[med-svn] [python-ruffus] 02/12: Imported Upstream version 2.5+dfsg

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository python-ruffus.

commit e17d203f8fbd6f212c2ede17e0984b11ccdd1081
Author: Andreas Tille <tille at debian.org>
Date:   Thu Feb 5 19:16:32 2015 +0100

    Imported Upstream version 2.5+dfsg
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-<g id="edge13" class="edge"><title>k5_0->k6_0</title>
-<path style="fill:none;stroke:#0044a0;" d="M126,-290C126,-286 126,-282 126,-278"/>
-<polygon style="fill:#0044a0;stroke:#0044a0;" points="129.5,-278 126,-268 122.5,-278 129.5,-278"/>
-</g>
-<!-- k7_0 -->
-<g id="node14" class="node"><title>k7_0</title>
-<polygon style="fill:#efa03b;stroke:#006000;" points="186,-172 70,-172 66,-168 66,-98 182,-98 186,-102 186,-172"/>
-<polyline style="fill:none;stroke:#006000;" points="182,-168 66,-168 "/>
-<polyline style="fill:none;stroke:#006000;" points="182,-168 182,-98 "/>
-<polyline style="fill:none;stroke:#006000;" points="182,-168 186,-172 "/>
-<text text-anchor="middle" x="126" y="-139.892" style="font-family:Times New Roman;font-size:20.0px;fill:#006000;">Up-to-date</text>
-<text text-anchor="middle" x="126" y="-116.892" style="font-family:Times New Roman;font-size:20.0px;fill:#006000;">Final target</text>
-</g>
-<!-- k6_0->k7_0 -->
-<g id="edge15" class="edge"><title>k6_0->k7_0</title>
-<path style="fill:none;stroke:#0044a0;" d="M126,-194C126,-190 126,-186 126,-182"/>
-<polygon style="fill:#0044a0;stroke:#0044a0;" points="129.5,-182 126,-172 122.5,-182 129.5,-182"/>
-</g>
-<!-- k8_0 -->
-<g id="node16" class="node"><title>k8_0</title>
-<polygon style="fill:#efa03b;stroke:black;" points="186,-75.5 70,-75.5 66,-71.5 66,-24.5 182,-24.5 186,-28.5 186,-75.5"/>
-<polyline style="fill:none;stroke:black;" points="182,-71.5 66,-71.5 "/>
-<polyline style="fill:none;stroke:black;" points="182,-71.5 182,-24.5 "/>
-<polyline style="fill:none;stroke:black;" points="182,-71.5 186,-75.5 "/>
-<text text-anchor="middle" x="126" y="-43.392" style="font-family:Times New Roman;font-size:20.0px;">Final target</text>
-</g>
-<!-- k7_0->k8_0 -->
-<g id="edge17" class="edge"><title>k7_0->k8_0</title>
-<path style="fill:none;stroke:gray;" d="M126,-98C126,-94 126,-90 126,-86"/>
-<polygon style="fill:gray;stroke:gray;" points="129.5,-86 126,-76 122.5,-86 129.5,-86"/>
-</g>
-<!-- k1_1 -->
-<g id="node19" class="node"><title>k1_1</title>
-<polygon style="fill:#d93611;stroke:white;" points="438,-637.5 306,-637.5 302,-633.5 302,-586.5 434,-586.5 438,-590.5 438,-637.5"/>
-<polyline style="fill:none;stroke:white;" points="434,-633.5 302,-633.5 "/>
-<polyline style="fill:none;stroke:white;" points="434,-633.5 434,-586.5 "/>
-<polyline style="fill:none;stroke:white;" points="434,-633.5 438,-637.5 "/>
-<text text-anchor="middle" x="370" y="-605.392" style="font-family:Times New Roman;font-size:20.0px;fill:white;">Vicious cycle</text>
-</g>
-<!-- k2_1 -->
-<g id="node20" class="node"><title>k2_1</title>
-<polygon style="fill:white;stroke:gray;" points="437,-563.5 307,-563.5 303,-559.5 303,-512.5 433,-512.5 437,-516.5 437,-563.5"/>
-<polyline style="fill:none;stroke:gray;" points="433,-559.5 303,-559.5 "/>
-<polyline style="fill:none;stroke:gray;" points="433,-559.5 433,-512.5 "/>
-<polyline style="fill:none;stroke:gray;" points="433,-559.5 437,-563.5 "/>
-<text text-anchor="middle" x="370" y="-531.392" style="font-family:Times New Roman;font-size:20.0px;fill:gray;">Down stream</text>
-</g>
-<!-- k1_1->k2_1 -->
-<g id="edge20" class="edge"><title>k1_1->k2_1</title>
-<path style="fill:none;stroke:#d93611;" d="M364,-586C363,-582 363,-578 363,-574"/>
-<polygon style="fill:#d93611;stroke:#d93611;" points="366.488,-574.299 364,-564 359.522,-573.602 366.488,-574.299"/>
-</g>
-<!-- k2_1->k1_1 -->
-<g id="edge22" class="edge"><title>k2_1->k1_1</title>
-<path style="fill:none;stroke:#d93611;" d="M376,-564C377,-568 377,-572 377,-576"/>
-<polygon style="fill:#d93611;stroke:#d93611;" points="373.512,-575.701 376,-586 380.478,-576.398 373.512,-575.701"/>
-</g>
-<!-- k3_1 -->
-<g id="node23" class="node"><title>k3_1</title>
-<polygon style="fill:#9ed983;stroke:#4b8c2e;" points="446,-489.5 298,-489.5 294,-485.5 294,-438.5 442,-438.5 446,-442.5 446,-489.5"/>
-<polyline style="fill:none;stroke:#4b8c2e;" points="442,-485.5 294,-485.5 "/>
-<polyline style="fill:none;stroke:#4b8c2e;" points="442,-485.5 442,-438.5 "/>
-<polyline style="fill:none;stroke:#4b8c2e;" points="442,-485.5 446,-489.5 "/>
-<text text-anchor="middle" x="370" y="-457.392" style="font-family:Times New Roman;font-size:20.0px;fill:#4b8c2e;">Up-to-date task</text>
-</g>
-<!-- k2_1->k3_1 -->
-<g id="edge24" class="edge"><title>k2_1->k3_1</title>
-<path style="fill:none;stroke:gray;" d="M370,-512C370,-508 370,-504 370,-500"/>
-<polygon style="fill:gray;stroke:gray;" points="373.5,-500 370,-490 366.5,-500 373.5,-500"/>
-</g>
-<!-- k4_1 -->
-<g id="node25" class="node"><title>k4_1</title>
-<polygon style="fill:none;stroke:black;" points="480,-415.5 264,-415.5 260,-411.5 260,-364.5 476,-364.5 480,-368.5 480,-415.5"/>
-<polyline style="fill:none;stroke:black;" points="476,-411.5 260,-411.5 "/>
-<polyline style="fill:none;stroke:black;" points="476,-411.5 476,-364.5 "/>
-<polyline style="fill:none;stroke:black;" points="476,-411.5 480,-415.5 "/>
-<text text-anchor="middle" x="370" y="-383.392" style="font-family:Times New Roman;font-size:20.0px;">Explicitly specified task</text>
-</g>
-<!-- k3_1->k4_1 -->
-<g id="edge26" class="edge"><title>k3_1->k4_1</title>
-<path style="fill:none;stroke:gray;" d="M370,-438C370,-434 370,-430 370,-426"/>
-<polygon style="fill:gray;stroke:gray;" points="373.5,-426 370,-416 366.5,-426 373.5,-426"/>
-</g>
-<!-- k5_1 -->
-<g id="node27" class="node"><title>k5_1</title>
-<polygon style="fill:none;stroke:#000ddf;" points="428,-341.5 316,-341.5 312,-337.5 312,-290.5 424,-290.5 428,-294.5 428,-341.5"/>
-<polyline style="fill:none;stroke:#000ddf;" points="424,-337.5 312,-337.5 "/>
-<polyline style="fill:none;stroke:#000ddf;" points="424,-337.5 424,-290.5 "/>
-<polyline style="fill:none;stroke:#000ddf;" points="424,-337.5 428,-341.5 "/>
-<text text-anchor="middle" x="370" y="-309.392" style="font-family:Times New Roman;font-size:20.0px;fill:#000ddf;">Task to run</text>
-</g>
-<!-- k4_1->k5_1 -->
-<g id="edge28" class="edge"><title>k4_1->k5_1</title>
-<path style="fill:none;stroke:#000ddf;" d="M370,-364C370,-360 370,-356 370,-352"/>
-<polygon style="fill:#000ddf;stroke:#000ddf;" points="373.5,-352 370,-342 366.5,-352 373.5,-352"/>
-</g>
-<!-- k6_1 -->
-<g id="node29" class="node"><title>k6_1</title>
-<polygon style="fill:none;stroke:#000ddf;stroke-dasharray:5,2;" points="446,-268 298,-268 294,-264 294,-194 442,-194 446,-198 446,-268"/>
-<polyline style="fill:none;stroke:#000ddf;stroke-dasharray:5,2;" points="442,-264 294,-264 "/>
-<polyline style="fill:none;stroke:#000ddf;stroke-dasharray:5,2;" points="442,-264 442,-194 "/>
-<polyline style="fill:none;stroke:#000ddf;stroke-dasharray:5,2;" points="442,-264 446,-268 "/>
-<text text-anchor="middle" x="370" y="-235.892" style="font-family:Times New Roman;font-size:20.0px;fill:#000ddf;">Up-to-date task</text>
-<text text-anchor="middle" x="370" y="-212.892" style="font-family:Times New Roman;font-size:20.0px;fill:#000ddf;">forced to rerun</text>
-</g>
-<!-- k5_1->k6_1 -->
-<g id="edge30" class="edge"><title>k5_1->k6_1</title>
-<path style="fill:none;stroke:#000ddf;" d="M370,-290C370,-286 370,-282 370,-278"/>
-<polygon style="fill:#000ddf;stroke:#000ddf;" points="373.5,-278 370,-268 366.5,-278 373.5,-278"/>
-</g>
-<!-- k7_1 -->
-<g id="node31" class="node"><title>k7_1</title>
-<polygon style="fill:#d98100;stroke:#d9d911;" points="430,-172 314,-172 310,-168 310,-98 426,-98 430,-102 430,-172"/>
-<polyline style="fill:none;stroke:#d9d911;" points="426,-168 310,-168 "/>
-<polyline style="fill:none;stroke:#d9d911;" points="426,-168 426,-98 "/>
-<polyline style="fill:none;stroke:#d9d911;" points="426,-168 430,-172 "/>
-<text text-anchor="middle" x="370" y="-139.892" style="font-family:Times New Roman;font-size:20.0px;fill:#d9d911;">Up-to-date</text>
-<text text-anchor="middle" x="370" y="-116.892" style="font-family:Times New Roman;font-size:20.0px;fill:#d9d911;">Final target</text>
-</g>
-<!-- k6_1->k7_1 -->
-<g id="edge32" class="edge"><title>k6_1->k7_1</title>
-<path style="fill:none;stroke:#000ddf;" d="M370,-194C370,-190 370,-186 370,-182"/>
-<polygon style="fill:#000ddf;stroke:#000ddf;" points="373.5,-182 370,-172 366.5,-182 373.5,-182"/>
-</g>
-<!-- k8_1 -->
-<g id="node33" class="node"><title>k8_1</title>
-<polygon style="fill:#d98100;stroke:black;" points="430,-75.5 314,-75.5 310,-71.5 310,-24.5 426,-24.5 430,-28.5 430,-75.5"/>
-<polyline style="fill:none;stroke:black;" points="426,-71.5 310,-71.5 "/>
-<polyline style="fill:none;stroke:black;" points="426,-71.5 426,-24.5 "/>
-<polyline style="fill:none;stroke:black;" points="426,-71.5 430,-75.5 "/>
-<text text-anchor="middle" x="370" y="-43.392" style="font-family:Times New Roman;font-size:20.0px;">Final target</text>
-</g>
-<!-- k7_1->k8_1 -->
-<g id="edge34" class="edge"><title>k7_1->k8_1</title>
-<path style="fill:none;stroke:gray;" d="M370,-98C370,-94 370,-90 370,-86"/>
-<polygon style="fill:gray;stroke:gray;" points="373.5,-86 370,-76 366.5,-86 373.5,-86"/>
-</g>
-<!-- k1_2 -->
-<g id="node36" class="node"><title>k1_2</title>
-<polygon style="fill:#a54a64;stroke:white;" points="682,-637.5 550,-637.5 546,-633.5 546,-586.5 678,-586.5 682,-590.5 682,-637.5"/>
-<polyline style="fill:none;stroke:white;" points="678,-633.5 546,-633.5 "/>
-<polyline style="fill:none;stroke:white;" points="678,-633.5 678,-586.5 "/>
-<polyline style="fill:none;stroke:white;" points="678,-633.5 682,-637.5 "/>
-<text text-anchor="middle" x="614" y="-605.392" style="font-family:Times New Roman;font-size:20.0px;fill:white;">Vicious cycle</text>
-</g>
-<!-- k2_2 -->
-<g id="node37" class="node"><title>k2_2</title>
-<polygon style="fill:white;stroke:gray;" points="681,-563.5 551,-563.5 547,-559.5 547,-512.5 677,-512.5 681,-516.5 681,-563.5"/>
-<polyline style="fill:none;stroke:gray;" points="677,-559.5 547,-559.5 "/>
-<polyline style="fill:none;stroke:gray;" points="677,-559.5 677,-512.5 "/>
-<polyline style="fill:none;stroke:gray;" points="677,-559.5 681,-563.5 "/>
-<text text-anchor="middle" x="614" y="-531.392" style="font-family:Times New Roman;font-size:20.0px;fill:gray;">Down stream</text>
-</g>
-<!-- k1_2->k2_2 -->
-<g id="edge37" class="edge"><title>k1_2->k2_2</title>
-<path style="fill:none;stroke:#a54a64;" d="M608,-586C607,-582 607,-578 607,-574"/>
-<polygon style="fill:#a54a64;stroke:#a54a64;" points="610.488,-574.299 608,-564 603.522,-573.602 610.488,-574.299"/>
-</g>
-<!-- k2_2->k1_2 -->
-<g id="edge39" class="edge"><title>k2_2->k1_2</title>
-<path style="fill:none;stroke:#a54a64;" d="M620,-564C621,-568 621,-572 621,-576"/>
-<polygon style="fill:#a54a64;stroke:#a54a64;" points="617.512,-575.701 620,-586 624.478,-576.398 617.512,-575.701"/>
-</g>
-<!-- k3_2 -->
-<g id="node40" class="node"><title>k3_2</title>
-<polygon style="fill:#99d1c1;stroke:#4a92a5;" points="690,-489.5 542,-489.5 538,-485.5 538,-438.5 686,-438.5 690,-442.5 690,-489.5"/>
-<polyline style="fill:none;stroke:#4a92a5;" points="686,-485.5 538,-485.5 "/>
-<polyline style="fill:none;stroke:#4a92a5;" points="686,-485.5 686,-438.5 "/>
-<polyline style="fill:none;stroke:#4a92a5;" points="686,-485.5 690,-489.5 "/>
-<text text-anchor="middle" x="614" y="-457.392" style="font-family:Times New Roman;font-size:20.0px;fill:#4a92a5;">Up-to-date task</text>
-</g>
-<!-- k2_2->k3_2 -->
-<g id="edge41" class="edge"><title>k2_2->k3_2</title>
-<path style="fill:none;stroke:gray;" d="M614,-512C614,-508 614,-504 614,-500"/>
-<polygon style="fill:gray;stroke:gray;" points="617.5,-500 614,-490 610.5,-500 617.5,-500"/>
-</g>
-<!-- k4_2 -->
-<g id="node42" class="node"><title>k4_2</title>
-<polygon style="fill:none;stroke:black;" points="724,-415.5 508,-415.5 504,-411.5 504,-364.5 720,-364.5 724,-368.5 724,-415.5"/>
-<polyline style="fill:none;stroke:black;" points="720,-411.5 504,-411.5 "/>
-<polyline style="fill:none;stroke:black;" points="720,-411.5 720,-364.5 "/>
-<polyline style="fill:none;stroke:black;" points="720,-411.5 724,-415.5 "/>
-<text text-anchor="middle" x="614" y="-383.392" style="font-family:Times New Roman;font-size:20.0px;">Explicitly specified task</text>
-</g>
-<!-- k3_2->k4_2 -->
-<g id="edge43" class="edge"><title>k3_2->k4_2</title>
-<path style="fill:none;stroke:gray;" d="M614,-438C614,-434 614,-430 614,-426"/>
-<polygon style="fill:gray;stroke:gray;" points="617.5,-426 614,-416 610.5,-426 617.5,-426"/>
-</g>
-<!-- k5_2 -->
-<g id="node44" class="node"><title>k5_2</title>
-<polygon style="fill:none;stroke:#4a64a5;" points="672,-341.5 560,-341.5 556,-337.5 556,-290.5 668,-290.5 672,-294.5 672,-341.5"/>
-<polyline style="fill:none;stroke:#4a64a5;" points="668,-337.5 556,-337.5 "/>
-<polyline style="fill:none;stroke:#4a64a5;" points="668,-337.5 668,-290.5 "/>
-<polyline style="fill:none;stroke:#4a64a5;" points="668,-337.5 672,-341.5 "/>
-<text text-anchor="middle" x="614" y="-309.392" style="font-family:Times New Roman;font-size:20.0px;fill:#4a64a5;">Task to run</text>
-</g>
-<!-- k4_2->k5_2 -->
-<g id="edge45" class="edge"><title>k4_2->k5_2</title>
-<path style="fill:none;stroke:#4a64a5;" d="M614,-364C614,-360 614,-356 614,-352"/>
-<polygon style="fill:#4a64a5;stroke:#4a64a5;" points="617.5,-352 614,-342 610.5,-352 617.5,-352"/>
-</g>
-<!-- k6_2 -->
-<g id="node46" class="node"><title>k6_2</title>
-<polygon style="fill:none;stroke:#4a64a5;stroke-dasharray:5,2;" points="690,-268 542,-268 538,-264 538,-194 686,-194 690,-198 690,-268"/>
-<polyline style="fill:none;stroke:#4a64a5;stroke-dasharray:5,2;" points="686,-264 538,-264 "/>
-<polyline style="fill:none;stroke:#4a64a5;stroke-dasharray:5,2;" points="686,-264 686,-194 "/>
-<polyline style="fill:none;stroke:#4a64a5;stroke-dasharray:5,2;" points="686,-264 690,-268 "/>
-<text text-anchor="middle" x="614" y="-235.892" style="font-family:Times New Roman;font-size:20.0px;fill:#4a64a5;">Up-to-date task</text>
-<text text-anchor="middle" x="614" y="-212.892" style="font-family:Times New Roman;font-size:20.0px;fill:#4a64a5;">forced to rerun</text>
-</g>
-<!-- k5_2->k6_2 -->
-<g id="edge47" class="edge"><title>k5_2->k6_2</title>
-<path style="fill:none;stroke:#4a64a5;" d="M614,-290C614,-286 614,-282 614,-278"/>
-<polygon style="fill:#4a64a5;stroke:#4a64a5;" points="617.5,-278 614,-268 610.5,-278 617.5,-278"/>
-</g>
-<!-- k7_2 -->
-<g id="node48" class="node"><title>k7_2</title>
-<polygon style="fill:#d2c24a;stroke:#4a92a5;" points="674,-172 558,-172 554,-168 554,-98 670,-98 674,-102 674,-172"/>
-<polyline style="fill:none;stroke:#4a92a5;" points="670,-168 554,-168 "/>
-<polyline style="fill:none;stroke:#4a92a5;" points="670,-168 670,-98 "/>
-<polyline style="fill:none;stroke:#4a92a5;" points="670,-168 674,-172 "/>
-<text text-anchor="middle" x="614" y="-139.892" style="font-family:Times New Roman;font-size:20.0px;fill:#4a92a5;">Up-to-date</text>
-<text text-anchor="middle" x="614" y="-116.892" style="font-family:Times New Roman;font-size:20.0px;fill:#4a92a5;">Final target</text>
-</g>
-<!-- k6_2->k7_2 -->
-<g id="edge49" class="edge"><title>k6_2->k7_2</title>
-<path style="fill:none;stroke:#4a64a5;" d="M614,-194C614,-190 614,-186 614,-182"/>
-<polygon style="fill:#4a64a5;stroke:#4a64a5;" points="617.5,-182 614,-172 610.5,-182 617.5,-182"/>
-</g>
-<!-- k8_2 -->
-<g id="node50" class="node"><title>k8_2</title>
-<polygon style="fill:#d2c24a;stroke:black;" points="674,-75.5 558,-75.5 554,-71.5 554,-24.5 670,-24.5 674,-28.5 674,-75.5"/>
-<polyline style="fill:none;stroke:black;" points="670,-71.5 554,-71.5 "/>
-<polyline style="fill:none;stroke:black;" points="670,-71.5 670,-24.5 "/>
-<polyline style="fill:none;stroke:black;" points="670,-71.5 674,-75.5 "/>
-<text text-anchor="middle" x="614" y="-43.392" style="font-family:Times New Roman;font-size:20.0px;">Final target</text>
-</g>
-<!-- k7_2->k8_2 -->
-<g id="edge51" class="edge"><title>k7_2->k8_2</title>
-<path style="fill:none;stroke:gray;" d="M614,-98C614,-94 614,-90 614,-86"/>
-<polygon style="fill:gray;stroke:gray;" points="617.5,-86 614,-76 610.5,-86 617.5,-86"/>
-</g>
-<!-- k1_3 -->
-<g id="node53" class="node"><title>k1_3</title>
-<polygon style="fill:#ff3e68;stroke:white;" points="926,-637.5 794,-637.5 790,-633.5 790,-586.5 922,-586.5 926,-590.5 926,-637.5"/>
-<polyline style="fill:none;stroke:white;" points="922,-633.5 790,-633.5 "/>
-<polyline style="fill:none;stroke:white;" points="922,-633.5 922,-586.5 "/>
-<polyline style="fill:none;stroke:white;" points="922,-633.5 926,-637.5 "/>
-<text text-anchor="middle" x="858" y="-605.392" style="font-family:Times New Roman;font-size:20.0px;fill:white;">Vicious cycle</text>
-</g>
-<!-- k2_3 -->
-<g id="node54" class="node"><title>k2_3</title>
-<polygon style="fill:white;stroke:gray;" points="925,-563.5 795,-563.5 791,-559.5 791,-512.5 921,-512.5 925,-516.5 925,-563.5"/>
-<polyline style="fill:none;stroke:gray;" points="921,-559.5 791,-559.5 "/>
-<polyline style="fill:none;stroke:gray;" points="921,-559.5 921,-512.5 "/>
-<polyline style="fill:none;stroke:gray;" points="921,-559.5 925,-563.5 "/>
-<text text-anchor="middle" x="858" y="-531.392" style="font-family:Times New Roman;font-size:20.0px;fill:gray;">Down stream</text>
-</g>
-<!-- k1_3->k2_3 -->
-<g id="edge54" class="edge"><title>k1_3->k2_3</title>
-<path style="fill:none;stroke:#ff3e68;" d="M852,-586C851,-582 851,-578 851,-574"/>
-<polygon style="fill:#ff3e68;stroke:#ff3e68;" points="854.488,-574.299 852,-564 847.522,-573.602 854.488,-574.299"/>
-</g>
-<!-- k2_3->k1_3 -->
-<g id="edge56" class="edge"><title>k2_3->k1_3</title>
-<path style="fill:none;stroke:#ff3e68;" d="M864,-564C865,-568 865,-572 865,-576"/>
-<polygon style="fill:#ff3e68;stroke:#ff3e68;" points="861.512,-575.701 864,-586 868.478,-576.398 861.512,-575.701"/>
-</g>
-<!-- k3_3 -->
-<g id="node57" class="node"><title>k3_3</title>
-<polygon style="fill:#c9d787;stroke:#7d8a2e;" points="934,-489.5 786,-489.5 782,-485.5 782,-438.5 930,-438.5 934,-442.5 934,-489.5"/>
-<polyline style="fill:none;stroke:#7d8a2e;" points="930,-485.5 782,-485.5 "/>
-<polyline style="fill:none;stroke:#7d8a2e;" points="930,-485.5 930,-438.5 "/>
-<polyline style="fill:none;stroke:#7d8a2e;" points="930,-485.5 934,-489.5 "/>
-<text text-anchor="middle" x="858" y="-457.392" style="font-family:Times New Roman;font-size:20.0px;fill:#7d8a2e;">Up-to-date task</text>
-</g>
-<!-- k2_3->k3_3 -->
-<g id="edge58" class="edge"><title>k2_3->k3_3</title>
-<path style="fill:none;stroke:gray;" d="M858,-512C858,-508 858,-504 858,-500"/>
-<polygon style="fill:gray;stroke:gray;" points="861.5,-500 858,-490 854.5,-500 861.5,-500"/>
-</g>
-<!-- k4_3 -->
-<g id="node59" class="node"><title>k4_3</title>
-<polygon style="fill:none;stroke:black;" points="968,-415.5 752,-415.5 748,-411.5 748,-364.5 964,-364.5 968,-368.5 968,-415.5"/>
-<polyline style="fill:none;stroke:black;" points="964,-411.5 748,-411.5 "/>
-<polyline style="fill:none;stroke:black;" points="964,-411.5 964,-364.5 "/>
-<polyline style="fill:none;stroke:black;" points="964,-411.5 968,-415.5 "/>
-<text text-anchor="middle" x="858" y="-383.392" style="font-family:Times New Roman;font-size:20.0px;">Explicitly specified task</text>
-</g>
-<!-- k3_3->k4_3 -->
-<g id="edge60" class="edge"><title>k3_3->k4_3</title>
-<path style="fill:none;stroke:gray;" d="M858,-438C858,-434 858,-430 858,-426"/>
-<polygon style="fill:gray;stroke:gray;" points="861.5,-426 858,-416 854.5,-426 861.5,-426"/>
-</g>
-<!-- k5_3 -->
-<g id="node61" class="node"><title>k5_3</title>
-<polygon style="fill:none;stroke:#bfb5ff;" points="916,-341.5 804,-341.5 800,-337.5 800,-290.5 912,-290.5 916,-294.5 916,-341.5"/>
-<polyline style="fill:none;stroke:#bfb5ff;" points="912,-337.5 800,-337.5 "/>
-<polyline style="fill:none;stroke:#bfb5ff;" points="912,-337.5 912,-290.5 "/>
-<polyline style="fill:none;stroke:#bfb5ff;" points="912,-337.5 916,-341.5 "/>
-<text text-anchor="middle" x="858" y="-309.392" style="font-family:Times New Roman;font-size:20.0px;fill:#bfb5ff;">Task to run</text>
-</g>
-<!-- k4_3->k5_3 -->
-<g id="edge62" class="edge"><title>k4_3->k5_3</title>
-<path style="fill:none;stroke:#bfb5ff;" d="M858,-364C858,-360 858,-356 858,-352"/>
-<polygon style="fill:#bfb5ff;stroke:#bfb5ff;" points="861.5,-352 858,-342 854.5,-352 861.5,-352"/>
-</g>
-<!-- k6_3 -->
-<g id="node63" class="node"><title>k6_3</title>
-<polygon style="fill:none;stroke:#bfb5ff;stroke-dasharray:5,2;" points="934,-268 786,-268 782,-264 782,-194 930,-194 934,-198 934,-268"/>
-<polyline style="fill:none;stroke:#bfb5ff;stroke-dasharray:5,2;" points="930,-264 782,-264 "/>
-<polyline style="fill:none;stroke:#bfb5ff;stroke-dasharray:5,2;" points="930,-264 930,-194 "/>
-<polyline style="fill:none;stroke:#bfb5ff;stroke-dasharray:5,2;" points="930,-264 934,-268 "/>
-<text text-anchor="middle" x="858" y="-235.892" style="font-family:Times New Roman;font-size:20.0px;fill:#bfb5ff;">Up-to-date task</text>
-<text text-anchor="middle" x="858" y="-212.892" style="font-family:Times New Roman;font-size:20.0px;fill:#bfb5ff;">forced to rerun</text>
-</g>
-<!-- k5_3->k6_3 -->
-<g id="edge64" class="edge"><title>k5_3->k6_3</title>
-<path style="fill:none;stroke:#bfb5ff;" d="M858,-290C858,-286 858,-282 858,-278"/>
-<polygon style="fill:#bfb5ff;stroke:#bfb5ff;" points="861.5,-278 858,-268 854.5,-278 861.5,-278"/>
-</g>
-<!-- k7_3 -->
-<g id="node65" class="node"><title>k7_3</title>
-<polygon style="fill:#fff1dc;stroke:#7d8a2e;" points="918,-172 802,-172 798,-168 798,-98 914,-98 918,-102 918,-172"/>
-<polyline style="fill:none;stroke:#7d8a2e;" points="914,-168 798,-168 "/>
-<polyline style="fill:none;stroke:#7d8a2e;" points="914,-168 914,-98 "/>
-<polyline style="fill:none;stroke:#7d8a2e;" points="914,-168 918,-172 "/>
-<text text-anchor="middle" x="858" y="-139.892" style="font-family:Times New Roman;font-size:20.0px;fill:#7d8a2e;">Up-to-date</text>
-<text text-anchor="middle" x="858" y="-116.892" style="font-family:Times New Roman;font-size:20.0px;fill:#7d8a2e;">Final target</text>
-</g>
-<!-- k6_3->k7_3 -->
-<g id="edge66" class="edge"><title>k6_3->k7_3</title>
-<path style="fill:none;stroke:#bfb5ff;" d="M858,-194C858,-190 858,-186 858,-182"/>
-<polygon style="fill:#bfb5ff;stroke:#bfb5ff;" points="861.5,-182 858,-172 854.5,-182 861.5,-182"/>
-</g>
-<!-- k8_3 -->
-<g id="node67" class="node"><title>k8_3</title>
-<polygon style="fill:#fff1dc;stroke:black;" points="918,-75.5 802,-75.5 798,-71.5 798,-24.5 914,-24.5 918,-28.5 918,-75.5"/>
-<polyline style="fill:none;stroke:black;" points="914,-71.5 798,-71.5 "/>
-<polyline style="fill:none;stroke:black;" points="914,-71.5 914,-24.5 "/>
-<polyline style="fill:none;stroke:black;" points="914,-71.5 918,-75.5 "/>
-<text text-anchor="middle" x="858" y="-43.392" style="font-family:Times New Roman;font-size:20.0px;">Final target</text>
-</g>
-<!-- k7_3->k8_3 -->
-<g id="edge68" class="edge"><title>k7_3->k8_3</title>
-<path style="fill:none;stroke:gray;" d="M858,-98C858,-94 858,-90 858,-86"/>
-<polygon style="fill:gray;stroke:gray;" points="861.5,-86 858,-76 854.5,-86 861.5,-86"/>
-</g>
-<!-- k1_4 -->
-<g id="node70" class="node"><title>k1_4</title>
-<polygon style="fill:#f54f29;stroke:white;" points="1170,-637.5 1038,-637.5 1034,-633.5 1034,-586.5 1166,-586.5 1170,-590.5 1170,-637.5"/>
-<polyline style="fill:none;stroke:white;" points="1166,-633.5 1034,-633.5 "/>
-<polyline style="fill:none;stroke:white;" points="1166,-633.5 1166,-586.5 "/>
-<polyline style="fill:none;stroke:white;" points="1166,-633.5 1170,-637.5 "/>
-<text text-anchor="middle" x="1102" y="-605.392" style="font-family:Times New Roman;font-size:20.0px;fill:white;">Vicious cycle</text>
-</g>
-<!-- k2_4 -->
-<g id="node71" class="node"><title>k2_4</title>
-<polygon style="fill:white;stroke:gray;" points="1169,-563.5 1039,-563.5 1035,-559.5 1035,-512.5 1165,-512.5 1169,-516.5 1169,-563.5"/>
-<polyline style="fill:none;stroke:gray;" points="1165,-559.5 1035,-559.5 "/>
-<polyline style="fill:none;stroke:gray;" points="1165,-559.5 1165,-512.5 "/>
-<polyline style="fill:none;stroke:gray;" points="1165,-559.5 1169,-563.5 "/>
-<text text-anchor="middle" x="1102" y="-531.392" style="font-family:Times New Roman;font-size:20.0px;fill:gray;">Down stream</text>
-</g>
-<!-- k1_4->k2_4 -->
-<g id="edge71" class="edge"><title>k1_4->k2_4</title>
-<path style="fill:none;stroke:#f54f29;" d="M1096,-586C1095,-582 1095,-578 1095,-574"/>
-<polygon style="fill:#f54f29;stroke:#f54f29;" points="1098.49,-574.299 1096,-564 1091.52,-573.602 1098.49,-574.299"/>
-</g>
-<!-- k2_4->k1_4 -->
-<g id="edge73" class="edge"><title>k2_4->k1_4</title>
-<path style="fill:none;stroke:#f54f29;" d="M1108,-564C1109,-568 1109,-572 1109,-576"/>
-<polygon style="fill:#f54f29;stroke:#f54f29;" points="1105.51,-575.701 1108,-586 1112.48,-576.398 1105.51,-575.701"/>
-</g>
-<!-- k3_4 -->
-<g id="node74" class="node"><title>k3_4</title>
-<polygon style="fill:#b8cc6e;stroke:#4b6000;" points="1178,-489.5 1030,-489.5 1026,-485.5 1026,-438.5 1174,-438.5 1178,-442.5 1178,-489.5"/>
-<polyline style="fill:none;stroke:#4b6000;" points="1174,-485.5 1026,-485.5 "/>
-<polyline style="fill:none;stroke:#4b6000;" points="1174,-485.5 1174,-438.5 "/>
-<polyline style="fill:none;stroke:#4b6000;" points="1174,-485.5 1178,-489.5 "/>
-<text text-anchor="middle" x="1102" y="-457.392" style="font-family:Times New Roman;font-size:20.0px;fill:#4b6000;">Up-to-date task</text>
-</g>
-<!-- k2_4->k3_4 -->
-<g id="edge75" class="edge"><title>k2_4->k3_4</title>
-<path style="fill:none;stroke:gray;" d="M1102,-512C1102,-508 1102,-504 1102,-500"/>
-<polygon style="fill:gray;stroke:gray;" points="1105.5,-500 1102,-490 1098.5,-500 1105.5,-500"/>
-</g>
-<!-- k4_4 -->
-<g id="node76" class="node"><title>k4_4</title>
-<polygon style="fill:none;stroke:black;" points="1212,-415.5 996,-415.5 992,-411.5 992,-364.5 1208,-364.5 1212,-368.5 1212,-415.5"/>
-<polyline style="fill:none;stroke:black;" points="1208,-411.5 992,-411.5 "/>
-<polyline style="fill:none;stroke:black;" points="1208,-411.5 1208,-364.5 "/>
-<polyline style="fill:none;stroke:black;" points="1208,-411.5 1212,-415.5 "/>
-<text text-anchor="middle" x="1102" y="-383.392" style="font-family:Times New Roman;font-size:20.0px;">Explicitly specified task</text>
-</g>
-<!-- k3_4->k4_4 -->
-<g id="edge77" class="edge"><title>k3_4->k4_4</title>
-<path style="fill:none;stroke:gray;" d="M1102,-438C1102,-434 1102,-430 1102,-426"/>
-<polygon style="fill:gray;stroke:gray;" points="1105.5,-426 1102,-416 1098.5,-426 1105.5,-426"/>
-</g>
-<!-- k5_4 -->
-<g id="node78" class="node"><title>k5_4</title>
-<polygon style="fill:none;stroke:#004460;" points="1160,-341.5 1048,-341.5 1044,-337.5 1044,-290.5 1156,-290.5 1160,-294.5 1160,-341.5"/>
-<polyline style="fill:none;stroke:#004460;" points="1156,-337.5 1044,-337.5 "/>
-<polyline style="fill:none;stroke:#004460;" points="1156,-337.5 1156,-290.5 "/>
-<polyline style="fill:none;stroke:#004460;" points="1156,-337.5 1160,-341.5 "/>
-<text text-anchor="middle" x="1102" y="-309.392" style="font-family:Times New Roman;font-size:20.0px;fill:#004460;">Task to run</text>
-</g>
-<!-- k4_4->k5_4 -->
-<g id="edge79" class="edge"><title>k4_4->k5_4</title>
-<path style="fill:none;stroke:#004460;" d="M1102,-364C1102,-360 1102,-356 1102,-352"/>
-<polygon style="fill:#004460;stroke:#004460;" points="1105.5,-352 1102,-342 1098.5,-352 1105.5,-352"/>
-</g>
-<!-- k6_4 -->
-<g id="node80" class="node"><title>k6_4</title>
-<polygon style="fill:none;stroke:#004460;stroke-dasharray:5,2;" points="1178,-268 1030,-268 1026,-264 1026,-194 1174,-194 1178,-198 1178,-268"/>
-<polyline style="fill:none;stroke:#004460;stroke-dasharray:5,2;" points="1174,-264 1026,-264 "/>
-<polyline style="fill:none;stroke:#004460;stroke-dasharray:5,2;" points="1174,-264 1174,-194 "/>
-<polyline style="fill:none;stroke:#004460;stroke-dasharray:5,2;" points="1174,-264 1178,-268 "/>
-<text text-anchor="middle" x="1102" y="-235.892" style="font-family:Times New Roman;font-size:20.0px;fill:#004460;">Up-to-date task</text>
-<text text-anchor="middle" x="1102" y="-212.892" style="font-family:Times New Roman;font-size:20.0px;fill:#004460;">forced to rerun</text>
-</g>
-<!-- k5_4->k6_4 -->
-<g id="edge81" class="edge"><title>k5_4->k6_4</title>
-<path style="fill:none;stroke:#004460;" d="M1102,-290C1102,-286 1102,-282 1102,-278"/>
-<polygon style="fill:#004460;stroke:#004460;" points="1105.5,-278 1102,-268 1098.5,-278 1105.5,-278"/>
-</g>
-<!-- k7_4 -->
-<g id="node82" class="node"><title>k7_4</title>
-<polygon style="fill:#fff0a3;stroke:#4b6000;" points="1162,-172 1046,-172 1042,-168 1042,-98 1158,-98 1162,-102 1162,-172"/>
-<polyline style="fill:none;stroke:#4b6000;" points="1158,-168 1042,-168 "/>
-<polyline style="fill:none;stroke:#4b6000;" points="1158,-168 1158,-98 "/>
-<polyline style="fill:none;stroke:#4b6000;" points="1158,-168 1162,-172 "/>
-<text text-anchor="middle" x="1102" y="-139.892" style="font-family:Times New Roman;font-size:20.0px;fill:#4b6000;">Up-to-date</text>
-<text text-anchor="middle" x="1102" y="-116.892" style="font-family:Times New Roman;font-size:20.0px;fill:#4b6000;">Final target</text>
-</g>
-<!-- k6_4->k7_4 -->
-<g id="edge83" class="edge"><title>k6_4->k7_4</title>
-<path style="fill:none;stroke:#004460;" d="M1102,-194C1102,-190 1102,-186 1102,-182"/>
-<polygon style="fill:#004460;stroke:#004460;" points="1105.5,-182 1102,-172 1098.5,-182 1105.5,-182"/>
-</g>
-<!-- k8_4 -->
-<g id="node84" class="node"><title>k8_4</title>
-<polygon style="fill:#fff0a3;stroke:black;" points="1162,-75.5 1046,-75.5 1042,-71.5 1042,-24.5 1158,-24.5 1162,-28.5 1162,-75.5"/>
-<polyline style="fill:none;stroke:black;" points="1158,-71.5 1042,-71.5 "/>
-<polyline style="fill:none;stroke:black;" points="1158,-71.5 1158,-24.5 "/>
-<polyline style="fill:none;stroke:black;" points="1158,-71.5 1162,-75.5 "/>
-<text text-anchor="middle" x="1102" y="-43.392" style="font-family:Times New Roman;font-size:20.0px;">Final target</text>
-</g>
-<!-- k7_4->k8_4 -->
-<g id="edge85" class="edge"><title>k7_4->k8_4</title>
-<path style="fill:none;stroke:gray;" d="M1102,-98C1102,-94 1102,-90 1102,-86"/>
-<polygon style="fill:gray;stroke:gray;" points="1105.5,-86 1102,-76 1098.5,-86 1105.5,-86"/>
-</g>
-<!-- k1_5 -->
-<g id="node87" class="node"><title>k1_5</title>
-<polygon style="fill:#ff0000;stroke:white;" points="1414,-637.5 1282,-637.5 1278,-633.5 1278,-586.5 1410,-586.5 1414,-590.5 1414,-637.5"/>
-<polyline style="fill:none;stroke:white;" points="1410,-633.5 1278,-633.5 "/>
-<polyline style="fill:none;stroke:white;" points="1410,-633.5 1410,-586.5 "/>
-<polyline style="fill:none;stroke:white;" points="1410,-633.5 1414,-637.5 "/>
-<text text-anchor="middle" x="1346" y="-605.392" style="font-family:Times New Roman;font-size:20.0px;fill:white;">Vicious cycle</text>
-</g>
-<!-- k2_5 -->
-<g id="node88" class="node"><title>k2_5</title>
-<polygon style="fill:white;stroke:gray;" points="1413,-563.5 1283,-563.5 1279,-559.5 1279,-512.5 1409,-512.5 1413,-516.5 1413,-563.5"/>
-<polyline style="fill:none;stroke:gray;" points="1409,-559.5 1279,-559.5 "/>
-<polyline style="fill:none;stroke:gray;" points="1409,-559.5 1409,-512.5 "/>
-<polyline style="fill:none;stroke:gray;" points="1409,-559.5 1413,-563.5 "/>
-<text text-anchor="middle" x="1346" y="-531.392" style="font-family:Times New Roman;font-size:20.0px;fill:gray;">Down stream</text>
-</g>
-<!-- k1_5->k2_5 -->
-<g id="edge88" class="edge"><title>k1_5->k2_5</title>
-<path style="fill:none;stroke:#ff0000;" d="M1340,-586C1339,-582 1339,-578 1339,-574"/>
-<polygon style="fill:#ff0000;stroke:#ff0000;" points="1342.49,-574.299 1340,-564 1335.52,-573.602 1342.49,-574.299"/>
-</g>
-<!-- k2_5->k1_5 -->
-<g id="edge90" class="edge"><title>k2_5->k1_5</title>
-<path style="fill:none;stroke:#ff0000;" d="M1352,-564C1353,-568 1353,-572 1353,-576"/>
-<polygon style="fill:#ff0000;stroke:#ff0000;" points="1349.51,-575.701 1352,-586 1356.48,-576.398 1349.51,-575.701"/>
-</g>
-<!-- k3_5 -->
-<g id="node91" class="node"><title>k3_5</title>
-<polygon style="fill:#44ff44;stroke:#007700;" points="1422,-489.5 1274,-489.5 1270,-485.5 1270,-438.5 1418,-438.5 1422,-442.5 1422,-489.5"/>
-<polyline style="fill:none;stroke:#007700;" points="1418,-485.5 1270,-485.5 "/>
-<polyline style="fill:none;stroke:#007700;" points="1418,-485.5 1418,-438.5 "/>
-<polyline style="fill:none;stroke:#007700;" points="1418,-485.5 1422,-489.5 "/>
-<text text-anchor="middle" x="1346" y="-457.392" style="font-family:Times New Roman;font-size:20.0px;fill:#007700;">Up-to-date task</text>
-</g>
-<!-- k2_5->k3_5 -->
-<g id="edge92" class="edge"><title>k2_5->k3_5</title>
-<path style="fill:none;stroke:gray;" d="M1346,-512C1346,-508 1346,-504 1346,-500"/>
-<polygon style="fill:gray;stroke:gray;" points="1349.5,-500 1346,-490 1342.5,-500 1349.5,-500"/>
-</g>
-<!-- k4_5 -->
-<g id="node93" class="node"><title>k4_5</title>
-<polygon style="fill:none;stroke:black;" points="1456,-415.5 1240,-415.5 1236,-411.5 1236,-364.5 1452,-364.5 1456,-368.5 1456,-415.5"/>
-<polyline style="fill:none;stroke:black;" points="1452,-411.5 1236,-411.5 "/>
-<polyline style="fill:none;stroke:black;" points="1452,-411.5 1452,-364.5 "/>
-<polyline style="fill:none;stroke:black;" points="1452,-411.5 1456,-415.5 "/>
-<text text-anchor="middle" x="1346" y="-383.392" style="font-family:Times New Roman;font-size:20.0px;">Explicitly specified task</text>
-</g>
-<!-- k3_5->k4_5 -->
-<g id="edge94" class="edge"><title>k3_5->k4_5</title>
-<path style="fill:none;stroke:gray;" d="M1346,-438C1346,-434 1346,-430 1346,-426"/>
-<polygon style="fill:gray;stroke:gray;" points="1349.5,-426 1346,-416 1342.5,-426 1349.5,-426"/>
-</g>
-<!-- k5_5 -->
-<g id="node95" class="node"><title>k5_5</title>
-<polygon style="fill:#aabbff;stroke:#1122ff;" points="1404,-341.5 1292,-341.5 1288,-337.5 1288,-290.5 1400,-290.5 1404,-294.5 1404,-341.5"/>
-<polyline style="fill:none;stroke:#1122ff;" points="1400,-337.5 1288,-337.5 "/>
-<polyline style="fill:none;stroke:#1122ff;" points="1400,-337.5 1400,-290.5 "/>
-<polyline style="fill:none;stroke:#1122ff;" points="1400,-337.5 1404,-341.5 "/>
-<text text-anchor="middle" x="1346" y="-309.392" style="font-family:Times New Roman;font-size:20.0px;fill:#1122ff;">Task to run</text>
-</g>
-<!-- k4_5->k5_5 -->
-<g id="edge96" class="edge"><title>k4_5->k5_5</title>
-<path style="fill:none;stroke:#1122ff;" d="M1346,-364C1346,-360 1346,-356 1346,-352"/>
-<polygon style="fill:#1122ff;stroke:#1122ff;" points="1349.5,-352 1346,-342 1342.5,-352 1349.5,-352"/>
-</g>
-<!-- k6_5 -->
-<g id="node97" class="node"><title>k6_5</title>
-<polygon style="fill:none;stroke:#1122ff;stroke-dasharray:5,2;" points="1422,-268 1274,-268 1270,-264 1270,-194 1418,-194 1422,-198 1422,-268"/>
-<polyline style="fill:none;stroke:#1122ff;stroke-dasharray:5,2;" points="1418,-264 1270,-264 "/>
-<polyline style="fill:none;stroke:#1122ff;stroke-dasharray:5,2;" points="1418,-264 1418,-194 "/>
-<polyline style="fill:none;stroke:#1122ff;stroke-dasharray:5,2;" points="1418,-264 1422,-268 "/>
-<text text-anchor="middle" x="1346" y="-235.892" style="font-family:Times New Roman;font-size:20.0px;fill:#1122ff;">Up-to-date task</text>
-<text text-anchor="middle" x="1346" y="-212.892" style="font-family:Times New Roman;font-size:20.0px;fill:#1122ff;">forced to rerun</text>
-</g>
-<!-- k5_5->k6_5 -->
-<g id="edge98" class="edge"><title>k5_5->k6_5</title>
-<path style="fill:none;stroke:#1122ff;" d="M1346,-290C1346,-286 1346,-282 1346,-278"/>
-<polygon style="fill:#1122ff;stroke:#1122ff;" points="1349.5,-278 1346,-268 1342.5,-278 1349.5,-278"/>
-</g>
-<!-- k7_5 -->
-<g id="node99" class="node"><title>k7_5</title>
-<polygon style="fill:#efa03b;stroke:#ffcc3b;" points="1406,-172 1290,-172 1286,-168 1286,-98 1402,-98 1406,-102 1406,-172"/>
-<polyline style="fill:none;stroke:#ffcc3b;" points="1402,-168 1286,-168 "/>
-<polyline style="fill:none;stroke:#ffcc3b;" points="1402,-168 1402,-98 "/>
-<polyline style="fill:none;stroke:#ffcc3b;" points="1402,-168 1406,-172 "/>
-<text text-anchor="middle" x="1346" y="-139.892" style="font-family:Times New Roman;font-size:20.0px;fill:#ffcc3b;">Up-to-date</text>
-<text text-anchor="middle" x="1346" y="-116.892" style="font-family:Times New Roman;font-size:20.0px;fill:#ffcc3b;">Final target</text>
-</g>
-<!-- k6_5->k7_5 -->
-<g id="edge100" class="edge"><title>k6_5->k7_5</title>
-<path style="fill:none;stroke:#1122ff;" d="M1346,-194C1346,-190 1346,-186 1346,-182"/>
-<polygon style="fill:#1122ff;stroke:#1122ff;" points="1349.5,-182 1346,-172 1342.5,-182 1349.5,-182"/>
-</g>
-<!-- k8_5 -->
-<g id="node101" class="node"><title>k8_5</title>
-<polygon style="fill:#efa03b;stroke:black;" points="1406,-75.5 1290,-75.5 1286,-71.5 1286,-24.5 1402,-24.5 1406,-28.5 1406,-75.5"/>
-<polyline style="fill:none;stroke:black;" points="1402,-71.5 1286,-71.5 "/>
-<polyline style="fill:none;stroke:black;" points="1402,-71.5 1402,-24.5 "/>
-<polyline style="fill:none;stroke:black;" points="1402,-71.5 1406,-75.5 "/>
-<text text-anchor="middle" x="1346" y="-43.392" style="font-family:Times New Roman;font-size:20.0px;">Final target</text>
-</g>
-<!-- k7_5->k8_5 -->
-<g id="edge102" class="edge"><title>k7_5->k8_5</title>
-<path style="fill:none;stroke:gray;" d="M1346,-98C1346,-94 1346,-90 1346,-86"/>
-<polygon style="fill:gray;stroke:gray;" points="1349.5,-86 1346,-76 1342.5,-86 1349.5,-86"/>
-</g>
-<!-- k1_6 -->
-<g id="node104" class="node"><title>k1_6</title>
-<polygon style="fill:#ff3232;stroke:white;" points="1658,-637.5 1526,-637.5 1522,-633.5 1522,-586.5 1654,-586.5 1658,-590.5 1658,-637.5"/>
-<polyline style="fill:none;stroke:white;" points="1654,-633.5 1522,-633.5 "/>
-<polyline style="fill:none;stroke:white;" points="1654,-633.5 1654,-586.5 "/>
-<polyline style="fill:none;stroke:white;" points="1654,-633.5 1658,-637.5 "/>
-<text text-anchor="middle" x="1590" y="-605.392" style="font-family:Times New Roman;font-size:20.0px;">Vicious cycle</text>
-</g>
-<!-- k2_6 -->
-<g id="node105" class="node"><title>k2_6</title>
-<polygon style="fill:white;stroke:gray;" points="1657,-563.5 1527,-563.5 1523,-559.5 1523,-512.5 1653,-512.5 1657,-516.5 1657,-563.5"/>
-<polyline style="fill:none;stroke:gray;" points="1653,-559.5 1523,-559.5 "/>
-<polyline style="fill:none;stroke:gray;" points="1653,-559.5 1653,-512.5 "/>
-<polyline style="fill:none;stroke:gray;" points="1653,-559.5 1657,-563.5 "/>
-<text text-anchor="middle" x="1590" y="-531.392" style="font-family:Times New Roman;font-size:20.0px;fill:gray;">Down stream</text>
-</g>
-<!-- k1_6->k2_6 -->
-<g id="edge105" class="edge"><title>k1_6->k2_6</title>
-<path style="fill:none;stroke:#ff3232;" d="M1584,-586C1583,-582 1583,-578 1583,-574"/>
-<polygon style="fill:#ff3232;stroke:#ff3232;" points="1586.49,-574.299 1584,-564 1579.52,-573.602 1586.49,-574.299"/>
-</g>
-<!-- k2_6->k1_6 -->
-<g id="edge107" class="edge"><title>k2_6->k1_6</title>
-<path style="fill:none;stroke:#ff3232;" d="M1596,-564C1597,-568 1597,-572 1597,-576"/>
-<polygon style="fill:#ff3232;stroke:#ff3232;" points="1593.51,-575.701 1596,-586 1600.48,-576.398 1593.51,-575.701"/>
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-<!-- k3_6 -->
-<g id="node108" class="node"><title>k3_6</title>
-<polygon style="fill:#6cb924;stroke:black;" points="1666,-489.5 1518,-489.5 1514,-485.5 1514,-438.5 1662,-438.5 1666,-442.5 1666,-489.5"/>
-<polyline style="fill:none;stroke:black;" points="1662,-485.5 1514,-485.5 "/>
-<polyline style="fill:none;stroke:black;" points="1662,-485.5 1662,-438.5 "/>
-<polyline style="fill:none;stroke:black;" points="1662,-485.5 1666,-489.5 "/>
-<text text-anchor="middle" x="1590" y="-457.392" style="font-family:Times New Roman;font-size:20.0px;">Up-to-date task</text>
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-<!-- k2_6->k3_6 -->
-<g id="edge109" class="edge"><title>k2_6->k3_6</title>
-<path style="fill:none;stroke:gray;" d="M1590,-512C1590,-508 1590,-504 1590,-500"/>
-<polygon style="fill:gray;stroke:gray;" points="1593.5,-500 1590,-490 1586.5,-500 1593.5,-500"/>
-</g>
-<!-- k4_6 -->
-<g id="node110" class="node"><title>k4_6</title>
-<polygon style="fill:none;stroke:black;" points="1700,-415.5 1484,-415.5 1480,-411.5 1480,-364.5 1696,-364.5 1700,-368.5 1700,-415.5"/>
-<polyline style="fill:none;stroke:black;" points="1696,-411.5 1480,-411.5 "/>
-<polyline style="fill:none;stroke:black;" points="1696,-411.5 1696,-364.5 "/>
-<polyline style="fill:none;stroke:black;" points="1696,-411.5 1700,-415.5 "/>
-<text text-anchor="middle" x="1590" y="-383.392" style="font-family:Times New Roman;font-size:20.0px;">Explicitly specified task</text>
-</g>
-<!-- k3_6->k4_6 -->
-<g id="edge111" class="edge"><title>k3_6->k4_6</title>
-<path style="fill:none;stroke:gray;" d="M1590,-438C1590,-434 1590,-430 1590,-426"/>
-<polygon style="fill:gray;stroke:gray;" points="1593.5,-426 1590,-416 1586.5,-426 1593.5,-426"/>
-</g>
-<!-- k5_6 -->
-<g id="node112" class="node"><title>k5_6</title>
-<polygon style="fill:#5f52ee;stroke:#0044a0;" points="1648,-341.5 1536,-341.5 1532,-337.5 1532,-290.5 1644,-290.5 1648,-294.5 1648,-341.5"/>
-<polyline style="fill:none;stroke:#0044a0;" points="1644,-337.5 1532,-337.5 "/>
-<polyline style="fill:none;stroke:#0044a0;" points="1644,-337.5 1644,-290.5 "/>
-<polyline style="fill:none;stroke:#0044a0;" points="1644,-337.5 1648,-341.5 "/>
-<text text-anchor="middle" x="1590" y="-309.392" style="font-family:Times New Roman;font-size:20.0px;fill:lightgrey;">Task to run</text>
-</g>
-<!-- k4_6->k5_6 -->
-<g id="edge113" class="edge"><title>k4_6->k5_6</title>
-<path style="fill:none;stroke:#0044a0;" d="M1590,-364C1590,-360 1590,-356 1590,-352"/>
-<polygon style="fill:#0044a0;stroke:#0044a0;" points="1593.5,-352 1590,-342 1586.5,-352 1593.5,-352"/>
-</g>
-<!-- k6_6 -->
-<g id="node114" class="node"><title>k6_6</title>
-<polygon style="fill:none;stroke:#0044a0;stroke-dasharray:5,2;" points="1666,-268 1518,-268 1514,-264 1514,-194 1662,-194 1666,-198 1666,-268"/>
-<polyline style="fill:none;stroke:#0044a0;stroke-dasharray:5,2;" points="1662,-264 1514,-264 "/>
-<polyline style="fill:none;stroke:#0044a0;stroke-dasharray:5,2;" points="1662,-264 1662,-194 "/>
-<polyline style="fill:none;stroke:#0044a0;stroke-dasharray:5,2;" points="1662,-264 1666,-268 "/>
-<text text-anchor="middle" x="1590" y="-235.892" style="font-family:Times New Roman;font-size:20.0px;fill:#0044a0;">Up-to-date task</text>
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-</g>
-<!-- k5_6->k6_6 -->
-<g id="edge115" class="edge"><title>k5_6->k6_6</title>
-<path style="fill:none;stroke:#0044a0;" d="M1590,-290C1590,-286 1590,-282 1590,-278"/>
-<polygon style="fill:#0044a0;stroke:#0044a0;" points="1593.5,-278 1590,-268 1586.5,-278 1593.5,-278"/>
-</g>
-<!-- k7_6 -->
-<g id="node116" class="node"><title>k7_6</title>
-<polygon style="fill:#ece116;stroke:black;" points="1650,-172 1534,-172 1530,-168 1530,-98 1646,-98 1650,-102 1650,-172"/>
-<polyline style="fill:none;stroke:black;" points="1646,-168 1530,-168 "/>
-<polyline style="fill:none;stroke:black;" points="1646,-168 1646,-98 "/>
-<polyline style="fill:none;stroke:black;" points="1646,-168 1650,-172 "/>
-<text text-anchor="middle" x="1590" y="-139.892" style="font-family:Times New Roman;font-size:20.0px;fill:#efa03b;">Up-to-date</text>
-<text text-anchor="middle" x="1590" y="-116.892" style="font-family:Times New Roman;font-size:20.0px;fill:#efa03b;">Final target</text>
-</g>
-<!-- k6_6->k7_6 -->
-<g id="edge117" class="edge"><title>k6_6->k7_6</title>
-<path style="fill:none;stroke:#0044a0;" d="M1590,-194C1590,-190 1590,-186 1590,-182"/>
-<polygon style="fill:#0044a0;stroke:#0044a0;" points="1593.5,-182 1590,-172 1586.5,-182 1593.5,-182"/>
-</g>
-<!-- k8_6 -->
-<g id="node118" class="node"><title>k8_6</title>
-<polygon style="fill:#ece116;stroke:black;" points="1650,-75.5 1534,-75.5 1530,-71.5 1530,-24.5 1646,-24.5 1650,-28.5 1650,-75.5"/>
-<polyline style="fill:none;stroke:black;" points="1646,-71.5 1530,-71.5 "/>
-<polyline style="fill:none;stroke:black;" points="1646,-71.5 1646,-24.5 "/>
-<polyline style="fill:none;stroke:black;" points="1646,-71.5 1650,-75.5 "/>
-<text text-anchor="middle" x="1590" y="-43.392" style="font-family:Times New Roman;font-size:20.0px;">Final target</text>
-</g>
-<!-- k7_6->k8_6 -->
-<g id="edge119" class="edge"><title>k7_6->k8_6</title>
-<path style="fill:none;stroke:gray;" d="M1590,-98C1590,-94 1590,-90 1590,-86"/>
-<polygon style="fill:gray;stroke:gray;" points="1593.5,-86 1590,-76 1586.5,-86 1593.5,-86"/>
-</g>
-<!-- k1_7 -->
-<g id="node121" class="node"><title>k1_7</title>
-<polygon style="fill:#b9495e;stroke:white;" points="1902,-637.5 1770,-637.5 1766,-633.5 1766,-586.5 1898,-586.5 1902,-590.5 1902,-637.5"/>
-<polyline style="fill:none;stroke:white;" points="1898,-633.5 1766,-633.5 "/>
-<polyline style="fill:none;stroke:white;" points="1898,-633.5 1898,-586.5 "/>
-<polyline style="fill:none;stroke:white;" points="1898,-633.5 1902,-637.5 "/>
-<text text-anchor="middle" x="1834" y="-605.392" style="font-family:Times New Roman;font-size:20.0px;fill:white;">Vicious cycle</text>
-</g>
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-<polygon style="fill:white;stroke:gray;" points="1901,-563.5 1771,-563.5 1767,-559.5 1767,-512.5 1897,-512.5 1901,-516.5 1901,-563.5"/>
-<polyline style="fill:none;stroke:gray;" points="1897,-559.5 1767,-559.5 "/>
-<polyline style="fill:none;stroke:gray;" points="1897,-559.5 1897,-512.5 "/>
-<polyline style="fill:none;stroke:gray;" points="1897,-559.5 1901,-563.5 "/>
-<text text-anchor="middle" x="1834" y="-531.392" style="font-family:Times New Roman;font-size:20.0px;fill:gray;">Down stream</text>
-</g>
-<!-- k1_7->k2_7 -->
-<g id="edge122" class="edge"><title>k1_7->k2_7</title>
-<path style="fill:none;stroke:#b9495e;" d="M1828,-586C1827,-582 1827,-578 1827,-574"/>
-<polygon style="fill:#b9495e;stroke:#b9495e;" points="1830.49,-574.299 1828,-564 1823.52,-573.602 1830.49,-574.299"/>
-</g>
-<!-- k2_7->k1_7 -->
-<g id="edge124" class="edge"><title>k2_7->k1_7</title>
-<path style="fill:none;stroke:#b9495e;" d="M1840,-564C1841,-568 1841,-572 1841,-576"/>
-<polygon style="fill:#b9495e;stroke:#b9495e;" points="1837.51,-575.701 1840,-586 1844.48,-576.398 1837.51,-575.701"/>
-</g>
-<!-- k3_7 -->
-<g id="node125" class="node"><title>k3_7</title>
-<polygon style="fill:#d3fae3;stroke:#87b379;" points="1910,-489.5 1762,-489.5 1758,-485.5 1758,-438.5 1906,-438.5 1910,-442.5 1910,-489.5"/>
-<polyline style="fill:none;stroke:#87b379;" points="1906,-485.5 1758,-485.5 "/>
-<polyline style="fill:none;stroke:#87b379;" points="1906,-485.5 1906,-438.5 "/>
-<polyline style="fill:none;stroke:#87b379;" points="1906,-485.5 1910,-489.5 "/>
-<text text-anchor="middle" x="1834" y="-457.392" style="font-family:Times New Roman;font-size:20.0px;fill:#87b379;">Up-to-date task</text>
-</g>
-<!-- k2_7->k3_7 -->
-<g id="edge126" class="edge"><title>k2_7->k3_7</title>
-<path style="fill:none;stroke:gray;" d="M1834,-512C1834,-508 1834,-504 1834,-500"/>
-<polygon style="fill:gray;stroke:gray;" points="1837.5,-500 1834,-490 1830.5,-500 1837.5,-500"/>
-</g>
-<!-- k4_7 -->
-<g id="node127" class="node"><title>k4_7</title>
-<polygon style="fill:none;stroke:black;" points="1944,-415.5 1728,-415.5 1724,-411.5 1724,-364.5 1940,-364.5 1944,-368.5 1944,-415.5"/>
-<polyline style="fill:none;stroke:black;" points="1940,-411.5 1724,-411.5 "/>
-<polyline style="fill:none;stroke:black;" points="1940,-411.5 1940,-364.5 "/>
-<polyline style="fill:none;stroke:black;" points="1940,-411.5 1944,-415.5 "/>
-<text text-anchor="middle" x="1834" y="-383.392" style="font-family:Times New Roman;font-size:20.0px;">Explicitly specified task</text>
-</g>
-<!-- k3_7->k4_7 -->
-<g id="edge128" class="edge"><title>k3_7->k4_7</title>
-<path style="fill:none;stroke:gray;" d="M1834,-438C1834,-434 1834,-430 1834,-426"/>
-<polygon style="fill:gray;stroke:gray;" points="1837.5,-426 1834,-416 1830.5,-426 1837.5,-426"/>
-</g>
-<!-- k5_7 -->
-<g id="node129" class="node"><title>k5_7</title>
-<polygon style="fill:none;stroke:#87bae4;" points="1892,-341.5 1780,-341.5 1776,-337.5 1776,-290.5 1888,-290.5 1892,-294.5 1892,-341.5"/>
-<polyline style="fill:none;stroke:#87bae4;" points="1888,-337.5 1776,-337.5 "/>
-<polyline style="fill:none;stroke:#87bae4;" points="1888,-337.5 1888,-290.5 "/>
-<polyline style="fill:none;stroke:#87bae4;" points="1888,-337.5 1892,-341.5 "/>
-<text text-anchor="middle" x="1834" y="-309.392" style="font-family:Times New Roman;font-size:20.0px;fill:#87bae4;">Task to run</text>
-</g>
-<!-- k4_7->k5_7 -->
-<g id="edge130" class="edge"><title>k4_7->k5_7</title>
-<path style="fill:none;stroke:#87bae4;" d="M1834,-364C1834,-360 1834,-356 1834,-352"/>
-<polygon style="fill:#87bae4;stroke:#87bae4;" points="1837.5,-352 1834,-342 1830.5,-352 1837.5,-352"/>
-</g>
-<!-- k6_7 -->
-<g id="node131" class="node"><title>k6_7</title>
-<polygon style="fill:none;stroke:#87bae4;stroke-dasharray:5,2;" points="1910,-268 1762,-268 1758,-264 1758,-194 1906,-194 1910,-198 1910,-268"/>
-<polyline style="fill:none;stroke:#87bae4;stroke-dasharray:5,2;" points="1906,-264 1758,-264 "/>
-<polyline style="fill:none;stroke:#87bae4;stroke-dasharray:5,2;" points="1906,-264 1906,-194 "/>
-<polyline style="fill:none;stroke:#87bae4;stroke-dasharray:5,2;" points="1906,-264 1910,-268 "/>
-<text text-anchor="middle" x="1834" y="-235.892" style="font-family:Times New Roman;font-size:20.0px;fill:#87bae4;">Up-to-date task</text>
-<text text-anchor="middle" x="1834" y="-212.892" style="font-family:Times New Roman;font-size:20.0px;fill:#87bae4;">forced to rerun</text>
-</g>
-<!-- k5_7->k6_7 -->
-<g id="edge132" class="edge"><title>k5_7->k6_7</title>
-<path style="fill:none;stroke:#87bae4;" d="M1834,-290C1834,-286 1834,-282 1834,-278"/>
-<polygon style="fill:#87bae4;stroke:#87bae4;" points="1837.5,-278 1834,-268 1830.5,-278 1837.5,-278"/>
-</g>
-<!-- k7_7 -->
-<g id="node133" class="node"><title>k7_7</title>
-<polygon style="fill:#fdba40;stroke:#87b379;" points="1894,-172 1778,-172 1774,-168 1774,-98 1890,-98 1894,-102 1894,-172"/>
-<polyline style="fill:none;stroke:#87b379;" points="1890,-168 1774,-168 "/>
-<polyline style="fill:none;stroke:#87b379;" points="1890,-168 1890,-98 "/>
-<polyline style="fill:none;stroke:#87b379;" points="1890,-168 1894,-172 "/>
-<text text-anchor="middle" x="1834" y="-139.892" style="font-family:Times New Roman;font-size:20.0px;fill:#87b379;">Up-to-date</text>
-<text text-anchor="middle" x="1834" y="-116.892" style="font-family:Times New Roman;font-size:20.0px;fill:#87b379;">Final target</text>
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-<g id="edge134" class="edge"><title>k6_7->k7_7</title>
-<path style="fill:none;stroke:#87bae4;" d="M1834,-194C1834,-190 1834,-186 1834,-182"/>
-<polygon style="fill:#87bae4;stroke:#87bae4;" points="1837.5,-182 1834,-172 1830.5,-182 1837.5,-182"/>
-</g>
-<!-- k8_7 -->
-<g id="node135" class="node"><title>k8_7</title>
-<polygon style="fill:#fdba40;stroke:black;" points="1894,-75.5 1778,-75.5 1774,-71.5 1774,-24.5 1890,-24.5 1894,-28.5 1894,-75.5"/>
-<polyline style="fill:none;stroke:black;" points="1890,-71.5 1774,-71.5 "/>
-<polyline style="fill:none;stroke:black;" points="1890,-71.5 1890,-24.5 "/>
-<polyline style="fill:none;stroke:black;" points="1890,-71.5 1894,-75.5 "/>
-<text text-anchor="middle" x="1834" y="-43.392" style="font-family:Times New Roman;font-size:20.0px;">Final target</text>
-</g>
-<!-- k7_7->k8_7 -->
-<g id="edge136" class="edge"><title>k7_7->k8_7</title>
-<path style="fill:none;stroke:gray;" d="M1834,-98C1834,-94 1834,-90 1834,-86"/>
-<polygon style="fill:gray;stroke:gray;" points="1837.5,-86 1834,-76 1830.5,-86 1837.5,-86"/>
-</g>
-</g>
-</svg>
diff --git a/doc/_build/html/_downloads/gallery_big_pipeline.svg b/doc/_build/html/_downloads/gallery_big_pipeline.svg
deleted file mode 100644
index 49ca7ed..0000000
--- a/doc/_build/html/_downloads/gallery_big_pipeline.svg
+++ /dev/null
@@ -1,2699 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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-<!-- Title: tree Pages: 1 -->
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- viewBox="0.00 0.00 432.00 48.31" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
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-<title>tree</title>
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-<g id="cluster2" class="cluster"><title>clustertasks</title>
-<polygon style="fill:none;stroke:black;" points="12,-16 12,-1218 10914,-1218 10914,-16 12,-16"/>
-<text text-anchor="middle" x="5463" y="-1187" style="font-family:Times New Roman;font-size:30.00;">Pipeline:</text>
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-<g id="cluster3" class="cluster"><title>clusterkey</title>
-<polygon style="fill:#e5e5e5;stroke:#e5e5e5;" points="10922,-872 10922,-1226 11090,-1226 11090,-872 10922,-872"/>
-<text text-anchor="middle" x="11006" y="-1195" style="font-family:Times New Roman;font-size:30.00;">Key:</text>
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-<!-- t0 -->
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-<polyline style="fill:none;stroke:green;" points="1979,-1164 1857,-1164 "/>
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-<polyline style="fill:none;stroke:green;" points="1979,-1164 1983,-1168 "/>
-<text text-anchor="middle" x="1920" y="-1143.5" style="font-family:Times New Roman;font-size:20.00;">indexGenome</text>
-</g>
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-<g id="node32" class="node"><title>t181</title>
-<polygon style="fill:none;stroke:blue;" points="1134,-312 1062,-312 1058,-308 1058,-276 1130,-276 1134,-280 1134,-312"/>
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-<polyline style="fill:none;stroke:blue;" points="1130,-308 1130,-276 "/>
-<polyline style="fill:none;stroke:blue;" points="1130,-308 1134,-312 "/>
-<text text-anchor="middle" x="1096" y="-287.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">prepare</text>
-</g>
-<!-- t0->t181 -->
-<g id="edge383" class="edge"><title>t0->t181</title>
-<path style="fill:none;stroke:gray;" d="M1913,-1132C1903,-1102 1885,-1043 1885,-991 1885,-991 1885,-991 1885,-664 1885,-602 1902,-577 1865,-528 1798,-436 1744,-449 1634,-418 1555,-395 1520,-440 1450,-396 1435,-385 1444,-369 1428,-360 1376,-327 1208,-361 1150,-338 1139,-333 1129,-326 1120,-319"/>
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-<!-- t16 -->
-<g id="node34" class="node"><title>t16</title>
-<polygon style="fill:#90ee90;stroke:green;" points="5835,-1094 5737,-1094 5733,-1090 5733,-1058 5831,-1058 5835,-1062 5835,-1094"/>
-<polyline style="fill:none;stroke:green;" points="5831,-1090 5733,-1090 "/>
-<polyline style="fill:none;stroke:green;" points="5831,-1090 5831,-1058 "/>
-<polyline style="fill:none;stroke:green;" points="5831,-1090 5835,-1094 "/>
-<text text-anchor="middle" x="5784" y="-1069.5" style="font-family:Times New Roman;font-size:20.00;">buildBAM</text>
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-<!-- t0->t16 -->
-<g id="edge21" class="edge"><title>t0->t16</title>
-<path style="fill:none;stroke:gray;" d="M1983,-1149C2442,-1140 5269,-1086 5723,-1077"/>
-<polygon style="fill:gray;stroke:gray;" points="5723,-1080.5 5733,-1077 5723,-1073.5 5723,-1080.5"/>
-</g>
-<!-- t39 -->
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-<!-- t36->t130 -->
-<g id="edge185" class="edge"><title>t36->t130</title>
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-<g id="edge189" class="edge"><title>t36->t131</title>
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-<g id="edge193" class="edge"><title>t36->t132</title>
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-<g id="edge197" class="edge"><title>t36->t133</title>
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-<polygon style="fill:gray;stroke:gray;" points="2559.5,-406 2556,-396 2552.5,-406 2559.5,-406"/>
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-<!-- t37->t181 -->
-<g id="edge353" class="edge"><title>t37->t181</title>
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-<!-- t176 -->
-<g id="node188" class="node"><title>t176</title>
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-<!-- t37->t176 -->
-<g id="edge169" class="edge"><title>t37->t176</title>
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-<!-- t32 -->
-<g id="node6" class="node"><title>t32</title>
-<polygon style="fill:#90ee90;stroke:green;" points="4626,-590 4484,-590 4480,-586 4480,-554 4622,-554 4626,-558 4626,-590"/>
-<polyline style="fill:none;stroke:green;" points="4622,-586 4480,-586 "/>
-<polyline style="fill:none;stroke:green;" points="4622,-586 4622,-554 "/>
-<polyline style="fill:none;stroke:green;" points="4622,-586 4626,-590 "/>
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-<g id="node7" class="node"><title>t40</title>
-<polygon style="fill:#90ee90;stroke:green;" points="4662,-480 4472,-480 4468,-476 4468,-444 4658,-444 4662,-448 4662,-480"/>
-<polyline style="fill:none;stroke:green;" points="4658,-476 4468,-476 "/>
-<polyline style="fill:none;stroke:green;" points="4658,-476 4658,-444 "/>
-<polyline style="fill:none;stroke:green;" points="4658,-476 4662,-480 "/>
-<text text-anchor="middle" x="4565" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">buildPromotorRegions</text>
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-<!-- t32->t40 -->
-<g id="edge3" class="edge"><title>t32->t40</title>
-<path style="fill:none;stroke:gray;" d="M4555,-554C4557,-537 4560,-511 4562,-490"/>
-<polygon style="fill:gray;stroke:gray;" points="4565.49,-490.299 4563,-480 4558.52,-489.602 4565.49,-490.299"/>
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-<!-- t41 -->
-<g id="node9" class="node"><title>t41</title>
-<polygon style="fill:#90ee90;stroke:green;" points="4836,-480 4684,-480 4680,-476 4680,-444 4832,-444 4836,-448 4836,-480"/>
-<polyline style="fill:none;stroke:green;" points="4832,-476 4680,-476 "/>
-<polyline style="fill:none;stroke:green;" points="4832,-476 4832,-444 "/>
-<polyline style="fill:none;stroke:green;" points="4832,-476 4836,-480 "/>
-<text text-anchor="middle" x="4758" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">buildTSSRegions</text>
-</g>
-<!-- t32->t41 -->
-<g id="edge5" class="edge"><title>t32->t41</title>
-<path style="fill:none;stroke:gray;" d="M4587,-554C4622,-535 4677,-506 4715,-485"/>
-<polygon style="fill:gray;stroke:gray;" points="4716.96,-487.916 4724,-480 4713.56,-481.797 4716.96,-487.916"/>
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-<!-- t34 -->
-<g id="node12" class="node"><title>t34</title>
-<polygon style="fill:#90ee90;stroke:green;" points="3027,-480 2873,-480 2869,-476 2869,-444 3023,-444 3027,-448 3027,-480"/>
-<polyline style="fill:none;stroke:green;" points="3023,-476 2869,-476 "/>
-<polyline style="fill:none;stroke:green;" points="3023,-476 3023,-444 "/>
-<polyline style="fill:none;stroke:green;" points="3023,-476 3027,-480 "/>
-<text text-anchor="middle" x="2948" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">importTranscripts</text>
-</g>
-<!-- t32->t34 -->
-<g id="edge7" class="edge"><title>t32->t34</title>
-<path style="fill:none;stroke:gray;" d="M4480,-565C4372,-555 4166,-536 3989,-528 3884,-522 3139,-531 3036,-506 3019,-502 3001,-494 2986,-485"/>
-<polygon style="fill:gray;stroke:gray;" points="2987.44,-481.797 2977,-480 2984.04,-487.916 2987.44,-481.797"/>
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-<!-- t32->t181 -->
-<g id="edge363" class="edge"><title>t32->t181</title>
-<path style="fill:none;stroke:gray;" d="M4480,-565C4372,-555 4166,-536 3989,-528 3864,-521 2982,-537 2860,-506 2760,-479 2725,-472 2655,-396 2644,-383 2655,-369 2640,-360 2572,-313 1228,-366 1150,-338 1139,-334 1129,-327 1120,-319"/>
-<polygon style="fill:gray;stroke:gray;" points="1122.55,-316.596 1113,-312 1117.6,-321.546 1122.55,-316.596"/>
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-<!-- t40->t42 -->
-<g id="edge337" class="edge"><title>t40->t42</title>
-<path style="fill:none;stroke:gray;" d="M4599,-444C4619,-434 4646,-423 4671,-418 4814,-388 9690,-407 9987,-396"/>
-<polygon style="fill:gray;stroke:gray;" points="9987.4,-399.478 9997,-395 9986.7,-392.512 9987.4,-399.478"/>
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-<!-- t40->t181 -->
-<g id="edge347" class="edge"><title>t40->t181</title>
-<path style="fill:none;stroke:gray;" d="M4531,-444C4511,-434 4484,-423 4459,-418 4374,-400 2964,-434 2885,-396 2867,-386 2876,-369 2857,-360 2773,-317 1240,-370 1150,-338 1139,-334 1129,-327 1120,-319"/>
-<polygon style="fill:gray;stroke:gray;" points="1122.55,-316.596 1113,-312 1117.6,-321.546 1122.55,-316.596"/>
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-<!-- t41->t42 -->
-<g id="edge11" class="edge"><title>t41->t42</title>
-<path style="fill:none;stroke:gray;" d="M4836,-454C4943,-443 5139,-425 5307,-418 5824,-395 9426,-438 9987,-396"/>
-<polygon style="fill:gray;stroke:gray;" points="9987.4,-399.478 9997,-395 9986.7,-392.512 9987.4,-399.478"/>
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-<!-- t41->t181 -->
-<g id="edge345" class="edge"><title>t41->t181</title>
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-<polygon style="fill:gray;stroke:gray;" points="1122.55,-316.596 1113,-312 1117.6,-321.546 1122.55,-316.596"/>
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-<g id="node11" class="node"><title>t35</title>
-<polygon style="fill:#90ee90;stroke:green;" points="2443,-396 2327,-396 2323,-392 2323,-360 2439,-360 2443,-364 2443,-396"/>
-<polyline style="fill:none;stroke:green;" points="2439,-392 2323,-392 "/>
-<polyline style="fill:none;stroke:green;" points="2439,-392 2439,-360 "/>
-<polyline style="fill:none;stroke:green;" points="2439,-392 2443,-396 "/>
-<text text-anchor="middle" x="2383" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">buildRepeats</text>
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-<!-- t35->t181 -->
-<g id="edge357" class="edge"><title>t35->t181</title>
-<path style="fill:none;stroke:gray;" d="M2323,-362C2318,-361 2314,-361 2309,-360 2246,-351 1209,-360 1148,-338 1137,-334 1128,-327 1119,-320"/>
-<polygon style="fill:gray;stroke:gray;" points="1121.22,-317.221 1112,-312 1115.95,-321.831 1121.22,-317.221"/>
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-<!-- t34->t181 -->
-<g id="edge359" class="edge"><title>t34->t181</title>
-<path style="fill:none;stroke:gray;" d="M2923,-444C2906,-431 2883,-413 2865,-396 2851,-381 2854,-368 2835,-360 2751,-319 1238,-369 1150,-338 1139,-334 1129,-327 1120,-319"/>
-<polygon style="fill:gray;stroke:gray;" points="1122.55,-316.596 1113,-312 1117.6,-321.546 1122.55,-316.596"/>
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-<!-- t8 -->
-<g id="node14" class="node"><title>t8</title>
-<polygon style="fill:#90ee90;stroke:green;" points="3105,-590 2895,-590 2891,-586 2891,-554 3101,-554 3105,-558 3105,-590"/>
-<polyline style="fill:none;stroke:green;" points="3101,-586 2891,-586 "/>
-<polyline style="fill:none;stroke:green;" points="3101,-586 3101,-554 "/>
-<polyline style="fill:none;stroke:green;" points="3101,-586 3105,-590 "/>
-<text text-anchor="middle" x="2998" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">importRegionsOfInterest</text>
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-<g id="node17" class="node"><title>t14</title>
-<polygon style="fill:#90ee90;stroke:green;" points="3257,-480 3049,-480 3045,-476 3045,-444 3253,-444 3257,-448 3257,-480"/>
-<polyline style="fill:none;stroke:green;" points="3253,-476 3045,-476 "/>
-<polyline style="fill:none;stroke:green;" points="3253,-476 3253,-444 "/>
-<polyline style="fill:none;stroke:green;" points="3253,-476 3257,-480 "/>
-<text text-anchor="middle" x="3151" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">exportRegionsOfInterest</text>
-</g>
-<!-- t8->t14 -->
-<g id="edge335" class="edge"><title>t8->t14</title>
-<path style="fill:none;stroke:gray;" d="M3023,-554C3049,-536 3090,-507 3118,-486"/>
-<polygon style="fill:gray;stroke:gray;" points="3120.1,-488.8 3126,-480 3115.9,-483.2 3120.1,-488.8"/>
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-<!-- t12 -->
-<g id="node30" class="node"><title>t12</title>
-<polygon style="fill:#90ee90;stroke:green;" points="2310,-480 2050,-480 2046,-476 2046,-444 2306,-444 2310,-448 2310,-480"/>
-<polyline style="fill:none;stroke:green;" points="2306,-476 2046,-476 "/>
-<polyline style="fill:none;stroke:green;" points="2306,-476 2306,-444 "/>
-<polyline style="fill:none;stroke:green;" points="2306,-476 2310,-480 "/>
-<text text-anchor="middle" x="2178" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">importRegionsOfInterestGenes</text>
-</g>
-<!-- t8->t12 -->
-<g id="edge343" class="edge"><title>t8->t12</title>
-<path style="fill:none;stroke:gray;" d="M2891,-560C2805,-551 2683,-538 2576,-528 2465,-517 2435,-527 2324,-506 2296,-501 2265,-491 2239,-483"/>
-<polygon style="fill:gray;stroke:gray;" points="2239.58,-479.521 2229,-480 2237.57,-486.226 2239.58,-479.521"/>
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-<!-- t8->t181 -->
-<g id="edge373" class="edge"><title>t8->t181</title>
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-<polygon style="fill:gray;stroke:gray;" points="1122.55,-316.596 1113,-312 1117.6,-321.546 1122.55,-316.596"/>
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-<!-- t8->t178 -->
-<g id="edge483" class="edge"><title>t8->t178</title>
-<path style="fill:none;stroke:gray;" d="M3105,-564C3249,-553 3512,-535 3737,-528 5421,-473 5843,-559 7526,-506 8377,-479 8594,-490 9443,-396"/>
-<polygon style="fill:gray;stroke:gray;" points="9443.4,-399.478 9453,-395 9442.7,-392.512 9443.4,-399.478"/>
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-<!-- t10 -->
-<g id="node15" class="node"><title>t10</title>
-<polygon style="fill:#90ee90;stroke:green;" points="2110.05,-559.794 2178,-532.5 2245.95,-559.794 2245.89,-603.956 2110.11,-603.956 2110.05,-559.794"/>
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-<text text-anchor="middle" x="2178" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">importGWAS</text>
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-<g id="edge333" class="edge"><title>t10->t14</title>
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-<!-- t10->t12 -->
-<g id="edge341" class="edge"><title>t10->t12</title>
-<path style="fill:none;stroke:gray;" d="M2178,-528C2178,-515 2178,-502 2178,-490"/>
-<polygon style="fill:gray;stroke:gray;" points="2181.5,-490 2178,-480 2174.5,-490 2181.5,-490"/>
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-<!-- t10->t181 -->
-<g id="edge371" class="edge"><title>t10->t181</title>
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-<!-- t11 -->
-<g id="node16" class="node"><title>t11</title>
-<polygon style="fill:#90ee90;stroke:green;" points="2360.83,-559.794 2462,-532.5 2563.17,-559.794 2563.08,-603.956 2360.92,-603.956 2360.83,-559.794"/>
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-<text text-anchor="middle" x="2462" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">importMergedGWAS</text>
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-<!-- t11->t14 -->
-<g id="edge9" class="edge"><title>t11->t14</title>
-<path style="fill:none;stroke:gray;" d="M2567,-561C2720,-546 2992,-517 3036,-506 3058,-500 3082,-492 3102,-484"/>
-<polygon style="fill:gray;stroke:gray;" points="3103.28,-487.26 3111,-480 3100.44,-480.863 3103.28,-487.26"/>
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-<g id="edge17" class="edge"><title>t11->t12</title>
-<path style="fill:none;stroke:gray;" d="M2395,-546C2346,-527 2280,-502 2234,-484"/>
-<polygon style="fill:gray;stroke:gray;" points="2235.56,-480.863 2225,-480 2232.72,-487.26 2235.56,-480.863"/>
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-<!-- t14->t181 -->
-<g id="edge365" class="edge"><title>t14->t181</title>
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-<polygon style="fill:gray;stroke:gray;" points="1122.55,-316.596 1113,-312 1117.6,-321.546 1122.55,-316.596"/>
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-<g id="node221" class="node"><title>t121</title>
-<polygon style="fill:none;stroke:blue;" points="6551,-396 6269,-396 6265,-392 6265,-360 6547,-360 6551,-364 6551,-396"/>
-<polyline style="fill:none;stroke:blue;" points="6547,-392 6265,-392 "/>
-<polyline style="fill:none;stroke:blue;" points="6547,-392 6547,-360 "/>
-<polyline style="fill:none;stroke:blue;" points="6547,-392 6551,-396 "/>
-<text text-anchor="middle" x="6408" y="-371.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">makeAnnotatorRegionsOfInterest</text>
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-<g id="edge201" class="edge"><title>t14->t121</title>
-<path style="fill:none;stroke:gray;" d="M3257,-452C3374,-441 3569,-424 3736,-418 4293,-394 5682,-431 6255,-396"/>
-<polygon style="fill:gray;stroke:gray;" points="6255.4,-399.478 6265,-395 6254.7,-392.512 6255.4,-399.478"/>
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-<g id="node236" class="node"><title>t160</title>
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-<polyline style="fill:none;stroke:blue;" points="3605,-392 3293,-392 "/>
-<polyline style="fill:none;stroke:blue;" points="3605,-392 3605,-360 "/>
-<polyline style="fill:none;stroke:blue;" points="3605,-392 3609,-396 "/>
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-<!-- t14->t160 -->
-<g id="edge217" class="edge"><title>t14->t160</title>
-<path style="fill:none;stroke:gray;" d="M3215,-444C3263,-431 3327,-413 3376,-399"/>
-<polygon style="fill:gray;stroke:gray;" points="3377.43,-402.226 3386,-396 3375.42,-395.521 3377.43,-402.226"/>
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-<g id="node240" class="node"><title>t161</title>
-<polygon style="fill:none;stroke:blue;" points="3255,-396 2913,-396 2909,-392 2909,-360 3251,-360 3255,-364 3255,-396"/>
-<polyline style="fill:none;stroke:blue;" points="3251,-392 2909,-392 "/>
-<polyline style="fill:none;stroke:blue;" points="3251,-392 3251,-360 "/>
-<polyline style="fill:none;stroke:blue;" points="3251,-392 3255,-396 "/>
-<text text-anchor="middle" x="3082" y="-371.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">makeAnnotatorRegionsOfInterestBottom</text>
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-<!-- t14->t161 -->
-<g id="edge221" class="edge"><title>t14->t161</title>
-<path style="fill:none;stroke:gray;" d="M3136,-444C3127,-432 3114,-417 3103,-404"/>
-<polygon style="fill:gray;stroke:gray;" points="3105.8,-401.9 3097,-396 3100.2,-406.1 3105.8,-401.9"/>
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-<!-- t151 -->
-<g id="node265" class="node"><title>t151</title>
-<polygon style="fill:none;stroke:blue;" points="4411,-396 4045,-396 4041,-392 4041,-360 4407,-360 4411,-364 4411,-396"/>
-<polyline style="fill:none;stroke:blue;" points="4407,-392 4041,-392 "/>
-<polyline style="fill:none;stroke:blue;" points="4407,-392 4407,-360 "/>
-<polyline style="fill:none;stroke:blue;" points="4407,-392 4411,-396 "/>
-<text text-anchor="middle" x="4226" y="-371.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">makeAnnotatorRegionsOfInterestWithMotif</text>
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-<g id="edge249" class="edge"><title>t14->t151</title>
-<path style="fill:none;stroke:gray;" d="M3257,-454C3374,-445 3569,-430 3736,-418 3865,-408 3899,-406 4031,-396"/>
-<polygon style="fill:gray;stroke:gray;" points="4031.4,-399.478 4041,-395 4030.7,-392.512 4031.4,-399.478"/>
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-<g id="node269" class="node"><title>t152</title>
-<polygon style="fill:none;stroke:blue;" points="4023,-396 3631,-396 3627,-392 3627,-360 4019,-360 4023,-364 4023,-396"/>
-<polyline style="fill:none;stroke:blue;" points="4019,-392 3627,-392 "/>
-<polyline style="fill:none;stroke:blue;" points="4019,-392 4019,-360 "/>
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-<text text-anchor="middle" x="3825" y="-371.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">makeAnnotatorRegionsOfInterestWithoutMotif</text>
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-<!-- t14->t152 -->
-<g id="edge253" class="edge"><title>t14->t152</title>
-<path style="fill:none;stroke:gray;" d="M3257,-449C3368,-435 3543,-413 3670,-397"/>
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-<polyline style="fill:none;stroke:green;" points="9431,-392 9265,-392 "/>
-<polyline style="fill:none;stroke:green;" points="9431,-392 9431,-360 "/>
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-<polygon style="fill:gray;stroke:gray;" points="9255.4,-399.478 9265,-395 9254.7,-392.512 9255.4,-399.478"/>
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-<!-- t42->t181 -->
-<g id="edge19" class="edge"><title>t42->t181</title>
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-<polygon style="fill:gray;stroke:gray;" points="1127.1,-315.2 1117,-312 1122.9,-320.8 1127.1,-315.2"/>
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-<!-- t60 -->
-<g id="node141" class="node"><title>t60</title>
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-<!-- t42->t60 -->
-<g id="edge125" class="edge"><title>t42->t60</title>
-<path style="fill:none;stroke:gray;" d="M10110,-360C10114,-354 10119,-346 10124,-339"/>
-<polygon style="fill:gray;stroke:gray;" points="10127.4,-340.262 10130,-330 10121.5,-336.379 10127.4,-340.262"/>
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-<!-- t62 -->
-<g id="node145" class="node"><title>t62</title>
-<polygon style="fill:#90ee90;stroke:green;" points="10693.9,-281.794 10788,-254.5 10882.1,-281.794 10882,-325.956 10694,-325.956 10693.9,-281.794"/>
-<polygon style="fill:none;stroke:green;" points="10689.9,-278.787 10788,-250.337 10886.1,-278.787 10886,-329.956 10690,-329.956 10689.9,-278.787"/>
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-<!-- t42->t62 -->
-<g id="edge129" class="edge"><title>t42->t62</title>
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-<polygon style="fill:gray;stroke:gray;" points="10699.4,-336.226 10708,-330 10697.4,-329.521 10699.4,-336.226"/>
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-<!-- t3 -->
-<g id="node22" class="node"><title>t3</title>
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-<polyline style="fill:none;stroke:green;" points="3976,-586 3746,-586 "/>
-<polyline style="fill:none;stroke:green;" points="3976,-586 3976,-554 "/>
-<polyline style="fill:none;stroke:green;" points="3976,-586 3980,-590 "/>
-<text text-anchor="middle" x="3863" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">importUCSCEncodeTracks</text>
-</g>
-<!-- t5 -->
-<g id="node23" class="node"><title>t5</title>
-<polygon style="fill:#90ee90;stroke:green;" points="4450,-480 4220,-480 4216,-476 4216,-444 4446,-444 4450,-448 4450,-480"/>
-<polyline style="fill:none;stroke:green;" points="4446,-476 4216,-476 "/>
-<polyline style="fill:none;stroke:green;" points="4446,-476 4446,-444 "/>
-<polyline style="fill:none;stroke:green;" points="4446,-476 4450,-480 "/>
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-<!-- t3->t5 -->
-<g id="edge13" class="edge"><title>t3->t5</title>
-<path style="fill:none;stroke:gray;" d="M3940,-554C4024,-535 4159,-503 4246,-482"/>
-<polygon style="fill:gray;stroke:gray;" points="4246.88,-485.393 4256,-480 4245.51,-478.529 4246.88,-485.393"/>
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-<!-- t3->t181 -->
-<g id="edge381" class="edge"><title>t3->t181</title>
-<path style="fill:none;stroke:gray;" d="M3746,-564C3599,-554 3338,-538 3114,-528 3045,-524 2553,-524 2485,-506 2405,-484 2395,-454 2319,-418 2298,-407 2288,-411 2269,-396 2254,-383 2262,-369 2244,-360 2191,-331 1208,-358 1150,-338 1139,-334 1129,-327 1120,-319"/>
-<polygon style="fill:gray;stroke:gray;" points="1122.55,-316.596 1113,-312 1117.6,-321.546 1122.55,-316.596"/>
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-<!-- t5->t181 -->
-<g id="edge379" class="edge"><title>t5->t181</title>
-<path style="fill:none;stroke:gray;" d="M4216,-444C4145,-434 4054,-423 3972,-418 3927,-414 2355,-418 2314,-396 2298,-386 2309,-369 2292,-360 2237,-328 1210,-359 1150,-338 1139,-334 1129,-327 1120,-319"/>
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-<!-- t5->t62 -->
-<g id="edge475" class="edge"><title>t5->t62</title>
-<path style="fill:none;stroke:gray;" d="M4374,-444C4398,-434 4430,-423 4459,-418 4502,-410 10633,-419 10668,-396 10683,-386 10672,-373 10683,-360 10691,-351 10699,-343 10709,-336"/>
-<polygon style="fill:gray;stroke:gray;" points="10711.1,-338.8 10717,-330 10706.9,-333.2 10711.1,-338.8"/>
-</g>
-<!-- t120 -->
-<g id="node201" class="node"><title>t120</title>
-<polygon style="fill:#90ee90;stroke:green;" points="5949,-396 5759,-396 5755,-392 5755,-360 5945,-360 5949,-364 5949,-396"/>
-<polyline style="fill:none;stroke:green;" points="5945,-392 5755,-392 "/>
-<polyline style="fill:none;stroke:green;" points="5945,-392 5945,-360 "/>
-<polyline style="fill:none;stroke:green;" points="5945,-392 5949,-396 "/>
-<text text-anchor="middle" x="5852" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">makeAnnotatorTracks</text>
-</g>
-<!-- t5->t120 -->
-<g id="edge181" class="edge"><title>t5->t120</title>
-<path style="fill:none;stroke:gray;" d="M4374,-444C4398,-434 4430,-423 4459,-418 4597,-393 5564,-408 5745,-396"/>
-<polygon style="fill:gray;stroke:gray;" points="5745.4,-399.478 5755,-395 5744.7,-392.512 5745.4,-399.478"/>
-</g>
-<!-- t149 -->
-<g id="node257" class="node"><title>t149</title>
-<polygon style="fill:none;stroke:blue;" points="4707,-396 4433,-396 4429,-392 4429,-360 4703,-360 4707,-364 4707,-396"/>
-<polyline style="fill:none;stroke:blue;" points="4703,-392 4429,-392 "/>
-<polyline style="fill:none;stroke:blue;" points="4703,-392 4703,-360 "/>
-<polyline style="fill:none;stroke:blue;" points="4703,-392 4707,-396 "/>
-<text text-anchor="middle" x="4568" y="-371.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">makeAnnotatorTracksWithMotif</text>
-</g>
-<!-- t5->t149 -->
-<g id="edge241" class="edge"><title>t5->t149</title>
-<path style="fill:none;stroke:gray;" d="M4383,-444C4419,-431 4469,-413 4507,-399"/>
-<polygon style="fill:gray;stroke:gray;" points="4508.43,-402.226 4517,-396 4506.42,-395.521 4508.43,-402.226"/>
-</g>
-<!-- t150 -->
-<g id="node261" class="node"><title>t150</title>
-<polygon style="fill:#90ee90;stroke:green;" points="5027,-396 4729,-396 4725,-392 4725,-360 5023,-360 5027,-364 5027,-396"/>
-<polyline style="fill:none;stroke:green;" points="5023,-392 4725,-392 "/>
-<polyline style="fill:none;stroke:green;" points="5023,-392 5023,-360 "/>
-<polyline style="fill:none;stroke:green;" points="5023,-392 5027,-396 "/>
-<text text-anchor="middle" x="4876" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">makeAnnotatorTracksWithoutMotif</text>
-</g>
-<!-- t5->t150 -->
-<g id="edge245" class="edge"><title>t5->t150</title>
-<path style="fill:none;stroke:gray;" d="M4376,-444C4400,-435 4431,-424 4459,-418 4569,-395 4600,-406 4715,-396"/>
-<polygon style="fill:gray;stroke:gray;" points="4715.4,-399.478 4725,-395 4714.7,-392.512 4715.4,-399.478"/>
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-<!-- t6 -->
-<g id="node25" class="node"><title>t6</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1925,-396 1685,-396 1681,-392 1681,-360 1921,-360 1925,-364 1925,-396"/>
-<polyline style="fill:none;stroke:green;" points="1921,-392 1681,-392 "/>
-<polyline style="fill:none;stroke:green;" points="1921,-392 1921,-360 "/>
-<polyline style="fill:none;stroke:green;" points="1921,-392 1925,-396 "/>
-<text text-anchor="middle" x="1803" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">importTranscriptInformation</text>
-</g>
-<!-- t6->t181 -->
-<g id="edge377" class="edge"><title>t6->t181</title>
-<path style="fill:none;stroke:gray;" d="M1681,-361C1678,-361 1675,-360 1672,-360 1614,-354 1203,-359 1148,-338 1137,-333 1128,-326 1119,-319"/>
-<polygon style="fill:gray;stroke:gray;" points="1121.55,-316.596 1112,-312 1116.6,-321.546 1121.55,-316.596"/>
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-<!-- t7 -->
-<g id="node26" class="node"><title>t7</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1663,-396 1463,-396 1459,-392 1459,-360 1659,-360 1663,-364 1663,-396"/>
-<polyline style="fill:none;stroke:green;" points="1659,-392 1459,-392 "/>
-<polyline style="fill:none;stroke:green;" points="1659,-392 1659,-360 "/>
-<polyline style="fill:none;stroke:green;" points="1659,-392 1663,-396 "/>
-<text text-anchor="middle" x="1561" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">importGeneInformation</text>
-</g>
-<!-- t7->t181 -->
-<g id="edge375" class="edge"><title>t7->t181</title>
-<path style="fill:none;stroke:gray;" d="M1459,-361C1454,-361 1450,-360 1445,-360 1380,-352 1210,-363 1148,-338 1137,-333 1128,-326 1119,-319"/>
-<polygon style="fill:gray;stroke:gray;" points="1121.55,-316.596 1112,-312 1116.6,-321.546 1121.55,-316.596"/>
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-<!-- t38->t181 -->
-<g id="edge351" class="edge"><title>t38->t181</title>
-<path style="fill:none;stroke:gray;" d="M2481,-362C2476,-361 2471,-360 2467,-360 2395,-352 1217,-363 1148,-338 1137,-334 1128,-327 1119,-320"/>
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-<!-- t33 -->
-<g id="node29" class="node"><title>t33</title>
-<polygon style="fill:#90ee90;stroke:green;" points="2225,-396 1967,-396 1963,-392 1963,-360 2221,-360 2225,-364 2225,-396"/>
-<polyline style="fill:none;stroke:green;" points="2221,-392 1963,-392 "/>
-<polyline style="fill:none;stroke:green;" points="2221,-392 2221,-360 "/>
-<polyline style="fill:none;stroke:green;" points="2221,-392 2225,-396 "/>
-<text text-anchor="middle" x="2094" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">buildAnnotatorGeneTerritories</text>
-</g>
-<!-- t33->t181 -->
-<g id="edge361" class="edge"><title>t33->t181</title>
-<path style="fill:none;stroke:gray;" d="M1963,-361C1958,-361 1954,-360 1949,-360 1861,-353 1232,-369 1148,-338 1137,-334 1128,-327 1119,-320"/>
-<polygon style="fill:gray;stroke:gray;" points="1121.22,-317.221 1112,-312 1115.95,-321.831 1121.22,-317.221"/>
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-<!-- t12->t181 -->
-<g id="edge369" class="edge"><title>t12->t181</title>
-<path style="fill:none;stroke:gray;" d="M2201,-444C2225,-421 2259,-384 2234,-360 2192,-316 1205,-359 1148,-338 1137,-334 1128,-327 1119,-320"/>
-<polygon style="fill:gray;stroke:gray;" points="1121.22,-317.221 1112,-312 1115.95,-321.831 1121.22,-317.221"/>
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-<!-- t191 -->
-<g id="node314" class="node"><title>t191</title>
-<polygon style="fill:#fff68f;stroke:black;" points="3551,-60 3501,-60 3497,-56 3497,-24 3547,-24 3551,-28 3551,-60"/>
-<polyline style="fill:none;stroke:black;" points="3547,-56 3497,-56 "/>
-<polyline style="fill:none;stroke:black;" points="3547,-56 3547,-24 "/>
-<polyline style="fill:none;stroke:black;" points="3547,-56 3551,-60 "/>
-<text text-anchor="middle" x="3524" y="-35.5" style="font-family:Times New Roman;font-size:20.00;">full</text>
-</g>
-<!-- t181->t191 -->
-<g id="edge331" class="edge"><title>t181->t191</title>
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-<!-- t17 -->
-<g id="node36" class="node"><title>t17</title>
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-<polyline style="fill:none;stroke:green;" points="9749,-1005 9613,-1005 "/>
-<polyline style="fill:none;stroke:green;" points="9749,-1005 9749,-973 "/>
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-<text text-anchor="middle" x="9683" y="-984.5" style="font-family:Times New Roman;font-size:20.00;">buildBAMStats</text>
-</g>
-<!-- t16->t17 -->
-<g id="edge23" class="edge"><title>t16->t17</title>
-<path style="fill:none;stroke:gray;" d="M5835,-1075C6252,-1066 9086,-1004 9603,-993"/>
-<polygon style="fill:gray;stroke:gray;" points="9603,-996.5 9613,-993 9603,-989.5 9603,-996.5"/>
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-<!-- t18 -->
-<g id="node38" class="node"><title>t18</title>
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-<polyline style="fill:none;stroke:green;" points="10044,-920 9806,-920 "/>
-<polyline style="fill:none;stroke:green;" points="10044,-920 10044,-888 "/>
-<polyline style="fill:none;stroke:green;" points="10044,-920 10048,-924 "/>
-<text text-anchor="middle" x="9927" y="-899.5" style="font-family:Times New Roman;font-size:20.00;">normalizeBAMPerReplicate</text>
-</g>
-<!-- t17->t18 -->
-<g id="edge25" class="edge"><title>t17->t18</title>
-<path style="fill:none;stroke:gray;" d="M9735,-973C9773,-960 9825,-942 9865,-927"/>
-<polygon style="fill:gray;stroke:gray;" points="9866.43,-930.226 9875,-924 9864.42,-923.521 9866.43,-930.226"/>
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-<!-- t20 -->
-<g id="node40" class="node"><title>t20</title>
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-<polyline style="fill:none;stroke:green;" points="9784,-920 9578,-920 "/>
-<polyline style="fill:none;stroke:green;" points="9784,-920 9784,-888 "/>
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-<text text-anchor="middle" x="9683" y="-899.5" style="font-family:Times New Roman;font-size:20.00;">normalizeBAMControls</text>
-</g>
-<!-- t17->t20 -->
-<g id="edge27" class="edge"><title>t17->t20</title>
-<path style="fill:none;stroke:gray;" d="M9683,-973C9683,-962 9683,-947 9683,-934"/>
-<polygon style="fill:gray;stroke:gray;" points="9686.5,-934 9683,-924 9679.5,-934 9686.5,-934"/>
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-<!-- t21 -->
-<g id="node42" class="node"><title>t21</title>
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-<polyline style="fill:none;stroke:green;" points="9913,-854 9819,-854 "/>
-<polyline style="fill:none;stroke:green;" points="9913,-854 9913,-822 "/>
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-<text text-anchor="middle" x="9868" y="-833.5" style="font-family:Times New Roman;font-size:20.00;">runMACS</text>
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-<!-- t18->t21 -->
-<g id="edge385" class="edge"><title>t18->t21</title>
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-<!-- t29 -->
-<g id="node54" class="node"><title>t29</title>
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-<polyline style="fill:none;stroke:green;" points="10458,-308 10458,-276 "/>
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-<text text-anchor="middle" x="10352" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">importCombinedIntervals</text>
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-<!-- t18->t29 -->
-<g id="edge393" class="edge"><title>t18->t29</title>
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-<!-- t20->t21 -->
-<g id="edge29" class="edge"><title>t20->t21</title>
-<path style="fill:none;stroke:gray;" d="M9734,-888C9757,-879 9785,-870 9809,-861"/>
-<polygon style="fill:gray;stroke:gray;" points="9811.02,-863.964 9819,-857 9808.42,-857.464 9811.02,-863.964"/>
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-<!-- t22 -->
-<g id="node44" class="node"><title>t22</title>
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-<polyline style="fill:none;stroke:green;" points="10143,-770 10023,-770 "/>
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-<text text-anchor="middle" x="10085" y="-749.5" style="font-family:Times New Roman;font-size:20.00;">importMACS</text>
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-<g id="edge31" class="edge"><title>t21->t22</title>
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-<g id="node56" class="node"><title>t23</title>
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-<g id="edge43" class="edge"><title>t21->t23</title>
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-<!-- t21->t179 -->
-<g id="edge163" class="edge"><title>t21->t179</title>
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-<!-- t25 -->
-<g id="node46" class="node"><title>t25</title>
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-<polyline style="fill:none;stroke:green;" points="10194,-678 10194,-646 "/>
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-<text text-anchor="middle" x="10102" y="-657.5" style="font-family:Times New Roman;font-size:20.00;">exportIntervalsAsBed</text>
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-<!-- t22->t25 -->
-<g id="edge33" class="edge"><title>t22->t25</title>
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-<!-- t26 -->
-<g id="node48" class="node"><title>t26</title>
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-<polyline style="fill:none;stroke:green;" points="10260,-586 10260,-554 "/>
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-<text text-anchor="middle" x="10181" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">combineReplicates</text>
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-<!-- t25->t26 -->
-<g id="edge35" class="edge"><title>t25->t26</title>
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-<polygon style="fill:gray;stroke:gray;" points="10162,-599.831 10166,-590 10156.8,-595.221 10162,-599.831"/>
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-<!-- t27 -->
-<g id="node50" class="node"><title>t27</title>
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-<polyline style="fill:none;stroke:green;" points="10202,-476 10036,-476 "/>
-<polyline style="fill:none;stroke:green;" points="10202,-476 10202,-444 "/>
-<polyline style="fill:none;stroke:green;" points="10202,-476 10206,-480 "/>
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-<!-- t25->t27 -->
-<g id="edge387" class="edge"><title>t25->t27</title>
-<path style="fill:none;stroke:gray;" d="M10096,-646C10093,-637 10090,-626 10089,-616 10084,-577 10081,-566 10089,-528 10092,-515 10098,-501 10105,-489"/>
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-</g>
-<!-- t31 -->
-<g id="node131" class="node"><title>t31</title>
-<polygon style="fill:#90ee90;stroke:green;" points="10432,-590 10316,-590 10312,-586 10312,-554 10428,-554 10432,-558 10432,-590"/>
-<polyline style="fill:none;stroke:green;" points="10428,-586 10312,-586 "/>
-<polyline style="fill:none;stroke:green;" points="10428,-586 10428,-554 "/>
-<polyline style="fill:none;stroke:green;" points="10428,-586 10432,-590 "/>
-<text text-anchor="middle" x="10372" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">makeMerged</text>
-</g>
-<!-- t25->t31 -->
-<g id="edge115" class="edge"><title>t25->t31</title>
-<path style="fill:none;stroke:gray;" d="M10174,-646C10205,-638 10241,-627 10273,-616 10291,-609 10309,-602 10325,-594"/>
-<polygon style="fill:gray;stroke:gray;" points="10326.3,-597.26 10334,-590 10323.4,-590.863 10326.3,-597.26"/>
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-<!-- t25->t60 -->
-<g id="edge467" class="edge"><title>t25->t60</title>
-<path style="fill:none;stroke:gray;" d="M10084,-646C10041,-602 9944,-487 10006,-418 10039,-382 10191,-431 10223,-396 10239,-378 10228,-356 10210,-337"/>
-<polygon style="fill:gray;stroke:gray;" points="10212.5,-334.596 10203,-330 10207.6,-339.546 10212.5,-334.596"/>
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-<!-- t26->t27 -->
-<g id="edge37" class="edge"><title>t26->t27</title>
-<path style="fill:none;stroke:gray;" d="M10171,-554C10161,-537 10147,-510 10136,-489"/>
-<polygon style="fill:gray;stroke:gray;" points="10138.9,-487.042 10131,-480 10132.8,-490.441 10138.9,-487.042"/>
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-<!-- t26->t29 -->
-<g id="edge391" class="edge"><title>t26->t29</title>
-<path style="fill:none;stroke:gray;" d="M10098,-556C10071,-546 10043,-530 10027,-506 10006,-473 10001,-446 10027,-418 10063,-379 10219,-424 10263,-396 10279,-385 10272,-374 10283,-360 10295,-345 10309,-330 10322,-319"/>
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-<!-- t26->t62 -->
-<g id="edge473" class="edge"><title>t26->t62</title>
-<path style="fill:none;stroke:gray;" d="M10192,-554C10200,-541 10209,-523 10215,-506 10229,-468 10205,-443 10235,-418 10275,-384 10656,-420 10701,-396 10719,-386 10716,-375 10728,-360 10734,-353 10741,-345 10747,-338"/>
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-<!-- t28 -->
-<g id="node52" class="node"><title>t28</title>
-<polygon style="fill:#90ee90;stroke:green;" points="10659,-396 10521,-396 10517,-392 10517,-360 10655,-360 10659,-364 10659,-396"/>
-<polyline style="fill:none;stroke:green;" points="10655,-392 10517,-392 "/>
-<polyline style="fill:none;stroke:green;" points="10655,-392 10655,-360 "/>
-<polyline style="fill:none;stroke:green;" points="10655,-392 10659,-396 "/>
-<text text-anchor="middle" x="10588" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">combineUnstim</text>
-</g>
-<!-- t27->t28 -->
-<g id="edge39" class="edge"><title>t27->t28</title>
-<path style="fill:none;stroke:gray;" d="M10154,-444C10173,-434 10197,-423 10220,-418 10342,-387 10380,-414 10507,-396"/>
-<polygon style="fill:gray;stroke:gray;" points="10507.9,-399.393 10517,-394 10506.5,-392.529 10507.9,-399.393"/>
-</g>
-<!-- t27->t29 -->
-<g id="edge389" class="edge"><title>t27->t29</title>
-<path style="fill:none;stroke:gray;" d="M10160,-444C10178,-435 10200,-426 10220,-418 10248,-407 10260,-414 10283,-396 10285,-394 10315,-350 10334,-321"/>
-<polygon style="fill:gray;stroke:gray;" points="10337.4,-322.262 10340,-312 10331.5,-318.379 10337.4,-322.262"/>
-</g>
-<!-- t27->t62 -->
-<g id="edge471" class="edge"><title>t27->t62</title>
-<path style="fill:none;stroke:gray;" d="M10154,-444C10173,-434 10197,-423 10220,-418 10321,-394 10591,-441 10683,-396 10702,-386 10699,-374 10713,-360 10721,-352 10729,-345 10738,-337"/>
-<polygon style="fill:gray;stroke:gray;" points="10740.4,-339.546 10745,-330 10735.5,-334.596 10740.4,-339.546"/>
-</g>
-<!-- t28->t29 -->
-<g id="edge41" class="edge"><title>t28->t29</title>
-<path style="fill:none;stroke:gray;" d="M10535,-360C10515,-353 10492,-345 10471,-338 10451,-331 10429,-323 10409,-315"/>
-<polygon style="fill:gray;stroke:gray;" points="10410.6,-311.842 10400,-312 10408.4,-318.483 10410.6,-311.842"/>
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-<!-- t28->t62 -->
-<g id="edge469" class="edge"><title>t28->t62</title>
-<path style="fill:none;stroke:gray;" d="M10631,-360C10649,-352 10671,-343 10693,-334"/>
-<polygon style="fill:gray;stroke:gray;" points="10694.3,-337.26 10702,-330 10691.4,-330.863 10694.3,-337.26"/>
-</g>
-<!-- t30 -->
-<g id="node60" class="node"><title>t30</title>
-<polygon style="fill:none;stroke:blue;" points="10128,-202 10006,-202 10002,-198 10002,-166 10124,-166 10128,-170 10128,-202"/>
-<polyline style="fill:none;stroke:blue;" points="10124,-198 10002,-198 "/>
-<polyline style="fill:none;stroke:blue;" points="10124,-198 10124,-166 "/>
-<polyline style="fill:none;stroke:blue;" points="10124,-198 10128,-202 "/>
-<text text-anchor="middle" x="10065" y="-177.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">buildIntervals</text>
-</g>
-<!-- t29->t30 -->
-<g id="edge47" class="edge"><title>t29->t30</title>
-<path style="fill:none;stroke:gray;" d="M10305,-276C10255,-257 10176,-227 10121,-206"/>
-<polygon style="fill:gray;stroke:gray;" points="10122.6,-202.863 10112,-202 10119.7,-209.26 10122.6,-202.863"/>
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-<!-- t24 -->
-<g id="node58" class="node"><title>t24</title>
-<polygon style="fill:#90ee90;stroke:green;" points="9968,-682 9772,-682 9768,-678 9768,-646 9964,-646 9968,-650 9968,-682"/>
-<polyline style="fill:none;stroke:green;" points="9964,-678 9768,-678 "/>
-<polyline style="fill:none;stroke:green;" points="9964,-678 9964,-646 "/>
-<polyline style="fill:none;stroke:green;" points="9964,-678 9968,-682 "/>
-<text text-anchor="middle" x="9868" y="-657.5" style="font-family:Times New Roman;font-size:20.00;">importMACSSummary</text>
-</g>
-<!-- t23->t24 -->
-<g id="edge45" class="edge"><title>t23->t24</title>
-<path style="fill:none;stroke:gray;" d="M9868,-712C9868,-706 9868,-699 9868,-692"/>
-<polygon style="fill:gray;stroke:gray;" points="9871.5,-692 9868,-682 9864.5,-692 9871.5,-692"/>
-</g>
-<!-- t24->t30 -->
-<g id="edge395" class="edge"><title>t24->t30</title>
-<path style="fill:none;stroke:gray;" d="M9870,-646C9878,-599 9904,-474 9983,-418 10025,-388 10175,-433 10208,-396 10219,-384 10219,-372 10208,-360 10170,-314 10116,-382 10075,-338 10044,-304 10050,-246 10058,-212"/>
-<polygon style="fill:gray;stroke:gray;" points="10061.5,-212.492 10060,-202 10054.6,-211.119 10061.5,-212.492"/>
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-<!-- t182 -->
-<g id="node63" class="node"><title>t182</title>
-<polygon style="fill:none;stroke:blue;" points="9700,-118 9620,-118 9616,-114 9616,-82 9696,-82 9700,-86 9700,-118"/>
-<polyline style="fill:none;stroke:blue;" points="9696,-114 9616,-114 "/>
-<polyline style="fill:none;stroke:blue;" points="9696,-114 9696,-82 "/>
-<polyline style="fill:none;stroke:blue;" points="9696,-114 9700,-118 "/>
-<text text-anchor="middle" x="9658" y="-93.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">intervals</text>
-</g>
-<!-- t30->t182 -->
-<g id="edge49" class="edge"><title>t30->t182</title>
-<path style="fill:none;stroke:blue;" d="M10002,-171C9922,-154 9785,-126 9710,-111"/>
-<polygon style="fill:blue;stroke:blue;" points="9710.49,-107.529 9700,-109 9709.12,-114.393 9710.49,-107.529"/>
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-<!-- t15 -->
-<g id="node62" class="node"><title>t15</title>
-<polygon style="fill:#90ee90;stroke:green;" points="9768,-202 9552,-202 9548,-198 9548,-166 9764,-166 9768,-170 9768,-202"/>
-<polyline style="fill:none;stroke:green;" points="9764,-198 9548,-198 "/>
-<polyline style="fill:none;stroke:green;" points="9764,-198 9764,-166 "/>
-<polyline style="fill:none;stroke:green;" points="9764,-198 9768,-202 "/>
-<text text-anchor="middle" x="9658" y="-177.5" style="font-family:Times New Roman;font-size:20.00;">importReferenceIntervals</text>
-</g>
-<!-- t15->t182 -->
-<g id="edge397" class="edge"><title>t15->t182</title>
-<path style="fill:none;stroke:gray;" d="M9658,-166C9658,-155 9658,-141 9658,-128"/>
-<polygon style="fill:gray;stroke:gray;" points="9661.5,-128 9658,-118 9654.5,-128 9661.5,-128"/>
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-<!-- t182->t191 -->
-<g id="edge329" class="edge"><title>t182->t191</title>
-<path style="fill:none;stroke:blue;" d="M9616,-100C9102,-95 4048,-47 3561,-42"/>
-<polygon style="fill:blue;stroke:blue;" points="3561,-38.5001 3551,-42 3561,-45.5001 3561,-38.5001"/>
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-<!-- t73 -->
-<g id="node65" class="node"><title>t73</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1826,-590 1720,-590 1716,-586 1716,-554 1822,-554 1826,-558 1826,-590"/>
-<polyline style="fill:none;stroke:green;" points="1822,-586 1716,-586 "/>
-<polyline style="fill:none;stroke:green;" points="1822,-586 1822,-554 "/>
-<polyline style="fill:none;stroke:green;" points="1822,-586 1826,-590 "/>
-<text text-anchor="middle" x="1771" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">makeMotifs</text>
-</g>
-<!-- t76 -->
-<g id="node69" class="node"><title>t76</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1214,-480 1104,-480 1100,-476 1100,-444 1210,-444 1214,-448 1214,-480"/>
-<polyline style="fill:none;stroke:green;" points="1210,-476 1100,-476 "/>
-<polyline style="fill:none;stroke:green;" points="1210,-476 1210,-444 "/>
-<polyline style="fill:none;stroke:green;" points="1210,-476 1214,-480 "/>
-<text text-anchor="middle" x="1157" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">runTomTom</text>
-</g>
-<!-- t73->t76 -->
-<g id="edge399" class="edge"><title>t73->t76</title>
-<path style="fill:none;stroke:gray;" d="M1744,-554C1728,-544 1707,-533 1687,-528 1518,-481 1465,-538 1292,-506 1266,-501 1237,-492 1213,-483"/>
-<polygon style="fill:gray;stroke:gray;" points="1213.58,-479.521 1203,-480 1211.57,-486.226 1213.58,-479.521"/>
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-<!-- t185 -->
-<g id="node80" class="node"><title>t185</title>
-<polygon style="fill:none;stroke:blue;" points="744,-312 632,-312 628,-308 628,-276 740,-276 744,-280 744,-312"/>
-<polyline style="fill:none;stroke:blue;" points="740,-308 628,-308 "/>
-<polyline style="fill:none;stroke:blue;" points="740,-308 740,-276 "/>
-<polyline style="fill:none;stroke:blue;" points="740,-308 744,-312 "/>
-<text text-anchor="middle" x="686" y="-287.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">build_motifs</text>
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-<!-- t73->t185 -->
-<g id="edge411" class="edge"><title>t73->t185</title>
-<path style="fill:none;stroke:gray;" d="M1744,-554C1728,-544 1707,-533 1687,-528 1554,-490 1509,-546 1376,-506 1301,-483 1299,-440 1223,-418 1138,-392 896,-444 820,-396 805,-386 815,-372 801,-360 784,-343 774,-349 753,-338 742,-332 731,-324 721,-318"/>
-<polygon style="fill:gray;stroke:gray;" points="722.262,-314.635 712,-312 718.379,-320.459 722.262,-314.635"/>
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-<!-- t79 -->
-<g id="node82" class="node"><title>t79</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1040,-312 946,-312 942,-308 942,-276 1036,-276 1040,-280 1040,-312"/>
-<polyline style="fill:none;stroke:green;" points="1036,-308 942,-308 "/>
-<polyline style="fill:none;stroke:green;" points="1036,-308 1036,-276 "/>
-<polyline style="fill:none;stroke:green;" points="1036,-308 1040,-312 "/>
-<text text-anchor="middle" x="991" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">runMAST</text>
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-<!-- t73->t79 -->
-<g id="edge417" class="edge"><title>t73->t79</title>
-<path style="fill:none;stroke:gray;" d="M1744,-554C1731,-545 1715,-536 1700,-528 1578,-461 1536,-466 1415,-396 1392,-382 1391,-369 1365,-360 1233,-312 1181,-387 1049,-338 1037,-333 1026,-326 1017,-319"/>
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-<!-- t91 -->
-<g id="node86" class="node"><title>t91</title>
-<polygon style="fill:none;stroke:blue;" points="924,-312 766,-312 762,-308 762,-276 920,-276 924,-280 924,-312"/>
-<polyline style="fill:none;stroke:blue;" points="920,-308 762,-308 "/>
-<polyline style="fill:none;stroke:blue;" points="920,-308 920,-276 "/>
-<polyline style="fill:none;stroke:blue;" points="920,-308 924,-312 "/>
-<text text-anchor="middle" x="843" y="-287.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">runGLAM2SCAN</text>
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-<!-- t73->t91 -->
-<g id="edge423" class="edge"><title>t73->t91</title>
-<path style="fill:none;stroke:gray;" d="M1749,-554C1735,-544 1718,-533 1700,-528 1597,-493 1553,-556 1456,-506 1400,-476 1398,-450 1365,-396 1357,-381 1365,-369 1350,-360 1313,-333 978,-349 933,-338 915,-333 897,-325 882,-317"/>
-<polygon style="fill:gray;stroke:gray;" points="883.441,-313.797 873,-312 880.042,-319.916 883.441,-313.797"/>
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-<!-- t58 -->
-<g id="node66" class="node"><title>t58</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1760,-682 1568,-682 1564,-678 1564,-646 1756,-646 1760,-650 1760,-682"/>
-<polyline style="fill:none;stroke:green;" points="1756,-678 1564,-678 "/>
-<polyline style="fill:none;stroke:green;" points="1756,-678 1756,-646 "/>
-<polyline style="fill:none;stroke:green;" points="1756,-678 1760,-682 "/>
-<text text-anchor="middle" x="1662" y="-657.5" style="font-family:Times New Roman;font-size:20.00;">exportMotifSequences</text>
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-<!-- t74 -->
-<g id="node67" class="node"><title>t74</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1678,-590 1582,-590 1578,-586 1578,-554 1674,-554 1678,-558 1678,-590"/>
-<polyline style="fill:none;stroke:green;" points="1674,-586 1578,-586 "/>
-<polyline style="fill:none;stroke:green;" points="1674,-586 1674,-554 "/>
-<polyline style="fill:none;stroke:green;" points="1674,-586 1678,-590 "/>
-<text text-anchor="middle" x="1628" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">runMEME</text>
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-<!-- t58->t74 -->
-<g id="edge51" class="edge"><title>t58->t74</title>
-<path style="fill:none;stroke:gray;" d="M1655,-646C1650,-633 1643,-615 1638,-600"/>
-<polygon style="fill:gray;stroke:gray;" points="1641.23,-598.573 1635,-590 1634.52,-600.584 1641.23,-598.573"/>
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-<!-- t75 -->
-<g id="node75" class="node"><title>t75</title>
-<polygon style="fill:#90ee90;stroke:green;" points="939,-396 833,-396 829,-392 829,-360 935,-360 939,-364 939,-396"/>
-<polyline style="fill:none;stroke:green;" points="935,-392 829,-392 "/>
-<polyline style="fill:none;stroke:green;" points="935,-392 935,-360 "/>
-<polyline style="fill:none;stroke:green;" points="935,-392 939,-396 "/>
-<text text-anchor="middle" x="884" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">runGLAM2</text>
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-<!-- t58->t75 -->
-<g id="edge59" class="edge"><title>t58->t75</title>
-<path style="fill:none;stroke:gray;" d="M1674,-646C1691,-617 1717,-560 1687,-528 1662,-501 1391,-517 1355,-506 1289,-483 1290,-441 1223,-418 1111,-378 1071,-415 949,-396"/>
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-<!-- t80 -->
-<g id="node78" class="node"><title>t80</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1540,-590 1388,-590 1384,-586 1384,-554 1536,-554 1540,-558 1540,-590"/>
-<polyline style="fill:none;stroke:green;" points="1536,-586 1384,-586 "/>
-<polyline style="fill:none;stroke:green;" points="1536,-586 1536,-554 "/>
-<polyline style="fill:none;stroke:green;" points="1536,-586 1540,-590 "/>
-<text text-anchor="middle" x="1462" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">runBioProspector</text>
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-<!-- t58->t80 -->
-<g id="edge61" class="edge"><title>t58->t80</title>
-<path style="fill:none;stroke:gray;" d="M1621,-646C1601,-637 1576,-626 1554,-616 1539,-609 1523,-602 1509,-594"/>
-<polygon style="fill:gray;stroke:gray;" points="1510.56,-590.863 1500,-590 1507.72,-597.26 1510.56,-590.863"/>
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-<!-- t58->t185 -->
-<g id="edge415" class="edge"><title>t58->t185</title>
-<path style="fill:none;stroke:gray;" d="M1609,-646C1594,-639 1579,-629 1569,-616 1545,-584 1580,-553 1549,-528 1508,-493 1107,-540 1066,-506 1036,-480 1079,-444 1048,-418 1012,-386 645,-431 611,-396 588,-371 619,-339 648,-318"/>
-<polygon style="fill:gray;stroke:gray;" points="650.621,-320.459 657,-312 646.738,-314.635 650.621,-320.459"/>
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-<!-- t58->t79 -->
-<g id="edge421" class="edge"><title>t58->t79</title>
-<path style="fill:none;stroke:gray;" d="M1760,-650C1800,-642 1838,-631 1850,-616 1874,-585 1874,-559 1850,-528 1828,-498 1805,-516 1769,-506 1620,-461 1565,-483 1435,-396 1418,-384 1424,-369 1405,-360 1335,-324 1124,-365 1049,-338 1037,-333 1026,-326 1017,-319"/>
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-<!-- t58->t91 -->
-<g id="edge427" class="edge"><title>t58->t91</title>
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-<!-- t74->t76 -->
-<g id="edge53" class="edge"><title>t74->t76</title>
-<path style="fill:none;stroke:gray;" d="M1608,-554C1596,-544 1580,-533 1564,-528 1442,-484 1399,-534 1272,-506 1250,-501 1226,-492 1205,-484"/>
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-<!-- t74->t185 -->
-<g id="edge409" class="edge"><title>t74->t185</title>
-<path style="fill:none;stroke:gray;" d="M1608,-554C1596,-544 1580,-533 1564,-528 1515,-511 1133,-538 1091,-506 1060,-480 1098,-443 1066,-418 1028,-387 657,-431 622,-396 600,-372 628,-341 653,-319"/>
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-<!-- t77 -->
-<g id="node71" class="node"><title>t77</title>
-<polygon style="fill:#90ee90;stroke:green;" points="771,-396 635,-396 631,-392 631,-360 767,-360 771,-364 771,-396"/>
-<polyline style="fill:none;stroke:green;" points="767,-392 631,-392 "/>
-<polyline style="fill:none;stroke:green;" points="767,-392 767,-360 "/>
-<polyline style="fill:none;stroke:green;" points="767,-392 771,-396 "/>
-<text text-anchor="middle" x="701" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">importTomTom</text>
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-<g id="edge55" class="edge"><title>t76->t77</title>
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-<polygon style="fill:gray;stroke:gray;" points="781.299,-391.512 771,-394 780.602,-398.478 781.299,-391.512"/>
-</g>
-<!-- t78 -->
-<g id="node73" class="node"><title>t78</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1065,-396 961,-396 957,-392 957,-360 1061,-360 1065,-364 1065,-396"/>
-<polyline style="fill:none;stroke:green;" points="1061,-392 957,-392 "/>
-<polyline style="fill:none;stroke:green;" points="1061,-392 1061,-360 "/>
-<polyline style="fill:none;stroke:green;" points="1061,-392 1065,-396 "/>
-<text text-anchor="middle" x="1011" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">filterMotifs</text>
-</g>
-<!-- t76->t78 -->
-<g id="edge57" class="edge"><title>t76->t78</title>
-<path style="fill:none;stroke:gray;" d="M1129,-444C1116,-436 1101,-426 1086,-418 1076,-413 1066,-407 1056,-401"/>
-<polygon style="fill:gray;stroke:gray;" points="1057.44,-397.797 1047,-396 1054.04,-403.916 1057.44,-397.797"/>
-</g>
-<!-- t76->t185 -->
-<g id="edge405" class="edge"><title>t76->t185</title>
-<path style="fill:none;stroke:gray;" d="M1135,-444C1121,-434 1104,-423 1086,-418 1027,-398 860,-427 805,-396 789,-386 794,-373 780,-360 770,-350 745,-333 723,-318"/>
-<polygon style="fill:gray;stroke:gray;" points="725.1,-315.2 715,-312 720.9,-320.8 725.1,-315.2"/>
-</g>
-<!-- t77->t185 -->
-<g id="edge403" class="edge"><title>t77->t185</title>
-<path style="fill:none;stroke:gray;" d="M698,-360C696,-349 693,-334 691,-322"/>
-<polygon style="fill:gray;stroke:gray;" points="694.393,-321.119 689,-312 687.529,-322.492 694.393,-321.119"/>
-</g>
-<!-- t78->t185 -->
-<g id="edge401" class="edge"><title>t78->t185</title>
-<path style="fill:none;stroke:gray;" d="M957,-362C954,-361 951,-361 948,-360 863,-343 836,-367 753,-338 740,-333 727,-325 716,-318"/>
-<polygon style="fill:gray;stroke:gray;" points="718.1,-315.2 708,-312 713.9,-320.8 718.1,-315.2"/>
-</g>
-<!-- t78->t79 -->
-<g id="edge65" class="edge"><title>t78->t79</title>
-<path style="fill:none;stroke:gray;" d="M1007,-360C1005,-349 1001,-334 998,-322"/>
-<polygon style="fill:gray;stroke:gray;" points="1001.23,-320.573 995,-312 994.521,-322.584 1001.23,-320.573"/>
-</g>
-<!-- t75->t185 -->
-<g id="edge407" class="edge"><title>t75->t185</title>
-<path style="fill:none;stroke:gray;" d="M829,-363C800,-354 767,-344 753,-338 741,-333 730,-325 719,-318"/>
-<polygon style="fill:gray;stroke:gray;" points="721.1,-315.2 711,-312 716.9,-320.8 721.1,-315.2"/>
-</g>
-<!-- t75->t91 -->
-<g id="edge69" class="edge"><title>t75->t91</title>
-<path style="fill:none;stroke:gray;" d="M875,-360C869,-349 863,-334 856,-321"/>
-<polygon style="fill:gray;stroke:gray;" points="859.26,-319.717 852,-312 852.863,-322.56 859.26,-319.717"/>
-</g>
-<!-- t59 -->
-<g id="node77" class="node"><title>t59</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1341,-396 1087,-396 1083,-392 1083,-360 1337,-360 1341,-364 1341,-396"/>
-<polyline style="fill:none;stroke:green;" points="1337,-392 1083,-392 "/>
-<polyline style="fill:none;stroke:green;" points="1337,-392 1337,-360 "/>
-<polyline style="fill:none;stroke:green;" points="1337,-392 1341,-396 "/>
-<text text-anchor="middle" x="1212" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">exportMotifControlSequences</text>
-</g>
-<!-- t59->t185 -->
-<g id="edge413" class="edge"><title>t59->t185</title>
-<path style="fill:none;stroke:gray;" d="M1083,-361C1080,-361 1077,-360 1074,-360 1003,-352 821,-360 753,-338 740,-333 727,-326 716,-318"/>
-<polygon style="fill:gray;stroke:gray;" points="718.1,-315.2 708,-312 713.9,-320.8 718.1,-315.2"/>
-</g>
-<!-- t59->t79 -->
-<g id="edge419" class="edge"><title>t59->t79</title>
-<path style="fill:none;stroke:gray;" d="M1111,-360C1090,-354 1068,-347 1049,-338 1038,-333 1028,-326 1019,-319"/>
-<polygon style="fill:gray;stroke:gray;" points="1020.83,-315.951 1011,-312 1016.22,-321.219 1020.83,-315.951"/>
-</g>
-<!-- t59->t91 -->
-<g id="edge425" class="edge"><title>t59->t91</title>
-<path style="fill:none;stroke:gray;" d="M1083,-360C1014,-350 941,-340 933,-338 916,-332 899,-324 884,-317"/>
-<polygon style="fill:gray;stroke:gray;" points="885.441,-313.797 875,-312 882.042,-319.916 885.441,-313.797"/>
-</g>
-<!-- t80->t185 -->
-<g id="edge63" class="edge"><title>t80->t185</title>
-<path style="fill:none;stroke:gray;" d="M1432,-554C1415,-544 1392,-533 1370,-528 1303,-510 1112,-548 1056,-506 1024,-480 1059,-442 1026,-418 988,-388 621,-431 587,-396 576,-384 580,-374 587,-360 591,-354 621,-334 647,-317"/>
-<polygon style="fill:gray;stroke:gray;" points="648.958,-319.916 656,-312 645.559,-313.797 648.958,-319.916"/>
-</g>
-<!-- t185->t191 -->
-<g id="edge325" class="edge"><title>t185->t191</title>
-<path style="fill:none;stroke:blue;" d="M707,-276C720,-266 737,-255 753,-250 808,-231 969,-265 1012,-228 1043,-201 1004,-168 1032,-140 1109,-62 1163,-95 1271,-82 1500,-52 3210,-43 3487,-42"/>
-<polygon style="fill:blue;stroke:blue;" points="3487,-45.5001 3497,-42 3487,-38.5001 3487,-45.5001"/>
-</g>
-<!-- t90 -->
-<g id="node84" class="node"><title>t90</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1396,-202 1276,-202 1272,-198 1272,-166 1392,-166 1396,-170 1396,-202"/>
-<polyline style="fill:none;stroke:green;" points="1392,-198 1272,-198 "/>
-<polyline style="fill:none;stroke:green;" points="1392,-198 1392,-166 "/>
-<polyline style="fill:none;stroke:green;" points="1392,-198 1396,-202 "/>
-<text text-anchor="middle" x="1334" y="-177.5" style="font-family:Times New Roman;font-size:20.00;">importMAST</text>
-</g>
-<!-- t79->t90 -->
-<g id="edge67" class="edge"><title>t79->t90</title>
-<path style="fill:none;stroke:gray;" d="M1009,-276C1020,-266 1034,-255 1049,-250 1138,-214 1173,-258 1263,-228 1277,-223 1291,-216 1303,-208"/>
-<polygon style="fill:gray;stroke:gray;" points="1305.1,-210.8 1311,-202 1300.9,-205.2 1305.1,-210.8"/>
-</g>
-<!-- t186 -->
-<g id="node90" class="node"><title>t186</title>
-<polygon style="fill:none;stroke:blue;" points="1388,-118 1284,-118 1280,-114 1280,-82 1384,-82 1388,-86 1388,-118"/>
-<polyline style="fill:none;stroke:blue;" points="1384,-114 1280,-114 "/>
-<polyline style="fill:none;stroke:blue;" points="1384,-114 1384,-82 "/>
-<polyline style="fill:none;stroke:blue;" points="1384,-114 1388,-118 "/>
-<text text-anchor="middle" x="1334" y="-93.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">find_motifs</text>
-</g>
-<!-- t79->t186 -->
-<g id="edge431" class="edge"><title>t79->t186</title>
-<path style="fill:none;stroke:gray;" d="M1009,-276C1020,-266 1034,-255 1049,-250 1087,-236 1378,-256 1405,-228 1432,-199 1425,-173 1405,-140 1402,-134 1397,-129 1391,-124"/>
-<polygon style="fill:gray;stroke:gray;" points="1393.1,-121.2 1383,-118 1388.9,-126.8 1393.1,-121.2"/>
-</g>
-<!-- t90->t186 -->
-<g id="edge429" class="edge"><title>t90->t186</title>
-<path style="fill:none;stroke:gray;" d="M1334,-166C1334,-155 1334,-141 1334,-128"/>
-<polygon style="fill:gray;stroke:gray;" points="1337.5,-128 1334,-118 1330.5,-128 1337.5,-128"/>
-</g>
-<!-- t92 -->
-<g id="node88" class="node"><title>t92</title>
-<polygon style="fill:none;stroke:blue;" points="1254,-202 1070,-202 1066,-198 1066,-166 1250,-166 1254,-170 1254,-202"/>
-<polyline style="fill:none;stroke:blue;" points="1250,-198 1066,-198 "/>
-<polyline style="fill:none;stroke:blue;" points="1250,-198 1250,-166 "/>
-<polyline style="fill:none;stroke:blue;" points="1250,-198 1254,-202 "/>
-<text text-anchor="middle" x="1160" y="-177.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">importGLAM2SCAN</text>
-</g>
-<!-- t91->t92 -->
-<g id="edge71" class="edge"><title>t91->t92</title>
-<path style="fill:none;stroke:blue;" d="M874,-276C891,-267 913,-256 933,-250 985,-233 1001,-243 1052,-228 1072,-222 1093,-214 1112,-206"/>
-<polygon style="fill:blue;stroke:blue;" points="1113.28,-209.26 1121,-202 1110.44,-202.863 1113.28,-209.26"/>
-</g>
-<!-- t91->t186 -->
-<g id="edge75" class="edge"><title>t91->t186</title>
-<path style="fill:none;stroke:blue;" d="M875,-276C892,-267 913,-257 933,-250 976,-235 1000,-258 1032,-228 1062,-200 1027,-166 1057,-140 1073,-126 1193,-112 1270,-106"/>
-<polygon style="fill:blue;stroke:blue;" points="1270.4,-109.478 1280,-105 1269.7,-102.512 1270.4,-109.478"/>
-</g>
-<!-- t92->t186 -->
-<g id="edge73" class="edge"><title>t92->t186</title>
-<path style="fill:none;stroke:blue;" d="M1197,-166C1223,-153 1259,-136 1287,-122"/>
-<polygon style="fill:blue;stroke:blue;" points="1288.28,-125.26 1296,-118 1285.44,-118.863 1288.28,-125.26"/>
-</g>
-<!-- t186->t191 -->
-<g id="edge323" class="edge"><title>t186->t191</title>
-<path style="fill:none;stroke:blue;" d="M1388,-90C1407,-87 1429,-84 1449,-82 1659,-63 3223,-45 3487,-42"/>
-<polygon style="fill:blue;stroke:blue;" points="3487,-45.5001 3497,-42 3487,-38.5001 3487,-45.5001"/>
-</g>
-<!-- t44 -->
-<g id="node93" class="node"><title>t44</title>
-<polygon style="fill:#90ee90;stroke:green;" points="693,-924 451,-924 447,-920 447,-888 689,-888 693,-892 693,-924"/>
-<polyline style="fill:none;stroke:green;" points="689,-920 447,-920 "/>
-<polyline style="fill:none;stroke:green;" points="689,-920 689,-888 "/>
-<polyline style="fill:none;stroke:green;" points="689,-920 693,-924 "/>
-<text text-anchor="middle" x="570" y="-899.5" style="font-family:Times New Roman;font-size:20.00;">importAffymetrixAnnotation</text>
-</g>
-<!-- t45 -->
-<g id="node94" class="node"><title>t45</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1105,-858 893,-858 889,-854 889,-822 1101,-822 1105,-826 1105,-858"/>
-<polyline style="fill:none;stroke:green;" points="1101,-854 889,-854 "/>
-<polyline style="fill:none;stroke:green;" points="1101,-854 1101,-822 "/>
-<polyline style="fill:none;stroke:green;" points="1101,-854 1105,-858 "/>
-<text text-anchor="middle" x="997" y="-833.5" style="font-family:Times New Roman;font-size:20.00;">buildProbeset2Transcript</text>
-</g>
-<!-- t44->t45 -->
-<g id="edge77" class="edge"><title>t44->t45</title>
-<path style="fill:none;stroke:gray;" d="M687,-888C747,-879 819,-867 879,-858"/>
-<polygon style="fill:gray;stroke:gray;" points="879.398,-861.478 889,-857 878.701,-854.512 879.398,-861.478"/>
-</g>
-<!-- t184 -->
-<g id="node128" class="node"><title>t184</title>
-<polygon style="fill:none;stroke:blue;" points="791,-118 695,-118 691,-114 691,-82 787,-82 791,-86 791,-118"/>
-<polyline style="fill:none;stroke:blue;" points="787,-114 691,-114 "/>
-<polyline style="fill:none;stroke:blue;" points="787,-114 787,-82 "/>
-<polyline style="fill:none;stroke:blue;" points="787,-114 791,-118 "/>
-<text text-anchor="middle" x="741" y="-93.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">expression</text>
-</g>
-<!-- t44->t184 -->
-<g id="edge461" class="edge"><title>t44->t184</title>
-<path style="fill:none;stroke:gray;" d="M447,-897C285,-882 21,-843 21,-756 21,-756 21,-756 21,-294 21,-225 -21,-188 26,-140 49,-116 512,-104 681,-101"/>
-<polygon style="fill:gray;stroke:gray;" points="681,-104.5 691,-101 681,-97.5001 681,-104.5"/>
-</g>
-<!-- t46 -->
-<g id="node96" class="node"><title>t46</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1111,-774 887,-774 883,-770 883,-738 1107,-738 1111,-742 1111,-774"/>
-<polyline style="fill:none;stroke:green;" points="1107,-770 883,-770 "/>
-<polyline style="fill:none;stroke:green;" points="1107,-770 1107,-738 "/>
-<polyline style="fill:none;stroke:green;" points="1107,-770 1111,-774 "/>
-<text text-anchor="middle" x="997" y="-749.5" style="font-family:Times New Roman;font-size:20.00;">importProbeset2Transcript</text>
-</g>
-<!-- t45->t46 -->
-<g id="edge79" class="edge"><title>t45->t46</title>
-<path style="fill:none;stroke:gray;" d="M997,-822C997,-811 997,-797 997,-784"/>
-<polygon style="fill:gray;stroke:gray;" points="1000.5,-784 997,-774 993.5,-784 1000.5,-784"/>
-</g>
-<!-- t45->t184 -->
-<g id="edge459" class="edge"><title>t45->t184</title>
-<path style="fill:none;stroke:gray;" d="M1065,-822C1084,-816 1103,-809 1120,-800 1238,-740 1299,-736 1352,-616 1368,-580 1379,-556 1352,-528 1303,-474 1079,-556 1026,-506 998,-478 1045,-444 1016,-418 981,-384 611,-431 577,-396 566,-384 572,-375 577,-360 582,-348 590,-349 595,-338 614,-301 588,-275 619,-250 681,-199 922,-285 976,-228 1003,-199 1002,-169 976,-140 965,-127 867,-113 801,-106"/>
-<polygon style="fill:gray;stroke:gray;" points="801.299,-102.512 791,-105 800.602,-109.478 801.299,-102.512"/>
-</g>
-<!-- t49 -->
-<g id="node98" class="node"><title>t49</title>
-<polygon style="fill:#90ee90;stroke:green;" points="903.007,-670.774 763,-685.92 622.993,-670.774 623.124,-646.266 902.876,-646.266 903.007,-670.774"/>
-<polygon style="fill:none;stroke:green;" points="907.026,-674.362 763,-689.944 618.974,-674.362 619.145,-642.266 906.855,-642.266 907.026,-674.362"/>
-<text text-anchor="middle" x="763" y="-657.5" style="font-family:Times New Roman;font-size:20.00;">buildExpressionTracks</text>
-</g>
-<!-- t46->t49 -->
-<g id="edge81" class="edge"><title>t46->t49</title>
-<path style="fill:none;stroke:gray;" d="M951,-738C915,-723 864,-703 824,-688"/>
-<polygon style="fill:gray;stroke:gray;" points="825.56,-684.863 815,-684 822.717,-691.26 825.56,-684.863"/>
-</g>
-<!-- t46->t184 -->
-<g id="edge457" class="edge"><title>t46->t184</title>
-<path style="fill:none;stroke:gray;" d="M1071,-738C1196,-704 1427,-626 1335,-528 1287,-476 1072,-549 1016,-506 984,-480 1021,-443 988,-418 950,-388 581,-431 547,-396 536,-384 541,-374 547,-360 554,-345 566,-350 575,-338 599,-304 572,-275 604,-250 667,-201 906,-285 960,-228 987,-199 986,-170 960,-140 940,-116 859,-106 801,-103"/>
-<polygon style="fill:gray;stroke:gray;" points="801.299,-99.5125 791,-102 800.602,-106.478 801.299,-99.5125"/>
-</g>
-<!-- t50 -->
-<g id="node100" class="node"><title>t50</title>
-<polygon style="fill:#90ee90;stroke:green;" points="868,-590 662,-590 658,-586 658,-554 864,-554 868,-558 868,-590"/>
-<polyline style="fill:none;stroke:green;" points="864,-586 658,-586 "/>
-<polyline style="fill:none;stroke:green;" points="864,-586 864,-554 "/>
-<polyline style="fill:none;stroke:green;" points="864,-586 868,-590 "/>
-<text text-anchor="middle" x="763" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">importExpressionTracks</text>
-</g>
-<!-- t49->t50 -->
-<g id="edge83" class="edge"><title>t49->t50</title>
-<path style="fill:none;stroke:gray;" d="M763,-642C763,-629 763,-614 763,-600"/>
-<polygon style="fill:gray;stroke:gray;" points="766.5,-600 763,-590 759.5,-600 766.5,-600"/>
-</g>
-<!-- t54 -->
-<g id="node102" class="node"><title>t54</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1116,-590 890,-590 886,-586 886,-554 1112,-554 1116,-558 1116,-590"/>
-<polyline style="fill:none;stroke:green;" points="1112,-586 886,-586 "/>
-<polyline style="fill:none;stroke:green;" points="1112,-586 1112,-554 "/>
-<polyline style="fill:none;stroke:green;" points="1112,-586 1116,-590 "/>
-<text text-anchor="middle" x="1001" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">importExpressionProbesets</text>
-</g>
-<!-- t49->t54 -->
-<g id="edge85" class="edge"><title>t49->t54</title>
-<path style="fill:none;stroke:gray;" d="M819,-642C857,-627 907,-608 944,-594"/>
-<polygon style="fill:gray;stroke:gray;" points="946.015,-596.964 954,-590 943.415,-590.464 946.015,-596.964"/>
-</g>
-<!-- t55 -->
-<g id="node104" class="node"><title>t55</title>
-<polygon style="fill:#90ee90;stroke:green;" points="1326,-590 1138,-590 1134,-586 1134,-554 1322,-554 1326,-558 1326,-590"/>
-<polyline style="fill:none;stroke:green;" points="1322,-586 1134,-586 "/>
-<polyline style="fill:none;stroke:green;" points="1322,-586 1322,-554 "/>
-<polyline style="fill:none;stroke:green;" points="1322,-586 1326,-590 "/>
-<text text-anchor="middle" x="1230" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">importExpressionMap</text>
-</g>
-<!-- t49->t55 -->
-<g id="edge87" class="edge"><title>t49->t55</title>
-<path style="fill:none;stroke:gray;" d="M907,-654C974,-647 1055,-635 1125,-616 1145,-610 1166,-602 1184,-594"/>
-<polygon style="fill:gray;stroke:gray;" points="1185.28,-597.26 1193,-590 1182.44,-590.863 1185.28,-597.26"/>
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-<!-- t51 -->
-<g id="node106" class="node"><title>t51</title>
-<polygon style="fill:#90ee90;stroke:green;" points="44.2538,-559.794 172,-532.5 299.746,-559.794 299.627,-603.956 44.373,-603.956 44.2538,-559.794"/>
-<polygon style="fill:none;stroke:green;" points="40.2451,-556.56 172,-528.41 303.755,-556.56 303.616,-607.956 40.3838,-607.956 40.2451,-556.56"/>
-<text text-anchor="middle" x="172" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">buildExpressionCorrelation</text>
-</g>
-<!-- t49->t51 -->
-<g id="edge89" class="edge"><title>t49->t51</title>
-<path style="fill:none;stroke:gray;" d="M619,-656C530,-649 414,-637 313,-616 305,-615 298,-613 291,-611"/>
-<polygon style="fill:gray;stroke:gray;" points="291.584,-607.521 281,-608 289.573,-614.226 291.584,-607.521"/>
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-<!-- t52 -->
-<g id="node108" class="node"><title>t52</title>
-<polygon style="fill:#90ee90;stroke:green;" points="325.802,-559.794 471,-532.5 616.198,-559.794 616.062,-603.956 325.938,-603.956 325.802,-559.794"/>
-<polygon style="fill:none;stroke:green;" points="321.805,-556.476 471,-528.43 620.195,-556.476 620.037,-607.956 321.963,-607.956 321.805,-556.476"/>
-<text text-anchor="middle" x="471" y="-565.5" style="font-family:Times New Roman;font-size:20.00;">buildExpressionFullCorrelation</text>
-</g>
-<!-- t49->t52 -->
-<g id="edge91" class="edge"><title>t49->t52</title>
-<path style="fill:none;stroke:gray;" d="M694,-642C664,-633 629,-622 595,-611"/>
-<polygon style="fill:gray;stroke:gray;" points="595.584,-607.521 585,-608 593.573,-614.226 595.584,-607.521"/>
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-<!-- t49->t184 -->
-<g id="edge455" class="edge"><title>t49->t184</title>
-<path style="fill:none;stroke:gray;" d="M684,-642C671,-636 658,-627 649,-616 624,-585 660,-554 629,-528 580,-485 385,-548 335,-506 305,-479 344,-445 315,-418 277,-380 247,-414 196,-396 146,-378 119,-383 91,-338 80,-319 76,-156 91,-140 112,-118 523,-106 681,-101"/>
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-<!-- t102 -->
-<g id="node112" class="node"><title>t102</title>
-<polygon style="fill:#90ee90;stroke:green;" points="922,-480 648,-480 644,-476 644,-444 918,-444 922,-448 922,-480"/>
-<polyline style="fill:none;stroke:green;" points="918,-476 644,-476 "/>
-<polyline style="fill:none;stroke:green;" points="918,-476 918,-444 "/>
-<polyline style="fill:none;stroke:green;" points="918,-476 922,-480 "/>
-<text text-anchor="middle" x="783" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">buildExpressionDifferencesSAM</text>
-</g>
-<!-- t50->t102 -->
-<g id="edge95" class="edge"><title>t50->t102</title>
-<path style="fill:none;stroke:gray;" d="M766,-554C769,-537 774,-511 778,-490"/>
-<polygon style="fill:gray;stroke:gray;" points="781.471,-490.492 780,-480 774.607,-489.119 781.471,-490.492"/>
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-<!-- t101 -->
-<g id="node114" class="node"><title>t101</title>
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-<polyline style="fill:none;stroke:green;" points="302,-476 306,-480 "/>
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-<polygon style="fill:gray;stroke:gray;" points="240.585,-480.464 230,-480 237.985,-486.964 240.585,-480.464"/>
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-<!-- t53->t184 -->
-<g id="edge449" class="edge"><title>t53->t184</title>
-<path style="fill:none;stroke:gray;" d="M160,-444C134,-422 93,-383 76,-338 61,-296 46,-172 76,-140 98,-118 521,-106 681,-101"/>
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-<polyline style="fill:none;stroke:green;" points="449,-392 205,-392 "/>
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-<polyline style="fill:none;stroke:green;" points="449,-392 453,-396 "/>
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-<!-- t102->t103 -->
-<g id="edge99" class="edge"><title>t102->t103</title>
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-<!-- t101->t103 -->
-<g id="edge435" class="edge"><title>t101->t103</title>
-<path style="fill:none;stroke:gray;" d="M452,-444C429,-432 397,-414 372,-401"/>
-<polygon style="fill:gray;stroke:gray;" points="373.441,-397.797 363,-396 370.042,-403.916 373.441,-397.797"/>
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-<polyline style="fill:none;stroke:green;" points="402,-198 100,-198 "/>
-<polyline style="fill:none;stroke:green;" points="402,-198 402,-166 "/>
-<polyline style="fill:none;stroke:green;" points="402,-198 406,-202 "/>
-<text text-anchor="middle" x="253" y="-177.5" style="font-family:Times New Roman;font-size:20.00;">exportDifferentiallyExpressedGenes</text>
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-<!-- t103->t104 -->
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-<polygon style="fill:gray;stroke:gray;" points="167.283,-209.26 175,-202 164.44,-202.863 167.283,-209.26"/>
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-<g id="node120" class="node"><title>t172</title>
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-<polyline style="fill:none;stroke:green;" points="310,-308 120,-308 "/>
-<polyline style="fill:none;stroke:green;" points="310,-308 310,-276 "/>
-<polyline style="fill:none;stroke:green;" points="310,-308 314,-312 "/>
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-<g id="edge103" class="edge"><title>t103->t172</title>
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-<polygon style="fill:gray;stroke:gray;" points="251.1,-315.2 241,-312 246.9,-320.8 251.1,-315.2"/>
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-<polygon style="fill:#90ee90;stroke:green;" points="490,-312 336,-312 332,-308 332,-276 486,-276 490,-280 490,-312"/>
-<polyline style="fill:none;stroke:green;" points="486,-308 332,-308 "/>
-<polyline style="fill:none;stroke:green;" points="486,-308 486,-276 "/>
-<polyline style="fill:none;stroke:green;" points="486,-308 490,-312 "/>
-<text text-anchor="middle" x="411" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">runExpressionGO</text>
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-<polygon style="fill:gray;stroke:gray;" points="388.404,-321.546 393,-312 383.454,-316.596 388.404,-321.546"/>
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-<path style="fill:none;stroke:gray;" d="M442,-360C468,-354 490,-347 499,-338 529,-309 493,-275 524,-250 589,-198 841,-288 897,-228 924,-199 921,-170 897,-140 886,-124 840,-114 801,-108"/>
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-<path style="fill:none;stroke:gray;" d="M313,-166C345,-157 384,-147 420,-140 510,-122 617,-111 681,-105"/>
-<polygon style="fill:gray;stroke:gray;" points="681.398,-108.478 691,-104 680.701,-101.512 681.398,-108.478"/>
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-<g id="node124" class="node"><title>t175</title>
-<polygon style="fill:none;stroke:blue;" points="666,-202 448,-202 444,-198 444,-166 662,-166 666,-170 666,-202"/>
-<polyline style="fill:none;stroke:blue;" points="662,-198 444,-198 "/>
-<polyline style="fill:none;stroke:blue;" points="662,-198 662,-166 "/>
-<polyline style="fill:none;stroke:blue;" points="662,-198 666,-202 "/>
-<text text-anchor="middle" x="555" y="-177.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">importExpressionGOSlim</text>
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-<!-- t172->t175 -->
-<g id="edge107" class="edge"><title>t172->t175</title>
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-<polygon style="fill:gray;stroke:gray;" points="500.283,-209.26 508,-202 497.44,-202.863 500.283,-209.26"/>
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-<!-- t172->t184 -->
-<g id="edge439" class="edge"><title>t172->t184</title>
-<path style="fill:none;stroke:gray;" d="M256,-276C276,-267 300,-257 323,-250 363,-237 386,-257 415,-228 444,-199 406,-167 435,-140 453,-123 597,-110 681,-104"/>
-<polygon style="fill:gray;stroke:gray;" points="681.398,-107.478 691,-103 680.701,-100.512 681.398,-107.478"/>
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-<g id="node126" class="node"><title>t174</title>
-<polygon style="fill:none;stroke:blue;" points="888,-202 708,-202 704,-198 704,-166 884,-166 888,-170 888,-202"/>
-<polyline style="fill:none;stroke:blue;" points="884,-198 704,-198 "/>
-<polyline style="fill:none;stroke:blue;" points="884,-198 884,-166 "/>
-<polyline style="fill:none;stroke:blue;" points="884,-198 888,-202 "/>
-<text text-anchor="middle" x="796" y="-177.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">importExpressionGO</text>
-</g>
-<!-- t173->t174 -->
-<g id="edge109" class="edge"><title>t173->t174</title>
-<path style="fill:none;stroke:gray;" d="M443,-276C460,-266 483,-256 504,-250 585,-227 610,-249 690,-228 710,-223 732,-214 751,-206"/>
-<polygon style="fill:gray;stroke:gray;" points="752.283,-209.26 760,-202 749.44,-202.863 752.283,-209.26"/>
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-<!-- t173->t184 -->
-<g id="edge437" class="edge"><title>t173->t184</title>
-<path style="fill:none;stroke:gray;" d="M443,-276C460,-266 483,-256 504,-250 541,-239 647,-253 675,-228 705,-201 675,-174 695,-140 698,-135 702,-130 707,-125"/>
-<polygon style="fill:gray;stroke:gray;" points="709.404,-127.546 714,-118 704.454,-122.596 709.404,-127.546"/>
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-<!-- t175->t184 -->
-<g id="edge111" class="edge"><title>t175->t184</title>
-<path style="fill:none;stroke:blue;" d="M595,-166C623,-153 662,-136 692,-122"/>
-<polygon style="fill:blue;stroke:blue;" points="693.283,-125.26 701,-118 690.44,-118.863 693.283,-125.26"/>
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-<!-- t174->t184 -->
-<g id="edge113" class="edge"><title>t174->t184</title>
-<path style="fill:none;stroke:blue;" d="M784,-166C777,-155 767,-139 758,-126"/>
-<polygon style="fill:blue;stroke:blue;" points="761.268,-124.625 753,-118 755.332,-128.335 761.268,-124.625"/>
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-<!-- t184->t191 -->
-<g id="edge327" class="edge"><title>t184->t191</title>
-<path style="fill:none;stroke:blue;" d="M791,-96C847,-92 941,-85 1022,-82 1532,-61 3214,-44 3487,-42"/>
-<polygon style="fill:blue;stroke:blue;" points="3487,-45.5001 3497,-42 3487,-38.5001 3487,-45.5001"/>
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-<!-- t69 -->
-<g id="node133" class="node"><title>t69</title>
-<polygon style="fill:#90ee90;stroke:green;" points="10456,-480 10248,-480 10244,-476 10244,-444 10452,-444 10456,-448 10456,-480"/>
-<polyline style="fill:none;stroke:green;" points="10452,-476 10244,-476 "/>
-<polyline style="fill:none;stroke:green;" points="10452,-476 10452,-444 "/>
-<polyline style="fill:none;stroke:green;" points="10452,-476 10456,-480 "/>
-<text text-anchor="middle" x="10350" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">makePeakvalCorrelation</text>
-</g>
-<!-- t31->t69 -->
-<g id="edge117" class="edge"><title>t31->t69</title>
-<path style="fill:none;stroke:gray;" d="M10368,-554C10365,-537 10360,-511 10356,-490"/>
-<polygon style="fill:gray;stroke:gray;" points="10359.4,-489.119 10354,-480 10352.5,-490.492 10359.4,-489.119"/>
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-<!-- t70 -->
-<g id="node135" class="node"><title>t70</title>
-<polygon style="fill:#90ee90;stroke:green;" points="10682,-480 10478,-480 10474,-476 10474,-444 10678,-444 10682,-448 10682,-480"/>
-<polyline style="fill:none;stroke:green;" points="10678,-476 10474,-476 "/>
-<polyline style="fill:none;stroke:green;" points="10678,-476 10678,-444 "/>
-<polyline style="fill:none;stroke:green;" points="10678,-476 10682,-480 "/>
-<text text-anchor="middle" x="10578" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">makeAvgvalCorrelation</text>
-</g>
-<!-- t31->t70 -->
-<g id="edge119" class="edge"><title>t31->t70</title>
-<path style="fill:none;stroke:gray;" d="M10406,-554C10442,-535 10497,-506 10535,-485"/>
-<polygon style="fill:gray;stroke:gray;" points="10537,-487.916 10544,-480 10533.6,-481.797 10537,-487.916"/>
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-<!-- t71 -->
-<g id="node137" class="node"><title>t71</title>
-<polygon style="fill:#90ee90;stroke:green;" points="10906,-480 10704,-480 10700,-476 10700,-444 10902,-444 10906,-448 10906,-480"/>
-<polyline style="fill:none;stroke:green;" points="10902,-476 10700,-476 "/>
-<polyline style="fill:none;stroke:green;" points="10902,-476 10902,-444 "/>
-<polyline style="fill:none;stroke:green;" points="10902,-476 10906,-480 "/>
-<text text-anchor="middle" x="10803" y="-455.5" style="font-family:Times New Roman;font-size:20.00;">makeLengthCorrelation</text>
-</g>
-<!-- t31->t71 -->
-<g id="edge121" class="edge"><title>t31->t71</title>
-<path style="fill:none;stroke:gray;" d="M10432,-563C10497,-552 10603,-532 10691,-506 10712,-500 10734,-492 10753,-484"/>
-<polygon style="fill:gray;stroke:gray;" points="10754.3,-487.26 10762,-480 10751.4,-480.863 10754.3,-487.26"/>
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-<!-- t72 -->
-<g id="node139" class="node"><title>t72</title>
-<polygon style="fill:#90ee90;stroke:green;" points="10897,-396 10741,-396 10737,-392 10737,-360 10893,-360 10897,-364 10897,-396"/>
-<polyline style="fill:none;stroke:green;" points="10893,-392 10737,-392 "/>
-<polyline style="fill:none;stroke:green;" points="10893,-392 10893,-360 "/>
-<polyline style="fill:none;stroke:green;" points="10893,-392 10897,-396 "/>
-<text text-anchor="middle" x="10817" y="-371.5" style="font-family:Times New Roman;font-size:20.00;">importCorrelation</text>
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-<!-- t69->t72 -->
-<g id="edge465" class="edge"><title>t69->t72</title>
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-<!-- t70->t72 -->
-<g id="edge463" class="edge"><title>t70->t72</title>
-<path style="fill:none;stroke:gray;" d="M10622,-444C10643,-436 10668,-426 10691,-418 10710,-411 10729,-405 10747,-399"/>
-<polygon style="fill:gray;stroke:gray;" points="10748.4,-402.226 10757,-396 10746.4,-395.521 10748.4,-402.226"/>
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-<!-- t71->t72 -->
-<g id="edge123" class="edge"><title>t71->t72</title>
-<path style="fill:none;stroke:gray;" d="M10806,-444C10808,-433 10810,-418 10812,-406"/>
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-<polyline style="fill:none;stroke:blue;" points="10623,-114 10525,-114 "/>
-<polyline style="fill:none;stroke:blue;" points="10623,-114 10623,-82 "/>
-<polyline style="fill:none;stroke:blue;" points="10623,-114 10627,-118 "/>
-<text text-anchor="middle" x="10576" y="-93.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">correlation</text>
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-<!-- t72->t188 -->
-<g id="edge137" class="edge"><title>t72->t188</title>
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-<g id="node143" class="node"><title>t61</title>
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-<polyline style="fill:none;stroke:green;" points="10380,-198 10380,-166 "/>
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-<!-- t60->t61 -->
-<g id="edge127" class="edge"><title>t60->t61</title>
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-<!-- t61->t188 -->
-<g id="edge479" class="edge"><title>t61->t188</title>
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-<g id="node147" class="node"><title>t63</title>
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-<!-- t62->t63 -->
-<g id="edge131" class="edge"><title>t62->t63</title>
-<path style="fill:none;stroke:gray;" d="M10782,-252C10780,-239 10777,-225 10776,-212"/>
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-<!-- t63->t188 -->
-<g id="edge477" class="edge"><title>t63->t188</title>
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-<g id="node149" class="node"><title>t64</title>
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-<polyline style="fill:none;stroke:green;" points="10495,-392 10317,-392 "/>
-<polyline style="fill:none;stroke:green;" points="10495,-392 10495,-360 "/>
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-<g id="edge133" class="edge"><title>t64->t65</title>
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-<polyline style="fill:none;stroke:blue;" points="10639,-198 10639,-166 "/>
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-<polygon style="fill:blue;stroke:blue;" points="3561,-38.5001 3551,-42 3561,-45.5001 3561,-38.5001"/>
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-<polyline style="fill:none;stroke:green;" points="9975,-392 9825,-392 "/>
-<polyline style="fill:none;stroke:green;" points="9975,-392 9975,-360 "/>
-<polyline style="fill:none;stroke:green;" points="9975,-392 9979,-396 "/>
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-<polyline style="fill:none;stroke:green;" points="10022,-308 9862,-308 "/>
-<polyline style="fill:none;stroke:green;" points="10022,-308 10022,-276 "/>
-<polyline style="fill:none;stroke:green;" points="10022,-308 10026,-312 "/>
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-<!-- t189 -->
-<g id="node190" class="node"><title>t189</title>
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-<polyline style="fill:none;stroke:blue;" points="9311,-198 9231,-198 "/>
-<polyline style="fill:none;stroke:blue;" points="9311,-198 9311,-166 "/>
-<polyline style="fill:none;stroke:blue;" points="9311,-198 9315,-202 "/>
-<text text-anchor="middle" x="9273" y="-177.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">annotate</text>
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-<!-- t94->t189 -->
-<g id="edge515" class="edge"><title>t94->t189</title>
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-<!-- t99 -->
-<g id="node162" class="node"><title>t99</title>
-<polygon style="fill:#90ee90;stroke:green;" points="8744,-312 8644,-312 8640,-308 8640,-276 8740,-276 8744,-280 8744,-312"/>
-<polyline style="fill:none;stroke:green;" points="8740,-308 8640,-308 "/>
-<polyline style="fill:none;stroke:green;" points="8740,-308 8740,-276 "/>
-<polyline style="fill:none;stroke:green;" points="8740,-308 8744,-312 "/>
-<text text-anchor="middle" x="8692" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">importTSS</text>
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-<!-- t97->t99 -->
-<g id="edge145" class="edge"><title>t97->t99</title>
-<path style="fill:none;stroke:gray;" d="M8577,-360C8593,-353 8611,-346 8626,-338 8637,-332 8648,-325 8659,-318"/>
-<polygon style="fill:gray;stroke:gray;" points="8661.1,-320.8 8667,-312 8656.9,-315.2 8661.1,-320.8"/>
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-<g id="edge509" class="edge"><title>t97->t189</title>
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-<!-- t99->t189 -->
-<g id="edge505" class="edge"><title>t99->t189</title>
-<path style="fill:none;stroke:gray;" d="M8714,-276C8726,-266 8742,-256 8758,-250 8842,-218 9107,-195 9221,-188"/>
-<polygon style="fill:gray;stroke:gray;" points="9221.4,-191.478 9231,-187 9220.7,-184.512 9221.4,-191.478"/>
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-<!-- t98 -->
-<g id="node164" class="node"><title>t98</title>
-<polygon style="fill:#90ee90;stroke:green;" points="9247,-396 9105,-396 9101,-392 9101,-360 9243,-360 9247,-364 9247,-396"/>
-<polyline style="fill:none;stroke:green;" points="9243,-392 9101,-392 "/>
-<polyline style="fill:none;stroke:green;" points="9243,-392 9243,-360 "/>
-<polyline style="fill:none;stroke:green;" points="9243,-392 9247,-396 "/>
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-<g id="node165" class="node"><title>t100</title>
-<polygon style="fill:#90ee90;stroke:green;" points="9444,-312 9316,-312 9312,-308 9312,-276 9440,-276 9444,-280 9444,-312"/>
-<polyline style="fill:none;stroke:green;" points="9440,-308 9312,-308 "/>
-<polyline style="fill:none;stroke:green;" points="9440,-308 9440,-276 "/>
-<polyline style="fill:none;stroke:green;" points="9440,-308 9444,-312 "/>
-<text text-anchor="middle" x="9378" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">importRepeats</text>
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-<!-- t98->t100 -->
-<g id="edge147" class="edge"><title>t98->t100</title>
-<path style="fill:none;stroke:gray;" d="M9237,-360C9257,-354 9279,-346 9298,-338 9312,-332 9326,-324 9339,-317"/>
-<polygon style="fill:gray;stroke:gray;" points="9340.96,-319.916 9348,-312 9337.56,-313.797 9340.96,-319.916"/>
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-<!-- t98->t189 -->
-<g id="edge507" class="edge"><title>t98->t189</title>
-<path style="fill:none;stroke:gray;" d="M9238,-360C9256,-353 9273,-346 9278,-338 9303,-300 9293,-245 9283,-212"/>
-<polygon style="fill:gray;stroke:gray;" points="9286.23,-210.573 9280,-202 9279.52,-212.584 9286.23,-210.573"/>
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-<!-- t100->t189 -->
-<g id="edge503" class="edge"><title>t100->t189</title>
-<path style="fill:none;stroke:gray;" d="M9361,-276C9343,-258 9317,-230 9297,-209"/>
-<polygon style="fill:gray;stroke:gray;" points="9299.55,-206.596 9290,-202 9294.6,-211.546 9299.55,-206.596"/>
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-<!-- t168 -->
-<g id="node169" class="node"><title>t168</title>
-<polygon style="fill:#90ee90;stroke:green;" points="9048,-312 8786,-312 8782,-308 8782,-276 9044,-276 9048,-280 9048,-312"/>
-<polyline style="fill:none;stroke:green;" points="9044,-308 8782,-308 "/>
-<polyline style="fill:none;stroke:green;" points="9044,-308 9044,-276 "/>
-<polyline style="fill:none;stroke:green;" points="9044,-308 9048,-312 "/>
-<text text-anchor="middle" x="8915" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">importTSSIntervalAssociations</text>
-</g>
-<!-- t167->t168 -->
-<g id="edge151" class="edge"><title>t167->t168</title>
-<path style="fill:none;stroke:gray;" d="M8784,-360C8809,-347 8843,-330 8870,-317"/>
-<polygon style="fill:gray;stroke:gray;" points="8871.96,-319.916 8879,-312 8868.56,-313.797 8871.96,-319.916"/>
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-<!-- t167->t189 -->
-<g id="edge493" class="edge"><title>t167->t189</title>
-<path style="fill:none;stroke:gray;" d="M8750,-360C8755,-326 8765,-257 8773,-250 8805,-219 9099,-195 9221,-188"/>
-<polygon style="fill:gray;stroke:gray;" points="9221.4,-191.478 9231,-187 9220.7,-184.512 9221.4,-191.478"/>
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-<!-- t168->t189 -->
-<g id="edge491" class="edge"><title>t168->t189</title>
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-<polygon style="fill:gray;stroke:gray;" points="9222.43,-203.226 9231,-197 9220.42,-196.521 9222.43,-203.226"/>
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-<!-- t166 -->
-<g id="node173" class="node"><title>t166</title>
-<polygon style="fill:#90ee90;stroke:green;" points="8602,-312 8370,-312 8366,-308 8366,-276 8598,-276 8602,-280 8602,-312"/>
-<polyline style="fill:none;stroke:green;" points="8598,-308 8366,-308 "/>
-<polyline style="fill:none;stroke:green;" points="8598,-308 8598,-276 "/>
-<polyline style="fill:none;stroke:green;" points="8598,-308 8602,-312 "/>
-<text text-anchor="middle" x="8484" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">importTSSIntervalDistance</text>
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-<!-- t165->t166 -->
-<g id="edge155" class="edge"><title>t165->t166</title>
-<path style="fill:none;stroke:gray;" d="M8359,-360C8383,-348 8415,-330 8441,-317"/>
-<polygon style="fill:gray;stroke:gray;" points="8442.96,-319.916 8450,-312 8439.56,-313.797 8442.96,-319.916"/>
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-<!-- t165->t189 -->
-<g id="edge497" class="edge"><title>t165->t189</title>
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-<polygon style="fill:gray;stroke:gray;" points="9221,-189.5 9231,-186 9221,-182.5 9221,-189.5"/>
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-<!-- t166->t189 -->
-<g id="edge495" class="edge"><title>t166->t189</title>
-<path style="fill:none;stroke:gray;" d="M8529,-276C8554,-267 8587,-256 8616,-250 8838,-202 9109,-189 9221,-185"/>
-<polygon style="fill:gray;stroke:gray;" points="9221,-188.5 9231,-185 9221,-181.5 9221,-188.5"/>
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-<!-- t95 -->
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-<polygon style="fill:#90ee90;stroke:green;" points="9807,-396 9673,-396 9669,-392 9669,-360 9803,-360 9807,-364 9807,-396"/>
-<polyline style="fill:none;stroke:green;" points="9803,-392 9669,-392 "/>
-<polyline style="fill:none;stroke:green;" points="9803,-392 9803,-360 "/>
-<polyline style="fill:none;stroke:green;" points="9803,-392 9807,-396 "/>
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-</g>
-<!-- t96 -->
-<g id="node176" class="node"><title>t96</title>
-<polygon style="fill:#90ee90;stroke:green;" points="9844,-312 9726,-312 9722,-308 9722,-276 9840,-276 9844,-280 9844,-312"/>
-<polyline style="fill:none;stroke:green;" points="9840,-308 9722,-308 "/>
-<polyline style="fill:none;stroke:green;" points="9840,-308 9840,-276 "/>
-<polyline style="fill:none;stroke:green;" points="9840,-308 9844,-312 "/>
-<text text-anchor="middle" x="9783" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">importTracks</text>
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-<!-- t95->t96 -->
-<g id="edge157" class="edge"><title>t95->t96</title>
-<path style="fill:none;stroke:gray;" d="M9748,-360C9754,-349 9762,-334 9768,-321"/>
-<polygon style="fill:gray;stroke:gray;" points="9771.2,-322.441 9773,-312 9765.08,-319.042 9771.2,-322.441"/>
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-<!-- t95->t189 -->
-<g id="edge513" class="edge"><title>t95->t189</title>
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-<!-- t96->t189 -->
-<g id="edge511" class="edge"><title>t96->t189</title>
-<path style="fill:none;stroke:gray;" d="M9758,-276C9744,-266 9726,-256 9708,-250 9637,-225 9614,-239 9539,-228 9465,-217 9379,-202 9325,-193"/>
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-<!-- t107 -->
-<g id="node180" class="node"><title>t107</title>
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-<polyline style="fill:none;stroke:green;" points="9250,-308 9066,-308 "/>
-<polyline style="fill:none;stroke:green;" points="9250,-308 9250,-276 "/>
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-<text text-anchor="middle" x="9160" y="-287.5" style="font-family:Times New Roman;font-size:20.00;">importIntervalCounts</text>
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-<!-- t106->t107 -->
-<g id="edge161" class="edge"><title>t106->t107</title>
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-<!-- t106->t189 -->
-<g id="edge501" class="edge"><title>t106->t189</title>
-<path style="fill:none;stroke:gray;" d="M9083,-361C9086,-361 9089,-360 9092,-360 9130,-354 9237,-365 9263,-338 9279,-320 9278,-251 9276,-212"/>
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-<!-- t107->t189 -->
-<g id="edge499" class="edge"><title>t107->t189</title>
-<path style="fill:none;stroke:gray;" d="M9179,-276C9198,-258 9227,-230 9247,-209"/>
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-<!-- t180 -->
-<g id="node184" class="node"><title>t180</title>
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-<polyline style="fill:none;stroke:green;" points="9660,-308 9482,-308 "/>
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-<!-- t179->t180 -->
-<g id="edge165" class="edge"><title>t179->t180</title>
-<path style="fill:none;stroke:gray;" d="M9406,-360C9425,-353 9448,-345 9468,-338 9486,-331 9506,-323 9523,-316"/>
-<polygon style="fill:gray;stroke:gray;" points="9524.28,-319.26 9532,-312 9521.44,-312.863 9524.28,-319.26"/>
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-<!-- t179->t189 -->
-<g id="edge485" class="edge"><title>t179->t189</title>
-<path style="fill:none;stroke:gray;" d="M9413,-360C9432,-353 9448,-346 9453,-338 9476,-305 9476,-282 9453,-250 9438,-229 9373,-208 9325,-196"/>
-<polygon style="fill:gray;stroke:gray;" points="9325.49,-192.529 9315,-194 9324.12,-199.393 9325.49,-192.529"/>
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-<!-- t180->t189 -->
-<g id="edge171" class="edge"><title>t180->t189</title>
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-<polygon style="fill:gray;stroke:gray;" points="9325.58,-196.521 9315,-197 9323.57,-203.226 9325.58,-196.521"/>
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-<g id="edge487" class="edge"><title>t178->t189</title>
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-<!-- t176->t189 -->
-<g id="edge489" class="edge"><title>t176->t189</title>
-<path style="fill:none;stroke:gray;" d="M8219,-276C8255,-267 8301,-256 8342,-250 8675,-199 9078,-188 9221,-185"/>
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-<g id="edge319" class="edge"><title>t189->t191</title>
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-<!-- t1 -->
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-<polyline style="fill:none;stroke:green;" points="5524,-586 5268,-586 "/>
-<polyline style="fill:none;stroke:green;" points="5524,-586 5524,-554 "/>
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-<polyline style="fill:none;stroke:green;" points="5476,-476 5316,-476 "/>
-<polyline style="fill:none;stroke:green;" points="5476,-476 5476,-444 "/>
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-<!-- t1->t2 -->
-<g id="edge173" class="edge"><title>t1->t2</title>
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-<polygon style="fill:gray;stroke:gray;" points="7911.4,-397.478 7921,-393 7910.7,-390.512 7911.4,-397.478"/>
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-<g id="edge521" class="edge"><title>t2->t120</title>
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-<polygon style="fill:gray;stroke:gray;" points="6255.4,-399.478 6265,-395 6254.7,-392.512 6255.4,-399.478"/>
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-<g id="edge525" class="edge"><title>t2->t118</title>
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-<polygon style="fill:gray;stroke:gray;" points="7445.4,-397.478 7455,-393 7444.7,-390.512 7445.4,-397.478"/>
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-<g id="edge527" class="edge"><title>t2->t119</title>
-<path style="fill:none;stroke:gray;" d="M5480,-461C5831,-456 7204,-435 7659,-396"/>
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-<g id="edge531" class="edge"><title>t2->t160</title>
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index c1fcd49..0000000
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diff --git a/doc/_build/html/_downloads/gallery_rna_seq.svg b/doc/_build/html/_downloads/gallery_rna_seq.svg
deleted file mode 100644
index 43a6e5b..0000000
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-<!-- t19->t22 -->
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-<!-- t35 -->
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diff --git a/doc/_build/html/_downloads/gallery_snp_annotation.svg b/doc/_build/html/_downloads/gallery_snp_annotation.svg
deleted file mode 100644
index 9a7995c..0000000
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deleted file mode 100644
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-<polygon style="fill:gray;stroke:gray;" points="965.1,-384.8 971,-376 960.9,-379.2 965.1,-384.8"/>
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-<polygon style="fill:gray;stroke:gray;" points="641.478,-301.602 637,-292 634.512,-302.299 641.478,-301.602"/>
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-<text text-anchor="middle" x="472" y="-564.5" style="font-family:Times New Roman;font-size:20.00;fill:gray;">buildGeneRegions</text>
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-<g id="node16" class="node"><title>t5</title>
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-<!-- t4->t5 -->
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-<path style="fill:none;stroke:gray;" d="M472,-553C472,-537 472,-514 472,-496"/>
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-<path style="fill:none;stroke:gray;" d="M472,-450C472,-433 472,-407 472,-386"/>
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-<!-- t6->t64 -->
-<g id="edge23" class="edge"><title>t6->t64</title>
-<path style="fill:none;stroke:gray;" d="M786,-340C755,-326 713,-309 681,-294"/>
-<polygon style="fill:gray;stroke:gray;" points="682.56,-290.863 672,-290 679.717,-297.26 682.56,-290.863"/>
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-<!-- t64->t68 -->
-<g id="edge69" class="edge"><title>t64->t68</title>
-<path style="fill:none;stroke:gray;" d="M640,-256C650,-230 668,-181 686,-140 697,-115 712,-88 723,-69"/>
-<polygon style="fill:gray;stroke:gray;" points="726.203,-70.4414 728,-60 720.084,-67.0418 726.203,-70.4414"/>
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-<!-- t49 -->
-<g id="node28" class="node"><title>t49</title>
-<polygon style="fill:white;stroke:gray;" points="19.9571,-345.794 114,-318.5 208.043,-345.794 207.955,-389.956 20.0448,-389.956 19.9571,-345.794"/>
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-</g>
-<!-- t50 -->
-<g id="node29" class="node"><title>t50</title>
-<polygon style="fill:white;stroke:gray;" points="299,-292 105,-292 101,-288 101,-256 295,-256 299,-260 299,-292"/>
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-<polyline style="fill:none;stroke:gray;" points="295,-288 299,-292 "/>
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-<!-- t49->t50 -->
-<g id="edge29" class="edge"><title>t49->t50</title>
-<path style="fill:none;stroke:gray;" d="M148,-324C156,-316 165,-307 174,-299"/>
-<polygon style="fill:gray;stroke:gray;" points="176.404,-301.546 181,-292 171.454,-296.596 176.404,-301.546"/>
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-<g id="node35" class="node"><title>t52</title>
-<polygon style="fill:white;stroke:gray;" points="176,-176 20,-176 16,-172 16,-140 172,-140 176,-144 176,-176"/>
-<polyline style="fill:none;stroke:gray;" points="172,-172 16,-172 "/>
-<polyline style="fill:none;stroke:gray;" points="172,-172 172,-140 "/>
-<polyline style="fill:none;stroke:gray;" points="172,-172 176,-176 "/>
-<text text-anchor="middle" x="96" y="-151.5" style="font-family:Times New Roman;font-size:20.00;fill:gray;">loadPolyphenMap</text>
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-<!-- t49->t52 -->
-<g id="edge35" class="edge"><title>t49->t52</title>
-<path style="fill:none;stroke:gray;" d="M99,-319C96,-310 93,-301 92,-292 87,-256 89,-213 92,-186"/>
-<polygon style="fill:gray;stroke:gray;" points="95.4875,-186.299 93,-176 88.5222,-185.602 95.4875,-186.299"/>
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-<polyline style="fill:none;stroke:gray;" points="438,-230 340,-230 "/>
-<polyline style="fill:none;stroke:gray;" points="438,-230 438,-198 "/>
-<polyline style="fill:none;stroke:gray;" points="438,-230 442,-234 "/>
-<text text-anchor="middle" x="391" y="-209.5" style="font-family:Times New Roman;font-size:20.00;fill:gray;">runPanther</text>
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-<!-- t49->t57 -->
-<g id="edge39" class="edge"><title>t49->t57</title>
-<path style="fill:none;stroke:gray;" d="M174,-332C189,-325 206,-319 221,-314 259,-301 277,-316 308,-292 323,-280 316,-269 328,-256 334,-250 340,-245 347,-240"/>
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-<polyline style="fill:none;stroke:gray;" points="282,-230 170,-230 "/>
-<polyline style="fill:none;stroke:gray;" points="282,-230 282,-198 "/>
-<polyline style="fill:none;stroke:gray;" points="282,-230 286,-234 "/>
-<text text-anchor="middle" x="228" y="-209.5" style="font-family:Times New Roman;font-size:20.00;fill:gray;">runPolyphen</text>
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-<!-- t50->t51 -->
-<g id="edge31" class="edge"><title>t50->t51</title>
-<path style="fill:none;stroke:gray;" d="M209,-256C211,-252 213,-248 215,-243"/>
-<polygon style="fill:gray;stroke:gray;" points="218.137,-244.56 219,-234 211.74,-241.717 218.137,-244.56"/>
-</g>
-<!-- t53 -->
-<g id="node33" class="node"><title>t53</title>
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-<polyline style="fill:none;stroke:gray;" points="314,-172 194,-172 "/>
-<polyline style="fill:none;stroke:gray;" points="314,-172 314,-140 "/>
-<polyline style="fill:none;stroke:gray;" points="314,-172 318,-176 "/>
-<text text-anchor="middle" x="256" y="-151.5" style="font-family:Times New Roman;font-size:20.00;fill:gray;">loadPolyphen</text>
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-<!-- t51->t53 -->
-<g id="edge33" class="edge"><title>t51->t53</title>
-<path style="fill:none;stroke:gray;" d="M237,-198C239,-194 241,-190 243,-185"/>
-<polygon style="fill:gray;stroke:gray;" points="246.137,-186.56 247,-176 239.74,-183.717 246.137,-186.56"/>
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-<polygon style="fill:white;stroke:gray;" points="359,-118 293,-118 289,-114 289,-82 355,-82 359,-86 359,-118"/>
-<polyline style="fill:none;stroke:gray;" points="355,-114 289,-114 "/>
-<polyline style="fill:none;stroke:gray;" points="355,-114 355,-82 "/>
-<polyline style="fill:none;stroke:gray;" points="355,-114 359,-118 "/>
-<text text-anchor="middle" x="324" y="-93.5" style="font-family:Times New Roman;font-size:20.00;fill:gray;">effects</text>
-</g>
-<!-- t53->t67 -->
-<g id="edge45" class="edge"><title>t53->t67</title>
-<path style="fill:none;stroke:gray;" d="M277,-140C283,-135 289,-130 295,-124"/>
-<polygon style="fill:gray;stroke:gray;" points="297.1,-126.8 303,-118 292.9,-121.2 297.1,-126.8"/>
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-<!-- t52->t67 -->
-<g id="edge47" class="edge"><title>t52->t67</title>
-<path style="fill:none;stroke:gray;" d="M167,-140C204,-131 248,-120 279,-111"/>
-<polygon style="fill:gray;stroke:gray;" points="279.881,-114.393 289,-109 278.508,-107.529 279.881,-114.393"/>
-</g>
-<!-- t12 -->
-<g id="node37" class="node"><title>t12</title>
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-<polyline style="fill:none;stroke:gray;" points="384,-372 230,-372 "/>
-<polyline style="fill:none;stroke:gray;" points="384,-372 384,-340 "/>
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-<!-- t56 -->
-<g id="node38" class="node"><title>t56</title>
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-<polyline style="fill:none;stroke:gray;" points="469,-288 337,-288 "/>
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-<polyline style="fill:none;stroke:gray;" points="469,-288 473,-292 "/>
-<text text-anchor="middle" x="405" y="-267.5" style="font-family:Times New Roman;font-size:20.00;fill:gray;">preparePanther</text>
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-<!-- t12->t56 -->
-<g id="edge37" class="edge"><title>t12->t56</title>
-<path style="fill:none;stroke:gray;" d="M330,-340C343,-328 361,-312 376,-299"/>
-<polygon style="fill:gray;stroke:gray;" points="378.779,-301.219 384,-292 374.169,-295.951 378.779,-301.219"/>
-</g>
-<!-- t56->t57 -->
-<g id="edge41" class="edge"><title>t56->t57</title>
-<path style="fill:none;stroke:gray;" d="M401,-256C400,-252 399,-248 398,-244"/>
-<polygon style="fill:gray;stroke:gray;" points="401.393,-243.119 396,-234 394.529,-244.492 401.393,-243.119"/>
-</g>
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-<g id="node43" class="node"><title>t58</title>
-<polygon style="fill:white;stroke:gray;" points="446,-176 340,-176 336,-172 336,-140 442,-140 446,-144 446,-176"/>
-<polyline style="fill:none;stroke:gray;" points="442,-172 336,-172 "/>
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-<text text-anchor="middle" x="391" y="-151.5" style="font-family:Times New Roman;font-size:20.00;fill:gray;">loadPanther</text>
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-<!-- t57->t58 -->
-<g id="edge43" class="edge"><title>t57->t58</title>
-<path style="fill:none;stroke:gray;" d="M391,-198C391,-194 391,-190 391,-186"/>
-<polygon style="fill:gray;stroke:gray;" points="394.5,-186 391,-176 387.5,-186 394.5,-186"/>
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-<!-- t58->t67 -->
-<g id="edge49" class="edge"><title>t58->t67</title>
-<path style="fill:none;stroke:gray;" d="M370,-140C364,-135 359,-130 353,-125"/>
-<polygon style="fill:gray;stroke:gray;" points="354.831,-121.951 345,-118 350.221,-127.219 354.831,-121.951"/>
-</g>
-<!-- t67->t68 -->
-<g id="edge73" class="edge"><title>t67->t68</title>
-<path style="fill:none;stroke:gray;" d="M359,-95C437,-84 621,-58 701,-47"/>
-<polygon style="fill:gray;stroke:gray;" points="701.398,-50.4778 711,-46 700.701,-43.5125 701.398,-50.4778"/>
-</g>
-<!-- t28 -->
-<g id="node52" class="node"><title>t28</title>
-<polygon style="fill:white;stroke:gray;" points="1040,-292 936,-292 932,-288 932,-256 1036,-256 1040,-260 1040,-292"/>
-<polyline style="fill:none;stroke:gray;" points="1036,-288 932,-288 "/>
-<polyline style="fill:none;stroke:gray;" points="1036,-288 1036,-256 "/>
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-<!-- t27->t28 -->
-<g id="edge55" class="edge"><title>t27->t28</title>
-<path style="fill:none;stroke:gray;" d="M993,-340C991,-329 990,-315 989,-302"/>
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-<polyline style="fill:none;stroke:gray;" points="854,-114 790,-114 "/>
-<polyline style="fill:none;stroke:gray;" points="854,-114 854,-82 "/>
-<polyline style="fill:none;stroke:gray;" points="854,-114 858,-118 "/>
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-<!-- t27->t66 -->
-<g id="edge61" class="edge"><title>t27->t66</title>
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-<!-- t28->t29 -->
-<g id="edge57" class="edge"><title>t28->t29</title>
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-<polygon style="fill:gray;stroke:gray;" points="898.56,-234.863 888,-234 895.717,-241.26 898.56,-234.863"/>
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-<!-- t28->t66 -->
-<g id="edge63" class="edge"><title>t28->t66</title>
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-<!-- t30 -->
-<g id="node56" class="node"><title>t30</title>
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-<!-- t29->t30 -->
-<g id="edge59" class="edge"><title>t29->t30</title>
-<path style="fill:none;stroke:gray;" d="M838,-198C837,-194 835,-190 834,-186"/>
-<polygon style="fill:gray;stroke:gray;" points="836.964,-183.985 830,-176 830.464,-186.585 836.964,-183.985"/>
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-<!-- t29->t66 -->
-<g id="edge65" class="edge"><title>t29->t66</title>
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-<!-- t30->t66 -->
-<g id="edge67" class="edge"><title>t30->t66</title>
-<path style="fill:none;stroke:gray;" d="M824,-140C824,-136 824,-132 824,-128"/>
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-<!-- t66->t68 -->
-<g id="edge75" class="edge"><title>t66->t68</title>
-<path style="fill:none;stroke:gray;" d="M797,-82C790,-77 781,-71 773,-66"/>
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-<!-- k1 -->
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-<text text-anchor="middle" x="1286" y="-576" style="font-family:Times New Roman;font-size:20.00;fill:gray;">Up-to-date</text>
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-<!-- k2 -->
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-<!-- k1->k2 -->
-<g id="edge78" class="edge"><title>k1->k2</title>
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diff --git a/doc/_build/html/_downloads/play_with_colours.py b/doc/_build/html/_downloads/play_with_colours.py
deleted file mode 100644
index 5054aa4..0000000
--- a/doc/_build/html/_downloads/play_with_colours.py
+++ /dev/null
@@ -1,268 +0,0 @@
-#!/usr/bin/env python
-"""
-
-    play_with_colours.py
-    [--log_file PATH]
-    [--verbose]
-
-"""
-
-################################################################################
-#
-#   test
-#
-#
-#   Copyright (c) 7/13/2010 Leo Goodstadt
-#
-#   Permission is hereby granted, free of charge, to any person obtaining a copy
-#   of this software and associated documentation files (the "Software"), to deal
-#   in the Software without restriction, including without limitation the rights
-#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-#   copies of the Software, and to permit persons to whom the Software is
-#   furnished to do so, subject to the following conditions:
-#
-#   The above copyright notice and this permission notice shall be included in
-#   all copies or substantial portions of the Software.
-#
-#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-#   THE SOFTWARE.
-#################################################################################
-
-import sys, os
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   options
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-from optparse import OptionParser
-import StringIO
-
-parser = OptionParser(version="%play_with_colours 1.0",
-                      usage = "\n\n    play_with_colours "
-                                "--flowchart FILE [options] "
-                                "[--colour_scheme_index INT ] "
-                                "[--key_legend_in_graph]")
-
-#
-#   pipeline
-#
-parser.add_option("--flowchart", dest="flowchart",
-                    metavar="FILE",
-                    type="string",
-                    help="Don't actually run any commands; just print the pipeline "
-                         "as a flowchart.")
-parser.add_option("--colour_scheme_index", dest="colour_scheme_index",
-                    metavar="INTEGER",
-                    type="int",
-                    help="Index of colour scheme for flow chart.")
-parser.add_option("--key_legend_in_graph", dest="key_legend_in_graph",
-                    action="store_true", default=False,
-                    help="Print out legend and key for dependency graph.")
-
-(options, remaining_args) = parser.parse_args()
-if not options.flowchart:
-    raise Exception("Missing mandatory parameter: --flowchart.\n")
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   imports
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-from ruffus import *
-from ruffus.ruffus_exceptions import JobSignalledBreak
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Pipeline
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-#
-# up to date tasks
-#
- at check_if_uptodate (lambda : (False, ""))
-def Up_to_date_task1(infile, outfile):
-    pass
-
- at check_if_uptodate (lambda : (False, ""))
- at follows(Up_to_date_task1)
-def Up_to_date_task2(infile, outfile):
-    pass
-
- at check_if_uptodate (lambda : (False, ""))
- at follows(Up_to_date_task2)
-def Up_to_date_task3(infile, outfile):
-    pass
-
-
- at check_if_uptodate (lambda : (False, ""))
- at follows(Up_to_date_task3)
-def Up_to_date_final_target(infile, outfile):
-    pass
-
-
-#
-# Explicitly specified
-#
- at check_if_uptodate (lambda : (False, ""))
- at follows(Up_to_date_task1)
-def Explicitly_specified_task(infile, outfile):
-    pass
-
-
-
-#
-# Tasks to run
-#
- at follows(Explicitly_specified_task)
-def Task_to_run1(infile, outfile):
-    pass
-
-
- at follows(Task_to_run1)
-def Task_to_run2(infile, outfile):
-    pass
-
- at follows(Task_to_run2)
-def Task_to_run3(infile, outfile):
-    pass
-
- at check_if_uptodate (lambda : (False, ""))
- at follows(Task_to_run2)
-def Up_to_date_task_forced_to_rerun(infile, outfile):
-    pass
-
-
-#
-# Final target
-#
- at follows(Up_to_date_task_forced_to_rerun, Task_to_run3)
-def Final_target(infile, outfile):
-    pass
-
-#
-# Ignored downstream
-#
- at follows(Final_target)
-def Downstream_task1_ignored(infile, outfile):
-    pass
-
- at follows(Final_target)
-def Downstream_task2_ignored(infile, outfile):
-    pass
-
-
-
-
-
-
-
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Main logic
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-from collections import defaultdict
-custom_flow_chart_colour_scheme = defaultdict(dict)
-
-#
-#   Base chart on this overall colour scheme index
-#
-custom_flow_chart_colour_scheme["colour_scheme_index"] = options.colour_scheme_index
-
-#
-#   Overriding colours
-#
-if options.colour_scheme_index == None:
-    custom_flow_chart_colour_scheme["Vicious cycle"]["linecolor"]                        = '"#FF3232"'
-    custom_flow_chart_colour_scheme["Pipeline"]["fontcolor"]                             = '"#FF3232"'
-    custom_flow_chart_colour_scheme["Key"]["fontcolor"]                                  = "black"
-    custom_flow_chart_colour_scheme["Key"]["fillcolor"]                                  = '"#F6F4F4"'
-    custom_flow_chart_colour_scheme["Task to run"]["linecolor"]                          = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Up-to-date"]["linecolor"]                           = "gray"
-    custom_flow_chart_colour_scheme["Final target"]["fillcolor"]                         = '"#EFA03B"'
-    custom_flow_chart_colour_scheme["Final target"]["fontcolor"]                         = "black"
-    custom_flow_chart_colour_scheme["Final target"]["color"]                             = "black"
-    custom_flow_chart_colour_scheme["Final target"]["dashed"]                            = 0
-    custom_flow_chart_colour_scheme["Vicious cycle"]["fillcolor"]                        = '"#FF3232"'
-    custom_flow_chart_colour_scheme["Vicious cycle"]["fontcolor"]                        = 'white'
-    custom_flow_chart_colour_scheme["Vicious cycle"]["color"]                            = "white"
-    custom_flow_chart_colour_scheme["Vicious cycle"]["dashed"]                           = 0
-    custom_flow_chart_colour_scheme["Up-to-date task"]["fillcolor"]                      = '"#B8CC6E"'
-    custom_flow_chart_colour_scheme["Up-to-date task"]["fontcolor"]                      = '"#006000"'
-    custom_flow_chart_colour_scheme["Up-to-date task"]["color"]                          = '"#006000"'
-    custom_flow_chart_colour_scheme["Up-to-date task"]["dashed"]                         = 0
-    custom_flow_chart_colour_scheme["Down stream"]["fillcolor"]                          = "white"
-    custom_flow_chart_colour_scheme["Down stream"]["fontcolor"]                          = "gray"
-    custom_flow_chart_colour_scheme["Down stream"]["color"]                              = "gray"
-    custom_flow_chart_colour_scheme["Down stream"]["dashed"]                             = 0
-    custom_flow_chart_colour_scheme["Explicitly specified task"]["fillcolor"]            = "transparent"
-    custom_flow_chart_colour_scheme["Explicitly specified task"]["fontcolor"]            = "black"
-    custom_flow_chart_colour_scheme["Explicitly specified task"]["color"]                = "black"
-    custom_flow_chart_colour_scheme["Explicitly specified task"]["dashed"]               = 0
-    custom_flow_chart_colour_scheme["Task to run"]["fillcolor"]                          = '"#EBF3FF"'
-    custom_flow_chart_colour_scheme["Task to run"]["fontcolor"]                          = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Task to run"]["color"]                              = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Task to run"]["dashed"]                             = 0
-    custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["fillcolor"]      = 'transparent'
-    custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["fontcolor"]      = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["color"]          = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["dashed"]         = 1
-    custom_flow_chart_colour_scheme["Up-to-date Final target"]["fillcolor"]              = '"#EFA03B"'
-    custom_flow_chart_colour_scheme["Up-to-date Final target"]["fontcolor"]              = '"#006000"'
-    custom_flow_chart_colour_scheme["Up-to-date Final target"]["color"]                  = '"#006000"'
-    custom_flow_chart_colour_scheme["Up-to-date Final target"]["dashed"]                 = 0
-
-if __name__ == '__main__':
-    pipeline_printout_graph (
-
-                                    open(options.flowchart, "w"),
-                                    # use flowchart file name extension to decide flowchart format
-                                    #   e.g. svg, jpg etc.
-                                    os.path.splitext(options.flowchart)[1][1:],
-
-                                    # final targets
-                                    [Final_target, Up_to_date_final_target],
-
-                                    # Explicitly specified tasks
-                                    [Explicitly_specified_task],
-
-                                    # Do we want key legend
-                                    no_key_legend   = not options.key_legend_in_graph,
-
-                                    # Print all the task types whether used or not
-                                    minimal_key_legend             = False,
-
-                                    user_colour_scheme = custom_flow_chart_colour_scheme,
-                                    pipeline_name = "Colour schemes")
-
-
-
-
-
-
-
-
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diff --git a/doc/_build/html/_images/history_html_flowchart.png b/doc/_build/html/_images/history_html_flowchart.png
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diff --git a/doc/_build/html/_images/history_html_flowchart.svg b/doc/_build/html/_images/history_html_flowchart.svg
deleted file mode 100644
index 268a187..0000000
--- a/doc/_build/html/_images/history_html_flowchart.svg
+++ /dev/null
@@ -1,269 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
- "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.36.0 (20140111.2315)
- -->
-<!-- Title: Pipeline: Pages: 1 -->
-<svg width="673pt" height="633pt"
- viewBox="0.00 0.00 673.00 633.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 629)">
-<title>Pipeline:</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-629 669,-629 669,4 -4,4"/>
-<g id="clust1" class="cluster"><title>clustertasks</title>
-<polygon fill="none" stroke="black" points="8,-8 8,-617 519,-617 519,-8 8,-8"/>
-<text text-anchor="middle" x="263.5" y="-589" font-family="Times,serif" font-size="30.00" fill="#ff3232">Pipeline:</text>
-</g>
-<g id="clust2" class="cluster"><title>clusterkey1</title>
-<polygon fill="#f6f4f4" stroke="#f6f4f4" points="527,-66 527,-610 657,-610 657,-66 527,-66"/>
-<text text-anchor="middle" x="592" y="-590" font-family="Times,serif" font-size="20.00">Key:</text>
-</g>
-<!-- t0 -->
-<g id="node1" class="node"><title>t0</title>
-<polygon fill="#b8cc6e" stroke="#006000" points="370.25,-568 215.75,-568 211.75,-564 211.75,-532 366.25,-532 370.25,-536 370.25,-568"/>
-<polyline fill="none" stroke="#006000" points="366.25,-564 211.75,-564 "/>
-<polyline fill="none" stroke="#006000" points="366.25,-564 366.25,-532 "/>
-<polyline fill="none" stroke="#006000" points="366.25,-564 370.25,-568 "/>
-<text text-anchor="middle" x="291" y="-545" font-family="Times,serif" font-size="20.00" fill="#006000">Up_to_date_task1</text>
-</g>
-<!-- t4 -->
-<g id="node2" class="node"><title>t4</title>
-<polygon fill="#b8cc6e" stroke="#006000" points="293.25,-454 82.75,-454 78.75,-450 78.75,-418 289.25,-418 293.25,-422 293.25,-454"/>
-<polyline fill="none" stroke="#006000" points="289.25,-450 78.75,-450 "/>
-<polyline fill="none" stroke="#006000" points="289.25,-450 289.25,-418 "/>
-<polyline fill="none" stroke="#006000" points="289.25,-450 293.25,-454 "/>
-<text text-anchor="middle" x="186" y="-431" font-family="Times,serif" font-size="20.00" fill="#006000">Explicitly_specified_task</text>
-</g>
-<!-- t0->t4 -->
-<g id="edge1" class="edge"><title>t0->t4</title>
-<path fill="none" stroke="gray" d="M275.053,-531.99C257.476,-513.241 229.048,-482.918 209.048,-461.585"/>
-<polygon fill="gray" stroke="gray" points="211.49,-459.072 202.097,-454.17 206.383,-463.86 211.49,-459.072"/>
-</g>
-<!-- t1 -->
-<g id="node8" class="node"><title>t1</title>
-<g id="a_node8"><a xlink:href="http://cnn.com" xlink:title="What is this?<BR/> What <FONT COLOR="red">is</FONT>this???">
-<polygon fill="#b8cc6e" stroke="#006000" points="466,-490 328,-490 328,-486 324,-486 324,-482 328,-482 328,-390 324,-390 324,-386 328,-386 328,-382 466,-382 466,-490"/>
-<polyline fill="none" stroke="#006000" points="328,-486 332,-486 332,-482 328,-482 "/>
-<polyline fill="none" stroke="#006000" points="328,-390 332,-390 332,-386 328,-386 "/>
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-<text text-anchor="start" x="345.5" y="-441" font-family="Times,serif" font-size="20.00" fill="#006000">What is this?</text>
-<text text-anchor="start" x="336" y="-421" font-family="Times,serif" font-size="20.00" fill="#006000"> What </text>
-<text text-anchor="start" x="390" y="-421" font-family="Times,serif" font-size="20.00" fill="red">is</text>
-<text text-anchor="start" x="403" y="-421" font-family="Times,serif" font-size="20.00" fill="#006000">this???</text>
-</a>
-</g>
-</g>
-<!-- t0->t1 -->
-<g id="edge8" class="edge"><title>t0->t1</title>
-<path fill="none" stroke="gray" d="M307.099,-531.99C312.118,-526.687 318.013,-520.458 324.344,-513.768"/>
-<polygon fill="gray" stroke="gray" points="327.033,-516.019 331.365,-506.351 321.949,-511.208 327.033,-516.019"/>
-</g>
-<!-- t5 -->
-<g id="node3" class="node"><title>t5</title>
-<polygon fill="#ebf3ff" stroke="#0044a0" points="248.25,-340 127.75,-340 123.75,-336 123.75,-304 244.25,-304 248.25,-308 248.25,-340"/>
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-<text text-anchor="middle" x="186" y="-317" font-family="Times,serif" font-size="20.00" fill="#0044a0">Task_to_run1</text>
-</g>
-<!-- t4->t5 -->
-<g id="edge2" class="edge"><title>t4->t5</title>
-<path fill="none" stroke="gray" d="M186,-417.99C186,-400.063 186,-371.555 186,-350.442"/>
-<polygon fill="gray" stroke="gray" points="189.5,-350.17 186,-340.17 182.5,-350.171 189.5,-350.17"/>
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-<!-- t6 -->
-<g id="node4" class="node"><title>t6</title>
-<polygon fill="#ebf3ff" stroke="#0044a0" points="248.25,-267 127.75,-267 123.75,-263 123.75,-231 244.25,-231 248.25,-235 248.25,-267"/>
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-<text text-anchor="middle" x="186" y="-244" font-family="Times,serif" font-size="20.00" fill="#0044a0">Task_to_run2</text>
-</g>
-<!-- t5->t6 -->
-<g id="edge3" class="edge"><title>t5->t6</title>
-<path fill="none" stroke="#0044a0" d="M186,-303.813C186,-295.789 186,-286.047 186,-277.069"/>
-<polygon fill="#0044a0" stroke="#0044a0" points="189.5,-277.029 186,-267.029 182.5,-277.029 189.5,-277.029"/>
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-<!-- t8 -->
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-<polygon fill="none" stroke="#0044a0" stroke-dasharray="5,2" points="312.25,-187 29.75,-187 25.75,-183 25.75,-151 308.25,-151 312.25,-155 312.25,-187"/>
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-  <h1>All modules for which code is available</h1>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-            
-  <h1>Source code for ruffus.proxy_logger</h1><div class="highlight"><pre>
-<span class="c">#!/usr/bin/env python</span>
-<span class="c">################################################################################</span>
-<span class="c">#</span>
-<span class="c">#   proxy_logger.py</span>
-<span class="c">#</span>
-<span class="c">#</span>
-<span class="c">#   Copyright (c) 10/9/2009 Leo Goodstadt</span>
-<span class="c">#</span>
-<span class="c">#   Permission is hereby granted, free of charge, to any person obtaining a copy</span>
-<span class="c">#   of this software and associated documentation files (the "Software"), to deal</span>
-<span class="c">#   in the Software without restriction, including without limitation the rights</span>
-<span class="c">#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
-<span class="c">#   copies of the Software, and to permit persons to whom the Software is</span>
-<span class="c">#   furnished to do so, subject to the following conditions:</span>
-<span class="c">#</span>
-<span class="c">#   The above copyright notice and this permission notice shall be included in</span>
-<span class="c">#   all copies or substantial portions of the Software.</span>
-<span class="c">#</span>
-<span class="c">#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
-<span class="c">#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
-<span class="c">#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
-<span class="c">#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
-<span class="c">#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
-<span class="c">#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN</span>
-<span class="c">#   THE SOFTWARE.</span>
-<span class="c">#################################################################################</span>
-<span class="sd">"""</span>
-<span class="sd">****************************************************************************</span>
-<span class="sd">Create proxy for logging for use with multiprocessing</span>
-<span class="sd">****************************************************************************</span>
-
-<span class="sd">These can be safely sent (marshalled) across process boundaries</span>
-
-
-<span class="sd">===========</span>
-<span class="sd">Example 1</span>
-<span class="sd">===========</span>
-
-<span class="sd">    Set up logger from config file::</span>
-
-<span class="sd">        from proxy_logger import *</span>
-<span class="sd">        args={}</span>
-<span class="sd">        args["config_file"] = "/my/config/file"</span>
-
-<span class="sd">        (logger_proxy,</span>
-<span class="sd">         logging_mutex) = make_shared_logger_and_proxy (setup_std_shared_logger,</span>
-<span class="sd">                                                        "my_logger", args)</span>
-
-
-<span class="sd">===========</span>
-<span class="sd">Example 2</span>
-<span class="sd">===========</span>
-
-<span class="sd">    Log to file ``"/my/lg.log"`` in the specified format (Time / Log name / Event type / Message).</span>
-
-<span class="sd">    Delay file creation until first log.</span>
-
-<span class="sd">    Only log ``Debug`` messages</span>
-
-<span class="sd">        Other alternatives for the logging threshold (``args["level"]``) include</span>
-
-<span class="sd">            * ``logging.DEBUG``</span>
-<span class="sd">            * ``logging.INFO``</span>
-<span class="sd">            * ``logging.WARNING``</span>
-<span class="sd">            * ``logging.ERROR``</span>
-<span class="sd">            * ``logging.CRITICAL``</span>
-
-<span class="sd">    ::</span>
-
-<span class="sd">        from proxy_logger import *</span>
-<span class="sd">        args={}</span>
-<span class="sd">        args["file_name"] = "/my/lg.log"</span>
-<span class="sd">        args["formatter"] = "%(asctime)s - %(name)s - %(levelname)6s - %(message)s"</span>
-<span class="sd">        args["delay"]     = True</span>
-<span class="sd">        args["level"]     = logging.DEBUG</span>
-
-<span class="sd">        (logger_proxy,</span>
-<span class="sd">         logging_mutex) = make_shared_logger_and_proxy (setup_std_shared_logger,</span>
-<span class="sd">                                                        "my_logger", args)</span>
-
-<span class="sd">===========</span>
-<span class="sd">Example 3</span>
-<span class="sd">===========</span>
-
-<span class="sd">    Rotate log files every 20 Kb, with up to 10 backups.</span>
-<span class="sd">    ::</span>
-
-<span class="sd">        from proxy_logger import *</span>
-<span class="sd">        args={}</span>
-<span class="sd">        args["file_name"] = "/my/lg.log"</span>
-<span class="sd">        args["rotating"] = True</span>
-<span class="sd">        args["maxBytes"]=20000</span>
-<span class="sd">        args["backupCount"]=10</span>
-<span class="sd">        (logger_proxy,</span>
-<span class="sd">         logging_mutex) = make_shared_logger_and_proxy (setup_std_shared_logger,</span>
-<span class="sd">                                                        "my_logger", args)</span>
-
-
-
-<span class="sd">==============</span>
-<span class="sd">To use:</span>
-<span class="sd">==============</span>
-
-<span class="sd">    ::</span>
-
-<span class="sd">        (logger_proxy,</span>
-<span class="sd">         logging_mutex) = make_shared_logger_and_proxy (setup_std_shared_logger,</span>
-<span class="sd">                                                        "my_logger", args)</span>
-
-<span class="sd">        with logging_mutex:</span>
-<span class="sd">            my_log.debug('This is a debug message')</span>
-<span class="sd">            my_log.info('This is an info message')</span>
-<span class="sd">            my_log.warning('This is a warning message')</span>
-<span class="sd">            my_log.error('This is an error message')</span>
-<span class="sd">            my_log.critical('This is a critical error message')</span>
-<span class="sd">            my_log.log(logging.DEBUG, 'This is a debug message')</span>
-
-<span class="sd">    Note that the logging function ``exception()`` is not included because python</span>
-<span class="sd">    stack trace information is not well-marshalled</span>
-<span class="sd">    (`pickle <http://docs.python.org/library/pickle.html>`_\ d) across processes.</span>
-
-<span class="sd">"""</span>
-
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   imports</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span><span class="nn">os</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Shared logging</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="kn">import</span> <span class="nn">multiprocessing</span>
-<span class="kn">import</span> <span class="nn">multiprocessing.managers</span>
-
-
-<span class="kn">import</span> <span class="nn">logging</span>
-<span class="kn">import</span> <span class="nn">logging.handlers</span>
-
-
-
-<span class="c">#</span>
-<span class="c">#   setup_logger</span>
-<span class="c">#</span>
-<div class="viewcode-block" id="setup_std_shared_logger"><a class="viewcode-back" href="../../proxy_logger.html#ruffus.proxy_logger.setup_std_shared_logger">[docs]</a><span class="k">def</span> <span class="nf">setup_std_shared_logger</span><span class="p">(</span><span class="n">logger_name</span><span class="p">,</span> <span class="n">args</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    This function is a simple around wrapper around the python</span>
-<span class="sd">    `logging <http://docs.python.org/library/logging.html>`_ module.</span>
-
-<span class="sd">    This *logger_factory* example creates logging objects which can</span>
-<span class="sd">    then be managed by proxy via ``ruffus.proxy_logger.make_shared_logger_and_proxy()``</span>
-
-<span class="sd">    This can be:</span>
-
-<span class="sd">        * a `disk log file <http://docs.python.org/library/logging.html#filehandler>`_</span>
-<span class="sd">        * a automatically backed-up `(rotating) log <http://docs.python.org/library/logging.html#rotatingfilehandler>`_.</span>
-<span class="sd">        * any log specified in a `configuration file <http://docs.python.org/library/logging.html#configuration-file-format>`_</span>
-
-<span class="sd">    These are specified in the ``args`` dictionary forwarded by ``make_shared_logger_and_proxy()``</span>
-
-<span class="sd">    :param logger_name: name of log</span>
-<span class="sd">    :param args: a dictionary of parameters forwarded from ``make_shared_logger_and_proxy()``</span>
-
-<span class="sd">        Valid entries include:</span>
-
-<span class="sd">            .. describe:: "level"</span>
-
-<span class="sd">                Sets the `threshold <http://docs.python.org/library/logging.html#logging.Handler.setLevel>`_ for the logger.</span>
-
-<span class="sd">            .. describe:: "config_file"</span>
-
-<span class="sd">                The logging object is configured from this `configuration file <http://docs.python.org/library/logging.html#configuration-file-format>`_.</span>
-
-<span class="sd">            .. describe:: "file_name"</span>
-
-<span class="sd">                Sets disk log file name.</span>
-
-<span class="sd">            .. describe:: "rotating"</span>
-
-<span class="sd">                Chooses a `(rotating) log <http://docs.python.org/library/logging.html#rotatingfilehandler>`_.</span>
-
-<span class="sd">            .. describe:: "maxBytes"</span>
-
-<span class="sd">                Allows the file to rollover at a predetermined size</span>
-
-<span class="sd">            .. describe:: "backupCount"</span>
-
-<span class="sd">                If backupCount is non-zero, the system will save old log files by appending the extensions ``.1``, ``.2``, ``.3`` etc., to the filename.</span>
-
-<span class="sd">            .. describe:: "delay"</span>
-
-<span class="sd">                Defer file creation until the log is written to.</span>
-
-<span class="sd">            .. describe:: "formatter"</span>
-
-<span class="sd">                `Converts <http://docs.python.org/library/logging.html#formatter-objects>`_ the message to a logged entry string.</span>
-<span class="sd">                For example,</span>
-<span class="sd">                ::</span>
-
-<span class="sd">                    "%(asctime)s - %(name)s - %(levelname)6s - %(message)s"</span>
-
-
-
-<span class="sd">    """</span>
-
-    <span class="c">#</span>
-    <span class="c">#   Log file name with logger level</span>
-    <span class="c">#</span>
-    <span class="n">new_logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="n">logger_name</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">"level"</span><span class="p">):</span>
-        <span class="n">new_logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s">"level"</span><span class="p">])</span>
-
-    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">"config_file"</span><span class="p">):</span>
-        <span class="n">logging</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">fileConfig</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s">"config_file"</span><span class="p">])</span>
-
-    <span class="k">else</span><span class="p">:</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">"file_name"</span><span class="p">):</span>
-            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Missing file name for log. Remember to set 'file_name'"</span><span class="p">)</span>
-        <span class="n">log_file_name</span> <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="s">"file_name"</span><span class="p">]</span>
-
-        <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">"rotating"</span><span class="p">):</span>
-            <span class="n">rotating_args</span> <span class="o">=</span> <span class="p">{}</span>
-            <span class="c"># override default</span>
-            <span class="n">rotating_args</span><span class="p">[</span><span class="s">"maxBytes"</span><span class="p">]</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">"maxBytes"</span><span class="p">,</span> <span class="mi">100000</span><span class="p">)</span>
-            <span class="n">rotating_args</span><span class="p">[</span><span class="s">"backupCount"</span><span class="p">]</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">"backupCount"</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
-            <span class="n">handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">handlers</span><span class="o">.</span><span class="n">RotatingFileHandler</span><span class="p">(</span> <span class="n">log_file_name</span><span class="p">,</span> <span class="o">**</span><span class="n">rotating_args</span><span class="p">)</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">defer_loggin</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">"delay"</span><span class="p">)</span>
-            <span class="n">handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">handlers</span><span class="o">.</span><span class="n">RotatingFileHandler</span><span class="p">(</span> <span class="n">log_file_name</span><span class="p">,</span> <span class="n">delay</span><span class="o">=</span><span class="n">defer_loggin</span><span class="p">)</span>
-
-        <span class="c">#       %(name)s</span>
-        <span class="c">#       %(levelno)s</span>
-        <span class="c">#       %(levelname)s</span>
-        <span class="c">#       %(pathname)s</span>
-        <span class="c">#       %(filename)s</span>
-        <span class="c">#       %(module)s</span>
-        <span class="c">#       %(funcName)s</span>
-        <span class="c">#       %(lineno)d</span>
-        <span class="c">#       %(created)f</span>
-        <span class="c">#       %(relativeCreated)d</span>
-        <span class="c">#       %(asctime)s</span>
-        <span class="c">#       %(msecs)d</span>
-        <span class="c">#       %(thread)d</span>
-        <span class="c">#       %(threadName)s</span>
-        <span class="c">#       %(process)d</span>
-        <span class="c">#       %(message)s</span>
-        <span class="c">#</span>
-        <span class="c"># E.g.: "%(asctime)s - %(name)s - %(levelname)6s - %(message)s"</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="s">"formatter"</span><span class="p">):</span>
-            <span class="n">my_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="s">"formatter"</span><span class="p">])</span>
-            <span class="n">handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">my_formatter</span><span class="p">)</span>
-
-        <span class="n">new_logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">handler</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   This log object will be wrapped in proxy</span>
-    <span class="c">#</span>
-    <span class="k">return</span> <span class="n">new_logger</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Proxy object for logging</span>
-<span class="c">#       Logging messages will be marshalled (forwarded) to the process where the</span>
-<span class="c">#       shared log lives</span>
-<span class="c">#</span></div>
-<span class="k">class</span> <span class="nc">LoggerProxy</span><span class="p">(</span><span class="n">multiprocessing</span><span class="o">.</span><span class="n">managers</span><span class="o">.</span><span class="n">BaseProxy</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">debug</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_callmethod</span><span class="p">(</span><span class="s">'debug'</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">log</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_callmethod</span><span class="p">(</span><span class="s">'log'</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">info</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_callmethod</span><span class="p">(</span><span class="s">'info'</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">warning</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_callmethod</span><span class="p">(</span><span class="s">'warning'</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">error</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_callmethod</span><span class="p">(</span><span class="s">'error'</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">critical</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_callmethod</span><span class="p">(</span><span class="s">'critical'</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">log</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_callmethod</span><span class="p">(</span><span class="s">'log'</span><span class="p">,</span> <span class="n">args</span><span class="p">,</span> <span class="n">kwargs</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">__str__</span> <span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">return</span> <span class="s">"<LoggingProxy>"</span>
-
-<span class="c">#</span>
-<span class="c">#   Register the setup_logger function as a proxy for setup_logger</span>
-<span class="c">#</span>
-<span class="c">#   We use SyncManager as a base class so we can get a lock proxy for synchronising</span>
-<span class="c">#       logging later on</span>
-<span class="c">#</span>
-<span class="k">class</span> <span class="nc">LoggingManager</span><span class="p">(</span><span class="n">multiprocessing</span><span class="o">.</span><span class="n">managers</span><span class="o">.</span><span class="n">SyncManager</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Logging manager sets up its own process and will create the real Log object there</span>
-<span class="sd">    We refer to this (real) log via proxies</span>
-<span class="sd">    """</span>
-    <span class="k">pass</span>
-
-
-
-
-<div class="viewcode-block" id="make_shared_logger_and_proxy"><a class="viewcode-back" href="../../proxy_logger.html#ruffus.proxy_logger.make_shared_logger_and_proxy">[docs]</a><span class="k">def</span> <span class="nf">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">logger_factory</span><span class="p">,</span> <span class="n">logger_name</span><span class="p">,</span> <span class="n">args</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Make a `logging <http://docs.python.org/library/logging.html>`_ object</span>
-<span class="sd">    called "\ ``logger_name``\ " by calling ``logger_factory``\ (``args``\ )</span>
-
-<span class="sd">    This function will return a proxy to the shared logger which can be copied to jobs</span>
-<span class="sd">    in other processes, as well as a mutex which can be used to prevent simultaneous logging</span>
-<span class="sd">    from happening.</span>
-
-<span class="sd">    :param logger_factory: functions which creates and returns an object with the</span>
-<span class="sd">                           `logging <http://docs.python.org/library/logging.html>`_ interface.</span>
-<span class="sd">                           ``setup_std_shared_logger()`` is one example of a logger factory.</span>
-<span class="sd">    :param logger_name: name of log</span>
-<span class="sd">    :param args: parameters passed (as a single argument) to ``logger_factory``</span>
-<span class="sd">    :returns: a proxy to the shared logger which can be copied to jobs in other processes</span>
-<span class="sd">    :returns: a mutex which can be used to prevent simultaneous logging from happening</span>
-
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   make shared log and proxy</span>
-    <span class="c">#</span>
-    <span class="n">manager</span> <span class="o">=</span> <span class="n">LoggingManager</span><span class="p">()</span>
-    <span class="n">manager</span><span class="o">.</span><span class="n">register</span><span class="p">(</span>   <span class="s">'setup_logger'</span><span class="p">,</span>
-                        <span class="n">logger_factory</span><span class="p">,</span>
-                        <span class="n">proxytype</span><span class="o">=</span><span class="n">LoggerProxy</span><span class="p">,</span>
-                        <span class="n">exposed</span> <span class="o">=</span> <span class="p">(</span> <span class="s">'critical'</span><span class="p">,</span> <span class="s">'log'</span><span class="p">,</span>
-                                    <span class="s">'info'</span><span class="p">,</span> <span class="s">'debug'</span><span class="p">,</span> <span class="s">'warning'</span><span class="p">,</span> <span class="s">'error'</span><span class="p">))</span>
-    <span class="n">manager</span><span class="o">.</span><span class="n">start</span><span class="p">()</span>
-    <span class="n">logger_proxy</span> <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">setup_logger</span><span class="p">(</span><span class="n">logger_name</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   make sure we are not logging at the same time in different processes</span>
-    <span class="c">#</span>
-    <span class="n">logging_mutex</span> <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Lock</span><span class="p">()</span>
-
-    <span class="k">return</span> <span class="n">logger_proxy</span><span class="p">,</span> <span class="n">logging_mutex</span>
-
-
-</div>
-<span class="kn">import</span> <span class="nn">unittest</span><span class="o">,</span> <span class="nn">os</span><span class="o">,</span><span class="nn">sys</span>
-<span class="kn">from</span> <span class="nn">proxy_logger</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">traceback</span>
-
-
-<span class="k">class</span> <span class="nc">Test_Logging</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
-
-
-
-    <span class="k">def</span> <span class="nf">test_rotating_log</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">            test rotating via proxy</span>
-<span class="sd">        """</span>
-        <span class="nb">open</span><span class="p">(</span><span class="s">"/tmp/lg.log"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-        <span class="n">args</span><span class="o">=</span><span class="p">{}</span>
-        <span class="n">args</span><span class="p">[</span><span class="s">"file_name"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"/tmp/lg.log"</span>
-        <span class="n">args</span><span class="p">[</span><span class="s">"rotating"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
-        <span class="n">args</span><span class="p">[</span><span class="s">"maxBytes"</span><span class="p">]</span><span class="o">=</span><span class="mi">20000</span>
-        <span class="n">args</span><span class="p">[</span><span class="s">"backupCount"</span><span class="p">]</span><span class="o">=</span><span class="mi">10</span>
-        <span class="c">#args["level"]= logging.INFO</span>
-        <span class="p">(</span><span class="n">my_log</span><span class="p">,</span>
-         <span class="n">logging_mutex</span><span class="p">)</span> <span class="o">=</span> <span class="n">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">setup_std_shared_logger</span><span class="p">,</span>
-                                                        <span class="s">"my_logger"</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
-        <span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-            <span class="n">my_log</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">'This is a debug message'</span><span class="p">)</span>
-            <span class="n">my_log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">'This is an info message'</span><span class="p">)</span>
-            <span class="n">my_log</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s">'This is a warning message'</span><span class="p">)</span>
-            <span class="n">my_log</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s">'This is an error message'</span><span class="p">)</span>
-            <span class="n">my_log</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s">'This is a critical error message'</span><span class="p">)</span>
-            <span class="n">my_log</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">ERROR</span><span class="p">,</span> <span class="s">'This is a debug message'</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">assert_</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="s">"/tmp/lg.log"</span><span class="p">)</span> <span class="o">.</span><span class="n">read</span><span class="p">()</span> <span class="o">==</span> \
-<span class="sd">"""This is a warning message</span>
-<span class="sd">This is an error message</span>
-<span class="sd">This is a critical error message</span>
-<span class="sd">This is a debug message</span>
-<span class="sd">"""</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   debug code not run if called as a module</span>
-<span class="c">#</span>
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
-    <span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"--debug"</span><span class="p">):</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s">"--debug"</span><span class="p">)</span>
-    <span class="n">unittest</span><span class="o">.</span><span class="n">main</span><span class="p">()</span>
-</pre></div>
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
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-<div id="searchbox" style="display: none">
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
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-    <h3> Quick Reference:</h3>
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-        <ul>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
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-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
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-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <h1>Source code for ruffus.task</h1><div class="highlight"><pre>
-<span class="c">#!/usr/bin/env python</span>
-<span class="c">################################################################################</span>
-<span class="c">#</span>
-<span class="c">#</span>
-<span class="c">#   task.py</span>
-<span class="c">#</span>
-<span class="c">#   Copyright (c) 10/9/2009 Leo Goodstadt</span>
-<span class="c">#</span>
-<span class="c">#   Permission is hereby granted, free of charge, to any person obtaining a copy</span>
-<span class="c">#   of this software and associated documentation files (the "Software"), to deal</span>
-<span class="c">#   in the Software without restriction, including without limitation the rights</span>
-<span class="c">#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
-<span class="c">#   copies of the Software, and to permit persons to whom the Software is</span>
-<span class="c">#   furnished to do so, subject to the following conditions:</span>
-<span class="c">#</span>
-<span class="c">#   The above copyright notice and this permission notice shall be included in</span>
-<span class="c">#   all copies or substantial portions of the Software.</span>
-<span class="c">#</span>
-<span class="c">#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
-<span class="c">#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
-<span class="c">#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
-<span class="c">#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
-<span class="c">#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
-<span class="c">#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN</span>
-<span class="c">#   THE SOFTWARE.</span>
-<span class="c">#################################################################################</span>
-<span class="sd">"""</span>
-
-<span class="sd">********************************************</span>
-<span class="sd">:mod:`ruffus.task` -- Overview</span>
-<span class="sd">********************************************</span>
-
-<span class="sd">.. moduleauthor:: Leo Goodstadt <ruffus at llew.org.uk></span>
-
-<span class="sd">Initial implementation of @active_if by Jacob Biesinger</span>
-
-<span class="sd">============================</span>
-<span class="sd">Decorator syntax:</span>
-<span class="sd">============================</span>
-
-<span class="sd">    Pipelined tasks are created by "decorating" a function with the following syntax::</span>
-
-<span class="sd">        def func_a():</span>
-<span class="sd">            pass</span>
-
-<span class="sd">        @follows(func_a)</span>
-<span class="sd">        def func_b ():</span>
-<span class="sd">            pass</span>
-
-
-<span class="sd">    Each task is a single function which is applied one or more times to a list of parameters</span>
-<span class="sd">    (typically input files to produce a list of output files).</span>
-
-<span class="sd">    Each of these is a separate, independent job (sharing the same code) which can be</span>
-<span class="sd">    run in parallel.</span>
-
-
-<span class="sd">============================</span>
-<span class="sd">Running the pipeline</span>
-<span class="sd">============================</span>
-<span class="sd">    To run the pipeline::</span>
-
-<span class="sd">            pipeline_run(target_tasks, forcedtorun_tasks = [], multiprocess = 1,</span>
-<span class="sd">                            logger = stderr_logger,</span>
-<span class="sd">                            gnu_make_maximal_rebuild_mode  = True,</span>
-<span class="sd">                            cleanup_log = "../cleanup.log")</span>
-
-<span class="sd">            pipeline_cleanup(cleanup_log = "../cleanup.log")</span>
-
-
-
-
-
-
-<span class="sd">"""</span>
-
-
-<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">with_statement</span>
-<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span><span class="nn">sys</span><span class="o">,</span><span class="nn">copy</span><span class="o">,</span> <span class="nn">multiprocessing</span>
-<span class="c">#from collections import namedtuple</span>
-<span class="kn">import</span> <span class="nn">collections</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   imports</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="kn">import</span> <span class="nn">logging</span>
-<span class="kn">import</span> <span class="nn">re</span>
-<span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">defaultdict</span>
-<span class="kn">from</span> <span class="nn">multiprocessing</span> <span class="kn">import</span> <span class="n">Pool</span>
-<span class="kn">from</span> <span class="nn">multiprocessing.pool</span> <span class="kn">import</span> <span class="n">ThreadPool</span>
-<span class="kn">import</span> <span class="nn">traceback</span>
-<span class="kn">import</span> <span class="nn">types</span>
-<span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">imap</span>
-<span class="kn">import</span> <span class="nn">textwrap</span>
-<span class="kn">import</span> <span class="nn">time</span>
-<span class="kn">from</span> <span class="nn">multiprocessing.managers</span> <span class="kn">import</span> <span class="n">SyncManager</span>
-<span class="kn">from</span> <span class="nn">contextlib</span> <span class="kn">import</span> <span class="n">contextmanager</span>
-<span class="kn">import</span> <span class="nn">cPickle</span> <span class="kn">as</span> <span class="nn">pickle</span>
-<span class="kn">import</span> <span class="nn">dbdict</span>
-
-
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
-    <span class="kn">import</span> <span class="nn">sys</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="s">"."</span><span class="p">)</span>
-
-<span class="kn">from</span> <span class="nn">graph</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">print_dependencies</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus_exceptions</span> <span class="kn">import</span>  <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus_utility</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">file_name_parameters</span> <span class="kn">import</span>  <span class="o">*</span>
-
-
-<span class="c">#</span>
-<span class="c"># use simplejson in place of json for python < 2.6</span>
-<span class="c">#</span>
-<span class="k">try</span><span class="p">:</span>
-    <span class="kn">import</span> <span class="nn">json</span>
-<span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
-    <span class="kn">import</span> <span class="nn">simplejson</span>
-    <span class="n">json</span> <span class="o">=</span> <span class="n">simplejson</span>
-<span class="n">dumps</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span>
-
-<span class="kn">import</span> <span class="nn">Queue</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#</span>
-<span class="c">#   light weight logging objects</span>
-<span class="c">#</span>
-<span class="c">#</span>
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<div class="viewcode-block" id="t_black_hole_logger"><a class="viewcode-back" href="../../task.html#ruffus.task.t_black_hole_logger">[docs]</a><span class="k">class</span> <span class="nc">t_black_hole_logger</span><span class="p">:</span>
-    <span class="sd">"""</span>
-<span class="sd">    Does nothing!</span>
-<span class="sd">    """</span>
-    <span class="k">def</span> <span class="nf">info</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">pass</span>
-    <span class="k">def</span> <span class="nf">debug</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">pass</span>
-    <span class="k">def</span> <span class="nf">warning</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">pass</span>
-    <span class="k">def</span> <span class="nf">error</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">pass</span>
-
-</div>
-<div class="viewcode-block" id="t_stderr_logger"><a class="viewcode-back" href="../../task.html#ruffus.task.t_stderr_logger">[docs]</a><span class="k">class</span> <span class="nc">t_stderr_logger</span><span class="p">:</span>
-    <span class="sd">"""</span>
-<span class="sd">    Everything to stderr</span>
-<span class="sd">    """</span>
-    <span class="k">def</span> <span class="nf">__init__</span> <span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">unique_prefix</span> <span class="o">=</span> <span class="s">""</span>
-    <span class="k">def</span> <span class="nf">add_unique_prefix</span> <span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="kn">import</span> <span class="nn">random</span>
-        <span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">()</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">unique_prefix</span><span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">1000</span><span class="p">))</span> <span class="o">+</span> <span class="s">" "</span>
-    <span class="k">def</span> <span class="nf">info</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">unique_prefix</span> <span class="o">+</span> <span class="n">message</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">warning</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n\n</span><span class="s">"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">unique_prefix</span> <span class="o">+</span> <span class="s">"WARNING:</span><span class="se">\n</span><span class="s">    "</span> <span  [...]
-    <span class="k">def</span> <span class="nf">error</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n\n</span><span class="s">"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">unique_prefix</span> <span class="o">+</span> <span class="s">"ERROR:</span><span class="se">\n</span><span class="s">    "</span> <span cl [...]
-    <span class="k">def</span> <span class="nf">debug</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">unique_prefix</span> <span class="o">+</span> <span class="n">message</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-</div>
-<span class="k">class</span> <span class="nc">t_stream_logger</span><span class="p">:</span>
-    <span class="sd">"""</span>
-<span class="sd">    Everything to stderr</span>
-<span class="sd">    """</span>
-    <span class="k">def</span> <span class="nf">__init__</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">stream</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">stream</span> <span class="o">=</span> <span class="n">stream</span>
-    <span class="k">def</span> <span class="nf">info</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">message</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">warning</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n\n</span><span class="s">WARNING:</span><span class="se">\n</span><span class="s">    "</span> <span class="o">+</span> <span class="n">message</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n\n</span><span class="s">"</span><span class="p [...]
-    <span class="k">def</span> <span class="nf">error</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n\n</span><span class="s">ERROR:</span><span class="se">\n</span><span class="s">    "</span> <span class="o">+</span> <span class="n">message</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n\n</span><span class="s">"</span><span class="p"> [...]
-    <span class="k">def</span> <span class="nf">debug</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">message</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-
-<span class="n">black_hole_logger</span> <span class="o">=</span> <span class="n">t_black_hole_logger</span><span class="p">()</span>
-<span class="n">stderr_logger</span>     <span class="o">=</span> <span class="n">t_stderr_logger</span><span class="p">()</span>
-
-<span class="k">class</span> <span class="nc">t_verbose_logger</span><span class="p">:</span>
-    <span class="k">def</span> <span class="nf">__init__</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="n">verbose</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">logger</span> <span class="o">=</span> <span class="n">logger</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">runtime_data</span> <span class="o">=</span> <span class="n">runtime_data</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   logging helper function</span>
-<span class="c">#</span>
-<span class="c">#________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="n">message_level</span><span class="p">,</span> <span class="n">verbose_level</span><span class="p">,</span> <span class="n">msg</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    writes to log if message_level > verbose level</span>
-<span class="sd">    """</span>
-    <span class="k">if</span> <span class="n">message_level</span> <span class="o"><=</span> <span class="n">verbose_level</span><span class="p">:</span>
-        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
-
-
-
-
-
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-
-<span class="c">#   queue management objects</span>
-
-<span class="c">#       inserted into queue like job parameters to control multi-processing queue</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c"># fake parameters to signal in queue</span>
-<span class="k">class</span> <span class="nc">all_tasks_complete</span><span class="p">:</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">waiting_for_more_tasks_to_complete</span><span class="p">:</span>
-    <span class="k">pass</span>
-
-
-<span class="c">#</span>
-<span class="c"># synchronisation data</span>
-<span class="c">#</span>
-<span class="c">#SyncManager()</span>
-<span class="c">#syncmanager.start()</span>
-
-<span class="c">#</span>
-<span class="c"># do nothing semaphore</span>
-<span class="c">#</span>
-<span class="nd">@contextmanager</span>
-<span class="k">def</span> <span class="nf">do_nothing_semaphore</span><span class="p">():</span>
-    <span class="k">yield</span>
-
-
-
-
-
-
-
-
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   task_decorator</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="k">class</span> <span class="nc">task_decorator</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        Adds task to the "pipeline_task" attribute of this function but</span>
-<span class="sd">        otherwise leaves function untouched</span>
-<span class="sd">    """</span>
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">decoratorArgs</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">            saves decorator arguments</span>
-<span class="sd">        """</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="n">decoratorArgs</span>
-
-    <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">func</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">            calls func in task with the same name as the class</span>
-<span class="sd">        """</span>
-        <span class="c"># add task as attribute of this function</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="s">"pipeline_task"</span><span class="p">):</span>
-            <span class="n">func</span><span class="o">.</span><span class="n">pipeline_task</span> <span class="o">=</span> <span class="n">_task</span><span class="o">.</span><span class="n">create_task</span><span class="p">(</span><span class="n">func</span><span class="p">)</span>
-
-
-        <span class="c"># call the method called</span>
-        <span class="c">#   "task.task_decorator"</span>
-        <span class="c">#   where "task_decorator" is the name of this class</span>
-        <span class="n">decorator_function_name</span> <span class="o">=</span> <span class="s">"task_"</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="o">.</span><span class="n">__name__</span>
-        <span class="n">task_decorator_function</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">func</span><span class="o">.</span><span class="n">pipeline_task</span><span class="p">,</span> <span class="n">decorator_function_name</span><span class="p">)</span>
-        <span class="n">task_decorator_function</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c">#   don't change the function so we can call it unaltered</span>
-        <span class="c">#</span>
-        <span class="k">return</span> <span class="n">func</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Basic decorators</span>
-<span class="c">#</span>
-<span class="k">class</span> <span class="nc">follows</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">files</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-
-
-
-
-<span class="c">#</span>
-<span class="c">#   Core</span>
-<span class="c">#</span>
-<span class="k">class</span> <span class="nc">split</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">transform</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">subdivide</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">originate</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">merge</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">posttask</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">jobs_limit</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Advanced</span>
-<span class="c">#</span>
-<span class="k">class</span> <span class="nc">collate</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">active_if</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="c">#</span>
-<span class="c">#   Esoteric</span>
-<span class="c">#</span>
-<span class="k">class</span> <span class="nc">check_if_uptodate</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="k">class</span> <span class="nc">parallel</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Obsolete</span>
-<span class="c">#</span>
-<span class="k">class</span> <span class="nc">files_re</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   indicator objects</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   mkdir</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">class</span> <span class="nc">mkdir</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="c">#def __init__ (self, *args):</span>
-    <span class="c">#    self.args = args</span>
-    <span class="k">pass</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   touch_file</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">class</span> <span class="nc">touch_file</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">__init__</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="n">args</span>
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   inputs</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">class</span> <span class="nc">inputs</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">__init__</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="n">args</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   add_inputs</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">class</span> <span class="nc">add_inputs</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">__init__</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="n">args</span>
-
-<span class="c">#8888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#       job descriptors</span>
-
-<span class="c">#           given parameters, returns strings describing job</span>
-<span class="c">#           First returned parameter is string in strong form</span>
-<span class="c">#           Second returned parameter is a list of strings for input, output and extra parameters</span>
-<span class="c">#               intended to be reformatted with indentation</span>
-<span class="c">#           main use in error logging</span>
-
-<span class="c">#8888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="k">def</span> <span class="nf">generic_job_descriptor</span> <span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">):</span>
-    <span class="k">if</span> <span class="n">param</span> <span class="ow">in</span> <span class="p">([],</span> <span class="bp">None</span><span class="p">):</span>
-        <span class="n">m</span> <span class="o">=</span> <span class="s">"Job"</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">m</span> <span class="o">=</span> <span class="s">"Job  = </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">ignore_unknown_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
-
-    <span class="k">return</span> <span class="n">m</span><span class="p">,</span> <span class="p">[</span><span class="n">m</span><span class="p">]</span>
-
-<span class="k">def</span> <span class="nf">io_files_job_descriptor</span> <span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">):</span>
-    <span class="n">extra_param</span> <span class="o">=</span> <span class="s">", "</span> <span class="o">+</span> <span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">2</span><span class="p">:])[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class=" [...]
-    <span class="n">out_param</span>   <span class="o">=</span>        <span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span> <span class="k">else</span> <span class="s">"??&qu [...]
-    <span class="n">in_param</span>    <span class="o">=</span>        <span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span> <span class="k">else</span> <span class="s">"??&qu [...]
-
-    <span class="k">return</span> <span class="p">(</span><span class="s">"Job  = [</span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s%s</span><span class="s">]"</span> <span class="o">%</span> <span class="p">(</span><span class="n">in_param</span><span class="p">,</span> <span class="n">out_param</span><span class="p">,</span> <span class="n">extra_param</span><span class="p">),</span>
-            <span class="p">[</span><span class="s">"Job  = [</span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">in_param</span><span class="p">,</span> <span class="s">"-> "</span> <span class="o">+</span> <span class="n">out_param</span> <span class="o">+</span> <span class="n">extra_param</span> <span class="o">+</span> <span class="s">"]"</span><span class="p">])</span>
-
-
-<span class="k">def</span> <span class="nf">io_files_one_to_many_job_descriptor</span> <span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">):</span>
-
-    <span class="n">extra_param</span> <span class="o">=</span> <span class="s">", "</span> <span class="o">+</span> <span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">2</span><span class="p">:])[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class=" [...]
-    <span class="n">out_param</span>   <span class="o">=</span>        <span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span> <span class="k">else</span> <span class="s">"??&qu [...]
-    <span class="n">in_param</span>    <span class="o">=</span>        <span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span> <span class="k">else</span> <span class="s">"??&qu [...]
-
-    <span class="c"># start with input parameter</span>
-    <span class="n">ret_params</span> <span class="o">=</span> <span class="p">[</span><span class="s">"Job  = [</span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">in_param</span><span class="p">]</span>
-
-    <span class="c"># add output parameter to list,</span>
-    <span class="c">#   processing one by one if multiple output parameters</span>
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">)):</span>
-            <span class="n">ret_params</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="s">"-> "</span> <span class="o">+</span> <span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">p</span><span class="p">)</span> <span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">ret_params</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"-> "</span> <span class="o">+</span> <span class="n">out_param</span><span class="p">)</span>
-
-    <span class="c"># add extra</span>
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">></span> <span class="mi">2</span> <span class="p">:</span>
-        <span class="n">ret_params</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">" , "</span> <span class="o">+</span> <span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">2</span><span class="p">:])[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
-
-    <span class="c"># add closing bracket</span>
-    <span class="n">ret_params</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">+=</span><span class="s">"]"</span>
-
-    <span class="k">return</span> <span class="p">(</span><span class="s">"Job  = [</span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s%s</span><span class="s">]"</span> <span class="o">%</span> <span class="p">(</span><span class="n">in_param</span><span class="p">,</span> <span class="n">out_param</span><span class="p">,</span> <span class="n">extra_param</span><span class="p">),</span> <span class="n">ret_params</span><span class="p">)</span>
-
-
-<span class="k">def</span> <span class="nf">mkdir_job_descriptor</span> <span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">):</span>
-    <span class="c"># input, output and parameters</span>
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
-        <span class="n">m</span> <span class="o">=</span> <span class="s">"Make directories </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
-    <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
-        <span class="n">m</span> <span class="o">=</span> <span class="s">"Make directories </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="k">return</span> <span class="p">[],</span> <span class="p">[]</span>
-    <span class="k">return</span> <span class="n">m</span><span class="p">,</span> <span class="p">[</span><span class="n">m</span><span class="p">]</span>
-
-
-<span class="c">#8888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#       job wrappers</span>
-<span class="c">#           registers files/directories for cleanup</span>
-
-<span class="c">#8888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   generic job wrapper</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<div class="viewcode-block" id="job_wrapper_generic"><a class="viewcode-back" href="../../task.html#ruffus.task.job_wrapper_generic">[docs]</a><span class="k">def</span> <span class="nf">job_wrapper_generic</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">user_defined_work_func</span><span class="p">,</span> <span class="n">register_cleanup</span><span class="p">,</span> <span class="n">touch_files_only</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    run func</span>
-<span class="sd">    """</span>
-    <span class="k">assert</span><span class="p">(</span><span class="n">user_defined_work_func</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">user_defined_work_func</span><span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">)</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   job wrapper for all that deal with i/o files</span>
-
-<span class="c">#_________________________________________________________________________________________</span></div>
-<div class="viewcode-block" id="job_wrapper_io_files"><a class="viewcode-back" href="../../task.html#ruffus.task.job_wrapper_io_files">[docs]</a><span class="k">def</span> <span class="nf">job_wrapper_io_files</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">user_defined_work_func</span><span class="p">,</span> <span class="n">register_cleanup</span><span class="p">,</span> <span class="n">touch_files_only</span><span class="p">,</span> < [...]
-    <span class="sd">"""</span>
-<span class="sd">    run func on any i/o if not up to date</span>
-<span class="sd">    """</span>
-    <span class="k">assert</span><span class="p">(</span><span class="n">user_defined_work_func</span><span class="p">)</span>
-
-    <span class="n">i</span><span class="p">,</span><span class="n">o</span> <span class="o">=</span> <span class="n">param</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
-
-    <span class="k">if</span> <span class="n">touch_files_only</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-        <span class="c"># @originate only uses output files</span>
-        <span class="k">if</span> <span class="n">output_files_only</span><span class="p">:</span>
-            <span class="n">ret_val</span> <span class="o">=</span> <span class="n">user_defined_work_func</span><span class="p">(</span><span class="o">*</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">:]))</span>
-        <span class="c"># all other decorators</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">ret_val</span> <span class="o">=</span> <span class="n">user_defined_work_func</span><span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">)</span>
-    <span class="k">elif</span> <span class="n">touch_files_only</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
-        <span class="c">#job_history = dbdict.open(RUFFUS_HISTORY_FILE, picklevalues=True)</span>
-
-        <span class="c">#</span>
-        <span class="c">#   touch files only</span>
-        <span class="c">#</span>
-        <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">get_strings_in_nested_sequence</span><span class="p">(</span><span class="n">o</span><span class="p">):</span>
-            <span class="c">#</span>
-            <span class="c">#   race condition still possible...</span>
-            <span class="c">#</span>
-            <span class="k">with</span> <span class="nb">file</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="s">'a'</span><span class="p">):</span>
-                <span class="n">os</span><span class="o">.</span><span class="n">utime</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>
-            <span class="c">#if not os.path.exists(f):</span>
-            <span class="c">#    open(f, 'w')</span>
-            <span class="c">#    mtime = os.path.getmtime(f)</span>
-            <span class="c">#else:</span>
-            <span class="c">#    os.utime(f, None)</span>
-            <span class="c">#    mtime = os.path.getmtime(f)</span>
-
-
-            <span class="c">#chksum = JobHistoryChecksum(f, mtime, param[2:], user_defined_work_func.pipeline_task)</span>
-            <span class="c">#job_history[f] = chksum  # update file times and job details in history</span>
-
-
-
-    <span class="c">#</span>
-    <span class="c"># register strings in output file for cleanup</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">get_strings_in_nested_sequence</span><span class="p">(</span><span class="n">o</span><span class="p">):</span>
-        <span class="n">register_cleanup</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="s">"file"</span><span class="p">)</span>
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   job wrapper for all that only deals with output files</span>
-
-<span class="c">#_________________________________________________________________________________________</span></div>
-<span class="k">def</span> <span class="nf">job_wrapper_output_files</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">user_defined_work_func</span><span class="p">,</span> <span class="n">register_cleanup</span><span class="p">,</span> <span class="n">touch_files_only</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    run func on any output file if not up to date</span>
-<span class="sd">    """</span>
-    <span class="n">job_wrapper_io_files</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">user_defined_work_func</span><span class="p">,</span> <span class="n">register_cleanup</span><span class="p">,</span> <span class="n">touch_files_only</span><span class="p">,</span> <span class="n">output_files_only</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   job wrapper for mkdir</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<div class="viewcode-block" id="job_wrapper_mkdir"><a class="viewcode-back" href="../../task.html#ruffus.task.job_wrapper_mkdir">[docs]</a><span class="k">def</span> <span class="nf">job_wrapper_mkdir</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">user_defined_work_func</span><span class="p">,</span> <span class="n">register_cleanup</span><span class="p">,</span> <span class="n">touch_files_only</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    make directories if not exists</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   Just in case, swallow file exist errors because some other makedirs might be subpath</span>
-    <span class="c">#       of this directory</span>
-    <span class="c">#   Should not be necessary because of "sorted" in task_mkdir</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
-        <span class="n">dirs</span> <span class="o">=</span> <span class="n">param</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-
-    <span class="c"># if there are two parameters, they are i/o, and the directories to be created are the output</span>
-    <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
-        <span class="n">dirs</span> <span class="o">=</span> <span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Wrong number of arguments in mkdir check </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">param</span><span class="p">,))</span>
-
-    <span class="c"># get all file names in flat list</span>
-    <span class="n">dirs</span> <span class="o">=</span> <span class="n">get_strings_in_nested_sequence</span> <span class="p">(</span><span class="n">dirs</span><span class="p">)</span>
-
-    <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">dirs</span><span class="p">:</span>
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
-            <span class="n">register_cleanup</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="s">"makedirs"</span><span class="p">)</span>
-        <span class="k">except</span><span class="p">:</span>
-            <span class="c">#</span>
-            <span class="c">#   ignore exception if exception == OSError / "File exists"</span>
-            <span class="c">#</span>
-            <span class="n">exceptionType</span><span class="p">,</span> <span class="n">exceptionValue</span><span class="p">,</span> <span class="n">exceptionTraceback</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
-            <span class="k">if</span> <span class="n">exceptionType</span> <span class="o">==</span> <span class="ne">OSError</span> <span class="ow">and</span> <span class="s">"File exists"</span> <span class="ow">in</span> <span class="nb">str</span><span class="p">(</span><span class="n">exceptionValue</span><span class="p">):</span>
-                <span class="k">continue</span>
-            <span class="k">raise</span>
-
-        <span class="c">#   changed for compatibility with python 3.x</span>
-        <span class="c">#except OSError, e:</span>
-        <span class="c">#    if "File exists" not in e:</span>
-        <span class="c">#        raise</span>
-
-</div>
-<span class="n">JOB_ERROR</span>           <span class="o">=</span> <span class="mi">0</span>
-<span class="n">JOB_SIGNALLED_BREAK</span> <span class="o">=</span> <span class="mi">1</span>
-<span class="n">JOB_UP_TO_DATE</span>      <span class="o">=</span> <span class="mi">2</span>
-<span class="n">JOB_COMPLETED</span>       <span class="o">=</span> <span class="mi">3</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   t_job_result</span>
-<span class="c">#       Previously a collections.namedtuple (introduced in python 2.6)</span>
-<span class="c">#       Now using implementation from running</span>
-<span class="c">#           t_job_result = namedtuple('t_job_result', 'task_name state job_name return_value exception', verbose =1)</span>
-<span class="c">#           for compatibility with python 2.5</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">class</span> <span class="nc">t_job_result</span><span class="p">(</span><span class="nb">tuple</span><span class="p">):</span>
-        <span class="s">'t_job_result(task_name, state, job_name, return_value, exception, params)'</span>
-
-        <span class="n">__slots__</span> <span class="o">=</span> <span class="p">()</span>
-
-        <span class="n">fields</span> <span class="o">=</span> <span class="p">(</span><span class="s">'task_name'</span><span class="p">,</span> <span class="s">'state'</span><span class="p">,</span> <span class="s">'job_name'</span><span class="p">,</span> <span class="s">'return_value'</span><span class="p">,</span> <span class="s">'exception'</span><span class="p">,</span> <span class="s">'params'</span><span class="p">)</span>
-
-        <span class="k">def</span> <span class="nf">__new__</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">task_name</span><span class="p">,</span> <span class="n">state</span><span class="p">,</span> <span class="n">job_name</span><span class="p">,</span> <span class="n">return_value</span><span class="p">,</span> <span class="n">exception</span><span class="p">,</span> <span class="n">params</span><span class="p">):</span>
-            <span class="k">return</span> <span class="nb">tuple</span><span class="o">.</span><span class="n">__new__</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="p">(</span><span class="n">task_name</span><span class="p">,</span> <span class="n">state</span><span class="p">,</span> <span class="n">job_name</span><span class="p">,</span> <span class="n">return_value</span><span class="p">,</span> <span class="n">exception</span><span clas [...]
-
-        <span class="nd">@classmethod</span>
-        <span class="k">def</span> <span class="nf">make</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">iterable</span><span class="p">,</span> <span class="n">new</span><span class="o">=</span><span class="nb">tuple</span><span class="o">.</span><span class="n">__new__</span><span class="p">,</span> <span class="nb">len</span><span class="o">=</span><span class="nb">len</span><span class="p">):</span>
-            <span class="s">'Make a new t_job_result object from a sequence or iterable'</span>
-            <span class="n">result</span> <span class="o">=</span> <span class="n">new</span><span class="p">(</span><span class="n">cls</span><span class="p">,</span> <span class="n">iterable</span><span class="p">)</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">result</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">6</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s">'Expected 6 arguments, got </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">result</span><span class="p">))</span>
-            <span class="k">return</span> <span class="n">result</span>
-
-        <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-            <span class="k">return</span> <span class="s">'t_job_result(task_name=</span><span class="si">%r</span><span class="s">, state=</span><span class="si">%r</span><span class="s">, job_name=</span><span class="si">%r</span><span class="s">, return_value=</span><span class="si">%r</span><span class="s">, exception=</span><span class="si">%r</span><span class="s">, params=</span><span class="si">%r</span><span class="s">)'</span> <span class="o">%</span> <span class="bp">s [...]
-
-        <span class="k">def</span> <span class="nf">asdict</span><span class="p">(</span><span class="n">t</span><span class="p">):</span>
-            <span class="s">'Return a new dict which maps field names to their values'</span>
-            <span class="k">return</span> <span class="p">{</span><span class="s">'task_name'</span><span class="p">:</span> <span class="n">t</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'state'</span><span class="p">:</span> <span class="n">t</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'job_name'</span><span class="p">:</span> <span class="n">t</span><span cl [...]
-
-        <span class="k">def</span> <span class="nf">replace</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwds</span><span class="p">):</span>
-            <span class="s">'Return a new t_job_result object replacing specified fields with new values'</span>
-            <span class="n">result</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">make</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="n">kwds</span><span class="o">.</span><span class="n">pop</span><span class="p">,</span> <span class="p">(</span><span class="s">'task_name'</span><span class="p">,</span> <span class="s">'state'</span><span class="p">,</span> <span class="s" [...]
-            <span class="k">if</span> <span class="n">kwds</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">'Got unexpected field names: </span><span class="si">%r</span><span class="s">'</span> <span class="o">%</span> <span class="n">kwds</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
-            <span class="k">return</span> <span class="n">result</span>
-
-        <span class="k">def</span> <span class="nf">__getnewargs__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-            <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
-
-        <span class="n">task_name</span>   <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">itemgetter</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
-        <span class="n">state</span>       <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">itemgetter</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
-        <span class="n">job_name</span>    <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">itemgetter</span><span class="p">(</span><span class="mi">2</span><span class="p">))</span>
-        <span class="n">return_value</span><span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">itemgetter</span><span class="p">(</span><span class="mi">3</span><span class="p">))</span>
-        <span class="n">exception</span>   <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">itemgetter</span><span class="p">(</span><span class="mi">4</span><span class="p">))</span>
-        <span class="n">params</span>      <span class="o">=</span> <span class="nb">property</span><span class="p">(</span><span class="n">itemgetter</span><span class="p">(</span><span class="mi">5</span><span class="p">))</span>
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   multiprocess_callback</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">run_pooled_job_without_exceptions</span> <span class="p">(</span><span class="n">process_parameters</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    handles running jobs in parallel</span>
-<span class="sd">    Make sure exceptions are caught here:</span>
-<span class="sd">        Otherwise, these will kill the thread/process</span>
-<span class="sd">        return any exceptions which will be rethrown at the other end:</span>
-<span class="sd">        See RethrownJobError /  run_all_jobs_in_task</span>
-<span class="sd">    """</span>
-
-    <span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">task_name</span><span class="p">,</span> <span class="n">job_name</span><span class="p">,</span> <span class="n">job_wrapper</span><span class="p">,</span> <span class="n">user_defined_work_func</span><span class="p">,</span>
-            <span class="n">job_limit_semaphore</span><span class="p">,</span> <span class="n">touch_files_only</span><span class="p">)</span> <span class="o">=</span> <span class="n">process_parameters</span>
-
-    <span class="c">##job_history = dbdict.open(RUFFUS_HISTORY_FILE, picklevalues=True)</span>
-    <span class="c">##outfile = param[1] if len(param) > 1 else None   # mkdir has no output</span>
-    <span class="c">##if not isinstance(outfile, list):</span>
-    <span class="c">##    outfile = [outfile]</span>
-    <span class="c">##for o in outfile:</span>
-    <span class="c">##    job_history.pop(o, None)  # remove outfile from history if it exists</span>
-
-    <span class="k">if</span> <span class="n">job_limit_semaphore</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">job_limit_semaphore</span> <span class="o">=</span> <span class="n">do_nothing_semaphore</span><span class="p">()</span>
-
-    <span class="k">try</span><span class="p">:</span>
-        <span class="k">with</span> <span class="n">job_limit_semaphore</span><span class="p">:</span>
-            <span class="n">return_value</span> <span class="o">=</span>  <span class="n">job_wrapper</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">user_defined_work_func</span><span class="p">,</span> <span class="n">register_cleanup</span><span class="p">,</span> <span class="n">touch_files_only</span><span class="p">)</span>
-
-            <span class="c">#</span>
-            <span class="c">#   ensure one second between jobs</span>
-            <span class="c">#</span>
-            <span class="c">#if one_second_per_job:</span>
-            <span class="c">#    time.sleep(1.01)</span>
-            <span class="k">return</span> <span class="n">t_job_result</span><span class="p">(</span><span class="n">task_name</span><span class="p">,</span> <span class="n">JOB_COMPLETED</span><span class="p">,</span> <span class="n">job_name</span><span class="p">,</span> <span class="n">return_value</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">param</span><span class="p">)</span>
-    <span class="k">except</span><span class="p">:</span>
-        <span class="c">#   Wrap up one or more exceptions rethrown across process boundaries</span>
-        <span class="c">#</span>
-        <span class="c">#       See multiprocessor.Server.handle_request/serve_client for an analogous function</span>
-        <span class="n">exceptionType</span><span class="p">,</span> <span class="n">exceptionValue</span><span class="p">,</span> <span class="n">exceptionTraceback</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
-        <span class="n">exception_stack</span>  <span class="o">=</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">(</span><span class="n">exceptionTraceback</span><span class="p">)</span>
-        <span class="n">exception_name</span>   <span class="o">=</span> <span class="n">exceptionType</span><span class="o">.</span><span class="n">__module__</span> <span class="o">+</span> <span class="s">'.'</span> <span class="o">+</span> <span class="n">exceptionType</span><span class="o">.</span><span class="n">__name__</span>
-        <span class="n">exception_value</span>  <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">exceptionValue</span><span class="p">)</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">exception_value</span><span class="p">):</span>
-            <span class="n">exception_value</span> <span class="o">=</span> <span class="s">"(</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="n">exception_value</span>
-
-        <span class="k">if</span> <span class="n">exceptionType</span> <span class="o">==</span> <span class="n">JobSignalledBreak</span><span class="p">:</span>
-            <span class="n">job_state</span> <span class="o">=</span> <span class="n">JOB_SIGNALLED_BREAK</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">job_state</span> <span class="o">=</span> <span class="n">JOB_ERROR</span>
-        <span class="k">return</span> <span class="n">t_job_result</span><span class="p">(</span><span class="n">task_name</span><span class="p">,</span> <span class="n">job_state</span><span class="p">,</span> <span class="n">job_name</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span>
-                            <span class="p">[</span><span class="n">task_name</span><span class="p">,</span>
-                             <span class="n">job_name</span><span class="p">,</span>
-                             <span class="n">exception_name</span><span class="p">,</span>
-                             <span class="n">exception_value</span><span class="p">,</span>
-                             <span class="n">exception_stack</span><span class="p">],</span> <span class="n">param</span><span class="p">)</span>
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Helper function</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   register_cleanup</span>
-
-<span class="c">#       to do</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">register_cleanup</span> <span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="n">operation</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   _task</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="k">class</span> <span class="nc">_task</span> <span class="p">(</span><span class="n">node</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    pipeline task</span>
-<span class="sd">    """</span>
-
-    <span class="n">action_names</span> <span class="o">=</span> <span class="p">[</span><span class="s">"unspecified"</span><span class="p">,</span>
-                    <span class="s">"task"</span><span class="p">,</span>
-                    <span class="s">"task_files_re"</span><span class="p">,</span>
-                    <span class="s">"task_split"</span><span class="p">,</span>
-                    <span class="s">"task_merge"</span><span class="p">,</span>
-                    <span class="s">"task_transform"</span><span class="p">,</span>
-                    <span class="s">"task_collate"</span><span class="p">,</span>
-                    <span class="s">"task_files_func"</span><span class="p">,</span>
-                    <span class="s">"task_files"</span><span class="p">,</span>
-                    <span class="s">"task_mkdir"</span><span class="p">,</span>
-                    <span class="s">"task_parallel"</span><span class="p">,</span>
-                    <span class="s">"task_active_if"</span><span class="p">,</span>
-                    <span class="s">"task_product"</span><span class="p">,</span>
-                    <span class="s">"task_permutations"</span><span class="p">,</span>
-                    <span class="s">"task_combinations"</span><span class="p">,</span>
-                    <span class="s">"task_combinations_with_replacement"</span><span class="p">,</span>
-                    <span class="s">"task_subdivide"</span><span class="p">,</span>
-                    <span class="s">"task_originate"</span><span class="p">,</span>
-                    <span class="p">]</span>
-    <span class="n">action_unspecified</span>                          <span class="o">=</span>  <span class="mi">0</span>
-    <span class="n">action_task</span>                                 <span class="o">=</span>  <span class="mi">1</span>
-    <span class="n">action_task_files_re</span>                        <span class="o">=</span>  <span class="mi">2</span>
-    <span class="n">action_task_split</span>                           <span class="o">=</span>  <span class="mi">3</span>
-    <span class="n">action_task_merge</span>                           <span class="o">=</span>  <span class="mi">4</span>
-    <span class="n">action_task_transform</span>                       <span class="o">=</span>  <span class="mi">5</span>
-    <span class="n">action_task_collate</span>                         <span class="o">=</span>  <span class="mi">6</span>
-    <span class="n">action_task_files_func</span>                      <span class="o">=</span>  <span class="mi">7</span>
-    <span class="n">action_task_files</span>                           <span class="o">=</span>  <span class="mi">8</span>
-    <span class="n">action_mkdir</span>                                <span class="o">=</span>  <span class="mi">9</span>
-    <span class="n">action_parallel</span>                             <span class="o">=</span> <span class="mi">10</span>
-    <span class="n">action_active_if</span>                            <span class="o">=</span> <span class="mi">11</span>
-    <span class="n">action_task_product</span>                         <span class="o">=</span> <span class="mi">12</span>
-    <span class="n">action_task_permutations</span>                    <span class="o">=</span> <span class="mi">13</span>
-    <span class="n">action_task_combinations</span>                    <span class="o">=</span> <span class="mi">14</span>
-    <span class="n">action_task_combinations_with_replacement</span>   <span class="o">=</span> <span class="mi">15</span>
-    <span class="n">action_task_subdivide</span>                       <span class="o">=</span> <span class="mi">16</span>
-    <span class="n">action_task_originate</span>                       <span class="o">=</span> <span class="mi">17</span>
-
-
-
-    <span class="n">multiple_jobs_outputs</span>    <span class="o">=</span> <span class="mi">0</span>
-    <span class="n">single_job_single_output</span> <span class="o">=</span> <span class="mi">1</span>
-    <span class="n">job_single_matches_parent</span><span class="o">=</span> <span class="mi">2</span>
-
-    <span class="n">job_limit_semaphores</span> <span class="o">=</span> <span class="p">{}</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   create_task / __init__</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">create_task</span><span class="p">(</span><span class="n">func</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Create task if the name as not been previously specified</span>
-<span class="sd">        Note that the task function may not have been created yet.</span>
-<span class="sd">        This allows us to create tasks and dependencies out of order</span>
-<span class="sd">        """</span>
-        <span class="n">func_name</span>   <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">__name__</span>
-        <span class="n">module_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">func</span><span class="o">.</span><span class="n">__module__</span><span class="p">)</span>
-        <span class="n">task_name</span>   <span class="o">=</span> <span class="n">module_name</span> <span class="o">+</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">func_name</span>
-
-        <span class="c"># Link to existing dependency if task name has previously been specified</span>
-        <span class="k">if</span> <span class="n">node</span><span class="o">.</span><span class="n">is_node</span><span class="p">(</span><span class="n">task_name</span><span class="p">):</span>
-            <span class="n">t</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">lookup_node_from_name</span><span class="p">(</span><span class="n">task_name</span><span class="p">)</span>
-            <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">user_defined_work_func</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">error_duplicate_task_name</span><span class="p">(</span><span class="s">"Same task name </span><span class="si">%s</span><span class="s"> specified multiple times in the same module"</span> <span class="o">%</span> <span class="n">task_name</span><span class="p">)</span>
-        <span class="c">#   otherwise create new</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">t</span> <span class="o">=</span> <span class="n">_task</span><span class="p">(</span><span class="n">module_name</span><span class="p">,</span> <span class="n">func_name</span><span class="p">)</span>
-
-        <span class="n">t</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task</span><span class="p">)</span>
-        <span class="n">t</span><span class="o">.</span><span class="n">user_defined_work_func</span> <span class="o">=</span> <span class="n">func</span>
-        <span class="k">assert</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">_name</span> <span class="o">==</span> <span class="n">task_name</span><span class="p">)</span>
-        <span class="c"># convert description into one line</span>
-        <span class="k">if</span> <span class="n">func</span><span class="o">.</span><span class="n">__doc__</span><span class="p">:</span>
-            <span class="n">t</span><span class="o">.</span><span class="n">_description</span>           <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">\s+"</span><span class="p">,</span> <span class="s">" "</span><span class="p">,</span> <span class="n">func</span><span class="o">.</span><span class="n">__doc__</span><span cl [...]
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">t</span><span class="o">.</span><span class="n">_description</span> <span class="o">=</span> <span class="s">""</span>
-
-        <span class="k">return</span> <span class="n">t</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   get_action_name</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">get_action_name</span> <span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">_task</span><span class="o">.</span><span class="n">action_names</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_action_type</span><span class="p">]</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   __init__</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">__init__</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">module_name</span><span class="p">,</span> <span class="n">func_name</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Does nothing because this might just be a dependency.</span>
-<span class="sd">        If it does not get initialised by a real task</span>
-<span class="sd">            (a task is depending on an unknown function/task),</span>
-<span class="sd">            throw an exception when running the pipeline</span>
-
-<span class="sd">        """</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_module_name</span> <span class="o">=</span> <span class="n">module_name</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_func_name</span>   <span class="o">=</span> <span class="n">func_name</span>
-
-        <span class="n">node</span><span class="o">.</span><span class="n">__init__</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">module_name</span> <span class="o">+</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">func_name</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_action_type</span>  <span class="o">=</span> <span class="n">_task</span><span class="o">.</span><span class="n">action_unspecified</span>
-
-        <span class="c">#   Each task has its own checksum level</span>
-        <span class="c">#   At the moment this is really so multiple pipelines in the same script can have</span>
-        <span class="c">#       different checksum levels</span>
-        <span class="c">#   Though set by pipeline_xxxx functions, have initial valid value so unit tests work :-|</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">checksum_level</span>             <span class="o">=</span> <span class="n">CHECKSUM_FILE_TIMESTAMPS</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span>       <span class="o">=</span> <span class="bp">None</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>          <span class="o">=</span> <span class="bp">None</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>                <span class="o">=</span> <span class="n">job_wrapper_generic</span>
-
-        <span class="c">#</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>             <span class="o">=</span> <span class="n">generic_job_descriptor</span>
-
-        <span class="c"># jobs which produce a single output.</span>
-        <span class="c"># special handling for task.get_output_files for dependency chaining</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span>  <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">multiple_jobs_outputs</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>            <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-        <span class="c"># function which is decorated and does the actual work</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">user_defined_work_func</span> <span class="o">=</span> <span class="bp">None</span>
-
-        <span class="c"># functions which will be called when task completes</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">posttask_functions</span>         <span class="o">=</span> <span class="p">[]</span>
-
-        <span class="c"># give makedir automatically made parent tasks unique names</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">cnt_task_mkdir</span>             <span class="o">=</span> <span class="mi">0</span>
-
-        <span class="c"># whether only task function itself knows what output it will produce</span>
-        <span class="c"># i.e. output is a glob or something similar</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">indeterminate_output</span>       <span class="o">=</span> <span class="mi">0</span>
-
-        <span class="c"># cache output file names here</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span>           <span class="o">=</span> <span class="bp">None</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">semaphore_name</span>             <span class="o">=</span> <span class="n">module_name</span> <span class="o">+</span> <span class="s">"."</span> <span class="o">+</span> <span class="n">func_name</span>
-
-        <span class="c"># do not test for whether task is active</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span>           <span class="o">=</span> <span class="bp">None</span>
-
-        <span class="c"># extra flag for outputfiles</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">is_active</span>                  <span class="o">=</span> <span class="bp">True</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   init_for_pipeline</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">init_for_pipeline</span> <span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Initialize variables for pipeline run / printout</span>
-
-<span class="sd">        **********</span>
-<span class="sd">          BEWARE</span>
-<span class="sd">        **********</span>
-
-<span class="sd">        Because state is stored, ruffus is *not* reentrant.</span>
-
-<span class="sd">        **********</span>
-<span class="sd">          BEWARE</span>
-<span class="sd">        **********</span>
-<span class="sd">        """</span>
-
-        <span class="c"># cache output file names here</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span> <span class="o">=</span> <span class="bp">None</span>
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   set_action_type</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">set_action_type</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new_action_type</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Save how this task</span>
-<span class="sd">            1) tests whether it is up-to-date and</span>
-<span class="sd">            2) handles input/output files</span>
-
-<span class="sd">        Checks that the task has not been defined with conflicting actions</span>
-
-<span class="sd">        """</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_action_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_unspecified</span><span class="p">,</span> <span class="n">_task</span><span class="o">.</span><span class="n">action_task</span><span class="p">):</span>
-            <span class="n">old_action</span> <span class="o">=</span> <span class="n">_task</span><span class="o">.</span><span class="n">action_names</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_action_type</span><span class="p">]</span>
-            <span class="n">new_action</span> <span class="o">=</span> <span class="n">_task</span><span class="o">.</span><span class="n">action_names</span><span class="p">[</span><span class="n">new_action_type</span><span class="p">]</span>
-            <span class="n">actions</span> <span class="o">=</span> <span class="s">" and "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">((</span><span class="n">old_action</span><span class="p">,</span> <span class="n">new_action</span><span class="p">))))</span>
-            <span class="n">task_name</span> <span class="o">=</span> <span class="s">"def </span><span class="si">%s</span><span class="s">(...)"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_name</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"__main__."</span><span class="p">,</span> <span class="s">""</span><span class="p">)</span>
-            <span class="k">raise</span> <span class="n">error_decorator_args</span><span class="p">((</span><span class="s">"    </span><span class="si">%s</span><span class="se">\n</span><span class="s">      has duplicate task specifications: (</span><span class="si">%s</span><span class="s">)</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span> <span class="o">%</span>
-                                        <span class="p">(</span><span class="n">task_name</span><span class="p">,</span> <span class="n">actions</span><span class="p">))</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_action_type</span> <span class="o">=</span> <span class="n">new_action_type</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_action_type_desc</span> <span class="o">=</span> <span class="n">_task</span><span class="o">.</span><span class="n">action_names</span><span class="p">[</span><span class="n">new_action_type</span><span class="p">]</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   get_job_name</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">get_job_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">descriptive_param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Use job descriptor to return short name for job, including any parameters</span>
-
-<span class="sd">            runtime_data is not (yet) used but may be used to add context in future</span>
-<span class="sd">        """</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span><span class="p">(</span><span class="n">descriptive_param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   get_task_name</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">get_task_name</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">in_func_format</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Returns name of task function, removing __main__ namespace if necessary</span>
-
-<span class="sd">        if in_func_format is true, will return def task_func(...):</span>
-
-<span class="sd">        """</span>
-
-        <span class="n">task_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_name</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">"__main__."</span><span class="p">,</span> <span class="s">""</span><span class="p">)</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_action_type</span> <span class="o">!=</span> <span class="n">_task</span><span class="o">.</span><span class="n">action_mkdir</span> <span class="ow">and</span> <span class="n">in_func_format</span><span class="p">:</span>
-            <span class="k">return</span> <span class="s">"def </span><span class="si">%s</span><span class="s">(...):"</span> <span class="o">%</span> <span class="n">task_name</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">task_name</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   update_active_state</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">update_active_state</span> <span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="c">#</span>
-        <span class="c">#   If has an @active_if decorator, check if the task needs to be run</span>
-        <span class="c">#       @active_if parameters may be call back functions or booleans</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span> <span class="o">!=</span> <span class="bp">None</span> <span class="ow">and</span>
-            <span class="nb">any</span><span class="p">(</span> <span class="ow">not</span> <span class="n">arg</span><span class="p">()</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span><span class="p">)</span> <span class="k">else</span> <span class="ow">not</span> <span class="n">arg</span>
-                     <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span><span class="p">)):</span>
-                <span class="c"># flip is active to false.</span>
-                <span class="c">#   ( get_output_files() will return empty if inactive )</span>
-                <span class="c">#   Remember each iteration of pipeline_printout pipeline_run will have</span>
-                <span class="c">#   another bite at changing this value</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">is_active</span> <span class="o">=</span> <span class="bp">False</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="c"># flip is active to True so that downstream dependencies will be correct</span>
-            <span class="c">#   ( get_output_files() will return empty if inactive )</span>
-            <span class="c">#   Remember each iteration of pipeline_printout pipeline_run will have</span>
-            <span class="c">#   another bite at changing this value</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">is_active</span> <span class="o">=</span> <span class="bp">True</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   printout</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">printout</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">,</span> <span class="n">force_rerun</span><span class="p">,</span> <span class="n">job_history</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">indent</span> <span class="o">=</span> <span class="m [...]
-        <span class="sd">"""</span>
-<span class="sd">        Print out all jobs for this task</span>
-
-<span class="sd">                verbose = 1 : print task name</span>
-<span class="sd">                          2 : print task description if exists</span>
-<span class="sd">                          3 : print job names for jobs to be run</span>
-<span class="sd">                          4 : print job names for up-to- date jobs</span>
-<span class="sd">        """</span>
-
-        <span class="k">def</span> <span class="nf">get_job_names</span> <span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">indent_str</span><span class="p">):</span>
-            <span class="n">job_names</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">job_names</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
-                <span class="n">job_names</span> <span class="o">=</span> <span class="p">([</span><span class="n">indent_str</span> <span class="o">+</span> <span class="n">job_names</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>  <span class="o">+</span>
-                             <span class="p">[</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"      "</span> <span class="o">+</span> <span class="n">jn</span> <span class="k">for</span> <span class="n">jn</span> <span class="ow">in</span> <span class="n">job_names</span><span class="p">[</span><span class="mi">1</span><span class="p">:]])</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="n">job_names</span> <span class="o">=</span> <span class="p">([</span><span class="n">indent_str</span> <span class="o">+</span> <span class="n">job_names</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
-            <span class="k">return</span> <span class="n">job_names</span>
-
-
-
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">verbose</span><span class="p">:</span>
-            <span class="k">return</span> <span class="p">[]</span>
-
-        <span class="n">indent_str</span> <span class="o">=</span> <span class="s">' '</span> <span class="o">*</span> <span class="n">indent</span>
-
-        <span class="n">messages</span> <span class="o">=</span> <span class="p">[]</span>
-
-        <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"Task = "</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">()</span> <span class="o">+</span> <span class="p">(</span><span class="s">"    >>Forced to rerun<<"</span> <span class="k">if</span> <span class="n">force_rerun</span> <span class=" [...]
-        <span class="k">if</span> <span class="n">verbose</span> <span class="o">==</span><span class="mi">1</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">messages</span>
-
-        <span class="k">if</span> <span class="n">verbose</span> <span class="o">>=</span> <span class="mi">2</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_description</span><span class="p">):</span>
-            <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">'"'</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">_description</span> <span class="o">+</span> <span class="s">'"'</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c">#   single job state</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="n">verbose</span> <span class="o">></span> <span class="mi">5</span><span class="p">:</span>
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">single_job_single_output</span><span class="p">:</span>
-                <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"    Single job single output"</span><span class="p">)</span>
-            <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">multiple_jobs_outputs</span><span class="p">:</span>
-                <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"    Multiple jobs Multiple outputs"</span><span class="p">)</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"    Single jobs status depends on </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span><span class="o">.</span><span class="n">_name</span><span class="p">)</span>
-
-
-        <span class="k">if</span> <span class="n">verbose</span> <span class="o"><=</span> <span class="mi">2</span> <span class="p">:</span>
-            <span class="k">return</span> <span class="n">messages</span>
-
-        <span class="c"># increase indent for jobs up to date status</span>
-        <span class="n">indent_str</span> <span class="o">+=</span> <span class="s">" "</span> <span class="o">*</span> <span class="mi">3</span>
-
-        <span class="c">#</span>
-        <span class="c">#   If has an @active_if decorator, check if the task needs to be run</span>
-        <span class="c">#       @active_if parameters may be call back functions or booleans</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_active</span><span class="p">:</span>
-            <span class="k">if</span> <span class="n">verbose</span> <span class="o"><=</span> <span class="mi">3</span><span class="p">:</span>
-                <span class="k">return</span> <span class="n">messages</span>
-            <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"Task is inactive"</span><span class="p">)</span>
-            <span class="c"># add spacer line</span>
-            <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">""</span><span class="p">)</span>
-            <span class="k">return</span> <span class="n">messages</span>
-
-        <span class="c">#</span>
-        <span class="c">#   No parameters: just call task function</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-            <span class="k">if</span> <span class="n">verbose</span> <span class="o"><=</span> <span class="mi">3</span><span class="p">:</span>
-                <span class="k">return</span> <span class="n">messages</span>
-
-            <span class="c">#</span>
-            <span class="c">#   needs update func = None: always needs update</span>
-            <span class="c">#</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span><span class="p">:</span>
-                <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"Task needs update: No function to check if up-to-date or not"</span><span class="p">)</span>
-                <span class="k">return</span> <span class="n">messages</span>
-
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="o">==</span> <span class="n">needs_update_check_modify_time</span><span class="p">:</span>
-                <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">(</span><span class="n">task</span><span class="o">=</span><span class="bp">self</span><span class="p">,</span> <span class="n">job_history</span> <span class="o">=</span> <span class="n">job_history</span><span class="p">)</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">()</span>
-
-            <span class="k">if</span> <span class="n">needs_update</span><span class="p">:</span>
-                <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"Task needs update: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">msg</span><span class="p">)</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"Task up-to-date"</span><span class="p">)</span>
-
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">runtime_data</span><span class="p">[</span><span class="s">"MATCH_FAILURE"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
-            <span class="c">#</span>
-            <span class="c">#   return messages description per job</span>
-            <span class="c">#</span>
-            <span class="n">cnt_jobs</span> <span class="o">=</span> <span class="mi">0</span>
-            <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">descriptive_param</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">):</span>
-                <span class="n">cnt_jobs</span> <span class="o">+=</span> <span class="mi">1</span>
-
-                <span class="c">#</span>
-                <span class="c">#   needs update func = None: always needs update</span>
-                <span class="c">#</span>
-                <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span><span class="p">:</span>
-                    <span class="n">messages</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">get_job_names</span> <span class="p">(</span><span class="n">descriptive_param</span><span class="p">,</span> <span class="n">indent_str</span><span class="p">))</span>
-                    <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"  Jobs needs update: No function to check if up-to-date or not"</span><span class="p">)</span>
-                    <span class="k">continue</span>
-
-                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="o">==</span> <span class="n">needs_update_check_modify_time</span><span class="p">:</span>
-                    <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">,</span> <span class="n">task</span><span class="o">=</span><span class="bp">self</span><span class="p">,</span> <span class="n">job_history</span> <span class="o">=</span> <s [...]
-                <span class="k">else</span><span class="p">:</span>
-                    <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">)</span>
-
-                <span class="k">if</span> <span class="n">needs_update</span><span class="p">:</span>
-                    <span class="n">messages</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">get_job_names</span> <span class="p">(</span><span class="n">descriptive_param</span><span class="p">,</span> <span class="n">indent_str</span><span class="p">))</span>
-                    <span class="n">per_job_messages</span> <span class="o">=</span> <span class="p">[(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="n">s</span><span class="p">)</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="p">(</span><span class="s">"  Job needs update: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">msg</span><span class="p" [...]
-                    <span class="n">messages</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">per_job_messages</span><span class="p">)</span>
-                <span class="k">else</span><span class="p">:</span>
-                    <span class="k">if</span> <span class="n">verbose</span> <span class="o">></span> <span class="mi">4</span><span class="p">:</span>
-                        <span class="n">messages</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">get_job_names</span> <span class="p">(</span><span class="n">descriptive_param</span><span class="p">,</span> <span class="n">indent_str</span><span class="p">))</span>
-                        <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"  Job up-to-date"</span><span class="p">)</span>
-
-            <span class="k">if</span> <span class="n">cnt_jobs</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-                <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"!!! No jobs for this task. "</span>
-                                             <span class="s">"Are you sure there is not a error in your "</span>
-                                             <span class="s">"code / regular expression?"</span><span class="p">)</span>
-            <span class="k">if</span> <span class="n">verbose</span> <span class="o">>=</span> <span class="mi">3</span> <span class="ow">or</span> <span class="p">(</span><span class="n">verbose</span> <span class="ow">and</span> <span class="n">cnt_jobs</span> <span class="o">==</span> <span class="mi">0</span><span class="p">):</span>
-                <span class="k">if</span> <span class="n">runtime_data</span> <span class="ow">and</span> <span class="s">"MATCH_FAILURE"</span> <span class="ow">in</span> <span class="n">runtime_data</span><span class="p">:</span>
-                    <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">runtime_data</span><span class="p">[</span><span class="s">"MATCH_FAILURE"</span><span class="p">]:</span>
-                        <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">indent_str</span> <span class="o">+</span> <span class="s">"Warning: File match failure: "</span> <span class="o">+</span> <span class="n">s</span><span class="p">)</span>
-            <span class="n">runtime_data</span><span class="p">[</span><span class="s">"MATCH_FAILURE"</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="n">messages</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">""</span><span class="p">)</span>
-        <span class="k">return</span> <span class="n">messages</span>
-
-
-
-
-    <span class="c">#_____________________________________________________________________________________</span>
-
-    <span class="c">#   signal</span>
-    <span class="c">#</span>
-    <span class="c">#       returns whether up to date</span>
-    <span class="c">#</span>
-    <span class="c">#_____________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">signal</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">verbose_logger_job_history</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        If up to date: signal = true</span>
-<span class="sd">        If true, depth first search will not pass through this node</span>
-<span class="sd">        """</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">verbose_logger_job_history</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"verbose_logger_job_history is None"</span><span class="p">)</span>
-
-        <span class="n">verbose_logger</span> <span class="o">=</span> <span class="n">verbose_logger_job_history</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-        <span class="n">job_history</span> <span class="o">=</span> <span class="n">verbose_logger_job_history</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">logger</span>       <span class="o">=</span> <span class="n">verbose_logger</span><span class="o">.</span><span class="n">logger</span>
-            <span class="n">verbose</span>      <span class="o">=</span> <span class="n">verbose_logger</span><span class="o">.</span><span class="n">verbose</span>
-            <span class="n">runtime_data</span> <span class="o">=</span> <span class="n">verbose_logger</span><span class="o">.</span><span class="n">runtime_data</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span>
-                            <span class="s">"  Task = "</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">())</span>
-
-            <span class="c">#</span>
-            <span class="c">#   If job is inactive, always consider it up-to-date</span>
-            <span class="c">#</span>
-            <span class="k">if</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span> <span class="o">!=</span> <span class="bp">None</span> <span class="ow">and</span>
-                <span class="nb">any</span><span class="p">(</span> <span class="ow">not</span> <span class="n">arg</span><span class="p">()</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span><span class="p">)</span> <span class="k">else</span> <span class="ow">not</span> <span class="n">arg</span>
-                         <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span><span class="p">)):</span>
-                <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span>
-                                <span class="s">"    Inactive task: treat as Up to date"</span><span class="p">)</span>
-                <span class="c">#print 'signaling that the inactive task is up to date'</span>
-                <span class="k">return</span> <span class="bp">True</span>
-
-            <span class="c">#</span>
-            <span class="c">#   Always needs update if no way to check if up to date</span>
-            <span class="c">#</span>
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-                <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span>
-                                <span class="s">"    No update function: treat as out of date"</span><span class="p">)</span>
-                <span class="k">return</span> <span class="bp">False</span>
-
-            <span class="c">#</span>
-            <span class="c">#   if no parameters, just return the results of needs update</span>
-            <span class="c">#</span>
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span><span class="p">:</span>
-                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="o">==</span> <span class="n">needs_update_check_modify_time</span><span class="p">:</span>
-                        <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">(</span><span class="n">task</span><span class="o">=</span><span class="bp">self</span><span class="p">,</span> <span class="n">job_history</span> <span class="o">=</span> <span class="n">job_history</span><span class="p">)</span>
-                    <span class="k">else</span><span class="p">:</span>
-                        <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">()</span>
-                    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span>
-                                    <span class="s">"    Needs update = </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">needs_update</span><span class="p">)</span>
-                    <span class="k">return</span> <span class="ow">not</span> <span class="n">needs_update</span>
-                <span class="k">else</span><span class="p">:</span>
-                    <span class="k">return</span> <span class="bp">True</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="c">#</span>
-                <span class="c">#   return not up to date if ANY jobs needs update</span>
-                <span class="c">#</span>
-                <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">descriptive_param</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">):</span>
-                    <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="o">==</span> <span class="n">needs_update_check_modify_time</span><span class="p">:</span>
-                        <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">,</span> <span class="n">task</span><span class="o">=</span><span class="bp">self</span><span class="p">,</span> <span class="n">job_history</span> <span class="o">=</span [...]
-                    <span class="k">else</span><span class="p">:</span>
-                        <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">)</span>
-                    <span class="k">if</span> <span class="n">needs_update</span><span class="p">:</span>
-                        <span class="k">if</span> <span class="n">verbose</span> <span class="o">>=</span> <span class="mi">4</span><span class="p">:</span>
-                            <span class="n">job_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_job_name</span><span class="p">(</span><span class="n">descriptive_param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">)</span>
-                            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span>
-                                            <span class="s">"    Needing update:</span><span class="se">\n</span><span class="s">      </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">job_name</span><span class="p">)</span>
-                        <span class="k">return</span> <span class="bp">False</span>
-
-                <span class="c">#</span>
-                <span class="c">#   Percolate warnings from parameter factories</span>
-                <span class="c">#</span>
-                <span class="k">if</span> <span class="p">(</span><span class="n">verbose</span> <span class="o">>=</span> <span class="mi">1</span> <span class="ow">and</span> <span class="s">"ruffus_WARNING"</span> <span class="ow">in</span> <span class="n">runtime_data</span> <span class="ow">and</span>
-                    <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="ow">in</span> <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ruffus_WARNING"</span><span class="p">]):</span>
-                    <span class="k">for</span> <span class="n">msg</span> <span class="ow">in</span> <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ruffus_WARNING"</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span><span class="p">]:</span>
-                        <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s">"    'In Task </span><span class="si">%s</span><span class="s">' </span><span class="si">%s</span><span class="s"> "</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">(</span><span class="bp">True</span><span class="p [...]
-
-
-                <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    All jobs up to date"</span><span class="p">)</span>
-
-
-
-
-                <span class="k">return</span> <span class="bp">True</span>
-
-        <span class="c">#</span>
-        <span class="c"># removed for compatibility with python 3.x</span>
-        <span class="c">#</span>
-        <span class="c"># rethrow exception after adding task name</span>
-        <span class="c">#except error_task, inst:</span>
-        <span class="c">#    inst.specify_task(self, "Exceptions in dependency checking")</span>
-        <span class="c">#    raise</span>
-
-        <span class="k">except</span><span class="p">:</span>
-            <span class="n">exceptionType</span><span class="p">,</span> <span class="n">exceptionValue</span><span class="p">,</span> <span class="n">exceptionTraceback</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
-
-            <span class="c">#</span>
-            <span class="c"># rethrow exception after adding task name</span>
-            <span class="c">#</span>
-            <span class="k">if</span> <span class="n">exceptionType</span> <span class="o">==</span> <span class="n">error_task</span><span class="p">:</span>
-                <span class="n">exceptionValue</span><span class="o">.</span><span class="n">specify</span>
-                <span class="n">inst</span><span class="o">.</span><span class="n">specify_task</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Exceptions in dependency checking"</span><span class="p">)</span>
-                <span class="k">raise</span>
-
-            <span class="n">exception_stack</span>  <span class="o">=</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">(</span><span class="n">exceptionTraceback</span><span class="p">)</span>
-            <span class="n">exception_name</span>   <span class="o">=</span> <span class="n">exceptionType</span><span class="o">.</span><span class="n">__module__</span> <span class="o">+</span> <span class="s">'.'</span> <span class="o">+</span> <span class="n">exceptionType</span><span class="o">.</span><span class="n">__name__</span>
-            <span class="n">exception_value</span>  <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">exceptionValue</span><span class="p">)</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">exception_value</span><span class="p">):</span>
-                <span class="n">exception_value</span> <span class="o">=</span> <span class="s">"(</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="n">exception_value</span>
-            <span class="n">errt</span> <span class="o">=</span> <span class="n">RethrownJobError</span><span class="p">([(</span><span class="bp">self</span><span class="o">.</span><span class="n">_name</span><span class="p">,</span>
-                                     <span class="s">""</span><span class="p">,</span>
-                                     <span class="n">exception_name</span><span class="p">,</span>
-                                     <span class="n">exception_value</span><span class="p">,</span>
-                                     <span class="n">exception_stack</span><span class="p">)])</span>
-            <span class="n">errt</span><span class="o">.</span><span class="n">specify_task</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Exceptions generating parameters"</span><span class="p">)</span>
-            <span class="k">raise</span> <span class="n">errt</span>
-
-
-
-    <span class="c">#_____________________________________________________________________________________</span>
-
-    <span class="c">#   get_output_files</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#_____________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">get_output_files</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">do_not_expand_single_job_tasks</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Cache output files</span>
-
-<span class="sd">            If flattened is True, returns file as a list of strings,</span>
-<span class="sd">                flattening any nested structures and discarding non string names</span>
-<span class="sd">            Normally returns a list with one item for each job or a just a list of file names.</span>
-<span class="sd">            For "single_job_single_output" i.e. @merge and @files with single jobs,</span>
-<span class="sd">                returns the output of a single job (i.e. can be a string)</span>
-<span class="sd">        """</span>
-
-        <span class="c">#</span>
-        <span class="c">#   N.B. active_if_checks is called once per task</span>
-        <span class="c">#        in make_job_parameter_generator() for consistency</span>
-        <span class="c">#</span>
-        <span class="c">#   self.is_active can be set using self.active_if_checks in that function,</span>
-        <span class="c">#       and therefore can be changed BETWEEN invocations of pipeline_run</span>
-        <span class="c">#</span>
-        <span class="c">#   self.is_active is not used anywhere else</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="p">(</span><span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_active</span><span class="p">):</span>
-            <span class="k">return</span> <span class="p">[]</span>
-
-        <span class="c">#</span>
-        <span class="c">#   This looks like the wrong place to flatten</span>
-        <span class="c">#</span>
-        <span class="n">flattened</span> <span class="o">=</span> <span class="bp">False</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-
-            <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span> <span class="o">=</span> <span class="p">[]</span>
-
-            <span class="c"># skip tasks which don't have parameters</span>
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
-
-                <span class="n">cnt_jobs</span> <span class="o">=</span> <span class="mi">0</span>
-                <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">descriptive_param</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">):</span>
-                    <span class="n">cnt_jobs</span> <span class="o">+=</span> <span class="mi">1</span>
-                    <span class="c"># skip tasks which don't have output parameters</span>
-                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">>=</span> <span class="mi">2</span><span class="p">:</span>
-                        <span class="c"># make sure each @split or @subdivide or @originate returns a list of jobs</span>
-                        <span class="c">#   i.e. each @split or @subdivide or @originate is always a ->many operation</span>
-                        <span class="c">#       even if len(many) can be 1 (or zero)</span>
-                        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">indeterminate_output</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">non_str_sequence</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
-                            <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">]])</span>
-                        <span class="k">else</span><span class="p">:</span>
-                            <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-
-
-                <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">single_job_single_output</span><span class="p">:</span>
-                    <span class="k">if</span> <span class="n">cnt_jobs</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
-                        <span class="k">raise</span> <span class="n">error_task_get_output</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
-                               <span class="s">"Task which is supposed to produce a single output "</span>
-                               <span class="s">"somehow has more than one job."</span><span class="p">)</span>
-
-                <span class="c">#</span>
-                <span class="c">#   The output of @split should be treated as multiple jobs</span>
-                <span class="c">#</span>
-                <span class="c">#       The output of @split is always a list of lists:</span>
-                <span class="c">#         1) There is a list of @split jobs</span>
-                <span class="c">#            A) For advanced (regex) @split</span>
-                <span class="c">#               this is a many -> many more operation</span>
-                <span class="c">#               So len(list) == many (i.e. the number of jobs</span>
-                <span class="c">#            B) For normal @split</span>
-                <span class="c">#               this is a  1   -> many operation</span>
-                <span class="c">#               So len(list)  = 1</span>
-                <span class="c">#</span>
-                <span class="c">#         2) The output of each @split job is a list</span>
-                <span class="c">#            The items in this list of lists are each a job in subsequent tasks</span>
-                <span class="c">#</span>
-                <span class="c">#</span>
-                <span class="c">#         So we need to concatenate these separate lists into a single list of output</span>
-                <span class="c">#</span>
-                <span class="c">#         For example:</span>
-                <span class="c">#         @split(["a.1", "b.1"], regex(r"(.)\.1"), r"\1.*.2")</span>
-                <span class="c">#         def example(input, output):</span>
-                <span class="c">#             # JOB 1</span>
-                <span class="c">#             #   a.1 -> a.i.2</span>
-                <span class="c">#             #       -> a.j.2</span>
-                <span class="c">#</span>
-                <span class="c">#             # JOB 2</span>
-                <span class="c">#             #   b.1 -> b.i.2</span>
-                <span class="c">#             #       -> b.j.2</span>
-                <span class="c">#</span>
-                <span class="c">#         output_filenames = [ [a.i.2, a.j.2], [b.i.2, b.j.2] ]</span>
-                <span class="c">#</span>
-                <span class="c">#         we want [ a.i.2, a.j.2, b.i.2, b.j.2 ]</span>
-                <span class="c">#</span>
-                <span class="c">#         This also works for simple @split</span>
-                <span class="c">#</span>
-                <span class="c">#         @split("a.1", r"a.*.2")</span>
-                <span class="c">#         def example(input, output):</span>
-                <span class="c">#             # only job</span>
-                <span class="c">#             #   a.1 -> a.i.2</span>
-                <span class="c">#             #       -> a.j.2</span>
-                <span class="c">#</span>
-                <span class="c">#         output_filenames = [ [a.i.2, a.j.2] ]</span>
-                <span class="c">#</span>
-                <span class="c">#         we want [ a.i.2, a.j.2 ]</span>
-                <span class="c">#</span>
-                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="p">)</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">indeterminate_output</span><span class="p">:</span>
-                    <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span> <span class="o">=</span> <span class="nb">reduce</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">:</span> <span class="n">x</span> <span class="o">+</span> <span class="n">y</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_ [...]
-
-
-        <span class="k">if</span> <span class="n">flattened</span><span class="p">:</span>
-            <span class="c"># if single file name, return that</span>
-            <span class="c"># accepts unicode</span>
-            <span class="k">if</span> <span class="p">(</span><span class="n">do_not_expand_single_job_tasks</span> <span class="ow">and</span>
-                <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="p">)</span> <span class="ow">and</span>
-                <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">basestring</span><span class="p">)):</span>
-                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span>
-            <span class="c"># if it is flattened, might as well sort it</span>
-            <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">get_strings_in_nested_sequence</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="p">))</span>
-
-        <span class="k">else</span><span class="p">:</span>
-            <span class="c"># special handling for jobs which have a single task,</span>
-            <span class="k">if</span> <span class="p">(</span><span class="n">do_not_expand_single_job_tasks</span> <span class="ow">and</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="ow">and</span>
-                <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="p">)</span> <span class="p">):</span>
-                <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-
-            <span class="c">#</span>
-            <span class="c"># sort by jobs so it is just a weeny little bit less deterministic</span>
-            <span class="c">#</span>
-            <span class="k">return</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="p">)</span>
-
-
-
-    <span class="c">#_____________________________________________________________________________________</span>
-
-    <span class="c">#   completed</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#_____________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">completed</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">jobs_uptodate</span> <span class="o">=</span> <span class="bp">False</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        called even when all jobs are up to date</span>
-<span class="sd">        """</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">is_active</span><span class="p">:</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"Inactive Task = "</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">())</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span> <span class="o">=</span> <span class="bp">None</span>
-            <span class="k">return</span>
-
-        <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">posttask_functions</span><span class="p">:</span>
-            <span class="n">f</span><span class="p">()</span>
-        <span class="k">if</span> <span class="n">jobs_uptodate</span><span class="p">:</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"Uptodate Task = "</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">())</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"Completed Task = "</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">())</span>
-
-
-        <span class="c">#</span>
-        <span class="c">#   indeterminate output. Check actual output again if someother tasks job function depend on it</span>
-        <span class="c">#       used for @split</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">indeterminate_output</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span> <span class="o">=</span> <span class="bp">None</span>
-
-
-
-
-
-
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   handle_tasks_globs_in_inputs</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">input_params</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Helper function for tasks which</span>
-<span class="sd">            1) Notes globs and tasks</span>
-<span class="sd">            2) Replaces tasks names and functions with actual tasks</span>
-<span class="sd">            3) Adds task dependencies automatically via task_follows</span>
-<span class="sd">        """</span>
-        <span class="c">#</span>
-        <span class="c"># get list of function/function names and globs</span>
-        <span class="c">#</span>
-        <span class="n">function_or_func_names</span><span class="p">,</span> <span class="n">globs</span><span class="p">,</span> <span class="n">runtime_data_names</span> <span class="o">=</span> <span class="n">get_nested_tasks_or_globs</span><span class="p">(</span><span class="n">input_params</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">tasks</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">task_follows</span><span class="p">(</span><span class="n">function_or_func_names</span><span class="p">)</span>
-        <span class="n">functions_to_tasks</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">function_or_func_names</span><span class="p">,</span> <span class="n">tasks</span><span class="p">))</span>
-        <span class="n">input_params</span> <span class="o">=</span> <span class="n">replace_func_names_with_tasks</span><span class="p">(</span><span class="n">input_params</span><span class="p">,</span> <span class="n">functions_to_tasks</span><span class="p">)</span>
-
-        <span class="k">return</span> <span class="n">t_params_tasks_globs_run_time_data</span><span class="p">(</span><span class="n">input_params</span><span class="p">,</span> <span class="n">tasks</span><span class="p">,</span> <span class="n">globs</span><span class="p">,</span> <span class="n">runtime_data_names</span><span class="p">)</span>
-
-
-
-
-
-    <span class="c">#8888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-    <span class="c">#       task handlers</span>
-
-    <span class="c">#         sets</span>
-    <span class="c">#               1) action_type</span>
-    <span class="c">#               2) param_generator_func</span>
-    <span class="c">#               3) needs_update_func</span>
-    <span class="c">#               4) job wrapper</span>
-
-
-    <span class="c">#8888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   do_task_subdivide</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">do_task_subdivide</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">            @subdivide and @split are synonyms</span>
-<span class="sd">            Common code here</span>
-<span class="sd">        """</span>
-
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-
-
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-        <span class="c">#   allows split to take a single file or task</span>
-        <span class="n">input_files_task_globs</span><span class="o">.</span><span class="n">single_file_to_list</span><span class="p">()</span>
-
-        <span class="c"># how to transform input to output file name</span>
-        <span class="n">file_names_transform</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">choose_file_names_transform</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">error_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="n">orig_args</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
-
-        <span class="c">#   inputs can also be defined by pattern match</span>
-        <span class="n">extra_inputs</span><span class="p">,</span> <span class="n">replace_inputs</span><span class="p">,</span> <span class="n">output_pattern</span><span class="p">,</span> <span class="n">extra_params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_extra_inputs_outputs_extra</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</ [...]
-
-        <span class="c">#</span>
-        <span class="c">#   output globs will be replaced with files. But there should not be tasks here!</span>
-        <span class="c">#</span>
-        <span class="n">output_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">output_pattern</span><span class="p">)</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">output_files_task_globs</span><span class="o">.</span><span class="n">tasks</span><span class="p">):</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> cannot output to another task. "</span>
-                                          <span class="s">"Do not include tasks in output parameters."</span><span class="p">)</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">subdivide_param_factory</span> <span class="p">(</span>   <span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                                <span class="bp">False</span><span class="p">,</span> <span class="c"># flatten input</span>
-                                                                <span class="n">file_names_transform</span><span class="p">,</span>
-                                                                <span class="n">extra_inputs</span><span class="p">,</span>
-                                                                <span class="n">replace_inputs</span><span class="p">,</span>
-                                                                <span class="n">output_files_task_globs</span><span class="p">,</span>
-                                                                <span class="o">*</span><span class="n">extra_params</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="c">#self.job_descriptor       = io_files_job_descriptor # (orig_args[0], output_runtime_data_names)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_one_to_many_job_descriptor</span>
-
-        <span class="c"># output is a glob</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">indeterminate_output</span> <span class="o">=</span> <span class="mi">2</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>       <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_split</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">do_task_simple_split</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">):</span>
-
-        <span class="c">#check enough arguments</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-        <span class="c">#</span>
-        <span class="c">#   replace output globs with files</span>
-        <span class="c">#</span>
-        <span class="n">output_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">output_files_task_globs</span><span class="o">.</span><span class="n">tasks</span><span class="p">):</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> cannot output to another task. "</span>
-                                    <span class="s">"Do not include tasks in output parameters."</span><span class="p">)</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="n">extra_params</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">split_param_factory</span> <span class="p">(</span><span class="n">input_files_task_globs</span><span class="p">,</span> <span class="n">output_files_task_globs</span><span class="p">,</span> <span class="o">*</span><span class="n">extra_params</span><span class="p">)</span>
-
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="c">#self.job_descriptor       = io_files_job_descriptor# (orig_args[1], output_runtime_data_names)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_one_to_many_job_descriptor</span>
-
-        <span class="c"># output is a glob</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">indeterminate_output</span> <span class="o">=</span> <span class="mi">1</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>       <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">one_to_many</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_split</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_split</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Splits a single set of input files into multiple output file names,</span>
-<span class="sd">            where the number of output files may not be known beforehand.</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span>  <span class="o">=</span> <span class="s">"@split"</span>
-        <span class="n">error_type</span>      <span class="o">=</span> <span class="n">error_task_split</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_split</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c">#   This is actually @subdivide</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">regex</span><span class="p">):</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">do_task_subdivide</span><span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c">#   This is actually @split</span>
-        <span class="c">#</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">do_task_simple_split</span><span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">)</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_originate</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_originate</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Splits out multiple output file names,</span>
-<span class="sd">            where the number of output files may or may not be known beforehand.</span>
-<span class="sd">            This is a synonym for @split(None,...)</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span>  <span class="o">=</span> <span class="s">"@originate"</span>
-        <span class="n">error_type</span>      <span class="o">=</span> <span class="n">error_task_originate</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_originate</span><span class="p">)</span>
-
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">1</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> takes a single argument"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="n">output_params</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-
-        <span class="c"># make sure output_params is a list.</span>
-        <span class="c"># Each of these will be called as an output</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">non_str_sequence</span> <span class="p">(</span><span class="n">output_params</span><span class="p">):</span>
-            <span class="n">output_params</span> <span class="o">=</span> <span class="p">[</span><span class="n">output_params</span><span class="p">]</span>
-
-        <span class="c">#</span>
-        <span class="c">#   output globs will be replaced with files. But there should not be tasks here!</span>
-        <span class="c">#</span>
-        <span class="n">list_output_files_task_globs</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">oo</span><span class="p">)</span> <span class="k">for</span> <span class="n">oo</span> <span class="ow">in</span> <span class="n">output_params</span><span class="p">]</span>
-        <span class="k">for</span> <span class="n">oftg</span> <span class="ow">in</span> <span class="n">list_output_files_task_globs</span><span class="p">:</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">oftg</span><span class="o">.</span><span class="n">tasks</span><span class="p">):</span>
-                <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> cannot output to another task. "</span>
-                                              <span class="s">"Do not include tasks in output parameters."</span><span class="p">)</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">originate_param_factory</span> <span class="p">(</span><span class="n">list_output_files_task_globs</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_output_files</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_one_to_many_job_descriptor</span>
-
-        <span class="c"># output is not a glob</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">indeterminate_output</span> <span class="o">=</span> <span class="mi">0</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>       <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-
-
-
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_subdivide</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_subdivide</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Splits a single set of input files into multiple output file names,</span>
-<span class="sd">            where the number of output files may not be known beforehand.</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span>  <span class="o">=</span> <span class="s">"@subdivide"</span>
-        <span class="n">error_type</span>      <span class="o">=</span> <span class="n">error_task_subdivide</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_subdivide</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">do_task_subdivide</span><span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">)</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   get_extra_inputs</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">get_extra_inputs_outputs_extra</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        shared code for subdivide, transform, product etc for parsing orig_args into</span>
-<span class="sd">            add_inputs/inputs, output, extra</span>
-<span class="sd">        """</span>
-
-        <span class="c">#</span>
-        <span class="c">#   inputs can also be defined by pattern match</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">inputs</span><span class="p">):</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">args</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">error_task_transform_inputs_multiple_args</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
-                                    <span class="s">"inputs(...) expects only a single argument. "</span>
-                                    <span class="s">"This can be, for example, a file name, "</span>
-                                    <span class="s">"a regular expression pattern, or any "</span>
-                                    <span class="s">"nested structure. If the intention was to "</span>
-                                    <span class="s">"specify a tuple as the input parameter, "</span>
-                                    <span class="s">"please wrap the elements of the tuple "</span>
-                                    <span class="s">"in brackets in the decorator</span><span class="se">\n\n</span><span class="s">"</span>
-                                    <span class="s">"</span><span class="si">%s</span><span class="s">(..., inputs(...), ...)</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">decorator_name</span><span class="p">))</span>
-            <span class="n">replace_inputs</span> <span class="o">=</span> <span class="n">t_extra_inputs</span><span class="o">.</span><span class="n">REPLACE_INPUTS</span>
-            <span class="n">extra_inputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-            <span class="n">output_pattern</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-            <span class="n">extra_params</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
-        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">add_inputs</span><span class="p">):</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-            <span class="n">replace_inputs</span> <span class="o">=</span> <span class="n">t_extra_inputs</span><span class="o">.</span><span class="n">ADD_TO_INPUTS</span>
-            <span class="n">extra_inputs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
-            <span class="n">output_pattern</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-            <span class="n">extra_params</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">replace_inputs</span> <span class="o">=</span> <span class="n">t_extra_inputs</span><span class="o">.</span><span class="n">KEEP_INPUTS</span>
-            <span class="n">extra_inputs</span> <span class="o">=</span> <span class="bp">None</span>
-            <span class="n">output_pattern</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-            <span class="n">extra_params</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
-
-        <span class="k">return</span> <span class="n">extra_inputs</span><span class="p">,</span> <span class="n">replace_inputs</span><span class="p">,</span> <span class="n">output_pattern</span><span class="p">,</span> <span class="n">extra_params</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   choose_file_names_transform</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">choose_file_names_transform</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name_transform_tag</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">valid_tags</span> <span class="o">=</span> <span class="p">(</span><span class="n">regex</span><span class="p">,</span> <span [...]
-        <span class="sd">"""</span>
-<span class="sd">        shared code for subdivide, transform, product etc for choosing method for transform input file to output files</span>
-<span class="sd">        """</span>
-        <span class="n">valid_tag_names</span> <span class="o">=</span> <span class="p">[];</span>
-        <span class="c"># regular expression match</span>
-        <span class="k">if</span> <span class="p">(</span><span class="n">regex</span> <span class="ow">in</span> <span class="n">valid_tags</span><span class="p">):</span>
-            <span class="n">valid_tag_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"regex()"</span><span class="p">)</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">file_name_transform_tag</span><span class="p">,</span> <span class="n">regex</span><span class="p">):</span>
-                <span class="k">return</span> <span class="n">t_regex_file_names_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name_transform_tag</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="c"># simulate end of string (suffix) match</span>
-        <span class="k">if</span> <span class="p">(</span><span class="n">suffix</span> <span class="ow">in</span> <span class="n">valid_tags</span><span class="p">):</span>
-            <span class="n">valid_tag_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"suffix()"</span><span class="p">)</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">file_name_transform_tag</span><span class="p">,</span> <span class="n">suffix</span><span class="p">):</span>
-                <span class="k">return</span> <span class="n">t_suffix_file_names_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name_transform_tag</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="c"># new style string.format()</span>
-        <span class="k">if</span> <span class="p">(</span><span class="n">formatter</span> <span class="ow">in</span> <span class="n">valid_tags</span><span class="p">):</span>
-            <span class="n">valid_tag_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"formatter()"</span><span class="p">)</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">file_name_transform_tag</span><span class="p">,</span> <span class="n">formatter</span><span class="p">):</span>
-                <span class="k">return</span> <span class="n">t_formatter_file_names_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name_transform_tag</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> expects one of </span><span class="si">%s</span><span class="s"> as the second argument"</span> <span class="o">%</span> <span class="p">(</span><span class="n">decorator_name</span><span class="p">,</span> <span class="s">", "</span><span class="o">.</span> [...]
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_product</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_product</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        all versus all</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span>  <span class="o">=</span> <span class="s">"@product"</span>
-        <span class="n">error_type</span>      <span class="o">=</span> <span class="n">error_task_product</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c">#   get all pairs of tasks / globs and formatter()</span>
-        <span class="c">#</span>
-        <span class="n">list_input_files_task_globs</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="n">list_formatter</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="k">while</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">>=</span> <span class="mi">3</span><span class="p">:</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">formatter</span><span class="p">):</span>
-                <span class="n">list_input_files_task_globs</span> <span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-                <span class="n">list_formatter</span>              <span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-                <span class="n">orig_args</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">break</span>
-
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">list_formatter</span><span class="p">):</span>
-            <span class="k">raise</span> <span class="n">error_task_product</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"@product expects formatter() as the second argument"</span><span class="p">)</span>
-
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_product</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">list_input_files_task_globs</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">ii</span><span class="p">)</span> <span class="k">for</span> <span class="n">ii</span> <span class="ow">in</span> <span class="n">list_input_files_task_globs</span><span class="p">]</span>
-
-
-        <span class="c"># list of new style string.format()</span>
-        <span class="n">file_names_transform</span> <span class="o">=</span> <span class="n">t_nested_formatter_file_names_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">list_formatter</span><span class="p">,</span> <span class="n">error_task_product</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-
-        <span class="c">#</span>
-        <span class="c">#   inputs can also be defined by pattern match</span>
-        <span class="c">#</span>
-        <span class="n">extra_inputs</span><span class="p">,</span> <span class="n">replace_inputs</span><span class="p">,</span> <span class="n">output_pattern</span><span class="p">,</span> <span class="n">extra_params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_extra_inputs_outputs_extra</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</ [...]
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">product_param_factory</span> <span class="p">(</span> <span class="n">list_input_files_task_globs</span><span class="p">,</span>
-                                                            <span class="bp">False</span><span class="p">,</span> <span class="c"># flatten input</span>
-                                                            <span class="n">file_names_transform</span><span class="p">,</span>
-                                                            <span class="n">extra_inputs</span><span class="p">,</span>
-                                                            <span class="n">replace_inputs</span><span class="p">,</span>
-                                                            <span class="n">output_pattern</span><span class="p">,</span>
-                                                            <span class="o">*</span><span class="n">extra_params</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_job_descriptor</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>      <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_combinatorics</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_combinatorics</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">,</span> <span class="n">combinatorics_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">            Common code for task_permutations, task_combinations_with_replacement, task_combinations</span>
-<span class="sd">        """</span>
-
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">4</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">formatter</span><span class="p">):</span>
-            <span class="k">raise</span> <span class="n">error_task_product</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> expects formatter() as the second argument"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">input_files_task_globs</span>  <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-        <span class="n">k_tuple</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-
-        <span class="c"># how to transform input to output file name: len(k-tuples) of (identical) formatters</span>
-        <span class="n">file_names_transform</span> <span class="o">=</span> <span class="n">t_nested_formatter_file_names_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="p">[</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="o">*</span> <span class="n">k_tuple</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</span> <span c [...]
-
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_permutations</span><span class="p">)</span>
-
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="nb">int</span><span class="p">):</span>
-            <span class="k">raise</span> <span class="n">error_task_product</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> expects an integer number as the third argument specifying the number of elements in each tuple."</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-
-        <span class="n">orig_args</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">3</span><span class="p">:]</span>
-
-
-        <span class="c">#</span>
-        <span class="c">#   inputs can also be defined by pattern match</span>
-        <span class="c">#</span>
-        <span class="n">extra_inputs</span><span class="p">,</span> <span class="n">replace_inputs</span><span class="p">,</span> <span class="n">output_pattern</span><span class="p">,</span> <span class="n">extra_params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_extra_inputs_outputs_extra</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</ [...]
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">combinatorics_param_factory</span> <span class="p">(</span>   <span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                                    <span class="bp">False</span><span class="p">,</span> <span class="c"># flatten input</span>
-                                                                    <span class="n">combinatorics_type</span><span class="p">,</span>
-                                                                    <span class="n">k_tuple</span><span class="p">,</span>
-                                                                    <span class="n">file_names_transform</span><span class="p">,</span>
-                                                                    <span class="n">extra_inputs</span><span class="p">,</span>
-                                                                    <span class="n">replace_inputs</span><span class="p">,</span>
-                                                                    <span class="n">output_pattern</span><span class="p">,</span>
-                                                                    <span class="o">*</span><span class="n">extra_params</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_job_descriptor</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>      <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_permutations</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_permutations</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">            k-permutations of n</span>
-
-<span class="sd">            k-length tuples, all possible orderings, no self vs self</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span>      <span class="o">=</span> <span class="s">"@permutations"</span>
-        <span class="n">error_type</span>          <span class="o">=</span> <span class="n">error_task_permutations</span>
-        <span class="n">combinatorics_type</span>  <span class="o">=</span> <span class="n">t_combinatorics_type</span><span class="o">.</span><span class="n">COMBINATORICS_PERMUTATIONS</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">task_combinatorics</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">combinatorics_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">)</span>
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_combinations</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_combinations</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">            k-length tuples</span>
-<span class="sd">                Single (sorted) ordering, i.e. AB is the same as BA,</span>
-<span class="sd">                No repeats. No AA, BB</span>
-
-<span class="sd">            E.g.</span>
-<span class="sd">                combinations("ABCD", 3) = ['ABC', 'ABD', 'ACD', 'BCD']</span>
-<span class="sd">                combinations("ABCD", 2) = ['AB', 'AC', 'AD', 'BC', 'BD', 'CD']</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span>      <span class="o">=</span> <span class="s">"@combinations"</span>
-        <span class="n">error_type</span>          <span class="o">=</span> <span class="n">error_task_combinations</span>
-        <span class="n">combinatorics_type</span>  <span class="o">=</span> <span class="n">t_combinatorics_type</span><span class="o">.</span><span class="n">COMBINATORICS_COMBINATIONS</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">task_combinatorics</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">combinatorics_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">)</span>
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_combinations_with_replacement</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_combinations_with_replacement</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">            k-length tuples</span>
-<span class="sd">                Single (sorted) ordering, i.e. AB is the same as BA,</span>
-<span class="sd">                Repeats. AA, BB, AAC etc.</span>
-
-<span class="sd">            E.g.</span>
-<span class="sd">                combinations_with_replacement("ABCD", 3) = ['AAA', 'AAB', 'AAC', 'AAD',</span>
-<span class="sd">                                                            'ABB', 'ABC', 'ABD',</span>
-<span class="sd">                                                            'ACC', 'ACD',</span>
-<span class="sd">                                                            'ADD',</span>
-<span class="sd">                                                            'BBB', 'BBC', 'BBD',</span>
-<span class="sd">                                                            'BCC', 'BCD',</span>
-<span class="sd">                                                            'BDD',</span>
-<span class="sd">                                                            'CCC', 'CCD',</span>
-<span class="sd">                                                            'CDD',</span>
-<span class="sd">                                                            'DDD']</span>
-<span class="sd">                combinations_with_replacement("ABCD", 2) = ['AA', 'AB', 'AC', 'AD',</span>
-<span class="sd">                                                            'BB', 'BC', 'BD',</span>
-<span class="sd">                                                            'CC', 'CD',</span>
-<span class="sd">                                                            'DD']</span>
-
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span>      <span class="o">=</span> <span class="s">"@combinations_with_replacement"</span>
-        <span class="n">error_type</span>          <span class="o">=</span> <span class="n">error_task_combinations_with_replacement</span>
-        <span class="n">combinatorics_type</span>  <span class="o">=</span> <span class="n">t_combinatorics_type</span><span class="o">.</span><span class="n">COMBINATORICS_COMBINATIONS_WITH_REPLACEMENT</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">task_combinatorics</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">combinatorics_type</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="n">error_type</span><span class="p">)</span>
-
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_transform</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_transform</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Merges multiple input files into a single output.</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span>  <span class="o">=</span> <span class="s">"@transform"</span>
-        <span class="n">error_type</span>      <span class="o">=</span> <span class="n">error_task_transform</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_transform</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-
-        <span class="c">#_________________________________________________________________________________</span>
-        <span class="c">#</span>
-        <span class="c">#       single_job_single_output is bad policy. Can we remove it?</span>
-        <span class="c">#       What does this actually mean in Ruffus semantics?</span>
-        <span class="c">#</span>
-        <span class="c">#</span>
-        <span class="c">#   allows transform to take a single file or task</span>
-        <span class="k">if</span> <span class="n">input_files_task_globs</span><span class="o">.</span><span class="n">single_file_to_list</span><span class="p">():</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">single_job_single_output</span>
-
-        <span class="c">#</span>
-        <span class="c">#   whether transform generates a list of jobs or not will depend on the parent task</span>
-        <span class="c">#</span>
-        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">input_files_task_globs</span><span class="o">.</span><span class="n">params</span><span class="p">,</span> <span class="n">_task</span><span class="p">):</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">=</span> <span class="n">input_files_task_globs</span><span class="o">.</span><span class="n">params</span>
-
-        <span class="c">#_________________________________________________________________________________</span>
-
-        <span class="c"># how to transform input to output file name</span>
-        <span class="n">file_names_transform</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">choose_file_names_transform</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">error_task_transform</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="n">orig_args</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
-
-
-        <span class="c">#</span>
-        <span class="c">#   inputs can also be defined by pattern match</span>
-        <span class="c">#</span>
-        <span class="n">extra_inputs</span><span class="p">,</span> <span class="n">replace_inputs</span><span class="p">,</span> <span class="n">output_pattern</span><span class="p">,</span> <span class="n">extra_params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_extra_inputs_outputs_extra</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</ [...]
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">transform_param_factory</span> <span class="p">(</span>   <span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                                <span class="bp">False</span><span class="p">,</span> <span class="c"># flatten input</span>
-                                                                <span class="n">file_names_transform</span><span class="p">,</span>
-                                                                <span class="n">extra_inputs</span><span class="p">,</span>
-                                                                <span class="n">replace_inputs</span><span class="p">,</span>
-                                                                <span class="n">output_pattern</span><span class="p">,</span>
-                                                                <span class="o">*</span><span class="n">extra_params</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_job_descriptor</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>      <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_collate</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_collate</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Merges multiple input files into a single output.</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span> <span class="o">=</span> <span class="s">"@collate"</span>
-        <span class="n">error_type</span>      <span class="o">=</span> <span class="n">error_task_collate</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_collate</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-
-        <span class="c"># how to transform input to output file name</span>
-        <span class="n">file_names_transform</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">choose_file_names_transform</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">error_task_collate</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">,</span> <span class="p">(</span><span class="n">regex</span>< [...]
-
-        <span class="n">orig_args</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
-
-        <span class="c">#</span>
-        <span class="c">#   inputs also defined by pattern match</span>
-        <span class="c">#</span>
-        <span class="n">extra_inputs</span><span class="p">,</span> <span class="n">replace_inputs</span><span class="p">,</span> <span class="n">output_pattern</span><span class="p">,</span> <span class="n">extra_params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_extra_inputs_outputs_extra</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">error_type</span><span class="p">,</ [...]
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>           <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">collate_param_factory</span> <span class="p">(</span> <span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                            <span class="bp">False</span><span class="p">,</span> <span class="c"># flatten input</span>
-                                                            <span class="n">file_names_transform</span><span class="p">,</span>
-                                                            <span class="n">extra_inputs</span><span class="p">,</span>
-                                                            <span class="n">replace_inputs</span><span class="p">,</span>
-                                                            <span class="n">output_pattern</span><span class="p">,</span>
-                                                            <span class="o">*</span><span class="n">extra_params</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_job_descriptor</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_merge</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_merge</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Merges multiple input files into a single output.</span>
-<span class="sd">        """</span>
-        <span class="c">#</span>
-        <span class="c">#   check enough arguments</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_task_merge</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for @merge"</span><span class="p">)</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_merge</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-        <span class="n">extra_params</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">merge_param_factory</span> <span class="p">(</span><span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                           <span class="o">*</span><span class="n">extra_params</span><span class="p">)</span>
-
-
-<span class="c">#        self._single_job_single_output = self.multiple_jobs_outputs</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">single_job_single_output</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>           <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_one</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_job_descriptor</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_parallel</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_parallel</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        calls user function in parallel</span>
-<span class="sd">            with either each of a list of parameters</span>
-<span class="sd">            or using parameters generated by a custom function</span>
-<span class="sd">        """</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_parallel</span><span class="p">)</span>
-
-        <span class="c">#   unmodified from __init__</span>
-        <span class="c">#</span>
-        <span class="c"># self.needs_update_func      = None</span>
-        <span class="c"># self.job_wrapper          = job_wrapper_generic</span>
-        <span class="c"># self.job_descriptor       = io_files_job_descriptor</span>
-
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_task_parallel</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for @parallel"</span><span class="p">)</span>
-
-        <span class="c">#   Use parameters generated by a custom function</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span><span class="p"> [...]
-        <span class="c">#if len(orig_args) == 1 and type(orig_args[0]) == types.FunctionType:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">args_param_factory</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">]())</span>
-
-        <span class="c"># list of  params</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
-                <span class="c"># single jobs</span>
-                <span class="n">params</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">([</span><span class="n">orig_args</span><span class="p">])</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">single_job_single_output</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="c"># multiple jobs with input/output parameters etc.</span>
-                <span class="n">params</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-                <span class="n">check_parallel_parameters</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">params</span><span class="p">,</span> <span class="n">error_task_parallel</span><span class="p">)</span>
-
-            <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">args_param_factory</span> <span class="p">(</span><span class="n">params</span><span class="p">)</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_files</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_files</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        calls user function in parallel</span>
-<span class="sd">            with either each of a list of parameters</span>
-<span class="sd">            or using parameters generated by a custom function</span>
-
-<span class="sd">            In the parameter list,</span>
-<span class="sd">                The first two items of each set of parameters must</span>
-<span class="sd">                be input/output files or lists of files or Null</span>
-<span class="sd">        """</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_job_descriptor</span>
-
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_task_files</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for @files"</span><span class="p">)</span>
-
-        <span class="c">#   Use parameters generated by a custom function</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span><span class="p"> [...]
-            <span class="c">#if len(orig_args) == 1 and type(orig_args[0]) == types.FunctionType:</span>
-
-            <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_files_func</span><span class="p">)</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">files_custom_generator_param_factory</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-            <span class="c"># assume</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>           <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-        <span class="c">#   Use parameters in supplied list</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_files</span><span class="p">)</span>
-
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
-
-                <span class="c"># single jobs</span>
-                <span class="c"># This is true even if the previous task has multiple output</span>
-                <span class="c"># These will all be joined together at the hip (like @merge)</span>
-                <span class="c"># If you want different behavior, use @transform</span>
-                <span class="n">params</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">([</span><span class="n">orig_args</span><span class="p">])</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">single_job_single_output</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>           <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">one_to_one</span>
-
-
-            <span class="k">else</span><span class="p">:</span>
-
-                <span class="c"># multiple jobs with input/output parameters etc.</span>
-                <span class="n">params</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">multiple_jobs_outputs</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>           <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-            <span class="n">check_files_io_parameters</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">params</span><span class="p">,</span> <span class="n">error_task_files</span><span class="p">)</span>
-
-            <span class="c">#</span>
-            <span class="c"># get list of function/function names and globs for all job params</span>
-            <span class="c">#</span>
-
-            <span class="c">#</span>
-            <span class="c"># replace function / function names with tasks</span>
-            <span class="c">#</span>
-            <span class="n">input_patterns</span> <span class="o">=</span> <span class="p">[</span><span class="n">j</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">params</span><span class="p">]</span>
-            <span class="n">input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">input_patterns</span><span class="p">)</span>
-
-
-            <span class="c">#</span>
-            <span class="c">#   extra params</span>
-            <span class="c">#</span>
-            <span class="n">output_extra_params</span> <span class="o">=</span> <span class="p">[</span><span class="nb">tuple</span><span class="p">(</span><span class="n">j</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span> <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">params</span><span class="p">]</span>
-
-            <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">files_param_factory</span> <span class="p">(</span><span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                             <span class="bp">False</span><span class="p">,</span> <span class="c"># flatten input</span>
-                                                             <span class="bp">True</span><span class="p">,</span>  <span class="c"># do_not_expand_single_job_tasks</span>
-                                                             <span class="n">output_extra_params</span><span class="p">)</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_files_re</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_files_re</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">old_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        calls user function in parallel</span>
-<span class="sd">            with input_files, output_files, parameters</span>
-<span class="sd">            These needed to be generated on the fly by</span>
-<span class="sd">                getting all file names in the supplied list/glob pattern</span>
-<span class="sd">            There are two variations:</span>
-
-<span class="sd">            1)    inputfiles = all files in glob which match the regular expression</span>
-<span class="sd">                  outputfile = generated from the replacement string</span>
-
-<span class="sd">            2)    inputfiles = all files in glob which match the regular expression and</span>
-<span class="sd">                                          generated from the "from" replacement string</span>
-<span class="sd">                  outputfiles = all files in glob which match the regular expression and</span>
-<span class="sd">                                          generated from the "to" replacement string</span>
-<span class="sd">        """</span>
-        <span class="c">#</span>
-        <span class="c">#   check enough arguments</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">old_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="n">error_task_files_re</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for @files_re"</span><span class="p">)</span>
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_task_files_re</span><span class="p">)</span>
-
-        <span class="c"># check if parameters wrapped in combine</span>
-        <span class="n">combining_all_jobs</span><span class="p">,</span> <span class="n">orig_args</span> <span class="o">=</span> <span class="n">is_file_re_combining</span><span class="p">(</span><span class="n">old_args</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># replace function / function names with tasks</span>
-        <span class="c">#</span>
-        <span class="n">input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-        <span class="n">file_names_transform</span> <span class="o">=</span> <span class="n">t_regex_file_names_transform</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span> <span class="n">error_task_files_re</span><span class="p">,</span> <span class="s">"@files_re"</span><span class="p"> [...]
-
-
-        <span class="c"># if the input file term is missing, just use the original</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
-            <span class="n">extra_input_files_task_globs</span> <span class="o">=</span> <span class="bp">None</span>
-            <span class="n">output_and_extras</span> <span class="o">=</span> <span class="p">[</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">]]</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">extra_input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
-            <span class="n">output_and_extras</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">3</span><span class="p">:]</span>
-
-
-        <span class="k">if</span> <span class="n">combining_all_jobs</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>           <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">collate_param_factory</span> <span class="p">(</span><span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                                <span class="bp">False</span><span class="p">,</span>                  <span class="c"># flatten</span>
-                                                                <span class="n">file_names_transform</span><span class="p">,</span>
-                                                                <span class="n">extra_input_files_task_globs</span><span class="p">,</span>
-                                                                <span class="n">t_extra_inputs</span><span class="o">.</span><span class="n">REPLACE_INPUTS</span><span class="p">,</span>
-                                                                <span class="o">*</span><span class="n">output_and_extras</span><span class="p">)</span>
-        <span class="k">else</span><span class="p">:</span>
-
-            <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>           <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">transform_param_factory</span> <span class="p">(</span><span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                                    <span class="bp">False</span><span class="p">,</span>              <span class="c"># flatten</span>
-                                                                    <span class="n">file_names_transform</span><span class="p">,</span>
-                                                                    <span class="n">extra_input_files_task_globs</span><span class="p">,</span>
-                                                                    <span class="n">t_extra_inputs</span><span class="o">.</span><span class="n">REPLACE_INPUTS</span><span class="p">,</span>
-                                                                    <span class="o">*</span><span class="n">output_and_extras</span><span class="p">)</span>
-
-
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_modify_time</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_io_files</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">io_files_job_descriptor</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_mkdir</span>
-
-    <span class="c">#       only called within task_follows</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_mkdir</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">cnt_task_mkdir</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="c"># give unique name to this instance of mkdir</span>
-        <span class="n">unique_name</span> <span class="o">=</span> <span class="s">r"(mkdir </span><span class="si">%d</span><span class="s">) before "</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">cnt_task_mkdir</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">_name</span>
-        <span class="n">new_node</span> <span class="o">=</span> <span class="n">_task</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_module_name</span><span class="p">,</span> <span class="n">unique_name</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">new_node</span><span class="p">)</span>
-        <span class="n">new_node</span><span class="o">.</span><span class="n">do_task_mkdir</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span>
-        <span class="n">new_node</span><span class="o">.</span><span class="n">display_name</span> <span class="o">=</span> <span class="n">new_node</span><span class="o">.</span><span class="n">_description</span>
-
-
-    <span class="k">def</span> <span class="nf">do_task_mkdir</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        list of directory names or a single argument which is aa list of directory names</span>
-<span class="sd">        Creates directory if missing</span>
-<span class="sd">        """</span>
-        <span class="n">decorator_name</span> <span class="o">=</span> <span class="s">"mkdir"</span>
-        <span class="n">error_type</span>      <span class="o">=</span> <span class="n">error_task_mkdir</span>
-
-        <span class="c">#   jump through hoops</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_action_type</span> <span class="p">(</span><span class="n">_task</span><span class="o">.</span><span class="n">action_mkdir</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>    <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="ow">or</span> <span class="n">needs_update_check_directory_missing</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_description</span>         <span class="o">=</span> <span class="s">"Make directories </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">shorten_filenames_encoder</span><span class="p">(</span><span class="n">orig_args</span><span class="p">))</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>          <span class="o">=</span> <span class="n">job_wrapper_mkdir</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">job_descriptor</span>       <span class="o">=</span> <span class="n">mkdir_job_descriptor</span>
-
-        <span class="c"># doesn't have a real function</span>
-        <span class="c">#  use job_wrapper just so it is not None</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">user_defined_work_func</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">job_wrapper</span>
-
-
-        <span class="c">#</span>
-        <span class="c"># @transform like behaviour with regex / suffix or formatter</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="p">(</span><span class="n">formatter</span><span class="p">,</span> <span class="n">suffix [...]
-            <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>      <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">many_to_many</span>
-
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too few arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-            <span class="c">#</span>
-            <span class="c"># replace function / function names with tasks</span>
-            <span class="c">#</span>
-            <span class="n">input_files_task_globs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">handle_tasks_globs_in_inputs</span><span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-
-            <span class="c"># how to transform input to output file name</span>
-            <span class="n">file_names_transform</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">choose_file_names_transform</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">error_task_transform</span><span class="p">,</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-            <span class="n">orig_args</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">2</span><span class="p">:]</span>
-
-            <span class="c">#</span>
-            <span class="c">#   inputs can also be defined by pattern match</span>
-            <span class="c">#</span>
-            <span class="n">extra_inputs</span><span class="p">,</span> <span class="n">replace_inputs</span><span class="p">,</span> <span class="n">output_pattern</span><span class="p">,</span> <span class="n">extra_params</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_extra_inputs_outputs_extra</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">,</span> <span class="n">error_type</span><span class="p" [...]
-
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">extra_params</span><span class="p">):</span>
-                <span class="k">raise</span> <span class="n">error_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">"Too many arguments for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">decorator_name</span><span class="p">)</span>
-
-
-            <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">transform_param_factory</span> <span class="p">(</span>   <span class="n">input_files_task_globs</span><span class="p">,</span>
-                                                                    <span class="bp">False</span><span class="p">,</span> <span class="c"># flatten input</span>
-                                                                    <span class="n">file_names_transform</span><span class="p">,</span>
-                                                                    <span class="n">extra_inputs</span><span class="p">,</span>
-                                                                    <span class="n">replace_inputs</span><span class="p">,</span>
-                                                                    <span class="n">output_pattern</span><span class="p">,</span>
-                                                                    <span class="o">*</span><span class="n">extra_params</span><span class="p">)</span>
-
-        <span class="c">#</span>
-        <span class="c"># simple behaviour: just make directories in list of strings</span>
-        <span class="c">#</span>
-        <span class="c"># the mkdir decorator accepts one string, multiple strings or a list of strings</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">single_multi_io</span>        <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">one_to_one</span>
-
-            <span class="c">#</span>
-            <span class="c">#</span>
-            <span class="c">#</span>
-            <span class="c"># if a single argument collection of parameters, keep that as is</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-                <span class="n">mkdir_params</span> <span class="o">=</span> <span class="p">[]</span>
-            <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">orig_args</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
-                <span class="n">mkdir_params</span> <span class="o">=</span> <span class="n">orig_args</span>
-            <span class="c"># len(orig_args) == 1: unpack orig_args[0]</span>
-            <span class="k">elif</span> <span class="n">non_str_sequence</span> <span class="p">(</span><span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
-                <span class="n">mkdir_params</span> <span class="o">=</span> <span class="n">orig_args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-            <span class="c"># single string or other non collection types</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="n">mkdir_params</span> <span class="o">=</span> <span class="n">orig_args</span>
-
-            <span class="c">#   all directories created in one job to reduce race conditions</span>
-            <span class="c">#    so we are converting [a,b,c] into [   [(a, b,c)]   ]</span>
-            <span class="c">#    where orig_args = (a,b,c)</span>
-            <span class="c">#   i.e. one job whose solitory argument is a tuple/list of directory names</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">=</span> <span class="n">args_param_factory</span><span class="p">([[</span><span class="nb">sorted</span><span class="p">(</span><span class="n">mkdir_params</span><span class="p">)]])</span>
-
-
-
-
-
-
-
-
-    <span class="c">#8888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-    <span class="c">#   Other task handlers</span>
-
-
-
-    <span class="c">#8888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-
-
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_follows</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_follows</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Saved decorator arguments should be:</span>
-<span class="sd">                (string/task,...)</span>
-<span class="sd">        """</span>
-        <span class="n">new_tasks</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">args</span><span class="p">:</span>
-            <span class="c">#</span>
-            <span class="c">#   specified by string: unicode or otherwise</span>
-            <span class="c">#</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
-                <span class="c"># string looks up to defined task, use that</span>
-                <span class="k">if</span> <span class="n">node</span><span class="o">.</span><span class="n">is_node</span><span class="p">(</span><span class="n">arg</span><span class="p">):</span>
-                    <span class="n">arg</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">lookup_node_from_name</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
-                <span class="c"># string looks up to defined task in main module, use that</span>
-                <span class="k">elif</span> <span class="n">node</span><span class="o">.</span><span class="n">is_node</span><span class="p">(</span><span class="s">"__main__."</span> <span class="o">+</span> <span class="n">arg</span><span class="p">):</span>
-                    <span class="n">arg</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">lookup_node_from_name</span><span class="p">(</span><span class="s">"__main__."</span> <span class="o">+</span> <span class="n">arg</span><span class="p">)</span>
-
-                <span class="c">#</span>
-                <span class="c"># string does not look up to defined task: defer</span>
-                <span class="c">#</span>
-                <span class="k">else</span><span class="p">:</span>
-                    <span class="c">#   no module: use same module as current task</span>
-                    <span class="n">names</span> <span class="o">=</span> <span class="n">arg</span><span class="o">.</span><span class="n">rsplit</span><span class="p">(</span><span class="s">"."</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
-                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">names</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
-                        <span class="n">arg</span> <span class="o">=</span> <span class="n">_task</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_module_name</span><span class="p">,</span> <span class="n">arg</span><span class="p">)</span>
-                    <span class="k">else</span><span class="p">:</span>
-                        <span class="n">arg</span> <span class="o">=</span> <span class="n">_task</span><span class="p">(</span><span class="o">*</span><span class="n">names</span><span class="p">)</span>
-
-                <span class="c">#</span>
-                <span class="c">#   add dependency</span>
-                <span class="c">#       duplicate dependencies are ignore automatically</span>
-                <span class="c">#</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
-                <span class="n">new_tasks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
-
-
-            <span class="c">#</span>
-            <span class="c">#   for mkdir, automatically generate task with unique name</span>
-            <span class="c">#</span>
-            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="n">mkdir</span><span class="p">):</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">cnt_task_mkdir</span> <span class="o">+=</span> <span class="mi">1</span>
-                <span class="c"># give unique name to this instance of mkdir</span>
-                <span class="n">unique_name</span> <span class="o">=</span> <span class="s">r"(mkdir </span><span class="si">%d</span><span class="s">) before "</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">cnt_task_mkdir</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">_name</span>
-                <span class="n">new_node</span> <span class="o">=</span> <span class="n">_task</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_module_name</span><span class="p">,</span> <span class="n">unique_name</span><span class="p">)</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">new_node</span><span class="p">)</span>
-                <span class="n">new_node</span><span class="o">.</span><span class="n">do_task_mkdir</span><span class="p">(</span><span class="n">arg</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
-                <span class="n">new_node</span><span class="o">.</span><span class="n">display_name</span> <span class="o">=</span> <span class="n">new_node</span><span class="o">.</span><span class="n">_description</span>
-                <span class="n">new_tasks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">new_node</span><span class="p">)</span>
-
-
-
-
-            <span class="c">#</span>
-            <span class="c">#   Is this a function?</span>
-            <span class="c">#       Turn this function into a task</span>
-            <span class="c">#           (add task as attribute of this function)</span>
-            <span class="c">#       Add self as dependent</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="c">#if type(arg) != types.FunctionType:</span>
-                <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span><span class="p">):</span>
-
-                    <span class="k">raise</span> <span class="n">error_decorator_args</span><span class="p">(</span><span class="s">"Dependencies must be functions or function names in "</span> <span class="o">+</span>
-                                                <span class="s">"@task_follows </span><span class="si">%s</span><span class="s">:</span><span class="se">\n</span><span class="s">[</span><span class="si">%s</span><span class="s">]"</span> <span class="o">%</span>
-                                                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_name</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">arg</span><span class="p">)))</span>
-
-                <span class="c"># add task as attribute of this function</span>
-                <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="s">"pipeline_task"</span><span class="p">):</span>
-                    <span class="n">arg</span><span class="o">.</span><span class="n">pipeline_task</span> <span class="o">=</span> <span class="n">_task</span><span class="o">.</span><span class="n">create_task</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">arg</span><span class="o">.</span><span class="n">pipeline_task</span><span class="p">)</span>
-                <span class="n">new_tasks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">arg</span><span class="o">.</span><span class="n">pipeline_task</span><span class="p">)</span>
-
-        <span class="k">return</span> <span class="n">new_tasks</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_check_if_uptodate</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_check_if_uptodate</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Saved decorator arguments should be:</span>
-<span class="sd">                a function which takes the appropriate number of arguments for each job</span>
-<span class="sd">        """</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">1</span> <span class="ow">or</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span [...]
-        <span class="c">#if len(args) != 1 or type(args[0]) != types.FunctionType:</span>
-            <span class="k">raise</span> <span class="n">error_decorator_args</span><span class="p">(</span><span class="s">"Expecting a single function in  "</span> <span class="o">+</span>
-                                                <span class="s">"@task_check_if_uptodate </span><span class="si">%s</span><span class="s">:</span><span class="se">\n</span><span class="s">[</span><span class="si">%s</span><span class="s">]"</span> <span class="o">%</span>
-                                                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_name</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">args</span><span class="p">)))</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">needs_update_func</span>        <span class="o">=</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
-
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_posttask</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_posttask</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Saved decorator arguments should be:</span>
-<span class="sd">                one or more functions which will be called if the task completes</span>
-<span class="sd">        """</span>
-        <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="n">args</span><span class="p">:</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="n">touch_file</span><span class="p">):</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">posttask_functions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">touch_file_factory</span> <span class="p">(</span><span class="n">arg</span><span class="o">.</span><span class="n">args</span><span class="p">,</span> <span class="n">register_cleanup</span><span class="p">))</span>
-            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">arg</span><span class="p">,</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span><span class="p">):</span>
-            <span class="c">#elif type(arg) == types.FunctionType:</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">posttask_functions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">arg</span><span class="p">)</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">PostTaskArgumentError</span><span class="p">(</span><span class="s">"Expecting simple functions or touch_file in  "</span> <span class="o">+</span>
-                                                <span class="s">"@posttask(...)</span><span class="se">\n</span><span class="s"> Task = </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span>
-                                                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_name</span><span class="p">))</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_jobs_limit</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_jobs_limit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">args</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Limit the number of concurrent jobs</span>
-<span class="sd">        """</span>
-        <span class="n">maximum_jobs</span><span class="p">,</span> <span class="n">name</span> <span class="o">=</span> <span class="p">(</span><span class="n">args</span> <span class="o">+</span> <span class="p">(</span><span class="bp">None</span><span class="p">,))[</span><span class="mi">0</span><span class="p">:</span><span class="mi">2</span><span class="p">]</span>
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">maximum_jobs_num</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">maximum_jobs</span><span class="p">)</span>
-            <span class="k">assert</span><span class="p">(</span><span class="n">maximum_jobs_num</span> <span class="o">>=</span> <span class="mi">1</span><span class="p">)</span>
-        <span class="k">except</span><span class="p">:</span>
-            <span class="n">limit_name</span> <span class="o">=</span> <span class="s">", "</span> <span class="o">+</span> <span class="n">name</span> <span class="k">if</span> <span class="n">name</span> <span class="k">else</span> <span class="s">""</span>
-            <span class="k">raise</span> <span class="n">JobsLimitArgumentError</span><span class="p">((</span><span class="s">'In @jobs_limit(</span><span class="si">%s%s</span><span class="s">), the limit '</span>
-                                          <span class="s">'must be an integer number greater than or '</span>
-                                          <span class="s">'equal to 1'</span><span class="p">)</span> <span class="o">%</span>
-                                         <span class="p">(</span><span class="n">maximum_jobs_num</span><span class="p">,</span> <span class="n">limit_name</span><span class="p">))</span>
-        <span class="k">if</span> <span class="n">name</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">semaphore_name</span> <span class="o">=</span> <span class="n">name</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">semaphore_name</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">job_limit_semaphores</span><span class="p">:</span>
-            <span class="n">curr_maximum_jobs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">job_limit_semaphores</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">semaphore_name</span><span class="p">]</span>
-            <span class="k">if</span> <span class="n">curr_maximum_jobs</span> <span class="o">!=</span> <span class="n">maximum_jobs_num</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">JobsLimitArgumentError</span><span class="p">((</span><span class="s">'@jobs_limit(</span><span class="si">%d</span><span class="s">, "</span><span class="si">%s</span><span class="s">") cannot '</span> <span class="o">+</span>
-                                            <span class="s">'re-defined with a different limit of </span><span class="si">%d</span><span class="s">'</span><span class="p">)</span> <span class="o">%</span>
-                                             <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">semaphore_name</span><span class="p">,</span> <span class="n">curr_maximum_jobs</span><span class="p">,</span>
-                                                <span class="n">maximum_jobs_num</span><span class="p">))</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="c">#</span>
-            <span class="c">#   save semaphore and limit</span>
-            <span class="c">#</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">job_limit_semaphores</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">semaphore_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">maximum_jobs_num</span>
-
-
-    <span class="c">#_________________________________________________________________________________________</span>
-
-    <span class="c">#   task_active_if</span>
-
-    <span class="c">#_________________________________________________________________________________________</span>
-    <span class="k">def</span> <span class="nf">task_active_if</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">active_if_checks</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        If any of active_checks is False or returns False, then the task is</span>
-<span class="sd">        marked as "inactive" and its outputs removed.</span>
-<span class="sd">        """</span>
-        <span class="c">#print 'job is active:', active_checks, [</span>
-        <span class="c">#                arg() if isinstance(arg, collections.Callable) else arg</span>
-        <span class="c">#                for arg in active_checks]</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">active_if_checks</span><span class="p">)</span>
-        <span class="k">print</span> <span class="bp">self</span><span class="o">.</span><span class="n">active_if_checks</span>
-
-
-<span class="k">class</span> <span class="nc">task_encoder</span><span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">JSONEncoder</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">default</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">):</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="nb">set</span><span class="p">):</span>
-            <span class="k">return</span> <span class="nb">list</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">defaultdict</span><span class="p">):</span>
-            <span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">obj</span><span class="p">)</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">_task</span><span class="p">):</span>
-            <span class="k">return</span> <span class="n">obj</span><span class="o">.</span><span class="n">_name</span> <span class="c">#, _task.action_names[obj.action_task], obj._description]</span>
-        <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">JSONEncoder</span><span class="o">.</span><span class="n">default</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obj</span><span class="p">)</span>
-
-
-
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Functions</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   link_task_names_to_functions</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">link_task_names_to_functions</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    Make sure all tasks in dependency list are linked to real functions</span>
-<span class="sd">        Call this before running anything else</span>
-<span class="sd">    """</span>
-
-    <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">_all_nodes</span><span class="p">:</span>
-        <span class="k">if</span> <span class="n">n</span><span class="o">.</span><span class="n">user_defined_work_func</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-            <span class="n">dependent_display_task_name</span> <span class="o">=</span> <span class="n">n</span><span class="o">.</span><span class="n">_inward</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">()</span>
-            <span class="k">if</span> <span class="n">n</span><span class="o">.</span><span class="n">_module_name</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">:</span>
-                <span class="n">module</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="n">n</span><span class="o">.</span><span class="n">_module_name</span><span class="p">]</span>
-                <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">module</span><span class="p">,</span> <span class="n">n</span><span class="o">.</span><span class="n">_func_name</span><span class="p">):</span>
-                    <span class="n">n</span><span class="o">.</span><span class="n">user_defined_work_func</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">module</span><span class="p">,</span> <span class="n">n</span><span class="o">.</span><span class="n">_func_name</span><span class="p">)</span>
-                <span class="k">else</span><span class="p">:</span>
-                    <span class="k">raise</span> <span class="n">error_decorator_args</span><span class="p">((</span><span class="s">"Module '</span><span class="si">%s</span><span class="s">' has no function '</span><span class="si">%s</span><span class="s">' in "</span> <span class="o">+</span>
-                                                <span class="s">"</span><span class="se">\n</span><span class="s">@task_follows('</span><span class="si">%s</span><span class="s">')</span><span class="se">\n</span><span class="s">def </span><span class="si">%s</span><span class="s">..."</span><span class="p">)</span> <span class="o">%</span>
-                                        <span class="p">(</span><span class="n">n</span><span class="o">.</span><span class="n">_module_name</span><span class="p">,</span> <span class="n">n</span><span class="o">.</span><span class="n">_func_name</span><span class="p">,</span> <span class="n">n</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">(),</span> <span class="n">dependent_display_task_name</span><span class="p">))</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">error_decorator_args</span><span class="p">(</span><span class="s">"Module '</span><span class="si">%s</span><span class="s">' not found in "</span> <span class="o">+</span>
-                                        <span class="s">"</span><span class="se">\n</span><span class="s">@task_follows('</span><span class="si">%s</span><span class="s">')</span><span class="se">\n</span><span class="s">def </span><span class="si">%s</span><span class="s">..."</span> <span class="o">%</span>
-                                <span class="p">(</span><span class="n">n</span><span class="o">.</span><span class="n">_module_name</span><span class="p">,</span> <span class="n">n</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">(),</span> <span class="n">dependent_display_task_name</span><span class="p">))</span>
-
-
-        <span class="c">#</span>
-        <span class="c"># some jobs single state status mirrors parent's state</span>
-        <span class="c">#   and parent task not known until know</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">n</span><span class="o">.</span><span class="n">_single_job_single_output</span><span class="p">,</span> <span class="n">_task</span><span class="p">):</span>
-            <span class="n">n</span><span class="o">.</span><span class="n">_single_job_single_output</span> <span class="o">=</span> <span class="n">n</span><span class="o">.</span><span class="n">_single_job_single_output</span><span class="o">.</span><span class="n">_single_job_single_output</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   update_checksum_level_on_tasks</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">update_checksum_level_on_tasks</span> <span class="p">(</span><span class="n">checksum_level</span><span class="p">):</span>
-    <span class="sd">"""Reset the checksum level for all tasks"""</span>
-    <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">_all_nodes</span><span class="p">:</span>
-        <span class="n">n</span><span class="o">.</span><span class="n">checksum_level</span> <span class="o">=</span> <span class="n">checksum_level</span>
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   update_active_states_for_all_tasks</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">update_active_states_for_all_tasks</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-
-<span class="sd">    @active_if decorated tasks can change their active state every time</span>
-<span class="sd">      pipeline_run / pipeline_printout / pipeline_printout_graph is called</span>
-
-<span class="sd">    update_active_states_for_all_tasks ()</span>
-
-<span class="sd">    """</span>
-    <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">_all_nodes</span><span class="p">:</span>
-        <span class="n">n</span><span class="o">.</span><span class="n">update_active_state</span><span class="p">()</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   task_names_to_tasks</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">task_names_to_tasks</span> <span class="p">(</span><span class="n">task_description</span><span class="p">,</span> <span class="n">task_names</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Given a list of task names, look up the corresponding tasks</span>
-<span class="sd">    Will just pass through if the task_name is already a task</span>
-<span class="sd">    """</span>
-
-    <span class="c">#</span>
-    <span class="c">#   In case we are given a single item instead of a list</span>
-    <span class="c">#       accepts unicode</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">task_names</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">)</span> <span class="ow">or</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">task_names</span><span class="p">,</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span><span class="p">):</span>
-    <span class="c">#if isinstance(task_names, basestring) or type(task_names) == types.FunctionType:</span>
-        <span class="n">task_names</span> <span class="o">=</span> <span class="p">[</span><span class="n">task_names</span><span class="p">]</span>
-
-    <span class="n">task_nodes</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="k">for</span> <span class="n">task_name</span> <span class="ow">in</span> <span class="n">task_names</span><span class="p">:</span>
-
-        <span class="c"># Is this already a function, don't do mapping if already is task</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">task_name</span><span class="p">,</span> <span class="n">collections</span><span class="o">.</span><span class="n">Callable</span><span class="p">):</span>
-        <span class="c">#if type(task_name) == types.FunctionType:</span>
-            <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">task_name</span><span class="p">,</span> <span class="s">"pipeline_task"</span><span class="p">):</span>
-                <span class="n">task_nodes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">task_name</span><span class="o">.</span><span class="n">pipeline_task</span><span class="p">)</span>
-                <span class="k">continue</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="c"># blow up for unwrapped function</span>
-                <span class="k">raise</span> <span class="n">error_function_is_not_a_task</span><span class="p">((</span><span class="s">"Function def </span><span class="si">%s</span><span class="s">(...): is not a pipelined task in ruffus."</span> <span class="o">%</span>
-                                                    <span class="n">task_name</span><span class="o">.</span><span class="n">__name__</span><span class="p">)</span> <span class="o">+</span>
-                                                    <span class="s">" To include this, this function needs to have a ruffus "</span><span class="o">+</span>
-                                                    <span class="s">"decoration like '@parallel', '@files', or named as a dependent "</span><span class="o">+</span>
-                                                    <span class="s">"of some other Ruffus task function via '@follows'."</span><span class="p">)</span>
-
-        <span class="c"># assumes is some kind of string</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">node</span><span class="o">.</span><span class="n">is_node</span><span class="p">(</span><span class="n">task_name</span><span class="p">):</span>
-            <span class="k">if</span>  <span class="n">node</span><span class="o">.</span><span class="n">is_node</span><span class="p">(</span><span class="s">"__main__."</span> <span class="o">+</span> <span class="n">task_name</span><span class="p">):</span>
-                <span class="n">task_nodes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">lookup_node_from_name</span><span class="p">(</span><span class="s">"__main__."</span> <span class="o">+</span> <span class="n">task_name</span><span class="p">))</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="n">error_node_not_task</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> task '</span><span class="si">%s</span><span class="s">' is not a pipelined task in Ruffus. Have you mis-spelt the function name?"</span> <span class="o">%</span> <span class="p">(</span>
-                                                        <span class="n">task_description</span><span class="p">,</span> <span class="n">task_name</span><span class="p">))</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">task_nodes</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">node</span><span class="o">.</span><span class="n">lookup_node_from_name</span><span class="p">(</span><span class="n">task_name</span><span class="p">))</span>
-    <span class="k">return</span> <span class="n">task_nodes</span>
-
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   pipeline_printout_in_dot_format</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<div class="viewcode-block" id="pipeline_printout_graph"><a class="viewcode-back" href="../../task.html#ruffus.task.pipeline_printout_graph">[docs]</a><span class="k">def</span> <span class="nf">pipeline_printout_graph</span> <span class="p">(</span><span class="n">stream</span><span class="p">,</span>
-                             <span class="n">output_format</span>                  <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                             <span class="n">target_tasks</span>                   <span class="o">=</span> <span class="p">[],</span>
-                             <span class="n">forcedtorun_tasks</span>              <span class="o">=</span> <span class="p">[],</span>
-                             <span class="n">draw_vertically</span>                <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
-                             <span class="n">ignore_upstream_of_target</span>      <span class="o">=</span> <span class="bp">False</span><span class="p">,</span>
-                             <span class="n">skip_uptodate_tasks</span>            <span class="o">=</span> <span class="bp">False</span><span class="p">,</span>
-                             <span class="n">gnu_make_maximal_rebuild_mode</span>  <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
-                             <span class="n">test_all_task_for_update</span>       <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
-                             <span class="n">no_key_legend</span>                  <span class="o">=</span> <span class="bp">False</span><span class="p">,</span>
-                             <span class="n">minimal_key_legend</span>             <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
-                             <span class="n">user_colour_scheme</span>             <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                             <span class="n">pipeline_name</span>                  <span class="o">=</span> <span class="s">"Pipeline:"</span><span class="p">,</span>
-                             <span class="n">size</span>                           <span class="o">=</span> <span class="p">(</span><span class="mi">11</span><span class="p">,</span><span class="mi">8</span><span class="p">),</span>
-                             <span class="n">dpi</span>                            <span class="o">=</span> <span class="mi">120</span><span class="p">,</span>
-                             <span class="n">runtime_data</span>                   <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                             <span class="n">checksum_level</span>                 <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                             <span class="n">history_file</span>                   <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
-                             <span class="c"># Remember to add further extra parameters here to "extra_pipeline_printout_graph_options" inside cmdline.py</span>
-                             <span class="c"># This will forward extra parameters from the command line to pipeline_printout_graph</span>
-    <span class="sd">"""</span>
-<span class="sd">    print out pipeline dependencies in various formats</span>
-
-<span class="sd">    :param stream: where to print to</span>
-<span class="sd">    :type stream: file-like object with ``write()`` function</span>
-<span class="sd">    :param output_format: ["dot", "jpg", "svg", "ps", "png"]. All but the first depends on the `dot <http://www.graphviz.org>`_ program.</span>
-<span class="sd">    :param target_tasks: targets task functions which will be run if they are out-of-date.</span>
-<span class="sd">    :param forcedtorun_tasks: task functions which will be run whether or not they are out-of-date.</span>
-<span class="sd">    :param draw_vertically: Top to bottom instead of left to right.</span>
-<span class="sd">    :param ignore_upstream_of_target: Don't draw upstream tasks of targets.</span>
-<span class="sd">    :param skip_uptodate_tasks: Don't draw up-to-date tasks if possible.</span>
-<span class="sd">    :param gnu_make_maximal_rebuild_mode: Defaults to re-running *all* out-of-date tasks. Runs minimal</span>
-<span class="sd">                                          set to build targets if set to ``True``. Use with caution.</span>
-<span class="sd">    :param test_all_task_for_update: Ask all task functions if they are up-to-date.</span>
-<span class="sd">    :param no_key_legend: Don't draw key/legend for graph.</span>
-<span class="sd">    :param checksum_level: Several options for checking up-to-dateness are available: Default is level 1.</span>
-<span class="sd">                    level 0 : Use only file timestamps</span>
-<span class="sd">                    level 1 : above, plus timestamp of successful job completion</span>
-<span class="sd">                    level 2 : above, plus a checksum of the pipeline function body</span>
-<span class="sd">                    level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</span>
-<span class="sd">    """</span>
-
-
-    <span class="k">if</span> <span class="n">checksum_level</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">checksum_level</span> <span class="o">=</span> <span class="n">get_default_checksum_level</span><span class="p">()</span>
-
-    <span class="n">link_task_names_to_functions</span> <span class="p">()</span>
-    <span class="n">update_checksum_level_on_tasks</span> <span class="p">(</span><span class="n">checksum_level</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c"># @active_if decorated tasks can change their active state every time</span>
-    <span class="c">#   pipeline_run / pipeline_printout / pipeline_printout_graph is called</span>
-    <span class="c">#</span>
-    <span class="n">update_active_states_for_all_tasks</span> <span class="p">()</span>
-
-    <span class="c">#</span>
-    <span class="c">#   run time data</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">runtime_data</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">runtime_data</span> <span class="o">=</span> <span class="p">{}</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"pipeline_run parameter runtime_data should be a dictionary of "</span>
-                        <span class="s">"values passes to jobs at run time."</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   If we aren't using checksums, and history file hasn't been specified,</span>
-    <span class="c">#       we might be a bit surprised to find Ruffus writing to a sqlite db anyway.</span>
-    <span class="c">#       Let us just use a in memory db which will be thrown away</span>
-    <span class="c">#   Of course, if history_file is specified, we presume you know what you are doing</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">checksum_level</span> <span class="o">==</span> <span class="n">CHECKSUM_FILE_TIMESTAMPS</span> <span class="ow">and</span> <span class="n">history_file</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">history_file</span> <span class="o">=</span> <span class="s">':memory:'</span>
-
-    <span class="c">#</span>
-    <span class="c"># load previous job history if it exists, otherwise create an empty history</span>
-    <span class="c">#</span>
-    <span class="n">job_history</span> <span class="o">=</span> <span class="n">open_job_history</span> <span class="p">(</span><span class="n">history_file</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   target jobs</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">target_tasks</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">target_tasks</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="k">if</span> <span class="n">forcedtorun_tasks</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">forcedtorun_tasks</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="n">target_tasks</span>        <span class="o">=</span> <span class="n">task_names_to_tasks</span> <span class="p">(</span><span class="s">"Target"</span><span class="p">,</span> <span class="n">target_tasks</span><span class="p">)</span>
-    <span class="n">forcedtorun_tasks</span>   <span class="o">=</span> <span class="n">task_names_to_tasks</span> <span class="p">(</span><span class="s">"Forced to run"</span><span class="p">,</span> <span class="n">forcedtorun_tasks</span><span class="p">)</span>
-
-
-    <span class="p">(</span><span class="n">topological_sorted</span><span class="p">,</span> <span class="n">ignore_param1</span><span class="p">,</span> <span class="n">ignore_param2</span><span class="p">,</span>
-         <span class="n">ignore_param3</span><span class="p">)</span> <span class="o">=</span> <span class="n">topologically_sorted_nodes</span><span class="p">(</span><span class="n">target_tasks</span><span class="p">,</span> <span class="n">forcedtorun_tasks</span><span class="p">,</span>
-                                                        <span class="n">gnu_make_maximal_rebuild_mode</span><span class="p">,</span>
-                                                        <span class="n">extra_data_for_signal</span> <span class="o">=</span> <span class="p">[</span><span class="n">t_verbose_logger</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">),</span> <span class="n">job_history</span><span class="p">])</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">target_tasks</span><span class="p">):</span>
-        <span class="n">target_tasks</span> <span class="o">=</span> <span class="n">topological_sorted</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">:]</span>
-
-
-
-    <span class="c"># open file if (unicode?) string</span>
-    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">stream</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">):</span>
-        <span class="n">stream</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">stream</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-    <span class="c"># derive format automatically from name</span>
-    <span class="k">if</span> <span class="n">output_format</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">output_format</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">stream</span><span class="o">.</span><span class="n">name</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lstrip</span><span class="p">(</span><span class="s">"."</span> [...]
-
-
-
-    <span class="n">graph_printout</span> <span class="p">(</span>  <span class="n">stream</span><span class="p">,</span>
-                      <span class="n">output_format</span><span class="p">,</span>
-                      <span class="n">target_tasks</span><span class="p">,</span>
-                      <span class="n">forcedtorun_tasks</span><span class="p">,</span>
-                      <span class="n">draw_vertically</span><span class="p">,</span>
-                      <span class="n">ignore_upstream_of_target</span><span class="p">,</span>
-                      <span class="n">skip_uptodate_tasks</span><span class="p">,</span>
-                      <span class="n">gnu_make_maximal_rebuild_mode</span><span class="p">,</span>
-                      <span class="n">test_all_task_for_update</span><span class="p">,</span>
-                      <span class="n">no_key_legend</span><span class="p">,</span>
-                      <span class="n">minimal_key_legend</span><span class="p">,</span>
-                      <span class="n">user_colour_scheme</span><span class="p">,</span>
-                      <span class="n">pipeline_name</span><span class="p">,</span>
-                      <span class="n">size</span><span class="p">,</span>
-                      <span class="n">dpi</span><span class="p">,</span>
-                      <span class="n">extra_data_for_signal</span> <span class="o">=</span> <span class="p">[</span><span class="n">t_verbose_logger</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">),</span> <span class="n">job_history</span><span class="p">])</span>
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   pipeline_printout</span>
-
-<span class="c">#_________________________________________________________________________________________</span></div>
-<div class="viewcode-block" id="pipeline_printout"><a class="viewcode-back" href="../../task.html#ruffus.task.pipeline_printout">[docs]</a><span class="k">def</span> <span class="nf">pipeline_printout</span><span class="p">(</span>  <span class="n">output_stream</span>                   <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                        <span class="n">target_tasks</span>                    <span class="o">=</span> <span class="p">[],</span>
-                        <span class="n">forcedtorun_tasks</span>               <span class="o">=</span> <span class="p">[],</span>
-                        <span class="n">verbose</span>                         <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
-                        <span class="n">indent</span>                          <span class="o">=</span> <span class="mi">4</span><span class="p">,</span>
-                        <span class="n">gnu_make_maximal_rebuild_mode</span>   <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
-                        <span class="n">wrap_width</span>                      <span class="o">=</span> <span class="mi">100</span><span class="p">,</span>
-                        <span class="n">runtime_data</span>                    <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                        <span class="n">checksum_level</span>                  <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                        <span class="n">history_file</span>                    <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
-                      <span class="c"># Remember to add further extra parameters here to "extra_pipeline_printout_options" inside cmdline.py</span>
-                      <span class="c"># This will forward extra parameters from the command line to pipeline_printout</span>
-    <span class="sd">"""</span>
-<span class="sd">    Printouts the parts of the pipeline which will be run</span>
-
-<span class="sd">    Because the parameters of some jobs depend on the results of previous tasks, this function</span>
-<span class="sd">    produces only the current snap-shot of task jobs. In particular, tasks which generate</span>
-<span class="sd">    variable number of inputs into following tasks will not produce the full range of jobs.</span>
-
-<span class="sd">    ::</span>
-
-<span class="sd">        verbose = 0 : nothing</span>
-<span class="sd">        verbose = 1 : print task name</span>
-<span class="sd">        verbose = 2 : print task description if exists</span>
-<span class="sd">        verbose = 3 : print job names for jobs to be run</span>
-<span class="sd">        verbose = 4 : print list of up-to-date tasks and job names for jobs to be run</span>
-<span class="sd">        verbose = 5 : print job names for all jobs whether up-to-date or not</span>
-
-<span class="sd">    :param output_stream: where to print to</span>
-<span class="sd">    :type output_stream: file-like object with ``write()`` function</span>
-<span class="sd">    :param target_tasks: targets task functions which will be run if they are out-of-date</span>
-<span class="sd">    :param forcedtorun_tasks: task functions which will be run whether or not they are out-of-date</span>
-<span class="sd">    :param verbose: level 0 : nothing</span>
-<span class="sd">                    level 1 : logs task names and warnings</span>
-<span class="sd">                    level 2 : logs task description if exists</span>
-<span class="sd">                    level 3 : logs job names for jobs to be run</span>
-<span class="sd">                    level 4 : logs list of up-to-date tasks and job names for jobs to be run</span>
-<span class="sd">                    level 5 : logs job names for all jobs whether up-to-date or not</span>
-<span class="sd">                    level 10: logs messages useful only for debugging ruffus pipeline code</span>
-<span class="sd">    :param indent: How much indentation for pretty format.</span>
-<span class="sd">    :param gnu_make_maximal_rebuild_mode: Defaults to re-running *all* out-of-date tasks. Runs minimal</span>
-<span class="sd">                                          set to build targets if set to ``True``. Use with caution.</span>
-<span class="sd">    :param wrap_width: The maximum length of each line</span>
-<span class="sd">    :param runtime_data: Experimental feature for passing data to tasks at run time</span>
-<span class="sd">    :param checksum_level: Several options for checking up-to-dateness are available: Default is level 1.</span>
-<span class="sd">                    level 0 : Use only file timestamps</span>
-<span class="sd">                    level 1 : above, plus timestamp of successful job completion</span>
-<span class="sd">                    level 2 : above, plus a checksum of the pipeline function body</span>
-<span class="sd">                    level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</span>
-<span class="sd">    """</span>
-    <span class="k">if</span> <span class="n">verbose</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-        <span class="k">return</span>
-
-    <span class="k">if</span> <span class="n">output_stream</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="kn">import</span> <span class="nn">sys</span>
-        <span class="n">output_stream</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span>
-
-
-    <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">output_stream</span><span class="p">,</span> <span class="s">"write"</span><span class="p">):</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"The first parameter to pipeline_printout needs to be an output file, e.g. sys.stdout and not </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">output_stream</span><span class="p">))</span>
-
-    <span class="k">if</span> <span class="n">runtime_data</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">runtime_data</span> <span class="o">=</span> <span class="p">{}</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"pipeline_run parameter runtime_data should be a dictionary of "</span>
-                        <span class="s">"values passes to jobs at run time."</span><span class="p">)</span>
-
-    <span class="k">if</span> <span class="n">checksum_level</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">checksum_level</span> <span class="o">=</span> <span class="n">get_default_checksum_level</span><span class="p">()</span>
-
-    <span class="n">link_task_names_to_functions</span> <span class="p">()</span>
-    <span class="n">update_checksum_level_on_tasks</span><span class="p">(</span><span class="n">checksum_level</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c"># @active_if decorated tasks can change their active state every time</span>
-    <span class="c">#   pipeline_run / pipeline_printout / pipeline_printout_graph is called</span>
-    <span class="c">#</span>
-    <span class="n">update_active_states_for_all_tasks</span> <span class="p">()</span>
-
-    <span class="c">#</span>
-    <span class="c">#   target jobs</span>
-    <span class="c">#</span>
-    <span class="n">target_tasks</span> <span class="o">=</span> <span class="n">task_names_to_tasks</span> <span class="p">(</span><span class="s">"Target"</span><span class="p">,</span> <span class="n">target_tasks</span><span class="p">)</span>
-    <span class="n">forcedtorun_tasks</span> <span class="o">=</span> <span class="n">task_names_to_tasks</span> <span class="p">(</span><span class="s">"Forced to run"</span><span class="p">,</span> <span class="n">forcedtorun_tasks</span><span class="p">)</span>
-
-    <span class="n">logging_strm</span> <span class="o">=</span> <span class="n">t_verbose_logger</span><span class="p">(</span><span class="n">verbose</span><span class="p">,</span> <span class="n">t_stream_logger</span><span class="p">(</span><span class="n">output_stream</span><span class="p">),</span> <span class="n">runtime_data</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   If we aren't using checksums, and history file hasn't been specified,</span>
-    <span class="c">#       we might be a bit surprised to find Ruffus writing to a sqlite db anyway.</span>
-    <span class="c">#       Let us just use a in memory db which will be thrown away</span>
-    <span class="c">#   Of course, if history_file is specified, we presume you know what you are doing</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">checksum_level</span> <span class="o">==</span> <span class="n">CHECKSUM_FILE_TIMESTAMPS</span> <span class="ow">and</span> <span class="n">history_file</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">history_file</span> <span class="o">=</span> <span class="s">':memory:'</span>
-
-    <span class="c">#</span>
-    <span class="c"># load previous job history if it exists, otherwise create an empty history</span>
-    <span class="c">#</span>
-    <span class="n">job_history</span> <span class="o">=</span> <span class="n">open_job_history</span> <span class="p">(</span><span class="n">history_file</span><span class="p">)</span>
-
-    <span class="p">(</span><span class="n">topological_sorted</span><span class="p">,</span>
-    <span class="n">self_terminated_nodes</span><span class="p">,</span>
-    <span class="n">dag_violating_edges</span><span class="p">,</span>
-    <span class="n">dag_violating_nodes</span><span class="p">)</span> <span class="o">=</span> <span class="n">topologically_sorted_nodes</span><span class="p">(</span><span class="n">target_tasks</span><span class="p">,</span> <span class="n">forcedtorun_tasks</span><span class="p">,</span>
-                                                        <span class="n">gnu_make_maximal_rebuild_mode</span><span class="p">,</span>
-                                                        <span class="n">extra_data_for_signal</span> <span class="o">=</span> <span class="p">[</span><span class="n">t_verbose_logger</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">),</span> <span class="n">job_history</span><span class="p">])</span>
-
-
-    <span class="c">#</span>
-    <span class="c">#   raise error if DAG violating nodes</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">dag_violating_nodes</span><span class="p">):</span>
-        <span class="n">dag_violating_tasks</span> <span class="o">=</span> <span class="s">", "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">_name</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">dag_violating_nodes</span><span class="p">)</span>
-
-        <span class="n">e</span> <span class="o">=</span> <span class="n">error_circular_dependencies</span><span class="p">(</span><span class="s">"Circular dependencies found in the "</span>
-                                        <span class="s">"pipeline involving one or more of (</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span>
-                                            <span class="p">(</span><span class="n">dag_violating_tasks</span><span class="p">))</span>
-        <span class="k">raise</span> <span class="n">e</span>
-
-    <span class="n">wrap_indent</span> <span class="o">=</span> <span class="s">" "</span> <span class="o">*</span> <span class="p">(</span><span class="n">indent</span> <span class="o">+</span> <span class="mi">11</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   Get updated nodes as all_nodes - nodes_to_run</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">verbose</span> <span class="o">>=</span> <span class="mi">4</span><span class="p">:</span>
-        <span class="p">(</span><span class="n">all_tasks</span><span class="p">,</span> <span class="n">ignore_param1</span><span class="p">,</span> <span class="n">ignore_param2</span><span class="p">,</span>
-         <span class="n">ignore_param3</span><span class="p">)</span> <span class="o">=</span> <span class="n">topologically_sorted_nodes</span><span class="p">(</span><span class="n">target_tasks</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span>
-                                                     <span class="n">gnu_make_maximal_rebuild_mode</span><span class="p">,</span>
-                                                     <span class="n">extra_data_for_signal</span> <span class="o">=</span> <span class="p">[</span><span class="n">t_verbose_logger</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">),</span> <span class="n">job_history</span><span class="p">])</span>
-
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">all_tasks</span><span class="p">)</span> <span class="o">></span> <span class="nb">len</span><span class="p">(</span><span class="n">topological_sorted</span><span class="p">):</span>
-            <span class="n">output_stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">Tasks which are up-to-date:</span><span class="se">\n\n</span><span class [...]
-            <span class="n">pipelined_tasks_to_run</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">topological_sorted</span><span class="p">)</span>
-
-            <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">all_tasks</span><span class="p">:</span>
-                <span class="k">if</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">pipelined_tasks_to_run</span><span class="p">:</span>
-                    <span class="k">continue</span>
-                <span class="n">messages</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">printout</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">,</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">forcedtorun_tasks</span><span class="p">,</span> <span class="n">job_history</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="n">indent</s [...]
-                <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">messages</span><span class="p">:</span>
-                    <span class="n">output_stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">textwrap</span><span class="o">.</span><span class="n">fill</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">subsequent_indent</span> <span class="o">=</span> <span class="n">wrap_indent</span><span class="p">,</span> <span class="n">width</span> <span class="o">=</span> <span class="n">wrap_width [...]
-
-    <span class="n">output_stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span> <span class="o">+</span> <span class="s">"_"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">Tasks which will be run:</span><span class="se">\n\n</span><span class="s">" [...]
-    <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">topological_sorted</span><span class="p">:</span>
-        <span class="n">messages</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">printout</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">,</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">forcedtorun_tasks</span><span class="p">,</span> <span class="n">job_history</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="n">indent</span><spa [...]
-        <span class="k">for</span> <span class="n">m</span> <span class="ow">in</span> <span class="n">messages</span><span class="p">:</span>
-            <span class="n">output_stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">textwrap</span><span class="o">.</span><span class="n">fill</span><span class="p">(</span><span class="n">m</span><span class="p">,</span> <span class="n">subsequent_indent</span> <span class="o">=</span> <span class="n">wrap_indent</span><span class="p">,</span> <span class="n">width</span> <span class="o">=</span> <span class="n">wrap_width</span>< [...]
-
-    <span class="k">if</span> <span class="n">verbose</span><span class="p">:</span>
-        <span class="n">output_stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"_"</span> <span class="o">*</span> <span class="mi">40</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   get_semaphore</span>
-
-<span class="c">#_________________________________________________________________________________________</span></div>
-<span class="k">def</span> <span class="nf">get_semaphore</span> <span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="n">job_limit_semaphores</span><span class="p">,</span> <span class="n">syncmanager</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    return semaphore to limit the number of concurrent jobs</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   Is this task limited in the number of jobs?</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">semaphore_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">t</span><span class="o">.</span><span class="n">job_limit_semaphores</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">None</span>
-
-
-    <span class="c">#</span>
-    <span class="c">#   create semaphore if not yet created</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">semaphore_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">job_limit_semaphores</span><span class="p">:</span>
-        <span class="n">maximum_jobs_num</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">job_limit_semaphores</span><span class="p">[</span><span class="n">t</span><span class="o">.</span><span class="n">semaphore_name</span><span class="p">]</span>
-        <span class="n">job_limit_semaphores</span><span class="p">[</span><span class="n">t</span><span class="o">.</span><span class="n">semaphore_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">syncmanager</span><span class="o">.</span><span class="n">BoundedSemaphore</span><span class="p">(</span><span class="n">maximum_jobs_num</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">job_limit_semaphores</span><span class="p">[</span><span class="n">t</span><span class="o">.</span><span class="n">semaphore_name</span><span class="p">]</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   Parameter generator for all jobs / tasks</span>
-<span class="c">#</span>
-<span class="c">#________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">make_job_parameter_generator</span> <span class="p">(</span><span class="n">incomplete_tasks</span><span class="p">,</span> <span class="n">task_parents</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">forcedtorun_tasks</span><span class="p">,</span>
-                                    <span class="n">task_with_completed_job_q</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span>
-                                    <span class="n">syncmanager</span><span class="p">,</span>
-                                    <span class="n">touch_files_only</span><span class="p">,</span> <span class="n">job_history</span><span class="p">):</span>
-
-    <span class="n">inprogress_tasks</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-    <span class="n">job_limit_semaphores</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
-
-    <span class="k">def</span> <span class="nf">parameter_generator</span><span class="p">():</span>
-        <span class="n">count_remaining_jobs</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span>
-        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   job_parameter_generator BEGIN"</span><span class="p">)</span>
-        <span class="k">while</span> <span class="nb">len</span><span class="p">(</span><span class="n">incomplete_tasks</span><span class="p">):</span>
-            <span class="n">cnt_jobs_created_for_all_tasks</span> <span class="o">=</span> <span class="mi">0</span>
-            <span class="n">cnt_tasks_processed</span> <span class="o">=</span> <span class="mi">0</span>
-
-            <span class="c">#</span>
-            <span class="c">#   get rid of all completed tasks first</span>
-            <span class="c">#       Completion is signalled from pipeline_run</span>
-            <span class="c">#</span>
-            <span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
-                <span class="k">try</span><span class="p">:</span>
-                    <span class="n">item</span> <span class="o">=</span> <span class="n">task_with_completed_job_q</span><span class="o">.</span><span class="n">get_nowait</span><span class="p">()</span>
-                    <span class="n">job_completed_task</span><span class="p">,</span> <span class="n">job_completed_task_name</span><span class="p">,</span> <span class="n">job_completed_name</span> <span class="o">=</span> <span class="n">item</span>
-
-
-                    <span class="k">if</span> <span class="ow">not</span> <span class="n">job_completed_task</span> <span class="ow">in</span> <span class="n">incomplete_tasks</span><span class="p">:</span>
-                        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Last job </span><span class="si">%s</span><span class="s"> for </span><span class="si">%s</span><span class="s">. Missing from incomplete tasks in make_job_parameter_generator"</span> <span class="o">%</span> <span class="p">(</span><span class="n">job_completed_name</span><span class="p">,</span> <span class="n">job_completed_task_name</span><span clas [...]
-                    <span class="n">count_remaining_jobs</span><span class="p">[</span><span class="n">job_completed_task</span><span class="p">]</span> <span class="o">=</span> <span class="n">count_remaining_jobs</span><span class="p">[</span><span class="n">job_completed_task</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span>
-                    <span class="c">#</span>
-                    <span class="c">#   This is bad: something has gone very wrong</span>
-                    <span class="c">#</span>
-                    <span class="k">if</span> <span class="n">count_remaining_jobs</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
-                        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"job </span><span class="si">%s</span><span class="s"> for </span><span class="si">%s</span><span class="s"> causes job count < 0."</span> <span class="o">%</span> <span class="p">(</span><span class="n">job_completed_name</span><span class="p">,</span> <span class="n">job_completed_task_name</span><span class="p">))</span>
-
-                    <span class="c">#</span>
-                    <span class="c">#   This Task completed</span>
-                    <span class="c">#</span>
-                    <span class="k">if</span> <span class="n">count_remaining_jobs</span><span class="p">[</span><span class="n">job_completed_task</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-                        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Last job for </span><span class="si">%s</span><span class="s">. Retired from incomplete tasks in pipeline_run "</span> <span class="o">%</span> <span class="n">job_completed_task</span><span class="o">.</span><span cla [...]
-                        <span class="n">incomplete_tasks</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">job_completed_task</span><span class="p">)</span>
-                        <span class="n">job_completed_task</span><span class="o">.</span><span class="n">completed</span> <span class="p">(</span><span class="n">logger</span><span class="p">)</span>
-                <span class="k">except</span> <span class="n">Queue</span><span class="o">.</span><span class="n">Empty</span><span class="p">:</span>
-                    <span class="k">break</span>
-
-            <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">incomplete_tasks</span><span class="p">):</span>
-                <span class="c">#</span>
-                <span class="c">#   wrap in execption handler so that we know which task exception</span>
-                <span class="c">#       came from</span>
-                <span class="c">#</span>
-                <span class="k">try</span><span class="p">:</span>
-                    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   job_parameter_generator consider task = </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">t</span><span class="o">.</span><span class="n">_name</span><span class="p">)</span>
-
-                    <span class="c"># ignore tasks in progress</span>
-                    <span class="k">if</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">inprogress_tasks</span><span class="p">:</span>
-                        <span class="k">continue</span>
-                    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   job_parameter_generator task </span><span class="si">%s</span><span class="s"> not in progress"</span> <span class="o">%</span> <span class="n">t</span><span class="o">.</span><span class="n">_name</span><span class="p">)</span>
-
-                    <span class="c"># ignore tasks with incomplete dependencies</span>
-                    <span class="n">incomplete_parent</span> <span class="o">=</span> <span class="bp">False</span>
-                    <span class="k">for</span> <span class="n">parent</span> <span class="ow">in</span> <span class="n">task_parents</span><span class="p">[</span><span class="n">t</span><span class="p">]:</span>
-                        <span class="k">if</span> <span class="n">parent</span> <span class="ow">in</span> <span class="n">incomplete_tasks</span><span class="p">:</span>
-                            <span class="n">incomplete_parent</span> <span class="o">=</span> <span class="bp">True</span>
-                            <span class="k">break</span>
-                    <span class="k">if</span> <span class="n">incomplete_parent</span><span class="p">:</span>
-                        <span class="k">continue</span>
-
-                    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   job_parameter_generator start task </span><span class="si">%s</span><span class="s"> (parents completed)"</span> <span class="o">%</span> <span class="n">t</span><span class="o">.</span><span class="n">_name</span><span cl [...]
-                    <span class="n">force_rerun</span> <span class="o">=</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">forcedtorun_tasks</span>
-                    <span class="c">#</span>
-                    <span class="c"># Only log active task</span>
-                    <span class="c">#</span>
-                    <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">is_active</span><span class="p">:</span>
-                        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"Task enters queue = "</span> <span class="o">+</span> <span class="n">t</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">()</span> <span class="o">+</span> <span class="p">(</span><span cla [...]
-                        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="n">t</span><span class="o">.</span><span class="n">_description</span><span class="p">)</span>
-                    <span class="n">inprogress_tasks</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
-                    <span class="n">cnt_tasks_processed</span> <span class="o">+=</span> <span class="mi">1</span>
-
-
-                    <span class="c">#</span>
-                    <span class="c">#   Use output parameters actually generated by running task</span>
-                    <span class="c">#</span>
-                    <span class="n">t</span><span class="o">.</span><span class="n">output_filenames</span> <span class="o">=</span> <span class="p">[]</span>
-
-
-
-                    <span class="c">#</span>
-                    <span class="c">#   If no parameters: just call task function (empty list)</span>
-                    <span class="c">#</span>
-                    <span class="c">#if (t.active_if_checks != None):</span>
-                    <span class="c">#    t.is_active = all(arg() if isinstance(arg, collections.Callable) else arg</span>
-                    <span class="c">#                        for arg in t.active_if_checks)</span>
-                    <span class="k">if</span> <span class="ow">not</span> <span class="n">t</span><span class="o">.</span><span class="n">is_active</span><span class="p">:</span>
-                        <span class="n">parameters</span> <span class="o">=</span> <span class="p">[]</span>
-
-
-
-                    <span class="c">#</span>
-                    <span class="c">#   If no parameters: just call task function (empty list)</span>
-                    <span class="c">#</span>
-                    <span class="k">elif</span> <span class="n">t</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-                        <span class="n">parameters</span> <span class="o">=</span> <span class="p">([[],</span> <span class="p">[]],)</span>
-                    <span class="k">else</span><span class="p">:</span>
-                        <span class="n">parameters</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">param_generator_func</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">)</span>
-
-                    <span class="c">#</span>
-                    <span class="c">#   iterate through parameters</span>
-                    <span class="c">#</span>
-                    <span class="n">cnt_jobs_created</span> <span class="o">=</span> <span class="mi">0</span>
-                    <span class="k">for</span> <span class="n">param</span><span class="p">,</span> <span class="n">descriptive_param</span> <span class="ow">in</span> <span class="n">parameters</span><span class="p">:</span>
-
-                        <span class="c">#</span>
-                        <span class="c">#   save output even if uptodate</span>
-                        <span class="c">#</span>
-                        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">param</span><span class="p">)</span> <span class="o">>=</span> <span class="mi">2</span><span class="p">:</span>
-                            <span class="n">t</span><span class="o">.</span><span class="n">output_filenames</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-
-                        <span class="n">job_name</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">get_job_name</span><span class="p">(</span><span class="n">descriptive_param</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">)</span>
-
-                        <span class="c">#</span>
-                        <span class="c">#    don't run if up to date unless force to run</span>
-                        <span class="c">#</span>
-                        <span class="k">if</span> <span class="n">force_rerun</span><span class="p">:</span>
-                            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    force task </span><span class="si">%s</span><span class="s"> to rerun "</span> <span class="o">%</span> <span class="n">job_name</span><span class="p">)</span>
-                        <span class="k">else</span><span class="p">:</span>
-                            <span class="k">if</span> <span class="ow">not</span> <span class="n">t</span><span class="o">.</span><span class="n">needs_update_func</span><span class="p">:</span>
-                                <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    </span><span class="si">%s</span><span class="s"> no function to check if up-to-date "</span> <span class="o">%</span> <span class="n">job_name</span><span class="p">)</span>
-                            <span class="k">else</span><span class="p">:</span>
-                                <span class="c"># extra clunky hack to also pass task info--</span>
-                                <span class="c"># makes sure that there haven't been code or arg changes</span>
-                                <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="o">==</span> <span class="n">needs_update_check_modify_time</span><span class="p">:</span>
-                                    <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">,</span> <span class="n">task</span><span class="o">=</span><span class="n">t</span><span class="p">,</span> <span class="n">job_history</span> <span class="o">=</ [...]
-                                <span class="k">else</span><span class="p">:</span>
-                                    <span class="n">needs_update</span><span class="p">,</span> <span class="n">msg</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">)</span>
-
-                                <span class="k">if</span> <span class="ow">not</span> <span class="n">needs_update</span><span class="p">:</span>
-                                    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    </span><span class="si">%s</span><span class="s"> unnecessary: already up to date "</span> <span class="o">%</span> <span class="n">job_name</span><span class="p">)</span>
-                                    <span class="k">continue</span>
-                                <span class="k">else</span><span class="p">:</span>
-                                    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> "</span> <span class="o">%</span> <span class="p">(</span><span class="n">job_name</span><span class="p">, [...]
-
-                        <span class="c">#</span>
-                        <span class="c">#   Clunky hack to make sure input files exists right before</span>
-                        <span class="c">#        job is called for better error messages</span>
-                        <span class="c">#</span>
-                        <span class="k">if</span> <span class="n">t</span><span class="o">.</span><span class="n">needs_update_func</span> <span class="o">==</span> <span class="n">needs_update_check_modify_time</span><span class="p">:</span>
-                            <span class="n">check_input_files_exist</span> <span class="p">(</span><span class="o">*</span><span class="n">param</span><span class="p">)</span>
-
-                        <span class="c"># pause for one second before first job of each tasks</span>
-                        <span class="c"># @originate tasks do not need to pause, because they depend on nothing!</span>
-                        <span class="k">if</span> <span class="n">cnt_jobs_created</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">touch_files_only</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span>
-                            <span class="k">if</span> <span class="s">"ONE_SECOND_PER_JOB"</span> <span class="ow">in</span> <span class="n">runtime_data</span> <span class="ow">and</span> <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ONE_SECOND_PER_JOB"</span><span class="p">]</span> <span class="ow">and</span> <span class="n">t</span><span class="o">.</span><span class="n">_action_type</span> <span class="o">!=</span> <span class="n">_t [...]
-                                <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   1 second PAUSE in job_parameter_generator</span><span class="se">\n\n\n</span><span class="s">"</span><span class="p">)</span>
-                                <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mf">1.01</span><span class="p">)</span>
-                            <span class="k">else</span><span class="p">:</span>
-                                <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mf">0.1</span><span class="p">)</span>
-
-
-                        <span class="n">count_remaining_jobs</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
-                        <span class="n">cnt_jobs_created</span> <span class="o">+=</span> <span class="mi">1</span>
-                        <span class="n">cnt_jobs_created_for_all_tasks</span> <span class="o">+=</span> <span class="mi">1</span>
-                        <span class="k">yield</span> <span class="p">(</span><span class="n">param</span><span class="p">,</span>
-                                <span class="n">t</span><span class="o">.</span><span class="n">_name</span><span class="p">,</span>
-                                <span class="n">job_name</span><span class="p">,</span>
-                                <span class="n">t</span><span class="o">.</span><span class="n">job_wrapper</span><span class="p">,</span>
-                                <span class="n">t</span><span class="o">.</span><span class="n">user_defined_work_func</span><span class="p">,</span>
-                                <span class="n">get_semaphore</span> <span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="n">job_limit_semaphores</span><span class="p">,</span> <span class="n">syncmanager</span><span class="p">),</span>
-                                <span class="n">touch_files_only</span><span class="p">)</span>
-
-                    <span class="c"># if no job came from this task, this task is complete</span>
-                    <span class="c">#   we need to retire it here instead of normal completion at end of job tasks</span>
-                    <span class="c">#   precisely because it created no jobs</span>
-                    <span class="k">if</span> <span class="n">cnt_jobs_created</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-                        <span class="n">incomplete_tasks</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
-                        <span class="n">t</span><span class="o">.</span><span class="n">completed</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
-                        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   No jobs created for </span><span class="si">%s</span><span class="s">. Retired in parameter_generator "</span> <span class="o">%</span> <span class="n">t</span><span class="o">.</span><span class="n">_name</span><span  [...]
-
-                        <span class="c">#</span>
-                        <span class="c">#   Add extra warning if no regular expressions match:</span>
-                        <span class="c">#   This is a common class of frustrating errors</span>
-                        <span class="c">#</span>
-                        <span class="k">if</span> <span class="p">(</span><span class="n">verbose</span> <span class="o">>=</span> <span class="mi">1</span> <span class="ow">and</span> <span class="s">"ruffus_WARNING"</span> <span class="ow">in</span> <span class="n">runtime_data</span> <span class="ow">and</span>
-                            <span class="n">t</span><span class="o">.</span><span class="n">param_generator_func</span> <span class="ow">in</span> <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ruffus_WARNING"</span><span class="p">]):</span>
-                            <span class="k">for</span> <span class="n">msg</span> <span class="ow">in</span> <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ruffus_WARNING"</span><span class="p">][</span><span class="n">t</span><span class="o">.</span><span class="n">param_generator_func</span><span class="p">]:</span>
-                                <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s">"    'In Task def </span><span class="si">%s</span><span class="s">(...):' </span><span class="si">%s</span><span class="s"> "</span> <span class="o">%</span> <span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">get_task_name</span><span class="p">(),</span> <span class="n">msg</span [...]
-
-
-                <span class="c">#</span>
-                <span class="c">#   GeneratorExit is thrown when this generator does not complete.</span>
-                <span class="c">#       I.e. there is a break in the pipeline_run loop.</span>
-                <span class="c">#       This happens where there are exceptions signalled from within a job</span>
-                <span class="c">#</span>
-                <span class="c">#   This is not really an exception, more a way to exit the generator loop</span>
-                <span class="c">#       asynchrononously so that cleanups can happen (e.g. the "with" statement</span>
-                <span class="c">#       or finally.)</span>
-                <span class="c">#</span>
-                <span class="c">#   We could write except Exception: below which will catch everything but</span>
-                <span class="c">#       KeyboardInterrupt and StopIteration and GeneratorExit in python 2.6</span>
-                <span class="c">#</span>
-                <span class="c">#   However, in python 2.5, GeneratorExit inherits from Exception. So</span>
-                <span class="c">#       we explicitly catch and rethrow GeneratorExit.</span>
-                <span class="k">except</span> <span class="ne">GeneratorExit</span><span class="p">:</span>
-                    <span class="k">raise</span>
-                <span class="k">except</span><span class="p">:</span>
-                    <span class="n">exceptionType</span><span class="p">,</span> <span class="n">exceptionValue</span><span class="p">,</span> <span class="n">exceptionTraceback</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">exc_info</span><span class="p">()</span>
-                    <span class="n">exception_stack</span>  <span class="o">=</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">(</span><span class="n">exceptionTraceback</span><span class="p">)</span>
-                    <span class="n">exception_name</span>   <span class="o">=</span> <span class="n">exceptionType</span><span class="o">.</span><span class="n">__module__</span> <span class="o">+</span> <span class="s">'.'</span> <span class="o">+</span> <span class="n">exceptionType</span><span class="o">.</span><span class="n">__name__</span>
-                    <span class="n">exception_value</span>  <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">exceptionValue</span><span class="p">)</span>
-                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">exception_value</span><span class="p">):</span>
-                        <span class="n">exception_value</span> <span class="o">=</span> <span class="s">"(</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="n">exception_value</span>
-                    <span class="n">errt</span> <span class="o">=</span> <span class="n">RethrownJobError</span><span class="p">([(</span><span class="n">t</span><span class="o">.</span><span class="n">_name</span><span class="p">,</span>
-                                             <span class="s">""</span><span class="p">,</span>
-                                             <span class="n">exception_name</span><span class="p">,</span>
-                                             <span class="n">exception_value</span><span class="p">,</span>
-                                             <span class="n">exception_stack</span><span class="p">)])</span>
-                    <span class="n">errt</span><span class="o">.</span><span class="n">specify_task</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="s">"Exceptions generating parameters"</span><span class="p">)</span>
-                    <span class="k">raise</span> <span class="n">errt</span>
-
-
-
-            <span class="c"># extra tests incase final tasks do not result in jobs</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">incomplete_tasks</span><span class="p">)</span> <span class="ow">and</span> <span class="p">(</span><span class="ow">not</span> <span class="n">cnt_tasks_processed</span> <span class="ow">or</span> <span class="n">cnt_jobs_created_for_all_tasks</span><span class="p">):</span>
-                <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    incomplete tasks = "</span> <span class="o">+</span>
-                                       <span class="s">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">t</span><span class="o">.</span><span class="n">_name</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">incomplete_tasks</span><span class="p">]</span> <span class="p">))</span>
-                <span class="k">yield</span> <span class="n">waiting_for_more_tasks_to_complete</span><span class="p">()</span>
-
-        <span class="k">yield</span> <span class="n">all_tasks_complete</span><span class="p">()</span>
-        <span class="c"># This function is done</span>
-        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   job_parameter_generator END"</span><span class="p">)</span>
-
-    <span class="k">return</span> <span class="n">parameter_generator</span>
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   feed_job_params_to_process_pool</span>
-<span class="c">#</span>
-<span class="c">#</span>
-<span class="c">#________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">feed_job_params_to_process_pool_factory</span> <span class="p">(</span><span class="n">parameter_q</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">verbose</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Process pool gets its parameters from this generator</span>
-<span class="sd">    Use factory function to save parameter_queue</span>
-<span class="sd">    """</span>
-    <span class="k">def</span> <span class="nf">feed_job_params_to_process_pool</span> <span class="p">():</span>
-        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Send param to Pooled Process START"</span><span class="p">)</span>
-        <span class="k">while</span> <span class="mi">1</span><span class="p">:</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Get next parameter size = </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span>
-                                                        <span class="n">parameter_q</span><span class="o">.</span><span class="n">qsize</span><span class="p">())</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="n">parameter_q</span><span class="o">.</span><span class="n">qsize</span><span class="p">():</span>
-                <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mf">0.1</span><span class="p">)</span>
-            <span class="n">param</span> <span class="o">=</span> <span class="n">parameter_q</span><span class="o">.</span><span class="n">get</span><span class="p">()</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Get next parameter done"</span><span class="p">)</span>
-
-            <span class="c"># all tasks done</span>
-            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">all_tasks_complete</span><span class="p">):</span>
-                <span class="k">break</span>
-
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Send param to Pooled Process=>"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
-            <span class="k">yield</span> <span class="n">param</span>
-
-        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Send param to Pooled Process END"</span><span class="p">)</span>
-
-    <span class="c"># return generator</span>
-    <span class="k">return</span> <span class="n">feed_job_params_to_process_pool</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   fill_queue_with_job_parameters</span>
-<span class="c">#</span>
-<span class="c">#________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">fill_queue_with_job_parameters</span> <span class="p">(</span><span class="n">job_parameters</span><span class="p">,</span> <span class="n">parameter_q</span><span class="p">,</span> <span class="n">POOL_SIZE</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">verbose</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Ensures queue is filled with number of parameters > jobs / slots (POOL_SIZE)</span>
-<span class="sd">    """</span>
-    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    fill_queue_with_job_parameters START"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">param</span> <span class="ow">in</span> <span class="n">job_parameters</span><span class="p">:</span>
-
-        <span class="c"># stop if no more jobs available</span>
-        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">waiting_for_more_tasks_to_complete</span><span class="p">):</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    fill_queue_with_job_parameters WAITING for task to complete"</span><span class="p">)</span>
-            <span class="k">break</span>
-
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">param</span><span class="p">,</span> <span class="n">all_tasks_complete</span><span class="p">):</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    fill_queue_with_job_parameters=>"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">param</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
-
-        <span class="c"># put into queue</span>
-        <span class="n">parameter_q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">param</span><span class="p">)</span>
-
-        <span class="c"># queue size needs to be at least 2 so that the parameter queue never consists of a single</span>
-        <span class="c">#   waiting_for_task_to_complete entry which will cause</span>
-        <span class="c">#   a loop and everything to hang!</span>
-        <span class="k">if</span> <span class="n">parameter_q</span><span class="o">.</span><span class="n">qsize</span><span class="p">()</span> <span class="o">></span> <span class="n">POOL_SIZE</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span>
-            <span class="k">break</span>
-    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"    fill_queue_with_job_parameters END"</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   How the job queue works:</span>
-<span class="c">#</span>
-<span class="c">#   Main loop</span>
-<span class="c">#       iterates pool.map using feed_job_params_to_process_pool()</span>
-<span class="c">#       (calls parameter_q.get() until all_tasks_complete)</span>
-<span class="c">#</span>
-<span class="c">#           if errors but want to finish tasks already in pipeine:</span>
-<span class="c">#               parameter_q.put(all_tasks_complete())</span>
-<span class="c">#               keep going</span>
-<span class="c">#        else:</span>
-<span class="c">#</span>
-<span class="c">#            loops through jobs until no more jobs in non-dependent tasks</span>
-<span class="c">#               separate loop in generator so that list of incomplete_tasks does not</span>
-<span class="c">#               get updated half way through</span>
-<span class="c">#               causing race conditions</span>
-<span class="c">#</span>
-<span class="c">#               parameter_q.put(param)</span>
-<span class="c">#               until waiting_for_more_tasks_to_complete</span>
-<span class="c">#               until queue is full (check *after*)</span>
-<span class="c">#</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#   pipeline_run</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<div class="viewcode-block" id="pipeline_run"><a class="viewcode-back" href="../../task.html#ruffus.task.pipeline_run">[docs]</a><span class="k">def</span> <span class="nf">pipeline_run</span><span class="p">(</span><span class="n">target_tasks</span>                     <span class="o">=</span> <span class="p">[],</span>
-                 <span class="n">forcedtorun_tasks</span>                <span class="o">=</span> <span class="p">[],</span>
-                 <span class="n">multiprocess</span>                     <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
-                 <span class="n">logger</span>                           <span class="o">=</span> <span class="n">stderr_logger</span><span class="p">,</span>
-                 <span class="n">gnu_make_maximal_rebuild_mode</span>    <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
-                 <span class="n">verbose</span>                          <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
-                 <span class="n">runtime_data</span>                     <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                 <span class="n">one_second_per_job</span>               <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                 <span class="n">touch_files_only</span>                 <span class="o">=</span> <span class="bp">False</span><span class="p">,</span>
-                 <span class="n">exceptions_terminate_immediately</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span>
-                 <span class="n">log_exceptions</span>                   <span class="o">=</span> <span class="bp">False</span><span class="p">,</span>
-                 <span class="n">checksum_level</span>                   <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
-                 <span class="n">multithread</span>                      <span class="o">=</span> <span class="mi">0</span><span class="p">,</span>
-                 <span class="n">history_file</span>                     <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
-                 <span class="c"># Remember to add further extra parameters here to "extra_pipeline_run_options" inside cmdline.py</span>
-                 <span class="c"># This will forward extra parameters from the command line to pipeline_run</span>
-    <span class="sd">"""</span>
-<span class="sd">    Run pipelines.</span>
-
-<span class="sd">    :param target_tasks: targets task functions which will be run if they are out-of-date</span>
-<span class="sd">    :param forcedtorun_tasks: task functions which will be run whether or not they are out-of-date</span>
-<span class="sd">    :param multiprocess: The number of concurrent jobs running on different processes.</span>
-<span class="sd">    :param multithread: The number of concurrent jobs running as different threads. If > 1, ruffus will use multithreading *instead of* multiprocessing (and ignore the multiprocess parameter). Using multi threading is particularly useful to manage high performance clusters which otherwise are prone to "processor storms" when large number of cores finish jobs at the same time. (Thanks Andreas Heger)</span>
-<span class="sd">    :param logger: Where progress will be logged. Defaults to stderr output.</span>
-<span class="sd">    :type logger: `logging <http://docs.python.org/library/logging.html>`_ objects</span>
-<span class="sd">    :param verbose: level 0 : nothing</span>
-<span class="sd">                    level 1 : logs task names and warnings</span>
-<span class="sd">                    level 2 : logs task description if exists</span>
-<span class="sd">                    level 3 : logs job names for jobs to be run</span>
-<span class="sd">                    level 4 : logs list of up-to-date tasks and job names for jobs to be run</span>
-<span class="sd">                    level 5 : logs job names for all jobs whether up-to-date or not</span>
-<span class="sd">                    level 10: logs messages useful only for debugging ruffus pipeline code</span>
-<span class="sd">    :param touch_files_only: Create or update input/output files only to simulate running the pipeline. Do not run jobs. If set to CHECKSUM_REGENERATE, will regenerate the checksum history file to reflect the existing i/o files on disk.</span>
-<span class="sd">    :param exceptions_terminate_immediately: Exceptions cause immediate termination</span>
-<span class="sd">                        rather than waiting for N jobs to finish where N = multiprocess</span>
-<span class="sd">    :param log_exceptions: Print exceptions to the logger as soon as they occur.</span>
-<span class="sd">    :param checksum_level: Several options for checking up-to-dateness are available: Default is level 1.</span>
-<span class="sd">                           level 0 : Use only file timestamps</span>
-<span class="sd">                           level 1 : above, plus timestamp of successful job completion</span>
-<span class="sd">                           level 2 : above, plus a checksum of the pipeline function body</span>
-<span class="sd">                           level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</span>
-<span class="sd">    :param history_file: The database file which stores checksums and file timestamps for input/output files.</span>
-<span class="sd">    :param one_second_per_job: To work around poor file timepstamp resolution for some file systems. Defaults to True if checksum_level is 0 forcing Tasks to take a minimum of 1 second to complete.</span>
-<span class="sd">    :param runtime_data: Experimental feature for passing data to tasks at run time</span>
-<span class="sd">    :param gnu_make_maximal_rebuild_mode: Defaults to re-running *all* out-of-date tasks. Runs minimal</span>
-<span class="sd">                                          set to build targets if set to ``True``. Use with caution.</span>
-<span class="sd">    """</span>
-    <span class="k">if</span> <span class="n">touch_files_only</span> <span class="o">==</span> <span class="bp">False</span><span class="p">:</span>
-        <span class="n">touch_files_only</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">elif</span> <span class="n">touch_files_only</span> <span class="o">==</span> <span class="bp">True</span><span class="p">:</span>
-        <span class="n">touch_files_only</span> <span class="o">=</span> <span class="mi">1</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">touch_files_only</span> <span class="o">=</span> <span class="mi">2</span>
-        <span class="c"># we are not running anything so do it as quickly as possible</span>
-        <span class="n">one_second_per_job</span> <span class="o">=</span> <span class="bp">False</span>
-
-    <span class="n">syncmanager</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Manager</span><span class="p">()</span>
-
-    <span class="k">if</span> <span class="n">runtime_data</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">runtime_data</span> <span class="o">=</span> <span class="p">{}</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">runtime_data</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"pipeline_run parameter runtime_data should be a dictionary of "</span>
-                        <span class="s">"values passes to jobs at run time."</span><span class="p">)</span>
-
-
-    <span class="c">#</span>
-    <span class="c">#   whether using multiprocessing or multithreading</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">multithread</span><span class="p">:</span>
-        <span class="n">pool</span> <span class="o">=</span> <span class="n">ThreadPool</span><span class="p">(</span><span class="n">multithread</span><span class="p">)</span>
-        <span class="n">parallelism</span> <span class="o">=</span> <span class="n">multithread</span>
-    <span class="k">elif</span> <span class="n">multiprocess</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
-        <span class="n">pool</span> <span class="o">=</span> <span class="n">Pool</span><span class="p">(</span><span class="n">multiprocess</span><span class="p">)</span>
-        <span class="n">parallelism</span> <span class="o">=</span> <span class="n">multiprocess</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">parallelism</span> <span class="o">=</span> <span class="mi">1</span>
-        <span class="n">pool</span> <span class="o">=</span> <span class="bp">None</span>
-
-    <span class="k">if</span> <span class="n">checksum_level</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">checksum_level</span> <span class="o">=</span> <span class="n">get_default_checksum_level</span><span class="p">()</span>
-
-    <span class="c">#</span>
-    <span class="c">#   Supplement mtime with system clock if using CHECKSUM_HISTORY_TIMESTAMPS</span>
-    <span class="c">#       we don't need to default to adding 1 second delays between jobs</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">one_second_per_job</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-         <span class="k">if</span> <span class="n">checksum_level</span> <span class="o">==</span> <span class="n">CHECKSUM_FILE_TIMESTAMPS</span><span class="p">:</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Checksums rely on FILE TIMESTAMPS only and we don't know if the system file time resolution: Pause 1 second..."</span><span class="p">)</span>
-            <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ONE_SECOND_PER_JOB"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
-         <span class="k">else</span><span class="p">:</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Checksum use calculated time as well: No 1 second pause..."</span><span class="p">)</span>
-            <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ONE_SECOND_PER_JOB"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">False</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   One second per job specified to be </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">one_second_per_job</span><span class="p">)</span>
-        <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ONE_SECOND_PER_JOB"</span><span class="p">]</span> <span class="o">=</span> <span class="n">one_second_per_job</span>
-
-
-    <span class="k">if</span> <span class="n">verbose</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-        <span class="n">logger</span> <span class="o">=</span> <span class="n">black_hole_logger</span>
-    <span class="k">elif</span> <span class="n">verbose</span> <span class="o">>=</span> <span class="mi">11</span><span class="p">:</span>
-        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="s">"add_unique_prefix"</span><span class="p">):</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">add_unique_prefix</span><span class="p">()</span>
-
-    <span class="k">if</span> <span class="n">touch_files_only</span> <span class="ow">and</span> <span class="n">verbose</span> <span class="o">>=</span> <span class="mi">1</span><span class="p">:</span>
-        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"Touch output files instead of remaking them."</span><span class="p">)</span>
-
-    <span class="n">link_task_names_to_functions</span> <span class="p">()</span>
-    <span class="n">update_checksum_level_on_tasks</span> <span class="p">(</span><span class="n">checksum_level</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   If we aren't using checksums, and history file hasn't been specified,</span>
-    <span class="c">#       we might be a bit surprised to find Ruffus writing to a sqlite db anyway.</span>
-    <span class="c">#       Let us just use a in-memory db which will be thrown away</span>
-    <span class="c">#   Of course, if history_file is specified, we presume you know what you are doing</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">checksum_level</span> <span class="o">==</span> <span class="n">CHECKSUM_FILE_TIMESTAMPS</span> <span class="ow">and</span> <span class="n">history_file</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">history_file</span> <span class="o">=</span> <span class="s">':memory:'</span>
-
-    <span class="n">job_history</span> <span class="o">=</span> <span class="n">open_job_history</span> <span class="p">(</span><span class="n">history_file</span><span class="p">)</span>
-
-
-
-
-    <span class="c">#</span>
-    <span class="c"># @active_if decorated tasks can change their active state every time</span>
-    <span class="c">#   pipeline_run / pipeline_printout / pipeline_printout_graph is called</span>
-    <span class="c">#</span>
-    <span class="n">update_active_states_for_all_tasks</span> <span class="p">()</span>
-
-
-    <span class="c">#</span>
-    <span class="c">#   target jobs</span>
-    <span class="c">#</span>
-    <span class="n">target_tasks</span> <span class="o">=</span> <span class="n">task_names_to_tasks</span> <span class="p">(</span><span class="s">"Target"</span><span class="p">,</span> <span class="n">target_tasks</span><span class="p">)</span>
-    <span class="n">forcedtorun_tasks</span> <span class="o">=</span> <span class="n">task_names_to_tasks</span> <span class="p">(</span><span class="s">"Forced to run"</span><span class="p">,</span> <span class="n">forcedtorun_tasks</span><span class="p">)</span>
-
-
-    <span class="c">#</span>
-    <span class="c">#   To update the checksum file, we force all tasks to rerun but then don't actually call the task function...</span>
-    <span class="c">#</span>
-    <span class="c">#   So starting with target_tasks and forcedtorun_tasks, we harvest all upstream dependencies willy, nilly</span>
-    <span class="c">#           and assign the results to forcedtorun_tasks</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">touch_files_only</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
-        <span class="p">(</span><span class="n">forcedtorun_tasks</span><span class="p">,</span> <span class="n">ignore_param1</span><span class="p">,</span> <span class="n">ignore_param2</span><span class="p">,</span>
-         <span class="n">ignore_param3</span><span class="p">)</span> <span class="o">=</span> <span class="n">topologically_sorted_nodes</span><span class="p">(</span><span class="n">target_tasks</span> <span class="o">+</span> <span class="n">forcedtorun_tasks</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span>
-                                                     <span class="n">gnu_make_maximal_rebuild_mode</span><span class="p">,</span>
-                                                     <span class="n">extra_data_for_signal</span> <span class="o">=</span> <span class="p">[</span><span class="n">t_verbose_logger</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="bp">None</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">),</span> <span class="n">job_history</span><span class="p">])</span>
-
-
-
-    <span class="p">(</span><span class="n">topological_sorted</span><span class="p">,</span>
-    <span class="n">self_terminated_nodes</span><span class="p">,</span>
-    <span class="n">dag_violating_edges</span><span class="p">,</span>
-    <span class="n">dag_violating_nodes</span><span class="p">)</span> <span class="o">=</span> <span class="n">topologically_sorted_nodes</span><span class="p">(</span>  <span class="n">target_tasks</span><span class="p">,</span> <span class="n">forcedtorun_tasks</span><span class="p">,</span>
-                                                        <span class="n">gnu_make_maximal_rebuild_mode</span><span class="p">,</span>
-                                                        <span class="n">extra_data_for_signal</span> <span class="o">=</span> <span class="p">[</span><span class="n">t_verbose_logger</span><span class="p">(</span><span class="n">verbose</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">runtime_data</span><span class="p">),</span> <span class="n">job_history</span><span class="p">])</span>
-
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">dag_violating_nodes</span><span class="p">):</span>
-        <span class="n">dag_violating_tasks</span> <span class="o">=</span> <span class="s">", "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">_name</span> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">dag_violating_nodes</span><span class="p">)</span>
-
-        <span class="n">e</span> <span class="o">=</span> <span class="n">error_circular_dependencies</span><span class="p">(</span><span class="s">"Circular dependencies found in the "</span>
-                                        <span class="s">"pipeline involving one or more of (</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span>
-                                            <span class="p">(</span><span class="n">dag_violating_tasks</span><span class="p">))</span>
-        <span class="k">raise</span> <span class="n">e</span>
-
-
-
-    <span class="c">#</span>
-    <span class="c"># get dependencies. Only include tasks which will be run</span>
-    <span class="c">#</span>
-    <span class="n">incomplete_tasks</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">topological_sorted</span><span class="p">)</span>
-    <span class="n">task_parents</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">set</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">incomplete_tasks</span><span class="p">:</span>
-        <span class="n">task_parents</span><span class="p">[</span><span class="n">t</span><span class="p">]</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">parent</span> <span class="ow">in</span> <span class="n">t</span><span class="o">.</span><span class="n">_outward</span><span class="p">:</span>
-            <span class="k">if</span> <span class="n">parent</span> <span class="ow">in</span> <span class="n">incomplete_tasks</span><span class="p">:</span>
-                <span class="n">task_parents</span><span class="p">[</span><span class="n">t</span><span class="p">]</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">parent</span><span class="p">)</span>
-    <span class="c">#print json.dumps(task_parents.items(), indent=4, cls=task_encoder)</span>
-
-
-    <span class="c"># prepare tasks for pipeline run</span>
-    <span class="c">#    **********</span>
-    <span class="c">#      BEWARE</span>
-    <span class="c">#    **********</span>
-    <span class="c">#</span>
-    <span class="c">#    Because state is stored, ruffus is *not* reentrant.</span>
-    <span class="c">#</span>
-    <span class="c">#    **********</span>
-    <span class="c">#      BEWARE</span>
-    <span class="c">#    **********</span>
-    <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">topological_sorted</span><span class="p">:</span>
-        <span class="n">t</span><span class="o">.</span><span class="n">init_for_pipeline</span><span class="p">()</span>
-
-
-    <span class="c">#</span>
-    <span class="c"># prime queue with initial set of job parameters</span>
-    <span class="c">#</span>
-    <span class="n">parameter_q</span> <span class="o">=</span> <span class="n">Queue</span><span class="o">.</span><span class="n">Queue</span><span class="p">()</span>
-    <span class="n">task_with_completed_job_q</span> <span class="o">=</span> <span class="n">Queue</span><span class="o">.</span><span class="n">Queue</span><span class="p">()</span>
-    <span class="n">parameter_generator</span> <span class="o">=</span> <span class="n">make_job_parameter_generator</span> <span class="p">(</span><span class="n">incomplete_tasks</span><span class="p">,</span> <span class="n">task_parents</span><span class="p">,</span>
-                                                        <span class="n">logger</span><span class="p">,</span> <span class="n">forcedtorun_tasks</span><span class="p">,</span>
-                                                        <span class="n">task_with_completed_job_q</span><span class="p">,</span>
-                                                        <span class="n">runtime_data</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span>
-                                                        <span class="n">syncmanager</span><span class="p">,</span>
-                                                        <span class="n">touch_files_only</span><span class="p">,</span> <span class="n">job_history</span><span class="p">)</span>
-    <span class="n">job_parameters</span> <span class="o">=</span> <span class="n">parameter_generator</span><span class="p">()</span>
-    <span class="n">fill_queue_with_job_parameters</span><span class="p">(</span><span class="n">job_parameters</span><span class="p">,</span> <span class="n">parameter_q</span><span class="p">,</span> <span class="n">parallelism</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">verbose</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   N.B.</span>
-    <span class="c">#   Handling keyboard shortcuts may require</span>
-    <span class="c">#       See http://stackoverflow.com/questions/1408356/keyboard-interrupts-with-pythons-multiprocessing-pool</span>
-    <span class="c">#</span>
-    <span class="c">#   When waiting for a condition in threading.Condition.wait(), KeyboardInterrupt is never sent</span>
-    <span class="c">#       unless a timeout is specified</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#   #</span>
-    <span class="c">#   #   whether using multiprocessing</span>
-    <span class="c">#   #</span>
-    <span class="c">#   pool = Pool(parallelism) if multiprocess > 1 else None</span>
-    <span class="c">#   if pool:</span>
-    <span class="c">#       pool_func = pool.imap_unordered</span>
-    <span class="c">#       job_iterator_timeout = []</span>
-    <span class="c">#   else:</span>
-    <span class="c">#       pool_func = imap</span>
-    <span class="c">#       job_iterator_timeout = [999999999999]</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#   ....</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#   it = pool_func(run_pooled_job_without_exceptions, feed_job_params_to_process_pool())</span>
-    <span class="c">#   while 1:</span>
-    <span class="c">#      try:</span>
-    <span class="c">#          job_result = it.next(*job_iterator_timeout)</span>
-    <span class="c">#</span>
-    <span class="c">#          ...</span>
-    <span class="c">#</span>
-    <span class="c">#      except StopIteration:</span>
-    <span class="c">#          break</span>
-
-
-
-
-    <span class="k">if</span> <span class="n">pool</span><span class="p">:</span>
-        <span class="n">pool_func</span> <span class="o">=</span> <span class="n">pool</span><span class="o">.</span><span class="n">imap_unordered</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">pool_func</span> <span class="o">=</span> <span class="n">imap</span>
-
-
-
-    <span class="n">feed_job_params_to_process_pool</span> <span class="o">=</span> <span class="n">feed_job_params_to_process_pool_factory</span> <span class="p">(</span><span class="n">parameter_q</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">verbose</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   for each result from job</span>
-    <span class="c">#</span>
-    <span class="n">job_errors</span> <span class="o">=</span> <span class="n">RethrownJobError</span><span class="p">()</span>
-    <span class="n">tasks_with_errors</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-
-
-    <span class="c">#</span>
-    <span class="c">#   job_result.job_name / job_result.return_value</span>
-    <span class="c">#       Reserved for returning result from job...</span>
-    <span class="c">#       How?</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">job_result</span> <span class="ow">in</span> <span class="n">pool_func</span><span class="p">(</span><span class="n">run_pooled_job_without_exceptions</span><span class="p">,</span> <span class="n">feed_job_params_to_process_pool</span><span class="p">()):</span>
-        <span class="n">t</span> <span class="o">=</span> <span class="n">node</span><span class="o">.</span><span class="n">lookup_node_from_name</span><span class="p">(</span><span class="n">job_result</span><span class="o">.</span><span class="n">task_name</span><span class="p">)</span>
-
-        <span class="c"># remove failed jobs from history-- their output is bogus now!</span>
-        <span class="k">if</span> <span class="n">job_result</span><span class="o">.</span><span class="n">state</span> <span class="ow">in</span> <span class="p">(</span><span class="n">JOB_ERROR</span><span class="p">,</span> <span class="n">JOB_SIGNALLED_BREAK</span><span class="p">):</span>
-
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">job_result</span><span class="o">.</span><span class="n">params</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>  <span class="c"># some jobs have no outputs</span>
-                <span class="n">output_file_name</span> <span class="o">=</span> <span class="n">job_result</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-                <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span> <span class="c"># some have multiple outputs from one job</span>
-                    <span class="n">output_file_name</span> <span class="o">=</span> <span class="p">[</span><span class="n">output_file_name</span><span class="p">]</span>
-                <span class="c">#</span>
-                <span class="c"># N.B. output parameters are not necessary all strings</span>
-                <span class="c">#</span>
-                <span class="k">for</span> <span class="n">o_f_n</span> <span class="ow">in</span> <span class="n">get_strings_in_nested_sequence</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">):</span>
-                    <span class="c">#</span>
-                    <span class="c"># use paths relative to working directory</span>
-                    <span class="c">#</span>
-                    <span class="n">o_f_n</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">relpath</span><span class="p">(</span><span class="n">o_f_n</span><span class="p">)</span>
-                    <span class="n">job_history</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">o_f_n</span><span class="p">,</span> <span class="bp">None</span><span class="p">)</span>  <span class="c"># remove outfile from history if it exists</span>
-
-        <span class="c"># only save poolsize number of errors</span>
-        <span class="k">if</span> <span class="n">job_result</span><span class="o">.</span><span class="n">state</span> <span class="o">==</span> <span class="n">JOB_ERROR</span><span class="p">:</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Exception caught for </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">job_result</span><span class="o">.</span><span class="n">job_name</span><span class="p">)</span>
-            <span class="n">job_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">job_result</span><span class="o">.</span><span class="n">exception</span><span class="p">)</span>
-            <span class="n">tasks_with_errors</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
-
-            <span class="c">#</span>
-            <span class="c"># print to logger immediately</span>
-            <span class="c">#</span>
-            <span class="k">if</span> <span class="n">log_exceptions</span><span class="p">:</span>
-                <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Log Exception"</span><span class="p">)</span>
-                <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">job_errors</span><span class="o">.</span><span class="n">get_nth_exception_str</span><span class="p">())</span>
-
-            <span class="c">#</span>
-            <span class="c"># break if too many errors</span>
-            <span class="c">#</span>
-            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">job_errors</span><span class="p">)</span> <span class="o">>=</span> <span class="n">parallelism</span> <span class="ow">or</span> <span class="n">exceptions_terminate_immediately</span><span class="p">:</span>
-                <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Break loop </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> "</span> <span class="o">%</span> <span class="p">(</span><span cl [...]
-                <span class="n">parameter_q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">all_tasks_complete</span><span class="p">())</span>
-                <span class="k">break</span>
-
-
-        <span class="c"># break immediately if the user says stop</span>
-        <span class="k">elif</span> <span class="n">job_result</span><span class="o">.</span><span class="n">state</span> <span class="o">==</span> <span class="n">JOB_SIGNALLED_BREAK</span><span class="p">:</span>
-            <span class="n">job_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">job_result</span><span class="o">.</span><span class="n">exception</span><span class="p">)</span>
-            <span class="n">job_errors</span><span class="o">.</span><span class="n">specify_task</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="s">"Exceptions running jobs"</span><span class="p">)</span>
-            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Break loop JOB_SIGNALLED_BREAK </span><span class="si">%s</span><span class="s"> </span><span class="si">%s</span><span class="s"> "</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p" [...]
-            <span class="n">parameter_q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">all_tasks_complete</span><span class="p">())</span>
-            <span class="k">break</span>
-
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">if</span> <span class="n">job_result</span><span class="o">.</span><span class="n">state</span> <span class="o">==</span> <span class="n">JOB_UP_TO_DATE</span><span class="p">:</span>
-                <span class="k">if</span> <span class="n">verbose</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
-                    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"    </span><span class="si">%s</span><span class="s"> unnecessary: already up to date"</span> <span class="o">%</span> <span class="n">job_result</span><span class="o">.</span><span class="n">job_name</span><span class="p">)</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">if</span> <span class="n">verbose</span><span class="p">:</span>
-                    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"    </span><span class="si">%s</span><span class="s"> completed"</span> <span class="o">%</span> <span class="n">job_result</span><span class="o">.</span><span class="n">job_name</span><span class="p">)</span>
-                <span class="c"># save this task name and the job (input and output files)</span>
-                <span class="c"># alternatively, we could just save the output file and its</span>
-                <span class="c"># completion time, or on the other end of the spectrum,</span>
-                <span class="c"># we could save a checksum of the function that generated</span>
-                <span class="c"># this file, something akin to:</span>
-                <span class="c"># chksum = md5.md5(marshal.dumps(t.user_defined_work_func.func_code.co_code))</span>
-                <span class="c"># we could even checksum the arguments to the function that</span>
-                <span class="c"># generated this file:</span>
-                <span class="c"># chksum2 = md5.md5(marshal.dumps(t.user_defined_work_func.func_defaults) +</span>
-                <span class="c">#                   marshal.dumps(t.args))</span>
-
-                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">job_result</span><span class="o">.</span><span class="n">params</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>  <span class="c"># some jobs have no outputs</span>
-                    <span class="n">output_file_name</span> <span class="o">=</span> <span class="n">job_result</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-                    <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span> <span class="c"># some have multiple outputs from one job</span>
-                        <span class="n">output_file_name</span> <span class="o">=</span> <span class="p">[</span><span class="n">output_file_name</span><span class="p">]</span>
-                    <span class="c">#</span>
-                    <span class="c"># N.B. output parameters are not necessary all strings</span>
-                    <span class="c">#       and not all files have been successfully created,</span>
-                    <span class="c">#       even though the task apparently completed properly!</span>
-                    <span class="c">#</span>
-                    <span class="k">for</span> <span class="n">o_f_n</span> <span class="ow">in</span> <span class="n">get_strings_in_nested_sequence</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">):</span>
-                        <span class="c">#</span>
-                        <span class="c"># use paths relative to working directory</span>
-                        <span class="c">#</span>
-                        <span class="n">o_f_n</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">relpath</span><span class="p">(</span><span class="n">o_f_n</span><span class="p">)</span>
-                        <span class="k">try</span><span class="p">:</span>
-                            <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Job History for : "</span> <span class="o">+</span> <span class="n">o_f_n</span><span class="p">)</span>
-                            <span class="n">mtime</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">getmtime</span><span class="p">(</span><span class="n">o_f_n</span><span class="p">)</span>
-                            <span class="c">#</span>
-                            <span class="c">#   use probably higher resolution time.time() over mtime</span>
-                            <span class="c">#       which might have 1 or 2s resolutions, unless there is</span>
-                            <span class="c">#       clock skew and the filesystem time > system time</span>
-                            <span class="c">#       (e.g. for networks)</span>
-                            <span class="c">#</span>
-                            <span class="n">epoch_seconds</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
-                            <span class="c"># Aargh. go back to insert one second between jobs</span>
-                            <span class="k">if</span> <span class="n">epoch_seconds</span> <span class="o"><</span> <span class="n">mtime</span><span class="p">:</span>
-                                <span class="k">if</span> <span class="n">one_second_per_job</span> <span class="o">==</span> <span class="bp">None</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ONE_SECOND_PER_JOB"</span><span class="p">]:</span>
-                                    <span class="n">log_at_level</span> <span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="mi">6</span><span class="p">,</span> <span class="n">verbose</span><span class="p">,</span> <span class="s">"   Switch to one second per job"</span><span class="p">)</span>
-                                    <span class="n">runtime_data</span><span class="p">[</span><span class="s">"ONE_SECOND_PER_JOB"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
-                            <span class="k">elif</span>  <span class="n">epoch_seconds</span> <span class="o">-</span> <span class="n">mtime</span> <span class="o"><</span> <span class="mf">1.1</span><span class="p">:</span>
-                                <span class="n">mtime</span> <span class="o">=</span> <span class="n">epoch_seconds</span>
-                            <span class="n">chksum</span> <span class="o">=</span> <span class="n">JobHistoryChecksum</span><span class="p">(</span><span class="n">o_f_n</span><span class="p">,</span> <span class="n">mtime</span><span class="p">,</span> <span class="n">job_result</span><span class="o">.</span><span class="n">params</span><span class="p">[</span><span class="mi">2</span><span class="p">:],</span> <span class="n">t</span><span class="p">)</span>
-                            <span class="n">job_history</span><span class="p">[</span><span class="n">o_f_n</span><span class="p">]</span> <span class="o">=</span> <span class="n">chksum</span>
-                        <span class="k">except</span><span class="p">:</span>
-                            <span class="k">pass</span>
-
-                <span class="c">##for output_file_name in t.output_filenames:</span>
-                <span class="c">##    # could use current time instead...</span>
-                <span class="c">##    if not isinstance(output_file_name, list):</span>
-                <span class="c">##        output_file_name = [output_file_name]</span>
-                <span class="c">##    for o_f_n in output_file_name:</span>
-                <span class="c">##        mtime = os.path.getmtime(o_f_n)</span>
-                <span class="c">##        chksum = JobHistoryChecksum(o_f_n, mtime, job_result.params[2:], t)</span>
-                <span class="c">##        job_history[o_f_n] = chksum</span>
-
-
-        <span class="c">#</span>
-        <span class="c">#   signal completed task after checksumming</span>
-        <span class="c">#</span>
-        <span class="n">task_with_completed_job_q</span><span class="o">.</span><span class="n">put</span><span class="p">((</span><span class="n">t</span><span class="p">,</span> <span class="n">job_result</span><span class="o">.</span><span class="n">task_name</span><span class="p">,</span> <span class="n">job_result</span><span class="o">.</span><span class="n">job_name</span><span class="p">))</span>
-
-
-        <span class="c"># make sure queue is still full after each job is retired</span>
-        <span class="c"># do this after undating which jobs are incomplete</span>
-        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">job_errors</span><span class="p">):</span>
-            <span class="c">#parameter_q.clear()</span>
-            <span class="c">#if len(job_errors) == 1 and not parameter_q._closed:</span>
-            <span class="n">parameter_q</span><span class="o">.</span><span class="n">put</span><span class="p">(</span><span class="n">all_tasks_complete</span><span class="p">())</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">fill_queue_with_job_parameters</span><span class="p">(</span><span class="n">job_parameters</span><span class="p">,</span> <span class="n">parameter_q</span><span class="p">,</span> <span class="n">parallelism</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">verbose</span><span class="p">)</span>
-
-
-    <span class="n">syncmanager</span><span class="o">.</span><span class="n">shutdown</span><span class="p">()</span>
-
-
-    <span class="k">if</span> <span class="n">pool</span><span class="p">:</span>
-        <span class="n">pool</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-        <span class="n">pool</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span>
-
-
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">job_errors</span><span class="p">):</span>
-        <span class="k">raise</span> <span class="n">job_errors</span>
-
-
-
-<span class="c">#   use high resolution timestamps where available</span>
-<span class="c">#       default in python 2.5 and greater</span>
-<span class="c">#   N.B. File modify times / stat values have 1 second precision for many file systems</span>
-<span class="c">#       and may not be accurate to boot, especially over the network.</span></div>
-<span class="n">os</span><span class="o">.</span><span class="n">stat_float_times</span><span class="p">(</span><span class="bp">True</span><span class="p">)</span>
-
-
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
-    <span class="kn">import</span> <span class="nn">unittest</span>
-
-
-
-
-    <span class="c">#</span>
-    <span class="c">#   debug parameter ignored if called as a module</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s">"--debug"</span><span class="p">):</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s">"--debug"</span><span class="p">)</span>
-    <span class="n">unittest</span><span class="o">.</span><span class="n">main</span><span class="p">()</span>
-</pre></div>
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../../genindex.html" title="General Index"
-             >index</a></li>
-        Ruffus v. 2.5
-            <li><a href="../../index.html">Home</a> | </li>
-            <li><a href="../../contents.html">Contents</a> | </li>
-            <li><a href="../../installation.html">Install</a>  | </li>
-            <li><a href="../../tutorials/new_tutorial/introduction.html">Manual</a>  / </li>
-            <li><a href="../../tutorials/new_tutorial/manual_contents.html">(TOC)</a>  | </li>
-            <li><a href="../../faq.html">FAQ</a>  | </li>
-            <li><a href="../../cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="../../tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="../../gallery.html">Gallery</a> |  </li>
-            <li><a href="../../history.html">Latest Changes</a> » </li>
-
-          <li><a href="../index.html" >Module code</a> »</li> 
-      </ul>
-    </div>
-    <div class="footer">
-        © Copyright 2009-2013 Leo Goodstadt.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
-    </div>
-  </body>
-</html>
\ No newline at end of file
diff --git a/doc/_build/html/_sources/cheatsheet.txt b/doc/_build/html/_sources/cheatsheet.txt
deleted file mode 100644
index aa5585d..0000000
--- a/doc/_build/html/_sources/cheatsheet.txt
+++ /dev/null
@@ -1,85 +0,0 @@
-.. include:: global.inc
-.. _cheat_sheet:
-
-
-#####################
-Cheat Sheet
-#####################
-
-The ``ruffus`` module is a lightweight way to add support
-for running computational pipelines.
-
-| Each stage or **task** in a computational pipeline is represented by a python function
-| Each python function can be called in parallel to run multiple **jobs**.
-
-================================================
-1. Annotate functions with **Ruffus** decorators
-================================================
-
-
-******
-Core
-******
-.. csv-table::
-   :header: "Decorator", "Syntax"
-   :widths: 100, 600,1
-
-   "@originate (:ref:`Manual <new_manual.originate>`)
-   ", "
-   :ref:`@originate <decorators.originate>` ( ``output_files``, [``extra_parameters``,...] )
-   ", ""
-   "@split (:ref:`Manual <new_manual.split>`)
-   ", "
-   :ref:`@split <decorators.split>` ( ``tasks_or_file_names``, ``output_files``, [``extra_parameters``,...] )
-   ", ""
-   "@transform (:ref:`Manual <new_manual.transform>`)
-   ", "
-   | :ref:`@transform <decorators.transform>` ( ``tasks_or_file_names``, :ref:`suffix <decorators.transform.suffix_string>`\ *(*\ ``suffix_string``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-   | :ref:`@transform <decorators.transform>` ( ``tasks_or_file_names``, :ref:`regex <decorators.transform.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-
-   ", ""
-   "@merge (:ref:`Manual <new_manual.merge>`)
-   ", "
-   :ref:`@merge <decorators.merge>` (``tasks_or_file_names``, ``output``, [``extra_parameters``,...] )
-   ", ""
-   "@posttask (:ref:`Manual <new_manual.posttask>`)
-   ", "
-   | :ref:`@posttask <decorators.posttask>` ( ``signal_task_completion_function`` )
-   | :ref:`@posttask <decorators.posttask>` (:ref:`touch_file <decorators.touch_file>`\ ( ``'task1.completed'`` ))
-
-   ", ""
-
-************************************************************************************************
-See :ref:`Decorators <decorators>` for a complete list of decorators
-************************************************************************************************
-
-
-
-================================================
-2. Print dependency graph if necessary
-================================================
-
-- For a graphical flowchart in ``jpg``, ``svg``, ``dot``, ``png``, ``ps``, ``gif`` formats::
-
-        pipeline_printout_graph ( "flowchart.svg")
-
-.. comment
-
-        This requires the `dot programme <http://www.graphviz.org/>`_ to be installed
-
-- For a text printout of all jobs ::
-
-        pipeline_printout()
-
-
-================================================
-3. Run the pipeline
-================================================
-
-::
-
-    pipeline_run(multiprocess = N_PARALLEL_JOBS)
-
-
-
-
diff --git a/doc/_build/html/_sources/contents.txt b/doc/_build/html/_sources/contents.txt
deleted file mode 100644
index 0e91439..0000000
--- a/doc/_build/html/_sources/contents.txt
+++ /dev/null
@@ -1,197 +0,0 @@
-.. include:: global.inc
-***************************
-**Ruffus** documentation
-***************************
-==========================================
-Start Here:
-==========================================
-.. toctree::
-   :maxdepth: 2
-
-   installation.rst
-   tutorials/new_tutorial/manual_contents.rst
-   tutorials/new_tutorial/introduction.rst
-   tutorials/new_tutorial/transform.rst
-   tutorials/new_tutorial/transform_in_parallel.rst
-   tutorials/new_tutorial/originate.rst
-   tutorials/new_tutorial/pipeline_printout.rst
-   tutorials/new_tutorial/command_line.rst
-   tutorials/new_tutorial/pipeline_printout_graph.rst
-   tutorials/new_tutorial/output_file_names.rst
-   tutorials/new_tutorial/mkdir.rst
-   tutorials/new_tutorial/checkpointing.rst
-   tutorials/new_tutorial/decorators_compendium.rst
-   tutorials/new_tutorial/split.rst
-   tutorials/new_tutorial/merge.rst
-   tutorials/new_tutorial/multiprocessing.rst
-   tutorials/new_tutorial/logging.rst
-   tutorials/new_tutorial/subdivide_collate.rst
-   tutorials/new_tutorial/combinatorics.rst
-   tutorials/new_tutorial/active_if.rst
-   tutorials/new_tutorial/posttask.rst
-   tutorials/new_tutorial/inputs.rst
-   tutorials/new_tutorial/onthefly.rst
-   tutorials/new_tutorial/parallel.rst
-   tutorials/new_tutorial/check_if_uptodate.rst
-   tutorials/new_tutorial/flowchart_colours.rst
-   tutorials/new_tutorial/dependencies.rst
-   tutorials/new_tutorial/exceptions.rst
-   tutorials/new_tutorial/list_of_ruffus_names.rst
-   tutorials/new_tutorial/deprecated_files.rst
-   tutorials/new_tutorial/deprecated_files_re.rst
-
-
-Example code for:
-
-.. toctree::
-   :maxdepth: 1
-
-   tutorials/new_tutorial/introduction_code.rst
-   tutorials/new_tutorial/transform_code.rst
-   tutorials/new_tutorial/transform_in_parallel_code.rst
-   tutorials/new_tutorial/originate_code.rst
-   tutorials/new_tutorial/pipeline_printout_code.rst
-   tutorials/new_tutorial/pipeline_printout_graph_code.rst
-   tutorials/new_tutorial/output_file_names_code.rst
-   tutorials/new_tutorial/mkdir_code.rst
-   tutorials/new_tutorial/checkpointing_code.rst
-   tutorials/new_tutorial/split_code.rst
-   tutorials/new_tutorial/merge_code.rst
-   tutorials/new_tutorial/multiprocessing_code.rst
-   tutorials/new_tutorial/logging_code.rst
-   tutorials/new_tutorial/subdivide_collate_code.rst
-   tutorials/new_tutorial/combinatorics_code.rst
-   tutorials/new_tutorial/inputs_code.rst
-   tutorials/new_tutorial/onthefly_code.rst
-   tutorials/new_tutorial/flowchart_colours_code.rst
-
-
-
-=====================
-Overview:
-=====================
-.. toctree::
-   :maxdepth: 2
-
-   cheatsheet.rst
-   pipeline_functions.rst
-   drmaa_wrapper_functions.rst
-   installation.rst
-   design.rst
-   Bugs and Updates <history>
-   Future plans <todo>
-   Implementation_notes <implementation_notes.rst>
-   faq.rst
-   glossary.rst
-   gallery.rst
-   why_ruffus.rst
-
-=====================
-Examples
-=====================
-.. toctree::
-   :maxdepth: 2
-
-   examples/bioinformatics/index.rst
-   examples/bioinformatics/part2.rst
-   examples/bioinformatics/part1_code.rst
-   examples/bioinformatics/part2_code.rst
-   examples/paired_end_data.py.rst
-
-
-
-=====================
-Reference:
-=====================
-######################
-Decorators
-######################
-.. toctree::
-    :maxdepth: 1
-
-    decorators/decorators.rst
-    decorators/indicator_objects.rst
-
-
-.. topic::
-    Core
-
-    .. toctree::
-        :maxdepth: 1
-
-        decorators/originate.rst
-        decorators/split.rst
-        decorators/transform.rst
-        decorators/merge.rst
-
-.. topic::
-    For advanced users
-
-    .. toctree::
-        :maxdepth: 1
-
-        decorators/subdivide.rst
-        decorators/transform_ex.rst
-        decorators/collate.rst
-        decorators/collate_ex.rst
-        decorators/graphviz.rst
-        decorators/mkdir.rst
-        decorators/jobs_limit.rst
-        decorators/posttask.rst
-        decorators/active_if.rst
-        decorators/follows.rst
-
-.. topic::
-    Combinatorics
-
-    .. toctree::
-        :maxdepth: 1
-
-        decorators/product.rst
-        decorators/permutations.rst
-        decorators/combinations.rst
-        decorators/combinations_with_replacement.rst
-
-.. topic::
-    Esoteric
-
-    .. toctree::
-        :maxdepth: 1
-
-        decorators/files_ex.rst
-        decorators/check_if_uptodate.rst
-        decorators/parallel.rst
-
-.. topic::
-    Deprecated
-
-    .. toctree::
-        :maxdepth: 1
-
-        decorators/files.rst
-        decorators/files_re.rst
-
-
-######################
-Modules:
-######################
-
-.. toctree::
-   :maxdepth: 2
-
-   task.rst
-   proxy_logger.rst
-
-.. comment
-   graph.rst
-   print_dependencies.rst
-   adjacent_pairs_iterate.rst
-
-
-=====================
-Indices and tables
-=====================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/doc/_build/html/_sources/decorators/active_if.txt b/doc/_build/html/_sources/decorators/active_if.txt
deleted file mode 100644
index 1b02e1f..0000000
--- a/doc/_build/html/_sources/decorators/active_if.txt
+++ /dev/null
@@ -1,110 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.active_if:
-.. index::
-    pair: @active_if; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-    * More on @active_if in the ``Ruffus`` :ref:`Manual <new_manual.active_if>`
-
-
-############
- at active_if
-############
-
-.. Comment. These are parameter names
-
-.. |on_or_off| replace:: `on_or_off`
-.. _on_or_off: `decorators.active_if.on_or_off`_
-
-***************************************************************************************************************************************************
-*@active_if*\ (on_or_off1, [on_or_off2,...])
-***************************************************************************************************************************************************
-    **Purpose:**
-
-        * Switches tasks on and off at run time depending on its parameters
-        * Evaluated each time ``pipeline_run``, ``pipeline_printout`` or ``pipeline_printout_graph`` is called.
-        * The Design and initial implementation were contributed by Jacob Biesinger
-        * Dormant tasks behave as if they are up to date and have no output.
-
-    **Example**:
-
-        .. code-block:: python
-            :emphasize-lines: 20
-
-            from ruffus import *
-            run_if_true_1 = True
-            run_if_true_2 = False
-            run_if_true_3 = True
-
-
-            #
-            #    task1
-            #
-            @originate(['a.foo', 'b.foo'])
-            def create_files(outfile):
-                """
-                create_files
-                """
-                open(outfile, "w").write(outfile + "\n")
-
-            #
-            #   Only runs if all three run_if_true conditions are met
-            #
-            #   @active_if determines if task is active
-            @active_if(run_if_true_1, lambda: run_if_true_2)
-            @active_if(run_if_true_3)
-            @transform(create_files, suffix(".foo"), ".bar")
-            def this_task_might_be_inactive(infile, outfile):
-                open(outfile, "w").write("%s -> %s\n" % (infile, outfile))
-
-
-            # @active_if switches off task because run_if_true_2 == False
-            pipeline_run(verbose = 3)
-
-            # @active_if switches on task because all run_if_true conditions are met
-            run_if_true_2 = True
-            pipeline_run(verbose = 3)
-
-
-        Produces the following output:
-
-            .. code-block:: pycon
-                :emphasize-lines: 1,13
-
-                >>> # @active_if switches off task "this_task_might_be_inactive" because run_if_true_2 == False
-                >>> pipeline_run(verbose = 3)
-
-                Task enters queue = create_files
-                create_files
-                    Job  = [None -> a.foo] Missing file [a.foo]
-                    Job  = [None -> b.foo] Missing file [b.foo]
-                    Job  = [None -> a.foo] completed
-                    Job  = [None -> b.foo] completed
-                Completed Task = create_files
-                Inactive Task = this_task_might_be_inactive
-
-                >>> # @active_if switches on task "this_task_might_be_inactive" because all run_if_true conditions are met
-                >>> run_if_true_2 = True
-                >>> pipeline_run(verbose = 3)
-
-                Task enters queue = this_task_might_be_inactive
-
-                    Job  = [a.foo -> a.bar] Missing file [a.bar]
-                    Job  = [b.foo -> b.bar] Missing file [b.bar]
-                    Job  = [a.foo -> a.bar] completed
-                    Job  = [b.foo -> b.bar] completed
-                Completed Task = this_task_might_be_inactive
-
-
-    **Parameters:**
-
-.. _decorators.active_if.on_or_off:
-
-    * *on_or_off*:
-        A comma separated list of boolean conditions. These can be values, functions or callable objects which return True / False
-
-        Multiple ``@active_if`` decorators can be stacked for clarity as in the example
-
-
diff --git a/doc/_build/html/_sources/decorators/check_if_uptodate.txt b/doc/_build/html/_sources/decorators/check_if_uptodate.txt
deleted file mode 100644
index 893f430..0000000
--- a/doc/_build/html/_sources/decorators/check_if_uptodate.txt
+++ /dev/null
@@ -1,68 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.check_if_uptodate:
-
-.. index::
-    pair: @check_if_uptodate; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-.. |dependency_checking_function| replace:: `dependency_checking_function`
-.. _dependency_checking_function: `decorators.check_if_uptodate.dependency_checking_function`_
-
-########################
- at check_if_uptodate
-########################
-
-*******************************************************************************************
-*@check_if_uptodate* (|dependency_checking_function|_)
-*******************************************************************************************
-
-    **Purpose:**
-        Checks to see if a job is up to date, and needs to be run.
-
-        Usually used in conjunction with :ref:`@parallel() <decorators.parallel>`
-
-    **Example**::
-
-        from ruffus import *
-        import os
-        def check_file_exists(input_file, output_file):
-            if not os.path.exists(output_file):
-                return True, "Missing file %s" % output_file
-            else:
-                return False, "File %s exists" % output_file
-
-        @parallel([[None, "a.1"]])
-        @check_if_uptodate(check_file_exists)
-        def create_if_necessary(input_file, output_file):
-            open(output_file, "w")
-
-        pipeline_run([create_if_necessary])
-
-    Is equivalent to::
-
-        from ruffus import *
-        @files(None, "a.1")
-        def create_if_necessary(input_file, output_file):
-            open(output_file, "w")
-
-        pipeline_run([create_if_necessary])
-
-    Both produce the same output::
-
-        Task = create_if_necessary
-            Job = [null, "a.1"] completed
-
-    **Parameters:**
-
-.. _decorators.check_if_uptodate.dependency_checking_function:
-
-    * *dependency_checking_function*:
-            returns two parameters: if job needs to be run, and a message explaining why
-
-            dependency_checking_func() needs to handle the same number of parameters as the
-            task function e.g. ``input_file`` and ``output_file`` above.
-
-
diff --git a/doc/_build/html/_sources/decorators/collate.txt b/doc/_build/html/_sources/decorators/collate.txt
deleted file mode 100644
index 1121925..0000000
--- a/doc/_build/html/_sources/decorators/collate.txt
+++ /dev/null
@@ -1,154 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.collate:
-.. index::
-    pair: @collate; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-########################
- at collate
-########################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.collate.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.collate.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.collate.output_pattern`_
-.. |matching_regex| replace:: `matching_regex`
-.. _matching_regex: `decorators.collate.matching_regex`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.collate.matching_formatter`_
-
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@collate* ( |tasks_or_file_names|_, :ref:`regex<decorators.regex>`\ *(*\ |matching_regex|_\ *)* |  :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, |output_pattern|_, [|extra_parameters|_,...] )
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    **Purpose:**
-        Groups / collates sets of input files, each into a separate summary.
-
-        Only out of date tasks (comparing input and output files) will be run
-
-        Output file names and strings in the extra parameters
-        are determined from |tasks_or_file_names|_, i.e. from the output
-        of up stream tasks, or a list of file names.
-
-        String replacement occurs either through suffix matches via :ref:`suffix<decorators.suffix>` or
-        the :ref:`formatter<decorators.formatter>` or :ref:`regex<decorators.regex>` indicators.
-
-        ``@collate`` groups together all **Input** which result in identical **Output** and **extra**
-        parameters.
-
-        It is a **many to fewer** operation.
-
-
-    **Example**:
-        ``regex(r".*(\..+)"), "\1.summary"`` creates a separate summary file for each suffix::
-
-            animal_files = "a.fish", "b.fish", "c.mammals", "d.mammals"
-            # summarise by file suffix:
-            @collate(animal_files, regex(r"\.(.+)$"),  r'\1.summary')
-            def summarize(infiles, summary_file):
-                pass
-
-    **Parameters:**
-
-
-.. _decorators.collate.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-
-.. _decorators.collate.matching_regex:
-
-    * *matching_regex*
-       is a python regular expression string, which must be wrapped in
-       a :ref:`regex<decorators.regex>` indicator object
-       See python `regular expression (re) <http://docs.python.org/library/re.html>`_
-       documentation for details of regular expression syntax
-
-.. _decorators.collate.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-
-.. _decorators.collate.output_pattern:
-
-    * *output_pattern*
-        Specifies the resulting output file name(s).
-
-.. _decorators.collate.extra_parameters:
-
-    * *extra_parameters*
-        Any extra parameters are passed verbatim to the task function
-
-    #. *outputs* and optional extra parameters are passed to the functions after string
-       substitution in any strings. Non-string values are passed through unchanged.
-    #. Each collate job consists of input files which are aggregated by string substitution
-       to a single set of output / extra parameter matches
-    #. In the above cases, ``a.fish`` and ``b.fish`` both produce ``fish.summary`` after regular
-       expression subsitution, and are collated into a single job:
-       ``["a.fish", "b.fish" -> "fish.summary"]``
-       while ``c.mammals``, ``d.mammals`` both produce ``mammals.summary``, are collated in a separate job:
-       ``["c.mammals", "d.mammals" -> "mammals.summary"]``
-
-    **Example2**:
-
-        Suppose we had the following files::
-
-            cows.mammals.animal
-            horses.mammals.animal
-            sheep.mammals.animal
-
-            snake.reptile.animal
-            lizard.reptile.animal
-            crocodile.reptile.animal
-
-            pufferfish.fish.animal
-
-        and we wanted to end up with three different resulting output::
-
-            cow.mammals.animal
-            horse.mammals.animal
-            sheep.mammals.animal
-                -> mammals.results
-
-            snake.reptile.animal
-            lizard.reptile.animal
-            crocodile.reptile.animal
-                -> reptile.results
-
-            pufferfish.fish.animal
-                -> fish.results
-
-        This is the ``@collate`` code required::
-
-            animals = [     "cows.mammals.animal",
-                            "horses.mammals.animal",
-                            "sheep.mammals.animal",
-                            "snake.reptile.animal",
-                            "lizard.reptile.animal",
-                            "crocodile.reptile.animal",
-                            "pufferfish.fish.animal"]
-
-            @collate(animals, regex(r"(.+)\.(.+)\.animal"),  r"\2.results")
-            # \1 = species [cow, horse]
-            # \2 = phylogenetics group [mammals, reptile, fish]
-            def summarize_animals_into_groups(species_file, result_file):
-                " ... more code here"
-                pass
-
-
-
-See :ref:`@merge <decorators.merge>` for an alternative way to summarise files.
diff --git a/doc/_build/html/_sources/decorators/collate_ex.txt b/doc/_build/html/_sources/decorators/collate_ex.txt
deleted file mode 100644
index 50175f4..0000000
--- a/doc/_build/html/_sources/decorators/collate_ex.txt
+++ /dev/null
@@ -1,145 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.collate_ex:
-.. index::
-    pair: @collate (Advanced Usage); Syntax
-    pair: @collate, inputs(...); Syntax
-    pair: @collate, add_inputs(...); Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-####################################################
- at collate  with ``add_inputs`` and ``inputs``
-####################################################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.collate_ex.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.collate_ex.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.collate_ex.output_pattern`_
-.. |input_pattern_or_glob| replace:: `input_pattern_or_glob`
-.. _input_pattern_or_glob: `decorators.collate_ex.input_pattern_or_glob`_
-.. |matching_regex| replace:: `matching_regex`
-.. _matching_regex: `decorators.collate_ex.matching_regex`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.collate_ex.matching_formatter`_
-
-
-************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************ [...]
-*@collate* ( |tasks_or_file_names|_, :ref:`regex<decorators.regex>`\ *(*\ |matching_regex|_\ *)* |  :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, [:ref:`inputs<decorators.inputs>`\ *(*\ |input_pattern_or_glob|_\ *)* | :ref:`add_inputs<decorators.add_inputs>`\ *(*\ |input_pattern_or_glob|_\ *)*\] , |output_pattern|_, [|extra_parameters|_,...] )
-************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************ [...]
-    **Purpose:**
-        Groups / collates sets of input files, each into a separate summary.
-
-        This variant of ``@collate`` allows additional inputs or dependencies to be added
-        dynamically to the task.
-
-        Output file names are determined from |tasks_or_file_names|_, i.e. from the output
-        of up stream tasks, or a list of file names.
-
-        This variant of ``@collate`` allows input file names to be derived in the same way.
-
-        :ref:`add_inputs<decorators.add_inputs>` nests the the original input parameters in a list before adding additional dependencies.
-
-        :ref:`inputs<decorators.inputs>` replaces the original input parameters wholescale.
-
-        Only out of date tasks (comparing input and output files) will be run
-
-    **Example of** :ref:`add_inputs<decorators.add_inputs>`
-
-        ``regex(r".*(\..+)"), "\1.summary"`` creates a separate summary file for each suffix.
-        But we also add date of birth data for each species::
-
-            animal_files = "tuna.fish", "shark.fish", "dog.mammals", "cat.mammals"
-            # summarise by file suffix:
-            @collate(animal_files, regex(r".+\.(.+)$"),  add_inputs(r"\1.date_of_birth"), r'\1.summary')
-            def summarize(infiles, summary_file):
-                pass
-
-        This results in the following equivalent function calls::
-
-            summarize([ ["shark.fish",  "fish.date_of_birth"   ],
-                        ["tuna.fish",   "fish.date_of_birth"   ] ], "fish.summary")
-            summarize([ ["cat.mammals", "mammals.date_of_birth"],
-                        ["dog.mammals", "mammals.date_of_birth"] ], "mammals.summary")
-
-    **Example of** :ref:`add_inputs<decorators.inputs>`
-
-        using ``inputs(...)`` will summarise only the dates of births for each species group::
-
-            animal_files = "tuna.fish", "shark.fish", "dog.mammals", "cat.mammals"
-            # summarise by file suffix:
-            @collate(animal_files, regex(r".+\.(.+)$"),  inputs(r"\1.date_of_birth"), r'\1.summary')
-            def summarize(infiles, summary_file):
-                pass
-
-        This results in the following equivalent function calls::
-
-            summarize(["fish.date_of_birth"   ], "fish.summary")
-            summarize(["mammals.date_of_birth"], "mammals.summary")
-
-    **Parameters:**
-
-
-.. _decorators.collate_ex.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-
-.. _decorators.collate_ex.matching_regex:
-
-    * *matching_regex*
-       is a python regular expression string, which must be wrapped in
-       a :ref:`regex<decorators.regex>` indicator object
-       See python `regular expression (re) <http://docs.python.org/library/re.html>`_
-       documentation for details of regular expression syntax
-
-.. _decorators.collate_ex.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-.. _decorators.collate_ex.input_pattern_or_glob:
-
-    * *input_pattern*
-       Specifies the resulting input(s) to each job.
-       Must be wrapped in an :ref:`inputs<decorators.inputs>` or an :ref:`inputs<decorators.add_inputs>` indicator object.
-
-       Can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            Strings will be subject to substitution.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-            E.g.:``"a.*" => "a.1", "a.2"``
-
-
-
-.. _decorators.collate_ex.output_pattern:
-
-    * *output_pattern*
-        Specifies the resulting output file name(s).
-
-.. _decorators.collate_ex.extra_parameters:
-
-    * *extra_parameters*
-        Any extra parameters are passed verbatim to the task function
-
-    #. *outputs* and optional extra parameters are passed to the functions after string
-       substitution in any strings. Non-string values are passed through unchanged.
-    #. Each collate job consists of input files which are aggregated by string substitution
-       to a single set of output / extra parameter matches
-
-
-See :ref:`@collate <decorators.collate>` for more straightforward ways to use collate.
diff --git a/doc/_build/html/_sources/decorators/combinations.txt b/doc/_build/html/_sources/decorators/combinations.txt
deleted file mode 100644
index 65f9ec9..0000000
--- a/doc/_build/html/_sources/decorators/combinations.txt
+++ /dev/null
@@ -1,153 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.combinations:
-.. index::
-    pair: @combinations; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-########################
- at combinations
-########################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.combinations.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.combinations.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.combinations.output_pattern`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.combinations.matching_formatter`_
-
-
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@combinations* ( |tasks_or_file_names|_, :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, |output_pattern|_, [|extra_parameters|_,...] )
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    **Purpose:**
-
-        Generates the **combinations**, between all the elements of a set of **Input** (e.g. **A B C D**),
-        i.e. r-length tuples of *input* elements with no repeated elements (**A A**)
-        and where order of the tuples is irrelevant (either **A B** or  **B A**, not both).
-
-        The effect is analogous to the python `itertools  <http://docs.python.org/2/library/itertools.html#itertools.combinations>`__
-        function of the same name:
-
-        .. code-block:: pycon
-            :emphasize-lines: 2
-
-            >>> from itertools import combinations
-            >>> # combinations('ABCD', 3) --> ABC ABD ACD BCD
-            >>> [ "".join(a) for a in combinations("ABCD", 3)]
-            ['ABC', 'ABD', 'ACD', 'BCD']
-
-        Only out of date tasks (comparing input and output files) will be run
-
-        Output file names and strings in the extra parameters
-        are determined from |tasks_or_file_names|_, i.e. from the output
-        of up stream tasks, or a list of file names, after string replacement via
-        :ref:`formatter<decorators.formatter>`.
-
-        The replacement strings require an extra level of indirection to refer to
-        parsed components:
-
-            #. The first level refers to which *set* in each tuple of inputs.
-            #. The second level refers to which input file in any particular *set* of inputs.
-
-    **Example**:
-
-        Calculates the **@combinations** of **A,B,C,D** files
-
-        .. code-block:: python
-            :emphasize-lines: 13,17,20,25,28-30
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   initial file pairs
-            @originate([ ['A.1_start', 'A.2_start'],
-                         ['B.1_start', 'B.2_start'],
-                         ['C.1_start', 'C.2_start'],
-                         ['D.1_start', 'D.2_start']])
-            def create_initial_files_ABCD(output_files):
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-            #   @combinations
-            @combinations(create_initial_files_ABCD,      # Input
-                          formatter(),                    # match input files
-
-                          # tuple of 3 at a time
-                          3,
-
-                          # Output Replacement string
-                          "{path[0][0]}/"
-                          "{basename[0][1]}_vs_"
-                          "{basename[1][1]}_vs_"
-                          "{basename[2][1]}.combinations",
-
-                          # Extra parameter: path for 1st set of files, 1st file name
-                          "{path[0][0]}",
-
-                          # Extra parameter
-                          ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                           "{basename[1][0]}",  #              2nd
-                           "{basename[2][0]}",  #              3rd
-                           ])
-            def combinations_task(input_file, output_parameter, shared_path, basenames):
-                print " - ".join(basenames)
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-        This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-            A - B - C
-            A - B - D
-            A - C - D
-            B - C - D
-
-
-    **Parameters:**
-
-
-.. _decorators.combinations.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-
-.. _decorators.combinations.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-
-.. _decorators.combinations.output_pattern:
-
-    * *output_pattern*
-        Specifies the resulting output file name(s) after string
-        substitution
-
-
-.. _decorators.combinations.extra_parameters:
-
-    * *extra_parameters*
-        Optional extra parameters are passed to the functions after string
-        substitution
-
diff --git a/doc/_build/html/_sources/decorators/combinations_with_replacement.txt b/doc/_build/html/_sources/decorators/combinations_with_replacement.txt
deleted file mode 100644
index fbb0daf..0000000
--- a/doc/_build/html/_sources/decorators/combinations_with_replacement.txt
+++ /dev/null
@@ -1,157 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.combinations_with_replacement:
-.. index::
-    pair: @combinations_with_replacement; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-################################################
- at combinations_with_replacement
-################################################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.combinations_with_replacement.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.combinations_with_replacement.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.combinations_with_replacement.output_pattern`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.combinations_with_replacement.matching_formatter`_
-
-
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@combinations_with_replacement* ( |tasks_or_file_names|_, :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, |output_pattern|_, [|extra_parameters|_,...] )
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    **Purpose:**
-
-        Generates the **combinations_with_replacement**, between all the elements of a set of **Input** (e.g. **A B C D**),
-        i.e. r-length tuples of *input* elements included repeated elements (**A A**)
-        and where order of the tuples is irrelevant (either **A B** or  **B A**, not both).
-
-        The effect is analogous to the python `itertools  <http://docs.python.org/2/library/itertools.html#itertools.combinations_with_replacement>`__
-        function of the same name:
-
-        .. code-block:: pycon
-            :emphasize-lines: 2
-
-            >>> from itertools import combinations_with_replacement
-            >>> # combinations_with_replacement('ABCD', 2) --> AA AB AC AD BB BC BD CC CD DD
-            >>> [ "".join(a) for a in combinations_with_replacement('ABCD', 2)]
-            ['AA', 'AB', 'AC', 'AD', 'BB', 'BC', 'BD', 'CC', 'CD', 'DD']
-
-        Only out of date tasks (comparing input and output files) will be run
-
-        Output file names and strings in the extra parameters
-        are determined from |tasks_or_file_names|_, i.e. from the output
-        of up stream tasks, or a list of file names, after string replacement via
-        :ref:`formatter<decorators.formatter>`.
-
-        The replacement strings require an extra level of indirection to refer to
-        parsed components:
-
-            #. The first level refers to which *set* in each tuple of inputs.
-            #. The second level refers to which input file in any particular *set* of inputs.
-
-    **Example**:
-
-        Calculates the **@combinations_with_replacement** of **A,B,C,D** files
-
-        .. code-block:: python
-            :emphasize-lines: 13,17,20,25,28-30
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   initial file pairs
-            @originate([ ['A.1_start', 'A.2_start'],
-                         ['B.1_start', 'B.2_start'],
-                         ['C.1_start', 'C.2_start'],
-                         ['D.1_start', 'D.2_start']])
-            def create_initial_files_ABCD(output_files):
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-            #   @combinations_with_replacement
-            @combinations_with_replacement(create_initial_files_ABCD,   # Input
-                          formatter(),                                  # match input files
-
-                          # tuple of 2 at a time
-                          2,
-
-                          # Output Replacement string
-                          "{path[0][0]}/"
-                          "{basename[0][1]}_vs_"
-                          "{basename[1][1]}.combinations_with_replacement",
-
-                          # Extra parameter: path for 1st set of files, 1st file name
-                          "{path[0][0]}",
-
-                          # Extra parameter
-                          ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                           "{basename[1][0]}",  #              2rd
-                           ])
-            def combinations_with_replacement_task(input_file, output_parameter, shared_path, basenames):
-                print " - ".join(basenames)
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-        This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-            A - A
-            A - B
-            A - C
-            A - D
-            B - B
-            B - C
-            B - D
-            C - C
-            C - D
-            D - D
-
-
-    **Parameters:**
-
-
-.. _decorators.combinations_with_replacement.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-
-.. _decorators.combinations_with_replacement.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-
-.. _decorators.combinations_with_replacement.output_pattern:
-
-    * *output_pattern*
-        Specifies the resulting output file name(s) after string
-        substitution
-
-
-.. _decorators.combinations_with_replacement.extra_parameters:
-
-    * *extra_parameters*
-        Optional extra parameters are passed to the functions after string
-        substitution
-
diff --git a/doc/_build/html/_sources/decorators/decorators.txt b/doc/_build/html/_sources/decorators/decorators.txt
deleted file mode 100644
index 5d70df8..0000000
--- a/doc/_build/html/_sources/decorators/decorators.txt
+++ /dev/null
@@ -1,296 +0,0 @@
-.. include:: ../global.inc
-#######################
-Ruffus Decorators
-#######################
-
-.. seealso::
-    :ref:`Indicator objects <decorators.indicator_objects>`
-
-.. _decorators:
-
-
-=============================================
-*Core*
-=============================================
-.. csv-table::
-   :header: "Decorator", "Examples"
-   :widths: 400, 600,1
-
-   "**@originate** (:ref:`Summary <decorators.originate>` / :ref:`Manual <new_manual.originate>`)
-
-    - Creates (originates) a set of starting file without dependencies from scratch  (*ex nihilo*!)
-    - Only called to create files which do not exist.
-    - Invoked onces (a job created) per item in the ``output_files`` list.
-
-   ", "
-   * :ref:`@originate <decorators.originate>` ( ``output_files``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-   "**@split** (:ref:`Summary <decorators.split>` / :ref:`Manual <new_manual.split>`)
-
-   - Splits a single input into multiple output
-   - Globs in ``output`` can specify an indeterminate number of files.
-
-   ", "
-   * :ref:`@split <decorators.split>` ( ``tasks_or_file_names``, ``output_files``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-   "**@transform** (:ref:`Summary <decorators.transform>` / :ref:`Manual <new_manual.transform>`)
-
-   - Applies the task function to transform input data to output.
-
-   ", "
-   * :ref:`@transform <decorators.transform>` ( ``tasks_or_file_names``, :ref:`suffix <decorators.transform.suffix_string>`\ *(*\ ``suffix_string``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-              \
-   * :ref:`@transform <decorators.transform>` ( ``tasks_or_file_names``, :ref:`regex <decorators.transform.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-           \
-   * :ref:`@transform <decorators.transform>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.transform.matching_formatter>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-   "**@merge** (:ref:`Summary <decorators.merge>` / :ref:`Manual <new_manual.merge>`)
-
-   - Merges multiple input files into a single output.
-
-   ", "
-   * :ref:`@merge <decorators.merge>` (``tasks_or_file_names``, ``output``, [``extra_parameters``,...] )
-           \
-
-          ", ""
-
-.. _decorators.combinatorics:
-
-=============================================
-*Combinatorics*
-=============================================
-.. csv-table::
-   :header: "Decorator", "Examples"
-   :widths: 400, 600,1
-
-   "**@product** (:ref:`Summary <decorators.product>` / :ref:`Manual <new_manual.product>`)
-
-    - Generates the **product**, i.e. all vs all comparisons, between sets of input files.
-   ", "
-   * :ref:`@product <decorators.product>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *])* ,*[* ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *]), ]*, ``output_pattern``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-   "**@permutations** (:ref:`Summary <decorators.permutations>` / :ref:`Manual <new_manual.permutations>`)
-
-    - Generates the **permutations**, between all the elements of a set of **Input**
-    - Analogous to the python `itertools.permutations <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__
-    - permutations('ABCD', 2) --> AB AC AD BA BC BD CA CB CD DA DB DC
-
-   ", "
-   * :ref:`@permutations <decorators.permutations>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *])*, ``tuple_size``, ``output_pattern``, [``extra_parameters``,...] )
-           \
-   ", ""
-   "**@combinations** (:ref:`Summary <decorators.combinations>` / :ref:`Manual <new_manual.combinations>`)
-
-    - Generates the **permutations**, between all the elements of a set of **Input**
-    - Analogous to the python `itertools.combinations <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__
-    - combinations('ABCD', 3) --> ABC ABD ACD BCD
-    - Generates the **combinations**, between all the elements of a set of **Input**:
-      i.e. r-length tuples of *input* elements with no repeated elements (**A A**)
-      and where order of the tuples is irrelevant (either **A B** or  **B A**, not both).
-
-   ", "
-   * :ref:`@combinations <decorators.permutations>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *])*, ``tuple_size``, ``output_pattern``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-   "**@combinations_with_replacement** (:ref:`Summary <decorators.combinations_with_replacement>` / :ref:`Manual <new_manual.combinations_with_replacement>`)
-
-    - Generates the **permutations**, between all the elements of a set of **Input**
-    - Analogous to the python `itertools.permutations <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__
-    - combinations('ABCD', 3) --> ABC ABD ACD BCD
-    - Generates the **combinations_with_replacement**, between all the elements of a set of **Input**:
-      i.e. r-length tuples of *input* elements with no repeated elements (**A A**)
-      and where order of the tuples is irrelevant (either **A B** or  **B A**, not both).
-
-   ", "
-   * :ref:`@combinations_with_replacement <decorators.permutations>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *])*, ``tuple_size``, ``output_pattern``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-
-=============================================
-*Advanced*
-=============================================
- .. csv-table::
-   :header: "Decorator", "Examples"
-   :widths: 400, 600,1
-
-   "**@subdivide** (:ref:`Summary <decorators.subdivide>` / :ref:`Manual <new_manual.subdivide>`)
-   - Subdivides a set of *Inputs* each further into multiple *Outputs*.
-   - The number of files in each *Output* can be set at runtime by the use of globs.
-   - **Many to Even More** operator.
-   - The use of **split** is a synonym for subdivide is deprecated.
-
-   ", "
-   * :ref:`@subdivide <decorators.subdivide>` ( ``tasks_or_file_names``, :ref:`regex <decorators.subdivide.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , [ :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ] ``output_pattern``, [``extra_parameters``,...] )
-           \
-   * :ref:`@subdivide <decorators.subdivide>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.subdivide.matching_formatter>`\ *(*\ [``regex_pattern``] *)*\ , [ :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ] ``output_pattern``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-   "**@transform** (:ref:`Summary <decorators.transform_ex>` / :ref:`Manual <new_manual.inputs>`)
-
-   - Infers input as well as output from regular expression substitutions
-   - Useful for adding additional file dependencies
-
-   ", "
-   * :ref:`@transform <decorators.transform_ex>` ( ``tasks_or_file_names``, :ref:`regex <decorators.transform.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , [ :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ] ``output_pattern``, [``extra_parameters``,...] )
-           \
-   * :ref:`@transform <decorators.transform_ex>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.transform.matching_formatter>`\ *(*\ ``regex_pattern``\ *)*\ , [ :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ] ``output_pattern``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-   "**@collate** (:ref:`Summary <decorators.collate>` / :ref:`Manual <new_manual.collate>`)
-
-   - Groups multiple input files using regular expression matching
-   - Input resulting in the same output after substitution will be collated together.
-
-   ", "
-   * :ref:`@collate <decorators.collate>` (``tasks_or_file_names``, :ref:`regex <decorators.collate.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-           \
-   * :ref:`@collate <decorators.collate_ex>` (``tasks_or_file_names``, :ref:`regex <decorators.collate_ex.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-           \
-   * :ref:`@collate <decorators.collate>` (``tasks_or_file_names``, :ref:`formatter <decorators.collate.matching_formatter>`\ *(*\ ``formatter_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-           \
-   * :ref:`@collate <decorators.collate_ex>` (``tasks_or_file_names``, :ref:`formatter <decorators.collate_ex.matching_formatter>`\ *(*\ ``formatter_pattern``\ *)*\ , :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
-           \
-
-   ", ""
-   "**@follows** (:ref:`Summary <decorators.follows>` / :ref:`Manual <new_manual.follows>`)
-
-   - Indicates task dependency
-   - optional :ref:`mkdir <decorators.follows.directory_name>` prerequisite (:ref:`see Manual <new_manual.follows.mkdir>`)
-
-   ", "
-   * :ref:`@follows <decorators.follows>` ( ``task1``, ``'task2'`` ))
-      \
-   * :ref:`@follows <decorators.follows>` ( ``task1``,  :ref:`mkdir <decorators.follows.directory_name>`\ ( ``'my/directory/'`` ))
-      \
-
-   ", ""
-   "**@posttask** (:ref:`Summary <decorators.posttask>` / :ref:`Manual <new_manual.posttask>`)
-
-   - Calls function after task completes
-   - Optional :ref:`touch_file <decorators.posttask.file_name>` indicator (:ref:`Manual <new_manual.posttask.touch_file>`)
-
-   ", "
-   * :ref:`@posttask <decorators.posttask>` ( ``signal_task_completion_function`` )
-           \
-   * :ref:`@posttask <decorators.posttask>` (:ref:`touch_file <decorators.touch_file>`\ ( ``'task1.completed'`` ))
-           \
-
-   ", ""
-   "**@active_if** (:ref:`Summary <decorators.active_if>` / :ref:`Manual <new_manual.active_if>`)
-
-    - Switches tasks on and off at run time depending on its parameters
-    - Evaluated each time :ref:`pipeline_run(...) <pipeline_functions.pipeline_run>`, :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` or :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>` is called.
-    - Dormant tasks behave as if they are up to date and have no output.
-
-   ", "
-   * :ref:`@active_if <decorators.active_if>` ( ``on_or_off1, [on_or_off2, ...]`` )
-           \
-
-   ", ""
-   "**@jobs_limit** (:ref:`Summary <decorators.jobs_limit>` / :ref:`Manual <new_manual.jobs_limit>`)
-
-   - Limits the amount of multiprocessing for the specified task
-   - Ensures that fewer than N jobs for this task are run in parallel
-   - Overrides ``multiprocess`` parameter in :ref:`pipeline_run(...) <pipeline_functions.pipeline_run>`
-   ", "
-   * :ref:`@jobs_limit <decorators.jobs_limit>` ( ``NUMBER_OF_JOBS_RUNNING_CONCURRENTLY`` )
-           \
-
-   ", ""
-   "**@mkdir** (:ref:`Summary <decorators.mkdir>` / :ref:`Manual <new_manual.mkdir>`)
-
-   - Generates paths for `os.makedirs  <http://docs.python.org/2/library/os.html#os.makedirs>`__
-
-   ", "
-   * :ref:`@mkdir <decorators.mkdir>` ( ``tasks_or_file_names``, :ref:`suffix <decorators.mkdir.suffix_string>`\ *(*\ ``suffix_string``\ *)*\ , ``output_pattern`` )
-              \
-   * :ref:`@mkdir <decorators.mkdir>` ( ``tasks_or_file_names``, :ref:`regex <decorators.mkdir.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern`` )
-           \
-   * :ref:`@mkdir <decorators.mkdir>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.mkdir.matching_formatter>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``)
-           \
-
-   ", ""
-   "**@graphviz** (:ref:`Summary <decorators.graphviz>` / :ref:`Manual <new_manual.pipeline_printout_graph>`)
-
-   - Customise the graphic for each task in printed flowcharts
-
-   ", "
-   * :ref:`@graphviz <decorators.graphviz>` ( ``graphviz_parameter = XXX``, ``[graphviz_parameter2 = YYY ...]``)
-           \
-
-   ", ""
-
-
-
-=============================================
-*Esoteric!*
-=============================================
- .. csv-table::
-   :header: "Decorator", "Examples"
-   :widths: 400, 600,1
-
-   "**@files** (:ref:`Summary <decorators.files>` / :ref:`Manual <new_manual.deprecated_files>`)
-
-   - I/O parameters
-   - skips up-to-date jobs
-   - Should use :ref:`@transform <decorators.transform>` etc instead
-
-   ", "
-   * :ref:`@files <decorators.files>`\ ( ``parameter_list`` )
-           \
-   * :ref:`@files <decorators.files>`\ ( ``parameter_generating_function`` )
-           \
-   * :ref:`@files <decorators.files>` ( ``input_file``, ``output_file``, ``other_params``, ... )
-           \
-
-   ", ""
-   "**@parallel** (:ref:`Summary <decorators.parallel>` / :ref:`Manual <new_manual.deprecated_parallel>`)
-
-   - By default, does not check if jobs are up to date
-   - Best used in conjuction with :ref:`@check_if_uptodate <decorators.check_if_uptodate>`
-
-   ", "
-   * :ref:`@parallel <decorators.parallel>` ( ``parameter_list`` ) (:ref:`see Manual <new_manual.deprecated_parallel>`)
-           \
-   * :ref:`@parallel <decorators.parallel>` ( ``parameter_generating_function`` ) (:ref:`see Manual <new_manual.on_the_fly>`)
-           \
-
-   ", ""
-   "**@check_if_uptodate** (:ref:`Summary <decorators.check_if_uptodate>` / :ref:`Manual <new_manual.check_if_uptodate>`)
-
-   - Custom function to determine if jobs need to be run
-
-   ", "
-   * :ref:`@check_if_uptodate <decorators.check_if_uptodate>` ( ``is_task_up_to_date_function`` )
-           \
-
-   ", ""
-   ".. tip::
-     The use of this overly complicated function is discouraged.
-       **@files_re** (:ref:`Summary <decorators.files_re>`)
-
-       - I/O file names via regular
-         expressions
-       - start from lists of file names
-         or |glob|_ results
-       - skips up-to-date jobs
-   ", "
-   * :ref:`@files_re <decorators.files_re>` ( ``tasks_or_file_names``, ``matching_regex``, [``input_pattern``,] ``output_pattern``, ``...`` )
-       ``input_pattern``/``output_pattern`` are regex patterns
-       used to create input/output file names from the starting
-       list of either glob_str or file names
-
-   ", ""
-
diff --git a/doc/_build/html/_sources/decorators/files.txt b/doc/_build/html/_sources/decorators/files.txt
deleted file mode 100644
index 8f73ba5..0000000
--- a/doc/_build/html/_sources/decorators/files.txt
+++ /dev/null
@@ -1,155 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.files:
-.. index::
-    pair: @files; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-
-.. |input| replace:: `input`
-.. _input: `decorators.files.input`_
-.. |input1| replace:: `input1`
-.. _input1: `decorators.files.input1`_
-.. |output| replace:: `output`
-.. _output: `decorators.files.output`_
-.. |output1| replace:: `output1`
-.. _output1: `decorators.files.output1`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.files.extra_parameters`_
-.. |extra_parameters1| replace:: `extra_parameters1`
-.. _extra_parameters1: `decorators.files.extra_parameters1`_
-
-
-########################
- at files
-########################
-
-*******************************************************************************************
-*@files* (|input1|_, |output1|_, [|extra_parameters1|_, ...])
-*******************************************************************************************
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- at files for single jobs
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-    **Purpose:**
-        Provides parameters to run a task.
-
-        The first two parameters in each set represent the input and output which are
-        used to see if the job is out of date and needs to be (re-)run.
-
-        By default, out of date checking uses input/output file timestamps.
-        (On some file systems, timestamps have a resolution in seconds.)
-        See :ref:`@check_if_uptodate() <decorators.check_if_uptodate>` for alternatives.
-
-
-    **Example**:
-        ::
-
-            from ruffus import *
-            @files('a.1', 'a.2', 'A file')
-            def transform_files(infile, outfile, text):
-                pass
-            pipeline_run([transform_files])
-
-    If ``a.2`` is missing or was created before ``a.1``, then the following will be called:
-        ::
-
-            transform_files('a.1', 'a.2', 'A file')
-
-    **Parameters:**
-
-.. _decorators.files.input1:
-
-    * *input*
-        Input file names
-
-
-.. _decorators.files.output1:
-
-    * *output*
-        Output file names
-
-
-.. _decorators.files.extra_parameters1:
-
-    * *extra_parameters*
-        optional ``extra_parameters`` are passed verbatim to each job.
-
-
-    **Checking if jobs are up to date:**
-        Strings in ``input`` and ``output`` (including in nested sequences) are interpreted as file names and
-        used to check if jobs are up-to-date.
-
-        See :ref:`above <decorators.files.check_up_to_date>` for more details
-
-
-*******************************************************************************************
-*@files* ( *((* |input|_, |output|_, [|extra_parameters|_,...] *), (...), ...)* )
-*******************************************************************************************
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- at files in parallel
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    **Purpose:**
-
-        Passes each set of parameters to separate jobs which can run in parallel
-
-        The first two parameters in each set represent the input and output which are
-        used to see if the job is out of date and needs to be (re-)run.
-
-        By default, out of date checking uses input/output file timestamps.
-        (On some file systems, timestamps have a resolution in seconds.)
-        See :ref:`@check_if_uptodate() <decorators.check_if_uptodate>` for alternatives.
-
-    **Example**:
-        ::
-
-            from ruffus import *
-            parameters = [
-                                [ 'a.1', 'a.2', 'A file'], # 1st job
-                                [ 'b.1', 'b.2', 'B file'], # 2nd job
-                          ]
-
-            @files(parameters)
-            def parallel_io_task(infile, outfile, text):
-                pass
-            pipeline_run([parallel_io_task])
-
-    is the equivalent of calling:
-        ::
-
-            parallel_io_task('a.1', 'a.2', 'A file')
-            parallel_io_task('b.1', 'b.2', 'B file')
-
-    **Parameters:**
-
-.. _decorators.files.input:
-
-    * *input*
-        Input file names
-
-
-.. _decorators.files.output:
-
-    * *output*
-        Output file names
-
-
-.. _decorators.files.extra_parameters:
-
-    * *extra_parameters*
-        optional ``extra_parameters`` are passed verbatim to each job.
-
-.. _decorators.files.check_up_to_date:
-
-    **Checking if jobs are up to date:**
-        #. Strings in ``input`` and ``output`` (including in nested sequences) are interpreted as file names and
-           used to check if jobs are up-to-date.
-        #. In the absence of input files (e.g. ``input == None``), the job will run if any output file is missing.
-        #. In the absence of output files (e.g. ``output == None``), the job will always run.
-        #. If any of the output files is missing, the job will run.
-        #. If any of the input files is missing when the job is run, a
-           ``MissingInputFileError`` exception will be raised.
-
-
diff --git a/doc/_build/html/_sources/decorators/files_ex.txt b/doc/_build/html/_sources/decorators/files_ex.txt
deleted file mode 100644
index d200d85..0000000
--- a/doc/_build/html/_sources/decorators/files_ex.txt
+++ /dev/null
@@ -1,77 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.files_on_the_fly:
-.. index::
-    pair: @files (on-the-fly parameter generation); Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-
-.. |custom_function| replace:: `custom_function`
-.. _custom_function: `decorators.files.custom_function`_
-
-
-################################################
-Generating parameters on the fly for @files
-################################################
-
-*******************************************************************************************
-*@files* (|custom_function|_)
-*******************************************************************************************
-    **Purpose:**
-
-        Uses a custom function to generate sets of parameters to separate jobs which can run in parallel.
-
-        The first two parameters in each set represent the input and output which are
-        used to see if the job is out of date and needs to be (re-)run.
-
-        By default, out of date checking uses input/output file timestamps.
-        (On some file systems, timestamps have a resolution in seconds.)
-        See :ref:`@check_if_uptodate() <decorators.check_if_uptodate>` for alternatives.
-
-    **Example**:
-        ::
-
-            from ruffus import *
-            def generate_parameters_on_the_fly():
-                parameters = [
-                                    ['input_file1', 'output_file1', 1, 2], # 1st job
-                                    ['input_file2', 'output_file2', 3, 4], # 2nd job
-                                    ['input_file3', 'output_file3', 5, 6], # 3rd job
-                             ]
-                for job_parameters in parameters:
-                    yield job_parameters
-
-            @files(generate_parameters_on_the_fly)
-            def parallel_io_task(input_file, output_file, param1, param2):
-                pass
-
-            pipeline_run([parallel_task])
-
-    is the equivalent of calling:
-        ::
-
-            parallel_io_task('input_file1', 'output_file1', 1, 2)
-            parallel_io_task('input_file2', 'output_file2', 3, 4)
-            parallel_io_task('input_file3', 'output_file3', 5, 6)
-
-
-    **Parameters:**
-
-
-.. _decorators.files.custom_function:
-
-        * *custom_function*:
-            Generator function which yields each time a complete set of parameters for one job
-
-    **Checking if jobs are up to date:**
-        Strings in ``input`` and ``output`` (including in nested sequences) are interpreted as file names and
-        used to check if jobs are up-to-date.
-
-        See :ref:`above <decorators.files.check_up_to_date>` for more details
-
-
-
-
-
diff --git a/doc/_build/html/_sources/decorators/files_re.txt b/doc/_build/html/_sources/decorators/files_re.txt
deleted file mode 100644
index 8d3df68..0000000
--- a/doc/_build/html/_sources/decorators/files_re.txt
+++ /dev/null
@@ -1,130 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.files_re:
-
-.. index::
-    pair: @files_re; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-
-########################
- at files_re
-########################
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.files_re.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.files_re.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.files_re.output_pattern`_
-.. |input_pattern| replace:: `input_pattern`
-.. _input_pattern: `decorators.files_re.input_pattern`_
-.. |matching_regex| replace:: `matching_regex`
-.. _matching_regex: `decorators.files_re.matching_regex`_
-
-*****************************************************************************************************************************************
-*@files_re* (|tasks_or_file_names|_, |matching_regex|_, [|input_pattern|_], |output_pattern|_, [|extra_parameters|_,...])
-*****************************************************************************************************************************************
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Legacy design now deprecated. We suggest using :ref:`@transform() <decorators.transform>` instead
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-    **Purpose:**
-
-        All singing, all dancing decorator which can do everything that :ref:`@merge() <decorators.merge>` and
-        :ref:`@transform() <decorators.transform>` can do.
-
-        Applies the task function to transform data from input to output files.
-
-        Output file names are determined from |tasks_or_file_names|_, i.e. from the output
-        of specified tasks, or a list of file names, using regular expression pattern substitutions.
-
-        Only out of date tasks (comparing input and output files) will be run.
-
-    **Example**:
-        ::
-
-            from ruffus import *
-            #
-            #   convert all files ending in ".1" into files ending in ".2"
-            #
-            @files_re('*.1', '(.*).1', r'\1.2')
-            def transform_func(infile, outfile):
-                open(outfile, "w").write(open(infile).read() + "\nconverted\n")
-
-            pipeline_run([task_re])
-
-    If the following files are present ``a.1``, ``b.1``, ``c.1``, this will result in the following function calls:
-        ::
-
-            transform_func("a.1", "a.2")
-            transform_func("b.1", "b.2")
-            transform_func("c.1", "c.2")
-
-    **Parameters:**
-
-.. _decorators.files_re.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_ .
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-.. _decorators.files_re.matching_regex:
-
-    * *matching_regex*
-       a python regular expression string.
-
-       | See python `regular expression (re) <http://docs.python.org/library/re.html>`_ documentation for details of regular expression syntax
-       | Each output file name is created using regular expression substitution with |output_pattern|_
-
-.. _decorators.files_re.input_pattern:
-
-    * *input_pattern*
-       Optionally specifies the resulting input file name(s).
-
-.. _decorators.files_re.output_pattern:
-
-    * *output_pattern*
-       Specifies the resulting output file name(s).
-
-.. _decorators.files_re.extra_parameters:
-
-    * [*extra_parameters, ...*]
-       Any extra parameters are passed to the task function.
-
-       | Regular expression substitution is first applied to (even nested) string parameters.
-       | Other data types are passed verbatim.
-
-       For example:
-        ::
-
-            from ruffus import *
-            #
-            #   convert all files ending in ".1" into files ending in ".2"
-            #
-            @files_re('*.1', '(.*).1', r'\1.2', [r'\1', 55], 17)
-            def transform_func(infile, outfile, extras, extra3):
-                extra1, extra2 = extras
-                open(outfile, "w").write(open(infile).read() + "\nconverted%s\n" % (extra1, extra2, extra3))
-
-            pipeline_run([transform_func])
-
-       If the following files are present ``a.1``, ``b.1``, ``c.1``, this will result in the following function calls:
-        ::
-
-            transform_func("a.1", "a.2", ["a", 55], 17)
-            transform_func("b.1", "b.2", ["b", 55], 17)
-            transform_func("c.1", "c.2", ["c", 55], 17)
-
-
-
-
-
-
diff --git a/doc/_build/html/_sources/decorators/follows.txt b/doc/_build/html/_sources/decorators/follows.txt
deleted file mode 100644
index 58e6d5c..0000000
--- a/doc/_build/html/_sources/decorators/follows.txt
+++ /dev/null
@@ -1,82 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.follows:
-.. index::
-    pair: @follows; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-    * More on @follows in the ``Ruffus`` :ref:`Manual <new_manual.follows>`
-
-    .. note::
-
-        Only missing directories are created.
-
-        In other words, the same directory can be specified multiple times safely without, for example, being recreated repeatedly.
-        Sometimes, for pipelines with multiple entry points, this is the only way to make sure that certain working or output
-        directories are always created or available *before* the pipeline runs.
-
-
-############
- at follows
-############
-
-.. _decorators.follows.mkdir:
-
-.. |task| replace:: `task`
-.. _task: `decorators.follows.task`_
-.. |task_name| replace:: `"task_name"`
-.. _task_name: `decorators.follows.task_name`_
-.. |directory_name| replace:: `directory_name`
-.. _directory_name: `decorators.follows.directory_name`_
-
-***************************************************************************************************************************************************
-*@follows*\ (|task|_ | |task_name|_ | :ref:`mkdir<decorators.mkdir>` (|directory_name|_), [more_tasks, ...])
-***************************************************************************************************************************************************
-    **Purpose:**
-
-        Indicates either
-
-            * task dependencies
-            * that the task requires a directory to be created first *if necessary*. (Existing directories will not be overwritten)
-
-
-    **Example**::
-
-        def task1():
-            print "doing task 1"
-
-        @follows(task1)
-        def task2():
-            print "doing task 2"
-
-
-    **Parameters:**
-
-.. _decorators.follows.task:
-
-    * *task*:
-        a list of tasks which have to be run **before** this function
-
-.. _decorators.follows.task_name:
-
-    * *"task_name"*:
-        Dependencies can be quoted function names.
-        Quoted function names allow dependencies to be added before the function is defined.
-
-        Functions in other modules need to be fully qualified.
-
-
-.. _decorators.follows.directory_name:
-
-    * *directory_name*:
-        Directories which need to be created (*only if they don't exist*) before
-        the task is run can be specified via a ``mkdir`` indicator object:
-
-            ::
-
-                @follows(task_x, mkdir("/output/directory") ...)
-                def task():
-                    pass
-
-
diff --git a/doc/_build/html/_sources/decorators/graphviz.txt b/doc/_build/html/_sources/decorators/graphviz.txt
deleted file mode 100644
index ebda4df..0000000
--- a/doc/_build/html/_sources/decorators/graphviz.txt
+++ /dev/null
@@ -1,92 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.graphviz:
-.. index::
-    pair: @graphviz; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-########################
- at graphviz
-########################
-
-.. |graphviz_parameters| replace:: `graphviz_parameters`
-.. _graphviz_parameters: `decorators.graphviz.graphviz_parameters`_
-
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@graphviz* ( |graphviz_parameters|_,...] )
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    *Contributed by Sean Davis, with improved syntax via Jake Biesinger*
-
-    **Purpose:**
-        Customise the graphic for each task in printed flowcharts by adding
-        `graphviz attributes  <http://www.graphviz.org/doc/info/attrs.html>`__,
-        (URL, shape, colour) to that node.
-
-        * This allows HTML formatting in the task names (using the ``label`` parameter as in the following example).
-          HTML labels **must** be enclosed in ``<`` and ``>``. E.g.
-
-          .. code-block:: python
-
-            label = "<Line <BR/> wrapped task_name()>"
-
-        * You can also opt to keep the task name and wrap it with a prefix and suffix:
-
-          .. code-block:: python
-
-            label_suffix = "??? ", label_prefix = ": What is this?"
-
-        * The ``URL`` attribute allows the generation of clickable svg, and also client / server
-          side image maps usable in web pages.
-          See `Graphviz documentation  <http://www.graphviz.org/content/output-formats#dimap>`__
-
-
-    **Example**:
-        .. code-block:: python
-
-
-            @graphviz(URL='"http://cnn.com"', fillcolor = '"#FFCCCC"',
-                            color = '"#FF0000"', pencolor='"#FF0000"', fontcolor='"#4B6000"',
-                            label_suffix = "???", label_prefix = "What is this?<BR/> ",
-                            label = "<What <FONT COLOR=\"red\">is</FONT>this>",
-                            shape= "component", height = 1.5, peripheries = 5,
-                            style="dashed")
-            def Up_to_date_task2(infile, outfile):
-                pass
-
-            #   Can use dictionary if you wish...
-            graphviz_params = {"URL":"http://cnn.com", "fontcolor": '"#FF00FF"'}
-            @graphviz(**graphviz_params)
-            def myTask(input,output):
-                pass
-
-        .. **
-
-        .. image:: ../images/history_html_flowchart.png
-           :scale: 30
-
-    **Parameters:**
-
-
-.. _decorators.graphviz.graphviz_parameters:
-
-    * named *graphviz_parameters*
-
-        Including among others:
-
-            * URL (e.g. ``"www.ruffus.org.uk"``)
-            * fillcolor
-            * color
-            * pencolor
-            * fontcolor
-            * label_suffix (appended to task name)
-            * label_prefix (precedes task name)
-            * label (replaces task name)
-            * shape (e.g. ``"component", "box", "diamond", "doubleoctagon"`` etc., see `graphviz <http://www.graphviz.org/doc/info/shapes.html>`__ )
-            * height
-            * peripheries (Number of borders)
-            * style (e.g. ``"solid", "wedged", "dashed"``  etc., see `graphviz <http://www.graphviz.org/doc/info/attrs.html#k:style>`__ )
-
-        Colours may specified as ``'"#FFCCCC"', 'red', 'red:blue', '/bugn9/7'`` etc. see  `color names <http://www.graphviz.org/doc/info/attrs.html#k:color>`__ and `colour schemes <http://www.graphviz.org/doc/info/colors.html>`__
diff --git a/doc/_build/html/_sources/decorators/indicator_objects.txt b/doc/_build/html/_sources/decorators/indicator_objects.txt
deleted file mode 100644
index e41cc4c..0000000
--- a/doc/_build/html/_sources/decorators/indicator_objects.txt
+++ /dev/null
@@ -1,547 +0,0 @@
-.. include:: ../global.inc
-
-
-.. seealso::
-    :ref:`Decorators <decorators>`
-
-.. index::
-    single: Indicator Object (Disambiguating parameters)
-
-.. _decorators.indicator_objects:
-
-
-########################
-Indicator Objects
-########################
-
-
-
-    How *ruffus* disambiguates certain parameters to decorators.
-
-    They are like `keyword arguments <http://docs.python.org/tutorial/controlflow.html#keyword-arguments>`_ in python, a little more verbose but they make the syntax much simpler.
-
-    Indicator objects are also "self-documenting" so you can see
-    exactly what is happening clearly.
-
-
-.. index::
-    pair: formatter; Indicator Object (Disambiguating parameters)
-
-.. _decorators.formatter:
-
-
-*********************************************
-*formatter*
-*********************************************
-
-    **formatter([** ``regex | None`` **, regex | None...])**
-
-    * The optional enclosed parameters are a python regular expression strings
-    * Each regular expression matches a corresponding *Input* file name string
-    * *formatter* parses each file name string into path and regular expression components
-    * Parsing fails altogether if the regular expression is not matched
-
-    Path components include:
-
-        * ``basename``: The `base name <http://docs.python.org/2/library/os.path.html#os.path.basename>`__ *excluding* `extension  <http://docs.python.org/2/library/os.path.html#os.path.splitext>`__, ``"file.name"``
-        * ``ext``     : The `extension <http://docs.python.org/2/library/os.path.html#os.path.splitext>`__, ``".ext"``
-        * ``path``    : The `dirname <http://docs.python.org/2/library/os.path.html#os.path.dirname>`__, ``"/directory/to/a"``
-        * ``subdir``  : A list of sub-directories in the ``path`` in reverse order, ``["a", "to", "directory", "/"]``
-        * ``subpath`` : A list of descending sub-paths in reverse order, ``["/directory/to/a", "/directory/to", "/directory", "/"]``
-
-    The replacement string refers to these components using python `string.format <http://docs.python.org/2/library/string.html#string-formatting>`__ style curly braces. ``{NAME}``
-
-    We refer to an element from the Nth input string by index, for example:
-
-       * ``"{ext[0]}"``     is the extension of the first input string.
-       * ``"{basename[1]}"`` is the basename of the second input string.
-       * ``"{basename[1][0:3]}"`` are the first three letters from the basename of the second input string.
-
-    **Used by:**
-        * :ref:`@split <decorators.split>`
-        * :ref:`@transform <decorators.transform>`
-        * :ref:`@merge <decorators.merge>`
-        * :ref:`@subdivide <decorators.subdivide>`
-        * :ref:`@collate <decorators.collate>`
-        * :ref:`@product <decorators.product>`
-        * :ref:`@permutations <decorators.permutations>`
-        * :ref:`@combinations <decorators.combinations>`
-        * :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`
-
-    **@transform example**:
-
-        .. code-block:: python
-            :emphasize-lines: 14, 18,19
-
-            from ruffus import *
-
-            #   create initial file pairs
-            @originate([   ['job1.a.start', 'job1.b.start'],
-                           ['job2.a.start', 'job2.b.start'],
-                           ['job3.a.start', 'job3.c.start']    ])
-            def create_initial_file_pairs(output_files):
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-
-            #---------------------------------------------------------------
-            #
-            #   formatter
-            #
-            @transform(create_initial_file_pairs,                               # Input
-
-                        formatter(".+/job(?P<JOBNUMBER>\d+).a.start",           # Extract job number
-                                  ".+/job[123].b.start"),                       # Match only "b" files
-
-                        ["{path[0]}/jobs{JOBNUMBER[0]}.output.a.1",             # Replacement list
-                         "{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"])
-            def first_task(input_files, output_parameters):
-                print "input_parameters = ", input_files
-                print "output_parameters = ", output_parameters
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-        This produces:
-
-        .. code-block:: pycon
-
-            input_parameters  =  ['job1.a.start',
-                                  'job1.b.start']
-            output_parameters =  ['/home/lg/src/temp/jobs1.output.a.1',
-                                  '/home/lg/src/temp/jobs1.output.b.1', 45]
-
-            input_parameters  =  ['job2.a.start',
-                                  'job2.b.start']
-            output_parameters =  ['/home/lg/src/temp/jobs2.output.a.1',
-                                  '/home/lg/src/temp/jobs2.output.b.1', 45]
-
-    **@permutations example**:
-
-        Combinatoric decorators such as :ref:`@product <decorators.product>` or
-        :ref:`@product <decorators.permutations>` behave much
-        like nested for loops in enumerating, combining, and permutating the original sets
-        of inputs.
-
-        The replacement strings require an extra level of indirection to refer to
-        parsed components:
-
-        .. code-block:: python
-            :emphasize-lines: 14, 18,19
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   create initial files
-            @originate([ 'a.start', 'b.start', 'c.start'])
-            def create_initial_files(output_file):
-                with open(output_file, "w") as oo: pass
-
-
-            #---------------------------------------------------------------
-            #
-            #   formatter
-            #
-            @permutations(create_initial_files,                                           # Input
-
-                        formatter("(.start)$"),                                           # match input file in permutations
-                        2,
-
-                        "{path[0][0]}/{basename[0][0]}_vs_{basename[1][0]}.product",    # Output Replacement string
-                        "{path[0][0]}",                                                 # path for 1st set of files, 1st file name
-                        ["{basename[0][0]}",                                            # basename for 1st set of files, 1st file name
-                         "{basename[1][0]}"])                                           # basename for 2nd set of files, 1st file name
-            def product_task(input_file, output_parameter, shared_path, basenames):
-                print "input_parameter  = ", input_file
-                print "output_parameter = ", output_parameter
-                print "shared_path      = ", shared_path
-                print "basenames        = ", basenames
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-        This produces:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-            input_parameter  =  ('a.start', 'b.start')
-            output_parameter =  /home/lg/src/oss/ruffus/a_vs_b.product
-            shared_path      =  /home/lg/src/oss/ruffus
-            basenames        =  ['a', 'b']
-
-            input_parameter  =  ('a.start', 'c.start')
-            output_parameter =  /home/lg/src/oss/ruffus/a_vs_c.product
-            shared_path      =  /home/lg/src/oss/ruffus
-            basenames        =  ['a', 'c']
-
-            input_parameter  =  ('b.start', 'a.start')
-            output_parameter =  /home/lg/src/oss/ruffus/b_vs_a.product
-            shared_path      =  /home/lg/src/oss/ruffus
-            basenames        =  ['b', 'a']
-
-            input_parameter  =  ('b.start', 'c.start')
-            output_parameter =  /home/lg/src/oss/ruffus/b_vs_c.product
-            shared_path      =  /home/lg/src/oss/ruffus
-            basenames        =  ['b', 'c']
-
-            input_parameter  =  ('c.start', 'a.start')
-            output_parameter =  /home/lg/src/oss/ruffus/c_vs_a.product
-            shared_path      =  /home/lg/src/oss/ruffus
-            basenames        =  ['c', 'a']
-
-            input_parameter  =  ('c.start', 'b.start')
-            output_parameter =  /home/lg/src/oss/ruffus/c_vs_b.product
-            shared_path      =  /home/lg/src/oss/ruffus
-            basenames        =  ['c', 'b']
-
-
-
-.. index::
-    pair: suffix; Indicator Object (Disambiguating parameters)
-
-.. _decorators.suffix:
-
-
-*********************************************
-*suffix*
-*********************************************
-
-    **suffix(** ``string`` **)**
-
-    The enclosed parameter is a string which must match *exactly* to the end
-    of a file name.
-
-
-    **Used by:**
-        * :ref:`@transform <decorators.transform>`
-
-    **Example**:
-        ::
-
-            #
-            #   Transforms ``*.c`` to ``*.o``::
-            #
-            @transform(previous_task, suffix(".c"), ".o")
-            def compile(infile, outfile):
-                pass
-
-.. index::
-    pair: regex; Indicator Object (Disambiguating parameters)
-
-.. _decorators.regex:
-
-*********************************************
-*regex*
-*********************************************
-
-    **regex(** ``regular_expression`` **)**
-
-
-    The enclosed parameter is a python regular expression string,
-    which must be wrapped in a ``regex`` indicator object.
-
-    See python `regular expression (re) <http://docs.python.org/library/re.html>`_
-    documentation for details of regular expression syntax
-
-
-    **Used by:**
-
-        * :ref:`@transform <decorators.transform>`
-        * :ref:`@subdivide <decorators.subdivide>`
-        * :ref:`@collate <decorators.collate>`
-        * The deprecated :ref:`@files_re <decorators.files_re>`
-
-    **Example**:
-        ::
-
-            @transform(previous_task, regex(r".c$"), ".o")
-            def compile(infile, outfile):
-                pass
-
-.. index::
-    pair: add_inputs; Indicator Object (Adding additional input parameters)
-
-.. _decorators.add_inputs:
-
-***********************************************
-*add_inputs*
-***********************************************
-
-    **add_inputs(** ``input_file_pattern`` **)**
-
-    The enclosed parameter(s) are pattern strings or a nested structure which is added to the
-    input for each job.
-
-    **Used by:**
-        * :ref:`@transform <decorators.transform_ex>`
-        * :ref:`@collate <decorators.transform_ex>`
-        * :ref:`@subdivide <decorators.subdivide>`
-
-    **Example @transform with suffix(...)**
-
-        A common task in compiling C code is to include the corresponding header file for the source.
-        To compile ``*.c`` to ``*.o``, adding ``*.h`` and the common header ``universal.h``:
-
-            ::
-
-                @transform(["1.c", "2.c"], suffix(".c"), add_inputs([r"\1.h", "universal.h"]),  ".o")
-                def compile(infile, outfile):
-                    # do something here
-                    pass
-
-        | The starting files names are ``1.c`` and ``2.c``.
-        | ``suffix(".c")`` matches ".c" so ``\1`` stands for the unmatched prefices  ``"1"`` and ``"2"``
-
-        This will result in the following functional calls:
-            ::
-
-                compile(["1.c", "1.h", "universal.h"], "1.o")
-                compile(["2.c", "2.h", "universal.h"], "2.o")
-
-
-        A string like ``universal.h`` in ``add_inputs`` will added *as is*.
-        ``r"\1.h"``, however, performs suffix substitution, with the special form ``r"\1"`` matching everything up to the suffix.
-        Remember to 'escape' ``r"\1"`` otherwise Ruffus will complain and throw an ``Exception`` to remind you.
-        The most convenient way is to use a python "raw" string.
-
-    **Example of add_inputs(...) with regex(...)**
-
-        The suffix match (``suffix(...)``) is exactly equivalent to the following code using regular expression (``regex(...)``):
-            ::
-
-                @transform(["1.c", "2.c"], regex(r"^(.+)\.c$"), add_inputs([r"\1.h", "universal.h"]),  r"\1.o")
-                def compile(infile, outfile):
-                    # do something here
-                    pass
-
-        The ``suffix(..)`` code is much simpler but the regular expression allows more complex substitutions.
-
-    **add_inputs(...) preserves original inputs**
-
-        ``add_inputs`` nests the the original input parameters in a list before adding additional dependencies.
-
-        This can be seen in the following example:
-            ::
-
-                @transform([    ["1.c", "A.c", 2]
-                                ["2.c", "B.c", "C.c", 3]],
-                                suffix(".c"), add_inputs([r"\1.h", "universal.h"]),  ".o")
-                def compile(infile, outfile):
-                    # do something here
-                    pass
-
-        This will result in the following functional calls:
-            ::
-
-                compile([["1.c", "A.c", 2],        "1.h", "universal.h"], "1.o")
-                compile([["3.c", "B.c", "C.c", 3], "2.h", "universal.h"], "2.o")
-
-
-        The original parameters are retained unchanged as the first item in a list
-
-
-
-
-.. index::
-    pair: inputs; Indicator Object (Replacing input parameters)
-
-.. _decorators.inputs:
-
-***************************************
-*inputs*
-***************************************
-
-    **inputs(** ``input_file_pattern`` **)**
-
-    **Used by:**
-        * :ref:`@transform <decorators.transform_ex>`
-        * :ref:`@collate <decorators.transform_ex>`
-        * :ref:`@subdivide <decorators.subdivide>`
-
-    The enclosed single parameter is a pattern string or a nested structure which is
-    used to construct the input for each job.
-
-    If more than one argument is supplied to inputs, an exception will be raised.
-
-    Use a tuple or list (as in the following example) to send multiple input arguments to each job.
-
-    **Used by:**
-        * The advanced form of :ref:`@transform <decorators.transform_ex>`
-
-    **inputs(...) replaces original inputs**
-
-        ``inputs(...)`` allows the original input parameters to be replaced wholescale.
-
-        This can be seen in the following example:
-            ::
-
-                @transform([    ["1.c", "A.c", 2]
-                                ["2.c", "B.c", "C.c", 3]],
-                                suffix(".c"), inputs([r"\1.py", "docs.rst"]),  ".pyc")
-                def compile(infile, outfile):
-                    # do something here
-                    pass
-
-        This will result in the following functional calls:
-            ::
-
-                compile(["1.py", "docs.rst"], "1.pyc")
-                compile(["2.py", "docs.rst"], "2.pyc")
-
-        In this example, the corresponding python files have been sneakily substituted
-        without trace in the place of the C source files.
-
-
-.. index::
-    single: @follows; mkdir (Syntax)
-    single: mkdir; @follows (Syntax)
-    single: Indicator Object (Disambiguating parameters); mkdir
-
-.. _decorators.indicator_objects.mkdir:
-
-
-******************************************************************************************
-*mkdir*
-******************************************************************************************
-
-    **mkdir(** ``directory_name1`` **, [** ``directory_name2`` **, ...] )**
-
-    The enclosed parameter is a directory name or a sequence of directory names.
-    These directories will be created as part of the prerequisites of running a task.
-
-    **Used by:**
-        * :ref:`@follows <decorators.follows>`
-
-    **Example:**
-        ::
-
-            @follows(mkdir("/output/directory"))
-            def task():
-                pass
-
-
-.. index::
-    single: @posttask; touch_file (Syntax)
-    single: touch_file; @posttask (Syntax)
-    single: Indicator Object (Disambiguating parameters); touch_file
-
-.. _decorators.touch_file:
-
-
-******************************************************************************************
-*touch_file*
-******************************************************************************************
-
-    **touch_file(** ``file_name`` **)**
-
-    The enclosed parameter is a file name. This file will be ``touch``\ -ed after a
-    task is executed.
-
-    This will change the date/time stamp of the ``file_name`` to the current date/time.
-    If the file does not exist, an empty file will be created.
-
-
-    **Used by:**
-        * :ref:`@posttask <decorators.posttask>`
-
-    **Example:**
-        ::
-
-            @posttask(touch_file("task_completed.flag"))
-            @files(None, "a.1")
-            def do_task(input_file, output_file):
-                pass
-
-
-.. index::
-    pair: output_from; Indicator Object (Disambiguating parameters)
-
-.. _decorators.output_from:
-
-******************************************************************************************
-*output_from*
-******************************************************************************************
-
-    **output_from (** ``file_name_string1`` **[,** ``file_name_string1`` **, ...] )**
-
-    Indicates that any enclosed strings are not file names but refer to task functions.
-
-    **Used by:**
-        * :ref:`@split <decorators.split>`
-        * :ref:`@transform <decorators.transform>`
-        * :ref:`@merge <decorators.merge>`
-        * :ref:`@collate <decorators.collate>`
-        * :ref:`@subdivide <decorators.subdivide>`
-        * :ref:`@product <decorators.product>`
-        * :ref:`@permutations <decorators.permutations>`
-        * :ref:`@combinations <decorators.combinations>`
-        * :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`
-        * :ref:`@files <decorators.files>`
-
-    **Example:**
-        ::
-
-            @split(["a.file", ("b.file", output_from("task1", 76, "task2"))], "*.split")
-            def task2(input, output):
-                pass
-
-
-        is equivalent to:
-
-        ::
-
-            @split(["a.file", ("b.file", (task1, 76, task2))], "*.split")
-            def task2(input, output):
-                pass
-
-
-
-
-.. index::
-    single: @files_re; combine (Deprecated Syntax)
-    single: combine; @follows (Deprecated Syntax)
-    single: Indicator Object (Disambiguating parameters); combine
-
-.. _decorators.combine:
-
-******************************************************************************************
-*combine*
-******************************************************************************************
-
-    **combine(** ``arguments`` **)**
-
-    .. warning::
-
-        This is deprecated syntax.
-
-        Please do not use!
-
-        :ref:`@merge <decorators.merge>` and :ref:`@collate <decorators.collate>` are more powerful
-        and have straightforward syntax.
-
-    Indicates that the *inputs* of :ref:`@files_re <decorators.files_re>` will be collated
-    or summarised into *outputs* by category. See the :ref:`Manual <new_manual.files_re.combine>`  or
-    :ref:` @collate <new_manual.collate>` for examples.
-
-
-    **Used by:**
-        * :ref:`@files_re <new_manual.files_re.combine>`
-
-    **Example:**
-        ::
-
-            @files_re('*.animals',                           # inputs = all *.animal files
-                        r'mammals.([^.]+)',                  # regular expression
-                        combine(r'\1/animals.in_my_zoo'),    # single output file per species
-                        r'\1' )                              # species name
-            def capture_mammals(infiles, outfile, species):
-                # summarise all animals of this species
-                ""
-
diff --git a/doc/_build/html/_sources/decorators/jobs_limit.txt b/doc/_build/html/_sources/decorators/jobs_limit.txt
deleted file mode 100644
index 1e0ee41..0000000
--- a/doc/_build/html/_sources/decorators/jobs_limit.txt
+++ /dev/null
@@ -1,73 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.jobs_limit:
-.. index::
-    pair: @jobs_limit; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-
-########################
- at jobs_limit
-########################
-
-.. |maximum_num_of_jobs| replace:: `maximum_num_of_jobs`
-.. _maximum_num_of_jobs: `decorators.jobs_limit.maximum_num_of_jobs`_
-.. |name| replace:: `name`
-.. _name: `decorators.jobs_limit.name`_
-
-*****************************************************************************************************************************************
-*@jobs_limit* ( |maximum_num_of_jobs|_, [ |name|_ ])
-*****************************************************************************************************************************************
-    **Purpose:**
-        | Manages the resources available for a task.
-        | Limits the number of concurrent jobs which can be run in parallel for this task
-        | Overrides the value for ``multiprocess`` in :ref:`pipeline_run <pipeline_functions.pipeline_run>`
-        | If an optional ``name`` is given, the same limit is shared across all tasks with the same @job_limit name.
-
-
-    **Parameters:**
-
-.. _decorators.jobs_limit.maximum_num_of_jobs:
-
-
-    * *maximum_num_of_jobs*
-       The maximum number of concurrent jobs for this task. Must be an integer number
-       greater than or equal to 1.
-
-.. _decorators.jobs_limit.name:
-
-    * *name*
-       Optional name for the limit. All tasks with the same name share the same limit if they
-       are running concurrently.
-
-    **Example**
-        ::
-
-            from ruffus import *
-
-            # make list of 10 files
-            @split(None, "*.stage1")
-            def make_files(input_file, output_files):
-                for i in range(10):
-                    open("%d.stage1" % i, "w")
-
-            @jobs_limit(2)
-            @transform(make_files, suffix(".stage1"), ".stage2")
-            def stage1(input_file, output_file):
-                open(output_file, "w")
-
-            @transform(stage1, suffix(".stage2"), ".stage3")
-            def stage2(input_file, output_file):
-                open(output_file, "w")
-
-            pipeline_run([stage2], multiprocess = 5)
-
-        will run the 10 jobs of ``stage1`` 2 at a time, while `` stage2`` will
-        run 5 at a time (from ``multiprocess = 5``):
-
-        .. image:: ../images/jobs_limit.png
-
-
-
diff --git a/doc/_build/html/_sources/decorators/merge.txt b/doc/_build/html/_sources/decorators/merge.txt
deleted file mode 100644
index bd85ee8..0000000
--- a/doc/_build/html/_sources/decorators/merge.txt
+++ /dev/null
@@ -1,64 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.merge:
-.. index::
-    pair: @merge; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.merge.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.merge.extra_parameters`_
-.. |output_file| replace:: `output_file`
-.. _output_file: `decorators.merge.output_file`_
-
-########################
- at merge
-########################
-
-************************************************************************************
-*@merge* ( |tasks_or_file_names|_, |output_file|_, [|extra_parameters|_,...] )
-************************************************************************************
-    **Purpose:**
-        Merges multiple input files into a single output.
-
-        Only out of date tasks (comparing input and output files) will be run
-
-    **Example**::
-
-        @merge(previous_task, 'all.summary')
-        def summarize(infiles, summary_file):
-            pass
-
-    **Parameters:**
-
-
-.. _decorators.merge.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-
-.. _decorators.merge.output_file:
-
-    * *output_file*
-        Specifies the resulting output file name(s).
-
-.. _decorators.merge.extra_parameters:
-
-    * *extra_parameters, ...*
-        Any optional extra parameters are passed verbatim to the task function
-
-
-
-See :ref:`here <decorators.collate>` for more advanced uses of merging.
-
-
diff --git a/doc/_build/html/_sources/decorators/mkdir.txt b/doc/_build/html/_sources/decorators/mkdir.txt
deleted file mode 100644
index b516b1a..0000000
--- a/doc/_build/html/_sources/decorators/mkdir.txt
+++ /dev/null
@@ -1,220 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.mkdir:
-.. index::
-    pair: @mkdir; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-    * More on @mkdir in the ``Ruffus`` :ref:`Manual <new_manual.mkdir>`
-    * :ref:`@follows(mkdir("dir")) <decorators.follows>` specifies the creation of a *single* directory as a task pre-requisite.
-
-########################
- at mkdir
-########################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.mkdir.tasks_or_file_names`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.mkdir.output_pattern`_
-.. |matching_regex| replace:: `matching_regex`
-.. _matching_regex: `decorators.mkdir.matching_regex`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.mkdir.matching_formatter`_
-.. |suffix_string| replace:: `suffix_string`
-.. _suffix_string: `decorators.mkdir.suffix_string`_
-
-******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@mkdir* ( |tasks_or_file_names|_, :ref:`suffix<decorators.suffix>`\ *(*\ |suffix_string|_\ *)*\ | :ref:`regex<decorators.regex>`\ *(*\ |matching_regex|_\ *)* |  :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, |output_pattern|_)
-******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    **Purpose:**
-
-        * Prepares directories to receive *Output* files
-        * Used when *Output* path names are generated at runtime from *Inputs*. **mkdir** can make sure these runtime specified paths exist.
-        * Directory names are generated from **Input** using string substitution via :ref:`formatter() <decorators.formatter>`,  :ref:`suffix() <decorators.suffix>` or  :ref:`regex() <decorators.regex>`.
-        * Behaves essentially like ``@transform`` but with its own (internal) function which does the actual work of making a directory
-        * Does *not* invoke the host task function to which it is attached
-        * Makes specified directories using `os.makedirs  <http://docs.python.org/2/library/os.html#os.makedirs>`__
-        * Multiple directories can be created in a list
-
-        .. note::
-
-            Only missing directories are created.
-
-            In other words, the same directory can be specified multiple times safely without, for example, being recreated repeatedly.
-
-            Sometimes, for pipelines with multiple entry points, this is the only way to make sure that certain working or output
-            directories are always created or available *before* the pipeline runs.
-
-    **Simple Example**
-
-        Creates multiple directories per job to hold the results of :ref:`@transform<decorators.transform>`
-
-            .. code-block:: python
-                :emphasize-lines: 10,20
-
-                from ruffus import *
-
-                #   initial files
-                @originate([ 'A.start',
-                             'B.start'])
-                def create_initial_files(output_file):
-                    with open(output_file, "w") as oo: pass
-
-
-                # create files without making directories -> ERROR
-                @transform( create_initial_files,
-                            formatter(),
-                            ["{path[0]}/{basename[0]}/processed.txt",
-                             "{path[0]}/{basename[0]}.tmp/tmp.processed.txt"])
-                def create_files_without_mkdir(input_file, output_files):
-                    open(output_files[0], "w")
-                    open(output_files[1], "w")
-
-
-                # create files after making corresponding directories
-                @mkdir( create_initial_files,
-                        formatter(),
-                        ["{path[0]}/{basename[0]}",         # create directory
-                         "{path[0]}/{basename[0]}.tmp"])    # create directory.tmp
-                @transform( create_initial_files,
-                            formatter(),
-                            ["{path[0]}/{basename[0]}/processed.txt",
-                             "{path[0]}/{basename[0]}.tmp/tmp.processed.txt"])
-                def create_files_with_mkdir(input_file, output_files):
-                    open(output_files[0], "w")
-                    open(output_files[1], "w")
-
-                pipeline_run([create_files_without_mkdir])
-                pipeline_run([create_files_with_mkdir])
-
-        Running without making the directories first gives errors:
-
-            .. code-block:: python
-                :emphasize-lines: 14-19
-
-                >>> pipeline_run([create_files_without_mkdir])
-                    Job  = [None -> A.start] completed
-                    Job  = [None -> B.start] completed
-                Completed Task = create_initial_files
-
-                    Traceback (most recent call last):
-                      File "<stdin>", line 1, in <module>
-                      File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 3738, in pipeline_run
-                        raise job_errors
-                    ruffus.ruffus_exceptions.RethrownJobError:
-
-                    Original exception:
-
-                >>> #    Exception #1
-                >>> #      'exceptions.IOError([Errno 2] No such file or directory: 'A/processed.txt')' raised in ...
-                >>> #       Task = def create_files_without_mkdir(...):
-                >>> #       Job  = [A.start -> [processed.txt, tmp.processed.txt]]
-
-
-        Running after making the directories first:
-
-            .. code-block:: python
-                :emphasize-lines: 15
-
-                >>> pipeline_run([create_files_with_mkdir])
-                    Job  = [None -> A.start] completed
-                    Job  = [None -> B.start] completed
-                Completed Task = create_initial_files
-                    Make directories [A, A.tmp] completed
-                    Make directories [B, B.tmp] completed
-                Completed Task = (mkdir 1) before create_files_with_mkdir
-                    Job  = [A.start -> [processed.txt, tmp.processed.txt]] completed
-                    Job  = [B.start -> [processed.txt, tmp.processed.txt]] completed
-                Completed Task = create_files_with_mkdir
-
-
-
-    **Escaping regular expression patterns**
-
-        A string like ``universal.h`` in ``add_inputs`` will added *as is*.
-        ``r"\1.h"``, however, performs suffix substitution, with the special form ``r"\1"`` matching everything up to the suffix.
-        Remember to 'escape' ``r"\1"`` otherwise Ruffus will complain and throw an Exception to remind you.
-        The most convenient way is to use a python "raw" string.
-
-    **Parameters:**
-
-.. _decorators.mkdir.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-.. _decorators.mkdir.suffix_string:
-
-    * *suffix_string*
-       must be wrapped in a :ref:`suffix<decorators.suffix>` indicator object.
-       The end of each input file name which matches ``suffix_string`` will be replaced by ``output_pattern``.
-
-       Input file names which do not match suffix_string will be ignored
-
-
-       The non-suffix part of the match can be referred to using the ``"\1"`` pattern. This
-       can be useful for putting the output in different directory, for example::
-
-
-            @mkdir(["1.c", "2.c"], suffix(".c"), r"my_path/\1.o")
-            def compile(infile, outfile):
-                pass
-
-       This results in the following function calls:
-
-            ::
-
-                # 1.c -> my_path/1.o
-                # 2.c -> my_path/2.o
-                compile("1.c", "my_path/1.o")
-                compile("2.c", "my_path/2.o")
-
-       For convenience and visual clarity, the  ``"\1"`` can be omitted from the output parameter.
-       However, the ``"\1"`` is mandatory for string substitutions in additional parameters, ::
-
-
-            @mkdir(["1.c", "2.c"], suffix(".c"), [r"\1.o", ".o"], "Compiling \1", "verbatim")
-            def compile(infile, outfile):
-                pass
-
-       Results in the following function calls:
-
-            ::
-
-                compile("1.c", ["1.o", "1.o"], "Compiling 1", "verbatim")
-                compile("2.c", ["2.o", "2.o"], "Compiling 2", "verbatim")
-
-       Since r"\1" is optional for the output parameter, ``"\1.o"`` and ``".o"`` are equivalent.
-       However, strings in other parameters which do not contain r"\1" will be included verbatim, much
-       like the string ``"verbatim"`` in the above example.
-
-
-
-
-.. _decorators.mkdir.matching_regex:
-
-    * *matching_regex*
-       is a python regular expression string, which must be wrapped in
-       a :ref:`regex<decorators.regex>`\  indicator object
-       See python `regular expression (re) <http://docs.python.org/library/re.html>`_
-       documentation for details of regular expression syntax
-       Each output file name is created using regular expression substitution with ``output_pattern``
-
-.. _decorators.mkdir.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-.. _decorators.mkdir.output_pattern:
-
-    * *output_pattern*
-       Specifies the resulting output file name(s).
-
diff --git a/doc/_build/html/_sources/decorators/originate.txt b/doc/_build/html/_sources/decorators/originate.txt
deleted file mode 100644
index 513a285..0000000
--- a/doc/_build/html/_sources/decorators/originate.txt
+++ /dev/null
@@ -1,79 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.originate:
-.. index::
-    pair: @originate; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-########################
- at originate
-########################
-
-.. |output_files| replace:: `output_files`
-.. _output_files: `decorators.originate.output_files`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.originate.extra_parameters`_
-
-
-***********************************************************************************************************************************************************
-*@originate* ( |output_files|_, [|extra_parameters|_,...] )
-***********************************************************************************************************************************************************
-    **Purpose:**
-        * Creates (originates) a set of starting file without dependencies from scratch  (*ex nihilo*!)
-        * Only called to create files which do not exist.
-        * Invoked onces (a job created) per item in the ``output_files`` list.
-
-        .. note::
-
-            The first argument for the task function is the *Output*. There is by definition no
-            *Input* for ``@originate``
-
-    **Example**:
-
-        .. code-block:: python
-
-            from ruffus import *
-            @originate(["a", "b", "c", "d"], "extra")
-            def test(output_file, extra):
-                open(output_file, "w")
-
-            pipeline_run()
-
-        .. code-block:: pycon
-            :emphasize-lines: 8,11
-
-            >>> pipeline_run()
-                Job  = [None -> a, extra] completed
-                Job  = [None -> b, extra] completed
-                Job  = [None -> c, extra] completed
-                Job  = [None -> d, extra] completed
-            Completed Task = test
-
-            >>> # all files exist: nothing to do
-            >>> pipeline_run()
-
-            >>> # delete 'a' so that it is missing
-            >>> import os
-            >>> os.unlink("a")
-
-            >>> pipeline_run()
-                Job  = [None -> a, extra] completed
-            Completed Task = test
-
-    **Parameters:**
-
-
-.. _decorators.originate.output_files:
-
-    * *output_files*
-       * Can be a single file name or a list of files
-       * Each item in the list is treated as the *Output* of a separate job
-
-
-.. _decorators.originate.extra_parameters:
-
-    * *extra_parameters*
-        Any extra parameters are passed verbatim to the task function
-
diff --git a/doc/_build/html/_sources/decorators/parallel.txt b/doc/_build/html/_sources/decorators/parallel.txt
deleted file mode 100644
index f16cd48..0000000
--- a/doc/_build/html/_sources/decorators/parallel.txt
+++ /dev/null
@@ -1,81 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.parallel:
-.. index::
-    pair: @parallel; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-
-########################
- at parallel
-########################
-
-.. |job_params| replace:: `job_params`
-.. _job_params: `decorators.parallel.job_params`_
-.. |parameter_generating_function| replace:: `parameter_generating_function`
-.. _parameter_generating_function: `decorators.parallel.parameter_generating_function`_
-
-
-*****************************************************************************************************************************************
-*@parallel* ( [ [|job_params|_, ...], [|job_params|_, ...]...] | |parameter_generating_function|_)
-*****************************************************************************************************************************************
-    **Purpose:**
-        To apply the (task) function to a set of parameters in parallel without file dependency checking.
-
-        Most useful allied to :ref:`@check_if_uptodate() <decorators.check_if_uptodate>`
-
-    **Example**::
-
-        from ruffus import *
-        parameters = [
-                         ['A', 1, 2], # 1st job
-                         ['B', 3, 4], # 2nd job
-                         ['C', 5, 6], # 3rd job
-                     ]
-        @parallel(parameters)
-        def parallel_task(name, param1, param2):
-            sys.stderr.write("    Parallel task %s: " % name)
-            sys.stderr.write("%d + %d = %d\\n" % (param1, param2, param1 + param2))
-
-        pipeline_run([parallel_task])
-
-    **Parameters:**
-
-
-.. _decorators.parallel.job_params:
-
-    * *job_params*:
-        Requires a sequence of parameters, one set for each job.
-
-        Each set of parameters can be one or more items in a sequence which will be passed to
-        the decorated task function iteratively (or in parallel)
-
-        For example::
-
-            parameters = [
-                             ['A', 1, 2], # 1st job
-                             ['B', 3, 4], # 2nd job
-                             ['C', 5, 6], # 3rd job
-                         ]
-            @parallel(parameters)
-            def parallel_task(name, param1, param2):
-                pass
-
-        Will result in the following function calls::
-
-            parallel_task('A', 1, 2)
-            parallel_task('B', 3, 4)
-            parallel_task('C', 5, 6)
-
-
-
-.. _decorators.parallel.parameter_generating_function:
-
-    * *parameter_generating_function*
-        #. A generator yielding  set of parameters (as above) in turn and on the fly
-        #. A function returning a sequence of parameter sets, as above
-
-
-
diff --git a/doc/_build/html/_sources/decorators/permutations.txt b/doc/_build/html/_sources/decorators/permutations.txt
deleted file mode 100644
index 1ef39a6..0000000
--- a/doc/_build/html/_sources/decorators/permutations.txt
+++ /dev/null
@@ -1,158 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.permutations:
-.. index::
-    pair: @permutations; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-########################
- at permutations
-########################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.permutations.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.permutations.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.permutations.output_pattern`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.permutations.matching_formatter`_
-
-
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@permutations* ( |tasks_or_file_names|_, :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, |output_pattern|_, [|extra_parameters|_,...] )
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    **Purpose:**
-
-        Generates the **permutations**, between all the elements of a set of **Input**
-
-        The effect is analogous to the python `itertools  <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__
-        function of the same name:
-
-        .. code-block:: pycon
-            :emphasize-lines: 2
-
-            >>> from itertools import permutations
-            >>> # permutations('ABCD', 2) --> AB AC AD BA BC BD CA CB CD DA DB DC
-            >>> [ "".join(a) for a in permutations("ABCD", 2)]
-            ['AB', 'AC', 'AD', 'BA', 'BC', 'BD', 'CA', 'CB', 'CD', 'DA', 'DB', 'DC']
-
-        Only out of date tasks (comparing input and output files) will be run
-
-        Output file names and strings in the extra parameters
-        are determined from |tasks_or_file_names|_, i.e. from the output
-        of up stream tasks, or a list of file names, after string replacement via
-        :ref:`formatter<decorators.formatter>`.
-
-        The replacement strings require an extra level of indirection to refer to
-        parsed components:
-
-            #. The first level refers to which *set* in each tuple of inputs.
-            #. The second level refers to which input file in any particular *set* of inputs.
-
-    **Example**:
-
-        Calculates the **@permutations** of **A,B,C,D** files
-
-        .. code-block:: python
-            :emphasize-lines: 13,17,20,25,28-30
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   initial file pairs
-            @originate([ ['A.1_start', 'A.2_start'],
-                         ['B.1_start', 'B.2_start'],
-                         ['C.1_start', 'C.2_start'],
-                         ['D.1_start', 'D.2_start']])
-            def create_initial_files_ABCD(output_files):
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-            #   @permutations
-            @permutations(create_initial_files_ABCD,      # Input
-                          formatter(),                    # match input files
-
-                          # tuple of 2 at a time
-                          2,
-
-                          # Output Replacement string
-                          "{path[0][0]}/"
-                          "{basename[0][1]}_vs_"
-                          "{basename[1][1]}.permutations",
-
-                          # Extra parameter: path for 1st set of files, 1st file name
-                          "{path[0][0]}",
-
-                          # Extra parameter
-                          ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                           "{basename[1][0]}",  #                                2nd
-                           ])
-            def permutations_task(input_file, output_parameter, shared_path, basenames):
-                print " - ".join(basenames)
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-        This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-
-            A - B
-            A - C
-            A - D
-            B - A
-            B - C
-            B - D
-            C - A
-            C - B
-            C - D
-            D - A
-            D - B
-            D - C
-
-
-    **Parameters:**
-
-
-.. _decorators.permutations.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-
-.. _decorators.permutations.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-
-.. _decorators.permutations.output_pattern:
-
-    * *output_pattern*
-        Specifies the resulting output file name(s) after string
-        substitution
-
-
-.. _decorators.permutations.extra_parameters:
-
-    * *extra_parameters*
-        Optional extra parameters are passed to the functions after string
-        substitution
-
diff --git a/doc/_build/html/_sources/decorators/posttask.txt b/doc/_build/html/_sources/decorators/posttask.txt
deleted file mode 100644
index e0a6a2f..0000000
--- a/doc/_build/html/_sources/decorators/posttask.txt
+++ /dev/null
@@ -1,70 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.posttask:
-.. index::
-    pair: @posttask; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-.. |function| replace:: `function`
-.. _function: `decorators.posttask.function`_
-.. |file_name| replace:: `file_name`
-.. _file_name: `decorators.posttask.file_name`_
-
-########################
- at posttask
-########################
-
-*****************************************************************************************************************************************
-*@posttask* (|function|_ | :ref:`touch_file<decorators.touch_file>`\ *(*\ |file_name|_\ *)*\)
-*****************************************************************************************************************************************
-    **Purpose:**
-        Calls functions to signal the completion of each task
-
-    **Example**::
-
-        from ruffus import *
-
-        def task_finished():
-            print "hooray"
-
-        @posttask(task_finished)
-        @files(None, "a.1")
-        def create_if_necessary(input_file, output_file):
-            open(output_file, "w")
-
-        pipeline_run([create_if_necessary])
-
-    **Parameters:**
-
-.. _decorators.posttask.function:
-
-    * *function*:
-        ``function()`` will be called when the ruffus passes through a task.
-
-        This may happen even if all of the jobs are up-to-date:
-        when a upstream task is out-of-date, and the execution passes through
-        this point in the pipeline
-
-.. _decorators.posttask.file_name:
-
-    * *file_name*
-        Files to be ``touch``\ -ed after the task is executed.
-
-        This will change the date/time stamp of the ``file_name`` to the current date/time.
-        If the file does not exist, an empty file will be created.
-
-        Requires to be wrapped in a :ref:`touch_file<decorators.touch_file>` indicator object::
-
-            from ruffus import *
-
-            @posttask(touch_file("task_completed.flag"))
-            @files(None, "a.1")
-            def create_if_necessary(input_file, output_file):
-                open(output_file, "w")
-
-            pipeline_run([create_if_necessary])
-
-
-
diff --git a/doc/_build/html/_sources/decorators/product.txt b/doc/_build/html/_sources/decorators/product.txt
deleted file mode 100644
index 5c77af4..0000000
--- a/doc/_build/html/_sources/decorators/product.txt
+++ /dev/null
@@ -1,192 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.product:
-.. index::
-    pair: @product; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-########################
- at product
-########################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.product.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.product.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.product.output_pattern`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.product.matching_formatter`_
-
-
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@product* ( |tasks_or_file_names|_, :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, [|tasks_or_file_names|_, :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, ... ], |output_pattern|_, [|extra_parameters|_,...] )
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    **Purpose:**
-
-        Generates the Cartesian **product**, i.e. all vs all comparisons, between sets of input files.
-
-        The effect is analogous to the python `itertools  <http://docs.python.org/2/library/itertools.html#itertools.product>`__
-        function of the same name, i.e. a nested for loop.
-
-        .. code-block:: pycon
-            :emphasize-lines: 2
-
-            >>> from itertools import product
-            >>> # product('ABC', 'XYZ') --> AX AY AZ BX BY BZ CX CY CZ
-            >>> [ "".join(a) for a in product('ABC', 'XYZ')]
-            ['AX', 'AY', 'AZ', 'BX', 'BY', 'BZ', 'CX', 'CY', 'CZ']
-
-        Only out of date tasks (comparing input and output files) will be run
-
-        Output file names and strings in the extra parameters
-        are determined from |tasks_or_file_names|_, i.e. from the output
-        of up stream tasks, or a list of file names, after string replacement via
-        :ref:`formatter<decorators.formatter>`.
-
-        The replacement strings require an extra level of indirection to refer to
-        parsed components:
-
-            #. The first level refers to which *set* of inputs (e.g. **A,B** or **P,Q** or **X,Y**
-               in the following example.)
-            #. The second level refers to which input file in any particular *set* of inputs.
-
-        For example, ``'{basename[2][0]}'`` is the `basename  <http://docs.python.org/2/library/os.path.html#os.path.basename>`__ for
-            * the third set of inputs (**X,Y**) and
-            * the first file name string in each **Input** of that set (``"x.1_start"`` and ``"y.1_start"``)
-
-    **Example**:
-
-        Calculates the **@product** of **A,B** and **P,Q** and **X, Y** files
-
-        .. code-block:: python
-            :emphasize-lines: 4,17,19,22,25,27,28,29,30,32,34,35,36
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   Three sets of initial files
-            @originate([ 'a.start', 'b.start'])
-            def create_initial_files_ab(output_file):
-                with open(output_file, "w") as oo: pass
-
-            @originate([ 'p.start', 'q.start'])
-            def create_initial_files_pq(output_file):
-                with open(output_file, "w") as oo: pass
-
-            @originate([ ['x.1_start', 'x.2_start'],
-                         ['y.1_start', 'y.2_start'] ])
-            def create_initial_files_xy(output_file):
-                with open(output_file, "w") as oo: pass
-
-            #   @product
-            @product(   create_initial_files_ab,        # Input
-                        formatter("(.start)$"),         # match input file set # 1
-
-                        create_initial_files_pq,        # Input
-                        formatter("(.start)$"),         # match input file set # 2
-
-                        create_initial_files_xy,        # Input
-                        formatter("(.start)$"),         # match input file set # 3
-
-                        "{path[0][0]}/"                 # Output Replacement string
-                        "{basename[0][0]}_vs_"          #
-                        "{basename[1][0]}_vs_"          #
-                        "{basename[2][0]}.product",     #
-
-                        "{path[0][0]}",                 # Extra parameter: path for 1st set of files, 1st file name
-
-                        ["{basename[0][0]}",            # Extra parameter: basename for 1st set of files, 1st file name
-                         "{basename[1][0]}",            #                               2nd
-                         "{basename[2][0]}",            #                               3rd
-                         ])
-            def product_task(input_file, output_parameter, shared_path, basenames):
-                print "# basenames      = ", " ".join(basenames)
-                print "input_parameter  = ", input_file
-                print "output_parameter = ", output_parameter, "\n"
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-        This results in:
-
-        .. code-block:: pycon
-            :emphasize-lines: 2,6,10,14,18,22,26,30
-
-            >>> pipeline_run(verbose=0)
-
-            # basenames      =  a p x
-            input_parameter  =  ('a.start', 'p.start', 'x.start')
-            output_parameter =  /home/lg/temp/a_vs_p_vs_x.product
-
-            # basenames      =  a p y
-            input_parameter  =  ('a.start', 'p.start', 'y.start')
-            output_parameter =  /home/lg/temp/a_vs_p_vs_y.product
-
-            # basenames      =  a q x
-            input_parameter  =  ('a.start', 'q.start', 'x.start')
-            output_parameter =  /home/lg/temp/a_vs_q_vs_x.product
-
-            # basenames      =  a q y
-            input_parameter  =  ('a.start', 'q.start', 'y.start')
-            output_parameter =  /home/lg/temp/a_vs_q_vs_y.product
-
-            # basenames      =  b p x
-            input_parameter  =  ('b.start', 'p.start', 'x.start')
-            output_parameter =  /home/lg/temp/b_vs_p_vs_x.product
-
-            # basenames      =  b p y
-            input_parameter  =  ('b.start', 'p.start', 'y.start')
-            output_parameter =  /home/lg/temp/b_vs_p_vs_y.product
-
-            # basenames      =  b q x
-            input_parameter  =  ('b.start', 'q.start', 'x.start')
-            output_parameter =  /home/lg/temp/b_vs_q_vs_x.product
-
-            # basenames      =  b q y
-            input_parameter  =  ('b.start', 'q.start', 'y.start')
-            output_parameter =  /home/lg/temp/b_vs_q_vs_y.product
-
-
-    **Parameters:**
-
-
-.. _decorators.product.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-
-.. _decorators.product.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-
-.. _decorators.product.output_pattern:
-
-    * *output_pattern*
-        Specifies the resulting output file name(s) after string
-        substitution
-
-
-.. _decorators.product.extra_parameters:
-
-    * *extra_parameters*
-        Optional extra parameters are passed to the functions after string
-        substitution
-
diff --git a/doc/_build/html/_sources/decorators/split.txt b/doc/_build/html/_sources/decorators/split.txt
deleted file mode 100644
index e0a6f5f..0000000
--- a/doc/_build/html/_sources/decorators/split.txt
+++ /dev/null
@@ -1,92 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.split:
-.. index::
-    pair: @split; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-
-########################
- at split
-########################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.split.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.split.extra_parameters`_
-.. |output_files| replace:: `output_files`
-.. _output_files: `decorators.split.output_files`_
-
-*****************************************************************************************************************************************
-*@split* ( |tasks_or_file_names|_, |output_files|_, [|extra_parameters|_,...]  )
-*****************************************************************************************************************************************
-    **Purpose:**
-        | Splits a single set of input files into multiple output file names, where the number of
-          output files may not be known beforehand.
-        | Only out of date tasks (comparing input and output files) will be run
-
-    **Example**::
-
-        @split("big_file", '*.little_files')
-        def split_big_to_small(input_file, output_files):
-            print "input_file = %s" % input_file
-            print "output_file = %s" % output_file
-
-    .
-
-        will produce::
-
-            input_file = big_file
-            output_file = *.little_files
-
-
-    **Parameters:**
-
-.. _decorators.split.tasks_or_file_names:
-
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  (Nested) list of file name strings (as in the example above).
-
-            | File names containing ``*[]?`` will be expanded as a |glob|_.
-            | E.g.:``"a.*" => "a.1", "a.2"``
-
-       #.  Task / list of tasks.
-
-            File names are taken from the output of the specified task(s)
-
-
-.. _decorators.split.output_files:
-
-    * *output_files*
-       Specifies the resulting output file name(s).
-
-       | These are used **only** to check if the task is up to date.
-       | Normally you would use either a |glob|_ (e.g. ``*.little_files`` as above) or  a "sentinel file"
-         to indicate that the task has completed successfully.
-       | You can of course do both:
-
-        ::
-
-            @split("big_file", ["sentinel.file", "*.little_files"])
-            def split_big_to_small(input_file, output_files):
-                pass
-
-
-.. _decorators.split.extra_parameters:
-
-    * [*extra_parameters, ...*]
-        Any extra parameters are passed verbatim to the task function
-
-
-
-########################################################################
- at split with ``regex(...)``, ``add_inputs`` and ``inputs``
-########################################################################
-
-    This deprecated syntax is a synonym for :ref:`@subdivide <decorators.subdivide>`.
-
diff --git a/doc/_build/html/_sources/decorators/subdivide.txt b/doc/_build/html/_sources/decorators/subdivide.txt
deleted file mode 100644
index b8df277..0000000
--- a/doc/_build/html/_sources/decorators/subdivide.txt
+++ /dev/null
@@ -1,189 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.subdivide:
-.. index::
-    pair: @subdivide; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-########################
- at subdivide
-########################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.subdivide.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.subdivide.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.subdivide.output_pattern`_
-.. |matching_regex| replace:: `matching_regex`
-.. _matching_regex: `decorators.subdivide.matching_regex`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.subdivide.matching_formatter`_
-.. |input_pattern_or_glob| replace:: `input_pattern_or_glob`
-.. _input_pattern_or_glob: `decorators.subdivide.input_pattern_or_glob`_
-
-
-************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@subdivide* ( |tasks_or_file_names|_, :ref:`regex<decorators.regex>`\ *(*\ |matching_regex|_\ *)* |  :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, [ :ref:`inputs<decorators.inputs>` *(*\ |input_pattern_or_glob|_\ *)* | :ref:`add_inputs<decorators.add_inputs>` *(*\ |input_pattern_or_glob|_\ *)* ], |output_pattern|_, [|extra_parameters|_,...]  )
-************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    **Purpose:**
-
-        * Subdivides a set of *Inputs* each further into multiple *Outputs*.
-
-        * **Many to Even More** operator
-
-        * The number of files in each *Output* can be set at runtime by the use of globs
-
-        * Output file names are specified using the :ref:`formatter<decorators.formatter>` or :ref:`regex<decorators.regex>` indicators from |tasks_or_file_names|_, i.e. from the output
-          of specified tasks, or a list of file names, or a |glob|_ matching pattern.
-
-        * Additional inputs or dependencies can be added dynamically to the task:
-            :ref:`add_inputs<decorators.add_inputs>` nests the the original input parameters in a list before adding additional dependencies.
-
-            :ref:`inputs<decorators.inputs>` replaces the original input parameters wholescale.
-
-        * Only out of date tasks (comparing input and output files) will be run.
-
-        .. note::
-
-            The use of **split** is a synonym for subdivide is deprecated.
-
-
-    **Example**:
-
-        .. code-block:: python
-            :emphasize-lines: 12,13,20
-
-            from ruffus import *
-            from random import randint
-            from random import os
-
-            @originate(['0.start', '1.start', '2.start'])
-            def create_files(output_file):
-                with open(output_file, "w"):
-                    pass
-
-
-            #
-            #   Subdivide each of 3 start files further into [NNN1, NNN2, NNN3] number of files
-            #      where NNN1, NNN2, NNN3 are determined at run time
-            #
-            @subdivide(create_files, formatter(),
-                        "{path[0]}/{basename[0]}.*.step1",  # Output parameter: Glob matches any number of output file names
-                        "{path[0]}/{basename[0]}")          # Extra parameter:  Append to this for output file names
-            def subdivide_files(input_file, output_files, output_file_name_root):
-                #
-                #   IMPORTANT: cleanup rubbish from previous run first
-                #
-                for oo in output_files:
-                    os.unlink(oo)
-                #   The number of output files is decided at run time
-                number_of_output_files = randint(2,4)
-                for ii in range(number_of_output_files):
-                    output_file_name = "{output_file_name_root}.{ii}.step1".format(**locals())
-                    with open(output_file_name, "w"):
-                        pass
-
-
-            #
-            #   Each output of subdivide_files results in a separate job for downstream tasks
-            #
-            @transform(subdivide_files, suffix(".step1"), ".step2")
-            def analyse_files(input_file, output_file_name):
-                with open(output_file_name, "w"):
-                    pass
-
-            pipeline_run()
-
-        .. comment **
-
-            The Ruffus printout shows how each of the jobs in ``subdivide_files()`` spawns
-            multiple *Output* leading to more jobs in ``analyse_files()``
-
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [None -> 0.start] completed
-                Job  = [None -> 1.start] completed
-                Job  = [None -> 2.start] completed
-            Completed Task = create_files
-                Job  = [0.start -> 0.*.step1, 0] completed
-                Job  = [1.start -> 1.*.step1, 1] completed
-                Job  = [2.start -> 2.*.step1, 2] completed
-            Completed Task = subdivide_files
-                Job  = [0.0.step1 -> 0.0.step2] completed
-                Job  = [0.1.step1 -> 0.1.step2] completed
-                Job  = [0.2.step1 -> 0.2.step2] completed
-                Job  = [1.0.step1 -> 1.0.step2] completed
-                Job  = [1.1.step1 -> 1.1.step2] completed
-                Job  = [1.2.step1 -> 1.2.step2] completed
-                Job  = [1.3.step1 -> 1.3.step2] completed
-                Job  = [2.0.step1 -> 2.0.step2] completed
-                Job  = [2.1.step1 -> 2.1.step2] completed
-                Job  = [2.2.step1 -> 2.2.step2] completed
-                Job  = [2.3.step1 -> 2.3.step2] completed
-            Completed Task = analyse_files
-
-
-
-
-    **Parameters:**
-
-
-.. _decorators.subdivide.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-
-.. _decorators.subdivide.matching_regex:
-
-    * *matching_regex*
-       is a python regular expression string, which must be wrapped in
-       a :ref:`regex<decorators.regex>` indicator object
-       See python `regular expression (re) <http://docs.python.org/library/re.html>`_
-       documentation for details of regular expression syntax
-
-.. _decorators.subdivide.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-.. _decorators.subdivide.output_pattern:
-
-    * *output_pattern*
-        Specifies the resulting output file name(s). Can include glob patterns.
-        Strings are subject to :ref:`regex<decorators.regex>` or :ref:`formatter<decorators.formatter>`
-        substitution.
-
-.. _decorators.subdivide.input_pattern_or_glob:
-
-    * *input_pattern*
-       Specifies the resulting input(s) to each job.
-       Must be wrapped in an :ref:`inputs<decorators.inputs>` or an :ref:`inputs<decorators.add_inputs>` indicator object.
-
-       Can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-
-       Strings are subject to :ref:`regex<decorators.regex>` or :ref:`formatter<decorators.formatter>` substitution.
-
-
-.. _decorators.subdivide.extra_parameters:
-
-    * *extra_parameters*
-        Any extra parameters are consumed by the task function and not forwarded further down the pipeline.
-        Strings are subject to :ref:`regex<decorators.regex>` or :ref:`formatter<decorators.formatter>`
-        substitution.
diff --git a/doc/_build/html/_sources/decorators/transform.txt b/doc/_build/html/_sources/decorators/transform.txt
deleted file mode 100644
index 494674e..0000000
--- a/doc/_build/html/_sources/decorators/transform.txt
+++ /dev/null
@@ -1,176 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.transform:
-.. index::
-    pair: @transform; Syntax
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-########################
- at transform
-########################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.transform.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.transform.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.transform.output_pattern`_
-.. |matching_regex| replace:: `matching_regex`
-.. _matching_regex: `decorators.transform.matching_regex`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.transform.matching_formatter`_
-.. |suffix_string| replace:: `suffix_string`
-.. _suffix_string: `decorators.transform.suffix_string`_
-
-******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-*@transform* ( |tasks_or_file_names|_, :ref:`suffix<decorators.suffix>`\ *(*\ |suffix_string|_\ *)*\ | :ref:`regex<decorators.regex>`\ *(*\ |matching_regex|_\ *)* |  :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, |output_pattern|_, [|extra_parameters|_,...] )
-******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-    **Purpose:**
-        Applies the task function to transform data from input to output files.
-
-        Output file names are specified from |tasks_or_file_names|_, i.e. from the output
-        of specified tasks, or a list of file names, or a |glob|_ matching pattern.
-
-        String replacement occurs either through suffix matches via :ref:`suffix<decorators.suffix>` or 
-        the :ref:`formatter<decorators.formatter>` or :ref:`regex<decorators.regex>` indicators.
-
-        Only out of date tasks (comparing input and output files) will be run
-
-    **Simple Example**
-
-        Transforms ``*.c`` to ``*.o``::
-
-            @transform(["1.c", "2.c"], suffix(".c"), ".o")
-            def compile(infile, outfile):
-                pass
-
-        Same example with a regular expression::
-
-            @transform(["1.c", "2.c"], regex(r".c$"), ".o")
-            def compile(infile, outfile):
-                pass
-
-        Both result in the following function calls:
-
-            ::
-
-                # 1.c -> 1.o
-                # 2.c -> 2.o
-                compile("1.c", "1.o")
-                compile("2.c", "2.o")
-
-
-    **Escaping regular expression patterns**
-
-        A string like ``universal.h`` in ``add_inputs`` will added *as is*.
-        ``r"\1.h"``, however, performs suffix substitution, with the special form ``r"\1"`` matching everything up to the suffix.
-        Remember to 'escape' ``r"\1"`` otherwise Ruffus will complain and throw an Exception to remind you.
-        The most convenient way is to use a python "raw" string.
-
-    **Parameters:**
-
-.. _decorators.transform.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-.. _decorators.transform.suffix_string:
-
-    * *suffix_string*
-       must be wrapped in a :ref:`suffix<decorators.suffix>` indicator object.
-       The end of each input file name which matches ``suffix_string`` will be replaced by ``output_pattern``.
-
-       Input file names which do not match suffix_string will be ignored
-
-
-       The non-suffix part of the match can be referred to using the ``"\1"`` pattern. This
-       can be useful for putting the output in different directory, for example::
-
-
-            @transform(["1.c", "2.c"], suffix(".c"), r"my_path/\1.o")
-            def compile(infile, outfile):
-                pass
-
-       This results in the following function calls:
-
-            ::
-
-                # 1.c -> my_path/1.o
-                # 2.c -> my_path/2.o
-                compile("1.c", "my_path/1.o")
-                compile("2.c", "my_path/2.o")
-
-       For convenience and visual clarity, the  ``"\1"`` can be omitted from the output parameter.
-       However, the ``"\1"`` is mandatory for string substitutions in additional parameters, ::
-
-
-            @transform(["1.c", "2.c"], suffix(".c"), [r"\1.o", ".o"], "Compiling \1", "verbatim")
-            def compile(infile, outfile):
-                pass
-
-       Results in the following function calls:
-
-            ::
-
-                compile("1.c", ["1.o", "1.o"], "Compiling 1", "verbatim")
-                compile("2.c", ["2.o", "2.o"], "Compiling 2", "verbatim")
-
-       Since r"\1" is optional for the output parameter, ``"\1.o"`` and ``".o"`` are equivalent.
-       However, strings in other parameters which do not contain r"\1" will be included verbatim, much
-       like the string ``"verbatim"`` in the above example.
-
-
-
-
-.. _decorators.transform.matching_regex:
-
-    * *matching_regex*
-       is a python regular expression string, which must be wrapped in
-       a :ref:`regex<decorators.regex>`\  indicator object
-       See python `regular expression (re) <http://docs.python.org/library/re.html>`_
-       documentation for details of regular expression syntax
-       Each output file name is created using regular expression substitution with ``output_pattern``
-
-.. _decorators.transform.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-.. _decorators.transform.output_pattern:
-
-    * *output_pattern*
-       Specifies the resulting output file name(s).
-
-.. _decorators.transform.extra_parameters:
-
-    * [*extra_parameters, ...*]
-       Any extra parameters are passed to the task function.
-
-       If ``regex(matching_regex)`` or ``formatter(...)``` is used, then substitution
-       is first applied to (even nested) string parameters. Other data types are passed
-       verbatim.
-
-       For example::
-
-             @transform(["a.c", "b.c"], regex(r"(.*).c"), r"\1.o", r"\1")
-             def compile(infile, outfile):
-                 pass
-
-       will result in the following function calls::
-
-            compile("a.c", "a.o", "a")
-            compile("b.c", "b.o", "b")
-
-
-
-
-See :ref:`here <decorators.transform_ex>` for more advanced uses of transform.
diff --git a/doc/_build/html/_sources/decorators/transform_ex.txt b/doc/_build/html/_sources/decorators/transform_ex.txt
deleted file mode 100644
index 2436696..0000000
--- a/doc/_build/html/_sources/decorators/transform_ex.txt
+++ /dev/null
@@ -1,190 +0,0 @@
-.. include:: ../global.inc
-.. _decorators.transform_ex:
-.. index::
-    pair: @transform, inputs(...); Syntax
-    pair: @transform, add_inputs(...); Syntax
-
-
-.. seealso::
-
-    * :ref:`Decorators <decorators>` for more decorators
-
-####################################################
- at transform  with ``add_inputs`` and ``inputs``
-####################################################
-
-.. |tasks_or_file_names| replace:: `tasks_or_file_names`
-.. _tasks_or_file_names: `decorators.transform.tasks_or_file_names`_
-.. |extra_parameters| replace:: `extra_parameters`
-.. _extra_parameters: `decorators.transform.extra_parameters`_
-.. |output_pattern| replace:: `output_pattern`
-.. _output_pattern: `decorators.transform.output_pattern`_
-.. |input_pattern_or_glob| replace:: `input_pattern_or_glob`
-.. _input_pattern_or_glob: `decorators.transform.input_pattern_or_glob`_
-.. |matching_regex| replace:: `matching_regex`
-.. _matching_regex: `decorators.transform.matching_regex`_
-.. |matching_formatter| replace:: `matching_formatter`
-.. _matching_formatter: `decorators.transform.matching_formatter`_
-.. |suffix_string| replace:: `suffix_string`
-.. _suffix_string: `decorators.transform.suffix_string`_
-
-
-
-
-
-************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************ [...]
-*@transform* ( |tasks_or_file_names|_, :ref:`suffix<decorators.suffix>`\ *(*\ |suffix_string|_\ *)*\ | :ref:`regex<decorators.regex>`\ *(*\ |matching_regex|_\ *)* |  :ref:`formatter<decorators.formatter>`\ *(*\ |matching_formatter|_\ *)*\, :ref:`inputs<decorators.inputs>` | :ref:`add_inputs<decorators.add_inputs>`\ *(*\ |input_pattern_or_glob|_\ *)*\ , |output_pattern|_, [|extra_parameters|_,...] )
-************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************ [...]
-    **Purpose:**
-        This variant of ``@transform`` allows additional inputs or dependencies to be added
-        dynamically to the task.
-
-        Output file names and strings in the extra parameters 
-        are determined from |tasks_or_file_names|_, i.e. from the output
-        of up stream tasks, or a list of file names.
-
-        This variant of ``@transform`` allows input file names to be derived in the same way.
-
-        String replacement occurs either through suffix matches via :ref:`suffix<decorators.suffix>` or 
-        the :ref:`formatter<decorators.formatter>` or :ref:`regex<decorators.regex>` indicators.
-
-        ``@collate`` groups together all **Input** which result in identical **Output** and **extra**
-        parameters.
-
-        It is a **many to fewer** operation.
-
-        :ref:`add_inputs<decorators.add_inputs>` nests the the original input parameters in a list before adding additional dependencies.
-
-        :ref:`inputs<decorators.inputs>` replaces the original input parameters wholescale.
-
-        Only out of date tasks (comparing input and output files) will be run
-
-    **Example of** :ref:`add_inputs<decorators.add_inputs>`
-
-        A common task in compiling C code is to include the corresponding header file for the source.
-
-        To compile ``*.c`` to ``*.o``, adding ``*.h`` and the common header ``universal.h``:
-            ::
-
-                @transform(["1.c", "2.c"], suffix(".c"), add_inputs([r"\1.h", "universal.h"]),  ".o")
-                def compile(infile, outfile):
-                    pass
-
-        This will result in the following functional calls:
-            ::
-
-                compile(["1.c", "1.h", "universal.h"], "1.o")
-                compile(["2.c", "2.h", "universal.h"], "2.o")
-
-    **Example of** :ref:`inputs<decorators.inputs>`
-
-        ``inputs(...)`` allows the original input parameters to be replaced wholescale.
-
-        This can be seen in the following example:
-            ::
-
-                @transform([    ["1.c", "A.c", 2]
-                                ["2.c", "B.c", "C.c", 3]],
-                                suffix(".c"), inputs([r"\1.py", "docs.rst"]),  ".pyc")
-                def compile(infile, outfile):
-                    pass
-
-        This will result in the following functional calls:
-            ::
-
-                compile(["1.py", "docs.rst"], "1.pyc")
-                compile(["2.py", "docs.rst"], "2.pyc")
-
-
-
-    **Parameters:**
-
-.. _decorators.transform.tasks_or_file_names:
-
-    * *tasks_or_file_names*
-       can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-             E.g.:``"a.*" => "a.1", "a.2"``
-
-.. _decorators.transform.suffix_string:
-
-    * *suffix_string*
-       must be wrapped in a :ref:`suffix<decorators.suffix>` indicator object.
-       The end of each file name which matches suffix_string will be replaced by `output_pattern`.
-       Thus::
-
-            @transform(["a.c", "b.c"], suffix(".c"), ".o")
-            def compile(infile, outfile):
-                pass
-
-       will result in the following function calls::
-
-           compile("a.c", "a.o")
-           compile("b.c", "b.o")
-
-       File names which do not match suffix_string will be ignored
-
-.. _decorators.transform.matching_regex:
-
-    * *matching_regex*
-       is a python regular expression string, which must be wrapped in
-       a :ref:`regex<decorators.regex>` indicator object
-       See python `regular expression (re) <http://docs.python.org/library/re.html>`_
-       documentation for details of regular expression syntax
-       Each output file name is created using regular expression substitution with ``output_pattern``
-
-.. _decorators.transform.matching_formatter:
-
-    * *matching_formatter*
-       a :ref:`formatter<decorators.formatter>` indicator object containing optionally
-       a  python `regular expression (re) <http://docs.python.org/library/re.html>`_.
-
-.. _decorators.transform.input_pattern_or_glob:
-
-    * *input_pattern*
-       Specifies the resulting input(s) to each job.
-       Must be wrapped in an :ref:`inputs<decorators.inputs>` or an :ref:`inputs<decorators.add_inputs>` indicator object.
-
-       Can be a:
-
-       #.  Task / list of tasks (as in the example above).
-            File names are taken from the output of the specified task(s)
-       #.  (Nested) list of file name strings.
-            Strings will be subject to substitution.
-            File names containing ``*[]?`` will be expanded as a |glob|_.
-            E.g.:``"a.*" => "a.1", "a.2"``
-
-
-
-.. _decorators.transform.output_pattern:
-
-    * *output_pattern*
-       Specifies the resulting output file name(s).
-
-.. _decorators.transform.extra_parameters:
-
-    * [*extra_parameters, ...*]
-       Any extra parameters are passed to the task function.
-
-       If the ``regex(...)`` or ``formatter(...)`` parameter is used, then substitution
-       is first applied to (even nested) string parameters. Other data types are passed
-       verbatim.
-
-       For example::
-
-             @transform(["a.c", "b.c"], regex(r"(.*).c"), inputs(r"\1.c", r"\1.h", "universal.h"),  r"\1.o", r"\1")
-             def compile(infiles, outfile, file_name_root):
-                 # do something here
-                 pass
-
-       will result in the following function calls::
-
-             compile(["1.c", "1.h", "universal.h"], "1.o", "1")
-             compile(["2.c", "2.h", "universal.h"], "2.o", "2")
-
-
-See :ref:`here <decorators.transform>` for more straightforward ways to use transform.
diff --git a/doc/_build/html/_sources/design.txt b/doc/_build/html/_sources/design.txt
deleted file mode 100644
index 2dd0b12..0000000
--- a/doc/_build/html/_sources/design.txt
+++ /dev/null
@@ -1,304 +0,0 @@
-.. Design:
-
-.. include:: global.inc
-
-.. index::
-    pair: Design; Ruffus
-
-###############################
-Design & Architecture
-###############################
-
-    The *ruffus* module has the following design goals:
-
-        * Simplicity.
-        * Intuitive
-        * Lightweight
-        * Unintrusive
-        * Flexible/Powerful
-
-
-    Computational pipelines, especially in science, are best thought of in terms of data
-    flowing through successive, dependent stages (**ruffus** calls these :term:`task`\ s).
-    Traditionally, files have been used to
-    link pipelined stages together. This means that computational pipelines can be managed
-    using traditional software construction (`build`) systems.
-
-=================================================
-`GNU Make`
-=================================================
-    The grand-daddy of these is UNIX `make <http://en.wikipedia.org/wiki/Make_(software)>`_.
-    `GNU make <http://www.gnu.org/software/make/>`_ is ubiquitous in the linux world for
-    installing and compiling software.
-    It has been widely used to build computational pipelines because it supports:
-
-    * Stopping and restarting computational processes
-    * Running multiple, even thousands of jobs in parallel
-
-.. _design.make_syntax_ugly:
-
-******************************************************
-Deficiencies of `make` / `gmake`
-******************************************************
-
-    However, make and `GNU make <http://www.gnu.org/software/make/>`_ use a specialised (domain-specific)
-    language, which has is been much criticised because of poor support for modern
-    programming languages features, such as variable scope, pattern matching, debugging.
-    Make scripts require large amounts of often obscure shell scripting
-    and makefiles can quickly become unmaintainable.
-
-.. _design.scons_and_rake:
-
-=================================================
-`Scons`, `Rake` and other `Make` alternatives
-=================================================
-
-    Many attempts have been made to produce a more modern version of make, with less of its
-    historical baggage. These include the Java-based `Apache ant <http://ant.apache.org/>`_ which is specified in xml.
-
-    More interesting are a new breed of build systems whose scripts are written in modern programming
-    languages, rather than a specially-invented "build" specificiation syntax.
-    These include the Python `scons <http://www.scons.org/>`_, Ruby `rake <http://rake.rubyforge.org/>`_ and
-    its python port `Smithy <http://packages.python.org/Smithy/>`_.
-
-    The great advantages are that computation pipelines do not need to be artificially parcelled out
-    between (the often second-class) workflow management code, and the logic which does the real computation
-    in the pipeline. It also means that workflow management can use all the standard language and library
-    features, for example, to read in directories, match file names using regular expressions and so on.
-
-    **Ruffus** is much like scons in that the modern dynamic programming language python is used seamlessly
-    throughout its pipeline scripts.
-
-.. _design.implicit_dependencies:
-
-**************************************************************************
-Implicit dependencies: disadvantages of `make` / `scons` / `rake`
-**************************************************************************
-
-    Although Python `scons <http://www.scons.org/>`_ and Ruby `rake <http://rake.rubyforge.org/>`_
-    are in many ways more powerful and easier to use for building software, they are still an
-    imperfect fit to the world of computational pipelines.
-
-    This is a result of the way dependencies are specified, an essential part of their design inherited
-    from `GNU make <http://www.gnu.org/software/make/>`_.
-
-    The order of operations in all of these tools is specified in a *declarative* rather than
-    *imperative* manner. This means that the sequence of steps that a build should take are
-    not spelled out explicity and directly. Instead recipes are provided for turning input files
-    of each type to another.
-
-    So, for example, knowing that ``a->b``, ``b->c``, ``c->d``, the build
-    system can infer how to get from ``a`` to ``d`` by performing the necessary operations in the correct order.
-
-    This is immensely powerful for three reasons:
-     #) The plumbing, such as dependency checking, passing output
-        from one stage to another, are handled automatically by the build system. (This is the whole point!)
-     #) The same *recipe* can be re-used at different points in the build.
-     #) | Intermediate files do not need to be retained.
-        | Given the automatic inference that ``a->b->c->d``,
-          we don't need to keep ``b`` and ``c`` files around once ``d`` has been produced.
-        |
-
-
-    The disadvantage is that because stages are specified only indirectly, in terms of
-    file name matches, the flow through a complex build or a pipeline can be difficult to trace, and nigh
-    impossible to debug when there are problems.
-
-
-.. _design.explicit_dependencies_in_ruffus:
-
-**************************************************************************
-Explicit dependencies in `Ruffus`
-**************************************************************************
-
-    **Ruffus** takes a different approach. The order of operations is specified explicitly rather than inferred
-    indirectly from the input and output types. So, for example, we would explicitly specify three successive and
-    linked operations ``a->b``, ``b->c``, ``c->d``. The build system knows that the operations always proceed in
-    this order.
-
-    Looking at a **Ruffus** script, it is always clear immediately what is the succession of computational steps
-    which will be taken.
-
-    **Ruffus** values clarity over syntactic cleverness.
-
-.. _design.static_dependencies:
-
-**************************************************************************
-Static dependencies: What `make` / `scons` / `rake` can't do (easily)
-**************************************************************************
-
-    `GNU make <http://www.gnu.org/software/make/>`_, `scons <http://www.scons.org/>`_ and `rake <http://rake.rubyforge.org/>`_
-    work by infer a static dependency (diacyclic) graph between all the files which
-    are used by a computational pipeline. These tools locate the target that they are supposed
-    to build and work backward through the dependency graph from that target,
-    rebuilding anything that is out of date.This is perfect for building software,
-    where the list of files data files can be computed **statically** at the beginning of the build.
-
-    This is not ideal matches for scientific computational pipelines because:
-
-        *  | Though the *stages* of a pipeline (i.e. `compile` or `DNA alignment`) are
-             invariably well-specified in advance, the number of
-             operations (*job*\s) involved at each stage may not be.
-           |
-
-        *  | A common approach is to break up large data sets into manageable chunks which
-             can be operated on in parallel in computational clusters or farms
-             (See `embarassingly parallel problems <http://en.wikipedia.org/wiki/Embarrassingly_parallel>`_).
-           | This means that the number of parallel operations or jobs varies with the data (the number of manageable chunks),
-             and dependency trees cannot be calculated statically beforehand.
-           |
-
-    Computational pipelines require **dynamic** dependencies which are not calculated up-front, but
-    at each stage of the pipeline
-
-    This is a *known* issue with traditional build systems each of which has partial strategies to work around
-    this problem:
-
-        * gmake always builds the dependencies when first invoked, so dynamic dependencies require (complex!) recursive calls to gmake
-        * `Rake dependencies unknown prior to running tasks <http://objectmix.com/ruby/759716-rake-dependencies-unknown-prior-running-tasks-2.html>`_.
-        * `Scons: Using a Source Generator to Add Targets Dynamically <http://www.scons.org/wiki/DynamicSourceGenerator>`_
-
-
-    **Ruffus** explicitly and straightforwardly handles tasks which produce an indeterminate (i.e. runtime dependent)
-    number of output, using its **@split**, **@transform**, **merge** function annotations.
-
-=============================================================================
-Managing pipelines stage-by-stage using **Ruffus**
-=============================================================================
-    **Ruffus** manages pipeline stages directly.
-
-        #) | The computational operations for each stage of the pipeline are written by you, in
-             separate python functions.
-           | (These correspond to `gmake pattern rules <http://www.gnu.org/software/make/manual/make.html#Pattern-Rules>`_)
-           |
-
-        #) | The dependencies between pipeline stages (python functions) are specified up-front.
-           | These can be displayed as a flow chart.
-
-           .. image:: images/front_page_flowchart.png
-
-        #) **Ruffus** makes sure pipeline stage functions are called in the right order,
-           with the right parameters, running in parallel using multiprocessing if necessary.
-
-        #) Data file timestamps can be used to automatically determine if all or any parts
-           of the pipeline are out-of-date and need to be rerun.
-
-        #) Separate pipeline stages, and operations within each pipeline stage,
-           can be run in parallel provided they are not inter-dependent.
-
-    Another way of looking at this is that **ruffus** re-constructs datafile dependencies dynamically
-    on-the-fly when it gets to each stage of the pipeline, giving much more flexibility.
-
-**************************************************************************
-Disadvantages of the Ruffus design
-**************************************************************************
-    Are there any disadvantages to this trade-off for additional clarity?
-
-        #) Each pipeline stage needs to take the right input and output. For example if we specified the
-           steps in the wrong order: ``a->b``, ``c->d``, ``b->c``, then no useful output would be produced.
-        #) We cannot re-use the same recipes in different parts of the pipeline
-        #) Intermediate files need to be retained.
-
-
-    In our experience, it is always obvious when pipeline operations are in the wrong order, precisely because the
-    order of computation is the very essense of the design of each pipeline. Ruffus produces extra diagnostics when
-    no output is created in a pipeline stage (usually happens for incorrectly specified regular expressions.)
-
-    Re-use of recipes is as simple as an extra call to common function code.
-
-    Finally, some users have proposed future enhancements to **Ruffus** to handle unnecessary temporary / intermediate files.
-
-
-.. index::
-    pair: Design; Comparison of Ruffus with alternatives
-
-=================================================
-Alternatives to **Ruffus**
-=================================================
-
-    A comparison of more make-like tools is available from `Ian Holmes' group <http://biowiki.org/MakeComparison>`_.
-
-    Build systems include:
-
-            * `GNU make <http://www.gnu.org/software/make/>`_
-            * `scons <http://www.scons.org/>`_
-            * `ant <http://ant.apache.org/>`_
-            * `rake <http://rake.rubyforge.org/>`_
-
-    There are also complete workload managements systems such as Condor.
-    Various bioinformatics pipelines are also available, including that used by the
-    leading genome annotation website Ensembl, Pegasys, GPIPE, Taverna, Wildfire, MOWserv,
-    Triana, Cyrille2 etc. These all are either hardwired to specific databases, and tasks,
-    or have steep learning curves for both the scientist/developer and the IT system
-    administrators.
-
-    **Ruffus** is designed to be lightweight and unintrusive enough to use for writing pipelines
-    with just 10 lines of code.
-
-
-.. seealso::
-
-
-   **Bioinformatics workload managements systems**
-
-    Condor:
-        http://www.cs.wisc.edu/condor/description.html
-
-    Ensembl Analysis pipeline:
-        http://www.ncbi.nlm.nih.gov/pubmed/15123589
-
-
-    Pegasys:
-        http://www.ncbi.nlm.nih.gov/pubmed/15096276
-
-    GPIPE:
-        http://www.biomedcentral.com/pubmed/15096276
-
-    Taverna:
-        http://www.ncbi.nlm.nih.gov/pubmed/15201187
-
-    Wildfire:
-        http://www.biomedcentral.com/pubmed/15788106
-
-    MOWserv:
-        http://www.biomedcentral.com/pubmed/16257987
-
-    Triana:
-        http://dx.doi.org/10.1007/s10723-005-9007-3
-
-    Cyrille2:
-        http://www.biomedcentral.com/1471-2105/9/96
-
-
-.. index::
-    single: Acknowledgements
-
-**************************************************
-Acknowledgements
-**************************************************
- *  Bruce Eckel's insightful article on
-    `A Decorator Based Build System <http://www.artima.com/weblogs/viewpost.jsp?thread=241209>`_
-    was the obvious inspiration for the use of decorators in *Ruffus*.
-
-    The rest of the *Ruffus* takes uses a different approach. In particular:
-        #. *Ruffus* uses task-based not file-based dependencies
-        #. *Ruffus* tries to have minimal impact on the functions it decorates.
-
-           Bruce Eckel's design wraps functions in "rule" objects.
-
-           *Ruffus* tasks are added as attributes of the functions which can be still be
-           called normally. This is how *Ruffus* decorators can be layered in any order
-           onto the same task.
-
- *  Languages like c++ and Java would probably use a "mixin" approach.
-    Python's easy support for reflection and function references,
-    as well as the necessity of marshalling over process boundaries, dictated the
-    internal architecture of *Ruffus*.
- *  The `Boost Graph library <http://www.boost.org>`_ for text book implementations of directed
-    graph traversals.
- *  `Graphviz <http://www.graphviz.org/>`_. Just works. Wonderful.
- *  Andreas Heger, Christoffer Nellåker and Grant Belgard for driving Ruffus towards
-    ever simpler syntax.
-
-
-
diff --git a/doc/_build/html/_sources/drmaa_wrapper_functions.txt b/doc/_build/html/_sources/drmaa_wrapper_functions.txt
deleted file mode 100644
index 5ad9ddc..0000000
--- a/doc/_build/html/_sources/drmaa_wrapper_functions.txt
+++ /dev/null
@@ -1,234 +0,0 @@
-.. include:: global.inc
-.. _drmaa_functions:
-
-.. comments: function name
-
-.. |run_job| replace:: `drmaa_wrapper.run_job`
-.. _run_job: `drmaa_wrapper.run_job`_
-
-.. comments: parameters
-
-.. |dw_cmd_str| replace:: `cmd_str`
-.. _dw_cmd_str: `drmaa_wrapper.run_job.cmd_str`_
-
-.. |dw_job_script_directory| replace:: `job_script_directory`
-.. _dw_job_script_directory: `drmaa_wrapper.run_job.job_script_directory`_
-.. |dw_job_environment| replace:: `job_environment`
-.. _dw_job_environment: `drmaa_wrapper.run_job.job_environment`_
-.. |dw_working_directory| replace:: `working_directory`
-.. _dw_working_directory: `drmaa_wrapper.run_job.working_directory`_
-.. |dw_retain_job_scripts| replace:: `retain_job_scripts`
-.. _dw_retain_job_scripts: `drmaa_wrapper.run_job.retain_job_scripts`_
-.. |dw_job_name| replace:: `job_name`
-.. _dw_job_name: `drmaa_wrapper.run_job.job_name`_
-.. |dw_job_other_options| replace:: `job_other_options`
-.. _dw_job_other_options: `drmaa_wrapper.run_job.job_other_options`_
-.. |dw_logger| replace:: `logger`
-.. _dw_logger: `drmaa_wrapper.run_job.logger`_
-.. |dw_drmaa_session| replace:: `drmaa_session`
-.. _dw_drmaa_session: `drmaa_wrapper.run_job.drmaa_session`_
-.. |dw_run_locally| replace:: `run_locally`
-.. _dw_run_locally: `drmaa_wrapper.run_job.run_locally`_
-.. |dw_output_files| replace:: `output_files`
-.. _dw_output_files: `drmaa_wrapper.run_job.output_files`_
-.. |dw_touch_only| replace:: `touch_only`
-.. _dw_touch_only: `drmaa_wrapper.run_job.touch_only`_
-
-
-################################################
-drmaa functions
-################################################
-
-    ``drmaa_wrapper`` is not exported automatically by ruffus and must be specified explicitly:
-
-        .. code-block:: python
-            :emphasize-lines: 1
-
-
-            # imported ruffus.drmaa_wrapper explicitly
-            from ruffus.drmaa_wrapper import run_job, error_drmaa_job
-
-.. _drmaa_wrapper.run_job:
-
-.. index::
-    single: drmaa ; run_job
-    pair: run_job; Run drmaa
-
-
-************************************************************************************************************************************************************************************************************************************************************************************
-*run_job*
-************************************************************************************************************************************************************************************************************************************************************************************
-**run_job** (|dw_cmd_str|_, |dw_job_name|_ = None, |dw_job_other_options|_ = None, |dw_job_script_directory|_ = None, |dw_job_environment|_ = None, |dw_working_directory|_ = None, |dw_logger|_ = None, |dw_drmaa_session|_ = None, |dw_retain_job_scripts|_ = False, |dw_run_locally|_ = False, |dw_output_files|_ = None, |dw_touch_only|_ = False)
-
-    **Purpose:**
-
-        ``ruffus.drmaa_wrapper.run_job`` dispatches a command with arguments to a cluster or Grid Engine node and waits for the command to complete.
-
-        It is the semantic equivalent of calling `os.system  <http://docs.python.org/2/library/os.html#os.system>`__  or
-        `subprocess.check_output  <http://docs.python.org/2/library/subprocess.html#subprocess.check_call>`__.
-
-    **Example**:
-
-        .. code-block:: python
-
-            from ruffus.drmaa_wrapper import run_job, error_drmaa_job
-            import drmaa
-            my_drmaa_session = drmaa.Session()
-            my_drmaa_session.initialize()
-
-            run_job("ls",
-                    job_name = "test",
-                    job_other_options="-P mott-flint.prja -q short.qa",
-                    job_script_directory = "test_dir",
-                    job_environment={ 'BASH_ENV' : '~/.bashrc' },
-                    retain_job_scripts = True, drmaa_session=my_drmaa_session)
-            run_job("ls",
-                    job_name = "test",
-                    job_other_options="-P mott-flint.prja -q short.qa",
-                    job_script_directory = "test_dir",
-                    job_environment={ 'BASH_ENV' : '~/.bashrc' },
-                    retain_job_scripts = True,
-                    drmaa_session=my_drmaa_session,
-                    working_directory = "/gpfs1/well/mott-flint/lg/src/oss/ruffus/doc")
-
-            #
-            #   catch exceptions
-            #
-            try:
-                stdout_res, stderr_res  = run_job(cmd,
-                                                  job_name          = job_name,
-                                                  logger            = logger,
-                                                  drmaa_session     = drmaa_session,
-                                                  run_locally       = options.local_run,
-                                                  job_other_options = get_queue_name())
-
-            # relay all the stdout, stderr, drmaa output to diagnose failures
-            except error_drmaa_job as err:
-                raise Exception("\n".join(map(str,
-                                    ["Failed to run:",
-                                     cmd,
-                                     err,
-                                     stdout_res,
-                                     stderr_res])))
-
-            my_drmaa_session.exit()
-
-
-
-    **Parameters:**
-
-.. _drmaa_wrapper.run_job.cmd_str:
-
-    * *cmd_str*
-
-        The command which will be run remotely including all parameters
-
-.. _drmaa_wrapper.run_job.job_name:
-
-    * *job_name*
-
-        A descriptive name for the command. This will be displayed by `SGE qstat  <http://gridscheduler.sourceforge.net/htmlman/htmlman1/qstat.html>`__, for example.
-        Defaults to "ruffus_job"
-
-.. _drmaa_wrapper.run_job.job_other_options:
-
-    * *job_other_options*
-
-        Other drmaa parameters can be passed verbatim as a string.
-
-        Examples for SGE include project name (``-P project_name``), parallel environment (``-pe parallel_environ``), account (``-A account_string``), resource (``-l resource=expression``),
-        queue name (``-q a_queue_name``), queue priority (``-p 15``).
-
-        These are parameters which you normally need to include when submitting jobs interactively, for example via
-        `SGE qsub  <http://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html>`__
-        or `SLURM  <http://apps.man.poznan.pl/trac/slurm-drmaa/wiki/WikiStart#Nativespecification>`__ (`srun <https://computing.llnl.gov/linux/slurm/srun.html>`__)
-
-.. _drmaa_wrapper.run_job.job_script_directory:
-
-    * *job_script_directory*
-
-        The directory where drmaa temporary script files will be found. Defaults to the current working directory.
-
-
-.. _drmaa_wrapper.run_job.job_environment:
-
-    * *job_environment*
-
-        A dictionary of key / values with environment variables. E.g. ``"{'BASH_ENV': '~/.bashrc'}"``
-
-
-.. _drmaa_wrapper.run_job.working_directory:
-
-    * *working_directory*
-
-        * Sets the working directory.
-        * Should be a fully qualified path.
-        * Defaults to the current working directory.
-
-
-.. _drmaa_wrapper.run_job.retain_job_scripts:
-
-    * *retain_job_scripts*
-
-        Do not delete temporary script files containg drmaa commands. Useful for
-        debugging, running on the command line directly, and can provide a useful record of the commands.
-
-.. _drmaa_wrapper.run_job.logger:
-
-    * *logger*
-
-        For logging messages indicating the progress of the pipeline in terms of tasks and jobs. Takes objects with the standard python
-        `logging  <https://docs.python.org/2/library/logging.html>`__ module interface.
-
-.. _drmaa_wrapper.run_job.drmaa_session:
-
-    * *drmaa_session*
-
-        A shared drmaa session created and managed separately.
-
-        In the main part of your **Ruffus** pipeline script somewhere there should be code looking like this:
-
-        .. code-block:: python
-
-            #
-            #   start shared drmaa session for all jobs / tasks in pipeline
-            #
-            import drmaa
-            drmaa_session = drmaa.Session()
-            drmaa_session.initialize()
-
-
-            #
-            #   pipeline functions
-            #
-
-            if __name__ == '__main__':
-                cmdline.run (options, multithread = options.jobs)
-                drmaa_session.exit()
-
-.. _drmaa_wrapper.run_job.run_locally:
-
-    * *run_locally*
-
-        Runs commands locally using the standard python `subprocess  <https://docs.python.org/2/library/subprocess.html>`__ module
-        rather than dispatching remotely. This allows scripts to be debugged easily
-
-.. _drmaa_wrapper.run_job.touch_only:
-
-    * *touch_only*
-
-        Create or update :ref:`Output files <drmaa_wrapper.run_job.output_files>`
-        only to simulate the running of the pipeline.
-        Does not dispatch commands remotely or locally. This is most useful to force a
-        pipeline to acknowledge that a particular part is now up-to-date.
-
-        See also: :ref:`pipeline_run(touch_files_only=True) <pipeline_functions.pipeline_run.touch_files_only>`
-
-
-.. _drmaa_wrapper.run_job.output_files:
-
-    * *output_files*
-
-        Output files which will be created or updated if  :ref:`touch_only <drmaa_wrapper.run_job.touch_only>` ``=True``
-
-
diff --git a/doc/_build/html/_sources/examples/bioinformatics/index.txt b/doc/_build/html/_sources/examples/bioinformatics/index.txt
deleted file mode 100644
index fe17943..0000000
--- a/doc/_build/html/_sources/examples/bioinformatics/index.txt
+++ /dev/null
@@ -1,290 +0,0 @@
-.. _examples_bioinformatics_part1:
-
-
-
-###################################################################
-Construction of a simple pipeline to run BLAST jobs
-###################################################################
-
-============
-Overview
-============
-
-    This is a simple example to illustrate the convenience **Ruffus**
-    brings to simple tasks in bioinformatics.
-
-        1. **Split** a problem into multiple fragments that can be
-        2. **Run in parallel** giving partial solutions that can be
-        3. **Recombined** into the complete solution.
-
-    The example code runs a `ncbi <http://blast.ncbi.nlm.nih.gov/>`__
-    `blast <http://en.wikipedia.org/wiki/BLAST>`__ search for four sequences
-    against the human `refseq <http://en.wikipedia.org/wiki/RefSeq>`_ protein sequence database.
-
-        #. **Split** each of the four sequences into a separate file.
-        #. **Run in parallel** Blastall on each sequence file
-        #. **Recombine** the BLAST results by simple concatenation.
-
-
-    In real life,
-
-        * `BLAST <http://blast.ncbi.nlm.nih.gov/>`__ already provides support for multiprocessing
-        * Sequence files would be split in much larger chunks, with many sequences
-        * The jobs would be submitted to large computational farms (in our case, using the SunGrid Engine).
-        * The High Scoring Pairs (HSPs) would be parsed / filtered / stored in your own formats.
-
-
-
-
-    .. note::
-
-        This bioinformatics example is intended to showcase *some* of the features of Ruffus.
-
-            #. See the :ref:`manual <new_manual.introduction>` to learn about the various features in Ruffus.
-
-
-========================
-Prerequisites
-========================
-
--------------
-1. Ruffus
--------------
-    To install Ruffus on most systems with python installed:
-
-        ::
-
-            easy_install -U ruffus
-
-    Otherwise, `download <http://code.google.com/p/ruffus/downloads/list>`_ Ruffus and run:
-
-        ::
-
-            tar -xvzf ruffus-xxx.tar.gz
-            cd ruffus-xxx
-            ./setup install
-
-    where xxx is the latest Ruffus version.
-
-
--------------
-2. BLAST
--------------
-    This example assumes that the `BLAST <http://blast.ncbi.nlm.nih.gov/>`__ ``blastall`` and ``formatdb`` executables are
-    installed and on the search path. Otherwise download from `here <http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download>`_.
-
-
----------------------------------------
-3. human refseq sequence database
----------------------------------------
-
-    We also need to download the human refseq sequence file and format the ncbi database:
-
-        ::
-
-            wget ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz
-            gunzip human.protein.faa.gz
-
-            formatdb -i human.protein.faa
-
----------------------------------------
-4. test sequences
----------------------------------------
-    Query sequences in FASTA format can be found in `original.fa <../../_static/examples/bioinformatics/original.fa>`_
-
-
-=========================
-Code
-=========================
-    The code for this example can be found :ref:`here <examples_bioinformatics_part1_code>`  and
-    pasted into the python command shell.
-
-
-================================================
-Step 1. Splitting up the query sequences
-================================================
-
-    We want each of our sequences in the query file `original.fa <../../_static/examples/bioinformatics/original.fa>`_ to be placed
-    in a separate files named ``XXX.segment`` where ``XXX`` = 1 -> the number of sequences.
-
-        ::
-
-            current_file_index = 0
-            for line in open("original.fa"):
-                # start a new file for each accession line
-                if line[0] == '>':
-                    current_file_index += 1
-                    current_file = open("%d.segment" % current_file_index, "w")
-                current_file.write(line)
-
-
-
-    To use this in a pipeline, we only need to wrap this in a function, "decorated" with the Ruffus
-    keyword :ref:`@split <new_manual.split>`:
-
-
-
-        .. image:: ../../images/examples_bioinformatics_split.jpg
-
-
-    | This indicates that we are splitting up the input file `original.fa <../../_static/examples/bioinformatics/original.fa>`_ into however many
-      ``*.segment`` files as it takes.
-    | The pipelined function itself takes two arguments, for the input and output.
-
-    We shall see later this simple :ref:`@split <new_manual.split>` decorator already gives all the benefits of:
-
-        * Dependency checking
-        * Flowchart printing
-
-================================================
-Step 2. Run BLAST jobs in parallel
-================================================
-
-    Assuming that blast is already installed, sequence matches can be found with this python
-    code:
-
-        ::
-
-            os.system("blastall -p blastp -d human.protein.faa -i 1.segment > 1.blastResult")
-
-    To pipeline this, we need to simply wrap in a function, decorated with the **Ruffus**
-    keyword :ref:`@transform <new_manual.transform>`.
-
-        .. image:: ../../images/examples_bioinformatics_transform.jpg
-
-    This indicates that we are taking all the output files from the previous ``splitFasta``
-    operation (``*.segment``) and :ref:`@transform <new_manual.transform>`-ing each to a new file with the ``.blastResult``
-    suffix. Each of these transformation operations can run in parallel if specified.
-
-
-================================================
-Step 3. Combining BLAST results
-================================================
-
-    The following python code will concatenate the results together
-        ::
-
-            output_file = open("final.blast_results",  "w")
-            for i in glob("*.blastResults"):
-                output_file.write(open(i).read())
-
-
-
-    To pipeline this, we need again to decorate with the **Ruffus** keyword :ref:`@merge <new_manual.merge>`.
-
-        .. image:: ../../images/examples_bioinformatics_merge.jpg
-
-    This indicates that we are taking all the output files from the previous ``runBlast``
-    operation (``*.blastResults``) and :ref:`@merge <new_manual.merge>`-ing them to the new file ``final.blast_results``.
-
-
-================================================
-Step 4. Running the pipeline
-================================================
-
-    We can run the completed pipeline using a maximum of 4 parallel processes by calling
-    :ref:`pipeline_run <pipeline_functions.pipeline_run>` :
-
-        ::
-
-            pipeline_run([combineBlastResults], verbose = 2, multiprocess = 4)
-
-
-    Though we have only asked Ruffus to run ``combineBlastResults``, it traces all the dependencies
-    of this task and runs all the necessary parts of the pipeline.
-
-
-    .. note ::
-
-        The full code for this example can be found  :ref:`here <examples_bioinformatics_part1_code>`
-        suitable for pasting into the python command shell.
-
-    The ``verbose`` parameter causes the following output to be printed to stderr as the pipeline
-    runs:
-
-        ::
-
-            >>> pipeline_run([combineBlastResults], verbose = 2, multiprocess = 4)
-                Job = [original.fa -> *.segment] completed
-            Completed Task = splitFasta
-                Job = [1.segment -> 1.blastResult] completed
-                Job = [3.segment -> 3.blastResult] completed
-                Job = [2.segment -> 2.blastResult] completed
-                Job = [4.segment -> 4.blastResult] completed
-            Completed Task = runBlast
-                Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult] -> final.blast_results] completed
-            Completed Task = combineBlastResults
-
-
-================================================
-Step 5. Testing dependencies
-================================================
-
-    If we invoked :ref:`pipeline_run <pipeline_functions.pipeline_run>` again, nothing
-    further would happen because the
-    pipeline is now up-to-date. But what if the pipeline had not run to completion?
-
-    We can simulate the failure of one of the ``blastall`` jobs by deleting its results:
-
-        ::
-
-            os.unlink("4.blastResult")
-
-    Let us use the :ref:`pipeline_printout <pipeline_functions.pipeline_printout>`
-    function to print out the dependencies of the pipeline at a high ``verbose`` level which
-    will show both complete and incomplete jobs:
-
-        ::
-
-            >>> import sys
-            >>> pipeline_printout(sys.stdout, [combineBlastResults], verbose = 4)
-
-            ________________________________________
-            Tasks which are up-to-date:
-
-            Task = splitFasta
-                "Split sequence file into as many fragments as appropriate depending on the size of
-                           original_fasta"
-
-
-            ________________________________________
-            Tasks which will be run:
-
-            Task = runBlast
-                "Run blast"
-                   Job = [4.segment
-                         ->4.blastResult]
-                     Job needs update: Missing file 4.blastResult
-
-            Task = combineBlastResults
-                "Combine blast results"
-                   Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult]
-                         ->final.blast_results]
-                     Job needs update: Missing file 4.blastResult
-
-            ________________________________________
-
-    Only the parts of the pipeline which involve the missing BLAST result will be rerun.
-    We can confirm this by invoking the pipeline.
-
-        ::
-
-            >>> pipeline_run([combineBlastResults], verbose = 2, multiprocess = 4)
-
-                Job = [1.segment -> 1.blastResult] unnecessary: already up to date
-                Job = [2.segment -> 2.blastResult] unnecessary: already up to date
-                Job = [3.segment -> 3.blastResult] unnecessary: already up to date
-                Job = [4.segment -> 4.blastResult] completed
-            Completed Task = runBlast
-                Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult] -> final.blast_results] completed
-            Completed Task = combineBlastResults
-
-================================================
-What is next?
-================================================
-
-
-    In the :ref:`next (short) part <examples_bioinformatics_part2>`,
-    we shall add some standard (boilerplate) code to
-    turn this BLAST pipeline into a (slightly more) useful python program.
-
diff --git a/doc/_build/html/_sources/examples/bioinformatics/part1_code.txt b/doc/_build/html/_sources/examples/bioinformatics/part1_code.txt
deleted file mode 100644
index c02232f..0000000
--- a/doc/_build/html/_sources/examples/bioinformatics/part1_code.txt
+++ /dev/null
@@ -1,70 +0,0 @@
-.. include:: ../../global.inc
-.. _examples_bioinformatics_part1_code:
-
-
-###################################################################
-Ruffus code
-###################################################################
-
-::
-    
-    import os, sys
-    
-    exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
-    sys.path.insert(0, os.path.abspath(os.path.join(exe_path,"..", "..","..")))
-    
-    from ruffus import *
-    
-    
-    original_fasta = "original.fa"
-    database_file  = "human.protein.faa"
-    
-    @split(original_fasta, "*.segment")
-    def splitFasta (seqFile, segments):
-        """Split sequence file into 
-           as many fragments as appropriate
-           depending on the size of original_fasta"""
-        current_file_index = 0
-        for line in open(original_fasta):
-            # 
-            # start a new file for each accession line
-            # 
-            if line[0] == '>':
-                current_file_index += 1
-                current_file = open("%d.segment" % current_file_index, "w")
-            current_file.write(line)
-    
-    
-    
-    @transform(splitFasta, suffix(".segment"), ".blastResult")
-    def runBlast(seqFile,  blastResultFile):
-        """Run blast"""
-        os.system("blastall -p blastp -d %s -i %s > %s" %
-                    (database_file, seqFile, blastResultFile))
-    
-    
-    @merge(runBlast, "final.blast_results")
-    def combineBlastResults (blastResultFiles, combinedBlastResultFile):
-        """Combine blast results"""
-        output_file = open(combinedBlastResultFile,  "w")
-        for i in blastResultFiles:
-            output_file.write(open(i).read())
-    
-    
-    pipeline_run([combineBlastResults], verbose = 2, multiprocess = 4)
-    
-
-    #
-    #   Simulate interuption of the pipeline by 
-    #        deleting the output of one of the BLAST jobs
-    #
-    os.unlink("4.blastResult")
-
-    pipeline_printout(sys.stdout, [combineBlastResults], verbose = 4) 
-    
-
-    #
-    #   Re-running the pipeline
-    #
-    pipeline_run([combineBlastResults], verbose = 2, multiprocess = 4)
-
diff --git a/doc/_build/html/_sources/examples/bioinformatics/part2.txt b/doc/_build/html/_sources/examples/bioinformatics/part2.txt
deleted file mode 100644
index 30e1343..0000000
--- a/doc/_build/html/_sources/examples/bioinformatics/part2.txt
+++ /dev/null
@@ -1,152 +0,0 @@
-.. _examples_bioinformatics_part2:
-
-
-###################################################################
-Part 2: A slightly more practical pipeline to run blasts jobs
-###################################################################
-
-============
-Overview
-============
-
-    :ref:`Previously <examples_bioinformatics_part1>`, we had built
-    a simple pipeline to split up a FASTA file of query sequences so
-    that these can be matched against a sequence database in parallel.
-
-    We shall wrap this code so that
-
-        * It is more robust to interruptions
-        * We can specify the file names on the command line
-
-==================================================================
-Step 1. Cleaning up any leftover junk from previous pipeline runs
-==================================================================
-
-    | We split up each of our sequences in the query file `original.fa <../../_static/examples/bioinformatics/original.fa>`_
-      into a separate files named ``XXX.segment`` where ``XXX`` is the number of sequences in
-      the FASTA file.
-
-    | However, if we start with 6 sequences (giving ``1.segment`` ... ``6.segment``), and we
-      then edited `original.fa <../../_static/examples/bioinformatics/original.fa>`_
-      so that only 5 were left, the file ``6.segment`` would still be left
-      hanging around as an unwanted, extraneous and confusing orphan.
-
-    As a general rule, it is a good idea to clean up the results of a previous run in
-    a :ref:`@split <manual.split>` operation:
-
-        ::
-
-            @split("original.fa", "*.segment")
-            def splitFasta (seqFile, segments):
-
-                #
-                #   Clean up any segment files from previous runs before creating new one
-                #
-                for i in glob.glob("*.segment"):
-                    os.unlink(i)
-
-                # code as before...
-
-.. _examples_bioinformatics_part2.step2:
-
-===============================================================
-Step 2. Adding a "flag" file to mark successful completion
-===============================================================
-
-    When pipelined tasks are interrupted half way through an operation, the output may
-    only contain part of the results in an incomplete or inconsistent state.
-    There are three general options to deal with this:
-
-        #. Catch any interrupting conditions and delete the incomplete output
-        #. Tag successfully completed output with a special marker at the end of the file
-        #. Create an empty "flag" file whose only point is to signal success
-
-    Option (3) is the most reliable way and involves the least amount of work in Ruffus.
-    We add flag files with the suffix ``.blastSuccess`` for our parallel BLAST jobs:
-
-        ::
-
-            @transform(splitFasta, suffix(".segment"), [".blastResult", ".blastSuccess"])
-            def runBlast(seqFile,  output_files):
-
-                blastResultFile, flag_file = output_files
-
-                #
-                #   Existing code unchanged
-                #
-                os.system("blastall -p blastp -d human.protein.faa "+
-                            "-i %s > %s" % (seqFile, blastResultFile))
-
-                #
-                #   "touch" flag file to indicate success
-                #
-                open(flag_file, "w")
-
-
-==============================================================
-Step 3. Allowing the script to be invoked on the command line
-==============================================================
-
-    We allow the query sequence file, as well as the sequence database and end results
-    to be specified at runtime using the standard python `optparse <http://docs.python.org/library/optparse.html>`_ module.
-    We find this approach to run time arguments generally useful for many Ruffus scripts.
-    The full code can be :ref:`viewed here <examples_bioinformatics_part2_code>` and
-    `downloaded from run_parallel_blast.py <../../_static/examples/bioinformatics/run_parallel_blast.py>`_.
-
-    The different options can be inspected by running the script with the ``--help`` or ``-h``
-    argument.
-
-    The following options are useful for developing Ruffus scripts:
-
-        ::
-
-            --verbose | -v    :  Print more detailed messages for each additional verbose level.
-                                 E.g. run_parallel_blast --verbose --verbose --verbose ... (or -vvv)
-
-            --jobs | -j       :  Specifies the number of jobs (operations) to run in parallel.
-
-            --flowchart FILE  :  Print flowchart of the pipeline to FILE. Flowchart format
-                                 depends on extension. Alternatives include (".dot", ".jpg",
-                                 "*.svg", "*.png" etc). Formats other than ".dot" require
-                                 the dot program to be installed (http://www.graphviz.org/).
-
-            --just_print | -n    Only print a trace (description) of the pipeline.
-                                 The level of detail is set by --verbose.
-
-
-============================================================
-Step 4. Printing out a flowchart for the pipeline
-============================================================
-    The ``--flowchart`` argument results in a call to ``pipeline_printout_graph(...)``
-    This prints out a flowchart of the pipeline. Valid formats include ".dot", ".jpg", ".svg", ".png"
-    but all except for the first require the ``dot`` program to be installed
-    (http://www.graphviz.org/).
-
-    The state of the pipeline is reflected in the flowchart:
-
-    .. image:: ../../images/examples_bioinformatics_pipeline.jpg
-
-
-============================================================
-Step 5. Errors
-============================================================
-    Because Ruffus scripts are just normal python functions, you can debug them using
-    your usual tools, or jump to the offending line(s) even when the pipeline is running in
-    parallel.
-
-    For example, these are the what the error messages would look like if we had mis-spelt ``blastal``.
-    In :ref:`run_parallel_blast.py <examples_bioinformatics_part2_code>`,
-    python exceptions are raised if the ``blastall`` command fails.
-
-    Each of the exceptions for the parallel operations are printed out with the
-    offending lines (line 204), and problems (``blastal`` not found)
-    highlighted in red.
-
-        .. image:: ../../images/examples_bioinformatics_error.png
-
-============================================================
-Step 6. Will it run?
-============================================================
-    The full code can be :ref:`viewed here <examples_bioinformatics_part2_code>` and
-    `downloaded from run_parallel_blast.py <../../_static/examples/bioinformatics/run_parallel_blast.py>`_.
-
diff --git a/doc/_build/html/_sources/examples/bioinformatics/part2_code.txt b/doc/_build/html/_sources/examples/bioinformatics/part2_code.txt
deleted file mode 100644
index 93b628d..0000000
--- a/doc/_build/html/_sources/examples/bioinformatics/part2_code.txt
+++ /dev/null
@@ -1,267 +0,0 @@
-.. include:: ../../global.inc
-.. _examples_bioinformatics_part2_code:
-
-
-###################################################################
-Ruffus code
-###################################################################
-
-::
-    
-    #!/usr/bin/env python
-    """
-    
-        run_parallel_blast.py
-        [--log_file PATH]
-        [--quiet]
-    
-    """
-    
-    ################################################################################
-    #
-    #   run_parallel_blast
-    #
-    #
-    #   Copyright (c) 4/21/2010 Leo Goodstadt
-    #   
-    #   Permission is hereby granted, free of charge, to any person obtaining a copy
-    #   of this software and associated documentation files (the "Software"), to deal
-    #   in the Software without restriction, including without limitation the rights
-    #   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-    #   copies of the Software, and to permit persons to whom the Software is
-    #   furnished to do so, subject to the following conditions:
-    #   
-    #   The above copyright notice and this permission notice shall be included in
-    #   all copies or substantial portions of the Software.
-    #   
-    #   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-    #   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-    #   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-    #   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-    #   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-    #   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-    #   THE SOFTWARE.
-    #################################################################################
-    import os, sys
-    exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
-    sys.path.insert(0,os.path.abspath(os.path.join(exe_path,"..", "..")))
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    #   options        
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    from optparse import OptionParser
-    import sys, os
-    
-    exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
-    
-    
-    parser = OptionParser(version="%prog 1.0", usage = "\n\n    %prog --input_file QUERY_FASTA --database_file FASTA_DATABASE [more_options]")
-    parser.add_option("-i", "--input_file", dest="input_file",
-                      metavar="FILE", 
-                      type="string",
-                      help="Name and path of query sequence file in FASTA format. ")
-    parser.add_option("-d", "--database_file", dest="database_file",
-                      metavar="FILE", 
-                      type="string",
-                      help="Name and path of FASTA database to search. ")
-    parser.add_option("--result_file", dest="result_file",
-                      metavar="FILE", 
-                      type="string",
-                      default="final.blast_results",
-                      help="Name and path of where the files should end up. ")
-    parser.add_option("-t", "--temp_directory", dest="temp_directory",
-                      metavar="PATH", 
-                      type="string",
-                      default="tmp",
-                      help="Name and path of temporary directory where calculations "
-                                "should take place. ")
-    
-    #
-    #   general options: verbosity / logging
-    # 
-    parser.add_option("-v", "--verbose", dest = "verbose",
-                      action="count", default=0,
-                      help="Print more detailed messages for each additional verbose level."
-                           " E.g. run_parallel_blast --verbose --verbose --verbose ... (or -vvv)")
-    
-    #
-    #   pipeline
-    # 
-    parser.add_option("-j", "--jobs", dest="jobs",
-                      default=1,
-                      metavar="jobs", 
-                      type="int",
-                      help="Specifies the number of jobs (operations) to run in parallel.")
-    parser.add_option("--flowchart", dest="flowchart",
-                      metavar="FILE", 
-                      type="string",
-                      help="Print flowchart of the pipeline to FILE. Flowchart format "
-                           "depends on extension. Alternatives include ('.dot', '.jpg', "
-                           "'*.svg', '*.png' etc). Formats other than '.dot' require "
-                           "the dot program to be installed (http://www.graphviz.org/).")
-    parser.add_option("-n", "--just_print", dest="just_print",
-                        action="store_true", default=False,
-                        help="Only print a trace (description) of the pipeline. "
-                             " The level of detail is set by --verbose.")
-    
-    (options, remaining_args) = parser.parse_args()
-    
-    
-    if not options.flowchart:
-        if not options.database_file:
-            parser.error("\n\n\tMissing parameter --database_file FILE\n\n")
-        if not options.input_file:
-            parser.error("\n\n\tMissing parameter --input_file FILE\n\n")
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    #   imports        
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    from ruffus import * 
-    import subprocess
-    
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    #   Functions        
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    def run_cmd(cmd_str):
-        """
-        Throw exception if run command fails
-        """
-        process = subprocess.Popen(cmd_str, stdout = subprocess.PIPE, 
-                                    stderr = subprocess.PIPE, shell = True)
-        stdout_str, stderr_str = process.communicate()
-        if process.returncode != 0:
-            raise Exception("Failed to run '%s'\n%s%sNon-zero exit status %s" %
-                                (cmd_str, stdout_str, stderr_str, process.returncode))
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    #   Logger
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    import logging
-    logger = logging.getLogger("run_parallel_blast")
-    # 
-    # We are interesting in all messages
-    # 
-    if options.verbose:
-        logger.setLevel(logging.DEBUG)
-        stderrhandler = logging.StreamHandler(sys.stderr)
-        stderrhandler.setFormatter(logging.Formatter("    %(message)s"))
-        stderrhandler.setLevel(logging.DEBUG)
-        logger.addHandler(stderrhandler)
-    
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    #   Pipeline tasks
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    original_fasta = options.input_file
-    database_file  = options.database_file
-    temp_directory = options.temp_directory
-    result_file    = options.result_file
-    
-    @follows(mkdir(temp_directory))
-    
-    @split(original_fasta, os.path.join(temp_directory, "*.segment"))
-    def splitFasta (seqFile, segments):
-        """Split sequence file into 
-           as many fragments as appropriate
-           depending on the size of original_fasta"""
-        # 
-        #   Clean up any segment files from previous runs before creating new one
-        #
-        for i in segments:
-            os.unlink(i)
-        #
-        current_file_index = 0
-        for line in open(original_fasta):
-            # 
-            # start a new file for each accession line
-            # 
-            if line[0] == '>':
-                current_file_index += 1
-                file_name = "%d.segment" % current_file_index
-                file_path = os.path.join(temp_directory, file_name)
-                current_file = open(file_path, "w")
-            current_file.write(line)
-    
-    
-    @transform(splitFasta, suffix(".segment"), [".blastResult", ".blastSuccess"])
-    def runBlast(seqFile,  output_files):
-        #
-        blastResultFile, flag_file = output_files
-        #
-        run_cmd("blastall -p blastp -d human.protein.faa -i %s > %s" % (seqFile, blastResultFile))
-        #
-        #   "touch" flag file to indicate success
-        #
-        open(flag_file, "w")            
-    
-    
-    @merge(runBlast, result_file)
-    def combineBlastResults (blastResult_and_flag_Files, combinedBlastResultFile):
-        """Combine blast results"""
-        #
-        output_file = open(combinedBlastResultFile,  "w")
-        for blastResult_file, flag_file in blastResult_and_flag_Files:
-            output_file.write(open(blastResult_file).read())
-    
-    
-    
-    
-    
-    
-    
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    #   Print list of tasks
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    if options.just_print:
-        pipeline_printout(sys.stdout, [combineBlastResults], verbose=options.verbose)
-    
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    #   Print flowchart
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    elif options.flowchart:
-        # use file extension for output format
-        output_format = os.path.splitext(options.flowchart)[1][1:]
-        pipeline_printout_graph (open(options.flowchart, "w"),
-                                 output_format,
-                                 [combineBlastResults],
-                                 no_key_legend = True)
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    
-    #   Run Pipeline
-    
-    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-    else:
-        pipeline_run([combineBlastResults],  multiprocess = options.jobs,
-                            logger = logger, verbose=options.verbose)
-    
-
diff --git a/doc/_build/html/_sources/examples/paired_end_data.py.txt b/doc/_build/html/_sources/examples/paired_end_data.py.txt
deleted file mode 100644
index cbf1b58..0000000
--- a/doc/_build/html/_sources/examples/paired_end_data.py.txt
+++ /dev/null
@@ -1,122 +0,0 @@
-.. _faq.paired_files.code:
-
-############################################################################################################################################################################################################
-Example code for :ref:`FAQ Good practices: "What is the best way of handling data in file pairs (or triplets etc.)?" <faq.paired_files>`
-############################################################################################################################################################################################################
-
-    .. seealso::
-
-        * :ref:`@collate <new_manual.collate>`
-
-
-    .. code-block:: python
-        :emphasize-lines: 10-21,29-31,40-43,70-74
-
-        #!/usr/bin/env python
-        import sys, os
-
-        from ruffus import *
-        import ruffus.cmdline as cmdline
-        from subprocess import check_call
-
-        parser = cmdline.get_argparse(description="Parimala's pipeline?")
-
-        #                                                                                 .
-        #   Very flexible handling of input files                                         .
-        #                                                                                 .
-        #      input files can be specified flexibly as:                                  .
-        #                 --input a.fastq b.fastq                                         .
-        #                 --input a.fastq --input b.fastq                                 .
-        #                 --input *.fastq --input other/*.fastq                           .
-        #                 --input "*.fastq"                                               .
-        #                                                                                 .
-        #       The last form is expanded in the script and avoids limitations on command .
-        #           line lengths                                                          .
-        #                                                                                 .
-        parser.add_argument('-i', '--input', nargs='+', metavar="FILE", action="append", help = "Fastq files")
-
-        options = parser.parse_args()
-
-        #  standard python logger which can be synchronised across concurrent Ruffus tasks
-        logger, logger_mutex = cmdline.setup_logging ("PARIMALA", options.log_file, options.verbose)
-
-        #                                                                                .
-        #   Useful code to turn input files into a flat list                             .
-        #                                                                                .
-        from glob import glob
-        original_data_files = [fn for grouped in options.input for glob_spec in grouped for fn in glob(glob_spec)] if options.input else []
-        if not original_data_files:
-            original_data_files = [["C1W1_R1.fastq.gz", "C1W1_R2.fastq.gz"]]
-            #raise Exception ("No matching files specified with --input.")
-
-        #   <<<----  pipelined functions go here
-
-        #_________________________________________________________________________________
-        #                                                                                .
-        #   Group together file pairs                                                    .
-        #_________________________________________________________________________________
-        @collate(original_data_files,
-                    # match file name up to the "R1.fastq.gz"
-                    formatter("([^/]+)R[12].fastq.gz$"),
-                    # Create output parameter supplied to next task
-                    ["{path[0]}/{1[0]}paired.R1.fastq.gz",  # paired file 1
-                     "{path[0]}/{1[0]}paired.R2.fastq.gz"], # paired file 2
-                    # Extra parameters for our own convenience and use
-                    ["{path[0]}/{1[0]}unpaired.R1.fastq.gz",  # unpaired file 1
-                     "{path[0]}/{1[0]}unpaired.R2.fastq.gz"], # unpaired file 2
-                    logger, logger_mutex)
-        def trim_fastq(input_files, output_paired_files, discarded_unpaired_files, logger, logger_mutex):
-            if len(input_files) != 2:
-                raise Exception("One of read pairs %s missing" % (input_files,))
-            cmd = ("java -jar ~/SPRING-SUMMER_2014/Softwares/Trimmomatic/Trimmomatic-0.32/trimmomatic-0.32.jar "
-                   " PE -phred33  "
-                   " {input_files[0]} {input_files[1]} "
-                   " {output_paired_files[0]} {output_paired_files[1]} "
-                   " {discarded_unpaired_files[0]} {discarded_unpaired_files[1]} "
-                   " LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:50 "
-                )
-
-            check_call(cmd.format(**locals()))
-
-            with logger_mutex:
-                    logger.debug("Hooray trim_fastq worked")
-
-        #_________________________________________________________________________________
-        #                                                                                .
-        #   Each file pair now makes its way down the rest of the pipeline as            .
-        #       a couple                                                                 .
-        #_________________________________________________________________________________
-        @transform(trim_fastq,
-                    # regular expression match on first of pe files
-                    formatter("([^/]+)paired.R1.fastq.gz$"),
-                    # Output parameter supplied to next task
-                    "{path[0]}/{1[0]}.sam"
-
-                   # Extra parameters for our own convenience and use
-                    "{path[0]}/{1[0]}.pe_soap_pe",        # soap intermediate file
-                    "{path[0]}/{1[0]}.pe_soap_se",        # soap intermediate file
-                    logger, logger_mutex)
-        def align_seq(input_files, output_file, soap_pe_output_file, soap_se_output_file, logger, logger_mutex):
-            if len(input_files) != 2:
-                raise Exception("One of read pairs %s missing" % (input_files,))
-            cmd = ("~/SPRING-SUMMER_2014/Softwares/soap2.21release/soap "
-                    " -a {input_files[0]} "
-                    " -b {input_files[1]} "
-                    " -D Y55_genome.fa.index* "
-                    " -o {soap_pe_output_file} -2 {soap_se_output_file} -m 400 -x 600")
-
-            check_call(cmd.format(**locals()))
-
-
-            #Soap_to_sam
-            cmd = " perl ~/SPRING-SUMMER_2014/Softwares/soap2sam.pl -p {soap_pe_output_file} > {output_file}"
-
-            check_call(cmd.format(**locals()))
-
-
-            with logger_mutex:
-                    logger.debug("Hooray align_seq worked")
-
-
-        cmdline.run (options)
-
diff --git a/doc/_build/html/_sources/faq.txt b/doc/_build/html/_sources/faq.txt
deleted file mode 100644
index 2b70f66..0000000
--- a/doc/_build/html/_sources/faq.txt
+++ /dev/null
@@ -1,980 +0,0 @@
-.. include:: global.inc
-#############
-FAQ
-#############
-
-**********************************************************
-Citations
-**********************************************************
-
-===============================================================
-Q. How should *Ruffus* be cited in academic publications?
-===============================================================
-
-    The official publication describing the original version of *Ruffus* is:
-
-        `Leo Goodstadt (2010) <http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524>`_ : **Ruffus: a lightweight Python library for computational pipelines.** *Bioinformatics* 26(21): 2778-2779
-
-
-**********************************************************
-Good practices
-**********************************************************
-
-==================================================================================================================
-Q. What is the best way of keeping my data and workings separate?
-==================================================================================================================
-
-    It is good practice to run your pipeline in a temporary, "working" directory away from your original data.
-
-    The first step of your pipeline might be to make softlinks to your original data in your working directory.
-    This is example (relatively paranoid) code to do just this:
-
-    .. code-block:: python
-        :emphasize-lines: 3,5
-
-            def re_symlink (input_file, soft_link_name, logger, logging_mutex):
-                """
-                Helper function: relinks soft symbolic link if necessary
-                """
-                # Guard agains soft linking to oneself: Disastrous consequences of deleting the original files!!
-                if input_file == soft_link_name:
-                    logger.debug("Warning: No symbolic link made. You are using the original data directory as the working directory.")
-                    return
-                # Soft link already exists: delete for relink?
-                if os.path.lexists(soft_link_name):
-                    # do not delete or overwrite real (non-soft link) file
-                    if not os.path.islink(soft_link_name):
-                        raise Exception("%s exists and is not a link" % soft_link_name)
-                    try:
-                        os.unlink(soft_link_name)
-                    except:
-                        with logging_mutex:
-                            logger.debug("Can't unlink %s" % (soft_link_name))
-                with logging_mutex:
-                    logger.debug("os.symlink(%s, %s)" % (input_file, soft_link_name))
-                #
-                #   symbolic link relative to original directory so that the entire path
-                #       can be moved around with breaking everything
-                #
-                os.symlink( os.path.relpath(os.path.abspath(input_file),
-                            os.path.abspath(os.path.dirname(soft_link_name))), soft_link_name)
-
-            #
-            #   First task should soft link data to working directory
-            #
-            @jobs_limit(1)
-            @mkdir(options.working_dir)
-            @transform( input_files,
-                        formatter(),
-                        # move to working directory
-                        os.path.join(options.working_dir, "{basename[0]}{ext[0]}"),
-                        logger, logging_mutex
-                       )
-            def soft_link_inputs_to_working_directory (input_file, soft_link_name, logger, logging_mutex):
-                """
-                Make soft link in working directory
-                """
-                with logging_mutex:
-                    logger.info("Linking files %(input_file)s -> %(soft_link_name)s\n" % locals())
-                re_symlink(input_file, soft_link_name, logger, logging_mutex)
-
-
-.. _faq.paired_files:
-
-==================================================================================================================
-Q. What is the best way of handling data in file pairs (or triplets etc.)
-==================================================================================================================
-
-
-    In Bioinformatics, DNA data often consists of only the nucleotide sequence at the two ends of larger fragments.
-    The `paired_end  <http://www.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.ilmn>`__ or
-    `mate pair  <http://en.wikipedia.org/wiki/Shotgun_sequencing#Whole_genome_shotgun_sequencing>`__ data frequently
-    consists of of file pairs with conveniently related names such as "*.R1.fastq" and "*.R2.fastq".
-
-    At some point in data pipeline, these file pairs or triplets must find each other and be analysed in the same job.
-
-    Provided these file pairs or triplets are named consistently, an easiest way to regroup them is to use the
-    Ruffus :ref:`@collate <new_manual.collate>` decorator. For example:
-
-
-    .. code-block:: python
-
-        @collate(original_data_files,
-
-                    # match file name up to the "R1.fastq.gz"
-                    formatter("([^/]+)R[12].fastq.gz$"),
-
-                    # Create output parameter supplied to next task
-                    "{path[0]}/{1[0]}.sam",
-                    logger, logger_mutex)
-        def handle_paired_end(input_files, output_paired_files, logger, logger_mutex):
-            # check that we really have a pair of two files not an orphaned singleton
-            if len(input_files) != 2:
-                raise Exception("One of read pairs %s missing" % (input_files,))
-
-            # do stuff here
-
-
-
-    This (incomplete, untested) :ref:`example code <faq.paired_files.code>` shows what this would look like *in vivo*.
-
-
-
-**********************************************************
-General
-**********************************************************
-
-=========================================================
-Q. *Ruffus* won't create dependency graphs
-=========================================================
-
-    A. You need to have installed ``dot`` from `Graphviz <http://www.graphviz.org/>`_ to produce
-    pretty flowcharts likes this:
-
-            .. image:: images/pretty_flowchart.png
-
-
-
-
-=========================================================
-Q. *Ruffus* seems to be hanging in the same place
-=========================================================
-
-    A. If *ruffus* is interrupted, for example, by a Ctrl-C,
-    you will often find the following lines of code highlighted::
-
-        File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 1904, in pipeline_run
-        File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 1380, in run_all_jobs_in_task
-        File "/xxxx/python2.6/multiprocessing/pool.py", line 507, in next
-          self._cond.wait(timeout)
-        File "/xxxxx/python2.6/threading.py", line 237, in wait
-          waiter.acquire()
-
-    This is *not* where *ruffus* is hanging but the boundary between the main programme process
-    and the sub-processes which run *ruffus* jobs in parallel.
-
-    This is naturally where broken execution threads get washed up onto.
-
-
-
-
-=========================================================
-Q. Regular expression substitutions don't work
-=========================================================
-
-    A. If you are using the special regular expression forms ``"\1"``, ``"\2"`` etc.
-    to refer to matching groups, remember to 'escape' the subsitution pattern string.
-    The best option is to use `'raw' python strings <http://docs.python.org/library/re.html>`_.
-    For example:
-
-        ::
-
-            r"\1_substitutes\2correctly\3four\4times"
-
-    Ruffus will throw an exception if it sees an unescaped ``"\1"`` or ``"\2"`` in a file name.
-
-========================================================================================
-Q. How to force a pipeline to appear up to date?
-========================================================================================
-
-    *I have made a trivial modification to one of my data files and now Ruffus wants to rerun my month long pipeline. How can I convince Ruffus that everything is fine and to leave things as they are?*
-
-    The standard way to do what you are trying to do is to touch all the files downstream...
-    That way the modification times of your analysis files would postdate your existing files.
-    You can do this manually but Ruffus also provides direct support:
-
-    .. code-block:: python
-
-        pipeline_run (touch_files_only = True)
-
-    pipeline_run will run your script normally stepping over up-to-date tasks and starting
-    with jobs which look out of date. However, after that, none of your pipeline task functions
-    will be called, instead, each non-up-to-date file is `touch  <https://en.wikipedia.org/wiki/Touch_(Unix)>`__-ed in
-    turn so that the file modification dates follow on successively.
-
-    See the documentation for :ref:`pipeline_run() <pipeline_functions.pipeline_run>`
-
-    It is even simpler if you are using the new Ruffus.cmdline support from version 2.4. You can just type
-
-        .. code-block:: bash
-
-            your script --touch_files_only [--other_options_of_your_own_etc]
-
-    See :ref:`command line <new_manual.cmdline>` documentation.
-
-========================================================================================
-Q. How can I use my own decorators with Ruffus?
-========================================================================================
-
-(Thanks to Radhouane Aniba for contributing to this answer.)
-
-A. With care! If the following two points are observed:
-
-____________________________________________________________________________________________________________________________________________________________________________________________________________________
-1. Use `@wraps <https://docs.python.org/2/library/functools.html#functools.wraps>`__  from ``functools`` or Michele Simionato's `decorator <https://pypi.python.org/pypi/decorator>`__ module
-____________________________________________________________________________________________________________________________________________________________________________________________________________________
-
-    These will automatically forward attributes from the task function correctly:
-
-    * ``__name__`` and ``__module__`` is used to identify functions uniquely in a Ruffus pipeline, and
-    * ``pipeline_task`` is used to hold per task data
-
-__________________________________________________________________________________________________________
-2. Always call Ruffus decorators first before your own decorators.
-__________________________________________________________________________________________________________
-
-    Otherwise, your decorator will be ignored.
-
-    So this works:
-
-    .. code-block:: python
-
-      @follows(prev_task)
-      @custom_decorator(something)
-      def test():
-          pass
-
-    This is a bit futile
-
-    .. code-block:: python
-
-        # ignore @custom_decorator
-        @custom_decorator(something)
-        @follows(prev_task)
-        def test():
-            pass
-
-
-    This order dependency is an unfortunate quirk of how python decorators work. The last (rather futile)
-    piece of code is equivalent to:
-
-    .. code-block:: python
-
-        test = custom_decorator(something)(ruffus.follows(prev_task)(test))
-
-    Unfortunately, Ruffus has no idea that someone else (``custom_decorator``) is also modifying the ``test()`` function
-    after it (``ruffus.follows``) has had its go.
-
-
-
-_____________________________________________________
-Example decorator:
-_____________________________________________________
-
-    Let us look at a decorator to time jobs:
-
-    .. code-block:: python
-
-        import sys, time
-        def time_func_call(func, stream, *args, **kwargs):
-            """prints elapsed time to standard out, or any other file-like object with a .write() method.
-            """
-           start = time.time()
-           # Run the decorated function.
-           ret = func(*args, **kwargs)
-           # Stop the timer.
-           end = time.time()
-           elapsed = end - start
-           stream.write("{} took {} seconds\n".format(func.__name__, elapsed))
-           return ret
-
-
-        from ruffus import *
-        import sys
-        import time
-
-        @time_job(sys.stderr)
-        def first_task():
-            print "First task"
-
-
-        @follows(first_task)
-        @time_job(sys.stderr)
-        def second_task():
-            print "Second task"
-
-
-        @follows(second_task)
-        @time_job(sys.stderr)
-        def final_task():
-            print "Final task"
-
-        pipeline_run()
-
-
-    What would ``@time_job`` look like?
-
-__________________________________________________________________________________________________________
-1. Using functools `@wraps <https://docs.python.org/2/library/functools.html#functools.wraps>`__
-__________________________________________________________________________________________________________
-
-
-    .. code-block:: python
-
-        import functools
-        def time_job(stream=sys.stdout):
-            def actual_time_job(func):
-                @functools.wraps(func)
-                def wrapper(*args, **kwargs):
-                    return time_func_call(func, stream, *args, **kwargs)
-                return wrapper
-            return actual_time_job
-
-__________________________________________________________________________________________________________
-2. Using Michele Simionato's `decorator <https://pypi.python.org/pypi/decorator>`__ module
-__________________________________________________________________________________________________________
-
-
-    .. code-block:: python
-
-        import decorator
-        def time_job(stream=sys.stdout):
-            def time_job(func, *args, **kwargs):
-                return time_func_call(func, stream, *args, **kwargs)
-            return decorator.decorator(time_job)
-
-
-_______________________________________________________________________________________________________________________________________________________________
-2. By hand, using a `callable object <https://docs.python.org/2/reference/datamodel.html#emulating-callable-objects>`__
-_______________________________________________________________________________________________________________________________________________________________
-
-
-    .. code-block:: python
-
-        class time_job(object):
-            def __init__(self, stream=sys.stdout):
-                self.stream = stream
-            def __call__(self, func):
-                def inner(*args, **kwargs):
-                    return time_func_call(func, self.stream, *args, **kwargs)
-                # remember to forward __name__
-                inner.__name__ = func.__name__
-                inner.__module__ = func.__module__
-                inner.__doc__ = func.__doc__
-                if hasattr(func, "pipeline_task"):
-                    inner.pipeline_task = func.pipeline_task
-                return inner
-
-
-
-
-
-========================================================================================
-Q. Can a task function in a *Ruffus* pipeline be called normally outside of Ruffus?
-========================================================================================
-    A. Yes. Most python decorators wrap themselves around a function. However, *Ruffus* leaves the
-    original function untouched and unwrapped. Instead, *Ruffus* adds a ``pipeline_task`` attribute
-    to the task function to signal that this is a pipelined function.
-
-    This means the original task function can be called just like any other python function.
-
-=====================================================================================================================
-Q. My  *Ruffus* tasks create two files at a time. Why is the second one ignored in successive stages of my pipeline?
-=====================================================================================================================
-    *This is my code:*
-
-        ::
-
-            from ruffus import *
-            import sys
-            @transform("start.input", regex(".+"), ("first_output.txt", "second_output.txt"))
-            def task1(i,o):
-                pass
-
-            @transform(task1, suffix(".txt"), ".result")
-            def task2(i, o):
-                pass
-
-            pipeline_printout(sys.stdout, [task2], verbose=3)
-
-        ::
-
-            ________________________________________
-            Tasks which will be run:
-
-            Task = task1
-                   Job = [start.input
-                         ->[first_output.txt, second_output.txt]]
-
-            Task = task2
-                   Job = [[first_output.txt, second_output.txt]
-                         ->first_output.result]
-
-            ________________________________________
-
-    A: This code produces a single output of a tuple of 2 files. In fact, you want two
-    outputs, each consisting of 1 file.
-
-    You want a single job (single input) to be produce multiple outputs (multiple jobs
-    in downstream tasks). This is a one-to-many operation which calls for
-    :ref:`@split <decorators.split>`:
-
-        ::
-
-            from ruffus import *
-            import sys
-            @split("start.input", ("first_output.txt", "second_output.txt"))
-            def task1(i,o):
-                pass
-
-            @transform(task1, suffix(".txt"), ".result")
-            def task2(i, o):
-                pass
-
-            pipeline_printout(sys.stdout, [task2], verbose=3)
-
-        ::
-
-            ________________________________________
-            Tasks which will be run:
-
-            Task = task1
-                   Job = [start.input
-                         ->[first_output.txt, second_output.txt]]
-
-            Task = task2
-                   Job = [first_output.txt
-                         ->first_output.result]
-                   Job = [second_output.txt
-                         ->second_output.result]
-
-            ________________________________________
-
-
-=======================================================================================
-Q. How can a *Ruffus* task produce output which goes off in different directions?
-=======================================================================================
-
-    A. As above, anytime there is a situation which requires a one-to-many operation, you should reach
-    for :ref:`@subdivide <decorators.subdivide>`. The advanced form takes a regular expression, making
-    it easier to produce multiple derivatives of the input file. The following example subdivides
-    *2* jobs each into *3*, so that the subsequence task will run *2* x *3* = *6* jobs.
-
-        ::
-
-            from ruffus import *
-            import sys
-            @subdivide(["1.input_file",
-                        "2.input_file"],
-                        regex(r"(.+).input_file"),      # match file prefix
-                       [r"\1.file_type1",
-                        r"\1.file_type2",
-                        r"\1.file_type3"])
-            def split_task(input, output):
-               pass
-
-
-            @transform(split_task, regex("(.+)"), r"\1.test")
-            def test_split_output(i, o):
-               pass
-
-            pipeline_printout(sys.stdout, [test_split_output], verbose = 3)
-
-        Each of the original 2 files have been split in three so that test_split_output will run
-        6 jobs simultaneously.
-
-            ::
-
-                ________________________________________
-                Tasks which will be run:
-
-                Task = split_task
-                       Job = [1.input_file ->[1.file_type1, 1.file_type2, 1.file_type3]]
-                       Job = [2.input_file ->[2.file_type1, 2.file_type2, 2.file_type3]]
-
-                Task = test_split_output
-                       Job = [1.file_type1 ->1.file_type1.test]
-                       Job = [1.file_type2 ->1.file_type2.test]
-                       Job = [1.file_type3 ->1.file_type3.test]
-                       Job = [2.file_type1 ->2.file_type1.test]
-                       Job = [2.file_type2 ->2.file_type2.test]
-                       Job = [2.file_type3 ->2.file_type3.test]
-                ________________________________________
-
-
-
-=======================================================================================
-Q. Can I call extra code before each job?
-=======================================================================================
-    A. This is easily accomplished by hijacking the process
-    for checking if jobs are up to date or not (:ref:`@check_if_uptodate <decorators.check_if_uptodate>`):
-
-        ::
-
-            from ruffus import *
-            import sys
-
-            def run_this_before_each_job (*args):
-                print "Calling function before each job using these args", args
-                # Remember to delegate to the default *Ruffus* code for checking if
-                #   jobs need to run.
-                return needs_update_check_modify_time(*args)
-
-            @check_if_uptodate(run_this_before_each_job)
-            @files([[None, "a.1"], [None, "b.1"]])
-            def task_func(input, output):
-                pass
-
-            pipeline_printout(sys.stdout, [task_func])
-
-        This results in:
-        ::
-
-            ________________________________________
-            >>> pipeline_run([task_func])
-            Calling function before each job using these args (None, 'a.1')
-            Calling function before each job using these args (None, 'a.1')
-            Calling function before each job using these args (None, 'b.1')
-                Job = [None -> a.1] completed
-                Job = [None -> b.1] completed
-            Completed Task = task_func
-
-        .. note::
-
-            Because ``run_this_before_each_job(...)`` is called whenever *Ruffus* checks to see if
-            a job is up to date or not, the function may be called twice for some jobs
-            (e.g. ``(None, 'a.1')`` above).
-
-
-=========================================================================================================
-Q. Does *Ruffus* allow checkpointing: to distinguish interrupted and completed results?
-=========================================================================================================
-
-_____________________________________________________
-A. Use the builtin sqlite checkpointing
-_____________________________________________________
-
-
-    By default, ``pipeline_run(...)`` will save the timestamps for output files from successfully run jobs to an sqlite database file (``.ruffus_history.sqlite``) in the current directory .
-
-    * If you are using ``Ruffus.cmdline``, you can change the checksum / timestamp database file name on the command line using  ``--checksum_file_name NNNN``
-    *
-
-
-    The level of timestamping / checksumming can be set via the ``checksum_level`` parameter:
-
-    .. code-block:: python
-
-        pipeline_run(..., checksum_level = N, ...)
-
-    where the default is 1::
-
-       level 0 : Use only file timestamps
-       level 1 : above, plus timestamp of successful job completion
-       level 2 : above, plus a checksum of the pipeline function body
-       level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-_____________________________________________________
-A. Use a flag file
-_____________________________________________________
-
-    When gmake is interrupted, it will delete the target file it is updating so that the target is
-    remade from scratch when make is next run. Ruffus, by design, does not do this because, more often than
-    not, the partial / incomplete file may be usefully if only to reveal, for example, what might have caused an interrupting error
-    or exception. It also seems a bit too clever and underhand to go around the programmer's back to delete files...
-
-    A common *Ruffus* convention is create an empty checkpoint or "flag" file whose sole purpose
-    is to record a modification-time and the successful completion of a job.
-
-    This would be task with a completion flag:
-
-    ::
-
-        #
-        #   Assuming a pipelined task function named "stage1"
-        #
-        @transform(stage1, suffix(".stage1"), [".stage2", ".stage2_finished"] )
-        def stage2 (input_files, output_files):
-            task_output_file, flag_file = output_files
-            cmd = ("do_something2 %(input_file)s >| %(task_output_file)s ")
-            cmd = cmd % {
-                            "input_file":               input_files[0],
-                            "task_output_file":         task_output_file
-                        }
-            if not os.system( cmd ):
-                #88888888888888888888888888888888888888888888888888888888888888888888888888888
-                #
-                #   It worked: Create completion flag_file
-                #
-                open(flag_file, "w")
-                #
-                #88888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-    The flag_files ``xxx.stage2_finished`` indicate that each job is finished. If this is missing,
-    ``xxx.stage2`` is only a partial, interrupted result.
-
-
-    The only thing to be aware of is that the flag file will appear in the list of inputs of the
-    downstream task, which should accordingly look like this:
-
-
-    ::
-
-        @transform(stage2, suffix(".stage2"), [".stage3", ".stage3_finished"] )
-        def stage3 (input_files, output_files):
-
-            #888888888888888888888888888888888888888888888888888888888888888888888888888888888
-            #
-            #   Note that the first parameter is a LIST of input files, the last of which
-            #       is the flag file from the previous task which we can ignore
-            #
-            input_file, previous_flag_file  = input_files
-            #
-            #888888888888888888888888888888888888888888888888888888888888888888888888888888888
-            task_output_file, flag_file     = output_files
-            cmd = ("do_something3 %(input_file)s >| %(task_output_file)s ")
-            cmd = cmd % {
-                            "input_file":               input_file,
-                            "task_output_file":         task_output_file
-                        }
-            # completion flag file for this task
-            if not os.system( cmd ):
-                open(flag_file, "w")
-
-
-    The :ref:`Bioinformatics example<examples_bioinformatics_part2.step2>` contains :ref:`code <examples_bioinformatics_part2_code>` for checkpointing.
-
-
-_____________________________________________________
-A. Use a temp file
-_____________________________________________________
-
-    Thanks to Martin Goodson for suggesting this and providing an example. In his words:
-
-    "I normally use a decorator to create a temporary file which is only renamed after the task has completed without any problems. This seems a more elegant solution to the problem:"
-
-
-        .. code-block:: python
-
-            def usetemp(task_func):
-                """ Decorate a function to write to a tmp file and then rename it. So half finished tasks cannot create up to date targets.
-                """
-                @wraps(task_func)
-                def wrapper_function(*args, **kwargs):
-                    args=list(args)
-                    outnames=args[1]
-                    if not isinstance(outnames, basestring) and  hasattr(outnames, '__getitem__'):
-                        tmpnames=[str(x)+".tmp" for x in outnames]
-                        args[1]=tmpnames
-                        task_func(*args, **kwargs)
-                        try:
-                            for tmp, name in zip(tmpnames, outnames):
-                                if os.path.exists(tmp):
-                                    os.rename(tmp, str(name))
-                        except BaseException as e:
-                            for name in outnames:
-                                if os.path.exists(name):
-                                    os.remove(name)
-                            raise (e)
-                    else:
-                        tmp=str(outnames)+'.tmp'
-                        args[1]=tmp
-                        task_func(*args, **kwargs)
-                        os.rename(tmp, str(outnames))
-            return wrapper_function
-
-
-    Use like this:
-
-        .. code-block:: python
-
-            @files(None, 'client1.price')
-            @usetemp
-            def getusers(inputfile, outputname):
-                #**************************************************
-                # code goes here
-                # outputname now refers to temporary file
-                pass
-
-
-
-
-
-**********************************************************
-Windows
-**********************************************************
-
-=========================================================
-Q. Windows seems to spawn *ruffus* processes recursively
-=========================================================
-
-    A. It is necessary to protect the "entry point" of the program under windows.
-    Otherwise, a new process will be started each time the main module is imported
-    by a new Python interpreter as an unintended side effects. Causing a cascade
-    of new processes.
-
-    See: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming
-
-    This code works::
-
-        if __name__ == '__main__':
-            try:
-                pipeline_run([parallel_task], multiprocess = 5)
-        except Exception, e:
-            print e.args
-
-
-
-**********************************************************
-Sun Grid Engine / PBS / SLURM etc
-**********************************************************
-
-==========================================================================================================================================
-Q. Can Ruffus be used to manage a cluster or grid based pipeline?
-==========================================================================================================================================
-    A. Some minimum modifications have to be made to your *Ruffus* script to allow it to submit jobs to a cluster
-
-    See :ref:`ruffus.drmaa_wrapper <new_manual.ruffus.drmaa_wrapper.run_job>`
-
-    Thanks to Andreas Heger and others at CGAT and Bernie Pope for contributing ideas and code.
-
-
-==========================================================================================================================================
-Q. When I submit lots of jobs via Sun Grid Engine (SGE), the head node occassionally freezes and dies
-==========================================================================================================================================
-
-    A. You need to use multithreading rather than multiprocessing. See :ref:`ruffus.drmaa_wrapper <new_manual.ruffus.drmaa_wrapper.run_job>`
-
-
-=====================================================================
-Q. Keeping Large intermediate files
-=====================================================================
-
-    Sometimes pipelines create a large number of intermediate files which might not be needed later.
-
-    Unfortunately, the current design of *Ruffus* requires these files to hang around otherwise the pipeline
-    will not know that it ran successfully.
-
-    We have some tentative plans to get around this but in the meantime, Bernie Pope suggests
-    truncating intermediate files in place, preserving timestamps::
-
-
-        # truncate a file to zero bytes, and preserve its original modification time
-        def zeroFile(file):
-            if os.path.exists(file):
-                # save the current time of the file
-                timeInfo = os.stat(file)
-                try:
-                    f = open(file,'w')
-                except IOError:
-                    pass
-                else:
-                    f.truncate(0)
-                    f.close()
-                    # change the time of the file back to what it was
-                    os.utime(file,(timeInfo.st_atime, timeInfo.st_mtime))
-
-**********************************************************************************
-Sharing python objects between Ruffus processes running concurrently
-**********************************************************************************
-
-    The design of Ruffus envisages that much of the data flow in pipelines occurs in files but it is also possible to pass python objects in memory.
-
-    Ruffus uses the `multiprocessing  <http://docs.python.org/2/library/multiprocessing.html>`_ module and much of the following is a summary of what is covered
-    in depth in the Python Standard Library `Documentation  <http://docs.python.org/2/library/multiprocessing.html#sharing-state-between-processes>`_.
-
-    Running Ruffus using ``pipeline_run(..., multiprocess = NNN)`` where ``NNN`` > 1 runs each job concurrently on up to ``NNN`` separate local processes.
-    Each task function runs independently in a different python intepreter, possibly on a different CPU, in the most efficient way.
-    However, this does mean we have to pay some attention to how data is sent across process boundaries (unlike the situation with ``pipeline_run(..., multithread = NNN)`` ).
-
-    The python code and data which comprises your multitasking Ruffus job is sent to a separate process in three ways:
-
-    #. The python function code and data objects are `pickled  <http://docs.python.org/2/library/pickle.html>`__, i.e. converting into a byte stream, by the master process, sent to the remote process
-       before being converted back into normal python (unpickling).
-    #. The parameters for your jobs, i.e. what Ruffus calls your task functions with, are separately `pickled  <http://docs.python.org/2/library/pickle.html>`__ and sent to the remote process via
-       `multiprocessing.Queue  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Queue>`_
-    #. You can share and synchronise other data yourselves. The canonical example is the logger provided by ``Ruffus.cmdline.setup_logging``
-
-    .. note::
-
-        Check that your function code and data can be `pickled  <http://docs.python.org/2/library/pickle.html#what-can-be-pickled-and-unpickled>`_.
-
-        Only functions, built-in functions and classes defined at the top level of a module are picklable.
-
-
-    The following answers are a short "how-to" for sharing and synchronising data yourselves.
-
-
-==============================================================================
-Can ordinary python objects be shared between processes?
-==============================================================================
-
-    A. Objects which can be `pickled  <http://docs.python.org/2/library/pickle.html>`__ can be shared as is. These include
-
-        * numbers
-        * strings
-        * tuples, lists, sets, and dictionaries containing only objects which can be `pickled  <http://docs.python.org/2/library/pickle.html>`__.
-
-    #. If these do not change during your pipeline, you can just use them without any further effort in your task.
-    #. If you need to use the value at the point when the task function is *called*, then you need to pass the python object as parameters to your task.
-       For example:
-
-       .. code-block:: python
-           :emphasize-lines: 1
-
-            # changing_list changes...
-            @transform(previous_task, suffix(".foo"), ".bar", changing_list)
-            def next_task(input_file, output_file, changing_list):
-                pass
-
-    #. If you need to use the value when the task function is *run* then see :ref:`the following answer. <how-about-synchronising-python-objects-in-real-time>`.
-
-
-================================================================================================
-Why am I getting ``PicklingError``?
-================================================================================================
-
-    What is happening? Didn't `Joan of Arc  <https://en.wikipedia.org/wiki/Battle_of_the_Herrings>`_ solve this once and for all?
-
-    A. Some of the data or code in your function cannot be `pickled  <http://docs.python.org/2/library/pickle.html>`__ and is being asked to be sent by python ``mulitprocessing`` across process boundaries.
-
-
-        When you run your pipeline using multiprocess:
-
-            .. code-block:: python
-
-                pipeline_run([], verbose = 5, multiprocess = 5, logger = ruffusLoggerProxy)
-
-        You will get the following errors:
-
-            .. code-block:: python
-
-                Exception in thread Thread-2:
-                Traceback (most recent call last):
-                  File "/path/to/python/python2.7/threading.py", line 808, in __bootstrap_inner
-                    self.run()
-                  File "/path/to/python/python2.7/threading.py", line 761, in run
-                    self.__target(*self.__args, * *self.__kwargs)
-                  File "/path/to/python/python2.7/multiprocessing/pool.py", line 342, in _handle_tasks
-                    put(task)
-                PicklingError: Can't pickle <type 'function'>: attribute lookup __builtin__.function failed
-
-
-        which go away when you set ``pipeline_run([], multiprocess = 1, ...)``
-
-
-
-
-    Unfortunately, pickling errors are particularly ill-served by standard python error messages. The only really good advice is to take the offending
-    code and try and `pickle  <http://docs.python.org/2/library/pickle.html>`__ it yourself and narrow down the errors. Check your objects against the list
-    in the `pickle  <http://docs.python.org/2/library/pickle.html#what-can-be-pickled-and-unpickled>`_ module.
-    Watch out especially for nested functions. These will have to be moved to file scope.
-    Other objects may have to be passed in proxy (see below).
-
-
-.. _how-about-synchronising-python-objects-in-real-time:
-
-================================================================================================
-How about synchronising python objects in real time?
-================================================================================================
-
-    A. You can use managers and proxy objects from the `multiprocessing  <http://docs.python.org/library/multiprocessing.html>`__ module.
-
-    The underlying python object would be owned and managed by a (hidden) server process. Other processes can access the shared objects transparently by using proxies. This is how the logger provided by
-    ``Ruffus.cmdline.setup_logging`` works:
-
-    .. code-block:: python
-
-        #  optional logger which can be passed to ruffus tasks
-        logger, logger_mutex = cmdline.setup_logging (__name__, options.log_file, options.verbose)
-
-    ``logger`` is a proxy for the underlying python `logger  <http://docs.python.org/2/library/logging.html>`__ object, and it can be shared freely between processes.
-
-    The best course is to pass ``logger`` as a parameter to a *Ruffus* task.
-
-    The only caveat is that we should make sure multiple jobs are not writting to the log at the same time. To synchronise logging, we use proxy to a non-reentrant `multiprocessing.lock <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Lock>`_.
-
-    .. code-block:: python
-
-        logger, logger_mutex = cmdline.setup_logging (__name__, options.log_file, options.verbose)
-
-
-        @transform(previous_task, suffix(".foo"), ".bar", logger, logger_mutex)
-        def next_task(input_file, output_file, logger, logger_mutex):
-            with logger_mutex:
-                logger.info("We are in the middle of next_task: %s -> %s" % (input_file, output_file))
-
-
-==============================================================================
-Can I  share and synchronise my own python classes via proxies?
-==============================================================================
-
-    A. `multiprocessing.managers.SyncManager  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.managers.SyncManager>`__ provides out of the box support for lists, arrays and dicts etc.
-
-        Most of the time, we can use a "vanilla" manager provided by `multiprocessing.Manager()  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.sharedctypes.multiprocessing.Manager>`_:
-
-        .. code-block:: python
-
-
-            import multiprocessing
-            manager = multiprocessing.Manager()
-
-            list_proxy = manager.list()
-            dict_proxy = manager.dict()
-            lock_proxy          = manager.Lock()
-            namespace_proxy     = manager.Namespace()
-            queue_proxy         = manager.Queue([maxsize])
-            rentrant_lock_proxy = manager.RLock()
-            semaphore_proxy     = manager.Semaphore([value])
-            char_array_proxy    = manager.Array('c')
-            integer_proxy       = manager.Value('i', 6)
-
-            @transform(previous_task, suffix(".foo"), ".bar", lock_proxy, dict_proxy, list_proxy)
-            def next_task(input_file, output_file, lock_proxy, dict_proxy, list_proxy):
-                with lock_proxy:
-                    list_proxy.append(3)
-                    dict_proxy['a'] = 5
-
-
-    However, you can also create proxy custom classes for your own objects.
-
-    In this case you may need to derive from  `multiprocessing.managers.SyncManager  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.managers.SyncManager>`_
-    and register proxy functions. See ``Ruffus.proxy_logger`` for an example of how to do this.
-
-============================================================================================================================================================
-How do I send python objects back and forth without tangling myself in horrible synchronisation code?
-============================================================================================================================================================
-
-    A. Sharing python objects by passing messages is a much more modern and safer way to coordinate multitasking than using synchronization primitives like locks.
-
-    The python `multiprocessing  <http://docs.python.org/2/library/multiprocessing.html#pipes-and-queues>`__ module provides support for passing python objects as messages between processes.
-    You can either use `pipes  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Pipe>`__
-    or `queues  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Queue>`__.
-    The idea is that one process pushes and object onto a `pipe  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Pipe>`__ or `queue  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Queue>`__
-    and the other processes pops it out at the other end. `Pipes  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Pipe>`__ are
-    only two ended so `queues  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Queue>`__ are usually a better fit for sending data to multiple Ruffus jobs.
-
-    Proxies for `queues  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.managers.SyncManager.Queue>`__ can be passed between processes as in the previous section
-
-
-==============================================================================
-How do I share large amounts of data efficiently across processes?
-==============================================================================
-
-    A. If it is really impractical to use data files on disk, you can put the data in shared memory.
-
-    It is possible to create shared objects using shared memory which can be inherited by child processes or passed as Ruffus parameters.
-    This is probably most efficently done via the `array  <http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Array>`_
-    interface. Again, it is easy to create locks and proxies for synchronised access:
-
-
-    .. code-block:: python
-
-        from multiprocessing import Process, Lock
-        from multiprocessing.sharedctypes import Value, Array
-        from ctypes import Structure, c_double
-
-        manager = multiprocessing.Manager()
-
-        lock_proxy          = manager.Lock()
-        int_array_proxy     = manager.Array('i', [123] * 100)
-
-        @transform(previous_task, suffix(".foo"), ".bar", lock_proxy, int_array_proxy)
-        def next_task(input_file, output_file, lock_proxy, int_array_proxy):
-            with lock_proxy:
-                int_array_proxy[23] = 71
-
-
-
-
diff --git a/doc/_build/html/_sources/gallery.txt b/doc/_build/html/_sources/gallery.txt
deleted file mode 100644
index 90ff20a..0000000
--- a/doc/_build/html/_sources/gallery.txt
+++ /dev/null
@@ -1,63 +0,0 @@
-.. include:: global.inc
-
-.. image:: images/logo.jpg
-
-******************************************************
-Hall of Fame: User contributed flowcharts
-******************************************************
-Please contribute your own work flows in your favourite colours with (an optional) short description
-to email: ruffus_lib at llew.org.uk
-
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-RNASeq pipeline
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    http://en.wikipedia.org/wiki/RNA-Seq
-
-    Mapping transcripts onto genomes using high-throughput sequencing technologies (:download:`svg <images/gallery/gallery_rna_seq.svg>`).
-
-    .. image:: images/gallery/gallery_rna_seq.png
-       :target: _downloads/gallery_rna_seq.svg
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-non-coding evolutionary constraints
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    http://en.wikipedia.org/wiki/Noncoding_DNA
-
-    Non-protein coding evolutionary constraints in different species (:download:`svg <images/gallery/gallery_dless.svg>`).
-
-    .. image:: images/gallery/gallery_dless.png
-       :target: _downloads/gallery_dless.svg
-
-^^^^^^^^^^^^^^^^^
-SNP annotation
-^^^^^^^^^^^^^^^^^
-Predicting impact of different Single Nucleotide Polymorphisms
-
-http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
-
-Population variation across genomes (:download:`svg <images/gallery/gallery_snp_annotation.svg>`).
-
-.. image:: images/gallery/gallery_snp_annotation.png
-       :target: _downloads/gallery_snp_annotation.svg
-
-Using "pseudo" targets to run only part of the pipeline (:download:`svg <images/gallery/gallery_snp_annotation_consequences.svg>`).
-
-.. image:: images/gallery/gallery_snp_annotation_consequences.png
-       :target: _downloads/gallery_snp_annotation_consequences.svg
-
-
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Chip-Seq analysis
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Analysing DNA binding sites with Chip-Seq
-http://en.wikipedia.org/wiki/Chip-Sequencing
-
-    (:download:`svg <images/gallery/gallery_big_pipeline.svg>`)
-
-    .. image:: images/gallery/gallery_big_pipeline.png
-       :target: _downloads/gallery_big_pipeline.svg
-
diff --git a/doc/_build/html/_sources/glossary.txt b/doc/_build/html/_sources/glossary.txt
deleted file mode 100644
index 9d86bab..0000000
--- a/doc/_build/html/_sources/glossary.txt
+++ /dev/null
@@ -1,81 +0,0 @@
-.. include:: global.inc
-****************
-Glossary
-****************
-.. _Glossary:
-
-.. _glossary.task:
-
-.. glossary::
-    
-    
-    
-    task
-        A stage in a computational pipeline.
-
-        Each **task** in *ruffus* is represented by a python function.
-    
-        For example, a task might be to find the products of a sets of two numbers::
-
-            4 x 5 = 20
-            5 x 6 = 30
-            2 x 7 = 14   
-
-    job
-        Any number of operations which can be run in parallel and make up
-        the work in a stage of a computional pipeline.
-        
-        Each **task** in *ruffus* is a separate call to the **task** function.
-        
-        For example, if a task is to find products of numbers, each of these will be a separate job.
-        
-            Job1::
-            
-                4 x 5 = 20
-            
-            Job2::
-            
-                5 x 6 = 30
-                    
-            Job3::
-            
-                2 x 7 = 14   
-            
-        Jobs need not complete in order.
-        
-    
-    decorator
-        Ruffus decorators allow functions to be incorporated into a computational
-        pipeline, with automatic generation of parameters, dependency checking etc.,
-        without modifying any code within the function.
-        Quoting from the `python wiki <http://wiki.python.org/moin/PythonDecorators>`_:
-
-            A Python decorator is a specific change to the Python syntax that 
-            allows us to more conveniently alter functions and methods.
-
-            Decorators dynamically alter the functionality of a function, method, or 
-            class without having to directly use subclasses or change the source code 
-            of the function being decorated.
-            
-
-    
-    generator
-        python generators are new to python 2.2 
-        (see `Charming Python: Iterators and simple generators <http://www.ibm.com/developerworks/library/l-pycon.html>`_).
-        They allow iterable data to be generated on the fly.
-        
-        Ruffus asks for generators when you want to generate **job** parameters dynamically.
-        
-        Each set of job parameters is returned by the ``yield`` keyword for 
-        greater clarity. For example,::
-        
-            def generate_job_parameters():
-                
-                for file_index, file_name in iterate(all_file_names):
-                
-                    # parameter for each job
-                    yield file_index, file_name
-    
-        Each job takes the parameters ``file_index`` and ``file_name``
-    
-         
diff --git a/doc/_build/html/_sources/history.txt b/doc/_build/html/_sources/history.txt
deleted file mode 100644
index c0a8f05..0000000
--- a/doc/_build/html/_sources/history.txt
+++ /dev/null
@@ -1,733 +0,0 @@
-.. include:: global.inc
-
-
-########################################
-Major Features added to Ruffus
-########################################
-
-.. note::
-
-    See :ref:`To do list <todo>` for future enhancements to Ruffus
-
-
-********************************************************************
-version 2.5RC
-********************************************************************
-
-    31st July 2014: Release Candidate
-
-    5th August 2014: Release
-
-============================================================================================================================================================
-1) Python3 compatability (but at least python 2.6 is now required)
-============================================================================================================================================================
-
-    Ruffus v2.5 is now python3 compatible. This has required surprisingly many changes to the codebase. Please report any bugs to me.
-
-    .. note::
-
-        **Ruffus now requires at least python 2.6**
-
-        It proved to be impossible to support python 2.5 and python 3.x at the same time.
-
-============================================================================================================================================================
-2) Ctrl-C interrupts
-============================================================================================================================================================
-
-    Ruffus now mostly(!) terminates gracefully when interrupted by Ctrl-C .
-
-    Please send me bug reports for when this doesn't work with a minimally reproducible case.
-
-    This means that, in general, if an ``Exception`` is thrown during your pipeline but you don't want to wait for the rest of the jobs to complete, you can still press Ctrl-C at any point.
-    Note that you may still need to clean up spawned processes, for example, using ``qdel`` if you are using ``Ruffus.drmaa_wrapper``
-
-============================================================================================================================================================
-3) Customising flowcharts in pipeline_printout_graph() with ``@graphviz``
-============================================================================================================================================================
-
-    *Contributed by Sean Davis, with improved syntax via Jake Biesinger*
-
-    The graphics for each task can have its own attributes (URL, shape, colour) etc. by adding
-    `graphviz attributes  <http://www.graphviz.org/doc/info/attrs.html>`__
-    using the ``@graphviz`` decorator.
-
-    * This allows HTML formatting in the task names (using the ``label`` parameter as in the following example).
-      HTML labels **must** be enclosed in ``<`` and ``>``. E.g.
-
-      .. code-block:: python
-
-        label = "<Line <BR/> wrapped task_name()>"
-
-    * You can also opt to keep the task name and wrap it with a prefix and suffix:
-
-      .. code-block:: python
-
-        label_suffix = "??? ", label_prefix = ": What is this?"
-
-    * The ``URL`` attribute allows the generation of clickable svg, and also client / server
-      side image maps usable in web pages.
-      See `Graphviz documentation  <http://www.graphviz.org/content/output-formats#dimap>`__
-
-
-    Example:
-
-        .. code-block:: python
-
-
-            @graphviz(URL='"http://cnn.com"', fillcolor = '"#FFCCCC"',
-                            color = '"#FF0000"', pencolor='"#FF0000"', fontcolor='"#4B6000"',
-                            label_suffix = "???", label_prefix = "What is this?<BR/> ",
-                            label = "<What <FONT COLOR=\"red\">is</FONT>this>",
-                            shape= "component", height = 1.5, peripheries = 5,
-                            style="dashed")
-            def Up_to_date_task2(infile, outfile):
-                pass
-
-            #   Can use dictionary if you wish...
-            graphviz_params = {"URL":"http://cnn.com", "fontcolor": '"#FF00FF"'}
-            @graphviz(**graphviz_params)
-            def myTask(input,output):
-                pass
-
-        .. **
-
-        .. image:: images/history_html_flowchart.png
-           :scale: 30
-
-
-============================================================================================================================================================
-4. Consistent verbosity levels
-============================================================================================================================================================
-
-    The verbosity levels are now more fine-grained and consistent between pipeline_printout and pipeline_run.
-    Note that At verbosity > 2, ``pipeline_run``  outputs lists of up-to-date tasks before running the pipeline.
-    Many users who defaulted to using a verbosity of 3 may want to move up to ``verbose = 4``.
-
-        * **level 0** : *Nothing*
-        * **level 1** : *Out-of-date Task names*
-        * **level 2** : *All Tasks (including any task function docstrings)*
-        * **level 3** : *Out-of-date Jobs in Out-of-date Tasks, no explanation*
-        * **level 4** : *Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings*
-        * **level 5** : *All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)*
-        * **level 6** : *All jobs in All Tasks whether out of date or not*
-        * **level 10**: *Logs messages useful only for debugging ruffus pipeline code*
-
-    * Defaults to **level 4** for pipeline_printout: *Out of date jobs, with explanations and warnings*
-    * Defaults to **level 1** for pipeline_run: *Out-of-date Task names*
-
-============================================================================================================================================================
-5. Allow abbreviated paths from ``pipeline_run`` or ``pipeline_printout``
-============================================================================================================================================================
-
-    .. note ::
-
-            Please contact me with suggestions if you find the abbreviations useful but "aesthetically challenged"!
-
-    Some pipelines produce interminable lists of long filenames. It would be nice to be able to abbreviate this
-    to just enough information to follow the progress.
-
-    Ruffus now allows either
-        1) Only the nth top level sub-directories to be included
-        2) The message to be truncated to a specified number of characters (to fit on a line, for example)
-
-           Note that the number of characters specified is the separate length of the input and output parameters,
-           not the entire message. You many need to specify a smaller limit that you expect (e.g. ``60`` rather than `80`)
-
-        .. code-block:: python
-
-            pipeline_printout(verbose_abbreviated_path = NNN)
-            pipeline_run(verbose_abbreviated_path = -MMM)
-
-
-    The ``verbose_abbreviated_path`` parameter restricts the length of input / output file paths to either
-
-        * NNN levels of nested paths
-        * A total of MMM characters, MMM is specified by setting ``verbose_abbreviated_path`` to -MMM (i.e. negative values)
-
-        ``verbose_abbreviated_path`` defaults to ``2``
-
-
-    For example:
-
-        Given ``["aa/bb/cc/dddd.txt", "aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt"]``
-
-
-        .. code-block:: python
-           :emphasize-lines: 1,4,8,19
-
-            # Original relative paths
-            "[aa/bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"
-
-            # Full abspath
-            verbose_abbreviated_path = 0
-            "[/test/ruffus/src/aa/bb/cc/dddd.txt, /test/ruffus/src/aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"
-
-            # Specifed level of nested directories
-            verbose_abbreviated_path = 1
-            "[.../dddd.txt, .../gggg.txt]"
-
-            verbose_abbreviated_path = 2
-            "[.../cc/dddd.txt, .../ffff/gggg.txt]"
-
-            verbose_abbreviated_path = 3
-            "[.../bb/cc/dddd.txt, .../eeee/ffff/gggg.txt]"
-
-
-            # Truncated to MMM characters
-            verbose_abbreviated_path = -60
-            "<???> /bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"
-
-
-    If you are using ``ruffus.cmdline``, the abbreviated path lengths can be specified on
-    the command line as an extension to the verbosity:
-
-        .. code-block:: bash
-           :emphasize-lines: 4,7
-
-            # verbosity of 4
-            yourscript.py --verbose 4
-
-            # display three levels of nested directories
-            yourscript.py --verbose 4:3
-
-            # restrict input and output parameters to 60 letters
-            yourscript.py --verbose 4:-60
-
-
-        The number after the colon is the abbreviated path length
-
-
-============================================================================================================================================================
-Other changes
-============================================================================================================================================================
-    * BUG FIX: Output producing wild cards was not saved in the checksum files!!!
-    * BUG FIX: @mkdir bug under Windows. Thanks to Sean Turley. (Aargh! Different exceptions are thrown in Windows vs. Linux for the same condition!)
-    * Added :ref:`pipeline_get_task_names(...) <pipeline_functions.pipeline_get_task_names>` which returns all task name as a list of strings. Thanks to Clare Sloggett
-
-
-********************************************************************
-version 2.4.1
-********************************************************************
-
-    26th April 2014
-
-    * Breaking changes to drmaa API suggested by Bernie Pope to ensure portability across different drmaa implementations (SGE, SLURM etc.)
-
-********************************************************************
-version 2.4
-********************************************************************
-
-    4th April 2014
-
-============================================================================================================================================================
-Additions to ``ruffus`` namespace
-============================================================================================================================================================
-
-    * :ref:`formatter() <new_manual.formatter>` (:ref:`syntax <decorators.formatter>`)
-    * :ref:`originate() <new_manual.originate>` (:ref:`syntax <decorators.originate>`)
-    * :ref:`subdivide() <new_manual.subdivide>` (:ref:`syntax <decorators.subdivide>`)
-
-============================================================================================================================================================
-Installation: use pip
-============================================================================================================================================================
-
-    ::
-
-        sudo pip install ruffus --upgrade
-
-============================================================================================================================================================
-1) Command Line support
-============================================================================================================================================================
-
-    The optional ``Ruffus.cmdline`` module provides support for a set of common command
-    line arguments which make writing *Ruffus* pipelines much more pleasant.
-    See :ref:`manual <new_manual.cmdline>`
-
-============================================================================================================================================================
-2) Check pointing
-============================================================================================================================================================
-
-    * Contributed by **Jake Biesinger**
-    * See :ref:`Manual <new_manual.checkpointing>`
-    * Uses a fault resistant sqlite database file to log i/o files, and additional checksums
-    * defaults to checking file timestamps stored in the current directory (``ruffus_utilility.RUFFUS_HISTORY_FILE = '.ruffus_history.sqlite'``)
-    * :ref:`pipeline_run(..., checksum_level = N, ...) <pipeline_functions.pipeline_run>`
-
-       * level 0 = CHECKSUM_FILE_TIMESTAMPS      : Classic mode. Use only file timestamps (no checksum file will be created)
-       * level 1 = CHECKSUM_HISTORY_TIMESTAMPS   : Also store timestamps in a database after successful job completion
-       * level 2 = CHECKSUM_FUNCTIONS            : As above, plus a checksum of the pipeline function body
-       * level 3 = CHECKSUM_FUNCTIONS_AND_PARAMS : As above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-       * defaults to level 1
-
-    * Can speed up trivial tasks: Previously Ruffus always added an extra 1 second pause between tasks
-      to guard against file systems (Ext3, FAT, some NFS) with low timestamp granularity.
-
-
-============================================================================================================================================================
-3) :ref:`subdivide() <new_manual.subdivide>` (:ref:`syntax <decorators.subdivide>`)
-============================================================================================================================================================
-
-    * Take a list of input jobs (like :ref:`@transform <decorators.transform>`) but further splits each into multiple jobs, i.e. it is a **many->even more** relationship
-    * synonym for the deprecated ``@split(..., regex(), ...)``
-
-========================================================================================================================================================================================================================================================================================================================
-4) :ref:`mkdir() <new_manual.mkdir>` (:ref:`syntax <decorators.mkdir>`) with :ref:`formatter() <new_manual.formatter>`, :ref:`suffix() <decorators.suffix>`  and :ref:`regex() <decorators.regex>`
-========================================================================================================================================================================================================================================================================================================================
-
-    * allows directories to be created depending on runtime parameters or the output of previous tasks
-    * behaves just like :ref:`@transform <decorators.transform>` but with its own (internal) function which does the actual work of making a directory
-    * Previous behavior is retained:``mkdir`` continues to work seamlessly inside :ref:`@follows <decorators.follows>`
-
-============================================================================================================================================================
-5) :ref:`originate() <new_manual.originate>` (:ref:`syntax <decorators.originate>`)
-============================================================================================================================================================
-
-    * Generates output files without dependencies from scratch  (*ex nihilo*!)
-    * For first step in a pipeline
-    * Task function obviously only takes output and not input parameters. (There *are* no inputs!)
-    * synonym for :ref:`@split(None,...) <decorators.split>`
-    * See :ref:`Summary <decorators.originate>` / :ref:`Manual <new_manual.originate>`
-
-========================================================================================================================================================================================================================================================================================================================
-6) New flexible :ref:`formatter() <new_manual.formatter>` (:ref:`syntax <decorators.formatter>`) alternative to :ref:`regex() <decorators.regex>`  & :ref:`suffix() <decorators.suffix>`
-========================================================================================================================================================================================================================================================================================================================
-
-    * Easy manipulation of path subcomponents in the style of `os.path.split()  <http://docs.python.org/2/library/os.path.html#os.path.split>`__
-    * Regular expressions are no longer necessary for path manipulation
-    * Familiar python syntax
-    * Optional regular expression matches
-    * Can refer to any in the list of N input files (not only the first file as for ``regex(...)``)
-    * Can even refer to individual letters within a match
-
-============================================================================================================================================================
-7) Combinatorics (all vs. all decorators)
-============================================================================================================================================================
-
-    * :ref:`@product <new_manual.product>`  (See `itertools.product  <http://docs.python.org/2/library/itertools.html#itertools.product>`__)
-    * :ref:`@permutations <new_manual.permutations>`  (See `itertools.permutations  <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__)
-    * :ref:`@combinations <new_manual.combinations>` (See `itertools.combinations  <http://docs.python.org/2/library/itertools.html#itertools.combinations>`__)
-    * :ref:`@combinations_with_replacement <new_manual.combinations_with_replacement>` (See `itertools.combinations_with_replacement  <http://docs.python.org/2/library/itertools.html#itertools.combinations_with_replacement>`__)
-    * in optional :ref:`combinatorics <new_manual.combinatorics>` module
-    * Only :ref:`formatter() <new_manual.formatter>` provides the necessary flexibility to construct the output. (:ref:`suffix() <decorators.suffix>` and :ref:`regex() <decorators.regex>` are not supported.)
-    * See :ref:`Summary <decorators.combinatorics>` / :ref:`Manual <new_manual.combinatorics>`
-
-
-
-============================================================================================================================================================
-8) drmaa support and multithreading:
-============================================================================================================================================================
-
-    * :ref:`ruffus.drmaa_wrapper.run_job() <new_manual.ruffus.drmaa_wrapper.run_job>` (:ref:`syntax <drmaa_wrapper.run_job>`)
-    * Optional helper module allows jobs to dispatch work to a computational cluster and wait until it completes.
-    * Requires ``multithread`` rather than ``multiprocess``
-
-============================================================================================================================================================
-9) ``pipeline_run(...)`` and exceptions
-============================================================================================================================================================
-    See :ref:`Manual <new_manual.exceptions>`
-
-    * Optionally terminate pipeline after first exception
-    * Display exceptions without delay
-
-
-============================================================================================================================================================
-10) Miscellaneous
-============================================================================================================================================================
-
-    Better error messages for ``formatter()``, ``suffix()`` and ``regex()`` for ``pipeline_printout(..., verbose >= 3, ...)``
-        * Error messages for showing mismatching regular expression and offending file name
-        * Wrong capture group names or out of range indices will raise informative Exception
-
-********************************************************************
-version 2.3
-********************************************************************
-    1st September, 2013
-
-    * ``@active_if`` turns off tasks at runtime
-        The Design and initial implementation were contributed by Jacob Biesinger
-
-        Takes one or more parameters which can be either booleans or functions or callable objects which return True / False::
-
-                run_if_true_1 = True
-                run_if_true_2 = False
-
-                @active_if(run_if_true, lambda: run_if_true_2)
-                def this_task_might_be_inactive():
-                    pass
-
-        The expressions inside @active_if are evaluated each time
-        ``pipeline_run``, ``pipeline_printout`` or ``pipeline_printout_graph`` is called.
-
-        Dormant tasks behave as if they are up to date and have no output.
-
-    * Command line parsing
-        * Supports both argparse (python 2.7) and optparse (python 2.6):
-        * ``Ruffus.cmdline`` module is optional.
-        * See :ref:`manual <new_manual.cmdline>`
-    * Optionally terminate pipeline after first exception
-        To have all exceptions interrupt immediately::
-
-                pipeline_run(..., exceptions_terminate_immediately = True)
-
-        By default ruffus accumulates ``NN`` errors before interrupting the pipeline prematurely. ``NN`` is the specified parallelism for ``pipeline_run(..., multiprocess = NN)``.
-
-        Otherwise, a pipeline will only be interrupted immediately if exceptions of type ``ruffus.JobSignalledBreak`` are thrown.
-
-    * Display exceptions without delay
-
-        By default, Ruffus re-throws exceptions in ensemble after pipeline termination.
-
-        To see exceptions as they occur::
-
-                pipeline_run(..., log_exceptions = True)
-
-        ``logger.error(...)`` will be invoked with the string representation of the each exception, and associated stack trace.
-
-        The default logger prints to sys.stderr, but this can be changed to any class from the logging module or compatible object via ``pipeline_run(..., logger = ???)``
-
-    * Improved ``pipeline_printout()``
-
-            * `@split` operations now show the 1->many output in pipeline_printout
-
-                This make it clearer that ``@split`` is creating multiple output parameters (rather than a single output parameter consisting of a list)::
-
-                        Task = split_animals
-                             Job = [None
-                                   -> cows
-                                   -> horses
-                                   -> pigs
-                                    , any_extra_parameters]
-            * File date and time are displayed in human readable form and out of date files are flagged with asterisks.
-
-
-
-********************************************************************
-version 2.2
-********************************************************************
-    22nd July, 2010
-
-    * Simplifying **@transform** syntax with **suffix(...)**
-
-        Regular expressions within ruffus are very powerful, and can allow files to be moved
-        from one directory to another and renamed at will.
-
-        However, using consistent file extensions and
-        ``@transform(..., suffix(...))`` makes the code much simpler and easier to read.
-
-        Previously, ``suffix(...)`` did not cooperate well with ``inputs(...)``.
-        For example, finding the corresponding header file (".h") for the matching input
-        required a complicated ``regex(...)`` regular expression and ``input(...)``. This simple case,
-        e.g. matching "something.c" with "something.h", is now much easier in Ruffus.
-
-
-        For example:
-          ::
-
-            source_files = ["something.c", "more_code.c"]
-            @transform(source_files, suffix(".c"), add_inputs(r"\1.h", "common.h"), ".o")
-            def compile(input_files, output_file):
-                ( source_file,
-                  header_file,
-                  common_header) = input_files
-                # call compiler to make object file
-
-          This is equivalent to calling:
-
-            ::
-
-              compile(["something.c", "something.h", "common.h"], "something.o")
-              compile(["more_code.c", "more_code.h", "common.h"], "more_code.o")
-
-        The ``\1`` matches everything *but* the suffix and will be applied to both ``glob``\ s and file names.
-
-    For simplicity and compatibility with previous versions, there is always an implied r"\1" before
-    the output parameters. I.e. output parameters strings are *always* substituted.
-
-
-    * Tasks and glob in **inputs(...)** and **add_inputs(...)**
-
-        ``glob``\ s and tasks can be added as the prerequisites / input files using
-        ``inputs(...)`` and ``add_inputs(...)``. ``glob`` expansions will take place when the task
-        is run.
-
-    * Advanced form of **@split** with **regex**:
-
-        The standard ``@split`` divided one set of inputs into multiple outputs (the number of which
-        can be determined at runtime).
-
-        This is a ``one->many`` operation.
-
-
-        An advanced form of ``@split`` has been added which can split each of several files further.
-
-        In other words, this is a ``many->"many more"`` operation.
-
-        For example, given three starting files:
-            ::
-
-                original_files = ["original_0.file",
-                                  "original_1.file",
-                                  "original_2.file"]
-        We can split each into its own set of sub-sections:
-            ::
-
-                @split(original_files,
-                   regex(r"starting_(\d+).fa"),                         # match starting files
-                         r"files.split.\1.*.fa"                         # glob pattern
-                         r"\1")                                         # index of original file
-                def split_files(input_file, output_files, original_index):
-                    """
-                        Code to split each input_file
-                            "original_0.file" -> "files.split.0.*.fa"
-                            "original_1.file" -> "files.split.1.*.fa"
-                            "original_2.file" -> "files.split.2.*.fa"
-                    """
-
-
-        This is, conceptually, the reverse of the @collate(...) decorator
-
-    * Ruffus will complain about unescaped regular expression special characters:
-
-        Ruffus uses "\\1" and "\\2" in regular expression substitutions. Even seasoned python
-        users may not remember that these have to be 'escaped' in strings. The best option is
-        to use 'raw' python strings e.g.
-
-            ::
-
-                r"\1_substitutes\2correctly\3four\4times"
-
-        Ruffus will throw an exception if it sees an unescaped "\\1" or "\\2" in a file name,
-        which should catch most of these bugs.
-
-    * Prettier output from *pipeline_printout_graph*
-
-        Changed to nicer colours, symbols etc. for a more professional look.
-        @split and @merge tasks now look different from @transform.
-        Colours, size and resolution are now fully customisable::
-
-            pipeline_printout_graph( #...
-                                     user_colour_scheme = {
-                                                            "colour_scheme_index":1,
-                                                            "Task to run"  : {"fillcolor":"blue"},
-                                                             pipeline_name : "My flowchart",
-                                                             size          : (11,8),
-                                                             dpi           : 120)})
-
-        An SVG bug in firefox has been worked around so that font size are displayed correctly.
-
-
-
-
-********************************************************************
-version 2.1.1
-********************************************************************
-    * **@transform(.., add_inputs(...))**
-        ``add_inputs(...)`` allows the addition of extra input dependencies / parameters for each job.
-
-        Unlike ``inputs(...)``, the original input parameter is retained:
-            ::
-
-                from ruffus import *
-                @transform(["a.input", "b.input"], suffix(".input"), add_inputs("just.1.more","just.2.more"), ".output")
-                def task(i, o):
-                ""
-
-        Produces:
-            ::
-
-                Job = [[a.input, just.1.more, just.2.more] ->a.output]
-                Job = [[b.input, just.1.more, just.2.more] ->b.output]
-
-
-        Like ``inputs``, ``add_inputs`` accepts strings, tasks and ``glob`` s
-        This minor syntactic change promises add much clarity to Ruffus code.
-        ``add_inputs()`` is available for ``@transform``, ``@collate`` and ``@split``
-
-
-********************************************************************
-version 2.1.0
-********************************************************************
-    * **@jobs_limit**
-      Some tasks are resource intensive and too many jobs should not be run at the
-      same time. Examples include disk intensive operations such as unzipping, or
-      downloading from FTP sites.
-
-      Adding::
-
-          @jobs_limit(4)
-          @transform(new_data_list, suffix(".big_data.gz"), ".big_data")
-          def unzip(i, o):
-            "unzip code goes here"
-
-      would limit the unzip operation to 4 jobs at a time, even if the rest of the
-      pipeline runs highly in parallel.
-
-      (Thanks to Rob Young for suggesting this.)
-
-********************************************************************
-version 2.0.10
-********************************************************************
-    * **touch_files_only** option for **pipeline_run**
-
-      When the pipeline runs, task functions will not be run. Instead, the output files for
-      each job (in each task) will be ``touch``\ -ed if necessary.
-      This can be useful for simulating a pipeline run so that all files look as
-      if they are up-to-date.
-
-      Caveats:
-
-        * This may not work correctly where output files are only determined at runtime, e.g. with **@split**
-        * Only the output from pipelined jobs which are currently out-of-date will be ``touch``\ -ed.
-          In other words, the pipeline runs *as normal*, the only difference is that the
-          output files are ``touch``\ -ed instead of being created by the python task functions
-          which would otherwise have been called.
-
-    * Parameter substitution for **inputs(...)**
-
-      The **inputs(...)** parameter in **@transform**, **@collate** can now take tasks and ``glob`` s,
-      and these will be expanded appropriately (after regular expression replacement).
-
-      For example::
-
-          @transform("dir/a.input", regex(r"(.*)\/(.+).input"),
-                        inputs((r"\1/\2.other", r"\1/*.more")), r"elsewhere/\2.output")
-          def task1(i, o):
-            """
-            Some pipeline task
-            """
-
-      Is equivalent to calling::
-
-            task1(("dir/a.other", "dir/1.more", "dir/2.more"), "elsewhere/a.output")
-
-      \
-
-          Here::
-
-                r"\1/*.more"
-
-          is first converted to::
-
-                r"dir/*.more"
-
-          which matches::
-
-                "dir/1.more"
-                "dir/2.more"
-
-
-********************************************************************
-version 2.0.9
-********************************************************************
-
-    * Better display of logging output
-    * Advanced form of **@split**
-      This is an experimental feature.
-
-      Hitherto, **@split** only takes 1 set of input (tasks/files/``glob`` s) and split these
-      into an indeterminate number of output.
-
-          This is a one->many operation.
-
-      Sometimes it is desirable to take multiple input files, and split each of them further.
-
-          This is a many->many (more) operation.
-
-      It is possible to hack something together using **@transform** but downstream tasks would not
-      aware that each job in **@transform** produces multiple outputs (rather than one input,
-      one output per job).
-
-      The syntax looks like::
-
-           @split(get_files, regex(r"(.+).original"), r"\1.*.split")
-           def split_files(i, o):
-                pass
-
-      If ``get_files()`` returned ``A.original``, ``B.original`` and ``C.original``,
-      ``split_files()`` might lead to the following operations::
-
-            A.original
-                    -> A.1.original
-                    -> A.2.original
-                    -> A.3.original
-            B.original
-                    -> B.1.original
-                    -> B.2.original
-            C.original
-                    -> C.1.original
-                    -> C.2.original
-                    -> C.3.original
-                    -> C.4.original
-                    -> C.5.original
-
-      Note that each input (``A/B/C.original``) can produce a number of output, the exact
-      number of which does not have to be pre-determined.
-      This is similar to **@split**
-
-      Tasks following ``split_files`` will have ten inputs corresponding to each of the
-      output from ``split_files``.
-
-      If **@transform** was used instead of **@split**, then tasks following ``split_files``
-      would only have 3 inputs.
-
-********************************************************************
-version 2.0.8
-********************************************************************
-
-    * File names can be in unicode
-    * File systems with 1 second timestamp granularity no longer cause problems.
-
-********************************************************************
-version 2.0.2
-********************************************************************
-
-    * Much prettier /useful output from :ref:`pipeline_printout <pipeline_functions.pipeline_printout>`
-    * New tutorial / manual
-
-
-
-********************************************************************
-version 2.0
-********************************************************************
-    * Revamped documentation:
-
-        * Rewritten tutorial
-        * Comprehensive manual
-        * New syntax help
-
-    * Major redesign. New decorators include
-
-        * :ref:`@split <new_manual.split>`
-        * :ref:`@transform <new_manual.transform>`
-        * :ref:`@merge <new_manual.merge>`
-        * :ref:`@collate <new_manual.collate>`
-
-    * Major redesign. Decorator *inputs* can mix
-
-        * Output from previous tasks
-        * |glob|_ patterns e.g. ``*.txt``
-        * Files names
-        * Any other data type
-
-********************************************************************
-version 1.1.4
-********************************************************************
-    Tasks can get their input by automatically chaining to the output from one or more parent tasks using :ref:`@files_re <decorators.files_re>`
-
-********************************************************************
-version 1.0.7
-********************************************************************
-    Added `proxy_logger` module for accessing a shared log across multiple jobs in different processes.
-
-********************************************************************
-version 1.0
-********************************************************************
-
-    Initial Release in Oxford
-
-########################################
-Fixed Bugs
-########################################
-
-    Full list at `"Latest Changes wiki entry" <http://code.google.com/p/ruffus/wiki/LatestChanges>`_
diff --git a/doc/_build/html/_sources/implementation_notes.txt b/doc/_build/html/_sources/implementation_notes.txt
deleted file mode 100644
index bba4374..0000000
--- a/doc/_build/html/_sources/implementation_notes.txt
+++ /dev/null
@@ -1,437 +0,0 @@
-##########################################
-Implementation Tips
-##########################################
-
-******************************************************************************
-Release
-******************************************************************************
-
-    * Change ``ruffus_version.py``
-
-    * Rebuild pdf and copy it to ``doc/static_data``
-
-        cd doc
-        make latexpdf
-        cp _build/latex/ruffus.pdf static_data
-
-    * Rebuild documentation::
-
-        make htmlsync
-
-    * tag git with, for example::
-
-        git tag -a v2.5RC -m "Version 2.5 Release Candidate"
-
-
-    * Upload to pypi::
-
-        python setup.py sdist --format=gztar upload
-
-******************************************************************************
-dbdict.py
-******************************************************************************
-
-    This is an sqlite backed dictionary originally written by Jacob Sondergaard and
-    contributed by Jake Biesinger who added automatic pickling of python objects.
-
-    The pickling code was refactored out by Leo Goodstadt into separate functions as
-    part of the preparation to make Ruffus python3 ready.
-
-    Python original saved (pickled) objects as 7 bit ASCII strings. Later formats
-    (protocol = -1 is the latest format) uses 8 bit strings and are rather more efficient.
-
-    These then need to be saved as BLOBs to sqlite3 rather than normal strings. We
-    can signal this by wrapping the pickled string in a object providing a "buffer interface".
-    This is ``buffer`` in python2.6/2.7 and ``memoryview`` in python3.
-
-    http://bugs.python.org/issue7723 suggests there is no portable python2/3 way to write
-    blobs to Sqlite without these two incompatible wrappers.
-    This would require conditional compilation:
-
-    .. code-block:: python
-
-        if sys.hexversion >= 0x03000000:
-            value = memoryview(pickle.dumps(value, protocol = -1))
-        else:
-            value = buffer(pickle.dumps(value, protocol = -1))
-
-
-    Despite the discussion on the bug report, sqlite3.Binary seems to work.
-    We shall see if this is portable to python3.
-
-******************************************************************************
-how to write new decorators
-******************************************************************************
-
-
-    New placeholder class. E.g. for ``@new_deco``
-
-    .. code-block:: python
-
-        class new_deco(task_decorator):
-            pass
-
-    Add to list of action names and ids:
-
-    .. code-block:: python
-
-        action_names = ["unspecified",
-                        ...
-                        "task_new_deco",
-
-        action_task_new_deco     =  15
-
-    Add function:
-
-    .. code-block:: python
-
-        def task_transform (self, orig_args):
-
-
-    Add documentation to:
-
-        * decorators/NEW_DECORATOR.rst
-        * decorators/decorators.rst
-        * _templates/layout.html
-        * manual
-
-
-
-
-##########################################
-Implementation notes
-##########################################
-
-N.B. Remember to cite Jake Biesinger and see if he is interested to be a co-author if we ever resubmit the drastically changed version...
-He contributed checkpointing, travis and tox etc.
-
-.. _todo.misfeatures:
-
-********************************************************************************************************
-``Ctrl-C`` handling
-********************************************************************************************************
-
-    Pressing ``Ctrl-C`` left dangling process in Ruffus 2.4 because ``KeyboardInterrupt`` does not play nice with python ``multiprocessing.Pool``
-    See http://stackoverflow.com/questions/1408356/keyboard-interrupts-with-pythons-multiprocessing-pool/1408476#1408476
-
-    http://bryceboe.com/2012/02/14/python-multiprocessing-pool-and-keyboardinterrupt-revisited/ provides a reimplementation of Pool which
-    however only works when you have a fixed number of jobs which should then run in parallel to completion. Ruffus is considerably more
-    complicated because we have a variable number of jobs completing and being submitted into the job queue at any one time. Think
-    of tasks stalling waiting for the dependent tasks to complete and then all the jobs of the task being released onto the queue
-
-    The solution is
-
-        #. Use a ``timeout`` parameter when using ``IMapIterator.next(timeout=None)`` to iterate through ``pool.imap_unordered`` because only timed ``condition`` s can be interruptible by signals...!!
-        #. This involves rewriting the ``for`` loop manually as a ``while`` loop
-        #. We use a timeout of ``99999999``, i.e. 3 years, which should be enough for any job to complete...
-        #. Googling after the fact, it looks like the galaxy guys (cool dudes or what) have written similar `code  <https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/objectstore/s3_multipart_upload.html>`__
-        #. ``next()`` for normal iterators do not take ``timeout`` as an extra parameter so we have to wrap next in a conditional :-(. The galaxy guys do a `shim  <http://en.wikipedia.org/wiki/Shim_(computing)>`__ around ``next()`` but that is as much obsfucation as a simple if...
-        #. After jobs are interrupted by a signal, we rethrow with our own exception because we want something that inherits from ``Exception`` unlike ``KeyboardInterrupt``
-        #. When a signal happens, we need to immediately stop ``feed_job_params_to_process_pool()`` from sending more parameters into the job queue (``parameter_q``)
-           We use a proxy to a ``multiprocessing.Event`` (via ``syncmanager.Event()``). When ``death_event`` is set, all further processing stops...
-        #. We also signal that all jobs should finish by putting ``all_tasks_complete()`` into ``parameter_q`` but only ``death_event`` prevents jobs already in the queue from going through
-        #. Ater signalling, some of the child processes appear to be dead by the time we start cleaning up. ``pool.terminate()`` sometimes tries and fails to
-           re-connect to the the ``death_event`` proxy via sockets and throws an exception. We should really figure out a better solution but in the meantime
-           wrapping it in a ``try / except`` allows a clean exit.
-        #. If a vanilla exception is raised without multiprocessing running, we still need to first save the exception in ``job_errors`` (even if it is just one) before
-           cleaning up, because the cleaning up process may lead to further (ignored) exceptions which would overwrite the current exception when we need to rethrow it
-
-
-    Exceptions thrown in the middle of a multiprocessing / multithreading job appear to be handled gracefully.
-
-    For drmaa jobs, ``qdel`` may still be necessary.
-
-
-******************************************************************************
-Python3 compatability
-******************************************************************************
-
-    Required extensive changes especially in unit test code.
-
-    Changes:
-
-    1. ``sort`` in python3 does not order mixed types, i.e. ``int()``, ``list()`` and ``str()`` are incommensurate
-
-       * In ``task.get_output_files (...)``, sort after conversion to string
-
-         .. code-block:: python
-
-           sorted(self.output_filenames, key = lambda x: str(x))
-
-       * In ``file_name_parameters.py``: ``collate_param_factory (...)``, ``sort`` after conversion to string, then ``groupby`` without string conversion. This is
-         because we can't guarantee that two different objects do not have the same string representation. But ``groupby`` requires that similar things are adjacent...
-
-         In other words, ``groupby`` is a refinement of ``sorted``
-
-         .. code-block:: python
-
-           for output_extra_params, grouped_params in groupby(sorted(io_params_iter, key = get_output_extras_str), key = get_output_extras):
-               pass
-
-    2. ``print()`` is a function
-
-       .. code-block:: python
-
-            from __future__ import print_function
-
-    3. ``items()`` only returns a list in python2. Rewrite ``dict.iteritems()`` whenever this might cause a performance bottleneck
-    4. ``zip`` and ``map`` return iterators. Conditionally import in python2
-
-       .. code-block:: python
-
-            import sys
-            if sys.hexversion < 0x03000000:
-                from future_builtins import zip, map
-
-    5. ``cPickle->pickle`` ``CStringIO->io`` need to be conditionally imported
-
-       .. code-block:: python
-
-            try:
-                import StringIO as io
-            except:
-                import io as io
-
-
-    6. ``map`` code can be changed to list comprehensions. Use ``2to3`` to do heavy lifting
-
-    7. All normal strings are unicode in python3. Have to use ``bytes`` to support 8-bit char arrays.
-       Normally, this means that ``str`` "just works". However, to provide special handling of
-       both 8-bit and unicode strings in python2, we often need to check for ``isinstance(xxx, basestring)``.
-
-       We need to conditionally define:
-
-       .. code-block:: python
-
-            if sys.hexversion >= 0x03000000:
-                # everything is unicode in python3
-                path_str_type = str
-            else:
-                path_str_type = basestring
-
-            # further down...
-            if isinstance(compiled_regex, path_str_type):
-                pass
-
-
-
-******************************************************************************
-Refactoring: parameter handling
-******************************************************************************
-
-    Though the code is still split in a not very sensible way between ``ruffus_utility.py``, ``file_name_parameters.py`` and ``task.py``,
-        some rationalisation has taken place, and comments added so further refactoring can be made more easily.
-
-    Common code for::
-
-        file_name_parameters.split_ex_param_factory()
-        file_name_parameters.transform_param_factory()
-        file_name_parameters.collate_param_factory()
-
-    has been moved to ``file_name_parameters.py.yield_io_params_per_job()``
-
-
-    unit tests added to ``test_file_name_parameters.py`` and ``test_ruffus_utility.py``
-
-
-
-
-******************************************************************************
-``formatter``
-******************************************************************************
-    ``get_all_paths_components(paths, regex_str)`` in ``ruffus_utility.py``
-
-    Input files names are first squished into a flat list of files.
-    ``get_all_paths_components()`` returns both the regular expression matches and the break down of the path.
-
-    In case of name clashes, the classes with higher priority override:
-
-        1) Captures by name
-        2) Captures by index
-        3) Path components:
-            'ext' = extension with dot
-            'basename' = file name without extension
-            'path' = path before basename, not ending with slash
-            'subdir' = list of directories starting with the most nested and ending with the root (if normalised)
-            'subpath' = list of 'path' with successive directories removed starting with the most nested and ending with the root (if normalised)
-
-        E.g.  ``name = '/a/b/c/sample1.bam'``, ``formatter=r"(.*)(?P<id>\d+)\.(.+)")`` returns:
-
-        .. code-block:: python
-
-                0:          '/a/b/c/sample1.bam',           // Entire match captured by index
-                1:          '/a/b/c/sample',                // captured by index
-                2:          'bam',                          // captured by index
-                'id':       '1'                             // captured by name
-                'ext':      '.bam',
-                'subdir':   ['c', 'b', 'a', '/'],
-                'subpath':  ['/a/b/c', '/a/b', '/a', '/'],
-                'path':     '/a/b/c',
-                'basename': 'sample1',
-
-
-    The code is in ``ruffus_utility.py``:
-
-    .. code-block:: python
-
-        results = get_all_paths_components(paths, regex_str)
-        string.format(results[2])
-
-
-    All the magic is hidden inside black boxes ``filename_transform`` classes:
-
-    .. code-block:: python
-
-
-        class t_suffix_filename_transform(t_filename_transform):
-        class t_regex_filename_transform(t_filename_transform):
-        class t_format_filename_transform(t_filename_transform):
-
-===================================================
-``formatter()``: ``regex()`` and ``suffix()``
-===================================================
-
-
-    The previous behaviour with regex() where mismatches fail even if no substitution is made is retained by the use of ``re.subn()``.
-    This is a corner case but I didn't want user code to break
-
-    .. code-block:: python
-
-        # filter on ".txt"
-        input_filenames = ["a.wrong", "b.txt"]
-        regex("(.txt)$")
-
-        # fails, no substitution possible
-        r"\1"
-
-        # fails anyway even through regular expression matches not referenced...
-        r"output.filename"
-
-
-************************************************************************************************************************************************************
- at product()
-************************************************************************************************************************************************************
-
-    * Use combinatoric generators from itertools and keep that naming scheme
-    * Put all new generators in an ``combinatorics`` submodule namespace to avoid breaking user code. (They can imported if necessary.)
-    * test code in test/test_combinatorics.py
-    * The ``itertools.product(repeat)`` parameter doesn't make sense for Ruffus and will not be used
-    * Flexible number of pairs of ``task`` / ``glob`` / file names + ``formatter()``
-    * Only ``formatter([OPTIONAl_REGEX])`` provides the necessary flexibility to construct the output so we won't bother with suffix and regex
-
-    * Similar to ``@transform`` but with extra level of nested-ness
-
-    Retain same code for ``@product`` and ``@transform`` by adding an additional level of indirection:
-        * generator wrap around ``get_strings_in_nested_sequence`` to convert nested input parameters either to a single flat list of file names or to nested lists of file names
-
-          .. code-block:: python
-
-              file_name_parameters.input_param_to_file_name_list (input_params)
-              file_name_parameters.list_input_param_to_file_name_list (input_params)
-
-        * ``t_file_names_transform`` class which stores a list of regular expressions, one for each ``formatter()`` object corresponding to a single set of input parameters
-
-          .. code-block:: python
-
-            t_formatter_file_names_transform
-            t_nested_formatter_file_names_transform
-
-        * string substitution functions which will apply a list of ``formatter`` changes
-
-          .. code-block:: python
-
-                ruffus.utility.t_formatter_replace()
-                ruffus.utility.t_nested_formatter_replace()
-
-        * ``ruffus_uilility.swap_doubly_nested_order()`` makes the syntax / implementation very orthogonal
-
-************************************************************************************************************************************************************
-``@permutations(...),`` ``@combinations(...),`` ``@combinations_with_replacement(...)``
-************************************************************************************************************************************************************
-
-    Similar to ``@product`` extra level of nested-ness is self versus self
-
-    Retain same code for ``@product``
-        * forward to a sinble ``file_name_parameters.combinatorics_param_factory()``
-        * use ``combinatorics_type`` to dispatch to ``combinatorics.permutations``, ``combinatorics.combinations`` and ``combinatorics.combinations_with_replacement``
-        * use ``list_input_param_to_file_name_list`` from ``file_name_parameters.product_param_factory()``
-
-
-
-************************************************************************************************************************************************************
-drmaa alternatives
-************************************************************************************************************************************************************
-
-    Alternative, non-drmaa polling code at
-
-    https://github.com/bjpop/rubra/blob/master/rubra/cluster_job.py
-
-
-
-************************************************************************************************************************************************************
-Task completion monitoring
-************************************************************************************************************************************************************
-
-===================================================
- How easy is it to abstract out the database?
-===================================================
-
-    * The database is Jacob Sondergaard's ``dbdict`` which is a nosql / key-value store wrapper around sqlite
-        .. code-block:: python
-
-            job_history = dbdict.open(RUFFUS_HISTORY_FILE, picklevalues=True)
-
-    * The key is the output file name, so it is important not to confuse Ruffus by having different tasks generate the same output file!
-    * Is it possible to abstract this so that **jobs** get timestamped as well?
-    * If we should ever want to abstract out ``dbdict``, we need to have a similar key-value store class,
-      and make sure that a single instance of ``dbdict`` is used through ``pipeline_run`` which is passed up
-      and down the function call chain. ``dbdict`` would then be drop-in replaceable by our custom (e.g. flat-file-based) dbdict alternative.
-
-
-    To peek into the database:
-
-        .. code-block:: bash
-
-            $ sqlite3 .ruffus_history.sqlite
-            sqlite> .tables
-            data
-            sqlite> .schema data
-            CREATE TABLE data (key PRIMARY KEY,value);
-            sqlite> select key from data order by key;
-
-======================================================================================================
- Can we query the database, get Job history / stats?
-======================================================================================================
-
-        Yes, if we write a function to read and dump the entire database but this is only useful with timestamps and task names. See below
-
-======================================================================================================
-  What are the run time performance implications?
-======================================================================================================
-
-  Should be fast: a single db connection is created and used inside ``pipeline_run``,  ``pipeline_printout``,  ``pipeline_printout_graph``
-
-
-
-===================================================
-  Avoid pauses between tasks
-===================================================
-
-    Allows Ruffus to avoid adding an extra 1 second pause between tasks to guard against file systems with low timestamp granularity.
-
-        * If the local file time looks to be in sync with the underlying file system, saved system time is used instead of file timestamps
-
-
-
-
-******************************************************************************************
-``@mkdir(...),``
-******************************************************************************************
-
-    * ``mkdir`` continues to work seamlessly inside ``@follows``) but also as its own decorator ``@mkdir`` due to the original happy orthogonal design
-    * fixed bug in checking so that Ruffus does't blow up if non strings are in the output (number...)
-    * note: adding the decorator to a previously undecorated function might have unintended consequences. The undecorated function turns into a zombie.
-    * fixed ugly bug in ``pipeline_printout`` for printing single line output
-    * fixed description and printout indent
-
-
diff --git a/doc/_build/html/_sources/installation.txt b/doc/_build/html/_sources/installation.txt
deleted file mode 100644
index f3ca116..0000000
--- a/doc/_build/html/_sources/installation.txt
+++ /dev/null
@@ -1,79 +0,0 @@
-.. include:: global.inc
-.. _Installation:
-
-************************************
-Installation
-************************************
-
-:mod:`Ruffus` is a lightweight python module for building computational pipelines.
-
-
-The easy way
-============
-
-    *Ruffus* is available as an
-    `easy-install <http://peak.telecommunity.com/DevCenter/EasyInstall>`_ -able package
-    on the `Python Package Index <http://pypi.python.org/pypi/Sphinx>`_.
-
-    ::
-
-        sudo pip install ruffus --upgrade
-
-    This may also work for older installations
-
-    #) Install setuptools::
-
-        wget peak.telecommunity.com/dist/ez_setup.py
-        sudo python ez_setup.py
-
-    #) Install *Ruffus* automatically::
-
-        easy_install -U ruffus
-
-
-The most up-to-date code:
-==============================
-        * `Download the latest sources <https://pypi.python.org/pypi/ruffus>`_ or
-
-        * Check out the latest code from Google using git::
-
-            git clone https://bunbun68@code.google.com/p/ruffus/ .
-
-        * Bleeding edge Ruffus development takes place on github::
-
-            git clone git at github.com:bunbun/ruffus.git .
-
-
-        * To install after downloading, change to the , type::
-
-             python ./setup.py install
-
-
-======================
-Graphical flowcharts
-======================
-
-    **Ruffus** relies on the ``dot`` programme from `Graphviz <http://www.graphviz.org/>`_
-    ("Graph visualisation") to make pretty flowchart representations of your pipelines in multiple
-    graphical formats (e.g. ``png``, ``jpg``). The crossplatform Graphviz package can be
-    `downloaded here <http://www.graphviz.org/Download.php>`_ for Windows,
-    Linux, Macs and Solaris. Some Linux
-    distributions may include prebuilt packages.
-
-    For Fedora, try
-        ::
-
-            yum list 'graphviz*'
-
-    For ubuntu / Debian, try
-        ::
-
-            sudo apt-get install graphviz
-
-
-
-
-
-
-
-
diff --git a/doc/_build/html/_sources/pipeline_functions.txt b/doc/_build/html/_sources/pipeline_functions.txt
deleted file mode 100644
index fd267fb..0000000
--- a/doc/_build/html/_sources/pipeline_functions.txt
+++ /dev/null
@@ -1,689 +0,0 @@
-.. include:: global.inc
-.. _pipeline_functions:
-
-See :ref:`Decorators <decorators>` for more decorators
-
-.. |pipeline_run| replace:: `pipeline_run`
-.. _pipeline_run: `pipeline_functions.pipeline_run`_
-.. |pipeline_printout| replace:: `pipeline_printout`
-.. _pipeline_printout: `pipeline_functions.pipeline_printout`_
-.. |pipeline_printout_graph| replace:: `pipeline_printout_graph`
-.. _pipeline_printout_graph: `pipeline_functions.pipeline_printout_graph`_
-.. |pipeline_get_task_names| replace:: `pipeline_get_task_names`
-.. _pipeline_get_task_names: `pipeline_functions.pipeline_get_task_names`_
-
-
-.. |pr_target_tasks| replace:: `target_tasks`
-.. _pr_target_tasks: `pipeline_functions.pipeline_run.target_tasks`_
-.. |pr_forcedtorun_tasks| replace:: `forcedtorun_tasks`
-.. _pr_forcedtorun_tasks: `pipeline_functions.pipeline_run.forcedtorun_tasks`_
-.. |pr_multiprocess| replace:: `multiprocess`
-.. _pr_multiprocess: `pipeline_functions.pipeline_run.multiprocess`_
-.. |pr_logger| replace:: `logger`
-.. _pr_logger: `pipeline_functions.pipeline_run.logger`_
-.. |pr_gnu_make| replace:: `gnu_make_maximal_rebuild_mode`
-.. _pr_gnu_make: `pipeline_functions.pipeline_run.gnu_make`_
-.. |pr_verbose| replace:: `verbose`
-.. _pr_verbose: `pipeline_functions.pipeline_run.verbose`_
-.. |pr_runtime_data| replace:: `runtime_data`
-.. _pr_runtime_data: `pipeline_functions.pipeline_run.runtime_data`_
-.. |pr_one_second_per_job| replace:: `one_second_per_job`
-.. _pr_one_second_per_job: `pipeline_functions.pipeline_run.one_second_per_job`_
-.. |pr_touch_files_only| replace:: `touch_files_only`
-.. _pr_touch_files_only: `pipeline_functions.pipeline_run.touch_files_only`_
-
-.. |pr_exceptions_terminate_immediately| replace:: `exceptions_terminate_immediately`
-.. _pr_exceptions_terminate_immediately: `pipeline_functions.pipeline_run.exceptions_terminate_immediately`_
-.. |pr_log_exceptions| replace:: `log_exceptions`
-.. _pr_log_exceptions: `pipeline_functions.pipeline_run.log_exceptions`_
-.. |pr_multithread| replace:: `multithread`
-.. _pr_multithread: `pipeline_functions.pipeline_run.multithread`_
-.. |pr_checksum_level| replace:: `checksum_level`
-.. _pr_checksum_level: `pipeline_functions.pipeline_run.checksum_level`_
-.. |pr_history_file| replace:: `history_file`
-.. _pr_history_file: `pipeline_functions.pipeline_run.history_file`_
-.. |pr_verbose_abbreviated_path| replace:: `verbose_abbreviated_path`
-.. _pr_verbose_abbreviated_path: `pipeline_functions.pipeline_run.verbose_abbreviated_path`_
-
-
-.. |pp_output_stream| replace:: `output_stream`
-.. _pp_output_stream: `pipeline_functions.pipeline_printout.output_stream`_
-.. |pp_target_tasks| replace:: `target_tasks`
-.. _pp_target_tasks: `pipeline_functions.pipeline_printout.target_tasks`_
-.. |pp_forcedtorun_tasks| replace:: `forcedtorun_tasks`
-.. _pp_forcedtorun_tasks: `pipeline_functions.pipeline_printout.forcedtorun_tasks`_
-.. |pp_verbose| replace:: `verbose`
-.. _pp_verbose: `pipeline_functions.pipeline_printout.verbose`_
-.. |pp_indent| replace:: `indent`
-.. _pp_indent: `pipeline_functions.pipeline_printout.indent`_
-.. |pp_wrap_width| replace:: `wrap_width`
-.. _pp_wrap_width: `pipeline_functions.pipeline_printout.wrap_width`_
-.. |pp_gnu_make| replace:: `gnu_make_maximal_rebuild_mode`
-.. _pp_gnu_make: `pipeline_functions.pipeline_printout.gnu_make`_
-.. |pp_runtime_data| replace:: `runtime_data`
-.. _pp_runtime_data: `pipeline_functions.pipeline_printout.runtime_data`_
-.. |pp_checksum_level| replace:: `checksum_level`
-.. _pp_checksum_level: `pipeline_functions.pipeline_printout.checksum_level`_
-.. |pp_history_file| replace:: `history_file`
-.. _pp_history_file: `pipeline_functions.pipeline_printout.history_file`_
-.. |pp_verbose_abbreviated_path| replace:: `verbose_abbreviated_path`
-.. _pp_verbose_abbreviated_path: `pipeline_functions.pipeline_printout.verbose_abbreviated_path`_
-
-
-
-.. |ppg_stream| replace:: `stream`
-.. _ppg_stream: `pipeline_functions.pipeline_printout_graph.stream`_
-.. |ppg_output_format| replace:: `output_format`
-.. _ppg_output_format: `pipeline_functions.pipeline_printout_graph.output_format`_
-.. |ppg_target_tasks| replace:: `target_tasks`
-.. _ppg_target_tasks: `pipeline_functions.pipeline_printout_graph.target_tasks`_
-.. |ppg_forcedtorun_tasks| replace:: `forcedtorun_tasks`
-.. _ppg_forcedtorun_tasks: `pipeline_functions.pipeline_printout_graph.forcedtorun_tasks`_
-.. |ppg_draw_vertically| replace:: `draw_vertically`
-.. _ppg_draw_vertically: `pipeline_functions.pipeline_printout_graph.draw_vertically`_
-.. |ppg_ignore_upstream_of_target| replace:: `ignore_upstream_of_target`
-.. _ppg_ignore_upstream_of_target: `pipeline_functions.pipeline_printout_graph.ignore_upstream_of_target`_
-.. |ppg_skip_uptodate_tasks| replace:: `skip_uptodate_tasks`
-.. _ppg_skip_uptodate_tasks: `pipeline_functions.pipeline_printout_graph.skip_uptodate_tasks`_
-.. |ppg_gnu_make| replace:: `gnu_make_maximal_rebuild_mode`
-.. _ppg_gnu_make: `pipeline_functions.pipeline_printout_graph.gnu_make`_
-.. |ppg_test_all_task_for_update| replace:: `test_all_task_for_update`
-.. _ppg_test_all_task_for_update: `pipeline_functions.pipeline_printout_graph.test_all_task_for_update`_
-.. |ppg_no_key_legend| replace:: `no_key_legend`
-.. _ppg_no_key_legend: `pipeline_functions.pipeline_printout_graph.no_key_legend`_
-.. |ppg_minimal_key_legend| replace:: `minimal_key_legend`
-.. _ppg_minimal_key_legend: `pipeline_functions.pipeline_printout_graph.minimal_key_legend`_
-.. |ppg_pipeline_name| replace:: `pipeline_name`
-.. _ppg_pipeline_name: `pipeline_functions.pipeline_printout_graph.pipeline_name`_
-.. |ppg_user_colour_scheme| replace:: `user_colour_scheme`
-.. _ppg_user_colour_scheme: `pipeline_functions.pipeline_printout_graph.user_colour_scheme`_
-.. |ppg_size| replace:: `size`
-.. _ppg_size: `pipeline_functions.pipeline_printout_graph.size`_
-.. |ppg_dpi| replace:: `dpi`
-.. _ppg_dpi: `pipeline_functions.pipeline_printout_graph.dpi`_
-.. |ppg_runtime_data| replace:: `runtime_data`
-.. _ppg_runtime_data: `pipeline_functions.pipeline_printout_graph.runtime_data`_
-.. |ppg_checksum_level| replace:: `checksum_level`
-.. _ppg_checksum_level: `pipeline_functions.pipeline_printout_graph.checksum_level`_
-.. |ppg_history_file| replace:: `history_file`
-.. _ppg_history_file: `pipeline_functions.pipeline_printout_graph.history_file`_
-
-
-
-
-
-
-
-
-
-
-################################################
-Pipeline functions
-################################################
-
-    There are only four functions for **Ruffus** pipelines:
-
-        * |pipeline_run|_ executes a pipeline
-        * |pipeline_printout|_ prints a list of tasks and jobs which will be run in a pipeline
-        * |pipeline_printout_graph|_ prints a schematic flowchart of pipeline tasks in various graphical formats
-        * |pipeline_get_task_names|_ returns a list of all task names in the pipeline
-
-.. _pipeline_functions.pipeline_run:
-
-.. index::
-    single: pipeline functions; pipeline_run
-    pair: pipeline_run; Run pipeline
-
-**************************************************************************************************************************************************************************************
-*pipeline_run*
-**************************************************************************************************************************************************************************************
-**pipeline_run** ( |pr_target_tasks|_ = [],  |pr_forcedtorun_tasks|_ = [], |pr_multiprocess|_ = 1, |pr_logger|_ = stderr_logger, |pr_gnu_make|_ = True, |pr_verbose|_ =1, |pr_runtime_data|_ = None, |pr_one_second_per_job|_ = True, |pr_touch_files_only|_ = False, |pr_exceptions_terminate_immediately|_ = None, |pr_log_exceptions|_ = None, |pr_history_file|_ = None, |pr_checksum_level|_ = None, |pr_multithread|_ = 0, |pr_verbose_abbreviated_path|_ = None)
-
-    **Purpose:**
-
-        Runs all specified pipelined functions if they or any antecedent tasks are
-        incomplete or out-of-date.
-
-    **Example**:
-
-        .. code-block:: python
-
-            #
-            #   Run task2 whatever its state, and also task1 and antecedents if they are incomplete
-            #   Do not log pipeline progress messages to stderr
-            #
-            pipeline_run([task1, task2], forcedtorun_tasks = [task2], logger = blackhole_logger)
-
-    **Parameters:**
-
-
-
-.. _pipeline_functions.pipeline_run.target_tasks:
-
-    * *target_tasks*
-        Pipeline functions and any necessary antecedents (specified implicitly or with :ref:`@follows <decorators.follows>`)
-        which should be invoked with the appropriate parameters if they are incomplete or out-of-date.
-
-.. _pipeline_functions.pipeline_run.forcedtorun_tasks:
-
-    * *forcedtorun_tasks*
-        Optional. These pipeline functions will be invoked regardless of their state.
-        Any antecedents tasks will also be executed if they are out-of-date or incomplete.
-
-.. _pipeline_functions.pipeline_run.multiprocess:
-
-    * *multiprocess*
-        Optional. The number of processes which should be dedicated to running in parallel independent
-        tasks and jobs within each task. If ``multiprocess`` is set to 1, the pipeline will
-        execute in the main process.
-
-.. _pipeline_functions.pipeline_run.multithread:
-
-    * *multithread*
-        Optional. The number of threads which should be dedicated to running in parallel independent
-        tasks and jobs within each task. Should be used only with drmaa. Otherwise the CPython `global interpreter lock (GIL) <https://wiki.python.org/moin/GlobalInterpreterLock>`__
-        will slow down your pipeline
-
-.. _pipeline_functions.pipeline_run.logger:
-
-    * *logger*
-        For logging messages indicating the progress of the pipeline in terms of tasks and jobs.
-        Defaults to outputting to sys.stderr.
-        Setting ``logger=blackhole_logger`` will prevent any logging output.
-
-.. _pipeline_functions.pipeline_run.gnu_make:
-
-    * *gnu_make_maximal_rebuild_mode*
-        .. warning ::
-            This is a dangerous option. Use rarely and with caution
-
-        Optional parameter governing how **Ruffus** determines which part of the pipeline is
-        out of date and needs to be re-run. If set to ``False``, **ruffus** will work back
-        from the ``target_tasks`` and only execute the pipeline after the first up-to-date
-        tasks that it encounters. For example, if there are four tasks:
-
-            ::
-
-                #
-                #   task1 -> task2 -> task3 -> task4 -> task5
-                #
-                target_tasks = [task5]
-
-        If ``task3()`` is up-to-date, then only ``task4()`` and ``task5()`` will be run.
-        This will be the case even if ``task2()`` and ``task1()`` are incomplete.
-
-        This allows you to remove all intermediate results produced by ``task1 -> task3``.
-
-
-
-.. _pipeline_functions.pipeline_run.verbose:
-
-    * *verbose*
-        Optional parameter indicating the verbosity of the messages sent to ``logger``:
-        (Defaults to level 1 if unspecified)
-
-        * level **0** : *nothing*
-        * level **1** : *Out-of-date Task names*
-        * level **2** : *All Tasks (including any task function docstrings)*
-        * level **3** : *Out-of-date Jobs in Out-of-date Tasks, no explanation*
-        * level **4** : *Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings*
-        * level **5** : *All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)*
-        * level **6** : *All jobs in All Tasks whether out of date or not*
-        * level **10**: *logs messages useful only for debugging ruffus pipeline code*
-
-
-        ``verbose >= 10`` are intended for debugging **Ruffus** by the developers and the details
-        are liable to change from release to release
-
-.. _pipeline_functions.pipeline_run.runtime_data:
-
-    * *runtime_data*
-        Experimental feature for passing data to tasks at run time
-
-.. _pipeline_functions.pipeline_run.one_second_per_job:
-
-    * *one_second_per_job*
-        To work around poor file timepstamp resolution for some file systems.
-        Defaults to True if checksum_level is 0 forcing Tasks to take a minimum of 1 second to complete.
-        If your file system has coarse grained time stamps, you can turn on this delay
-        by setting *one_second_per_job* to ``True``
-
-.. _pipeline_functions.pipeline_run.touch_files_only:
-
-    * *touch_files_only*
-        Create or update output files only to simulate the running of the pipeline.
-        Does not invoke real task functions to run jobs. This is most useful to force a
-        pipeline to acknowledge that a particular part is now up-to-date.
-
-        This will not work properly if the identities of some files are not known before hand,
-        and depend on run time. In other words, not recommended if ``@split`` or custom parameter generators are being used.
-
-
-
-.. _pipeline_functions.pipeline_run.exceptions_terminate_immediately:
-
-    * *exceptions_terminate_immediately*
-        Exceptions cause immediate termination of the pipeline.
-
-
-.. _pipeline_functions.pipeline_run.log_exceptions:
-
-    * *log_exceptions*
-        Print exceptions to the logger as soon as they occur.
-
-
-.. _pipeline_functions.pipeline_run.history_file:
-
-    * *history_file*
-        The database file which stores checksums and file timestamps for input/output files.
-        Defaults to ``.ruffus_history.sqlite`` if unspecified
-
-.. _pipeline_functions.pipeline_run.checksum_level:
-
-    * *checksum_level*
-        Several options for checking up-to-dateness are available: Default is level 1.
-
-           * level 0 : Use only file timestamps
-           * level 1 : above, plus timestamp of successful job completion
-           * level 2 : above, plus a checksum of the pipeline function body
-           * level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-.. _pipeline_functions.pipeline_run.verbose_abbreviated_path:
-
-    * *verbose_abbreviated_path*
-        Whether input and output paths are abbreviated. Defaults to 2 if unspecified
-
-          * level 0: The full (expanded, abspath) input or output path
-          * level > 1: The number of subdirectories to include. Abbreviated paths are prefixed with ``[,,,]/``
-          * level < 0: Input / Output parameters are truncated to ``MMM`` letters where ``verbose_abbreviated_path ==-MMM``. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by ``<???>``
-
-
-
-
-
-
-
-
-.. _pipeline_functions.pipeline_printout:
-
-.. index::
-    single: pipeline functions; pipeline_run
-    pair: pipeline_printout; Printout simulated run of the pipeline
-
-**********************************************************************************************************************************************************************************************************
-*pipeline_printout*
-**********************************************************************************************************************************************************************************************************
-**pipeline_printout** (|pp_output_stream|_ = sys.stdout, |pp_target_tasks|_ = [], |pp_forcedtorun_tasks|_ = [], |pp_verbose|_ = 1, |pp_indent|_ = 4, |pp_gnu_make|_ = True, |pp_wrap_width|_ = 100, |pp_runtime_data|_ = None, |pp_checksum_level|_ = None, |pp_history_file|_ = None, |pr_verbose_abbreviated_path|_ = None)
-
-    **Purpose:**
-
-        Prints out all the pipelined functions which will be invoked given specified ``target_tasks``
-        without actually running the pipeline. Because this is a simulation, some of the job
-        parameters may be incorrect. For example, the results of a :ref:`@split<new_manual.split>`
-        operation is not predetermined and will only be known after the pipelined function
-        splits up the original data. Parameters of all downstream pipelined functions will
-        be changed depending on this initial operation.
-
-    **Example**:
-        ::
-
-            #
-            #   Simulate running task2 whatever its state, and also task1 and antecedents
-            #     if they are incomplete
-            #   Print out results to STDOUT
-            #
-            pipeline_printout(sys.stdout, [task1, task2], forcedtorun_tasks = [task2], verbose = 1)
-
-    **Parameters:**
-
-.. _pipeline_functions.pipeline_printout.output_stream:
-
-    * *output_stream*
-        Where to printout the results of simulating the running of the pipeline.
-
-.. _pipeline_functions.pipeline_printout.target_tasks:
-
-    * *target_tasks*
-        As in :ref:`pipeline_run<pipeline_functions.pipeline_run>`: Pipeline functions and any necessary antecedents (specified implicitly or with :ref:`@follows <decorators.follows>`)
-        which should be invoked with the appropriate parameters if they are incomplete or out-of-date.
-
-
-.. _pipeline_functions.pipeline_printout.forcedtorun_tasks:
-
-    * *forcedtorun_tasks*
-        As in :ref:`pipeline_run<pipeline_functions.pipeline_run>`:These pipeline functions will be invoked regardless of their state.
-        Any antecedents tasks will also be executed if they are out-of-date or incomplete.
-
-
-.. _pipeline_functions.pipeline_printout.verbose:
-
-    * *verbose*
-        Optional parameter indicating the verbosity of the messages sent to ``logger``:
-        (Defaults to level 4 if unspecified)
-
-        * level **0** : *nothing*
-        * level **1** : *Out-of-date Task names*
-        * level **2** : *All Tasks (including any task function docstrings)*
-        * level **3** : *Out-of-date Jobs in Out-of-date Tasks, no explanation*
-        * level **4** : *Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings*
-        * level **5** : *All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)*
-        * level **6** : *All jobs in All Tasks whether out of date or not*
-        * level **10**: *logs messages useful only for debugging ruffus pipeline code*
-
-
-        ``verbose >= 10`` are intended for debugging **Ruffus** by the developers and the details
-        are liable to change from release to release
-
-.. _pipeline_functions.pipeline_printout.indent:
-
-    * *indent*
-        Optional parameter governing the indentation when printing out the component job
-        parameters of each task function.
-
-
-.. _pipeline_functions.pipeline_printout.gnu_make:
-
-    * *gnu_make_maximal_rebuild_mode*
-        .. warning ::
-            This is a dangerous option. Use rarely and with caution
-
-        See explanation in :ref:`pipeline_run <pipeline_functions.pipeline_run.gnu_make>`.
-
-.. _pipeline_functions.pipeline_printout.wrap_width:
-
-    * *wrap_width*
-        Optional parameter governing the length of each line before it starts wrapping
-        around.
-
-
-.. _pipeline_functions.pipeline_printout.runtime_data:
-
-    * *runtime_data*
-        Experimental feature for passing data to tasks at run time
-
-
-.. _pipeline_functions.pipeline_printout.history_file:
-
-    * *history_file*
-        The database file which stores checksums and file timestamps for input/output files.
-        Defaults to ``.ruffus_history.sqlite`` if unspecified
-
-.. _pipeline_functions.pipeline_printout.checksum_level:
-
-    * *checksum_level*
-        Several options for checking up-to-dateness are available: Default is level 1.
-
-           * level 0 : Use only file timestamps
-           * level 1 : above, plus timestamp of successful job completion
-           * level 2 : above, plus a checksum of the pipeline function body
-           * level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-
-.. _pipeline_functions.pipeline_printout.verbose_abbreviated_path:
-
-    * *verbose_abbreviated_path*
-        Whether input and output paths are abbreviated. Defaults to 2 if unspecified
-
-          * level 0: The full (expanded, abspath) input or output path
-          * level > 1: The number of subdirectories to include. Abbreviated paths are prefixed with ``[,,,]/``
-          * level < 0: Input / Output parameters are truncated to ``MMM`` letters where ``verbose_abbreviated_path ==-MMM``. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by ``<???>``
-
-
-.. _pipeline_functions.pipeline_printout_graph:
-
-.. index::
-    single: pipeline functions; pipeline_printout_graph
-    pair: pipeline_printout_graph; print flowchart representation of pipeline functions
-
-
-
-
-
-************************************************************************************************************************************************************************************************************************************************************************************
-*pipeline_printout_graph*
-************************************************************************************************************************************************************************************************************************************************************************************
-
-**pipeline_printout_graph** (|ppg_stream|_, |ppg_output_format|_ = None, |ppg_target_tasks|_ = [], |ppg_forcedtorun_tasks|_ = [], |ppg_ignore_upstream_of_target|_ = False, |ppg_skip_uptodate_tasks|_ = False, |ppg_gnu_make|_ = True, |ppg_test_all_task_for_update|_ = True, |ppg_no_key_legend|_  = False, |ppg_minimal_key_legend|_ = True, |ppg_user_colour_scheme|_ = None, |ppg_pipeline_name|_ = "Pipeline", |ppg_size|_ = (11,8), |ppg_dpi|_ = 120, |ppg_runtime_data|_ = None, |ppg_checksum_leve [...]
-
-    **Purpose:**
-
-        Prints out flowchart of all the pipelined functions which will be invoked given specified ``target_tasks``
-        without actually running the pipeline.
-
-        See :ref:`Flowchart colours <new_manual.flowchart_colours>`
-
-    **Example**:
-        ::
-
-            pipeline_printout_graph("flowchart.jpg", "jpg", [task1, task16],
-                                        forcedtorun_tasks = [task2],
-                                        no_key_legend = True)
-
-    **Customising appearance:**
-
-        The :ref:`user_colour_scheme <pipeline_functions.pipeline_printout_graph.user_colour_scheme>` parameter can be used to change
-        flowchart colours. This allows the default :ref:`Colour Schemes <new_manual.flowchart_colours>`
-        to be set. An example of customising flowchart appearance is available :ref:`(see code) <new_manual.flowchart_colours.code>` .
-
-
-
-
-    **Parameters:**
-
-.. _pipeline_functions.pipeline_printout_graph.stream:
-
-    * *stream*
-        The file or file-like object to which the flowchart should be printed.
-        If a string is provided, it is assumed that this is the name of the output file
-        which will be opened automatically.
-
-
-.. _pipeline_functions.pipeline_printout_graph.output_format:
-
-    * *output_format*
-        If missing, defaults to the extension of the *stream* file name (i.e. ``jpg`` for ``a.jpg``)
-
-        | If the programme ``dot`` can be found on the executio path, this
-          can be any number of `formats <http://www.graphviz.org/doc/info/output.html>`_
-          supported by `Graphviz <http://www.graphviz.org/>`_, including, for example,
-          ``jpg``, ``png``, ``pdf``, ``svg`` etc.
-        | Otherwise, **ruffus** will only output without error in the `dot <http://en.wikipedia.org/wiki/DOT_language>`_ format, which
-          is a plain-text graph description language.
-
-.. _pipeline_functions.pipeline_printout_graph.target_tasks:
-
-    * *target_tasks*
-        As in :ref:`pipeline_run<pipeline_functions.pipeline_run>`: Pipeline functions and any necessary antecedents (specified implicitly or with :ref:`@follows <decorators.follows>`)
-        which should be invoked with the appropriate parameters if they are incomplete or out-of-date.
-
-
-.. _pipeline_functions.pipeline_printout_graph.forcedtorun_tasks:
-
-    * *forcedtorun_tasks*
-        As in :ref:`pipeline_run<pipeline_functions.pipeline_run>`:These pipeline functions will be invoked regardless of their state.
-        Any antecedents tasks will also be executed if they are out-of-date or incomplete.
-
-.. _pipeline_functions.pipeline_printout_graph.draw_vertically:
-
-    * *draw_vertically*
-        Draw flowchart in vertical orientation
-
-.. _pipeline_functions.pipeline_printout_graph.ignore_upstream_of_target:
-
-    * *ignore_upstream_of_target*
-        Start drawing flowchart from specified target tasks. Do not draw tasks which are
-        downstream (subsequent) to the targets.
-
-.. _pipeline_functions.pipeline_printout_graph.skip_uptodate_tasks:
-
-    * *ignore_upstream_of_target*
-        Do not draw up-to-date / completed tasks in the flowchart unless they are
-        lie on the execution path of the pipeline.
-
-.. _pipeline_functions.pipeline_printout_graph.gnu_make:
-
-    * *gnu_make_maximal_rebuild_mode*
-        .. warning ::
-            This is a dangerous option. Use rarely and with caution
-
-        See explanation in :ref:`pipeline_run <pipeline_functions.pipeline_run.gnu_make>`.
-
-.. _pipeline_functions.pipeline_printout_graph.test_all_task_for_update:
-
-    * *test_all_task_for_update*
-        | Indicates whether intermediate tasks are out of date or not. Normally **Ruffus** will
-          stop checking dependent tasks for completion or whether they are out-of-date once it has
-          discovered the maximal extent of the pipeline which has to be run.
-        | For displaying the flow of the pipeline, this is hardly very informative.
-
-.. _pipeline_functions.pipeline_printout_graph.no_key_legend:
-
-    * *no_key_legend*
-        Do not include key legend explaining the colour scheme of the flowchart.
-
-
-.. _pipeline_functions.pipeline_printout_graph.minimal_key_legend:
-
-     * *minimal_key_legend*
-        Do not include unused task types in key legend.
-
-.. _pipeline_functions.pipeline_printout_graph.user_colour_scheme:
-
-     * *user_colour_scheme*
-        Dictionary specifying colour scheme for flowchart
-
-        See complete :ref:`list of Colour Schemes <new_manual.flowchart_colours>`.
-
-        | Colours can be names e.g. ``"black"`` or quoted hex e.g. ``'"#F6F4F4"'`` (note extra quotes)
-        | Default values will be used unless specified
-
-        .. csv-table::
-           :header: "key", "Subkey", ""
-
-           "
-           - ``'colour_scheme_index'`` ", "| index of default colour scheme,
-           | 0-7, defaults to 0 unless specified", ""
-           "
-           - ``'Final target'``
-           - ``'Explicitly specified task'``
-           - ``'Task to run'``
-           - ``'Down stream'``
-           - ``'Up-to-date Final target'``
-           - ``'Up-to-date task forced to rerun'``
-           - ``'Up-to-date task'``
-           - ``'Vicious cycle'``
-           ","
-           - ``'fillcolor'``
-           - ``'fontcolor'``
-           - ``'color'``
-           - ``'dashed'``   = ``0/1``
-           ", "Colours / attributes for each task type"
-           "
-           - ``'Vicious cycle'``
-           - ``'Task to run'``
-           - ``'Up-to-date'``", "- ``'linecolor'``", "Colours for arrows between tasks"
-           "- ``'Pipeline'``",  "- ``'fontcolor'``","Flowchart title colour"
-           "- ``'Key'``", "
-           - ``'fontcolor'``
-           - ``'fillcolor'``", "Legend colours"
-
-        Example:
-
-            Use colour scheme index  = 1
-            ::
-
-                pipeline_printout_graph ("flowchart.svg", "svg", [final_task],
-                                         user_colour_scheme = {
-                                                                "colour_scheme_index" :1,
-                                                                "Pipeline"      :{"fontcolor" : '"#FF3232"' },
-                                                                "Key"           :{"fontcolor" : "Red",
-                                                                                  "fillcolor" : '"#F6F4F4"' },
-                                                                "Task to run"   :{"linecolor" : '"#0044A0"' },
-                                                                "Final target"  :{"fillcolor" : '"#EFA03B"',
-                                                                                  "fontcolor" : "black",
-                                                                                  "dashed"    : 0           }
-                                                               })
-
-
-
-
-.. _pipeline_functions.pipeline_printout_graph.pipeline_name:
-
-     * *pipeline_name*
-        Specify title for flowchart
-
-.. _pipeline_functions.pipeline_printout_graph.size:
-
-     * *size*
-        Size in inches for flowchart
-
-.. _pipeline_functions.pipeline_printout_graph.dpi:
-
-     * *dpi*
-        Resolution in dots per inch. Ignored for svg output
-
-.. _pipeline_functions.pipeline_printout_graph.runtime_data:
-
-     * *runtime_data*
-        Experimental feature for passing data to tasks at run time
-
-.. _pipeline_functions.pipeline_printout_graph.history_file:
-
-    * *history_file*
-        The database file which stores checksums and file timestamps for input/output files.
-        Defaults to ``.ruffus_history.sqlite`` if unspecified
-
-.. _pipeline_functions.pipeline_printout_graph.checksum_level:
-
-    * *checksum_level*
-        Several options for checking up-to-dateness are available: Default is level 1.
-
-           * level 0 : Use only file timestamps
-           * level 1 : above, plus timestamp of successful job completion
-           * level 2 : above, plus a checksum of the pipeline function body
-           * level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-
-
-.. _pipeline_functions.pipeline_get_task_names:
-
-.. index::
-    single: pipeline functions; pipeline_get_task_names
-    pair: pipeline_get_task_names; print list of task names without running the pipeline
-
-
-**************************************************************************************************************************************************************************************
-*pipeline_get_task_names*
-**************************************************************************************************************************************************************************************
-**pipeline_get_task_names** ()
-
-    **Purpose:**
-
-        Returns a list of all task names in the pipeline without running the pipeline or checking to see if the tasks are connected correctly
-
-    **Example**:
-
-        Given:
-
-        .. code-block:: python
-
-            from ruffus import *
-
-            @originate([])
-            def create_data(output_files):
-                pass
-
-            @transform(create_data, suffix(".txt"), ".task1")
-            def task1(input_files, output_files):
-                pass
-
-            @transform(task1, suffix(".task1"), ".task2")
-            def task2(input_files, output_files):
-                pass
-
-        Produces a list of three task names:
-
-        .. code-block:: pycon
-
-            >>> pipeline_get_task_names ()
-            ['create_data', 'task1', 'task2']
diff --git a/doc/_build/html/_sources/proxy_logger.txt b/doc/_build/html/_sources/proxy_logger.txt
deleted file mode 100644
index 1e11a28..0000000
--- a/doc/_build/html/_sources/proxy_logger.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-.. include:: global.inc
-#####################
-ruffus.proxy_logger
-#####################
-
-.. _proxy-logger:
-
-.. automodule:: ruffus.proxy_logger
-      :undoc-members:
-      
-
-===========================
-Proxies for a log:
-===========================
-
-.. autofunction:: make_shared_logger_and_proxy
-
-===========================
-Create a logging object
-===========================
-
-
-.. autofunction:: setup_std_shared_logger
-
diff --git a/doc/_build/html/_sources/recipes.txt b/doc/_build/html/_sources/recipes.txt
deleted file mode 100644
index b31b8df..0000000
--- a/doc/_build/html/_sources/recipes.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-.. include:: global.inc
-************
-Recipes
-************
-
-^^^^^^^^^^^^^^^^^
-General
-^^^^^^^^^^^^^^^^^
-
diff --git a/doc/_build/html/_sources/refactoring_ruffus_notes.txt b/doc/_build/html/_sources/refactoring_ruffus_notes.txt
deleted file mode 100644
index 0148709..0000000
--- a/doc/_build/html/_sources/refactoring_ruffus_notes.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-
-    Remember to cite Jake Biesinger and see if he is interested to be a co-author if we ever resubmit the drastically changed version...
-
-
-
diff --git a/doc/_build/html/_sources/task.txt b/doc/_build/html/_sources/task.txt
deleted file mode 100644
index c84bee1..0000000
--- a/doc/_build/html/_sources/task.txt
+++ /dev/null
@@ -1,138 +0,0 @@
-.. include:: global.inc
-#####################
-ruffus.Task
-#####################
-
-.. automodule:: ruffus.task
-      :undoc-members:
-      :noindex:
-
-***************************************
-Decorators
-***************************************
-    Basic Task decorators are:
-    
-        :ref:`@follows() <decorators.follows>`      
-        
-        and
-        
-        :ref:`@files() <decorators.files>`      
-        
-    Task decorators include:
-    
-        :ref:`@split() <decorators.files>`      
-
-        :ref:`@transform() <decorators.files>`      
-
-        :ref:`@merge() <decorators.files>`      
-
-        :ref:`@posttask() <decorators.posttask>`      
-
-    More advanced users may require:
-    
-        :ref:`@transform() <decorators.transform_ex>`      
-        
-        :ref:`@collate() <decorators.collate>`      
-
-        :ref:`@parallel() <decorators.parallel>`      
-        
-        :ref:`@check_if_uptodate() <decorators.check_if_uptodate>`      
-
-        :ref:`@files_re() <decorators.files_re>`      
-        
-
-***************************************
-Pipeline functions
-***************************************
-========================
-pipeline_run
-========================
-.. autofunction:: pipeline_run (target_tasks, forcedtorun_tasks=[], multiprocess=1, logger=stderr_logger, gnu_make_maximal_rebuild_mode=True)
-
-========================
-pipeline_printout
-========================
-.. autofunction:: pipeline_printout
-
-========================
-pipeline_printout_graph
-========================
-.. autofunction:: pipeline_printout_graph
-
-
-.. ???
-    
-
-***************************************
-Logging
-***************************************
-.. autoclass:: t_black_hole_logger
-.. autoclass:: t_stderr_logger
-
-.. ???
-
-
-***************************************
-Implementation:
-***************************************
-=================================
-Parameter factories:
-=================================
-.. autofunction:: merge_param_factory
-.. autofunction:: collate_param_factory
-.. autofunction:: transform_param_factory
-.. autofunction:: files_param_factory
-.. autofunction:: args_param_factory
-.. autofunction:: split_param_factory
-
-.. ???
-    
-    
-=================================
-Wrappers around jobs:
-=================================
-.. autofunction:: job_wrapper_generic
-.. autofunction:: job_wrapper_io_files
-.. autofunction:: job_wrapper_mkdir
-
-.. ???
-    
-
-
-
-=================================
-Checking if job is update:
-=================================
-.. autofunction:: needs_update_check_modify_time
-.. autofunction:: needs_update_check_directory_missing
-
-.. ???
-
-
-***************************************
-Exceptions and Errors
-***************************************
-.. autoclass::task_FilesArgumentsError
-.. autoclass::task_FilesreArgumentsError
-.. autoclass::JobSignalledBreak
-.. autoclass::MissingInputFileError
-.. autoclass::PostTaskArgumentError
-.. autoclass::error_making_directory
-.. autoclass::error_duplicate_task_name
-.. autoclass::error_decorator_args
-.. autoclass::error_task_name_lookup_failed
-.. autoclass::error_task_decorator_takes_no_args
-.. autoclass::error_function_is_not_a_task
-.. autoclass::error_circular_dependencies
-.. autoclass::error_not_a_directory
-.. autoclass::error_missing_output
-.. autoclass::error_job_signalled_interrupt
-
-
-
-.. ???
-
-
-
-
-
diff --git a/doc/_build/html/_sources/todo.txt b/doc/_build/html/_sources/todo.txt
deleted file mode 100644
index 678f521..0000000
--- a/doc/_build/html/_sources/todo.txt
+++ /dev/null
@@ -1,500 +0,0 @@
-.. include:: global.inc
-
-.. _todo:
-
-##########################################
-Future Changes to Ruffus
-##########################################
-
-    I would appreciated feedback and help on all these issues and where next to take *ruffus*.
-
-
-    **Future Changes** are features where we more or less know where we are going and how to get there.
-
-    **Planned Improvements** describes features we would like in Ruffus but where the implementation
-    or syntax has not yet been (fully) worked out.
-
-    If you have suggestions or contributions, please either write to me ( ruffus_lib at llew.org.uk) or
-    send a pull request via the `git site  <https://github.com/bunbun/ruffus>`__.
-
-
-.. _todo.inactive_tasks_in_pipeline_printout_graph:
-
-********************************************************************************************************
-Todo: pipeline_printout_graph should print inactive tasks
-********************************************************************************************************
-
-
-.. _todo.dynamic_strings:
-
-********************************************************************************************************
-Todo: Mark input strings as non-file names, and add support for dynamically returned parameters
-********************************************************************************************************
-
-    1. Use indicator object.
-    2. What is a good name? ``"output_from()"``, ``"NOT_FILE_NAME"`` :-)
-    3. They will still participate in suffix, formatter and regex replacement
-
-    Bernie Pope suggests that we should generalise this:
-
-
-    If any object in the input parameters is a (non-list/tuple) class instance, check (getattr) whether it has a ``ruffus_params()`` function.
-    If it does, call it to obtain a list which is substituted in place.
-    If there are string nested within, these will also take part in Ruffus string substitution.
-    Objects with ``ruffus_params()`` always "decay" to the results of the function call
-
-    ``output_from`` would be a simple wrapper which returns the internal string via ``ruffus_params()``
-
-    .. code-block:: python
-
-        class output_from (object):
-            def __init__(self, str):
-                self.str = str
-            def ruffus_params(self):
-                return [self.str]
-
-    Returning a list should be like wildcards and should not introduce an unnecessary level of indirection for output parameters, i.e. suffix(".txt") or formatter() / "{basename[0]}" should work.
-
-    Check!
-
-
-.. _todo.extra_parameters:
-
-********************************************************************************************************
-Todo: Allow "extra" parameters to be used in output substitution
-********************************************************************************************************
-
-    Formatter substitution can refer to the original elements in the input and extra parameters (without converting them to strings either). This refers to the original (nested) data structure.
-
-    This will allow normal python datatypes to be handed down and slipstreamed into a pipeline more easily.
-
-    The syntax would use Ruffus (> version 2.4) formatter:
-
-    .. code-block:: python
-        :emphasize-lines: 2,3
-
-        @transform( ..., formatter(), [
-                                        "{EXTRAS[0][1][3]}",    # EXTRAS
-                                        "[INPUTS[1][2]]"],...)  # INPUTS
-        def taskfunc():
-            pass
-
-    ``EXTRA`` and ``INPUTS`` indicate that we are referring to the input and extra parameters.
-
-    These are the full (nested) parameters in all their original form. In the case of the input parameters, this obvious depends on the decorator, so
-
-    .. code-block:: python
-
-        @transform(["a.text", [1, "b.text"]], formatter(), "{INPUTS[0][0]}")
-        def taskfunc():
-            pass
-
-    would give
-
-    ::
-
-        job #1
-           input  == "a.text"
-           output == "a"
-
-        job #2
-           input  == [1, "b.text"]
-           output == 1
-
-
-    The entire string must consist of ``INPUTS`` or ``EXTRAS`` followed by optionally N levels of square brackets. i.e. They must match ``"(INPUTS|EXTRAS)(\[\d+\])+"``
-
-    No string conversion takes place.
-
-    For ``INPUTS`` or ``EXTRAS`` which have objects with a ``ruffus_params()`` function (see Todo item above),
-    the original object rather than the result of ``ruffus_params()`` is forwarded.
-
-
-
-.. _todo.pre_post_job:
-
-********************************************************************************************************
-Todo: Extra signalling before and after each task and job
-********************************************************************************************************
-
-    .. code-block:: python
-
-        @prejob(custom_func)
-        @postjob(custom_func)
-        def task():
-            pass
-
-    ``@prejob`` / ``@postjob`` would be run in the child processes.
-
-
-.. _todo.new_decorators:
-
-******************************************************************************
-Todo: ``@split`` / ``@subdivide`` returns the actual output created
-******************************************************************************
-
-    * **overrides** (not replaces) wild cards.
-    * Returns a list, each with output and extra paramters.
-    * Won't include extraneous files which were not created in the pipeline but which just happened to match the wild card
-    * We should have ``ruffus_output_params``, ``ruffus_extra_params`` wrappers for clarity:
-
-      .. code-block:: python
-
-        @split("a.file", "*.txt")
-        def split_into_txt_files(input_file, output_files):
-            output_files = ["a.txt", "b.txt", "c.txt"]
-            for output_file_name in output_files:
-                with open(output_file_name, "w") as oo:
-                    pass
-            return [
-                    ruffus_output("a.file"),
-                    [ruffus_output(["b.file", "c.file"]), ruffus_extras(13, 14)],
-                    ]
-
-
-    * Consider yielding?
-
-==========================================================================================
-Checkpointing
-==========================================================================================
-
-    * If checkpoint file is used, the actual files are saved and checked the next time
-    * If no files are generated, no files are checked the next time...
-    * The output files do not have to match the wildcard though we can output a warning message if that happens...
-      This is obviously dangerous because the behavior will change if the pipeline is rerun without using the checkpoint file
-    * What happens if the task function changes?
-
-***************************************
-Todo: New decorators
-***************************************
-
-==============================================================================
-Todo: ``@originate``
-==============================================================================
-
-    Each (serial) invocation returns lists of output parameters until returns
-    None. (Empty list = ``continue``, None = ``break``).
-
-
-
-==============================================================================
-Todo: ``@recombine``
-==============================================================================
-
-    Like ``@collate`` but automatically regroups jobs which were a result of a previous ``@subdivide`` / ``@split`` (even after intervening ``@transform`` )
-
-    This is the only way job trickling can work without stalling the pipeline: We would know
-    how many jobs were pending for each ``@recombine`` job and which jobs go together.
-
-****************************************************************************************
-Todo: Named parameters in decorators for clarity
-****************************************************************************************
-
-.. _todo.bioinformatics_example:
-
-********************************************************************************************************
-Todo: Bioinformatics example to end all examples
-********************************************************************************************************
-
-    Uses
-        * ``@product``
-        * ``@subdivide``
-        * ``@transform``
-        * ``@collate``
-        * ``@merge``
-
-****************************************************************************************
-Todo: Allow the next task to start before all jobs in the previous task have finished
-****************************************************************************************
-
-    Jake (Biesinger) calls this **Job Trickling**!
-
-    * A single long running job no longer will hold up the entire pipeline
-    * Calculates dependencies dynamically at the job level.
-    * Goal is to have a long running (months) pipeline to which we can keep adding input...
-    * We can choose between prioritising completion of the entire pipeline for some jobs
-      (depth first) or trying to complete as many tasks as possible (breadth first)
-
-==============================================================================
-Converting to per-job rather than per task dependencies
-==============================================================================
-    Some decorators prevent per job (rather than per task) dependency calculations, and
-    will call a pipeline stall until the dependent tasks are completed (the current situation):
-
-        * Some types of jobs unavoidably depend on an entire previous task completing:
-             * ``add_inputs()``, ``inputs()``
-             * ``@merge``
-             * ``@split`` (implicit ``@merge``)
-        * ``@split``, ``@originate`` produce variable amount of output at runtime and must be completed before the next task can be run.
-             * Should ``yield`` instead of return?
-        * ``@collate`` needs to pattern match all the inputs of a previous task
-             * Replace ``@collate`` with ``@recombine`` which "remembers" and reverses the results of a previous
-               ``@subdivide`` or ``@split``
-             * Jobs need unique job_id tag
-             * Jobs are assigned (nested) grouping id which accompany them down the
-               pipeline after ``@subdivide`` / ``@split`` and are removed after ``@recombine``
-             * Should have a count of jobs so we always know *when* an "input slot" is full
-        * Funny "single file" mode for ``@transform,`` ``@files`` needs to be
-          regularised so it is a syntactic (front end) convenience (oddity!)
-          and not plague the inards of ruffus
-
-
-    Breaking change: to force the entirety of the previous task to complete before the next one, use ``@follows``
-
-==============================================================================
-Implementation
-==============================================================================
-
-    * "Push" model. Completing jobs "check in" their outputs to "input slots" for all the sucessor jobs.
-    * When "input slots" are full for any job, it is put on the dispatch queue to be run.
-    * The priority (depth first or breadth first) can be set here.
-    * ``pipeline_run`` / ``Pipeline_printout`` create a task dependency tree structure (from decorator dependencies) (a runtime pipeline object)
-    * Each task in the pipeline object knows which other tasks wait on it.
-    * When output is created by a job, it sends messages to (i.e. function calls) all dependent tasks in the pipeline object with the new output
-    * Sets of output such as from ``@split`` and ``@subdivide`` and ``@originate`` have a
-      terminating condition and/or a associated count (# of output)
-    * Tasks in the pipeline object forward incoming inputs to task input slots (for slots common to all jobs in a
-      task: ``@inputs``, ``@add_inputs``) or to slots in new jobs in the pipeline object
-    * When all slots are full in each job, this triggers putting the job parameters onto the job submission queue
-    * The pipeline object should allow Ruffus to be reentrant?
-
-
-
-##########################################
-Planned Improvements to Ruffus
-##########################################
-
-.. _todo.run_on_cluster:
-
-
-
-    * ``@split`` needs to be able to specify at run time the number of
-      resulting jobs without using wild cards
-    * legacy support for wild cards and file names.
-
-
-********************************************************************************************************
-Planned: Running python code (task functions) transparently on remote cluster nodes
-********************************************************************************************************
-
-    Wait until next release.
-
-    Will bump Ruffus to v.3.0 if can run python jobs transparently on a cluster!
-
-    abstract out ``task.run_pooled_job_without_exceptions()`` as a function which can be supplied to ``pipeline_run``
-
-    Common "job" interface:
-
-         *  marshalled arguments
-         *  marshalled function
-         *  submission timestamp
-
-    Returns
-         *  completion timestamp
-         *  returned values
-         *  exception
-
-    #) Full version use libpythongrid?
-       * Christian Widmer <ckwidmer at gmail.com>
-       * Cheng Soon Ong <chengsoon.ong at unimelb.edu.au>
-       * https://code.google.com/p/pythongrid/source/browse/#git%2Fpythongrid
-       * Probably not good to base Ruffus entirely on libpythongrid to minimise dependencies, the use of sophisticated configuration policies etc.
-    #) Start with light-weight file-based protocol
-       * specify where the scripts should live
-       * use drmaa to start jobs
-       * have executable ruffus module which knows how to load deserialise (unmarshall) function / parameters from disk. This would be what drmaa starts up, given the marshalled data as an argument
-       * time stamp
-       * "heart beat" to check that the job is still running
-    #) Next step: socket-based protocol
-       * use specified master port in ruffus script
-       * start remote processes using drmaa
-       * child receives marshalled data and the address::port in the ruffus script (head node) to initiate hand shake or die
-       * process recycling: run successive jobs on the same remote process for reduced overhead, until exceeds max number of jobs on the same process, min/max time on the same process
-       * resubmit if die (Don't do sophisticated stuff like libpythongrid).
-
-.. _todo.job_trickling:
-
-
-
-.. _todo.custom_parameters:
-
-************************************
-Planned: Custom parameter generator
-************************************
-
-    Request on mailing list
-
-         I've often wished that I could use an arbitrary function to process the input filepath instead of just a regex.
-
-        .. code-block:: python
-
-           def f(inputs, outputs, extra_param1, extra_param2):
-                # do something to generate parameters
-                return new_output_param, new_extra_param1, new_extra_param2
-
-        now f() can be used inside a Ruffus decorator to generate the outputs from inputs, instead of being forced to use a regex for the job.
-
-        Cheers,
-        Bernie.
-
-    Leverages built-in Ruffus functionality.
-    Don't have to write entire parameter generation from scratch.
-
-    * Gets passed an iterator where you can do a for loop to get input parameters / a flattened list of files
-    * Other parameters are forwarded as is
-    * The duty of the function is to ``yield`` input, output, extra parameters
-
-
-    Simple to do but how do we prevent this from being a job-trickling barrier?
-
-    Postpone until we have an initial design for job-trickling: Ruffus v.4 ;-(
-
-
-.. _todo.gui:
-
-****************************************************************************
-Planned: Ruffus GUI interface.
-****************************************************************************
-
-    Desktop (PyQT or web-based solution?)  I'd love to see an svg pipeline picture that I could actually interact with
-
-
-********************************************************************************************************
-Planned: Non-decorator / Function interface to Ruffus
-********************************************************************************************************
-
-
-.. _todo.intermediate_files:
-
-********************************************************************************************************
-Planned: Remove intermediate files
-********************************************************************************************************
-
-    Often large intermediate files are produced in the middle of a pipeline which could be
-    removed. However, their absence would cause the pipeline to appear out of date. What is
-    the best way to solve this?
-
-    In gmake, all intermediate files which are not marked ``.PRECIOUS`` are deleted.
-
-    We do not want to manually mark intermediate files for several reasons:
-        * The syntax would be horrible and clunky
-        * The gmake distinction between ``implicit`` and ``explicit`` rules is not one we
-          would like to impose on Ruffus
-        * Gmake uses statically determined (DAG) dependency trees so it is quite natural and
-          easy to prune intermediate paths
-
-    Our preferred solution should impose little to no semantic load on Ruffus, i.e. it should
-    not make it more complex / difficult to use. There are several alternatives we are
-    considering:
-
-        #) Have an **update** mode in which pipeline_run would ignore missing files and only run tasks with existing, out-of-date files.
-        #) Optionally ignore all out-of-date dependencies beyond a specified point in the pipeline
-        #) Add a decorator to flag sections of the pipeline where intermediate files can be removed
-
-
-    Option (1) is rather unnerving because it makes inadvertent errors difficult to detect.
-
-    Option (2) involves relying on the user of a script to remember the corect chain of dependencies in
-    often complicated pipelines. It would be advised to keep a flowchart to hand. Again,
-    the chances of error are much greater.
-
-    Option (3) springs from the observation by Andreas Heger that parts of a pipeline with
-    disposable intermediate files can usually be encapsulated as an autonomous section.
-    Within this subpipeline, all is well provided that the outputs of the last task are complete
-    and up-to-date with reference to the inputs of the first task. Intermediate files
-    could be removed with impunity.
-
-    The suggestion is that these autonomous subpipelines could be marked out using the Ruffus
-    decorator syntax::
-
-        #
-        #   First task in autonomous subpipeline
-        #
-        @files("who.isit", "its.me")
-        def first_task(*args):
-            pass
-
-        #
-        #   Several intermediate tasks
-        #
-        @transform(subpipeline_task1, suffix(".me"), ".her")
-        def task2_etc(*args):
-           pass
-
-        #
-        #   Final task
-        #
-        @sub_pipeline(subpipeline_task1)
-        @transform(subpipeline_task1, suffix(".her"), ".you")
-        def final_task(*args):
-           pass
-
-    **@sub_pipeline** marks out all tasks between ``first_task`` and ``final_task`` and
-    intermediate files such as ``"its.me"``, ``"its.her`` can be deleted. The pipeline will
-    only run if ``"its.you"`` is missing or out-of-date compared with ``"who.isit"``.
-
-    Over the next few Ruffus releases we will see if this is a good design, and whether
-    better keyword can be found than **@sub_pipeline** (candidates include **@shortcut**
-    and **@intermediate**)
-
-
-.. _todo.retry:
-
-********************************************************************************************************
-Planned: @retry_on_error(NUM_OF_RETRIES)
-********************************************************************************************************
-
-.. _todo.cleanup:
-
-********************************************************************************************************
-Planned: Clean up
-********************************************************************************************************
-
-    The plan is to store the files and directories created via
-    a standard interface.
-
-    The placeholders for this are a function call ``register_cleanup``.
-
-    Jobs can specify the files they created and which need to be
-    deleted by returning a list of file names from the job function.
-
-    So::
-
-        raise Exception = Error
-
-        return False = halt pipeline now
-
-        return string / list of strings = cleanup files/directories later
-
-        return anything else = ignored
-
-
-    The cleanup file/directory store interface can be connected to
-    a text file or a database.
-
-    The cleanup function would look like this::
-
-        pipeline_cleanup(cleanup_log("../cleanup.log"), [instance ="october19th" ])
-        pipeline_cleanup(cleanup_msql_db("user", "password", "hash_record_table"))
-
-    The parameters for where and how to store the list of created files could be
-    similarly passed to pipeline_run as an extra parameter::
-
-        pipeline_run(cleanup_log("../cleanup.log"), [instance ="october19th" ])
-        pipeline_run(cleanup_msql_db("user", "password", "hash_record_table"))
-
-    where `cleanup_log` and `cleanup_msql_db` are classes which have functions for
-
-        #) storing file
-        #) retrieving file
-        #) clearing entries
-
-
-    * Files would be deleted in reverse order, and directories after files.
-    * By default, only empty directories would be removed.
-
-      But this could be changed with a ``--forced_remove_dir`` option
-
-    * An ``--remove_empty_parent_directories`` option would be
-      supported by `os.removedirs(path) <http://docs.python.org/library/os.html#os.removedirs>`_.
-
diff --git a/doc/_build/html/_sources/tutorials/manual/advanced_transform.txt b/doc/_build/html/_sources/tutorials/manual/advanced_transform.txt
deleted file mode 100644
index 3d211a2..0000000
--- a/doc/_build/html/_sources/tutorials/manual/advanced_transform.txt
+++ /dev/null
@@ -1,347 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.advanced_transform:
-
-######################################################################################################################################################
-|manual.transform_ex.chapter_num|: **add_inputs()** `and` **inputs()**: `Controlling both input and output files with` **@transform**
-######################################################################################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>`
-        * :ref:`@transform <decorators.transform>` syntax in detail
-
-
-    .. index::
-        pair: @transform (Advanced Usage); Manual
-
-
-    The standard :ref:`@transform <manual.transform>` allows you to send a list of data files
-    to the same pipelined function and for the resulting *outputs* parameter to be automatically
-    inferred from file names in the *inputs*.
-
-    There are two situations where you might desire additional flexibility:
-        #. You need to add additional prequisites or filenames to the *inputs* of every single one
-           of your jobs
-        #. (Less often,) the actual *inputs* file names are some variant of the *outputs* of another
-           task.
-
-    Either way, it is occasionally very useful to be able to generate the actual *inputs* as
-    well as *outputs* parameters by regular expression substitution. The following examples will show
-    you both how and why you would want to do this.
-
-====================================================================
-Adding additional *input* prerequisites per job
-====================================================================
-
-
-************************************************************************
-1.) Example: compiling c++ code
-************************************************************************
-
-    Suppose we wished to compile some c++ (``"*.cpp"``) files:
-        .. comment << Pythoncode
-
-        ::
-
-            source_files = "hasty.cpp", "tasty.cpp", "messy.cpp"
-            for source_file in source_files:
-                open(source_file, "w")
-
-    .. comment
-        Pythoncode
-
-
-    The ruffus code would look like this:
-        .. comment << Pythoncode
-
-        ::
-
-            from ruffus import *
-
-            @transform(source_files, suffix(".cpp"), ".o")
-            def compile(input_filename, output_file_name):
-                open(output_file_name, "w")
-
-    .. comment
-        Pythoncode
-
-
-    This results in the following jobs:
-        ::
-
-            >>> pipeline_run([compile], verbose = 2, multiprocess = 3)
-
-                Job = [None -> hasty.cpp] completed
-                Job = [None -> tasty.cpp] completed
-                Job = [None -> messy.cpp] completed
-            Completed Task = prepare_cpp_source
-
-                Job = [hasty.cpp -> hasty.o] completed
-                Job = [messy.cpp -> messy.o] completed
-                Job = [tasty.cpp -> tasty.o] completed
-            Completed Task = compile
-
-************************************************************************
-2.) Example: Adding a header file with **add_inputs(..)**
-************************************************************************
-
-
-    All this is plain vanilla **@transform** syntax. But suppose that we need to add a
-    common header file ``"universal.h"`` to our compilation.
-    The **add_inputs** provides for this with the minimum of fuss:
-
-        .. comment << Pythoncode
-
-        ::
-
-            # create header file
-            open("universal.h", "w")
-
-            # compile C++ files with extra header
-            @transform(prepare_cpp_source, suffix(".cpp"), add_inputs("universal.h"), ".o")
-            def compile(input_filename, output_file_name):
-                open(output_file_name, "w")
-
-    .. comment
-        Pythoncode
-
-    Now the input file is a python list, with ``"universal.h"`` added to each ``"*.cpp"``
-
-        ::
-
-            >>> pipeline_run([compile], verbose = 2, multiprocess = 3)
-
-                Job = [ [hasty.cpp, universal.h] -> hasty.o] completed
-                Job = [ [messy.cpp, universal.h] -> messy.o] completed
-                Job = [ [tasty.cpp, universal.h] -> tasty.o] completed
-            Completed Task = compile
-
-
-================================================================================
-Additional *input* prerequisites can be globs, tasks or pattern matches
-================================================================================
-
-    A common requirement is to include the corresponding header file in compilations.
-    It is easy to use **add_inputs** to look up additional files via pattern matches.
-
-************************************************************************
-3.) Example: Adding matching header file
-************************************************************************
-
-    To make this example more fun, we shall also:
-        #) Give each source code file its own ordinal
-        #) Use ``add_inputs`` to add files produced by another task function
-
-    .. comment << Pythoncode
-
-    ::
-
-        # each source file has its own index
-        source_names = [("hasty.cpp", 1),
-                        ("tasty.cpp", 2),
-                        ("messy.cpp", 3), ]
-        header_names = [sn.replace(".cpp", ".h") for (sn, i) in source_names]
-        header_names.append("universal.h")
-
-        #
-        #   create header and source files
-        #
-        for source, source_index in source_names:
-            open(source, "w")
-
-        for header in header_names:
-            open(header, "w")
-
-
-
-        from ruffus import *
-
-        #
-        #   lookup embedded strings in each source files
-        #
-        @transform(source_names, suffix(".cpp"), ".embedded")
-        def get_embedded_strings(input_filename, output_file_name):
-            open(output_file_name, "w")
-
-
-
-        # compile C++ files with extra header
-        @transform(source_names, suffix(".cpp"),
-                   add_inputs(  "universal.h",
-                                r"\1.h",
-                                get_embedded_strings     ), ".o")
-        def compile(input_params, output_file_name):
-            open(output_file_name, "w")
-
-
-        pipeline_run([compile], verbose = 2, multiprocess = 3)
-
-    .. comment
-        Pythoncode
-
-    This script gives the following output
-
-        ::
-
-                >>> pipeline_run([compile], verbose = 2, multiprocess = 3)
-
-                    Job = [[hasty.cpp,  1] -> hasty.embedded] completed
-                    Job = [[messy.cpp,  3] -> messy.embedded] completed
-                    Job = [[tasty.cpp,  2] -> tasty.embedded] completed
-                Completed Task = get_embedded_strings
-
-                    Job = [[[hasty.cpp,  1],                                            # inputs
-                            universal.h,                                                # common header
-                            hasty.h,                                                    # corresponding header
-                            hasty.embedded, messy.embedded, tasty.embedded]             # output of get_embedded_strings()
-                           -> hasty.o] completed
-                    Job = [[[messy.cpp, 3],                                             # inputs
-                            universal.h,                                                # common header
-                            messy.h,                                                    # corresponding header
-                            hasty.embedded, messy.embedded, tasty.embedded]             # output of get_embedded_strings()
-                           -> messy.o] completed
-                    Job = [[[tasty.cpp, 2],                                             # inputs
-                            universal.h,                                                # common header
-                            tasty.h,                                                    # corresponding header
-                            hasty.embedded, messy.embedded, tasty.embedded]             # output of get_embedded_strings()
-                           -> tasty.o] completed
-                Completed Task = compile
-
-    We can see that the ``compile(...)`` task now has four sets of *inputs*:
-        1) The original inputs (e.g. ``[hasty.cpp,  1]``)
-
-    And three additional added by **add_inputs(...)**
-        2) A header file (``universal.h``) common to all jobs
-        3) The matching header (e.g. ``hasty.h``)
-        4) The output from another task ``get_embedded_strings()`` (e.g. ``hasty.embedded, messy.embedded, tasty.embedded``)
-
-    .. note::
-        For input parameters with nested structures (lists or sets), the pattern matching is
-        on the first filename string Ruffus comes across (DFS).
-
-        So for ``["hasty.c", 0]``, the pattern matches ``"hasty.c"``.
-
-        If in doubt, use :ref:`pipeline_printout <manual.tracing_pipeline_parameters>` to
-        check what parameters Ruffus is using.
-
-
-************************************************************************
-4.) Example: Using **regex(..)** instead of **suffix(..)**
-************************************************************************
-    Suffix pattern matching is much simpler and hence is usually preferable to the more
-    powerful regular expressions. We can rewrite the above example to use **regex** as well
-    to give exactly the same output.
-
-    .. comment << Pythoncode
-
-    ::
-
-        # compile C++ files with extra header
-        @transform(source_names, regex(r"(.+)\.cpp"),
-                   add_inputs(  "universal.h",
-                                r"\1.h",
-                                get_embedded_strings     ), r"\1.o")
-        def compile(input_params, output_file_name):
-            open(output_file_name, "w")
-
-    .. comment
-        Pythoncode
-
-    .. note::
-        The backreference ``\g<0>`` usefully substitutes the entire substring matched by
-        the regular expression.
-
-
-
-====================================================================
-Replacing all input parameters with **inputs(...)**
-====================================================================
-
-    More rarely, it is necessary to replace all the input parameters wholescale.
-
-************************************************************************
-4.) Example: Running matching python scripts
-************************************************************************
-    In the following example, we are not compiling C++ source files but invoking
-    corresponding python scripts which have the same name.
-
-    Given three c++ files and their corresponding python scripts:
-
-        .. comment << Pythoncode
-
-        ::
-
-            # each source file has its own index
-            source_names = [("hasty.cpp", 1),
-                            ("tasty.cpp", 2),
-                            ("messy.cpp", 3), ]
-
-            #
-            #   create c++ source files and corresponding python files
-            #
-            for source, source_index in source_names:
-                open(source, "w")
-                open(source.replace(".cpp", ".py"), "w")
-
-        .. comment
-            Pythoncode
-
-    The Ruffus code will call each python script corresponding to their c++ counterpart:
-
-        .. comment << Pythoncode
-
-        ::
-
-            from ruffus import *
-
-
-            # run corresponding python files
-            @transform(source_names, suffix(".cpp"), inputs(  r"\1.py"), ".results")
-            def run_python_file(input_params, output_file_name):
-                open(output_file_name, "w")
-
-
-            pipeline_run([run_python_file], verbose = 2, multiprocess = 3)
-
-        .. comment
-            Pythoncode
-
-    Resulting in this output:
-        ::
-
-            >>> pipeline_run([run_python_file], verbose = 2, multiprocess = 3)
-                Job = [hasty.py -> hasty.results] completed
-                Job = [messy.py -> messy.results] completed
-                Job = [tasty.py -> tasty.results] completed
-            Completed Task = run_python_file
-
-
-************************************************************************
-5.) Example: Using **regex** instead of **suffix**
-************************************************************************
-
-    Again, the same code can be written (less clearly) using the more powerful
-    **regex** and python regular expressions:
-
-        .. comment << Pythoncode
-
-        ::
-
-            from ruffus import *
-
-
-            # run corresponding python files
-            @transform(source_names, regex(r"(.+)\.cpp"), inputs(  r"\1.py"), r\"1.results")
-            def run_python_file(input_params, output_file_name):
-                open(output_file_name, "w")
-
-
-            pipeline_run([run_python_file], verbose = 2, multiprocess = 3)
-
-        .. comment
-            Pythoncode
-
-
-    This is about as sophisticated as **@transform** ever gets!
diff --git a/doc/_build/html/_sources/tutorials/manual/check_if_uptodate.txt b/doc/_build/html/_sources/tutorials/manual/check_if_uptodate.txt
deleted file mode 100644
index bbfe447..0000000
--- a/doc/_build/html/_sources/tutorials/manual/check_if_uptodate.txt
+++ /dev/null
@@ -1,89 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.check_if_uptodate:
-
-#######################################################################################################################
-|manual.check_if_uptodate.chapter_num|: `Writing custom functions to decide which jobs are up to date`
-#######################################################################################################################
-
-    .. hlist::
-    
-        * :ref:`Manual overview <manual>` 
-        * :ref:`@check_if_uptodate  syntax in detail<decorators.check_if_uptodate>`
-    
-        
-    
-    .. index:: 
-        pair: @check_if_uptodate; Manual
-    
-******************************************************************************
-**@check_if_uptodate** : Manual dependency checking
-******************************************************************************
-    tasks specified with 
-        * :ref:`@files <manual.files>`
-        * :ref:`@split <manual.split>` 
-        * :ref:`@transform <manual.transform>`
-        * :ref:`@merge <manual.merge>`
-        * :ref:`@collate <manual.collate>`
-
-    have automatic dependency checking based on file modification times.
-    
-    Sometimes, you might want to decide have more control over whether to run jobs, especially
-    if a task does not rely on or produce files (i.e. with :ref:`@parallel <manual.parallel>`)
-    
-    You can write your own custom function to decide whether to run a job.
-    This takes as many parameters as your task function, and needs to return a
-    tuple for whether an update is required, and why (i.e. ``tuple(bool, str)``)
-    
-    This simple example which creates the file ``"a.1"`` if it does not exist:
-
-        ::
-            
-            from ruffus import *
-            @files(None, "a.1")
-            def create_if_necessary(input_file, output_file):
-                open(output_file, "w")
-                        
-            pipeline_run([create_if_necessary])
-    
-
-        
-    could be rewritten more laboriously as:
-
-        ::
-        
-            
-            from ruffus import *
-            import os
-            def check_file_exists(input_file, output_file):
-                if os.path.exists(output_file):
-                    return False, "File already exists"
-                return True, "%s is missing" % output_file
-            
-            @parallel([[None, "a.1"]])
-            @check_if_uptodate(check_file_exists)
-            def create_if_necessary(input_file, output_file):
-                open(output_file, "w")
-            
-            pipeline_run([create_if_necessary])
-            
-        
-
-    Both produce the same output:
-        ::
-        
-            Task = create_if_necessary
-                Job = [null, "a.1"] completed
-        
-
-    
-    
-.. note::
-    
-    The function specified by :ref:`@check_if_uptodate <manual.check_if_uptodate>` can be called
-    more than once for each job. 
-
-    See the :ref:`description here <manual.dependencies>` of how **Ruffus** decides which tasks to run.
-        
-
diff --git a/doc/_build/html/_sources/tutorials/manual/collate.txt b/doc/_build/html/_sources/tutorials/manual/collate.txt
deleted file mode 100644
index 13e98cf..0000000
--- a/doc/_build/html/_sources/tutorials/manual/collate.txt
+++ /dev/null
@@ -1,95 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.collate:
-
-######################################################################################################
-|manual.collate.chapter_num|: **@collate**\ : `group together disparate input into sets of results`
-######################################################################################################
-
-    .. hlist::
-    
-        * :ref:`Manual overview <manual>` 
-        * :ref:`@collate syntax in detail <decorators.collate>`
-    
-    It is often very useful to group together disparate *inputs* into several categories, each of which
-    lead to a separate *output*. In the example shown below, we produce separate summaries of results 
-    depending on which species the file belongs to.
-    
-    **Ruffus** uses the term ``collate`` in a rough analogy to the way printers group together
-    copies of documents appropriately.
-        
-    .. index:: 
-        pair: @collate; Manual
-        
-    
-
-
-
-====================================================
-Collating many *inputs* each into a single *output*
-====================================================
-
-    Our example starts with some files which presumably have been created by some
-    earlier stages of our pipeline. We simulate this here with this code:
-    
-        ::
-        
-            files_names = [     "mammals.tiger.wild.animals"
-                                "mammals.lion.wild.animals"
-                                "mammals.lion.handreared.animals"
-                                "mammals.dog.tame.animals"
-                                "mammals.dog.wild.animals"
-                                "mammals.dog.feral.animals"
-                                "reptiles.crocodile.wild.animals" ]
-            for f in files_names:
-                open(f, "w").write(f)
-
-    However, we are only interested in mammals, and we would like the files of each species to
-    end up in its own directory, i.e. ``tiger``, ``lion`` and ``dog``:
-    
-        ::
-        
-            import os
-            os.mkdir("tiger")
-            os.mkdir("lion")
-            os.mkdir("dog")
-
-    Now we would like to place each file in a different destination, depending on its
-    species. The following regular expression marks out the species name ``r'mammals.([^.]+)'``.
-    For ``mammals.tiger.wild.animals``, the first matching group (``\1``) == ``"tiger"``
-    
-    Then, the following::     
-    
-        from ruffus import *
-
-        @collate('*.animals',                     # inputs = all *.animal files
-                    regex(r'mammals.([^.]+)'),    # regular expression
-                    r'\1/animals.in_my_zoo',      # single output file per species
-                    r'\1' )                       # species name
-        def capture_mammals(infiles, outfile, species):
-            # summarise all animals of this species
-            print "Collating %s" % species
-            
-            o = open(outfile, "w")
-            for i in infiles:
-                o.write(open(infile).read() + "\ncaptured\n")
-        
-        pipeline_run([capture_mammals])
-        
-    .. ???
-
-    puts each captured mammal in its own directory::
-
-        Task = capture_mammals
-            Job = [(mammals.lion.handreared.animals, mammals.lion.wild.animals) -> lion/animals.in_my_zoo] completed
-            Job = [(mammals.tiger.wild.animals, ) -> tiger/animals.in_my_zoo] completed
-            Job = [(mammals.dog.tame.animals, mammals.dog.wild.animals, mammals.dog.feral.animals) -> dog/animals.in_my_zoo] completed
-
-        
-    .. ???
-
-    The crocodile has been discarded because it isn't a mammal and the file name
-    doesn't match the ``mammal`` part of the regular expression.
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/dependencies.txt b/doc/_build/html/_sources/tutorials/manual/dependencies.txt
deleted file mode 100644
index 1221c63..0000000
--- a/doc/_build/html/_sources/tutorials/manual/dependencies.txt
+++ /dev/null
@@ -1,158 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.dependencies:
-
-##################################################################################
-|manual.dependencies.chapter_num|: `Checking dependencies to run tasks in order`
-##################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>` 
-
-    
-    .. index:: 
-        pair: dependencies; Manual
-        
-    
-    
-    How does **Ruffus** decide how to run your pipeline? 
-    
-        * In which order should pipelined functions be called?
-        
-        * Which parts of the pipeline are up-to-date and do not need to be rerun?
-
-
-=============================================
-Running all out-of-date tasks and dependents
-=============================================
-
-    .. image:: ../../images/manual_dependencies_flowchart_intro.png
-    
-
-    By default, *ruffus* will 
-    
-        * build a flow chart (dependency tree) of pipelined tasks (functions) 
-        * start from the most ancestral tasks with the fewest dependencies (``task1`` and ``task4`` in the flowchart above).
-        * walk up the tree to find the first incomplete / out-of-date tasks (i.e. ``task3`` and ``task5``. 
-        * start running from there
-
-    All down-stream (dependent) tasks will be re-run anyway, so we don't have to test
-          whether they are up-to-date or not.
-
-    .. _manual.dependencies.checking_multiple_times:
-    
-    .. note::
-    
-        This means that **ruffus** *may* ask any task if their jobs are out of date more than once:
-    
-            * once when deciding which parts of the pipeline have to be run
-            * once just before executing the task.
-        
-    *Ruffus* tries to be clever / efficient, and does the minimal amount of querying.
-    
-    
-.. _manual.dependencies.example:
-    
-    
-=======================================
-A simple example
-=======================================
-
--------------------------------------
-    Four successive tasks to run:
--------------------------------------    
-        .. note::    
-            The full code is available :ref:`here <manual.dependencies.code>`.
-
-    
-        Suppose we have four successive tasks to run, whose flowchart we can print out
-        by running:
-        
-            ::
-            
-                pipeline_printout_graph ("flowchart.png", "png", [task4], 
-                                            draw_vertically = True)
-                
-        
-        .. image:: ../../images/manual_dependencies_flowchart1.png
-        
-        We can see that all four tasks need to run reach the target task4.
-   
-----------------------------------------
-    Pipeline tasks are up-to-date:
-----------------------------------------
-
-
-        After the pipeline runs (``python simpler.py -d ""``), all tasks are up to date and the flowchart shows:
-        
-        .. image:: ../../images/manual_dependencies_flowchart2.png
-    
--------------------------------------
-    Some tasks out of date:
--------------------------------------
-
-        If we then made task2 and task4 out of date by modifying their *inputs* files:
-            ::
-        
-                open("a.1", "w")
-                open("a.3", "w")
-                
-        
-        the flowchart would show:
-        
-        #. the pipeline only has to rerun from ``task2``.
-        #. ``task1`` is complete / up-to-date
-        #. ``task3`` will have to be re-run because it follows (depends on) ``task2``.
-
-        .. image:: ../../images/manual_dependencies_flowchart3.png
-            
-=======================================
-Forced Reruns
-=======================================
-    Even if a pipeline stage appears to be up to date,
-    you can always force the pipeline to include from one or more task functions.
-
-    This is particularly useful, for example, if the pipeline data hasn't changed but
-    the analysis or computional code has.
-
-        ::
-        
-            pipeline_run([task4], [task1])
-        
-
-        will run all tasks from ``task1`` to ``task4``
-        
-
-    Both the "target" and the "forced" lists can include as many tasks as you wish. All dependencies
-    are still carried out and out-of-date jobs rerun.
-            
-
-=======================================
-Esoteric option: Minimal Reruns
-=======================================
-
-    In the above example, you could point out that ``task3`` is not out of date. And if we were only interested
-    in the immediate dependencies or prerequisites leading up to ``task4``, we might not 
-    need task2 to rerun at all, only ``task4``.
-    
-    This rather dangerous option is useful if you don't want to keep all the intermediate 
-    files/results from upstream tasks. The pipeline will only not involve any incomplete
-    tasks which precede an up-to-date result. 
-    
-    This is seldom what you intend, and you should always check that the appropriate stages
-    of the pipeline are executed in the flowchart output.
-    
-    In such cases, we can rerun the pipeline with the following option:
-
-        ::
-    
-            pipeline_run([task4], gnu_make_maximal_rebuild_mode = False)
-
-    and only ``task4`` will rerun.
-    
-    
-        
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/dependencies_code.txt b/doc/_build/html/_sources/tutorials/manual/dependencies_code.txt
deleted file mode 100644
index 9e99198..0000000
--- a/doc/_build/html/_sources/tutorials/manual/dependencies_code.txt
+++ /dev/null
@@ -1,97 +0,0 @@
-.. include:: ../../global.inc
-.. _manual.dependencies.code:
-
-
-########################################################################################
-Code for Chapter 9: Checking dependencies to run tasks in order
-########################################################################################
-    * :ref:`Manual overview <manual>` 
-    * :ref:`Back <manual.dependencies.example>` 
-
-    This example shows how dependencies work
-              
-    
-************************************
-Code
-************************************
-    ::
-
-        from ruffus import *
-        import json
-        
-        import time
-        def task_helper(infile, outfile):
-            """
-            cat input file content to output file
-                after writing out job parameters
-            """
-            if infile:
-                output_text = "".join(sorted(open(infile).readlines()))
-            else:
-                output_text = "None"
-            output_text += json.dumps(infile) + " -> " + json.dumps(outfile) + "\n"
-            open(outfile, "w").write(output_text)
-
-
-
-        #
-        #    task1
-        #
-        @files(None, 'a.1')
-        def task1(infile, outfile):
-            """
-            First task
-            """
-            task_helper(infile, outfile)
-        
-        
-        
-        #
-        #    task2
-        #
-        @transform(task1, regex(r'.1'), '.2')
-        def task2(infile, outfile):
-            """
-            Second task
-            """
-            task_helper(infile, outfile)
-        
-        
-        
-        #
-        #    task3
-        #
-        @transform(task2, regex(r'.2'), '.3')
-        def task3(infile, outfile):
-            """
-            Third task
-            """
-            task_helper(infile, outfile)
-        
-        
-        
-        #
-        #    task4
-        #
-        @transform(task3, regex(r'.3'), '.4')
-        def task4(infile, outfile):
-            """
-            Fourth task
-            """
-            task_helper(infile, outfile)
-        
-        pipeline_printout_graph ("flowchart.png", "png", [task4], draw_vertically = True, no_key_legend = True)
-        pipeline_run([task4])
-
-************************************
-Resulting Output
-************************************
-    ::
-    
-        >>> pipeline_run([task4], multiprocess = 10, logger = logger_proxy)
-            job = [null, "a.1"]
-            job = ["a.1", "a.2"]
-            job = ["a.2", "a.3"]
-            job = ["a.3", "a.4"]
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/exceptions.txt b/doc/_build/html/_sources/tutorials/manual/exceptions.txt
deleted file mode 100644
index c0bd3b6..0000000
--- a/doc/_build/html/_sources/tutorials/manual/exceptions.txt
+++ /dev/null
@@ -1,82 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.exceptions:
-
-###################################################################################################
-|manual.exceptions.chapter_num|: `Exceptions thrown inside a pipeline`
-###################################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>` 
-
-    
-    .. index:: 
-        pair: Exceptions; Manual
-    
-
-    The goal for **Ruffus** is that exceptions should just work *out-of-the-box* without any fuss.
-    This is especially important for exceptions that come from your code which may be raised
-    in a different process. Often multiple parallel operations (jobs or tasks) fail at the
-    same time. **Ruffus** will forward each of these exceptions with the tracebacks so you
-    can jump straight to the offending line.
-    
-    This example shows separate exceptions from two jobs running in parallel:
-    
-        .. image:: ../../images/manual_exceptions.png
-
-
-.. _manual.exceptions.multiple_errors:
-
-.. index:: signalling, interrupts, break, errors, exceptions, multiple errors
-    
-=====================
-Multiple Errors
-=====================
-    For any task where exceptions are thrown, *Ruffus* will continue executing all the jobs
-    currently in progress (up to the maximum number of concurrent jobs 
-    (``multiprocess``) set in :ref:`pipeline_run <pipeline_functions.pipeline_run>`). 
-    Each of these may raise separate exceptions.
-    This seems a fair tradeoff between being able to gather detailed error information for
-    running jobs, and not wasting too much time for a task that is going to fail anyway.
-
-
-.. index:: signalling, interrupts, break, errors, exceptions
-
-.. _manual.exceptions.interrupting:
-
-=================================
-Interrupting the pipeline
-=================================
-
-    If your task function raises a ``Ruffus.JobSignalledBreak`` Exception, this will immediately
-    halt the pipeline at that point, without waiting for other jobs in the queue to complete:
-    
-        ::
-        
-            from ruffus import *
-            @parallel([['A', 1], ['B',3]])
-            def parallel_task(name, param1):
-                if name == 'A': return False
-            
-            pipeline_run([parallel_task])
-        
-            
-
-    produces the following (abbreviated):
-
-        ::
-        
-            task.RethrownJobError:
-            
-                Exceptions running jobs for
-                'def parallel_task(...):'
-            
-                Original exception:
-            
-                Exception #1
-                task.JobSignalledBreak: Job = ["A", 1] returned False
-                for Job = ["A", 1]
-        
-    
diff --git a/doc/_build/html/_sources/tutorials/manual/files.txt b/doc/_build/html/_sources/tutorials/manual/files.txt
deleted file mode 100644
index ebf7746..0000000
--- a/doc/_build/html/_sources/tutorials/manual/files.txt
+++ /dev/null
@@ -1,218 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.files:
-
-#######################################################################################
-|manual.files.chapter_num|: `Passing parameters to the pipeline with` **@files**
-#######################################################################################
-    .. hlist::
-    
-       * :ref:`Manual overview <manual>` 
-       * :ref:`@files syntax in detail <decorators.files>`
-
-
-    | The python functions which do the actual work of each stage  or
-      :term:`task` of a **Ruffus** pipeline are written by you.
-    | The role of **Ruffus** is to make sure these functions are called in the right order, 
-      with the right parameters, running in parallel using multiprocessing if desired.
-
-    The easiest way to specify parameters to *Ruffus* :term:`task` functions is to use 
-    the :ref:`@files <decorators.files>` decorator.
-    
-    .. index:: 
-        pair: @files; Manual
-    
-
-***************************************
-**@files**
-***************************************
-    
-    Running this code:
-    
-        ::    
-    
-            from ruffus import *
-    
-            @files('a.1', ['a.2', 'b.2'], 'A file')
-            def single_job_io_task(infile, outfiles, text):
-                for o in outfiles: open(o, "w")
-            
-            # prepare input file
-            open('a.1', "w")
-            
-            pipeline_run()
-            
-        
-        Is equivalent to calling:
-            ::
-            
-                single_job_io_task('a.1', ['a.2', 'b.2'], 'A file')
-
-                
-        And produces:
-            ::
-            
-                >>> pipeline_run()
-                    Job = [a.1 -> [a.2, b.2], A file] completed
-                Completed Task = single_job_io_task
-
-    **Ruffus** will automatically check if your task is up to date. The second time :ref:`pipeline_run() <pipeline_functions.pipeline_run>`
-    is called, nothing will happen. But if you update ``a.1``, the task will rerun:
-    
-        ::
-        
-            >>> open('a.1', "w")
-            >>> pipeline_run()
-                Job = [a.1 -> [a.2, b.2], A file] completed
-            Completed Task = single_job_io_task
-    
-    See :ref:`chapter 2<manual.skip_up_to_date>` for a more in-depth discussion of how **Ruffus**
-    decides which parts of the pipeline are complete and up-to-date.
-
-
-.. index:: 
-    pair: @files; in parallel
-
-.. _manual.files.parallel:
-
-******************************************************************************
-Running the same code on different parameters in parallel
-******************************************************************************
-
-    Your pipeline may require the same function to be called multiple times on independent parameters.
-    In which case, you can supply all the parameters to @files, each will be sent to separate jobs that 
-    may run in parallel if necessary. **Ruffus** will check if each separate :term:`job` is up-to-date using
-    the *inputs* and *outputs* (first two) parameters (See the :ref:`chapter 2<manual.io_parameters>` ).
-
-
-    For example, if a sequence
-    (e.g. a list or tuple) of 5 parameters are passed to **@files**, that indicates
-    there will also be 5 separate jobs:
-
-        ::
-
-            from ruffus import *
-            parameters = [
-                                [ 'job1.file'           ],             # 1st job
-                                [ 'job2.file', 4        ],             # 2st job
-                                [ 'job3.file', [3, 2]   ],             # 3st job
-                                [ 67, [13, 'job4.file'] ],             # 4st job
-                                [ 'job5.file'           ],             # 5st job
-                          ]
-            @files(parameters)
-            def task_file(*params):
-                ""
-
-    | **Ruffus** creates as many jobs as there are elements in ``parameters``.
-    | In turn, each of these elements consist of series of parameters which will be
-      passed to each separate job.
-    
-    Thus the above code is equivalent to calling:
-    
-        ::
-        
-             task_file('job1.file')
-             task_file('job2.file', 4)
-             task_file('job3.file', [3, 2])   
-             task_file(67, [13, 'job4.file'])
-             task_file('job5.file')
-        
-        
-    What ``task_file()`` does with these parameters is up to you!
-    
-    The only constraint on the parameters is that **Ruffus** will treat any first 
-    parameter of each job as the *inputs* and any second as the *output*. Any
-    strings in the *inputs* or *output* parameters (including those nested in sequences)
-    will be treated as file names.
-
-    Thus, to pick the parameters out of one of the above jobs:
-        
-        ::
-        
-             task_file(67, [13, 'job4.file'])
-    
-        | *inputs*  == ``67``
-        | *outputs* == ``[13, 'job4.file']``
-        |
-        |   The solitary output filename is ``job4.file``
-        
-
-.. index:: 
-    pair: @files; check if up to date
-    
-.. _manual.files.is_uptodate:
-.. _manual.files.example:
-
-=======================================
-Checking if jobs are up to date
-=======================================
-
-    | Usually we do not want to run all the stages in a pipeline but only where
-      the input data has changed or is no longer up to date.
-    | One easy way to do this is to check the modification times for files produced
-      at each stage of the pipeline.
-
-    | Let us first create our starting files ``a.1`` and ``b.1``
-    | We can then run the following pipeline function to create
-    
-        * ``a.2`` from ``a.1`` and
-        * ``b.2`` from ``b.1``
-        
-        ::
-        
-            # create starting files
-            open("a.1", "w")
-            open("b.1", "w")
-            
-        
-            from ruffus import *
-            parameters = [
-                                [ 'a.1', 'a.2', 'A file'], # 1st job
-                                [ 'b.1', 'b.2', 'B file'], # 2nd job
-                          ]
-            
-            @files(parameters)
-            def parallel_io_task(infile, outfile, text):
-                # copy infile contents to outfile
-                infile_text = open(infile).read()
-                f = open(outfile, "w").write(infile_text + "\n" + text)
-            
-            pipeline_run()
-       
-        
-    .. ???
-
-    This produces the following output:
-        ::
-        
-            >>> pipeline_run()
-                Job = [a.1 -> a.2, A file] completed
-                Job = [b.1 -> b.2, B file] completed
-            Completed Task = parallel_io_task
-
-        
-    | If you called :ref:`pipeline_run() <pipeline_functions.pipeline_run>` again, nothing would happen because the files are up to date:
-    | ``a.2`` is more recent than ``a.1`` and
-    | ``b.2`` is more recent than ``b.1``
-    
-    However, if you subsequently modified ``a.1`` again:
-        ::
-        
-            open("a.1", "w")
-            pipeline_run(verbose = 1)
-            
-    you would see the following::
-    
-        >>> pipeline_run([parallel_io_task])
-        Task = parallel_io_task
-            Job = ["a.1" -> "a.2", "A file"] completed
-            Job = ["b.1" -> "b.2", "B file"] unnecessary: already up to date
-        Completed Task = parallel_io_task    
-        
-    The 2nd job is up to date and will be skipped.
-
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/files_re.txt b/doc/_build/html/_sources/tutorials/manual/files_re.txt
deleted file mode 100644
index 5d8a396..0000000
--- a/doc/_build/html/_sources/tutorials/manual/files_re.txt
+++ /dev/null
@@ -1,135 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.files_re:
-
-###############################################################################################################
-|manual.files_re.chapter_num|: **@files_re**: Deprecated `syntax using regular expressions`
-###############################################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>`
-        * :ref:`@files_re <decorators.files_re>` syntax in detail
-
-
-    .. index::
-        pair: @files_re; Manual
-
-
-
-
-***************************************
-**@files_re**
-***************************************
-
-    This is older, now deprecated syntax.
-
-    **@files_re** combines the functionality of @transform, @collate and @merge in
-    one overloaded decorator.
-
-    This is the reason why its use is discouraged. **@files_re** syntax is far too overloaded
-    and context-dependent to support its myriad of different functions.
-
-    The following documentation is provided to help maintain historical **ruffus** usage.
-
-=======================================
-Transforming input and output filenames
-=======================================
-
-
-    For example, the following code from |manual.transform.chapter_num| takes files from
-    the previous pipeline task, and makes new output parameters with the ``.sums`` suffix
-    in place of the ``.chunks`` suffix:
-
-        ::
-
-            @transform(step_4_split_numbers_into_chunks, suffix(".chunks"), ".sums")
-            def step_5_calculate_sum_of_squares (input_file_name, output_file_name):
-                #
-                #   calculate sums and sums of squares for all values in the input_file_name
-                #       writing to output_file_name
-                ""
-
-    This can be written using @files_re equivalently:
-
-        ::
-
-            @files_re(step_4_split_numbers_into_chunks, r".chunks", r".sums")
-            def step_5_calculate_sum_of_squares (input_file_name, output_file_name):
-            ""
-
-.. _manual.files_re.combine:
-.. index::
-    pair: combine; Manual
-
-=====================================================
-Collating many *inputs* into a single *output*
-=====================================================
-
-    Similarly, the following code from :ref:`|manual.collate.chapter_num| <manual.collate>` collects **inputs**
-    from the same species in the same directory:
-
-        ::
-
-            @collate('*.animals',                     # inputs = all *.animal files
-                        regex(r'mammals.([^.]+)'),    # regular expression
-                        r'\1/animals.in_my_zoo',      # single output file per species
-                        r'\1' )                       # species name
-            def capture_mammals(infiles, outfile, species):
-                # summarise all animals of this species
-                ""
-
-    This can be written using @files_re equivalently using the :ref:`combine<decorators.combine>` indicator:
-
-        ::
-
-            @files_re('*.animals',                           # inputs = all *.animal files
-                        r'mammals.([^.]+)',                  # regular expression
-                        combine(r'\1/animals.in_my_zoo'),    # single output file per species
-                        r'\1' )                              # species name
-            def capture_mammals(infiles, outfile, species):
-                # summarise all animals of this species
-                ""
-
-
-
-==============================================================================
-Generating *input* and *output* parameter using regular expresssions
-==============================================================================
-
-    The following code generates additional *Input* prerequisite file names which match the original *Input* files names.
-
-    We want each job of our ``analyse()`` function to get corresponding pairs
-    of ``xx.chunks`` and ``xx.red_indian`` files when
-
-        ``*.chunks`` are generated by the task function ``split_up_problem()`` and
-        ``*.red_indian`` are generated by the task function ``make_red_indians()``:
-
-        ::
-
-            @follows(make_red_indians)
-            @transform(split_up_problem,                # starting set of *inputs*
-                        regex(r"(.*).chunks"),          # regular expression
-                        inputs([r"\g<0>",               # xx.chunks
-                                r"\1.red_indian"]),     # important.file
-                         r"\1.results"                  # xx.results
-                          )
-            def analyse(input_filenames, output_file_name):
-                "Do analysis here"
-
-
-    The equivalent code using @files_re looks very similar:
-
-        ::
-
-            @follows(make_red_indians)
-            @files_re( split_up_problem,        # starting set of *inputs*
-                       r"(.*).chunks",          # regular expression
-                       [r"\g<0>",               # xx.chunks
-                        r"\1.red_indian"]),     # important.file
-                         r"\1.results")         # xx.results
-            def analyse(input_filenames, output_file_name):
-                "Do analysis here"
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/follows.txt b/doc/_build/html/_sources/tutorials/manual/follows.txt
deleted file mode 100644
index 7486f9b..0000000
--- a/doc/_build/html/_sources/tutorials/manual/follows.txt
+++ /dev/null
@@ -1,193 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.follows:
-
-#################################################################################################
-|manual.follows.chapter_num| : `Arranging tasks into a pipeline with` **@follows**
-#################################################################################################
-
-    * :ref:`Manual overview <manual>` 
-    * :ref:`@follows syntax in detail <decorators.follows>`
-    
-    .. index:: 
-        pair: @follows; Manual
-
-
-***************************************
-**@follows**
-***************************************
-
-    The order in which stages or :term:`task`\ s of a pipeline are arranged are set
-    explicitly by the :ref:`@follows(...) <decorators.follows>` python decorator:
-    
-        ::
-    
-            from ruffus import *
-            import sys
-            
-            def first_task():
-                print "First task"
-        
-            @follows(first_task)
-            def second_task():
-                print "Second task"
-        
-            @follows(second_task)
-            def final_task():
-                print "Final task"
-
-    
-    the ``@follows`` decorator indicate that the ``first_task`` function precedes ``second_task`` in 
-    the pipeline.
-
-
-.. note::
-
-    We shall see in :ref:`Chapter 2 <manual.tasks_as_input>` that the order of pipeline :term:`task`\ s can also be inferred implicitly 
-    for the following decorators
-
-        * :ref:`@split(...) <manual.split>`
-        * :ref:`@transform(...) <manual.transform>`
-        * :ref:`@merge(...) <manual.merge>`
-        * :ref:`@collate(...) <manual.collate>`
-
-.. index:: 
-    pair: pipeline_run; Manual
-
-=====================
-Running
-=====================
-
-    Now we can run the pipeline by:
-        ::
-            
-            pipeline_run([final_task])
-    
-    
-    Because ``final_task`` depends on ``second_task`` which depends on ``first_task`` , all 
-    three functions will be executed in order.
-    
-.. index:: 
-    pair: pipeline_printout_graph; Manual
-    pair: pipeline_printout; Manual
-
-    
-=====================
-Displaying
-=====================
-
-    We can see a flowchart of our fledgling pipeline by executing:
-        ::
-        
-            pipeline_printout_graph ( "manual_follows1.png",
-                                     "png",
-                                     [final_task], 
-                                     no_key_legend=True)
-        
-    producing the following flowchart
-    
-        .. image:: ../../images/manual_follows1.png
-        
-
-    or in text format with:
-        ::
-        
-            pipeline_printout(sys.stdout, [final_task])
-        
-    which produces the following:
-        ::
-        
-            Task = first_task
-            Task = second_task
-            Task = final_task
-
-    
-
-.. index:: 
-    pair: @follows; referring to functions before they are defined
-    pair: @follows; out of order
-.. _manual.follows.out_of_order:
-
-***************************************
-Defining pipeline tasks out of order
-***************************************
-
-    All this assumes that all your pipelined tasks are defined in order.
-    (``first_task`` before ``second_task`` before ``final_task``)
-    
-    | This is usually the most sensible way to arrange your code.
-
-    If you wish to refer to tasks which are not yet defined, you can do so by quoting the function name as a string:
-
-        ::
-        
-            @follows("second_task")
-            def final_task():
-                print "Final task"
-
-    You can refer to tasks (functions) in other modules, in which case the full 
-    qualified name must be used:
-
-        ::
-        
-            @follows("other_module.second_task")
-            def final_task():
-                print "Final task"
-    
-.. index:: 
-    pair: @follows; multiple dependencies
-    
-.. _manual.follows.multiple_dependencies:
-
-***************************************
-Multiple dependencies
-***************************************
-            
-    Each task can depend on more than one antecedent task.
-    
-    This can be indicated either by stacking ``@follows``:
-        ::
-        
-            @follows(first_task)
-            @follows("second_task")
-            def final_task():
-                ""
-    
-    
-    or in a more concise way:
-        ::
-        
-            @follows(first_task, "second_task")
-            def final_task():
-                ""
-    
-.. _manual.follows.mkdir:
-
-.. index:: 
-    single: @follows; mkdir (Manual)
-    single: mkdir; @follows (Manual)
-
-
-******************************************************************************
-Making directories automatically with :ref:`mkdir <decorators.mkdir>`
-******************************************************************************
-
-    A common prerequisite for any computational task, is making sure that the destination
-    directories exist. 
-
-    **Ruffus** provides special syntax to support this, using the special 
-    :ref:`mkdir <decorators.mkdir>` dependency. For example:
-
-        ::
-    
-            @follows(first_task, mkdir("output/results/here"))
-            def second_task():
-                print "Second task"
-            
-    will make sure that ``output/results/here`` exists before `second_task` is run.
-    
-    In other words, it will make the ``output/results/here`` directory if it does not exist.
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/jobs_limit.txt b/doc/_build/html/_sources/tutorials/manual/jobs_limit.txt
deleted file mode 100644
index 50822c6..0000000
--- a/doc/_build/html/_sources/tutorials/manual/jobs_limit.txt
+++ /dev/null
@@ -1,80 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.jobs_limit:
-
-####################################################################################################################
-|manual.jobs_limit.chapter_num|: `Manage concurrency for a specific task with` **@jobs_limit**
-####################################################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>` 
-        * :ref:`@jobs_limit <decorators.jobs_limit>` syntax in detail
-
-    .. index:: 
-        pair: @jobs_limit; Manual
-    
-
-=================
-**@jobs_limit**
-=================
-    
-    Calling :ref:`pipeline_run(multiprocess = NNN)<pipeline_functions.pipeline_run>` allows
-    multiple jobs (from multiple independent tasks) to be run in parallel. However, there
-    are some operations which consume so many resources that we might want them to run
-    with less or no concurrency.
-    
-    For example, we might want to download some files via FTP but the server restricts 
-    requests from each IP address. Even if the rest of the pipeline is running 100 jobs in
-    parallel, the FTP downloading must be restricted to 2 files at a time. We would really
-    like to keep the pipeline running as is, but let this one operation run either serially,
-    or with little concurrency.
-    
-
-    If setting ``multiprocess = NNN`` sets the pipeline-wide concurrency to ``NNN``, then
-    ``@jobs_limit(MMM)`` sets concurrency at a much finer level, at ``MMM`` just for jobs
-    in the indicated task.
-    
-    The optional name (e.g. ``@jobs_limit(3, "ftp_download_limit")``) allows the same limit to
-    be shared across multiple tasks. To be pedantic: a limit of ``3`` jobs at a time would be applied
-    across all tasks which have a ``@jobs_limit`` named ``"ftp_download_limit"``:
-
-        ::
-    
-            from ruffus import *
-            
-            # make list of 10 files
-            @split(None, "*stage1")
-            def make_files(input_file, output_files):
-                for i in range(10):
-                    if i < 5:
-                        open("%d.small_stage1" % i, "w")
-                    else:
-                        open("%d.big_stage1" % i, "w")
-                
-            @jobs_limit(3, "ftp_download_limit")
-            @transform(make_files, suffix(".small_stage1"), ".stage2")
-            def stage1_small(input_file, output_file):
-                open(output_file, "w")
-
-            @jobs_limit(3, "ftp_download_limit")
-            @transform(make_files, suffix(".big_stage1"), ".stage2")
-            def stage1_big(input_file, output_file):
-                open(output_file, "w")
-    
-            @jobs_limit(5)
-            @transform([stage1_small, stage1_big], suffix(".stage2"), ".stage3")
-            def stage2(input_file, output_file):
-                open(output_file, "w")
-
-            pipeline_run([stage2], multiprocess = 10)
-
-        will run the 10 jobs of ``stage1_big`` and ``stage1_small`` 3 at a time (highlighted in blue), 
-        a limit shared across the two tasks. ``stage2`` jobs run 5 at a time (in red). 
-        These limits override the numbers set in ``pipeline_run`` (``multiprocess = 10``):
-        
-            .. image:: ../../images/jobs_limit2.png
-        
-        
-
diff --git a/doc/_build/html/_sources/tutorials/manual/logging.txt b/doc/_build/html/_sources/tutorials/manual/logging.txt
deleted file mode 100644
index 49a69bd..0000000
--- a/doc/_build/html/_sources/tutorials/manual/logging.txt
+++ /dev/null
@@ -1,185 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.logging:
-
-###################################################################################################
-|manual.logging.chapter_num|: `Logging progress through a pipeline`
-###################################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>` 
-
-    
-    .. index:: 
-        pair: Logging; Manual
-    
-
-    There are two parts to logging with **Ruffus**:
-        
-    * Logging progress through the pipeline
-    
-        This produces the sort of output displayed in this manual:
-        
-        ::
-        
-            >>> pipeline_run([parallel_io_task])
-            Task = parallel_io_task
-                Job = ["a.1" -> "a.2", "A file"] completed
-                Job = ["b.1" -> "b.2", "B file"] unnecessary: already up to date
-            Completed Task = parallel_io_task    
-                
-    
-    * Logging your own messages from within your pipelined functions.
-    
-        Because **Ruffus** may run these in separate process (multiprocessing), some
-        attention has to be paid to how to send and synchronise your log messages
-        across process boundaries.
-        
-    
-    We shall deal with these in turn.
-
-
-.. _manual.logging.pipeline:
-
-=================================
-Logging task/job completion
-=================================
-    By default, *Ruffus* logs each task and each job as it is completed to
-    ``sys.stderr``. 
-    
-    :ref:`pipeline_run() <pipeline_functions.pipeline_run>`  includes an optional ``logger`` parameter which defaults to
-    ``stderr_logger``. Set this to ``black_hole_logger`` to turn off all tracking messages as
-    the pipeline runs:
-    
-        ::
-                
-            pipeline_run([pipelined_task], logger = black_hole_logger)
-            
-
-**********************************
-Controlling logging verbosity
-**********************************
-    :ref:`pipeline_run() <pipeline_functions.pipeline_run>` currently has five levels of verbosity, set by the optional ``verbose``
-    parameter which defaults to 1:
-    
-        ::
-        
-                verbose = 0: nothing
-                verbose = 1: logs completed jobs/tasks; 
-                verbose = 2: logs up to date jobs in incomplete tasks
-                verbose = 3: logs reason for running job
-                verbose = 4: logs messages useful only for debugging ruffus pipeline code
-
-
-        ``Verbose`` > 2 are intended for debugging **Ruffus** by the developers and the details
-        are liable to change from release to release
-
-    
-**********************************
-Using your own logging
-**********************************
-    You can specify your own logging by providing a log object  to :ref:`pipeline_run() <pipeline_functions.pipeline_run>` .
-    This log object should have ``debug()`` and ``info()`` methods.
-    
-    Instead of writing your own, it is usually more convenient to use the python
-    `logging <http://docs.python.org/library/logging.html>`_
-    module which provides logging classes with rich functionality. The following sets up
-    a logger to a rotating set of files:
-
-        ::
-    
-            import logging
-            import logging.handlers
-            
-            LOG_FILENAME = '/tmp/ruffus.log'
-            
-            # Set up a specific logger with our desired output level
-            my_ruffus_logger = logging.getLogger('My_Ruffus_logger')
-            my_ruffus_logger.setLevel(logging.DEBUG)
-            
-            # Add the log message handler to the logger
-            handler = logging.handlers.RotatingFileHandler(
-                          LOG_FILENAME, maxBytes=2000, backupCount=5)
-            
-            my_ruffus_logger.addHandler(handler)
-            
-            
-            from ruffus import *
-            
-            @files(None, "a.1")
-            def create_if_necessary(input_file, output_file):
-                """Description: Create the file if it does not exists"""
-                open(output_file, "w")
-            
-            pipeline_run([create_if_necessary], [create_if_necessary], logger=my_ruffus_logger)
-            print open("/tmp/ruffus.log").read()
-    
-
-    The contents of ``/tmp/ruffus.log`` are as specified:
-        ::
-    
-            Task = create_if_necessary
-                Description: Create the file if it does not exists
-                Job = [null -> "a.1"] completed
-    
-.. _manual.logging.per_job:
-
-=======================================
-Your own logging *within* each job
-=======================================
-
-    It is often useful to log the messages from within each of your pipelined functions.
-    
-    However, each job runs in a separate process, and it is *not* a good
-    idea to pass the logging object itself between jobs:
-    
-    #. logging is not synchronised between processes
-    #. `logging <http://docs.python.org/library/logging.html>`_ objects can not be 
-       `pickle <http://docs.python.org/library/pickle.html>`_\ d and sent across processes
-        
-    The best thing to do is to have a centralised log and to have each job invoke the
-    logging methods (e.g. `debug`, `warning`, `info` etc.) across the process boundaries in
-    the centralised log.
-    
-    The **Ruffus** :ref:`proxy_logger <proxy-logger>` module provides an easy way to share 
-    `logging <http://docs.python.org/library/logging.html>`_ objects among
-    jobs. This requires just two simple steps:
-
-    .. note::    
-        :ref:`The full code <manual.logging_code>` shows how this can be coded.
-    
-    
-    
-****************************************
-    1. Set up log from config file
-****************************************
-    ::
-    
-        from ruffus.proxy_logger import *
-        (logger_proxy, 
-         logging_mutex) = make_shared_logger_and_proxy (setup_std_shared_logger, 
-                                                        "my_logger", 
-                                                        {"file_name" :"/my/lg.log"})
-                                                        
-****************************************
-    2. Give each job proxy to logger
-****************************************
-        Now, pass:
-        
-            * ``logger_proxy`` (which forwards logging calls across jobs) and
-            * ``logging_mutex`` (which prevents different jobs which are logging simultaneously 
-              from being jumbled up) 
-            
-        to each job::
-    
-            @files(None, 'a.1', logger_proxy, logging_mutex)
-            def task1(ignore_infile, outfile, logger_proxy, logging_mutex):
-                """
-                Log within task
-                """
-                open(outfile, "w").write("Here we go")
-                with logging_mutex:
-                    logger_proxy.info("Here we go logging")
-
diff --git a/doc/_build/html/_sources/tutorials/manual/logging_code.txt b/doc/_build/html/_sources/tutorials/manual/logging_code.txt
deleted file mode 100644
index 31ad70b..0000000
--- a/doc/_build/html/_sources/tutorials/manual/logging_code.txt
+++ /dev/null
@@ -1,187 +0,0 @@
-.. include:: ../../global.inc
-.. _manual.logging_code:
-
-########################################################################################
-Code for Chapter 16: Logging progress through a pipeline
-########################################################################################
-    * :ref:`Manual overview <manual>` 
-    * :ref:`Back <manual.logging.per_job>` 
-
-    This example shows how to log messages from within each of your pipelined functions.
-              
-    
-************************************
-Code
-************************************
-    ::
-
-        
-        from ruffus import *
-        from ruffus.proxy_logger import *
-        import logging
-        
-        import sys,os
-        # use simplejson in place of json for python < 2.6
-        try:
-            import json
-        except ImportError:
-            import simplejson
-            json = simplejson
-        
-            
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #   Shared logging
-        
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        logger_args={}
-        logger_args["file_name"] = "pipeline.log"
-        logger_args["level"] = logging.DEBUG
-        logger_args["rotating"] = True
-        logger_args["maxBytes"]=20000
-        logger_args["backupCount"]=10
-        logger_args["formatter"]="%(asctime)s - %(name)s - %(levelname)6s - %(message)s"
-    
-        (logger_proxy, 
-         logging_mutex) = make_shared_logger_and_proxy (setup_std_shared_logger, 
-                                                        "my_logger", logger_args)
-    
-        
-        
-            
-            
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #   Helper Function which writes to a shared log
-        
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        import time
-        def test_job_io(infiles, outfiles, extra_params):
-            """
-            cat input files content to output files
-                after writing out job parameters
-            """
-            #
-            # dump parameters
-            params = (infiles, outfiles)# + extra_params[0:-3]
-            #
-            logger_proxy, logging_mutex = extra_params
-            with logging_mutex:
-                logger_proxy.debug("job = %s, process name = %s" % 
-                                    (json.dumps(params),
-                                        multiprocessing.current_process().name))
-            #
-            #
-            sys.stdout.write('    job = %s\n' % json.dumps(params))
-            #
-            if isinstance(infiles, str):
-                infiles = [infiles]
-            elif infiles == None:
-                infiles = []
-            if isinstance(outfiles, str):
-                outfiles = [outfiles]
-            output_text = list()
-            for f in infiles:
-                output_text.append(open(f).read())
-            output_text = "".join(sorted(output_text))
-            output_text += json.dumps(infiles) + " -> " + json.dumps(outfiles) + "\n"
-            for f in outfiles:
-                open(f, "w").write(output_text)
-        
-            
-        
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #   Tasks
-        
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #
-        #    task1
-        #
-        @files(None, 'a.1', logger_proxy, logging_mutex)
-        def task1(infiles, outfiles, *extra_params):
-            """
-            First task
-            """
-            test_job_io(infiles, outfiles, extra_params)
-        
-        
-        
-        #
-        #    task2
-        #
-        @transform(task1, regex('.1'), '.2', logger_proxy, logging_mutex)
-        def task2(infiles, outfiles, *extra_params):
-            """
-            Second task
-            """
-            test_job_io(infiles, outfiles, extra_params)
-        
-        
-        
-        #
-        #    task3
-        #
-        @transform(task2, regex('.2'), '.3', logger_proxy, logging_mutex)
-        def task3(infiles, outfiles, *extra_params):
-            """
-            Third task
-            """
-            test_job_io(infiles, outfiles, extra_params)
-        
-        
-        
-        #
-        #    task4
-        #
-        @transform(task3, regex('.3'), '.4', logger_proxy, logging_mutex)
-        def task4(infiles, outfiles, *extra_params):
-            """
-            Fourth task
-            """
-            test_job_io(infiles, outfiles, extra_params)
-        
-
-        # 
-        #   Necessary to protect the "entry point" of the program under windows.
-        #       see: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming
-        #
-        pipeline_run([task4], multiprocess = 10, logger = logger_proxy)
-            
-
-************************************
-Resulting Output
-************************************
-    ::
-    
-        >>> pipeline_run([task4], multiprocess = 10, logger = logger_proxy)
-            job = [null, "a.1"]
-            job = ["a.1", "a.2"]
-            job = ["a.2", "a.3"]
-            job = ["a.3", "a.4"]
-
-    Pipeline.log will contain our unimaginative log messages:
-    
-    ::
-
-        2009-11-15 03:04:55,884 - my_logger -  DEBUG - job = [null, "a.1"], process name = PoolWorker-2
-        2009-11-15 03:04:56,941 - my_logger -   INFO -     Job = [None -> a.1, <LoggingProxy>, <thread.lock>] completed
-        2009-11-15 03:04:56,942 - my_logger -   INFO - Completed Task = task1
-        2009-11-15 03:04:56,945 - my_logger -  DEBUG - job = ["a.1", "a.2"], process name = PoolWorker-4
-        2009-11-15 03:04:57,962 - my_logger -   INFO -     Job = [a.1 -> a.2, <LoggingProxy>, <thread.lock>] completed
-        2009-11-15 03:04:57,962 - my_logger -   INFO - Completed Task = task2
-        2009-11-15 03:04:57,965 - my_logger -  DEBUG - job = ["a.2", "a.3"], process name = PoolWorker-3
-        2009-11-15 03:04:59,009 - my_logger -   INFO -     Job = [a.2 -> a.3, <LoggingProxy>, <thread.lock>] completed
-        2009-11-15 03:04:59,010 - my_logger -   INFO - Completed Task = task3
-        2009-11-15 03:04:59,013 - my_logger -  DEBUG - job = ["a.3", "a.4"], process name = PoolWorker-5
-        2009-11-15 03:05:00,024 - my_logger -   INFO -     Job = [a.3 -> a.4, <LoggingProxy>, <thread.lock>] completed
-        2009-11-15 03:05:00,025 - my_logger -   INFO - Completed Task = task4
-
diff --git a/doc/_build/html/_sources/tutorials/manual/manual_code.txt b/doc/_build/html/_sources/tutorials/manual/manual_code.txt
deleted file mode 100644
index 084d016..0000000
--- a/doc/_build/html/_sources/tutorials/manual/manual_code.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-.. include:: ../../global.inc
-.. _Manual_code:
-
-
-############################################################
-Code for the manual tutorial
-############################################################
-
-    * :ref:`The **Ruffus** manual<manual.introduction>`
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/manual_contents.txt b/doc/_build/html/_sources/tutorials/manual/manual_contents.txt
deleted file mode 100644
index 737919f..0000000
--- a/doc/_build/html/_sources/tutorials/manual/manual_contents.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-.. include:: ../../global.inc
-.. _manual:
-
-####################################################################
-**Ruffus** Manual: Table of Contents:
-####################################################################
-
-    :ref:`manual_introduction <manual.introduction>`
-
-    #) :ref:`follows <manual.follows>`
-    #) :ref:`tasks_as_recipes <manual.tasks_as_recipes>`
-    #) :ref:`files <manual.files>`
-    #) :ref:`tasks_and_globs_in_inputs <manual.tasks_and_globs_in_inputs>`
-    #) :ref:`tracing_pipeline_parameters <manual.tracing_pipeline_parameters>`
-    #) :ref:`parallel_processing <manual.multiprocessing>`
-    #) :ref:`split <manual.split>`
-    #) :ref:`transform <manual.transform>`
-    #) :ref:`merge <manual.merge>`
-    #) :ref:`posttask <manual.posttask>`
-    #) :ref:`jobs_limit <manual.jobs_limit>`
-    #) :ref:`dependencies <manual.dependencies>`
-    #) :ref:`onthefly <manual.on_the_fly>`
-    #) :ref:`collate <manual.collate>`
-    #) :ref:`advanced_transform <manual.advanced_transform>`
-    #) :ref:`parallel <manual.parallel>`
-    #) :ref:`check_if_uptodate <manual.check_if_uptodate>`
-    #) :ref:`exceptions <manual.exceptions>`
-    #) :ref:`logging <manual.logging>`
-    #) :ref:`files_re <manual.files_re>`
-
diff --git a/doc/_build/html/_sources/tutorials/manual/manual_introduction.txt b/doc/_build/html/_sources/tutorials/manual/manual_introduction.txt
deleted file mode 100644
index ea58a1a..0000000
--- a/doc/_build/html/_sources/tutorials/manual/manual_introduction.txt
+++ /dev/null
@@ -1,224 +0,0 @@
-.. include:: ../../global.inc
-.. _manual.introduction:
-
-.. index::
-    pair: manual; introduction
-
-
-####################################################################
-**Ruffus** Manual
-####################################################################
-
-| The chapters of this manual go through each of the features of **Ruffus** in turn.
-| Some of these (especially those labelled **esoteric** or **deprecated**) may not
-  be of interest to all users of **Ruffus**.
-
-If you are looking for a quick introduction to **Ruffus**, you may want to look at the
-:ref:`Simple Tutorial <Simple_Tutorial>` first, some of which content is shared with,
-or elaborated on, by this manual.
-
-
-***************************************
-Introduction
-***************************************
-
-    The **Ruffus** module is a lightweight way to run computational pipelines.
-
-    Computational pipelines often become quite simple
-    if we breakdown the process into simple stages.
-
-    .. note::
-
-        Ruffus refers to each stage of your pipeline as a :term:`task`.
-
-    | Let us start with the usual "Hello World".
-    | We have the following two python functions which
-      we would like to turn into an automatic pipeline:
-
-
-        .. image:: ../../images/simple_tutorial_hello_world.png
-
-    .. ::
-
-        ::
-
-            def first_task():
-                print "Hello "
-
-            def second_task():
-                print "world"
-
-
-    The simplest **Ruffus** pipeline would look like this:
-
-        .. image:: ../../images/simple_tutorial_intro_follows.png
-
-    .. ::
-
-        ::
-
-            from ruffus import *
-
-            def first_task():
-                print "Hello "
-
-            @follows(first_task)
-            def second_task():
-                print "world"
-
-            pipeline_run([second_task])
-
-
-    The functions which do the actual work of each stage of the pipeline remain unchanged.
-    The role of **Ruffus** is to make sure these functions are called in the right order,
-    with the right parameters, running in parallel using multiprocessing if desired.
-
-    There are three simple parts to building a **ruffus** pipeline
-
-        #. importing ruffus
-        #. "Decorating" functions which are part of the pipeline
-        #. Running the pipeline!
-
-.. _manual.introduction.import:
-
-.. index::
-    single: importing ruffus
-
-
-****************************
-Importing ruffus
-****************************
-
-    The most convenient way to use ruffus is to import the various names directly:
-
-        ::
-
-            from ruffus import *
-
-    This will allow **ruffus** terms to be used directly in your code. This is also
-    the style we have adopted for this manual.
-
-    .. csv-table::
-       :header: "Category", "Terms"
-       :stub-columns: 1
-
-       "*Pipeline functions*", "
-       ::
-
-         pipeline_printout
-         pipeline_printout_graph
-         pipeline_run
-         register_cleanup"
-       "*Decorators*", "
-       ::
-
-        @follows
-        @files
-        @split
-        @transform
-        @merge
-        @collate
-        @posttask
-        @jobs_limit
-        @parallel
-        @check_if_uptodate
-        @files_re"
-       "*Loggers*", "
-       ::
-
-         stderr_logger
-         black_hole_logger"
-       "*Parameter disambiguating Indicators*", "
-       ::
-
-         suffix
-         regex
-         inputs
-         touch_file
-         combine
-         mkdir
-         output_from"
-
-If any of these clash with names in your code, you can use qualified names instead:
-        ::
-
-            import ruffus
-
-            ruffus.pipeline_printout("...")
-
-
-.. index::
-    pair: decorators; Manual
-
-.. _manual.introduction.decorators:
-
-****************************
-"Decorating" functions
-****************************
-
-    You need to tag or :term:`decorator` existing code to tell **Ruffus** that they are part
-    of the pipeline.
-
-    .. note::
-
-        :term:`decorator`\ s are ways to tag or mark out functions.
-
-        They start with an ``@`` prefix and take a number of parameters in parenthesis.
-
-        .. image:: ../../images/simple_tutorial_decorator_syntax.png
-
-    The **ruffus** decorator :ref:`@follows <decorators.follows>` makes sure that
-    ``second_task`` follows ``first_task``.
-
-
-    | Multiple :term:`decorator`\ s can be used for each :term:`task` function to add functionality
-      to *Ruffus* pipeline functions.
-    | However, the decorated python functions can still be
-      called normally, outside of *Ruffus*.
-    | *Ruffus* :term:`decorator`\ s can be added to (stacked on top of) any function in any order.
-
-    * :ref:`More on @follows in |manual.follows.chapter_num| <manual.follows>`
-    * :ref:`@follows syntax in detail <decorators.follows>`
-
-.. index::
-    pair: Running the pipeline; Manual
-    pair: pipeline_run; Manual
-
-.. _manual.introduction.running_pipeline:
-
-****************************
-Running the pipeline
-****************************
-
-    We run the pipeline by specifying the **last** stage (:term:`task` function) of your pipeline.
-    Ruffus will know what other functions this depends on, following the appropriate chain of
-    dependencies automatically, making sure that the entire pipeline is up-to-date.
-
-    In our example above, because ``second_task`` depends on ``first_task``, both functions are executed in order.
-
-        ::
-
-            >>> pipeline_run([second_task], verbose = 1)
-
-    **Ruffus** by default prints out the ``verbose`` progress through your pipeline,
-    interleaved with our ``Hello`` and ``World``.
-
-        .. image:: ../../images/simple_tutorial_hello_world_output.png
-
-    .. ::
-
-        ::
-
-            >>> pipeline_run([second_task], verbose = 1)
-            Start Task = first_task
-            Hello
-                Job completed
-            Completed Task = first_task
-            Start Task = second_task
-            world
-                Job completed
-            Completed Task = second_task
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/merge.txt b/doc/_build/html/_sources/tutorials/manual/merge.txt
deleted file mode 100644
index 8dd0227..0000000
--- a/doc/_build/html/_sources/tutorials/manual/merge.txt
+++ /dev/null
@@ -1,102 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.merge:
-
-#########################################################################################
-|manual.merge.chapter_num|: **Merge** `multiple input into a single result`
-#########################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>` 
-        * :ref:`@merge <decorators.merge>` syntax in detail
-
-    At the conclusion of our pipeline, or at key selected points, we might need a 
-    summary of our progress, gathering data from a multitude of files or disparate *inputs*, 
-    and summarised in the *output*  of a single :term:`job`.
-    
-    *Ruffus* uses the :ref:`@merge <decorators.merge>` decorator for this purpose.
-    
-    Although, **@merge** tasks multiple *inputs* and produces a single *output*, **Ruffus**
-    is again agnostic as to the sort of data contained within *output*. It can be a single
-    (string) file name, or an arbitrary complicated nested structure with numbers, objects etc.
-    As always, strings contained (even with nested sequences) within *output* will be treated
-    as file names for the purpose of checking if the :term:`task` is up-to-date.
-    
-    .. index:: 
-        pair: @merge; Manual
-    
-
-=================
-**@merge**
-=================
-
-This example is borrowed from :ref:`step 6 <Simple_Tutorial_6th_step>` of the simple tutorial.
-
-    .. note:: :ref:`Accompanying Python Code  <Simple_Tutorial_6th_step_code>` 
-
-**************************************************************************************
-Combining partial solutions: Calculating variances
-**************************************************************************************
-
-    .. csv-table:: 
-        :widths: 1,99
-        :class: borderless
-
-        ".. centered::
-            Step 6 from:
-
-        .. image:: ../../images/simple_tutorial_step5_sans_key.png", "
-            We wanted to calculate the sample variance of a large list of random numbers. We                                 
-            have seen previously how we can split up this large problem into small pieces                                      
-            (using :ref:`@split <manual.split>` in |manual.split.chapter_num|), and work out the                                        
-            partial solutions for each sub-problem (calculating sums with :ref:`@transform<manual.transform>`
-            in |manual.transform.chapter_num| ).                                                                          
-                                                                                                                             
-            All that remains is to join up the partial solutions from the different ``.sums`` files                          
-            and turn these into the variance as follows::                                                                    
-                                                                                                                             
-                variance = (sum_squared - sum * sum / N)/N                                                                   
-                                                                                                                             
-            where ``N`` is the number of values                                                                              
-                                                                                                                             
-            See the `wikipedia <http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance>`_ entry for a discussion of
-            why this is a very naive approach!"
-
-    
-    
-    To do this, all we have to do is go through all the values in ``*.sums``, i.e.
-    add up the ``sums`` and ``sum_squared`` for each chunk. We can then apply the above (naive) formula.
-    
-    Merging files is straightforward in **Ruffus**:
-        ::
-
-            @merge(step_5_calculate_sum_of_squares, "variance.result")
-            def step_6_calculate_variance (input_file_names, output_file_name):
-                #
-                #   add together sums and sums of squares from each input_file_name
-                #       calculate variance and write to output_file_name
-                ""
-
-
-    The :ref:`@merge <decorators.merge>` decorator tells *Ruffus* to take all the files from the step 5 task (i.e. ``*.sums``),
-    and produced a merge file in the form of ``variance.result``.
-    
-    Thus if ``step_5_calculate_sum_of_squares`` created
-        | ``1.sums`` and 
-        | ``2.sums`` etc.
-        
-    This would result in the following function call:
-    
-        ::
-        
-            step_6_calculate_variance (["1.sums", "2.sums"], "variance.result")
-            
-
-    The final result is, of course, in ``variance.result``.
-            
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/onthefly.txt b/doc/_build/html/_sources/tutorials/manual/onthefly.txt
deleted file mode 100644
index 75f32d7..0000000
--- a/doc/_build/html/_sources/tutorials/manual/onthefly.txt
+++ /dev/null
@@ -1,138 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.on_the_fly:
-
-#######################################################################################################
-|manual.on_the_fly.chapter_num|: `Generating parameters on the fly with` **@files**
-#######################################################################################################
-    .. hlist::
-    
-       * :ref:`Manual overview <manual>` 
-       * :ref:`@files on-the-fly syntax in detail <decorators.files_on_the_fly>`
-
-    | Sometimes, it is necessary, or perhaps more convenient, to generate parameters on the fly or
-      at runtime. 
-    | This  powerful ability to generate the exact parameters you need is 
-      sometimes worth the slight increase in complexity.
-
-    .. index:: 
-        pair: @files; Tutorial on-the-fly parameter generation
-
-    
-***********************
-**@files**
-***********************
-    To generate parameters on the fly, pass the decorator **files** with a :term:`generator` function which 
-    yields one list / tuple of parameters per job. For example::
-    
-        from ruffus import *
-        def generate_parameters_on_the_fly():
-            """
-            returns one list of parameters per job
-            """
-            parameters = [
-                                ['A.input', 'A.output', (1, 2)], # 1st job
-                                ['B.input', 'B.output', (3, 4)], # 2nd job
-                                ['C.input', 'C.output', (5, 6)], # 3rd job
-                            ]
-            for job_parameters in parameters:
-                yield job_parameters
-        
-        @files(generate_parameters_on_the_fly)
-        def pipeline_task(input, output, extra):
-            open(output, "w").write(open(input).read())
-            sys.stderr.write("%d + %d => %d\n" % (extra[0] , extra[1], extra[0] + extra[1]))
-        
-        pipeline_run([pipeline_task])
-        
-        
-    .. ???
-
-    Produces::
-   
-        Task = parallel_task
-            1 + 2 = 3
-            Job = ["A", 1, 2] completed
-            3 + 4 = 7
-            Job = ["B", 3, 4] completed
-            5 + 6 = 11
-            Job = ["C", 5, 6] completed
-    
-        
-    .. note::
-    
-        Be aware that the parameter generating function may be invoked 
-        :ref:`more than once<manual.dependencies.checking_multiple_times>`:
-            
-            | The first time to check if this part of the pipeline is up-to-date.
-            | The second time when the pipeline task function is run.
-
-    The resulting *inputs*, *outputs* and any additional extra parameters per job are
-    treated normally for the purposes of checking to see if jobs are up-to-date and
-    need to be re-run.
-    
-
-**********************************************
- Permutations and Combinations
-**********************************************
-
-    The :ref:`accompanying example<manual.on_the_fly_code>` provides a more realistic reason why
-    you would want to generate parameters on the fly. It is a fun piece of code, which generates
-    N x M combinations from two sets of files as the *inputs* of a pipeline stage.
-
-    The *inputs* / *outputs* filenames are generated as a pair of nested for-loops to produce
-    the N (outside loop) x M (inside loop) combinations, with the appropriate parameters
-    for each job ``yield``\ed per iteration of the inner loop. The gist of this is:
-
-        ::
-        
-            #_________________________________________________________________________________________
-            #
-            #   Step 1:
-            #       
-            #        N x M jobs
-            #_________________________________________________________________________________________
-            def generate_simulation_params ():
-                """
-                Custom function to generate 
-                file names for gene/gwas simulation study
-                """
-                for sim_file in get_simulation_files():
-                    for (gene, gwas) in get_gene_gwas_file_pairs():
-                        result_file = "%s.%s.results" % (gene, sim_file)
-                        yield (gene, gwas, sim_file), result_file
-            
-    
-    
-            @files(generate_simulation_params)
-            def gwas_simulation(input_files, output_file):
-                "..."
-                                                     
-        If ``get_gene_gwas_file_pairs()`` produces:
-            ::
-            
-                ['a.sim', 'b.sim', 'c.sim']
-                
-        and ``get_gene_gwas_file_pairs()`` produces:
-            ::
-            
-                [('1.gene', '1.gwas'), ('2.gene', '2.gwas')]
-                
-        then we would end up with ``3`` x ``2`` = ``6`` jobs and the following equivalent function calls:
-        
-            ::
-            
-                gwas_simulation(('1.gene', '1.gwas', 'a.sim'), "1.gene.a.sim.results")                
-                gwas_simulation(('2.gene', '2.gwas', 'a.sim'), "2.gene.a.sim.results")                
-                gwas_simulation(('1.gene', '1.gwas', 'b.sim'), "1.gene.b.sim.results")                
-                gwas_simulation(('2.gene', '2.gwas', 'b.sim'), "2.gene.b.sim.results")                
-                gwas_simulation(('1.gene', '1.gwas', 'c.sim'), "1.gene.c.sim.results")                
-                gwas_simulation(('2.gene', '2.gwas', 'c.sim'), "2.gene.c.sim.results")                
-
-
-    The :ref:`accompanying code<manual.on_the_fly_code>` looks slightly more complicated because
-    of some extra bookkeeping.
-    
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/onthefly_code.txt b/doc/_build/html/_sources/tutorials/manual/onthefly_code.txt
deleted file mode 100644
index 2b10d0c..0000000
--- a/doc/_build/html/_sources/tutorials/manual/onthefly_code.txt
+++ /dev/null
@@ -1,320 +0,0 @@
-.. include:: ../../global.inc
-.. _manual.on_the_fly_code:
-
-###################################################################
-Code for Chapter 10: Generating parameters on the fly
-###################################################################
-    * :ref:`Manual overview <manual>` 
-    * :ref:`@files on-the-fly syntax in detail <decorators.files_on_the_fly>`
-    * :ref:`Back <manual.on_the_fly>` 
-
-
-    | This script takes N pairs of input file pairs (with the suffices .gene and .gwas)
-    | and runs them against M sets of simulation data (with the suffix .simulation)
-    | A summary per input file pair is then produced
-              
-    
-    In pseudo-code:
-        
-        STEP_1:
-        
-        ::
-        
-            for n_file in NNN_pairs_of_input_files:
-                for m_file in MMM_simulation_data:
-        
-                    [n_file.gene,
-                     n_file.gwas,
-                     m_file.simulation] -> n_file.m_file.simulation_res
-                     
-    
-        STEP_2:
-        
-        ::
-        
-            for n_file in NNN_pairs_of_input_files:
-                
-                n_file.*.simulation_res -> n_file.mean
-            
-    
-        | n = CNT_GENE_GWAS_FILES
-        | m = CNT_SIMULATION_FILES
-            
-************************************
-Code
-************************************
-    ::
-
-        from ruffus import *
-        import os
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #   constants
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        working_dir             = "temp_NxM"
-        simulation_data_dir     = os.path.join(working_dir, "simulation")
-        gene_data_dir           = os.path.join(working_dir, "gene")
-        CNT_GENE_GWAS_FILES     = 2
-        CNT_SIMULATION_FILES    = 3
-        
-
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #   imports        
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        import os, sys
-        from itertools import izip
-        import glob
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #   Functions
-        
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #_________________________________________________________________________________________
-        #
-        #   get gene gwas file pairs
-        #
-        #_________________________________________________________________________________________
-        def get_gene_gwas_file_pairs(  ):
-            """
-            Helper function to get all *.gene, *.gwas from the direction specified
-                in --gene_data_dir
-                
-            Returns 
-                file pairs with both .gene and .gwas extensions, 
-                corresponding roots (no extension) of each file
-            """
-            gene_files = glob.glob(os.path.join(gene_data_dir, "*.gene"))
-            gwas_files = glob.glob(os.path.join(gene_data_dir, "*.gwas"))
-            #
-            common_roots = set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gene_files))
-            common_roots &=set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gwas_files))
-            common_roots = list(common_roots)
-            #    
-            p = os.path; g_dir = gene_data_dir
-            file_pairs = [[p.join(g_dir, x + ".gene"), p.join(g_dir, x + ".gwas")] for x in common_roots]
-            return file_pairs, common_roots
-        
-        #_________________________________________________________________________________________
-        #
-        #   get simulation files
-        #
-        #_________________________________________________________________________________________
-        def get_simulation_files(  ):
-            """
-            Helper function to get all *.simulation from the direction specified
-                in --simulation_data_dir
-                Returns 
-                    file with .simulation extensions, 
-                    corresponding roots (no extension) of each file
-            """
-            simulation_files = glob.glob(os.path.join(simulation_data_dir, "*.simulation"))
-            simulation_roots =map(lambda x: os.path.splitext(os.path.split(x)[1])[0], simulation_files)
-            return simulation_files, simulation_roots
-        
-        
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        #   Main logic
-        
-        
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        
-        
-        
-        
-        
-        
-        
-        #_________________________________________________________________________________________
-        # 
-        #   setup_simulation_data
-        # 
-        #_________________________________________________________________________________________
-        
-        # 
-        # mkdir: makes sure output directories exist before task    
-        #
-        @follows(mkdir(gene_data_dir, simulation_data_dir))
-        def setup_simulation_data ():
-            """
-            create simulation files
-            """
-            for i in range(CNT_GENE_GWAS_FILES):
-                open(os.path.join(gene_data_dir, "%03d.gene" % i), "w")
-                open(os.path.join(gene_data_dir, "%03d.gwas" % i), "w")
-            #
-            # gene files without corresponding gwas and vice versa
-            open(os.path.join(gene_data_dir, "orphan1.gene"), "w")
-            open(os.path.join(gene_data_dir, "orphan2.gwas"), "w")
-            open(os.path.join(gene_data_dir, "orphan3.gwas"), "w")
-            #
-            for i in range(CNT_SIMULATION_FILES):
-                open(os.path.join(simulation_data_dir, "%03d.simulation" % i), "w")
-        
-        
-        
-        
-        #_________________________________________________________________________________________
-        # 
-        #   cleanup_simulation_data
-        # 
-        #_________________________________________________________________________________________
-        def try_rmdir (d):
-            if os.path.exists(d):
-                try:    
-                    os.rmdir(d)
-                except OSError:
-                    sys.stderr.write("Warning:\t%s is not empty and will not be removed.\n" % d)
-
-        
-
-        def cleanup_simulation_data ():
-            """
-            cleanup files
-            """
-            sys.stderr.write("Cleanup working directory and simulation files.\n")
-            #   
-            #   cleanup gene and gwas files
-            # 
-            for f in glob.glob(os.path.join(gene_data_dir, "*.gene")):
-                os.unlink(f)
-            for f in glob.glob(os.path.join(gene_data_dir, "*.gwas")):
-                os.unlink(f)
-            try_rmdir(gene_data_dir)
-            #   
-            #   cleanup simulation
-            # 
-            for f in glob.glob(os.path.join(simulation_data_dir, "*.simulation")):
-                os.unlink(f)
-            try_rmdir(simulation_data_dir)
-            #   
-            #   cleanup working_dir
-            # 
-            for f in glob.glob(os.path.join(working_dir, "simulation_results", "*.simulation_res")):
-                os.unlink(f)
-            try_rmdir(os.path.join(working_dir, "simulation_results"))
-            #
-            for f in glob.glob(os.path.join(working_dir, "*.mean")):
-                os.unlink(f)
-            try_rmdir(working_dir)
-        
-        
-        #_________________________________________________________________________________________
-        #
-        #   Step 1:
-        #       
-        #        for n_file in NNN_pairs_of_input_files:
-        #            for m_file in MMM_simulation_data:
-        #
-        #                [n_file.gene,
-        #                 n_file.gwas,
-        #                 m_file.simulation] -> working_dir/n_file.m_file.simulation_res
-        #
-        #_________________________________________________________________________________________
-        def generate_simulation_params ():
-            """
-            Custom function to generate 
-            file names for gene/gwas simulation study
-            """
-            simulation_files, simulation_file_roots    = get_simulation_files()
-            gene_gwas_file_pairs, gene_gwas_file_roots =  get_gene_gwas_file_pairs()
-            #
-            for sim_file, sim_file_root in izip(simulation_files, simulation_file_roots):
-                for (gene, gwas), gene_file_root in izip(gene_gwas_file_pairs, gene_gwas_file_roots):
-                    #
-                    result_file = "%s.%s.simulation_res" % (gene_file_root, sim_file_root)
-                    result_file_path = os.path.join(working_dir, "simulation_results", result_file)
-                    #
-                    yield [gene, gwas, sim_file], result_file_path, gene_file_root, sim_file_root, result_file
-        
-
-
-        # 
-        # mkdir: makes sure output directories exist before task    
-        #
-        @follows(mkdir(working_dir, os.path.join(working_dir, "simulation_results")))
-        @files(generate_simulation_params)
-        def gwas_simulation(input_files, result_file_path, gene_file_root, sim_file_root, result_file):
-            """
-            Dummy calculation of gene gwas vs simulation data
-            Normally runs in parallel on a computational cluster       
-            """
-            (gene_file,
-            gwas_file,
-            simulation_data_file) = input_files
-            #
-            simulation_res_file = open(result_file_path, "w")
-            simulation_res_file.write("%s + %s -> %s\n" % (gene_file_root, sim_file_root, result_file))
-        
-        
-        #_________________________________________________________________________________________
-        #
-        #   Step 2:
-        #       
-        #       Statistical summary per gene/gwas file pair
-        # 
-        #        for n_file in NNN_pairs_of_input_files:
-        #            working_dir/simulation_results/n.*.simulation_res
-        #               -> working_dir/n.mean
-        #       
-        #_________________________________________________________________________________________
-        
-        
-        @collate(gwas_simulation, regex(r"simulation_results/(\d+).\d+.simulation_res"), r"\1.mean")
-        @posttask(lambda : sys.stdout.write("\nOK\n"))
-        def statistical_summary (result_files, summary_file):
-            """
-            Simulate statistical summary
-            """
-            summary_file = open(summary_file, "w")
-            for f in result_files:
-                summary_file.write(open(f).read())
-        
-        
-        
-        pipeline_run([setup_simulation_data], multiprocess = 5, verbose = 2)
-        pipeline_run([statistical_summary], multiprocess = 5, verbose = 2)
-        
-        # uncomment to printout flowchar
-        #
-        # pipeline_printout(sys.stdout, [statistical_summary], verbose=2)
-        # graph_printout ("flowchart.jpg", "jpg", [statistical_summary])
-        #
-
-        cleanup_simulation_data ()
-        
-        
-            
-
-************************************
-Resulting Output
-************************************
-    ::
-        
-        >>> pipeline_run([setup_simulation_data], multiprocess = 5, verbose = 2)
-            Make directories [temp_NxM/gene, temp_NxM/simulation] completed
-        Completed Task = setup_simulation_data_mkdir_1
-            Job completed
-        Completed Task = setup_simulation_data
-
-
-        >>> pipeline_run([statistical_summary], multiprocess = 5, verbose = 2)
-            Make directories [temp_NxM, temp_NxM/simulation_results] completed
-        Completed Task = gwas_simulation_mkdir_1
-            Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/000.simulation] -> temp_NxM/simulation_results/001.000.simulation_res, 001, 000, 001.000.simulation_res] completed
-            Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/000.simulation] -> temp_NxM/simulation_results/000.000.simulation_res, 000, 000, 000.000.simulation_res] completed
-            Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/001.simulation] -> temp_NxM/simulation_results/001.001.simulation_res, 001, 001, 001.001.simulation_res] completed
-            Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/001.simulation] -> temp_NxM/simulation_results/000.001.simulation_res, 000, 001, 000.001.simulation_res] completed
-            Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/002.simulation] -> temp_NxM/simulation_results/000.002.simulation_res, 000, 002, 000.002.simulation_res] completed
-            Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/002.simulation] -> temp_NxM/simulation_results/001.002.simulation_res, 001, 002, 001.002.simulation_res] completed
-        Completed Task = gwas_simulation
-            Job = [[temp_NxM/simulation_results/000.000.simulation_res, temp_NxM/simulation_results/000.001.simulation_res, temp_NxM/simulation_results/000.002.simulation_res] -> temp_NxM/000.mean] completed
-            Job = [[temp_NxM/simulation_results/001.000.simulation_res, temp_NxM/simulation_results/001.001.simulation_res, temp_NxM/simulation_results/001.002.simulation_res] -> temp_NxM/001.mean] completed
diff --git a/doc/_build/html/_sources/tutorials/manual/parallel.txt b/doc/_build/html/_sources/tutorials/manual/parallel.txt
deleted file mode 100644
index 2f05355..0000000
--- a/doc/_build/html/_sources/tutorials/manual/parallel.txt
+++ /dev/null
@@ -1,65 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.parallel:
-
-#######################################################################################################################
-|manual.parallel.chapter_num|: `Esoteric: Running jobs in parallel without using files with` **@parallel**
-#######################################################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>` 
-        * :ref:`@parallel<decorators.parallel>` syntax in detail
-
-    
-    .. index:: 
-        pair: @parallel; Manual
-    
-
-
-
-
-***************************************
-**@parallel** 
-***************************************
-
-    **@parallel** supplies parameters for multiple **jobs** exactly like :ref:`@files<manual.files>` except that:
-    
-        #. The first two parameters are not treated like *inputs* and *ouputs* parameters, 
-           and strings are not assumed to be file names
-        #. Thus no checking of whether each job is up-to-date is made using *inputs* and *outputs* files
-        #. No expansions of |glob|_ patterns or *output* from previous tasks is carried out.
-        
-    This syntax is most useful when a pipeline stage does not involve creating or consuming any files, and
-    you wish to forego the conveniences of :ref:`@files<manual.files>`, :ref:`@transform<manual.transform>` etc.
-    
-    The following code performs some arithmetic in parallel:
-    
-        ::
-
-            import sys
-            from ruffus import *
-            parameters = [
-                             ['A', 1, 2], # 1st job
-                             ['B', 3, 4], # 2nd job
-                             ['C', 5, 6], # 3rd job
-                         ]
-            @parallel(parameters)                                                     
-            def parallel_task(name, param1, param2):                                  
-                sys.stderr.write("    Parallel task %s: " % name)                     
-                sys.stderr.write("%d + %d = %d\n" % (param1, param2, param1 + param2))
-            
-            pipeline_run([parallel_task])
-            
-        produces the following::
-        
-            Task = parallel_task
-                Parallel task A: 1 + 2 = 3
-                Job = ["A", 1, 2] completed
-                Parallel task B: 3 + 4 = 7
-                Job = ["B", 3, 4] completed
-                Parallel task C: 5 + 6 = 11
-                Job = ["C", 5, 6] completed
-            
-    
diff --git a/doc/_build/html/_sources/tutorials/manual/parallel_processing.txt b/doc/_build/html/_sources/tutorials/manual/parallel_processing.txt
deleted file mode 100644
index 08c4143..0000000
--- a/doc/_build/html/_sources/tutorials/manual/parallel_processing.txt
+++ /dev/null
@@ -1,52 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.multiprocessing:
-
-#######################################################################################
-|manual.multiprocessing.chapter_num|: `Running Tasks and Jobs in parallel`
-#######################################################################################
-    .. hlist::
-    
-       * :ref:`Manual overview <manual>` 
-
-=====================
-Multi Processing
-=====================
-
-    *Ruffus* uses python `multiprocessing <http://docs.python.org/library/multiprocessing.html>`_ to run
-    each job in a separate process.
-    
-    This means that jobs do *not* necessarily complete in the order of the defined parameters.
-    Task hierachies are, of course, inviolate: upstream tasks run before downstream, dependent tasks.
-    
-    Tasks that are independent (i.e. do not precede each other) may be run in parallel as well.
-    
-    The number of concurrent jobs can be set in :ref:`pipeline_run<pipeline_functions.pipeline_run>`:
-
-        ::
-        
-            pipeline_run([parallel_task], multiprocess = 5)
-        
-        
-    If ``multiprocess`` is set to 1, then jobs will be run on a single process.
-
-    
-=====================
-Data sharing
-=====================
-    
-    Running jobs in separate processes allows *Ruffus* to make full use of the multiple
-    processors in modern computers. However, some of the 
-    `multiprocessing guidelines <http://docs.python.org/library/multiprocessing.html#multiprocessing-programming>`_
-    should be borne in mind when writing *Ruffus* pipelines. In particular:
-    
-    * Try not to pass large amounts of data between jobs, or at least be aware that this has to be marshalled
-      across process boundaries.
-      
-    * Only data which can be `pickled <http://docs.python.org/library/pickle.html>`_ can be passed as 
-      parameters to *Ruffus* task functions. Happily, that applies to almost any Python data type.
-      The use of the rare, unpicklable object will cause python to complain (fail) loudly when *Ruffus* pipelines
-      are run.
-      
-
diff --git a/doc/_build/html/_sources/tutorials/manual/posttask.txt b/doc/_build/html/_sources/tutorials/manual/posttask.txt
deleted file mode 100644
index d974889..0000000
--- a/doc/_build/html/_sources/tutorials/manual/posttask.txt
+++ /dev/null
@@ -1,110 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.posttask:
-
-####################################################################################################################
-|manual.posttask.chapter_num|: `Signal the completion of each stage of our pipeline with` **@posttask**
-####################################################################################################################
-
-    .. hlist::
-
-        * :ref:`Manual overview <manual>` 
-        * :ref:`@posttask <decorators.posttask>` syntax in detail
-
-    It is often useful to signal the completion of each task by specifying a specific
-    action to be taken or function to be called. This can range from 
-    printing out some message, or ``touching`` some sentinel file,
-    to emailing the author.This is particular useful if the :term:`task` is a recipe apply to an unspecified number
-    of parameters in parallel in different :term:`job`\ s. If the task is never run, or if it
-    fails, needless-to-say no task completion action will happen.
-
-
-    *Ruffus* uses the :ref:`@posttask <decorators.posttask>` decorator for this purpose.
-    
-    .. index:: 
-        pair: @posttask; Manual
-    
-
-=================
-**@posttask**
-=================
-    
-    We can signal the completion of each task by specifying
-    one or more function(s) using ``@posttask`` ::
-    
-        from ruffus import *
-        
-        def task_finished():
-            print "hooray"
-            
-        @posttask(task_finished)
-        @files(None, "a.1")
-        def create_if_necessary(input_file, output_file):
-            open(output_file, "w")
-                    
-        pipeline_run([create_if_necessary])
-
-
-    This is such a short function, we might as well write it in-line:
-    
-        ::
-        
-            @posttask(lambda: sys.stdout.write("hooray\n"))
-            @files(None, "a.1")
-            def create_if_necessary(input_file, output_file):
-                open(output_file, "w")
-        
-    
-.. note::
-
-    The function(s) provided to ``@posttask`` will be called if the pipeline passes 
-    through a task, even if none of its jobs are run because they are up-to-date.
-    This happens when a upstream task is out-of-date, and the execution passes through
-    this point in the pipeline. See the example in :ref:`Chapter 9<manual.dependencies>` 
-    of this manual.
-    
-        
-.. index:: 
-    single: @posttask; touchfile (Manual)
-    single: touchfile ; @posttask (Manual)
-
-
-.. _manual.posttask.touch_file:
-
-============================================
-:ref:`touch_file<decorators.touch_file>`
-============================================
-
-    The most common way to note the completion of a task is to create some sort of
-    "flag" file. Each stage in a traditional ``make`` pipeline would contain a 
-    ``touch completed.flag``.
-    
-    This is so common that **Ruffus** provides a special shorthand called
-    :ref:`touch_file<decorators.touch_file>`::
-    
-        from ruffus import *
-        
-        @posttask(touch_file("task_completed.flag"))
-        @files(None, "a.1")
-        def create_if_necessary(input_file, output_file):
-            open(output_file, "w")
-                    
-        pipeline_run([create_if_necessary])
-        
-=======================================
-Adding several post task actions
-=======================================
-    You can, of course, add more than one different action to be taken on completion of the 
-    task, either by stacking up as many :ref:`@posttask<decorators.posttask>` decorators 
-    as necessary, or by including several functions in the same **@posttask**:
-    
-        ::
-        
-            @posttask(print_hooray, print_whoppee)
-            @posttask(print_hip_hip, touch_file("sentinel_flag"))
-            @files(None, "a.1")
-            def your_pipeline_function (input_file_names, output_file_name):
-                ""
-                
-
diff --git a/doc/_build/html/_sources/tutorials/manual/split.txt b/doc/_build/html/_sources/tutorials/manual/split.txt
deleted file mode 100644
index f7689fd..0000000
--- a/doc/_build/html/_sources/tutorials/manual/split.txt
+++ /dev/null
@@ -1,177 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.split:
-
-###################################################################################
-|manual.split.chapter_num|: `Splitting up large tasks / files with` **@split**
-###################################################################################
-    .. hlist::
-    
-        * :ref:`Manual overview <manual>` 
-        * :ref:`@split <decorators.split>` syntax in detail
-
-    A common requirement in computational pipelines is to split up a large task into
-    small jobs which can be run on different processors, (or sent to a computational
-    cluster). Very often, the number of jobs depends dynamically on the size of the
-    task, and cannot be known for sure beforehand. 
-
-    *Ruffus* uses the :ref:`@split <decorators.split>` decorator to indicate that
-    the :term:`task` function will produce an indeterminate number of output files.
-    
-    
-    
-    .. index:: 
-        pair: @split; Manual
-    
-
-=================
-**@split**
-=================
-This example is borrowed from :ref:`step 4 <Simple_Tutorial_5th_step>` of the simple tutorial.
-
-    .. note :: See :ref:`accompanying Python Code <Simple_Tutorial_5th_step_code>` 
-    
-**************************************************************************************
-Splitting up a long list of random numbers to calculate their variance
-**************************************************************************************
-
-    .. csv-table:: 
-        :widths: 1,99
-        :class: borderless
-
-        ".. centered::
-            Step 5 from the tutorial:
-
-        .. image:: ../../images/simple_tutorial_step5_sans_key.png", "
-            Suppose we had a list of 100,000 random numbers in the file ``random_numbers.list``:
-            
-                ::
-                
-                    import random
-                    f = open('random_numbers.list', 'w')
-                    for i in range(NUMBER_OF_RANDOMS):
-                        f.write('%g\n' % (random.random() * 100.0))
-            
-            
-            We might want to calculate the sample variance more quickly by splitting them 
-            into ``NNN`` parcels of 1000 numbers each and working on them in parallel. 
-            In this case we known that ``NNN == 100`` but usually the number of resulting files
-            is only apparent after we have finished processing our starting file."
-    
-
-    Our pipeline function needs to take the random numbers file ``random_numbers.list``,
-    read the random numbers from it, and write to a new file every 100 lines.
-    
-    The *Ruffus* decorator :ref:`@split<decorators.split>` is designed specifically for 
-    splitting up *inputs* into an indeterminate ``NNN`` number of *outputs*:
-    
-        .. image:: ../../images/simple_tutorial_split.png
-        
-    .. ::
-    
-        ::
-        
-            @split("random_numbers.list", "*.chunks")
-            def step_4_split_numbers_into_chunks (input_file_name, output_files):
-                #
-                """code goes here"""
-            
-
-    Ruffus will set 
-
-        | ``input_file_name`` to ``"random_numbers.list"``
-        | ``output_files`` to all files which match ``*.chunks`` (i.e. ``"1.chunks"``, ``"2.chunks"`` etc.).
-    
-
-    
-.. _manual.split.output_files:
-
-=================
-Output files
-=================
-
-    The *output* (second) parameter of **@split** usually contains a 
-    |glob|_ pattern like the ``*.chunks`` above. 
-
-    .. note::
-        **Ruffus** is quite relaxed about the contents of the ``output`` parameter.
-        Strings are treated as file names. Strings containing |glob|_ pattern are expanded.
-        Other types are passed verbatim to the decorated task function.
-    
-    The files which match the |glob|_ will be passed as the actual parameters to the job
-    function. Thus, the first time you run the example code ``*.chunks`` will return an empty list because
-    no ``.chunks`` files have been created, resulting in the following:
-    
-        ::
-        
-            step_4_split_numbers_into_chunks ("random_numbers.list", [])
-    
-    After that ``*.chunks`` will match the list of current ``.chunks`` files created by
-    the previous pipeline run. 
-
-
-
-    File names in *output* are generally out of date or superfluous. They are useful 
-    mainly for cleaning-up detritus from previous runs 
-    (have a look at :ref:`step_4_split_numbers_into_chunks(...) <Simple_Tutorial_5th_step_code>`).
-    
-    .. note ::
-
-        It is important, nevertheless, to specify correctly the list of *output* files.
-        Otherwise, dependent tasks will not know what files you have created, and it will
-        not be possible automatically to chain together the *ouput* of this pipeline task into the
-        *inputs* of the next step.
-        
-        You can specify multiple |glob|_ patterns to match *all* the files which are the
-        result of the splitting task function. These can even cover different directories, 
-        or groups of file names. This is a more extreme example:
-        
-            ::
-            
-                @split("input.file", ['a*.bits', 'b*.pieces', 'somewhere_else/c*.stuff'])
-                def split_function (input_filename, output_files):
-                    "Code to split up 'input.file'"
-                    
-
-
-    The actual resulting files of this task function are not constrained by the file names
-    in the *output* parameter of the function. The whole point of **@split** is that number 
-    of resulting output files cannot be known beforehand, after all. 
-    
-******************
-Example
-******************
-
-    
-    Suppose random_numbers.list can be split into four pieces, this function will create
-        ``1.chunks``, ``2.chunks``, ``3.chunks``, ``4.chunks``
-        
-    Subsequently, we receive a larger ``random_numbers.list`` which should be split into 10
-    pieces. If the pipeline is called again, the task function receives the following parameters:
-    
-        ::
-        
-            step_4_split_numbers_into_chunks("random_numbers.list", 
-                                             ["1.chunks",               #   previously created files
-                                              "2.chunks",               #
-                                              "3.chunks",               #
-                                              "4.chunks" ])             #
-
-
-    This doesn't stop the function from creating the extra ``5.chunks``, ``6.chunks`` etc.
-
-    .. note::
-    
-        Any tasks **@follow**\ ing and specifying 
-        ``step_4_split_numbers_into_chunks(...)`` as its *inputs* parameter is going to receive
-        ``1.chunks``, ``...``, ``10.chunks`` and not merely the first four files.
-
-        In other words, dependent / down-stream tasks which obtain output files automatically 
-        from the task decorated by **@split** receive the most current file list. 
-        The |glob|_ patterns will be matched again to see exactly what files the task function
-        has created in reality *after* the task completes.
-
-    
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/tasks_and_globs_in_inputs.txt b/doc/_build/html/_sources/tutorials/manual/tasks_and_globs_in_inputs.txt
deleted file mode 100644
index b915ca0..0000000
--- a/doc/_build/html/_sources/tutorials/manual/tasks_and_globs_in_inputs.txt
+++ /dev/null
@@ -1,265 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.tasks_and_globs_in_inputs:
-
-#################################################################################################################
-|manual.tasks_and_globs_in_inputs.chapter_num|: Chaining pipeline `Tasks` together automatically
-#################################################################################################################
-    * :ref:`Manual overview <manual>` 
-
-
-    .. index:: 
-        pair: tasks as recipes; Manual
-    
-    In the previous chapter, we explained that **ruffus** determines the data flow through
-    your pipeline by calling your :term:`task` functions (normal python functions written 
-    by you) with the right parameters at the right time, making sure that
-
-        #. only out-of-date parts of the pipeline will be re-run
-        #. multiple jobs can be run in parallel (on different processors if possible)
-        #. pipeline stages can be chained together automatically
-        
-    This chapter is devoted to the last item: how the output of one stage of the pipeline 
-    is piped into as the input of the next stage.
-    
-.. _manual.tasks_as_input:
-
-.. index:: 
-    pair: tasks; as input parameters (Manual)
-    pair: tasks as input parameters; Manual
-    pair: inputs parameters; tasks
-
-    
-   
-==========================================================
-Tasks in the *inputs* parameters: Implicit dependencies
-==========================================================
-    **Ruffus** treats the first two parameters of each job in each task as the *inputs* and
-    *outputs* parameters respectively. If the *inputs* parameter contains strings, these 
-    will be treated as the names of files required by that job. 
-
-    If the *inputs* parameter contains any :term:`task`\ s, **Ruffus** will take the output
-    from these specified tasks as part of the current *inputs* parameter. In addition, 
-    such tasks will be listed as prequisites, much as if you had included them in a 
-    separate ``@follows`` decorator.
-    
-    For example, supposed we wanted to take the output files from ``task1`` and feed
-    them automatically to ``task2``, we might write the following code
-
-        ::
-        
-            task1_ouput_files = ("task1.output_a", "task1.output_b", "task1.output_c")
-    
-            @follows(task1)
-            @files(task1_ouput_files, "task2.output")
-            def task2(input, output):
-                pass
-
-
-
-    This can be replaced by the much more concise syntax:
-
-        ::
-    
-            @files(task1, "task2.output")
-            def task2(input, output):
-                pass
-                        
-
-    This means: 
-        * Take the output from ``task1``, and feed it automatically into ``task2``. 
-        * Also make sure that ``task2`` becomes a dependency of ``task1``.
-
-            
-    In other words, ``task1`` and ``task2`` have been chained together automatically.
-    This is both a great convenience and makes the flow of data through a pipeline much clearer.
-    
-    
-
-.. index:: 
-    pair: tasks; refering to by name
-    pair: inputs parameters; refering to tasks by name            
-
-.. _manual.output_from:
-
-==========================================================
-Refering to tasks by name in the *inputs* parameters
-==========================================================
-
-    :ref:`Chapter 1 <manual.follows.out_of_order>` explains that task functions can be 
-    defined in any order so long as undefined tasks are referred to by their (fully qualified if
-    necessary) function name string.
-    
-    You can similarly refer to tasks in the *inputs* parameter by name, as a text string. 
-    Normally **Ruffus** assumes that strings are file names. To indicate that that 
-    you are referring to task function names instead, you need to
-    wrap the relevant parameter or (nested) parts of the parameter with the indicator object
-    :ref:`output_from("task_name") <decorators.output_from>`. Thus,
-    
-        ::
-        
-            @split(["a.file", ("b.file", output_from("task1", 76, "task2"))], "*.split")
-            def task2(input, output):
-                pass
-                        
-
-    is equivalent to:
-
-        ::
-        
-            @split(["a.file", ("b.file", (task1, 76, task2))], "*.split")
-            def task2(input, output):
-                pass
-    
-.. index:: 
-    pair: inputs parameters; globs
-    pair: globs in input parameters; Manual
-
-.. _manual.globs_as_input:
-
-=======================================
-Globs in the *inputs* parameters
-=======================================
-
-    As a syntactic convenience, **Ruffus** also allows you to specify a 
-    |glob|_ pattern (e.g. ``*.txt``) in the
-    *input* parameter, it will be expanded automatically to the actually matching 
-    file names. This applies to any strings within *inputs* which contain the letters: ``*?[]``.
-    
-    
-    
-.. index:: 
-    pair: tasks; combined with globs and files as input parameters (Manual)
-    pair: tasks combined with globs and files as input parameters; Manual
-    pair: globs; combined with tasks and files as input parameters (Manual)
-    pair: globs combined with tasks and files as input parameters; Manual
-
-    
-.. _manual.mixing_tasks_globs_files:
-    
-=========================================================
-Mixing globs, tasks and files as **inputs**
-=========================================================
-
-    **Ruffus** is very flexible in allowing you to mix 
-    |glob|_ patterns, references to tasks and file names
-    in the data structures you pass as the **inputs** parameters. 
-
-    Suppose, in the previous example, 
-
-        * that ``task1`` produces the files
-            ::
-
-            "task1.output_a"
-            "task1.output_b"
-            "task1.output_c"
-            
-        * that the following additional files are also present 
-            ::
-
-            "extra.a"
-            "extra.c"
-
-    Then,
-    
-        ::
-    
-            @files(["1_more.file", "2_more.file", task1, "extra.*"], "task2.output")
-            def task2(input, output):
-                pass
-                
-
-    would result in the combination of the specified file name, the expansion of the |glob|_, 
-    and the results from the previous task:
-    
-        ::
-    
-            input == [
-                        "1_more.file"   ,           # specified file
-                        "2_more.file"   ,           # specified file
-                        "task1.output_a",           # from previous task
-                        "task1.output_b",           # from previous task 
-                        "task1.output_c",           # from previous task 
-                        "extra.a"       ,           # from glob expansion
-                        "extra.c"       ,           # from glob expansion
-                     ]
-            
-
-    In other words, |glob|_ patterns and tasks are expanded "in place" when they are part of
-    python lists, sets, or tuples.
-    
-.. _manual.appending_tasks_globs_to_lists_sets_tuples:
-    
-===============================================================
-Appending globs or tasks to pre-existing lists, sets or tuples
-===============================================================
-
-    Sometimes we want to the *inputs* parameter to contain be a combination of |glob|_\ s and tasks,
-    and an existing list of file names.
-    
-    To elaborate on the above example, suppose we have a list of files:
-    
-        ::
-        
-            file_list = [   "1_more.file", 
-                            "2_more.file"]
-                            
-    Now we want the input to ``task2`` to be:
-    
-        ::
-        
-            file_list + task1 + "extra.*"
-            
-    The closest that we can express this in python syntax is by turning task1 and the |glob|_
-    to a list first then adding them together:
-    
-        ::
-    
-            @files(file_list + [task1] + ["extra.*"], "task2.output")
-            def task2(input, output):
-                pass
-    
-
-    The same also works with tuples:
-    
-        ::
-    
-            file_list = (   "1_more.file", 
-                            "2_more.file")
-
-            @files(file_list + (task1, "extra.*"), "task2.output")
-            def task2(input, output):
-                pass
-
-    
-    and sets (using the set concatenation operator):
-        
-        ::
-    
-            file_list = set([   "1_more.file", 
-                                "2_more.file"])
-
-            @files(file_list | set([task1 + "extra.*"]), "task2.output")
-            def task2(input, output):
-                pass
-
-.. _manual.understanding_complex_inputs:
-
-===============================================================
-Understanding complex *inputs* and *outputs* parameters
-===============================================================
-
-    In all cases, **Ruffus** tries to do the right thing, and to make the simple or
-    obvious case require the simplest, least onerous syntax.
-    
-    If sometimes **Ruffus** does not behave the way you expect, please write to the authors:
-    it may be a bug!
-    
-    In all other cases, the best thing to do, is write your **Ruffus** specifications, and 
-    check the results of :ref:`pipeline_printout <pipeline_functions.pipeline_printout>` 
-    to make sure that your wishes are properly
-    reflected in the parameters sent to your pipelined tasks.
-    
-    In other words, read the :ref:`next chapter <manual.tracing_pipeline_parameters>`!
-    
diff --git a/doc/_build/html/_sources/tutorials/manual/tasks_as_recipes.txt b/doc/_build/html/_sources/tutorials/manual/tasks_as_recipes.txt
deleted file mode 100644
index 39781b3..0000000
--- a/doc/_build/html/_sources/tutorials/manual/tasks_as_recipes.txt
+++ /dev/null
@@ -1,192 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.tasks_as_recipes:
-
-###################################################################
-|manual.tasks_as_recipes.chapter_num|: `Tasks and Recipes`
-###################################################################
-    * :ref:`Manual overview <manual>`
-
-
-    .. index::
-        pair: tasks as recipes; Manual
-
-
-    | The python functions which do the actual work of each stage  or
-      :term:`task` of a **Ruffus** pipeline are written by you.
-    | The role of **Ruffus** is to make sure these functions are called in the right order,
-      with the right parameters, running in parallel using multiprocessing if desired.
-
-    **Ruffus** manages the data flowing through your pipeline by supplying the correct
-    parameters to your pipeline functions. In this way, you will get the following features
-    for free:
-
-        #. only out-of-date parts of the pipeline will be re-run
-        #. multiple jobs can be run in parallel (on different processors if possible)
-        #. pipeline stages can be chained together automatically
-
-    Much of the functionality of **ruffus** involves determining the data flow through
-    your pipeline, by governing how the output of one stage of the pipeline is supplied
-    as parameters to the functions of the next.
-
-    .. index::
-        pair: skip up-to-date; Manual
-
-.. _manual.skip_up_to_date:
-
-=======================================
-Skip jobs which are up to date
-=======================================
-
-    Very often it will necessary to re-run a computational pipeline, because part of the
-    data has changed. **Ruffus** will run only those stages of the pipeline
-    which are absolutely necessary.
-
-    By default, **Ruffus** uses file modification times to see which parts of the pipeline
-    are out of date, and which :term:`task`\s need to be run again. This is so convenient that
-    even if a pipeline is not file-based (if it, for example, uses database tables instead),
-    it may be worth while to use dummy, "sentinel" files to manage the stages of a pipeline.
-
-    (It is also possible, as we shall
-    see later, to add custom functions to determine which parts of the pipeline are out
-    of date. see :ref:`@parallel <decorators.parallel>` and
-    :ref:`@check_if_uptodate <decorators.check_if_uptodate>`.)
-
-.. index::
-    single: inputs / outputs parameters
-
-.. _manual.io_parameters:
-
-.. index::
-    pair: inputs / outputs parameters; Manual
-
-=================================
-*Inputs* and *Outputs* parameters
-=================================
-    **Ruffus** treats the first two parameters of each job in each task as the *inputs* and
-    *outputs* parameters respectively. If these parameters are strings, or are sequences
-    which contain strings, these will be treated as the names of files required by and
-    produced by that job. The presence and modification times of the *inputs* and *outputs* files
-    will be used to check if it is necessry to rerun the job.
-
-    Apart from this, **Ruffus** imposes no other restrictions on the parameters for jobs, which
-    are passed verbatim to task functions.
-
-    Most of the time, it is sensible to stick with file names (strings) in the *inputs* and
-    *outputs* parameters but **Ruffus** does not try to second-guess what sort of data you
-    will be passing through your pipelines (except that strings represent file names).
-
-    Thus, given the following over-elaborate parameters (parameter passing will be discussed in
-    more detail from :ref:`|manual.files.chapter_num| <manual.files>`):
-
-        ::
-
-            [   [[1, 3], "afile.name", ("bfile.name", 72)],
-                [[56, 3.3], set(custom_object(), "output.file")],
-                33.3,
-                "oops"]
-
-    This will be passed `"as is"` to your task function:
-
-        ::
-
-            do_something([[1, 3], "afile.name", ("bfile.name", 72)],        # input
-                        [[56, 3.3], set(custom_object(), "output.file")],   # output
-                        33.3,                                               # extra parameter
-                        "oops")                                             # extra parameter
-
-
-        **Ruffus** will interprete this as:
-
-        ::
-
-            Input_parameter   = [[1, 3], "afile.name", ("bfile.name", 72)]
-            Output_parameter  = [[56, 3.3], set(custom_object(), "output.file")]
-            Other_parameter_1 = 33.3
-            Other_parameter_2 = "oops"
-
-        **Ruffus** disregards the *structure* of your data, only identifying the (nested) strings.
-        Thus there are 2 input files:
-
-            ::
-
-                "afile.name"
-                "bfile.name"
-
-        and 1 output file:
-
-            ::
-
-                "output.file"
-
-
-
-
-
-
-.. index::
-    pair: rules; for rerunning jobs
-
-.. _manual.skip_up_to_date.rules:
-
-=======================================
-Checking if files are up to date
-=======================================
-    The following simple rules are used by **Ruffus**.
-
-    #. The pipeline stage will be rerun if:
-
-        * If any of the *inputs* files are new (newer than the *output* files)
-        * If any of the *output* files are missing
-
-    #. In addition, it is possible to run jobs which create files from scratch.
-
-        * If no *inputs* file names are supplied, the job will only run if any *output* file is missing.
-
-    #. Finally, if no *outputs* file names are supplied, the job will always run.
-
-
-    The :ref:`example <manual.files.example>` in the next chapter shows how this works in practice.
-
-
-.. index::
-    pair: Exception; Missing input files
-
-=======================================
-Missing files
-=======================================
-
-    If the *inputs* files for a job are missing, the task function will have no way
-    to produce its *output*. In this case, a ``MissingInputFileError`` exception will be raised
-    automatically. For example,
-
-        ::
-
-            task.MissingInputFileError: No way to run job: Input file ['a.1'] does not exist
-            for Job = ["a.1" -> "a.2", "A file"]
-
-.. index::
-    single: Timestamp resolution
-
-=======================================
-Caveats: Timestamp resolution
-=======================================
-
-    | Note that modification times have precision to the nearest second under some older file systems
-      (ext2/ext3?). This may be also be true for networked file systems.
-    | **Ruffus** is very conservative, and assumes that files with *exactly* the same date stamp might have been
-      created in the wrong order, and will treat the job as out-of-date. This would result in some
-      jobs re-running unnecessarily, simple because an underlying coarse-grained file system does not
-      distinguish between successively created files with sufficiently accuracy.
-
-    To get around this, **Ruffus** makes sure that each task is punctuated by a 1 second pause
-    (via ``time.sleep()``). If this is gets in the way, and you are using a modern file system with
-    nanosecond timestamp resolution, you can turn off the delay by setting
-    ``one_second_per_job`` to ``False`` in :ref:`pipeline_run <pipeline_functions.pipeline_run>`
-
-    Later versions of **Ruffus** will allow file modification times to be saved at higher precision
-    in a log file or database to get around this.
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/tracing_pipeline_parameters.txt b/doc/_build/html/_sources/tutorials/manual/tracing_pipeline_parameters.txt
deleted file mode 100644
index 4890eda..0000000
--- a/doc/_build/html/_sources/tutorials/manual/tracing_pipeline_parameters.txt
+++ /dev/null
@@ -1,115 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.tracing_pipeline_parameters:
-
-#################################################################################################################
-|manual.tracing_pipeline_parameters.chapter_num|: Tracing pipeline parameters
-#################################################################################################################
-    * :ref:`Manual overview <manual>` 
-
-
-    .. index:: 
-        pair: pipeline_printout; Manual
-        pair: Tracing pipeline parameters; Manual
-        pair: Debugging; Manual
-    
-        
-    The trickiest part of developing pipelines is understanding how your
-    data flows through the pipeline.
-    
-    In **Ruffus**, your data is passed from one task function to another down
-    the pipeline by the chain of linked parameters. Sometimes, it may be difficult to 
-    choose the right **Ruffus** syntax at first, or to understand which parameters in
-    what format are being passed to your function.
-
-    Whether you are learning how to use **ruffus**, or trying out a new
-    feature in **ruffus**, or just have a horrendously complicated pipeline
-    to debug (we have colleagues with >100 criss-crossing pipelined stages),
-    your best friend is :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>`.
-    
-    **pipeline_printout** displays the parameters which would be passed to each task function
-    for each job in your pipeline. In other words, it traces how each of the functions in
-    the pipeline are called in detail.
-   
-    It makes good sense to alternate between calls to **pipeline_printout** and **pipeline_run** 
-    in the development of **Ruffus** pipelines (perhaps with the use of a command-line option), 
-    so that you always know exactly how the pipeline is being invoked. 
-    
-   
-=======================================
-Printing out which jobs will be run
-=======================================
-
-    **pipeline_printout** is called in exactly the same way as **pipeline_run** but 
-    instead of running the pipeline, just prints the tasks which are and are not up-to-date.
-        
-    The ``verbose`` parameter controls how much detail is displayed.
-
-        ::
-    
-            verbose = 0 : prints nothing
-            verbose = 1 : logs warnings and tasks which are not up-to-date and which will be run
-            verbose = 2 : logs doc strings for task functions as well
-            verbose = 3 : logs job parameters for jobs which are out-of-date
-            verbose = 4 : logs list of up-to-date tasks but parameters for out-of-date jobs
-            verbose = 5 : logs parameters for all jobs whether up-to-date or not
-            verbose = 10: logs messages useful only for debugging ruffus pipeline code
-
-    
-    Let us take the two step :ref:`pipeline<Simple_Tutorial_3nd_step_code>` from
-    the tutorial. :ref:`Pipeline_printout(...) <pipeline_functions.pipeline_printout>` 
-    by default merely lists the two tasks which will be run in the pipeline:
-
-
-        .. image:: ../../images/simple_tutorial_pipeline_printout1.png
-
-    .. ::
-    
-        ::
-    
-            >>> pipeline_printout(sys.stdout, [second_task])
-            
-            ________________________________________
-            Tasks which will be run:
-            
-            Task = first_task
-            Task = second_task
-            ________________________________________
-        
-
-    
-    To see the input and output parameters of out-of-date jobs in the pipeline, we can increase the verbosity from the default (``1``) to ``3``:
-
-        .. image:: ../../images/simple_tutorial_pipeline_printout2.png
-        
-    This is very useful for checking that the input and output parameters have been specified
-        correctly.
-
-=============================================
-Determining which jobs are out-of-date or not
-=============================================
-
-    It is often useful to see which tasks are or are not up-to-date. For example, if we
-    were to run the pipeline in full, and then modify one of the intermediate files, the
-    pipeline would be partially out of date.
-    
-
-    Let us start by run the pipeline in full but then modify ``job1.stage`` so that the second task is no longer up-to-date::
-        
-        pipeline_run([second_task])
-   
-        # modify job1.stage1
-        open("job1.stage1", "w").close()
-   
-
-    At a verbosity of ``5``, even jobs which are up-to-date will be displayed.
-    We can now see that the there is only one job in ``second_task(...)`` which needs to be re-run
-    because ``job1.stage1`` has been modified after ``job1.stage2`` (highlighted in blue):
-    
-        .. image:: ../../images/simple_tutorial_pipeline_printout3.png
-        
-
-
-            
-    
diff --git a/doc/_build/html/_sources/tutorials/manual/transform.txt b/doc/_build/html/_sources/tutorials/manual/transform.txt
deleted file mode 100644
index 6aa8870..0000000
--- a/doc/_build/html/_sources/tutorials/manual/transform.txt
+++ /dev/null
@@ -1,194 +0,0 @@
-.. include:: ../../global.inc
-.. include:: chapter_numbers.inc
-
-.. _manual.transform:
-
-#######################################################################################################################
-|manual.transform.chapter_num|: `Applying the same recipe to create many different files with` **@transform**
-#######################################################################################################################
-    .. hlist::
-    
-        * :ref:`Manual overview <manual>` 
-        * :ref:`@transform <decorators.transform>` syntax in detail
-
-    Sometimes you might have a list of data files which you might want to send to the
-    same pipelined function, to apply
-    the same operation. The best way to manage this would be to produce a corresponding 
-    list of results files:
-    
-        | Compiling c source files might *@transform* an ``a.c`` file to an ``a.o`` file.
-        | A ``grep`` operation might *@transform* a ``plays.king_lear.txt`` file to an ``plays.king_lear.counts`` file.
-    
-    *Ruffus* uses the :ref:`@transform <decorators.transform>` decorator for this purpose.
-
-    When you **@transform** your data from one file type to another, you are not restricted just
-    to changing the file suffix. We shall see how, with the full power of regular 
-    expressions behind you, you can sort the resulting
-    data into different directories, add indices and so on.
-    
-    
-    
-    .. index:: 
-        pair: @transform; Manual
-    
-
-=================
-**@transform**
-=================
-**************************************************************************************
-Worked example: calculating sums and sum of squares in parallel
-**************************************************************************************
-    This example is borrowed from :ref:`step 5 <Simple_Tutorial_5th_step>` of the simple tutorial.
-    
-        .. note:: See :ref:`example code here <Simple_Tutorial_5th_step_code>` 
-    
-
-    Given a set of files, each with a set of random numbers, we want to calculate thier
-    sums and sum of squares. The easiest way to do this is by providing a recipe for 
-    transforming a ``*.chunk`` file containing a list of numbers into a ``*.sums`` file 
-    with our sums and sum of squares.
-    
-    *Ruffus* magically takes care of applying the same recipe (task function) to all the different
-    data files in parallel.
-
-        .. image:: ../../images/simple_tutorial_transform.png
-
-    The :ref:`@transform <decorators.transform>` decorator tells *Ruffus* to take files from the step 4 task (i.e. ``*.chunks``),
-    and produce files having the ``.sums`` suffix instead.
-    ending.
-    
-    Thus if ``step_4_split_numbers_into_chunks`` created
-        ::
-        
-            "1.chunks"
-            "2.chunks"
-            "3.chunks"
-        
-    This would result in the following function calls:
-    
-        ::
-        
-            step_5_calculate_sum_of_squares ("1.chunk", "1.sums")
-            step_5_calculate_sum_of_squares ("2.chunk", "2.sums")
-            step_5_calculate_sum_of_squares ("3.chunk", "3.sums")
-            
-            # etc...
-            
-================================================================================================
-Using :ref:`suffix(...) <decorators.suffix>` to change give each output file a new suffix
-================================================================================================
-
-
-    The :ref:`suffix<decorators.suffix>` specification indicates that
-    
-        * only filenames with ending with the suffix term (e.g. ``.chunk``) should be considered
-        * The text matching the suffix term should be replaced with the string in the output pattern.
-        
-
-    This example assumes that both the *inputs* and the *outputs* consist each of a single string but
-    **Ruffus** places no such constraints on the data flowing through your pipeline. 
-
-        * If there are multiple file names (strings) contained within each *inputs* parameter,
-          then only the first will be used to generate the *output*
-        * Each string that is encountered in each *output* parameter will be used for suffix replacement.
-        
-        
-************************************************        
-An example with more complex data structures
-************************************************        
-    This will become much clearer with this example:
-    
-
-        ::
-    
-                inputs = [                                                                    
-                                ["file1.ext", 10   ],               #job 1
-                                [37.0, "file2.wrong_extension",     
-                                       "file2_ignored.ext"],        #job 2
-                                "file3.ext"                         #job 3
-                                ]
-            
-            @transform(inputs, suffix(".ext"), [(".ext1", ), ".ext2"])
-            def pipelinetask (input_file_name, output_file_name):
-                ""
-                
-
-    | Granted, it may seem rather odd that the *inputs* parameter including numbers as well
-      as file names, but **Ruffus** does not second guess how you wish to arrange your pipelines.
-    | ``inputs`` contains the parameters for three jobs.
-    | In each case, the first file name string encountered will be used to generate the *output* parameter:
-    
-        .. image:: ../../images/manual_transform_complex_outputs.png
-
-        .. note:: 
-            The first filename in the prospective job #2 does not have the ``.ext`` suffix so this job will be eliminated.
-    
-    Thus, the original code:
-    
-        ::
-        
-            @transform(inputs, suffix(".ext"), [(15, ".ext1"), ".ext2"])
-            def pipelinetask (input_file_name, output_file_name):
-                ""
-                
-    is equivalent to calling:
-            
-        ::
-        
-            pipelinetask(["file1.ext", 10], [(15, 'file1.ext1'), 'file1.ext2'])  # job 1
-            pipelinetask("file3.ext",       [(15, 'file3.ext1'), 'file3.ext2'])  # job 3
-            
-    Hopefully, your code will simpler than this rather pathological case!
-
-
-================================================================================================
-Regular expressions :ref:`regex(...) <decorators.regex>` provide maximum flexibility
-================================================================================================
-
-    Exactly the same function could be written using regular expressions:
-    
-        ::
-        
-            @transform(inputs, regex(".ext"), [(15, ".ext1"), ".ext2"])
-            def pipelinetask (input_file_name, output_file_name):
-                ""
-                
-
-    | However, regular expressions are not limited to suffix matches. 
-    | We can sort our *ouputs* to different subdirectories, depending on category.
-    |
-    | Our example starts off with data file for different zoo animals.
-    | We are only interested in mammals, and we would like the files of each species to 
-    | end up in its own directory after processing.                                     
-    | Starting with these species files:
-    
-        ::
-        
-            "mammals.tiger.wild.animals"     
-            "mammals.lion.wild.animals"      
-            "mammals.lion.handreared.animals"
-            "mammals.dog.tame.animals"       
-            "mammals.dog.wild.animals"       
-            "reptiles.crocodile.wild.animals"
-            
-    Then, the following:
-        .. image:: ../../images/manual_transform.png
-    
-    will put each captured mammal in its own directory:
-        ::
-
-            >>> pipeline_run([capture_mammals])
-                Job = [mammals.dog.tame.animals        -> dog/dog.tame.in_my_zoo, dog] completed
-                Job = [mammals.dog.wild.animals        -> dog/dog.wild.in_my_zoo, dog] completed
-                Job = [mammals.lion.handreared.animals -> lion/lion.handreared.in_my_zoo, lion] completed
-                Job = [mammals.lion.wild.animals       -> lion/lion.wild.in_my_zoo, lion] completed
-                Job = [mammals.tiger.wild.animals      -> tiger/tiger.wild.in_my_zoo, tiger] completed
-            Completed Task = capture_mammals
-
-    .. note:: The code can be found :ref:`here <manual.transform_code>` 
-
-
-        
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/manual/transform_code.txt b/doc/_build/html/_sources/tutorials/manual/transform_code.txt
deleted file mode 100644
index 092b899..0000000
--- a/doc/_build/html/_sources/tutorials/manual/transform_code.txt
+++ /dev/null
@@ -1,68 +0,0 @@
-.. include:: ../../global.inc
-.. _manual.transform_code:
-
-########################################################################################
-Code for Chapter 6: Applying the same recipe to create many different files
-########################################################################################
-    * :ref:`Manual overview <manual>` 
-    * :ref:`@transform syntax in detail <decorators.transform>`
-    * :ref:`Back <manual.transform>` 
-
-
-    | Our example starts off with data file for different zoo animals.
-    | We are only interested in mammals, and we would like the files of each species to 
-    | end up in its own directory after processing.                                     
-              
-    
-************************************
-Code
-************************************
-    ::
-
-        # 
-        #   Start with species files
-        #
-        open("mammals.tiger.wild.animals"     , "w")
-        open("mammals.lion.wild.animals"      , "w")
-        open("mammals.lion.handreared.animals", "w")
-        open("mammals.dog.tame.animals"       , "w")
-        open("mammals.dog.wild.animals"       , "w")
-        open("reptiles.crocodile.wild.animals", "w")
-        
-        # 
-        #   create destinations for each species
-        #
-        import os
-        for s in ("tiger", "lion", "dog"):
-            if not os.path.exists(s):
-                os.mkdir(s)                 
-    
-    
-        #
-        #   Now summarise files in directories organised by species
-        #        
-        from ruffus import *
-        @transform('*.animals', 
-                    regex(r'mammals\.(.+)\.(.+)\.animals'), # save species and wild/tame
-                    r'\1/\1.\2.in_my_zoo',                  # same species go together
-                    r'\1')                                  # extra species name
-        def capture_mammals(infile, outfile, species):
-            open(outfile, "w").write(open(infile).read() + "\ncaptured %s\n" % species)
-        
-        pipeline_run([capture_mammals])
-
-            
-
-************************************
-Resulting Output
-************************************
-    ::
-        
-        >>> pipeline_run([capture_mammals])
-            Job = [mammals.dog.tame.animals        -> dog/dog.tame.in_my_zoo, dog] completed
-            Job = [mammals.dog.wild.animals        -> dog/dog.wild.in_my_zoo, dog] completed
-            Job = [mammals.lion.handreared.animals -> lion/lion.handreared.in_my_zoo, lion] completed
-            Job = [mammals.lion.wild.animals       -> lion/lion.wild.in_my_zoo, lion] completed
-            Job = [mammals.tiger.wild.animals      -> tiger/tiger.wild.in_my_zoo, tiger] completed
-        Completed Task = capture_mammals
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/active_if.txt b/doc/_build/html/_sources/tutorials/new_tutorial/active_if.txt
deleted file mode 100644
index ce51051..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/active_if.txt
+++ /dev/null
@@ -1,149 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: @active_if; Tutorial
-
-.. _new_manual.active_if:
-
-##########################################################################################################################################
-|new_manual.active_if.chapter_num|: Turning parts of the pipeline on and off at runtime with :ref:`@active_if <decorators.active_if>`
-##########################################################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@active_if syntax in detail <decorators.active_if>`
-
-
-***************************************
-Overview
-***************************************
-
-    It is sometimes useful to be able to switch on and off parts of a pipeline. For example, a pipeline
-    might have two difference code paths depending on the type of data it is being asked to analyse.
-
-    One surprisingly easy way to do this is to use a python ``if`` statement around particular task functions:
-
-        .. code-block:: python
-           :emphasize-lines: 3,5
-
-            from ruffus import *
-
-            run_task1 = True
-
-            @originate(['a.foo', 'b.foo'])
-            def create_files(output_file):
-                open(output_file, "w")
-
-
-            if run_task1:
-                # might not run
-                @transform(create_files, suffix(".foo"), ".bar")
-                def foobar(input_file, output_file):
-                    open(output_file, "w")
-
-
-            @transform(foobar, suffix(".bar"), ".result")
-            def wrap_up(input_file, output_file):
-                    open(output_file, "w")
-
-
-            pipeline_run()
-
-
-    This simple solution has a number of drawbacks:
-        #. The on/off decision is a one off event that happens when the script is loaded. Ideally, we
-           would like some flexibility, and postpone the decision until ``pipeline_run()`` is invoked.
-        #. When ``if`` is false, the entire task function becomes invisible, and if there are any
-           downstream tasks, as in the above example, *Ruffus* will complain loudly about
-           missing dependencies.
-
-
-******************************************************************************
-:ref:`@active_if <decorators.active_if>`  controls the state of tasks
-******************************************************************************
-
-
-    * Switches tasks on and off at run time depending on its parameters
-    * Evaluated each time ``pipeline_run``, ``pipeline_printout`` or ``pipeline_printout_graph`` is called.
-    * Dormant tasks behave as if they are up to date and have no output.
-
-    The Design and initial implementation were contributed by Jacob Biesinger
-
-    The following example shows its flexibility and syntax:
-
-        .. code-block:: python
-            :emphasize-lines: 20
-
-            from ruffus import *
-            run_if_true_1 = True
-            run_if_true_2 = False
-            run_if_true_3 = True
-
-
-            #
-            #    task1
-            #
-            @originate(['a.foo', 'b.foo'])
-            def create_files(outfile):
-                """
-                create_files
-                """
-                open(outfile, "w").write(outfile + "\n")
-
-            #
-            #   Only runs if all three run_if_true conditions are met
-            #
-            #   @active_if determines if task is active
-            @active_if(run_if_true_1, lambda: run_if_true_2)
-            @active_if(run_if_true_3)
-            @transform(create_files, suffix(".foo"), ".bar")
-            def this_task_might_be_inactive(infile, outfile):
-                open(outfile, "w").write("%s -> %s\n" % (infile, outfile))
-
-
-            # @active_if switches off task because run_if_true_2 == False
-            pipeline_run(verbose = 3)
-
-            # @active_if switches on task because all run_if_true conditions are met
-            run_if_true_2 = True
-            pipeline_run(verbose = 3)
-
-
-    The task starts off inactive:
-
-
-        .. code-block:: pycon
-            :emphasize-lines: 1
-
-            >>> # @active_if switches off task "this_task_might_be_inactive" because run_if_true_2 == False
-            >>> pipeline_run(verbose = 3)
-
-            Task enters queue = create_files
-            create_files
-                Job  = [None -> a.foo] Missing file [a.foo]
-                Job  = [None -> b.foo] Missing file [b.foo]
-                Job  = [None -> a.foo] completed
-                Job  = [None -> b.foo] completed
-            Completed Task = create_files
-            Inactive Task = this_task_might_be_inactive
-
-    Now turn on the task:
-
-        .. code-block:: pycon
-            :emphasize-lines: 1
-
-            >>> # @active_if switches on task "this_task_might_be_inactive" because all run_if_true conditions are met
-            >>> run_if_true_2 = True
-            >>> pipeline_run(verbose = 3)
-
-            Task enters queue = this_task_might_be_inactive
-
-                Job  = [a.foo -> a.bar] Missing file [a.bar]
-                Job  = [b.foo -> b.bar] Missing file [b.bar]
-                Job  = [a.foo -> a.bar] completed
-                Job  = [b.foo -> b.bar] completed
-            Completed Task = this_task_might_be_inactive
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/check_if_uptodate.txt b/doc/_build/html/_sources/tutorials/new_tutorial/check_if_uptodate.txt
deleted file mode 100644
index 2323d29..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/check_if_uptodate.txt
+++ /dev/null
@@ -1,89 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: check_if_uptodate; Tutorial
-
-.. _new_manual.check_if_uptodate:
-
-########################################################################################################################################################################################################################################################################################################
-|new_manual.check_if_uptodate.chapter_num|: Esoteric: Writing custom functions to decide which jobs are up to date with :ref:`@check_if_uptodate<decorators.check_if_uptodate>`
-########################################################################################################################################################################################################################################################################################################
-
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@check_if_uptodate  syntax in detail<decorators.check_if_uptodate>`
-
-
-******************************************************************************
-**@check_if_uptodate** : Manual dependency checking
-******************************************************************************
-    tasks specified with most decorators such as
-        * :ref:`@split <decorators.split>`
-        * :ref:`@transform <decorators.transform>`
-        * :ref:`@merge <decorators.merge>`
-        * :ref:`@collate <decorators.collate>`
-        * :ref:`@collate <decorators.subdivide>`
-
-    have automatic dependency checking based on file modification times.
-
-    Sometimes, you might want to decide have more control over whether to run jobs, especially
-    if a task does not rely on or produce files (i.e. with :ref:`@parallel <decorators.parallel>`)
-
-    You can write your own custom function to decide whether to run a job.
-    This takes as many parameters as your task function, and needs to return a
-    tuple for whether an update is required, and why (i.e. ``tuple(bool, str)``)
-
-    This simple example which creates the file ``"a.1"`` if it does not exist:
-
-        ::
-
-            from ruffus import *
-            @originate("a.1")
-            def create_if_necessary(output_file):
-                open(output_file, "w")
-
-            pipeline_run([])
-
-
-
-    could be rewritten more laboriously as:
-
-        ::
-
-
-            from ruffus import *
-            import os
-            def check_file_exists(input_file, output_file):
-                if os.path.exists(output_file):
-                    return False, "File already exists"
-                return True, "%s is missing" % output_file
-
-            @parallel([[None, "a.1"]])
-            @check_if_uptodate(check_file_exists)
-            def create_if_necessary(input_file, output_file):
-                open(output_file, "w")
-
-            pipeline_run([create_if_necessary])
-
-
-
-    Both produce the same output:
-        ::
-
-            Task = create_if_necessary
-                Job = [null, "a.1"] completed
-
-
-
-
-.. note::
-
-    The function specified by :ref:`@check_if_uptodate <decorators.check_if_uptodate>` can be called
-    more than once for each job.
-
-    See the :ref:`description here <new_manual.dependencies>` of how *Ruffus* decides which tasks to run.
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/checkpointing.txt b/doc/_build/html/_sources/tutorials/new_tutorial/checkpointing.txt
deleted file mode 100644
index f512806..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/checkpointing.txt
+++ /dev/null
@@ -1,400 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: Up to date; Tutorial
-    pair: Task completion; Tutorial
-    pair: Exceptions; Tutorial
-    pair: Interrupted Pipeline; Tutorial
-
-.. _new_manual.checkpointing:
-
-######################################################################################################
-|new_manual.checkpointing.chapter_num|: Checkpointing: Interrupted Pipelines and Exceptions
-######################################################################################################
-
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-
-.. note::
-
-    Remember to look at the example code:
-
-    * :ref:`new_manual.checkpointing.code`
-
-
-
-***************************************
-Overview
-***************************************
-    .. image:: ../../images/theoretical_pipeline_schematic.png
-       :scale: 50
-
-    Computational pipelines transform your data in stages until the final result is produced.
-
-    By default, *Ruffus* uses file modification times for the **input** and **output** to determine
-    whether each stage of a pipeline is up-to-date or not. But what happens when the task
-    function is interrupted, whether from the command line or by error, half way through writing the output?
-
-    In this case, the half-formed, truncated and corrupt **Output** file will look newer than its **Input** and hence up-to-date.
-
-
-.. index::
-    pair: Tutorial; interrupting tasks
-
-.. _new_manual.interrupting_tasks:
-
-***************************************
-Interrupting tasks
-***************************************
-    Let us try with an example:
-
-        .. code-block:: python
-            :emphasize-lines: 20
-
-            from ruffus import *
-            import sys, time
-
-            #   create initial files
-            @originate(['job1.start'])
-            def create_initial_files(output_file):
-                with open(output_file, "w") as oo: pass
-
-
-            #---------------------------------------------------------------
-            #
-            #   long task to interrupt
-            #
-            @transform(create_initial_files, suffix(".start"), ".output")
-            def long_task(input_files, output_file):
-                with open(output_file, "w") as ff:
-                    ff.write("Unfinished...")
-                    # sleep for 2 seconds here so you can interrupt me
-                    sys.stderr.write("Job started. Press ^C to interrupt me now...\n")
-                    time.sleep(2)
-                    ff.write("\nFinished")
-                    sys.stderr.write("Job completed.\n")
-
-
-            #       Run
-            pipeline_run([long_task])
-
-
-    When this script runs, it pauses in the middle with this message::
-
-        Job started. Press ^C to interrupt me now...
-
-    If you interrupted the script by pressing Control-C at this point, you will see that ``job1.output`` contains only ``Unfinished...``.
-    However, if you should rerun the interrupted pipeline again, Ruffus ignores the corrupt, incomplete file:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run([long_task])
-            Job started. Press ^C to interrupt me now...
-            Job completed
-
-    And if you had run ``pipeline_printout``:
-
-        .. code-block:: pycon
-            :emphasize-lines: 8
-
-            >>> pipeline_printout(sys.stdout, [long_task], verbose=3)
-            ________________________________________
-            Tasks which will be run:
-
-            Task = long_task
-                   Job  = [job1.start
-                         -> job1.output]
-                     # Job needs update: Previous incomplete run leftover: [job1.output]
-
-
-    We can see that *Ruffus* magically knows that the previous run was incomplete, and that ``job1.output`` is detritus that needs to be discarded.
-
-
-.. _new_manual.logging_completed_jobs:
-
-******************************************
-Checkpointing: only log completed jobs
-******************************************
-
-    All is revealed if you were to look in the working directory. *Ruffus* has created a file called ``.ruffus_history.sqlite``.
-    In this `SQLite  <https://sqlite.org/>`_ database, *Ruffus* logs only those files which are the result of a completed job,
-    all other files are suspect.
-    This file checkpoint database is a fail-safe, not a substitute for checking file modification times. If the **Input** or **Output** files are
-    modified, the pipeline will rerun.
-
-    By default, *Ruffus* saves only file timestamps to the SQLite database but you can also add a checksum of the pipeline task function body or parameters.
-    This behaviour can be controlled by setting the ``checksum_level`` parameter
-    in ``pipeline_run()``. For example, if you do not want to save any timestamps or checksums:
-
-        .. code-block:: python
-
-            pipeline_run(checksum_level = 0)
-
-            CHECKSUM_FILE_TIMESTAMPS      = 0     # only rerun when the file timestamps are out of date (classic mode)
-            CHECKSUM_HISTORY_TIMESTAMPS   = 1     # Default: also rerun when the history shows a job as being out of date
-            CHECKSUM_FUNCTIONS            = 2     # also rerun when function body has changed
-            CHECKSUM_FUNCTIONS_AND_PARAMS = 3     # also rerun when function parameters or function body change
-
-
-    .. note::
-
-        Checksums are calculated from the `pickled  <http://docs.python.org/2/library/pickle.html>`_ string for the function code and parameters.
-        If pickling fails, Ruffus will degrade gracefully to saving just the timestamp in the SQLite database.
-
-.. _new_manual.history_files_cannot_be_shared:
-
-****************************************************************************
-Do not share the same checkpoint file across for multiple pipelines!
-****************************************************************************
-
-    The name of the Ruffus python script is not saved in the checkpoint file along side timestamps and checksums.
-    That means that you can rename your pipeline source code file without having to rerun the pipeline!
-    The tradeoff is that if multiple pipelines are run from the same directory, and save their histories to the
-    same SQlite database file, and if their file names overlap (all of these are bad ideas anyway!), this is
-    bound to be a source of confusion.
-
-    Luckily, the name and path of the checkpoint file can be also changed for each pipeline
-
-.. _new_manual.changing_history_file_name:
-
-****************************************************************************
-Setting checkpoint file names
-****************************************************************************
-
-    .. warning::
-
-        Some file systems do not appear to support SQLite at all:
-
-        There are reports that SQLite databases have `file locking problems  <http://beets.radbox.org/blog/sqlite-nightmare.html>`_ on Lustre.
-
-        The best solution would be to keep the SQLite database on an alternate compatible file system away from the working directory if possible.
-
-============================================================================================================================================================
-environment variable ``DEFAULT_RUFFUS_HISTORY_FILE``
-============================================================================================================================================================
-
-    The name of the checkpoint file is the value of the environment variable ``DEFAULT_RUFFUS_HISTORY_FILE``.
-
-        export DEFAULT_RUFFUS_HISTORY_FILE=/some/where/.ruffus_history.sqlite
-
-    This gives considerable flexibility, and allows a system-wide policy to be set so that all Ruffus checkpoint files are set logically to particular paths.
-
-    .. note::
-
-        It is your responsibility to make sure that the requisite destination directories for the checkpoint files exist beforehand!
-
-
-    Where this is missing, the checkpoint file defaults to ``.ruffus_history.sqlite`` in your working directory
-
-
-============================================================================================================================================================
-Setting the checkpoint file name manually
-============================================================================================================================================================
-
-    This checkpoint file name can always be overridden as a parameter to Ruffus functions:
-
-        .. code-block:: python
-
-            pipeline_run(history_file = "XXX")
-            pipeline_printout(history_file = "XXX")
-            pipeline_printout_graph(history_file = "XXX")
-
-
-    There is also built in support in ``Ruffus.cmdline``. So if you use this module, you can simply add to your command line:
-
-        .. code-block:: bash
-
-            # use a custom checkpoint file
-            myscript --checksum_file_name .myscript.ruffus_history.sqlite
-
-    This takes precedence over everything else.
-
-
-
-****************************************************************************
-Useful checkpoint file name policies ``DEFAULT_RUFFUS_HISTORY_FILE``
-****************************************************************************
-
-    If the pipeline script is called ``test/bin/scripts/run.me.py``, then these are the resulting checkpoint files locations:
-
-============================================================================================================================================================
-Example 1: same directory, different name
-============================================================================================================================================================
-    If the environment variable is:
-
-    .. code-block:: bash
-
-        export DEFAULT_RUFFUS_HISTORY_FILE=.{basename}.ruffus_history.sqlite
-
-    Then the job checkpoint database for ``run.me.py`` will be ``.run.me.ruffus_history.sqlite``
-
-    .. code-block:: bash
-
-        /test/bin/scripts/run.me.py
-        /common/path/for/job_history/scripts/.run.me.ruffus_history.sqlite
-
-============================================================================================================================================================
-Example 2: Different directory, same name
-============================================================================================================================================================
-
-    .. code-block:: bash
-
-        export DEFAULT_RUFFUS_HISTORY_FILE=/common/path/for/job_history/.{basename}.ruffus_history.sqlite
-
-    .. code-block:: bash
-
-        /common/path/for/job_history/.run.me.ruffus_history.sqlite
-
-
-============================================================================================================================================================
-Example 2: Different directory, same name but keep one level of subdirectory to disambiguate
-============================================================================================================================================================
-
-    .. code-block:: bash
-
-        export DEFAULT_RUFFUS_HISTORY_FILE=/common/path/for/job_history/{subdir[0]}/.{basename}.ruffus_history.sqlite
-
-
-    .. code-block:: bash
-
-        /common/path/for/job_history/scripts/.run.me.ruffus_history.sqlite
-
-
-
-============================================================================================================================================================
-Example 2: nested in common directory
-============================================================================================================================================================
-
-    .. code-block:: bash
-
-        export DEFAULT_RUFFUS_HISTORY_FILE=/common/path/for/job_history/{path}/.{basename}.ruffus_history.sqlite
-
-    .. code-block:: bash
-
-        /common/path/for/job_history/test/bin/scripts/.run.me.ruffus_history.sqlite
-
-
-
-
-.. index::
-    pair: Tutorial; Regenerating the checkpoint file
-
-.. _new_manual.regenerating_history_file:
-
-******************************************************************************
-Regenerating the checkpoint file
-******************************************************************************
-
-    Occasionally you may need to re-generate the checkpoint file.
-
-    This could be necessary:
-
-        * because you are upgrading from a previous version of Ruffus without checkpoint file support
-        * on the rare occasions when the SQLite file becomes corrupted and has to deleted
-        * if you wish to circumvent the file checking of Ruffus after making some manual changes!
-
-    To do this, it is only necessary to call ``pipeline_run`` appropriately:
-
-        .. code-block:: python
-
-            CHECKSUM_REGENERATE = 2
-            pipeline(touch_files_only = CHECKSUM_REGENERATE)
-
-
-    Similarly, if you are using ``Ruffus.cmdline``, you can call:
-
-        .. code-block:: bash
-
-            myscript --recreate_database
-
-
-    Note that this regenerates the checkpoint file to reflect the existing *Input*, *Output* files on disk.
-    In other words, the onus is on you to make sure there are no half-formed, corrupt files. On the other hand,
-    the pipeline does not need to have been previously run successfully for this to work. Essentially, Ruffus,
-    pretends to run the pipeline, while logging all the files with consistent file modication times, stopping
-    at the first tasks which appear out of date or incomplete.
-
-
-.. index::
-    pair: rules; for rerunning jobs
-
-.. _new_manual.skip_up_to_date.rules:
-
-******************************************************************************
-Rules for determining if files are up to date
-******************************************************************************
-    The following simple rules are used by *Ruffus*.
-
-    #. The pipeline stage will be rerun if:
-
-        * If any of the **Input** files are new (newer than the **Output** files)
-        * If any of the **Output** files are missing
-
-    #. In addition, it is possible to run jobs which create files from scratch.
-
-        * If no **Input** file names are supplied, the job will only run if any *output* file is missing.
-
-    #. Finally, if no **Output** file names are supplied, the job will always run.
-
-
-
-.. index::
-    pair: Exception; Missing input files
-
-******************************************************************************
-Missing files generate exceptions
-******************************************************************************
-
-    If the *inputs* files for a job are missing, the task function will have no way
-    to produce its *output*. In this case, a ``MissingInputFileError`` exception will be raised
-    automatically. For example,
-
-        ::
-
-            task.MissingInputFileError: No way to run job: Input file ['a.1'] does not exist
-            for Job = ["a.1" -> "a.2", "A file"]
-
-.. index::
-    pair: Manual; Timestamp resolution
-
-******************************************************************************
-Caveats: Coarse Timestamp resolution
-******************************************************************************
-
-    Note that modification times have precision to the nearest second under some older file systems
-    (ext2/ext3?). This may be also be true for networked file systems.
-
-    *Ruffus* supplements the file system time resolution by independently recording the timestamp at
-    full OS resolution (usually to at least the millisecond) at job completion, when presumably the **Output**
-    files will have been created.
-
-    However, *Ruffus* only does this if the discrepancy between file time and system time is less than a second
-    (due to poor file system timestamp resolution). If there are large mismatches between the two, due for example
-    to network time slippage, misconfiguration etc, *Ruffus* reverts to using the file system time and adds a one second
-    delay between jobs (via ``time.sleep()``) to make sure input and output file stamps are different.
-
-    If you know that your filesystem has coarse-grained timestamp resolution, you can always revert to this very conservative behaviour,
-    at the prices of some annoying 1s pauses, by setting :ref:`pipeline_run(one_second_per_job = True) <pipeline_functions.pipeline_run>`
-
-
-
-.. index::
-    pair: Manual; flag files
-
-******************************************************************************
-Flag files: Checkpointing for the paranoid
-******************************************************************************
-
-    One other way of checkpointing your pipelines is to create an extra "flag" file as an additional
-    **Output** file name. The flag file is only created or updated when everything else in the
-    job has completed successifully and written to disk. A missing or out of date flag file then
-    would be a sign for Ruffus that the task never completed properly in the first place.
-
-    This used to be much the best way of performing checkpointing in Ruffus and is still
-    the most bulletproof way of proceeding. For example, even the loss or corruption
-    of the checkpoint file, would not affect things greatly.
-
-    Nevertheless flag files are largely superfluous in modern *Ruffus*.
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/checkpointing_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/checkpointing_code.txt
deleted file mode 100644
index 27632e8..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/checkpointing_code.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.checkpointing.code:
-
-#################################################################################################################
-|new_manual.checkpointing.chapter_num|: Python Code for Checkpointing: Interrupted Pipelines and Exceptions
-#################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`Back to |new_manual.checkpointing.chapter_num|: Interrupted Pipelines and Exceptions <new_manual.checkpointing>`
-
-
-************************************************************************
-Code for .:ref:`suffix() <decorators.suffix>` example
-************************************************************************
-    .. code-block:: python
-
-        from ruffus import *
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/combinatorics.txt b/doc/_build/html/_sources/tutorials/new_tutorial/combinatorics.txt
deleted file mode 100644
index 3e89ca1..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/combinatorics.txt
+++ /dev/null
@@ -1,442 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: combinatorics; Tutorial
-
-.. _new_manual.combinatorics:
-
-##################################################################################################################################################################################################################################################
-|new_manual.combinatorics.chapter_num|: :ref:`@combinations<decorators.combinations>`, :ref:`@permutations<decorators.permutations>` and all versus all :ref:`@product<decorators.product>`
-##################################################################################################################################################################################################################################################
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`
-   * :ref:`@combinations <decorators.combinations>`
-   * :ref:`@permutations <decorators.permutations>`
-   * :ref:`@product <decorators.product>`
-   * :ref:`formatter() <decorators.formatter>`
-
-.. note::
-
-    Remember to look at the example code:
-
-        * :ref:`new_manual.combinatorics.code`
-
-
-**************************************
-Overview
-**************************************
-
-    A surprising number of computational problems involve some sort of all versus all calculations.
-    Previously, this would have required all the parameters to be supplied using a custom function
-    on the fly with :ref:`@files<decorators.files_on_the_fly>`.
-
-    From version 2.4, *Ruffus* supports  :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`,
-    :ref:`@combinations <decorators.combinations>`, :ref:`@permutations <decorators.permutations>`,
-    :ref:`@product <decorators.product>`.
-
-    These provide as far as possible all the functionality of the four combinatorics iterators
-    from the standard python `itertools  <http://docs.python.org/2/library/itertools.html>`__
-    functions of the same name.
-
-***************************************************************************
-Generating output with :ref:`formatter()<decorators.formatter>`
-***************************************************************************
-
-    String replacement always takes place via :ref:`formatter()<decorators.formatter>`. Unfortunately,
-    the other *Ruffus* workhorses of  :ref:`regex()<decorators.regex>` and  :ref:`suffix()<decorators.suffix>`
-    do not have sufficient syntactic flexibility.
-
-    Each combinatorics decorator deals with multiple sets of inputs whether this might be:
-
-        * a self-self comparison (such as :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`,
-          :ref:`@combinations <decorators.combinations>`, :ref:`@permutations <decorators.permutations>`) or,
-        * a self-other comparison (:ref:`@product <decorators.product>`)
-
-    The replacement strings thus require an extra level of indirection to refer to
-    parsed components.
-
-        #. The first level refers to which *set* of inputs.
-        #. The second level refers to which input file in any particular *set* of inputs.
-
-
-    For example, if the *inputs* are  **[A1,A2],[B1,B2],[C1,C2] vs [P1,P2],[Q1,Q2],[R1,R2] vs [X1,X2],[Y1,Y2],[Z1,Z2]**,
-    then ``'{basename[2][0]}'`` is the `basename  <http://docs.python.org/2/library/os.path.html#os.path.basename>`__ for
-
-        * the third set of inputs (**X,Y,Z**) and
-        * the first file name string in each **Input** of that set (**X1, Y1, Z1**)
-
-
-
-.. _new_manual.product:
-
-***************************************************************************
-All vs all comparisons with :ref:`@product <decorators.product>`
-***************************************************************************
-
-    :ref:`@product <decorators.product>` generates the Cartesian **product** between sets of input files,
-    i.e. all vs all comparisons.
-
-    The effect is analogous to a nested for loop.
-
-    :ref:`@product <decorators.product>` can be useful, for example, in bioinformatics for finding
-    the corresponding genes (orthologues) for a set of proteins in multiple species.
-
-    .. code-block:: pycon
-        :emphasize-lines: 2
-
-        >>> from itertools import product
-        >>> # product('ABC', 'XYZ') --> AX AY AZ BX BY BZ CX CY CZ
-        >>> [ "".join(a) for a in product('ABC', 'XYZ')]
-        ['AX', 'AY', 'AZ', 'BX', 'BY', 'BZ', 'CX', 'CY', 'CZ']
-
-
-
-    This example Calculates the **@product** of **A,B** and **P,Q** and **X,Y** files
-
-        .. code-block:: python
-            :emphasize-lines: 4,17,19,22,25,27,28,29,30,32,34,35,36
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   Three sets of initial files
-            @originate([ 'a.start', 'b.start'])
-            def create_initial_files_ab(output_file):
-                with open(output_file, "w") as oo: pass
-
-            @originate([ 'p.start', 'q.start'])
-            def create_initial_files_pq(output_file):
-                with open(output_file, "w") as oo: pass
-
-            @originate([ ['x.1_start', 'x.2_start'],
-                         ['y.1_start', 'y.2_start'] ])
-            def create_initial_files_xy(output_file):
-                with open(output_file, "w") as oo: pass
-
-            #   @product
-            @product(   create_initial_files_ab,        # Input
-                        formatter("(.start)$"),         # match input file set # 1
-
-                        create_initial_files_pq,        # Input
-                        formatter("(.start)$"),         # match input file set # 2
-
-                        create_initial_files_xy,        # Input
-                        formatter("(.start)$"),         # match input file set # 3
-
-                        "{path[0][0]}/"                 # Output Replacement string
-                        "{basename[0][0]}_vs_"          #
-                        "{basename[1][0]}_vs_"          #
-                        "{basename[2][0]}.product",     #
-
-                        "{path[0][0]}",                 # Extra parameter: path for 1st set of files, 1st file name
-
-                        ["{basename[0][0]}",            # Extra parameter: basename for 1st set of files, 1st file name
-                         "{basename[1][0]}",            #                               2nd
-                         "{basename[2][0]}",            #                               3rd
-                         ])
-            def product_task(input_file, output_parameter, shared_path, basenames):
-                print "# basenames      = ", " ".join(basenames)
-                print "input_parameter  = ", input_file
-                print "output_parameter = ", output_parameter, "\n"
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-    This results in:
-
-        .. code-block:: pycon
-            :emphasize-lines: 2,6,10,14,18,22,26,30
-
-            >>> pipeline_run(verbose=0)
-
-            # basenames      =  a p x
-            input_parameter  =  ('a.start', 'p.start', 'x.start')
-            output_parameter =  /home/lg/temp/a_vs_p_vs_x.product
-
-            # basenames      =  a p y
-            input_parameter  =  ('a.start', 'p.start', 'y.start')
-            output_parameter =  /home/lg/temp/a_vs_p_vs_y.product
-
-            # basenames      =  a q x
-            input_parameter  =  ('a.start', 'q.start', 'x.start')
-            output_parameter =  /home/lg/temp/a_vs_q_vs_x.product
-
-            # basenames      =  a q y
-            input_parameter  =  ('a.start', 'q.start', 'y.start')
-            output_parameter =  /home/lg/temp/a_vs_q_vs_y.product
-
-            # basenames      =  b p x
-            input_parameter  =  ('b.start', 'p.start', 'x.start')
-            output_parameter =  /home/lg/temp/b_vs_p_vs_x.product
-
-            # basenames      =  b p y
-            input_parameter  =  ('b.start', 'p.start', 'y.start')
-            output_parameter =  /home/lg/temp/b_vs_p_vs_y.product
-
-            # basenames      =  b q x
-            input_parameter  =  ('b.start', 'q.start', 'x.start')
-            output_parameter =  /home/lg/temp/b_vs_q_vs_x.product
-
-            # basenames      =  b q y
-            input_parameter  =  ('b.start', 'q.start', 'y.start')
-            output_parameter =  /home/lg/temp/b_vs_q_vs_y.product
-
-
-.. _new_manual.permutations:
-
-******************************************************************************************************************************************************
-Permute all k-tuple orderings of inputs without repeats using :ref:`@permutations <decorators.permutations>`
-******************************************************************************************************************************************************
-
-    Generates the **permutations** for all the elements of a set of **Input** (e.g. **A B C D**),
-        * r-length tuples of *input* elements
-        * excluding repeated elements (**A A**)
-        * and order of the tuples is significant (both **A B** and  **B A**).
-
-    .. code-block:: pycon
-        :emphasize-lines: 2
-
-        >>> from itertools import permutations
-        >>> # permutations('ABCD', 2) --> AB AC AD BA BC BD CA CB CD DA DB DC
-        >>> [ "".join(a) for a in permutations("ABCD", 2)]
-        ['AB', 'AC', 'AD', 'BA', 'BC', 'BD', 'CA', 'CB', 'CD', 'DA', 'DB', 'DC']
-
-    This following example calculates the **@permutations** of **A,B,C,D** files
-
-        .. code-block:: python
-            :emphasize-lines: 13,17,20,25,28-30
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   initial file pairs
-            @originate([ ['A.1_start', 'A.2_start'],
-                         ['B.1_start', 'B.2_start'],
-                         ['C.1_start', 'C.2_start'],
-                         ['D.1_start', 'D.2_start']])
-            def create_initial_files_ABCD(output_files):
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-            #   @permutations
-            @permutations(create_initial_files_ABCD,      # Input
-                          formatter(),                    # match input files
-
-                          # tuple of 2 at a time
-                          2,
-
-                          # Output Replacement string
-                          "{path[0][0]}/"
-                          "{basename[0][1]}_vs_"
-                          "{basename[1][1]}.permutations",
-
-                          # Extra parameter: path for 1st set of files, 1st file name
-                          "{path[0][0]}",
-
-                          # Extra parameter
-                          ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                           "{basename[1][0]}",  #                                2nd
-                           ])
-            def permutations_task(input_file, output_parameter, shared_path, basenames):
-                print " - ".join(basenames)
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-    This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-
-            A - B
-            A - C
-            A - D
-            B - A
-            B - C
-            B - D
-            C - A
-            C - B
-            C - D
-            D - A
-            D - B
-            D - C
-
-.. _new_manual.combinations:
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-Select unordered k-tuples within inputs excluding repeated elements using :ref:`@combinations <decorators.combinations>`
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-
-    Generates the **combinations** for all the elements of a set of **Input** (e.g. **A B C D**),
-        * r-length tuples of *input* elements
-        * without repeated elements (**A A**)
-        * where order of the tuples is irrelevant (either **A B** or  **B A**, not both).
-
-    :ref:`@combinations <decorators.combinations>` can be useful, for example, in calculating a transition probability matrix
-    for a set of states. The diagonals are meaningless "self-self" transitions which are excluded.
-
-    .. code-block:: pycon
-        :emphasize-lines: 2
-
-        >>> from itertools import combinations
-        >>> # combinations('ABCD', 3) --> ABC ABD ACD BCD
-        >>> [ "".join(a) for a in combinations("ABCD", 3)]
-        ['ABC', 'ABD', 'ACD', 'BCD']
-
-    This example calculates the **@combinations** of **A,B,C,D** files
-
-        .. code-block:: python
-            :emphasize-lines: 13,17,20,25,28-30
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   initial file pairs
-            @originate([ ['A.1_start', 'A.2_start'],
-                         ['B.1_start', 'B.2_start'],
-                         ['C.1_start', 'C.2_start'],
-                         ['D.1_start', 'D.2_start']])
-            def create_initial_files_ABCD(output_files):
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-            #   @combinations
-            @combinations(create_initial_files_ABCD,      # Input
-                          formatter(),                    # match input files
-
-                          # tuple of 3 at a time
-                          3,
-
-                          # Output Replacement string
-                          "{path[0][0]}/"
-                          "{basename[0][1]}_vs_"
-                          "{basename[1][1]}_vs_"
-                          "{basename[2][1]}.combinations",
-
-                          # Extra parameter: path for 1st set of files, 1st file name
-                          "{path[0][0]}",
-
-                          # Extra parameter
-                          ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                           "{basename[1][0]}",  #              2nd
-                           "{basename[2][0]}",  #              3rd
-                           ])
-            def combinations_task(input_file, output_parameter, shared_path, basenames):
-                print " - ".join(basenames)
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-    This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-            A - B - C
-            A - B - D
-            A - C - D
-            B - C - D
-
-.. _new_manual.combinations_with_replacement:
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-Select unordered k-tuples within inputs *including* repeated elements with :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-
-    Generates the **combinations_with_replacement** for all the elements of a set of **Input** (e.g. **A B C D**),
-        * r-length tuples of *input* elements
-        * including repeated elements (**A A**)
-        * where order of the tuples is irrelevant (either **A B** or  **B A**, not both).
-
-
-    :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>` can be useful,
-    for example, in bioinformatics for finding evolutionary relationships between genetic elements such as proteins
-    and genes. Self-self comparisons can be used a baseline for scaling similarity scores.
-
-    .. code-block:: pycon
-        :emphasize-lines: 2
-
-        >>> from itertools import combinations_with_replacement
-        >>> # combinations_with_replacement('ABCD', 2) --> AA AB AC AD BB BC BD CC CD DD
-        >>> [ "".join(a) for a in combinations_with_replacement('ABCD', 2)]
-        ['AA', 'AB', 'AC', 'AD', 'BB', 'BC', 'BD', 'CC', 'CD', 'DD']
-
-    This example calculates the **@combinations_with_replacement** of **A,B,C,D** files
-
-        .. code-block:: python
-            :emphasize-lines: 13,17,20,25,28-30
-
-            from ruffus import *
-            from ruffus.combinatorics import *
-
-            #   initial file pairs
-            @originate([ ['A.1_start', 'A.2_start'],
-                         ['B.1_start', 'B.2_start'],
-                         ['C.1_start', 'C.2_start'],
-                         ['D.1_start', 'D.2_start']])
-            def create_initial_files_ABCD(output_files):
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-            #   @combinations_with_replacement
-            @combinations_with_replacement(create_initial_files_ABCD,   # Input
-                          formatter(),                                  # match input files
-
-                          # tuple of 2 at a time
-                          2,
-
-                          # Output Replacement string
-                          "{path[0][0]}/"
-                          "{basename[0][1]}_vs_"
-                          "{basename[1][1]}.combinations_with_replacement",
-
-                          # Extra parameter: path for 1st set of files, 1st file name
-                          "{path[0][0]}",
-
-                          # Extra parameter
-                          ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                           "{basename[1][0]}",  #              2rd
-                           ])
-            def combinations_with_replacement_task(input_file, output_parameter, shared_path, basenames):
-                print " - ".join(basenames)
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-    This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-            A - A
-            A - B
-            A - C
-            A - D
-            B - B
-            B - C
-            B - D
-            C - C
-            C - D
-            D - D
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/combinatorics_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/combinatorics_code.txt
deleted file mode 100644
index 3113601..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/combinatorics_code.txt
+++ /dev/null
@@ -1,308 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.combinatorics.code:
-
-############################################################################################################################################################################################################
-|new_manual.combinatorics.chapter_num|: Python Code for :ref:`@combinations<decorators.combinations>`, :ref:`@permutations<decorators.permutations>` and all versus all :ref:`@product<decorators.product>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`
-   * :ref:`@combinations <decorators.combinations>`
-   * :ref:`@permutations <decorators.permutations>`
-   * :ref:`@product <decorators.product>`
-   * Back to |new_manual.combinatorics.chapter_num|: :ref:`Preparing directories for output with @combinatorics() <new_manual.combinatorics>`
-
-***************************************************************************
-Example code for :ref:`@product <decorators.product>`
-***************************************************************************
-
-    .. code-block:: python
-        :emphasize-lines: 4,17,19,22,25,27,28,29,30,32,34,35,36
-
-        from ruffus import *
-        from ruffus.combinatorics import *
-
-        #   Three sets of initial files
-        @originate([ 'a.start', 'b.start'])
-        def create_initial_files_ab(output_file):
-            with open(output_file, "w") as oo: pass
-
-        @originate([ 'p.start', 'q.start'])
-        def create_initial_files_pq(output_file):
-            with open(output_file, "w") as oo: pass
-
-        @originate([ ['x.1_start', 'x.2_start'],
-                     ['y.1_start', 'y.2_start'] ])
-        def create_initial_files_xy(output_file):
-            with open(output_file, "w") as oo: pass
-
-        #   @product
-        @product(   create_initial_files_ab,        # Input
-                    formatter("(.start)$"),         # match input file set # 1
-
-                    create_initial_files_pq,        # Input
-                    formatter("(.start)$"),         # match input file set # 2
-
-                    create_initial_files_xy,        # Input
-                    formatter("(.start)$"),         # match input file set # 3
-
-                    "{path[0][0]}/"                 # Output Replacement string
-                    "{basename[0][0]}_vs_"          #
-                    "{basename[1][0]}_vs_"          #
-                    "{basename[2][0]}.product",     #
-
-                    "{path[0][0]}",                 # Extra parameter: path for 1st set of files, 1st file name
-
-                    ["{basename[0][0]}",            # Extra parameter: basename for 1st set of files, 1st file name
-                     "{basename[1][0]}",            #                               2nd
-                     "{basename[2][0]}",            #                               3rd
-                     ])
-        def product_task(input_file, output_parameter, shared_path, basenames):
-            print "# basenames      = ", " ".join(basenames)
-            print "input_parameter  = ", input_file
-            print "output_parameter = ", output_parameter, "\n"
-
-
-        #
-        #       Run
-        #
-        pipeline_run(verbose=0)
-
-
-    This results in:
-
-        .. code-block:: pycon
-            :emphasize-lines: 2,6,10,14,18,22,26,30
-
-            >>> pipeline_run(verbose=0)
-
-            # basenames      =  a p x
-            input_parameter  =  ('a.start', 'p.start', 'x.start')
-            output_parameter =  /home/lg/temp/a_vs_p_vs_x.product
-
-            # basenames      =  a p y
-            input_parameter  =  ('a.start', 'p.start', 'y.start')
-            output_parameter =  /home/lg/temp/a_vs_p_vs_y.product
-
-            # basenames      =  a q x
-            input_parameter  =  ('a.start', 'q.start', 'x.start')
-            output_parameter =  /home/lg/temp/a_vs_q_vs_x.product
-
-            # basenames      =  a q y
-            input_parameter  =  ('a.start', 'q.start', 'y.start')
-            output_parameter =  /home/lg/temp/a_vs_q_vs_y.product
-
-            # basenames      =  b p x
-            input_parameter  =  ('b.start', 'p.start', 'x.start')
-            output_parameter =  /home/lg/temp/b_vs_p_vs_x.product
-
-            # basenames      =  b p y
-            input_parameter  =  ('b.start', 'p.start', 'y.start')
-            output_parameter =  /home/lg/temp/b_vs_p_vs_y.product
-
-            # basenames      =  b q x
-            input_parameter  =  ('b.start', 'q.start', 'x.start')
-            output_parameter =  /home/lg/temp/b_vs_q_vs_x.product
-
-            # basenames      =  b q y
-            input_parameter  =  ('b.start', 'q.start', 'y.start')
-            output_parameter =  /home/lg/temp/b_vs_q_vs_y.product
-
-******************************************************************************************************************************************************
-Example code for :ref:`@permutations <decorators.permutations>`
-******************************************************************************************************************************************************
-
-
-    .. code-block:: python
-        :emphasize-lines: 13,17,20,25,28-30
-
-        from ruffus import *
-        from ruffus.combinatorics import *
-
-        #   initial file pairs
-        @originate([ ['A.1_start', 'A.2_start'],
-                     ['B.1_start', 'B.2_start'],
-                     ['C.1_start', 'C.2_start'],
-                     ['D.1_start', 'D.2_start']])
-        def create_initial_files_ABCD(output_files):
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-        #   @permutations
-        @permutations(create_initial_files_ABCD,      # Input
-                      formatter(),                    # match input files
-
-                      # tuple of 2 at a time
-                      2,
-
-                      # Output Replacement string
-                      "{path[0][0]}/"
-                      "{basename[0][1]}_vs_"
-                      "{basename[1][1]}.permutations",
-
-                      # Extra parameter: path for 1st set of files, 1st file name
-                      "{path[0][0]}",
-
-                      # Extra parameter
-                      ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                       "{basename[1][0]}",  #                                2nd
-                       ])
-        def permutations_task(input_file, output_parameter, shared_path, basenames):
-            print " - ".join(basenames)
-
-
-        #
-        #       Run
-        #
-        pipeline_run(verbose=0)
-
-
-    This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-
-            A - B
-            A - C
-            A - D
-            B - A
-            B - C
-            B - D
-            C - A
-            C - B
-            C - D
-            D - A
-            D - B
-            D - C
-
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-Example code for :ref:`@combinations <decorators.combinations>`
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-
-    .. code-block:: python
-        :emphasize-lines: 13,17,20,25,28-30
-
-        from ruffus import *
-        from ruffus.combinatorics import *
-
-        #   initial file pairs
-        @originate([ ['A.1_start', 'A.2_start'],
-                     ['B.1_start', 'B.2_start'],
-                     ['C.1_start', 'C.2_start'],
-                     ['D.1_start', 'D.2_start']])
-        def create_initial_files_ABCD(output_files):
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-        #   @combinations
-        @combinations(create_initial_files_ABCD,      # Input
-                      formatter(),                    # match input files
-
-                      # tuple of 3 at a time
-                      3,
-
-                      # Output Replacement string
-                      "{path[0][0]}/"
-                      "{basename[0][1]}_vs_"
-                      "{basename[1][1]}_vs_"
-                      "{basename[2][1]}.combinations",
-
-                      # Extra parameter: path for 1st set of files, 1st file name
-                      "{path[0][0]}",
-
-                      # Extra parameter
-                      ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                       "{basename[1][0]}",  #              2nd
-                       "{basename[2][0]}",  #              3rd
-                       ])
-        def combinations_task(input_file, output_parameter, shared_path, basenames):
-            print " - ".join(basenames)
-
-
-        #
-        #       Run
-        #
-        pipeline_run(verbose=0)
-
-
-    This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-            A - B - C
-            A - B - D
-            A - C - D
-            B - C - D
-
-
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-Example code for :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`
-********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************
-
-    .. code-block:: python
-        :emphasize-lines: 13,17,20,25,28-30
-
-        from ruffus import *
-        from ruffus.combinatorics import *
-
-        #   initial file pairs
-        @originate([ ['A.1_start', 'A.2_start'],
-                     ['B.1_start', 'B.2_start'],
-                     ['C.1_start', 'C.2_start'],
-                     ['D.1_start', 'D.2_start']])
-        def create_initial_files_ABCD(output_files):
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-        #   @combinations_with_replacement
-        @combinations_with_replacement(create_initial_files_ABCD,   # Input
-                      formatter(),                                  # match input files
-
-                      # tuple of 2 at a time
-                      2,
-
-                      # Output Replacement string
-                      "{path[0][0]}/"
-                      "{basename[0][1]}_vs_"
-                      "{basename[1][1]}.combinations_with_replacement",
-
-                      # Extra parameter: path for 1st set of files, 1st file name
-                      "{path[0][0]}",
-
-                      # Extra parameter
-                      ["{basename[0][0]}",  # basename for 1st set of files, 1st file name
-                       "{basename[1][0]}",  #              2rd
-                       ])
-        def combinations_with_replacement_task(input_file, output_parameter, shared_path, basenames):
-            print " - ".join(basenames)
-
-
-        #
-        #       Run
-        #
-        pipeline_run(verbose=0)
-
-
-    This results in:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run(verbose=0)
-            A - A
-            A - B
-            A - C
-            A - D
-            B - B
-            B - C
-            B - D
-            C - C
-            C - D
-            D - D
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/command_line.txt b/doc/_build/html/_sources/tutorials/new_tutorial/command_line.txt
deleted file mode 100644
index e2a6419..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/command_line.txt
+++ /dev/null
@@ -1,352 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: command line; Tutorial
-
-.. _new_manual.cmdline:
-
-######################################################################################################
-|new_manual.cmdline.chapter_num|: Running *Ruffus* from the command line with ruffus.cmdline
-######################################################################################################
-
-.. seealso::
-
-   * :ref:`Manual table of Contents <new_manual.table_of_contents>`
-
-
-We find that much of our *Ruffus* pipeline code is built on the same template and this is generally
-a good place to start developing a new pipeline.
-
-From version 2.4, *Ruffus* includes an optional ``Ruffus.cmdline`` module that provides
-support for a set of common command line arguments. This makes writing *Ruffus* pipelines much more pleasant.
-
-
-.. _new_manual.cmdline.get_argparse:
-
-.. _new_manual.cmdline.run:
-
-.. _new_manual.cmdline.setup_logging:
-
-************************************************************************************************************
-Template for `argparse  <http://docs.python.org/2.7/library/argparse.html>`__
-************************************************************************************************************
-    All you need to do is copy these 6 lines
-
-
-    .. code-block:: python
-        :emphasize-lines: 5, 13
-
-        import ruffus.cmdline as cmdline
-
-        parser = cmdline.get_argparse(description='WHAT DOES THIS PIPELINE DO?')
-
-        #   <<<---- add your own command line options like --input_file here
-        # parser.add_argument("--input_file")
-
-        options = parser.parse_args()
-
-        #  standard python logger which can be synchronised across concurrent Ruffus tasks
-        logger, logger_mutex = cmdline.setup_logging (__name__, options.log_file, options.verbose)
-
-        #   <<<----  pipelined functions go here
-
-        cmdline.run (options)
-
-    You are recommended to use the standard `argparse  <http://docs.python.org/2.7/library/argparse.html>`__ module
-    but the deprecated `optparse  <http://docs.python.org/2.7/library/optparse.html>`__ module works as well. (See :ref:`below <code_template.optparse>` for the template)
-
-
-******************************************************
-Command Line Arguments
-******************************************************
-
-     ``Ruffus.cmdline`` by default provides these predefined options:
-
-        .. code-block:: bash
-            :emphasize-lines: 5,12,15,22
-
-            -v, --verbose
-                --version
-            -L, --log_file
-
-                # tasks
-            -T, --target_tasks
-                --forced_tasks
-            -j, --jobs
-                --use_threads
-
-
-                # printout
-            -n, --just_print
-
-                # flow chart
-                --flowchart
-                --key_legend_in_graph
-                --draw_graph_horizontally
-                --flowchart_format
-
-
-                # check sum
-                --touch_files_only
-                --checksum_file_name
-                --recreate_database
-
-
-******************************************************
-1) Logging
-******************************************************
-
-    The script provides for logging both to the command line:
-
-        .. code-block:: bash
-
-            myscript -v
-            myscript --verbose
-
-    and an optional log file:
-
-        .. code-block:: bash
-
-            # keep tabs on yourself
-            myscript --log_file /var/log/secret.logbook
-
-    Logging is ignored if neither ``--verbose`` or ``--log_file`` are specified on the command line
-
-    ``Ruffus.cmdline`` automatically allows you to write to a shared log file via a proxy from multiple processes.
-    However, you do need to use ``logging_mutex`` for the log files to be synchronised properly across different jobs:
-
-        .. code-block:: python
-
-            with logging_mutex:
-
-                logger_proxy.info("Look Ma. No hands")
-
-    Logging is set up so that you can write
-
-
-=================================
-        A) Only to the log file:
-=================================
-
-        .. code-block:: python
-
-                logger.info("A message")
-
-=================================
-        B) Only to the display:
-=================================
-
-        .. code-block:: python
-
-                logger.debug("A message")
-
-
-.. _new_manual.cmdline.MESSAGE:
-
-======================================
-        C) To both simultaneously:
-======================================
-
-        .. code-block:: python
-
-                from ruffus.cmdline import MESSAGE
-
-                logger.log(MESSAGE, "A message")
-
-
-******************************************************
-2) Tracing pipeline progress
-******************************************************
-
-    This is extremely useful for understanding what is happening with your pipeline, what tasks and which
-    jobs are up-to-date etc.
-
-    See :ref:`new_manual.pipeline_printout`
-
-    To trace the pipeline, call script with the following options
-
-        .. code-block:: bash
-
-            # well-mannered, reserved
-            myscript --just_print
-            myscript -n
-
-            or
-
-            # extremely loquacious
-            myscript --just_print --verbose 5
-            myscript -n -v5
-
-    Increasing levels of verbosity (``--verbose`` to ``--verbose 5``) provide more detailed output
-
-
-
-******************************************************
-3) Printing a flowchart
-******************************************************
-
-    This is the subject of :ref:`new_manual.pipeline_printout_graph`.
-
-    Flowcharts can be specified using the following option:
-
-        .. code-block:: bash
-
-            myscript --flowchart xxxchart.svg
-
-    The extension of the flowchart file indicates what format the flowchart should take,
-    for example, ``svg``, ``jpg`` etc.
-
-    Override with ``--flowchart_format``
-
-******************************************************
-4) Running in parallel on multiple processors
-******************************************************
-
-
-    Optionally specify the number of parallel strands of execution and which is the last *target* task to run.
-    The pipeline will run starting from any out-of-date tasks which precede the *target* and proceed no further
-    beyond the *target*.
-
-        .. code-block:: bash
-
-            myscript --jobs 15 --target_tasks "final_task"
-            myscript -j 15
-
-
-
-
-******************************************************************************************************
-5) Setup checkpointing so that *Ruffus* knows which files are out of date
-******************************************************************************************************
-
-    The :ref:`checkpoint file <new_manual.checkpointing>` uses to the value set in the
-    environment (``DEFAULT_RUFFUS_HISTORY_FILE``).
-
-    If this is not set, it will default to ``.ruffus_history.sqlite`` in the current working directory.
-
-    Either can be changed on the command line:
-
-        .. code-block:: bash
-
-            myscript --checksum_file_name mychecksum.sqlite
-
-
-============================================================================================================================================================
-Recreating checkpoints
-============================================================================================================================================================
-
-    Create or update the checkpoint file so that all existing files in completed jobs appear up to date
-
-    Will stop sensibly if current state is incomplete or inconsistent
-
-        ::
-
-            myscript --recreate_database
-
-============================================================================================================================================================
-Touch files
-============================================================================================================================================================
-
-    As far as possible, create empty files with the correct timestamp to make the pipeline appear up to date.
-
-    .. code-block:: bash
-
-        myscript --touch_files_only
-
-
-******************************************************************************************************
-6) Skipping specified options
-******************************************************************************************************
-    Note that particular options can be skipped (not added to the command line), if they conflict with your own options, for example:
-
-        .. code-block:: python
-            :emphasize-lines: 3
-
-            # see below for how to use get_argparse
-            parser = cmdline.get_argparse(  description='WHAT DOES THIS PIPELINE DO?',
-                                            # Exclude the following options: --log_file --key_legend_in_graph
-                                            ignored_args = ["log_file", "key_legend_in_graph"])
-
-
-******************************************************************************************************
-7) Specifying verbosity and abbreviating long paths
-******************************************************************************************************
-
-    The verbosity can be specified on the command line
-
-        .. code-block:: bash
-
-            myscript --verbose 5
-
-            # verbosity of 5 + 1 = 6
-            myscript --verbose 5 --verbose
-
-            # verbosity reset to 2
-            myscript --verbose 5 --verbose --verbose 2
-
-    If the printed paths are too long, and need to be abbreviated, or alternatively, if you want see the full absolute paths of your input and output parameters,
-    you can specify an extension to the verbosity. See the manual discussion of :ref:`verbose_abbreviated_path <new_manual.pipeline_printout.verbose_abbreviated_path>` for
-    more details. This is specified as ``--verbose VERBOSITY:VERBOSE_ABBREVIATED_PATH``. (No spaces!)
-
-    For example:
-
-        .. code-block:: bash
-           :emphasize-lines: 4,7
-
-            # verbosity of 4
-            myscript.py --verbose 4
-
-            # display three levels of nested directories
-            myscript.py --verbose 4:3
-
-            # restrict input and output parameters to 60 letters
-            myscript.py --verbose 4:-60
-
-
-******************************************************************************************************
-8) Displaying the version
-******************************************************************************************************
-    Note that the version for your script will default to ``"%(prog)s 1.0"`` unless specified:
-
-        .. code-block:: python
-
-            parser = cmdline.get_argparse(  description='WHAT DOES THIS PIPELINE DO?',
-                                            version = "my_programme.py v. 2.23")
-
-
-
-
-
-
-
-.. _code_template.optparse:
-
-************************************************************************************************************
-Template for `optparse  <http://docs.python.org/2.7/library/optparse.html>`__
-************************************************************************************************************
-
-    deprecated since python 2.7
-
-        .. code-block:: python
-            :emphasize-lines: 8,16
-
-            #
-            #   Using optparse (new in python v 2.6)
-            #
-            from ruffus import *
-
-            parser = cmdline.get_optgparse(version="%prog 1.0", usage = "\n\n    %prog [options]")
-
-            #   <<<---- add your own command line options like --input_file here
-            # parser.add_option("-i", "--input_file", dest="input_file", help="Input file")
-
-            (options, remaining_args) = parser.parse_args()
-
-            #  logger which can be passed to ruffus tasks
-            logger, logger_mutex = cmdline.setup_logging ("this_program", options.log_file, options.verbose)
-
-            #   <<<----  pipelined functions go here
-
-            cmdline.run (options)
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/decorators_compendium.txt b/doc/_build/html/_sources/tutorials/new_tutorial/decorators_compendium.txt
deleted file mode 100644
index f1b2862..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/decorators_compendium.txt
+++ /dev/null
@@ -1,154 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: decorators_compendium; Tutorial
-
-.. _new_manual.decorators_compendium:
-
-#####################################################################################################################
-|new_manual.decorators_compendium.chapter_num|: Pipeline topologies and a compendium of *Ruffus* decorators
-#####################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`decorators <decorators>`
-
-
-***************************************
-Overview
-***************************************
-
-    Computational pipelines transform your data in stages until the final result is produced.
-
-    You can visualise your pipeline data flowing like water down a system of pipes.
-    *Ruffus* has many ways of joining up your pipes to create different topologies.
-
-    .. note::
-
-        **The best way to design a pipeline is to:**
-
-            * **Write down the file names of the data as it flows across your pipeline.**
-            * **Draw lines between the file names to show how they should be connected together.**
-
-
-******************************************************************************
-:ref:`@transform <decorators.transform>`
-******************************************************************************
-
-
-    So far, our data files have been flowing through our pipelines independently in lockstep.
-
-    .. image:: ../../images/bestiary_transform.png
-       :scale: 50
-
-    If we drew a graph of the data files moving through the pipeline, all of our flowcharts would look like something like this.
-
-    The :ref:`@transform <decorators.transform>` decorator connects up your data files in 1 to 1 operations, ensuring that for every **Input**, a corresponding **Output** is
-    generated, ready to got into the next pipeline stage. If we start with three sets of starting data, we would end up with three final sets of results.
-
-******************************************************************************
-A bestiary of *Ruffus* decorators
-******************************************************************************
-
-    Very often, we would like to transform our data in more complex ways, this is where other *Ruffus* decorators come in.
-
-    .. image:: ../../images/bestiary_decorators.png
-       :scale: 50
-
-******************************************************************************
-:ref:`@originate <decorators.originate>`
-******************************************************************************
-
-    * Introduced in |new_manual.transform_in_parallel.chapter_num| :ref:`More on @transform-ing data and @originate <new_manual.transform_in_parallel>`,
-      :ref:`@originate <decorators.originate>` generates **Output** files from scratch without the benefits of any **Input** files.
-
-******************************************************************************
-:ref:`@merge <decorators.merge>`
-******************************************************************************
-    * A **many to one** operator.
-    * The last decorator at the far right to the figure, :ref:`@merge <decorators.merge>` merges multiple **Input** into one **Output**.
-
-******************************************************************************
-:ref:`@split <decorators.split>`
-******************************************************************************
-    * A  **one to many** operator,
-    * :ref:`@split <decorators.split>` is the evil twin of :ref:`@merge <decorators.merge>`. It takes a single set of **Input** and splits them into multiple smaller pieces.
-    * The best part of :ref:`@split <decorators.split>` is that we don't necessarily have to decide ahead of time *how many* smaller pieces it should produce. If we have encounter a larger file,
-      we might need to split it up into more fragments for greater parallelism.
-    * Since :ref:`@split <decorators.split>` is a  **one to many** operator, if you pass it **many** inputs (e.g. via :ref:`@transform <decorators.transform>`, it performs an implicit :ref:`@merge <decorators.merge>` step to make one
-      set of **Input** that you can redistribute into a different number of pieces. If you are looking to split *each* **Input** into further smaller fragments, then you
-      need :ref:`@subdivide <decorators.subdivide>`
-
-******************************************************************************
-:ref:`@subdivide <decorators.subdivide>`
-******************************************************************************
-    * A **many to even more** operator.
-    * It takes each of multiple **Input**, and further subdivides them.
-    * Uses :ref:`suffix() <decorators.suffix>`, :ref:`formatter() <decorators.formatter>` or :ref:`regex() <decorators.regex>` to generate **Output** names from its **Input** files but like :ref:`@split <decorators.split>`, we don't have to decide ahead of time
-      *how many* smaller pieces each **Input** should be further divided into. For example, a large **Input** files might be subdivided into 7 pieces while the next job might,
-      however, split its **Input** into just 4 pieces.
-
-******************************************************************************
-:ref:`@collate <decorators.collate>`
-******************************************************************************
-    * A **many to fewer** operator.
-    * :ref:`@collate <decorators.collate>` is the opposite twin of ``subdivide``: it takes multiple **Output** and groups or collates them into bundles of **Output**.
-    * :ref:`@collate <decorators.collate>` uses :ref:`formatter() <decorators.formatter>` or :ref:`regex() <decorators.regex>` to generate **Output** names.
-    * All **Input** files which map to the same **Output** are grouped together into one job (one task function call) which
-      produces one **Output**.
-
-******************************************************************************
-Combinatorics
-******************************************************************************
-
-    More rarely, we need to generate a set of **Output** based on a combination or permutation or product of the **Input**.
-
-    For example, in bioinformatics, we might need to look for all instances of a set of genes in the genomes of a different number of species.
-    In other words, we need to find the :ref:`@product <decorators.product>` of XXX genes x YYY species.
-
-    *Ruffus* provides decorators modelled on the "Combinatoric generators" in the Standard Python `itertools  <http://docs.python.org/2/library/itertools.html>`_ library.
-
-    To use combinatoric decorators, you need to explicitly include them from *Ruffus*:
-
-    .. code-block:: python
-
-
-        import ruffus
-        from ruffus import *
-        from ruffus.combinatorics import *
-
-    .. image:: ../../images/bestiary_combinatorics.png
-       :scale: 50
-
-******************************************************************************
-:ref:`@product <decorators.product>`
-******************************************************************************
-    * Given several sets of **Input**, it generates all versus all **Output**. For example, if there are four sets of **Input** files, :ref:`@product <decorators.product>` will generate ``WWW x XXX x YYY x ZZZ`` **Output**.
-    * Uses :ref:`formatter <decorators.transform>` to generate unique **Output** names from components parsed from *any* parts of *any* specified files in
-      all **Input** sets. In the above example, this allows the generation of  ``WWW x XXX x YYY x ZZZ`` unique names.
-
-******************************************************************************
-:ref:`@combinations <decorators.combinations>`
-******************************************************************************
-    * Given one set of **Input**, it generates the combinations of r-length tuples among them.
-    * Uses :ref:`formatter <decorators.transform>` to generate unique **Output** names from components parsed from *any* parts of *any* specified files in all **Input** sets.
-    * For example, given **Input** called ``A``, ``B`` and ``C``, it will generate: ``A-B``,  ``A-C``,  ``B-C``
-    * The order of **Input** items is ignored so either ``A-B`` or ``B-A`` will be included, not both
-    * Self-vs-self combinations (``A-A``) are excluded.
-
-************************************************************************************************************************************************************
-:ref:`@combinations_with_replacement <decorators.combinations_with_replacement>`
-************************************************************************************************************************************************************
-    * Given one set of **Input**, it generates the combinations of r-length tuples among them but includes self-vs-self conbinations.
-    * Uses :ref:`formatter <decorators.transform>` to generate unique **Output** names from components parsed from *any* parts of *any* specified files in all **Input** sets.
-    * For example, given **Input** called ``A``, ``B`` and ``C``, it will generate: ``A-A``, ``A-B``,  ``A-C``, ``B-B``, ``B-C``,  ``C-C``
-
-******************************************************************************
-:ref:`@permutations <decorators.permutations>`
-******************************************************************************
-    * Given one set of **Input**, it generates the permutations of r-length tuples among them. This excludes self-vs-self combinations but includes all orderings (``A-B`` and ``B-A``).
-    * Uses :ref:`formatter <decorators.transform>` to generate unique **Output** names from components parsed from *any* parts of *any* specified files in all **Input** sets.
-    * For example, given **Input** called ``A``, ``B`` and ``C``, it will generate: ``A-A``, ``A-B``,  ``A-C``, ``B-A``, ``B-C``, ``C-A``,  ``C-B``
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/dependencies.txt b/doc/_build/html/_sources/tutorials/new_tutorial/dependencies.txt
deleted file mode 100644
index 66600e4..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/dependencies.txt
+++ /dev/null
@@ -1,110 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: Checking dependencies; Tutorial
-
-.. _new_manual.dependencies:
-
-##################################################################################
-|new_manual.dependencies.chapter_num|: How dependency is checked
-##################################################################################
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-
-
-**************************************
-Overview
-**************************************
-
-    How does *Ruffus* decide how to run your pipeline?
-
-        * In which order should pipelined functions be called?
-
-        * Which parts of the pipeline are up-to-date and do not need to be rerun?
-
-
-=============================================
-Running all out-of-date tasks and dependents
-=============================================
-
-    .. image:: ../../images/manual_dependencies_flowchart_intro.png
-       :scale: 50
-
-
-    By default, *Ruffus* will
-
-        * build a flow chart (dependency tree) of pipelined tasks (functions)
-        * start from the most ancestral tasks with the fewest dependencies (``task1`` and ``task4`` in the flowchart above).
-        * walk up the tree to find the first incomplete / out-of-date tasks (i.e. ``task3`` and ``task5``.
-        * start running from there
-
-    All down-stream (dependent) tasks will be re-run anyway, so we don't have to test
-          whether they are up-to-date or not.
-
-    .. _new_manual.dependencies.checking_multiple_times:
-
-    .. note::
-
-        This means that *Ruffus* *may* ask any task if their jobs are out of date more than once:
-
-            * once when deciding which parts of the pipeline have to be run
-            * once just before executing the task.
-
-    *Ruffus* tries to be clever / efficient, and does the minimal amount of querying.
-
-
-.. _new_manual.dependencies.forced_reruns:
-
-=======================================
-Forced Reruns
-=======================================
-    Even if a pipeline stage appears to be up to date,
-    you can always force the pipeline to include from one or more task functions.
-
-    This is particularly useful, for example, if the pipeline data hasn't changed but
-    the analysis or computional code has.
-
-        ::
-
-            pipeline_run(forcedtorun_tasks = [up_to_date_task1])
-
-
-        will run all tasks from ``up_to_date_task1`` to ``final_task``
-
-
-    Both the "target" and the "forced" lists can include as many tasks as you wish. All dependencies
-    are still carried out and out-of-date jobs rerun.
-
-.. _new_manual.dependencies.minimal_reruns:
-
-=======================================
-Esoteric option: Minimal Reruns
-=======================================
-
-    In the above example, if we were to delete the results of ``up_to_date_task1``, *Ruffus*
-    would rerun ``up_to_date_task1``, ``up_to_date_task2`` and ``task3``.
-
-    However, you might argue that so long as ``up_to_date_task2`` is up-to-date, and it
-    is the only necessary prerequisite for ``task3``, we should not be concerned about
-    ``up_to_date_task1``.
-
-    This is enabled with:
-
-        .. code-block:: python
-
-            pipeline_run([task6], gnu_make_maximal_rebuild_mode = False)
-
-    This option walks down the dependency tree and proceeds no further when it encounters
-    an up-to-date task (``up_to_date_task2``) whatever the state of what lies beyond it.
-
-    This rather dangerous option is useful if you don't want to keep all the intermediate
-    files/results from upstream tasks. The pipeline will only not involve any incomplete
-    tasks which precede an up-to-date result.
-
-    This is seldom what you intend, and you should always check that the appropriate stages
-    of the pipeline are executed in the flowchart output.
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/deprecated_files.txt b/doc/_build/html/_sources/tutorials/new_tutorial/deprecated_files.txt
deleted file mode 100644
index 740d3b8..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/deprecated_files.txt
+++ /dev/null
@@ -1,238 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: deprecated @files; Tutorial
-
-.. _new_manual.deprecated_files:
-
-#####################################################################################################################
-|new_manual.deprecated_files.chapter_num|: **@files**: Deprecated syntax
-#####################################################################################################################
-
-.. warning ::
-
-    -
-
-        **This is deprecated syntax**
-
-        **which is no longer supported and**
-
-        **should NOT be used in new code.**
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`decorators <decorators>`
-    * :ref:`@files <decorators.files>` syntax in detail
-
-
-***************************************
-Overview
-***************************************
-
-
-    | The python functions which do the actual work of each stage  or
-      :term:`task` of a *Ruffus* pipeline are written by you.
-    | The role of *Ruffus* is to make sure these functions are called in the right order,
-      with the right parameters, running in parallel using multiprocessing if desired.
-
-    The easiest way to specify parameters to *Ruffus* :term:`task` functions is to use
-    the :ref:`@files <decorators.files>` decorator.
-
-    .. index::
-        pair: @files; Manual
-
-
-***************************************
-**@files**
-***************************************
-
-    Running this code:
-
-        ::
-
-            from ruffus import *
-
-            @files('a.1', ['a.2', 'b.2'], 'A file')
-            def single_job_io_task(infile, outfiles, text):
-                for o in outfiles: open(o, "w")
-
-            # prepare input file
-            open('a.1', "w")
-
-            pipeline_run()
-
-
-        Is equivalent to calling:
-            ::
-
-                single_job_io_task('a.1', ['a.2', 'b.2'], 'A file')
-
-
-        And produces:
-            ::
-
-                >>> pipeline_run()
-                    Job = [a.1 -> [a.2, b.2], A file] completed
-                Completed Task = single_job_io_task
-
-    *Ruffus* will automatically check if your task is up to date. The second time :ref:`pipeline_run() <pipeline_functions.pipeline_run>`
-    is called, nothing will happen. But if you update ``a.1``, the task will rerun:
-
-        ::
-
-            >>> open('a.1', "w")
-            >>> pipeline_run()
-                Job = [a.1 -> [a.2, b.2], A file] completed
-            Completed Task = single_job_io_task
-
-    See :ref:`chapter 2 <new_manual.skip_up_to_date.rules>` for a more in-depth discussion of how *Ruffus*
-    decides which parts of the pipeline are complete and up-to-date.
-
-
-.. index::
-    pair: @files; in parallel
-
-.. _new_manual.files.parallel:
-
-******************************************************************************
-Running the same code on different parameters in parallel
-******************************************************************************
-
-    Your pipeline may require the same function to be called multiple times on independent parameters.
-    In which case, you can supply all the parameters to @files, each will be sent to separate jobs that
-    may run in parallel if necessary. *Ruffus* will check if each separate :term:`job` is up-to-date using
-    the *inputs* and *outputs* (first two) parameters (See the :ref:`new_manual.only_rerun_out_of_date` ).
-
-
-    For example, if a sequence
-    (e.g. a list or tuple) of 5 parameters are passed to **@files**, that indicates
-    there will also be 5 separate jobs:
-
-        ::
-
-            from ruffus import *
-            parameters = [
-                                [ 'job1.file'           ],             # 1st job
-                                [ 'job2.file', 4        ],             # 2st job
-                                [ 'job3.file', [3, 2]   ],             # 3st job
-                                [ 67, [13, 'job4.file'] ],             # 4st job
-                                [ 'job5.file'           ],             # 5st job
-                          ]
-            @files(parameters)
-            def task_file(*params):
-                ""
-
-    | *Ruffus* creates as many jobs as there are elements in ``parameters``.
-    | In turn, each of these elements consist of series of parameters which will be
-      passed to each separate job.
-
-    Thus the above code is equivalent to calling:
-
-        ::
-
-             task_file('job1.file')
-             task_file('job2.file', 4)
-             task_file('job3.file', [3, 2])
-             task_file(67, [13, 'job4.file'])
-             task_file('job5.file')
-
-
-    What ``task_file()`` does with these parameters is up to you!
-
-    The only constraint on the parameters is that *Ruffus* will treat any first
-    parameter of each job as the *inputs* and any second as the *output*. Any
-    strings in the *inputs* or *output* parameters (including those nested in sequences)
-    will be treated as file names.
-
-    Thus, to pick the parameters out of one of the above jobs:
-
-        ::
-
-             task_file(67, [13, 'job4.file'])
-
-        | *inputs*  == ``67``
-        | *outputs* == ``[13, 'job4.file']``
-        |
-        |   The solitary output filename is ``job4.file``
-
-
-.. index::
-    pair: @files; check if up to date
-
-.. _new_manual.files.is_uptodate:
-.. _new_manual.files.example:
-
-=======================================
-Checking if jobs are up to date
-=======================================
-
-    | Usually we do not want to run all the stages in a pipeline but only where
-      the input data has changed or is no longer up to date.
-    | One easy way to do this is to check the modification times for files produced
-      at each stage of the pipeline.
-
-    | Let us first create our starting files ``a.1`` and ``b.1``
-    | We can then run the following pipeline function to create
-
-        * ``a.2`` from ``a.1`` and
-        * ``b.2`` from ``b.1``
-
-        ::
-
-            # create starting files
-            open("a.1", "w")
-            open("b.1", "w")
-
-
-            from ruffus import *
-            parameters = [
-                                [ 'a.1', 'a.2', 'A file'], # 1st job
-                                [ 'b.1', 'b.2', 'B file'], # 2nd job
-                          ]
-
-            @files(parameters)
-            def parallel_io_task(infile, outfile, text):
-                # copy infile contents to outfile
-                infile_text = open(infile).read()
-                f = open(outfile, "w").write(infile_text + "\n" + text)
-
-            pipeline_run()
-
-
-    .. ???
-
-    This produces the following output:
-        ::
-
-            >>> pipeline_run()
-                Job = [a.1 -> a.2, A file] completed
-                Job = [b.1 -> b.2, B file] completed
-            Completed Task = parallel_io_task
-
-
-    | If you called :ref:`pipeline_run() <pipeline_functions.pipeline_run>` again, nothing would happen because the files are up to date:
-    | ``a.2`` is more recent than ``a.1`` and
-    | ``b.2`` is more recent than ``b.1``
-
-    However, if you subsequently modified ``a.1`` again:
-        ::
-
-            open("a.1", "w")
-            pipeline_run(verbose = 1)
-
-    you would see the following::
-
-        >>> pipeline_run([parallel_io_task])
-        Task = parallel_io_task
-            Job = ["a.1" -> "a.2", "A file"] completed
-            Job = ["b.1" -> "b.2", "B file"] unnecessary: already up to date
-        Completed Task = parallel_io_task
-
-    The 2nd job is up to date and will be skipped.
-
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/deprecated_files_re.txt b/doc/_build/html/_sources/tutorials/new_tutorial/deprecated_files_re.txt
deleted file mode 100644
index 93782c5..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/deprecated_files_re.txt
+++ /dev/null
@@ -1,145 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: deprecated @files_re; Tutorial
-
-.. _new_manual.deprecated_files_re:
-
-#####################################################################################################################
-|new_manual.deprecated_files_re.chapter_num|: **@files_re**: Deprecated `syntax using regular expressions`
-#####################################################################################################################
-
-.. warning ::
-
-    -
-
-        **This is deprecated syntax**
-
-        **which is no longer supported and**
-
-        **should NOT be used in new code.**
-
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`decorators <decorators>`
-    * :ref:`@files_re <decorators.files_re>` syntax in detail
-
-
-***************************************
-Overview
-***************************************
-
-
-
-    **@files_re** combines the functionality of @transform, @collate and @merge in
-    one overloaded decorator.
-
-    This is the reason why its use is discouraged. **@files_re** syntax is far too overloaded
-    and context-dependent to support its myriad of different functions.
-
-    The following documentation is provided to help maintain historical *Ruffus* usage.
-
-=======================================
-Transforming input and output filenames
-=======================================
-
-
-    For example, the following code takes files from
-    the previous pipeline task, and makes new output parameters with the ``.sums`` suffix
-    in place of the ``.chunks`` suffix:
-
-        ::
-
-            @transform(step_4_split_numbers_into_chunks, suffix(".chunks"), ".sums")
-            def step_5_calculate_sum_of_squares (input_file_name, output_file_name):
-                #
-                #   calculate sums and sums of squares for all values in the input_file_name
-                #       writing to output_file_name
-                ""
-
-    This can be written using @files_re equivalently:
-
-        ::
-
-            @files_re(step_4_split_numbers_into_chunks, r".chunks", r".sums")
-            def step_5_calculate_sum_of_squares (input_file_name, output_file_name):
-            ""
-
-.. _new_manual.files_re.combine:
-.. index::
-    pair: combine; Manual
-
-=====================================================
-Collating many *inputs* into a single *output*
-=====================================================
-
-    Similarly, the following code collects **inputs**
-    from the same species in the same directory:
-
-        ::
-
-            @collate('*.animals',                     # inputs = all *.animal files
-                        regex(r'mammals.([^.]+)'),    # regular expression
-                        r'\1/animals.in_my_zoo',      # single output file per species
-                        r'\1' )                       # species name
-            def capture_mammals(infiles, outfile, species):
-                # summarise all animals of this species
-                ""
-
-    This can be written using @files_re equivalently using the :ref:`combine<decorators.combine>` indicator:
-
-        ::
-
-            @files_re('*.animals',                           # inputs = all *.animal files
-                        r'mammals.([^.]+)',                  # regular expression
-                        combine(r'\1/animals.in_my_zoo'),    # single output file per species
-                        r'\1' )                              # species name
-            def capture_mammals(infiles, outfile, species):
-                # summarise all animals of this species
-                ""
-
-
-
-==============================================================================
-Generating *input* and *output* parameter using regular expresssions
-==============================================================================
-
-    The following code generates additional
-    *input* prerequisite file names which match the original *input* files.
-
-    We want each job of our ``analyse()`` function to get corresponding pairs
-    of ``xx.chunks`` and ``xx.red_indian`` files when
-
-        ``*.chunks`` are generated by the task function ``split_up_problem()`` and
-        ``*.red_indian`` are generated by the task function ``make_red_indians()``:
-
-        ::
-
-            @follows(make_red_indians)
-            @transform(split_up_problem,                # starting set of *inputs*
-                        regex(r"(.*).chunks"),          # regular expression
-                        inputs([r"\g<0>",               # xx.chunks
-                                r"\1.red_indian"]),     # important.file
-                         r"\1.results"                  # xx.results
-                          )
-            def analyse(input_filenames, output_file_name):
-                "Do analysis here"
-
-
-    The equivalent code using @files_re looks very similar:
-
-        ::
-
-            @follows(make_red_indians)
-            @files_re( split_up_problem,        # starting set of *inputs*
-                       r"(.*).chunks",          # regular expression
-                       [r"\g<0>",               # xx.chunks
-                        r"\1.red_indian"]),     # important.file
-                         r"\1.results")         # xx.results
-            def analyse(input_filenames, output_file_name):
-                "Do analysis here"
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/exceptions.txt b/doc/_build/html/_sources/tutorials/new_tutorial/exceptions.txt
deleted file mode 100644
index 8a3ed92..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/exceptions.txt
+++ /dev/null
@@ -1,191 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: exceptions; Tutorial
-
-.. _new_manual.exceptions:
-
-###################################################################################################
-|new_manual.exceptions.chapter_num|: Exceptions thrown inside pipelines
-###################################################################################################
-
-**************************************
-Overview
-**************************************
-
-
-    The goal for *Ruffus* is that exceptions should just work *out-of-the-box* without any fuss.
-    This is especially important for exceptions that come from your code which may be raised
-    in a different process. Often multiple parallel operations (jobs or tasks) fail at the
-    same time. *Ruffus* will forward each of these exceptions with the tracebacks so you
-    can jump straight to the offending line.
-
-    This example shows separate exceptions from two jobs running in parallel:
-
-
-    .. code-block:: python
-
-            from ruffus import *
-
-            @originate(["a.start", "b.start", "c.start", "d.start", "e.start"])
-            def throw_exceptions_here(output_file):
-                raise Exception("OOPS")
-
-            pipeline_run(multiprocess = 2)
-
-    .. code-block:: pycon
-        :emphasize-lines: 5, 21
-
-            >>> pipeline_run(multiprocess = 2)
-
-            ruffus.ruffus_exceptions.RethrownJobError:
-
-            Original exceptions:
-
-                Exception #1
-                  'exceptions.Exception(OOPS)' raised in ...
-                   Task = def throw_exceptions_here(...):
-                   Job  = [None -> b.start]
-
-                Traceback (most recent call last):
-                  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 685, in run_pooled_job_without_exceptions
-                    return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
-                  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 549, in job_wrapper_output_files
-                    job_wrapper_io_files(param, user_defined_work_func, register_cleanup, touch_files_only, output_files_only = True)
-                  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 504, in job_wrapper_io_files
-                    ret_val = user_defined_work_func(*(param[1:]))
-                  File "<stdin>", line 3, in throw_exceptions_here
-                Exception: OOPS
-
-
-                Exception #2
-                  'exceptions.Exception(OOPS)' raised in ...
-                   Task = def throw_exceptions_here(...):
-                   Job  = [None -> a.start]
-
-                Traceback (most recent call last):
-                  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 685, in run_pooled_job_without_exceptions
-                    return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
-                  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 549, in job_wrapper_output_files
-                    job_wrapper_io_files(param, user_defined_work_func, register_cleanup, touch_files_only, output_files_only = True)
-                  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 504, in job_wrapper_io_files
-                    ret_val = user_defined_work_func(*(param[1:]))
-                  File "<stdin>", line 3, in throw_exceptions_here
-                Exception: OOPS
-
-
-        .. image:: ../../images/manual_exceptions.png
-
-
-.. _new_manual.exceptions.multiple_errors:
-
-.. index:: signalling, interrupts, break, errors, exceptions, multiple errors
-
-****************************************************************
-Pipelines running in parallel accumulate Exceptions
-****************************************************************
-
-    As show above, by default *Ruffus* accumulates ``NN`` exceptions before interrupting the pipeline prematurely where
-    ``NN`` is the specified parallelism for :ref:`pipeline_run(multiprocess = NN) <pipeline_functions.pipeline_run>`
-
-    This seems a fair tradeoff between being able to gather detailed error information for
-    running jobs, and not wasting too much time for a task that is going to fail anyway.
-
-
-****************************************************************
-Terminate pipeline immediately upon Exceptions
-****************************************************************
-
-
-==============================================================================================================================
-Set :ref:`pipeline_run(exceptions_terminate_immediately = True) <pipeline_functions.pipeline_run>`
-==============================================================================================================================
-
-    To have all exceptions interrupt the pipeline immediately, invoke:
-
-        .. code-block:: python
-
-            pipeline_run(exceptions_terminate_immediately = True)
-
-
-    For example, with this change, only a single exception will be thrown before the pipeline is interrupted:
-
-        .. code-block:: python
-
-            from ruffus import *
-
-            @originate(["a.start", "b.start", "c.start", "d.start", "e.start"])
-            def throw_exceptions_here(output_file):
-                raise Exception("OOPS")
-
-            pipeline_run(multiprocess = 2, exceptions_terminate_immediately = True)
-
-    .. code-block:: pycon
-        :emphasize-lines: 5, 21
-
-            >>> pipeline_run(multiprocess = 2)
-
-            ruffus.ruffus_exceptions.RethrownJobError:
-
-            Original exception:
-
-                Exception #1
-                  'exceptions.Exception(OOPS)' raised in ...
-                   Task = def throw_exceptions_here(...):
-                   Job  = [None -> a.start]
-
-                Traceback (most recent call last):
-                  [Tedious traceback snipped out!!!....]
-                Exception: OOPS
-
-
-==============================================================================================================================
-raise ``Ruffus.JobSignalledBreak``
-==============================================================================================================================
-
-    The same can be accomplished on a finer scale by throwing the ``Ruffus.JobSignalledBreak`` Exception. Unlike
-    other exceptions, this causes an immediate halt in pipeline execution. If there are other exceptions in play at that
-    point, they will be rethrown in the main process but no new exceptions will be added.
-
-        .. code-block:: python
-
-            from ruffus import *
-
-            @originate(["a.start", "b.start", "c.start", "d.start", "e.start"])
-            def throw_exceptions_here(output_file):
-                raise JobSignalledBreak("OOPS")
-
-            pipeline_run(multiprocess = 2)
-
-
-****************************************************************
-Display exceptions as they occur
-****************************************************************
-
-    In the following example, the jobs throw exceptions
-    at two second staggered intervals into the job. With ``log_exceptions = True``, the
-    exceptions are displayed as they occur even though the pipeline continues running.
-
-    logger.error(...) will be invoked with the string representation of the each exception, and associated stack trace.
-
-    The default logger prints to sys.stderr, but as usual can be changed to any class from the logging module or compatible object via
-    :ref:`pipeline_run(logger = XXX) <pipeline_functions.pipeline_run>`
-
-
-        .. code-block:: python
-
-            from ruffus import *
-            import time, os
-
-            @originate(["1.start", "2.start", "3.start", "4.start", "5.start"])
-            def throw_exceptions_here(output_file):
-                delay = int(os.path.splitext(output_file)[0])
-                time.sleep(delay * 2)
-                raise JobSignalledBreak("OOPS")
-
-            pipeline_run(log_exceptions = True, multiprocess = 5)
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/flowchart_colours.txt b/doc/_build/html/_sources/tutorials/new_tutorial/flowchart_colours.txt
deleted file mode 100644
index e03f171..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/flowchart_colours.txt
+++ /dev/null
@@ -1,61 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: flowchart colours; Tutorial
-
-.. _new_manual.flowchart_colours:
-
-##########################################################################################################################################################################################################################################
-|new_manual.flowchart_colours.chapter_num|: Flow Chart Colours with :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>`
-##########################################################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>`
-    * :download:`Download code <../../static_data/example_scripts/play_with_colours.py>`
-    * :ref:`Code <new_manual.flowchart_colours.code>` for experimenting with colours
-
-******************
-Flowchart colours
-******************
-
-The appearance of *Ruffus* flowcharts produced by :ref:`pipeline_printout_graph <pipeline_functions.pipeline_printout_graph>`
-can be extensively customised.
-
-This is mainly controlled by the :ref:`user_colour_scheme <pipeline_functions.pipeline_printout_graph.user_colour_scheme>`  (note UK spelling of "colour") parameter
-
-Example:
-
-    Use colour scheme index  = 1
-    ::
-
-        pipeline_printout_graph ("flowchart.svg", "svg", [final_task],
-                                 user_colour_scheme = {
-                                                        "colour_scheme_index" :1,
-                                                        "Pipeline"      :{"fontcolor" : '"#FF3232"' },
-                                                        "Key"           :{"fontcolor" : "Red",
-                                                                          "fillcolor" : '"#F6F4F4"' },
-                                                        "Task to run"   :{"linecolor" : '"#0044A0"' },
-                                                        "Final target"  :{"fillcolor" : '"#EFA03B"',
-                                                                          "fontcolor" : "black",
-                                                                          "dashed"    : 0           }
-                                                       })
-
-
-There are 8 colour schemes by setting ``"colour_scheme_index"``:
-    ::
-
-        pipeline_printout_graph ("flowchart.svg", "svg", [final_task],
-                                  user_colour_scheme = {"colour_scheme_index" :6})
-
-
-These colours were chosen after much fierce arguments between the authors and friends, and much
-inspiration from  http://kuler.adobe.com/#create/fromacolor. Please
-feel free to submit any additional sets of colours for our consideration.
-
-
-(Click here for image in :download:`svg <../../images/flowchart_colour_schemes.svg>`.)
-
-.. image:: ../../images/flowchart_colour_schemes.png
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/flowchart_colours_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/flowchart_colours_code.txt
deleted file mode 100644
index 13bb236..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/flowchart_colours_code.txt
+++ /dev/null
@@ -1,288 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: flowchart colours; Tutorial
-
-.. _new_manual.flowchart_colours.code:
-
-##########################################################################################################################################################################################################################################
-|new_manual.flowchart_colours.chapter_num|: Python code for Flow Chart Colours with :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>`
-##########################################################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>`
-    * :download:`Download code <../../static_data/example_scripts/play_with_colours.py>`
-    * Back to :ref:`Flowchart colours <new_manual.flowchart_colours>`
-
-    This example shows how flowchart colours can be customised.
-
-
-************************************
-Code
-************************************
-    ::
-
-        #!/usr/bin/env python
-        """
-
-            play_with_colours.py
-            [--log_file PATH]
-            [--verbose]
-
-        """
-
-        ################################################################################
-        #
-        #   play_with_colours.py
-        #
-        #
-        #   Copyright (c) 7/13/2010 Leo Goodstadt
-        #
-        #   Permission is hereby granted, free of charge, to any person obtaining a copy
-        #   of this software and associated documentation files (the "Software"), to deal
-        #   in the Software without restriction, including without limitation the rights
-        #   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        #   copies of the Software, and to permit persons to whom the Software is
-        #   furnished to do so, subject to the following conditions:
-        #
-        #   The above copyright notice and this permission notice shall be included in
-        #   all copies or substantial portions of the Software.
-        #
-        #   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        #   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        #   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        #   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        #   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        #   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-        #   THE SOFTWARE.
-        #################################################################################
-
-        import sys, os
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #   options
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-        from optparse import OptionParser
-        import StringIO
-
-        parser = OptionParser(version="%play_with_colours 1.0",
-                              usage = "\n\n    play_with_colours "
-                                        "--flowchart FILE [options] "
-                                        "[--colour_scheme_index INT ] "
-                                        "[--key_legend_in_graph]")
-
-        #
-        #   pipeline
-        #
-        parser.add_option("--flowchart", dest="flowchart",
-                            metavar="FILE",
-                            type="string",
-                            help="Don't actually run any commands; just print the pipeline "
-                                 "as a flowchart.")
-        parser.add_option("--colour_scheme_index", dest="colour_scheme_index",
-                            metavar="INTEGER",
-                            type="int",
-                            help="Index of colour scheme for flow chart.")
-        parser.add_option("--key_legend_in_graph", dest="key_legend_in_graph",
-                            action="store_true", default=False,
-                            help="Print out legend and key for dependency graph.")
-
-        (options, remaining_args) = parser.parse_args()
-        if not options.flowchart:
-            raise Exception("Missing mandatory parameter: --flowchart.\n")
-
-
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #   imports
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        from ruffus import *
-        from ruffus.ruffus_exceptions import JobSignalledBreak
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #   Pipeline
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-        #
-        # up to date tasks
-        #
-        @check_if_uptodate (lambda : (False, ""))
-        def Up_to_date_task1(infile, outfile):
-            pass
-
-        @check_if_uptodate (lambda : (False, ""))
-        @follows(Up_to_date_task1)
-        def Up_to_date_task2(infile, outfile):
-            pass
-
-        @check_if_uptodate (lambda : (False, ""))
-        @follows(Up_to_date_task2)
-        def Up_to_date_task3(infile, outfile):
-            pass
-
-
-        @check_if_uptodate (lambda : (False, ""))
-        @follows(Up_to_date_task3)
-        def Up_to_date_final_target(infile, outfile):
-            pass
-
-
-        #
-        # Explicitly specified
-        #
-        @check_if_uptodate (lambda : (False, ""))
-        @follows(Up_to_date_task1)
-        def Explicitly_specified_task(infile, outfile):
-            pass
-
-
-
-        #
-        # Tasks to run
-        #
-        @follows(Explicitly_specified_task)
-        def Task_to_run1(infile, outfile):
-            pass
-
-
-        @follows(Task_to_run1)
-        def Task_to_run2(infile, outfile):
-            pass
-
-        @follows(Task_to_run2)
-        def Task_to_run3(infile, outfile):
-            pass
-
-        @check_if_uptodate (lambda : (False, ""))
-        @follows(Task_to_run2)
-        def Up_to_date_task_forced_to_rerun(infile, outfile):
-            pass
-
-
-        #
-        # Final target
-        #
-        @follows(Up_to_date_task_forced_to_rerun, Task_to_run3)
-        def Final_target(infile, outfile):
-            pass
-
-        #
-        # Ignored downstream
-        #
-        @follows(Final_target)
-        def Downstream_task1_ignored(infile, outfile):
-            pass
-
-        @follows(Final_target)
-        def Downstream_task2_ignored(infile, outfile):
-            pass
-
-
-
-
-
-
-
-
-
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #   Main logic
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        from collections import defaultdict
-        custom_flow_chart_colour_scheme = defaultdict(dict)
-
-        #
-        #   Base chart on this overall colour scheme index
-        #
-        custom_flow_chart_colour_scheme["colour_scheme_index"] = options.colour_scheme_index
-
-        #
-        #   Overriding colours
-        #
-        if options.colour_scheme_index == None:
-            custom_flow_chart_colour_scheme["Vicious cycle"]["linecolor"]                        = '"#FF3232"'
-            custom_flow_chart_colour_scheme["Pipeline"]["fontcolor"]                             = '"#FF3232"'
-            custom_flow_chart_colour_scheme["Key"]["fontcolor"]                                  = "black"
-            custom_flow_chart_colour_scheme["Key"]["fillcolor"]                                  = '"#F6F4F4"'
-            custom_flow_chart_colour_scheme["Task to run"]["linecolor"]                          = '"#0044A0"'
-            custom_flow_chart_colour_scheme["Up-to-date"]["linecolor"]                           = "gray"
-            custom_flow_chart_colour_scheme["Final target"]["fillcolor"]                         = '"#EFA03B"'
-            custom_flow_chart_colour_scheme["Final target"]["fontcolor"]                         = "black"
-            custom_flow_chart_colour_scheme["Final target"]["color"]                             = "black"
-            custom_flow_chart_colour_scheme["Final target"]["dashed"]                            = 0
-            custom_flow_chart_colour_scheme["Vicious cycle"]["fillcolor"]                        = '"#FF3232"'
-            custom_flow_chart_colour_scheme["Vicious cycle"]["fontcolor"]                        = 'white'
-            custom_flow_chart_colour_scheme["Vicious cycle"]["color"]                            = "white"
-            custom_flow_chart_colour_scheme["Vicious cycle"]["dashed"]                           = 0
-            custom_flow_chart_colour_scheme["Up-to-date task"]["fillcolor"]                      = '"#B8CC6E"'
-            custom_flow_chart_colour_scheme["Up-to-date task"]["fontcolor"]                      = '"#006000"'
-            custom_flow_chart_colour_scheme["Up-to-date task"]["color"]                          = '"#006000"'
-            custom_flow_chart_colour_scheme["Up-to-date task"]["dashed"]                         = 0
-            custom_flow_chart_colour_scheme["Down stream"]["fillcolor"]                          = "white"
-            custom_flow_chart_colour_scheme["Down stream"]["fontcolor"]                          = "gray"
-            custom_flow_chart_colour_scheme["Down stream"]["color"]                              = "gray"
-            custom_flow_chart_colour_scheme["Down stream"]["dashed"]                             = 0
-            custom_flow_chart_colour_scheme["Explicitly specified task"]["fillcolor"]            = "transparent"
-            custom_flow_chart_colour_scheme["Explicitly specified task"]["fontcolor"]            = "black"
-            custom_flow_chart_colour_scheme["Explicitly specified task"]["color"]                = "black"
-            custom_flow_chart_colour_scheme["Explicitly specified task"]["dashed"]               = 0
-            custom_flow_chart_colour_scheme["Task to run"]["fillcolor"]                          = '"#EBF3FF"'
-            custom_flow_chart_colour_scheme["Task to run"]["fontcolor"]                          = '"#0044A0"'
-            custom_flow_chart_colour_scheme["Task to run"]["color"]                              = '"#0044A0"'
-            custom_flow_chart_colour_scheme["Task to run"]["dashed"]                             = 0
-            custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["fillcolor"]      = 'transparent'
-            custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["fontcolor"]      = '"#0044A0"'
-            custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["color"]          = '"#0044A0"'
-            custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["dashed"]         = 1
-            custom_flow_chart_colour_scheme["Up-to-date Final target"]["fillcolor"]              = '"#EFA03B"'
-            custom_flow_chart_colour_scheme["Up-to-date Final target"]["fontcolor"]              = '"#006000"'
-            custom_flow_chart_colour_scheme["Up-to-date Final target"]["color"]                  = '"#006000"'
-            custom_flow_chart_colour_scheme["Up-to-date Final target"]["dashed"]                 = 0
-
-        if __name__ == '__main__':
-            pipeline_printout_graph (
-
-                                            open(options.flowchart, "w"),
-                                            # use flowchart file name extension to decide flowchart format
-                                            #   e.g. svg, jpg etc.
-                                            os.path.splitext(options.flowchart)[1][1:],
-
-                                            # final targets
-                                            [Final_target, Up_to_date_final_target],
-
-                                            # Explicitly specified tasks
-                                            [Explicitly_specified_task],
-
-                                            # Do we want key legend
-                                            no_key_legend   = not options.key_legend_in_graph,
-
-                                            # Print all the task types whether used or not
-                                            minimal_key_legend             = False,
-
-                                            user_colour_scheme = custom_flow_chart_colour_scheme,
-                                            pipeline_name = "Colour schemes")
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/inputs.txt b/doc/_build/html/_sources/tutorials/new_tutorial/inputs.txt
deleted file mode 100644
index 823f187..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/inputs.txt
+++ /dev/null
@@ -1,239 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: inputs; Tutorial
-    pair: add_inputs; Tutorial
-    pair: string substiution for inputs; Tutorial
-
-.. _new_manual.inputs:
-
-###########################################################################################################################################################################################################################################################################################
-|new_manual.inputs.chapter_num|: Manipulating task inputs via string substitution using :ref:`inputs() <decorators.inputs>` and  :ref:`add_inputs() <decorators.add_inputs>`
-###########################################################################################################################################################################################################################################################################################
-
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`inputs() <decorators.inputs>` syntax
-    * :ref:`add_inputs() <decorators.add_inputs>` syntax
-
-.. note::
-
-    Remember to look at the example code:
-
-        * :ref:`new_manual.inputs.code`
-
-***********************
-Overview
-***********************
-
-    The previous chapters have been described how *Ruffus* allows the **Output** names for each job
-    to be generated from the *Input* names via string substitution. This is how *Ruffus* can
-    automatically chain multiple tasks in a pipeline together seamlessly.
-
-    Sometimes it is useful to be able to modify the **Input**  by string substitution
-    as well. There are two situations where this additional flexibility is needed:
-
-        #. You need to add additional prequisites or filenames to the **Input** of every single job
-        #. You need to add additional **Input** file names which are some variant of the existing ones.
-
-    Both will be much more obvious with some examples
-
-
-*******************************************************************************************************************
-Adding additional *input* prerequisites per job with :ref:`add_inputs() <decorators.add_inputs>`
-*******************************************************************************************************************
-
-
-===================================================================
-1. Example: compiling c++ code
-===================================================================
-
-    Let us first compile some c++ (``"*.cpp"``) files using plain :ref:`@transform <decorators.transform>` syntax:
-
-    .. code-block:: python
-
-            # source files exist before our pipeline
-            source_files = ["hasty.cpp", "tasty.cpp", "messy.cpp"]
-            for source_file in source_files:
-                open(source_file, "w")
-
-            from ruffus import *
-
-            @transform(source_files, suffix(".cpp"), ".o")
-            def compile(input_filename, output_file):
-                open(output_file, "w")
-
-            pipeline_run()
-
-
-======================================================================================================================================
-2. Example: Adding a common header file with :ref:`add_inputs() <decorators.add_inputs>`
-======================================================================================================================================
-
-    .. code-block:: python
-        :emphasize-lines: 11,17,19
-
-        # source files exist before our pipeline
-        source_files = ["hasty.cpp", "tasty.cpp", "messy.cpp"]
-        for source_file in source_files:
-            open(source_file, "w")
-
-        # common (universal) header exists before our pipeline
-        open("universal.h", "w")
-
-        from ruffus import *
-
-        # make header files
-        @transform(source_files, suffix(".cpp"), ".h")
-        def create_matching_headers(input_file, output_file):
-            open(output_file, "w")
-
-        @transform(source_files, suffix(".cpp"),
-                                # add header to the input of every job
-                    add_inputs("universal.h",
-                                # add result of task create_matching_headers to the input of every job
-                               create_matching_headers),
-                    ".o")
-        def compile(input_filename, output_file):
-            open(output_file, "w")
-
-        pipeline_run()
-
-            >>> pipeline_run()
-                Job  = [hasty.cpp -> hasty.h] completed
-                Job  = [messy.cpp -> messy.h] completed
-                Job  = [tasty.cpp -> tasty.h] completed
-            Completed Task = create_matching_headers
-                Job  = [[hasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> hasty.o] completed
-                Job  = [[messy.cpp, universal.h, hasty.h, messy.h, tasty.h] -> messy.o] completed
-                Job  = [[tasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> tasty.o] completed
-            Completed Task = compile
-
-
-=====================================================================
-3. Example: Additional *Input* can be tasks
-=====================================================================
-
-    We can also add a task name to :ref:`add_inputs() <decorators.add_inputs>`.
-    This chains the **Output**, i.e. run time results, of any previous task as
-    an additional **Input** to every single job in the task.
-
-        .. code-block:: python
-            :emphasize-lines: 1,7,9
-
-            # make header files
-            @transform(source_files, suffix(".cpp"), ".h")
-            def create_matching_headers(input_file, output_file):
-                open(output_file, "w")
-
-            @transform(source_files, suffix(".cpp"),
-                                    # add header to the input of every job
-                        add_inputs("universal.h",
-                                    # add result of task create_matching_headers to the input of every job
-                                   create_matching_headers),
-                        ".o")
-            def compile(input_filenames, output_file):
-                open(output_file, "w")
-
-            pipeline_run()
-
-
-        >>> pipeline_run()
-            Job  = [[hasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> hasty.o] completed
-            Job  = [[messy.cpp, universal.h, hasty.h, messy.h, tasty.h] -> messy.o] completed
-            Job  = [[tasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> tasty.o] completed
-        Completed Task = compile
-
-
-================================================================================================================================================================================================================================================
-4. Example: Add corresponding files using :ref:`add_inputs() <decorators.add_inputs>` with :ref:`formatter <decorators.formatter>` or :ref:`regex <decorators.regex>`
-================================================================================================================================================================================================================================================
-    The previous example created headers corresponding to our source files and added them
-    as the **Input** to the compilation. That is generally not what you want. Instead,
-    what is generally need is a way to
-
-        1) Look up the exact corresponding header for the *specific* job, and not add all
-           possible files to all jobs in a task. When compiling ``hasty.cpp``, we just need
-           to add ``hasty.h`` (and ``universal.h``).
-        2) Add a pre-existing file name (``hasty.h`` already exists. Don't create it via
-           another task.)
-
-    This is a surprisingly common requirement: In bioinformatics sometimes DNA or RNA
-    sequence files come singly in  `*.fastq  <http://en.wikipedia.org/wiki/FASTQ_format>`__
-    and sometimes in `matching pairs  <http://en.wikipedia.org/wiki/DNA_sequencing_theory#Pairwise_end-sequencing>`__:
-    ``*1.fastq, *2.fastq`` etc. In the latter case, we often need to make sure that both
-    sequence files are being processed in tandem. One way is to take one file name (``*1.fastq``)
-    and look up the other.
-
-     :ref:`add_inputs() <decorators.add_inputs>` uses standard *Ruffus* string substitution
-     via :ref:`formatter <decorators.formatter>` and :ref:`regex <decorators.regex>` to lookup (generate) **Input** file names.
-     (As a rule :ref:`suffix <decorators.suffix>` only substitutes **Output** file names.)
-
-    .. code-block:: python
-        :emphasize-lines: 3,5
-
-        @transform( source_files,
-                    formatter(".cpp$"),
-                                # corresponding header for each source file
-                    add_inputs("{basename[0]}.h",
-                               # add header to the input of every job
-                               "universal.h"),
-                    "{basename[0]}.o")
-        def compile(input_filenames, output_file):
-            open(output_file, "w")
-
-    This script gives the following output
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [[hasty.cpp, hasty.h, universal.h] -> hasty.o] completed
-                Job  = [[messy.cpp, messy.h, universal.h] -> messy.o] completed
-                Job  = [[tasty.cpp, tasty.h, universal.h] -> tasty.o] completed
-            Completed Task = compile
-
-
-********************************************************************************
-Replacing all input parameters with :ref:`inputs() <decorators.inputs>`
-********************************************************************************
-
-    The previous examples all *added* to the set of **Input** file names.
-    Sometimes it is necessary to replace all the **Input** parameters altogether.
-
-================================================================================================================================================================================================================================================
-5. Example: Running matching python scripts using :ref:`inputs() <decorators.inputs>`
-================================================================================================================================================================================================================================================
-
-    Here is a contrived example: we wish to find all cython/python files which have been
-    compiled into corresponding c++ source files.
-    Instead of compiling the c++, we shall invoke the corresponding python scripts.
-
-    Given three c++ files and their corresponding python scripts:
-
-        .. code-block:: python
-            :emphasize-lines: 4
-
-            @transform( source_files,
-                        formatter(".cpp$"),
-
-                        # corresponding python file for each source file
-                        inputs("{basename[0]}.py"),
-
-                        "{basename[0]}.results")
-            def run_corresponding_python(input_filenames, output_file):
-                open(output_file, "w")
-
-
-    The *Ruffus* code will call each python script corresponding to their c++ counterpart:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [hasty.py -> hasty.results] completed
-                Job  = [messy.py -> messy.results] completed
-                Job  = [tasty.py -> tasty.results] completed
-            Completed Task = run_corresponding_python
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/inputs_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/inputs_code.txt
deleted file mode 100644
index 050ae10..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/inputs_code.txt
+++ /dev/null
@@ -1,229 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.inputs.code:
-
-############################################################################################################################################################################################################
-|new_manual.inputs.chapter_num|: Python Code for Manipulating task inputs via string substitution using :ref:`inputs() <decorators.inputs>`  and  :ref:`add_inputs() <decorators.add_inputs>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`inputs() <decorators.inputs>` syntax
-    * :ref:`add_inputs() <decorators.add_inputs>` syntax
-    * Back to |new_manual.inputs.chapter_num|: :ref:`Manipulating task inputs via string substitution <new_manual.inputs>`
-
-******************************************************************************************************************************************************
-Example code for adding additional *input* prerequisites per job with :ref:`add_inputs() <decorators.add_inputs>`
-******************************************************************************************************************************************************
-
-.. _new_manual.inputs.example1:
-
-===================================================================
-1. Example: compiling c++ code
-===================================================================
-
-    .. code-block:: python
-
-        # source files exist before our pipeline
-        source_files = ["hasty.cpp", "tasty.cpp", "messy.cpp"]
-        for source_file in source_files:
-            open(source_file, "w")
-
-        from ruffus import *
-
-        @transform(source_files, suffix(".cpp"), ".o")
-        def compile(input_filename, output_file):
-            open(output_file, "w")
-
-        pipeline_run()
-
-
-    Giving:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [hasty.cpp -> hasty.o] completed
-                Job  = [messy.cpp -> messy.o] completed
-                Job  = [tasty.cpp -> tasty.o] completed
-            Completed Task = compile
-
-.. _new_manual.inputs.example2:
-
-======================================================================================================================================
-2. Example: Adding a common header file with :ref:`add_inputs() <decorators.add_inputs>`
-======================================================================================================================================
-
-
-    .. code-block:: python
-        :emphasize-lines: 12
-
-        # source files exist before our pipeline
-        source_files = ["hasty.cpp", "tasty.cpp", "messy.cpp"]
-        for source_file in source_files:
-            open(source_file, "w")
-
-        # common (universal) header exists before our pipeline
-        open("universal.h", "w")
-
-        from ruffus import *
-
-        @transform( source_files, suffix(".cpp"),
-                    # add header to the input of every job
-                    add_inputs("universal.h"),
-                    ".o")
-        def compile(input_filename, output_file):
-            open(output_file, "w")
-
-        pipeline_run()
-
-    Giving:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [[hasty.cpp, universal.h] -> hasty.o] completed
-                Job  = [[messy.cpp, universal.h] -> messy.o] completed
-                Job  = [[tasty.cpp, universal.h] -> tasty.o] completed
-            Completed Task = compile
-
-.. _new_manual.inputs.example3:
-
-=====================================================================
-3. Example: Additional *Input* can be tasks
-=====================================================================
-
-    .. code-block:: python
-        :emphasize-lines: 11,17,19
-
-        # source files exist before our pipeline
-        source_files = ["hasty.cpp", "tasty.cpp", "messy.cpp"]
-        for source_file in source_files:
-            open(source_file, "w")
-
-        # common (universal) header exists before our pipeline
-        open("universal.h", "w")
-
-        from ruffus import *
-
-        # make header files
-        @transform(source_files, suffix(".cpp"), ".h")
-        def create_matching_headers(input_file, output_file):
-            open(output_file, "w")
-
-        @transform(source_files, suffix(".cpp"),
-                                # add header to the input of every job
-                    add_inputs("universal.h",
-                                # add result of task create_matching_headers to the input of every job
-                               create_matching_headers),
-                    ".o")
-        def compile(input_filename, output_file):
-            open(output_file, "w")
-
-        pipeline_run()
-
-    Giving:
-
-        .. code-block:: pycon
-
-
-            >>> pipeline_run()
-                Job  = [hasty.cpp -> hasty.h] completed
-                Job  = [messy.cpp -> messy.h] completed
-                Job  = [tasty.cpp -> tasty.h] completed
-            Completed Task = create_matching_headers
-                Job  = [[hasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> hasty.o] completed
-                Job  = [[messy.cpp, universal.h, hasty.h, messy.h, tasty.h] -> messy.o] completed
-                Job  = [[tasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> tasty.o] completed
-            Completed Task = compile
-
-.. _new_manual.inputs.example4:
-
-================================================================================================================================================================================================================================================
-4. Example: Add corresponding files using :ref:`add_inputs() <decorators.add_inputs>` with :ref:`formatter <decorators.formatter>` or :ref:`regex <decorators.regex>`
-================================================================================================================================================================================================================================================
-
-    .. code-block:: python
-        :emphasize-lines: 11,17,19
-
-        # source files exist before our pipeline
-        source_files = ["hasty.cpp", "tasty.cpp", "messy.cpp"]
-        header_files = ["hasty.h", "tasty.h", "messy.h"]
-        for source_file in source_files + header_files:
-            open(source_file, "w")
-
-        # common (universal) header exists before our pipeline
-        open("universal.h", "w")
-
-        from ruffus import *
-
-        @transform( source_files,
-                    formatter(".cpp$"),
-                                # corresponding header for each source file
-                    add_inputs("{basename[0]}.h",
-                               # add header to the input of every job
-                               "universal.h"),
-                    "{basename[0]}.o")
-        def compile(input_filename, output_file):
-            open(output_file, "w")
-
-        pipeline_run()
-
-    Giving:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [[hasty.cpp, hasty.h, universal.h] -> hasty.o] completed
-                Job  = [[messy.cpp, messy.h, universal.h] -> messy.o] completed
-                Job  = [[tasty.cpp, tasty.h, universal.h] -> tasty.o] completed
-            Completed Task = compile
-
-*********************************************************************************************
-Example code for replacing all input parameters with :ref:`inputs() <decorators.inputs>`
-*********************************************************************************************
-
-.. _new_manual.inputs.example5:
-
-================================================================================================================================================================================================================================================
-5. Example: Running matching python scripts using :ref:`inputs() <decorators.inputs>`
-================================================================================================================================================================================================================================================
-
-    .. code-block:: python
-        :emphasize-lines: 11,17,19
-
-        # source files exist before our pipeline
-        source_files = ["hasty.cpp", "tasty.cpp", "messy.cpp"]
-        python_files = ["hasty.py", "tasty.py", "messy.py"]
-        for source_file in source_files + python_files:
-            open(source_file, "w")
-
-        # common (universal) header exists before our pipeline
-        open("universal.h", "w")
-
-        from ruffus import *
-
-        @transform( source_files,
-                    formatter(".cpp$"),
-                    # corresponding python file for each source file
-                    inputs("{basename[0]}.py"),
-
-                    "{basename[0]}.results")
-        def run_corresponding_python(input_filenames, output_file):
-            open(output_file, "w")
-
-
-        pipeline_run()
-
-    Giving:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [hasty.py -> hasty.results] completed
-                Job  = [messy.py -> messy.results] completed
-                Job  = [tasty.py -> tasty.results] completed
-            Completed Task = run_corresponding_python
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/introduction.txt b/doc/_build/html/_sources/tutorials/new_tutorial/introduction.txt
deleted file mode 100644
index d36354a..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/introduction.txt
+++ /dev/null
@@ -1,399 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. role:: raw-html(raw)
-   :format: html
-
-:raw-html:`<style> .blue {color:blue} </style>`
-
-:raw-html:`<style> .highlight-red {color:red} </style>`
-
-.. role:: highlight-red
-
-.. role:: blue
-
-
-.. index::
-    pair: overview; Tutorial
-
-.. _new_manual.introduction:
-
-######################################################################################################
-|new_manual.introduction.chapter_num|: An introduction to basic *Ruffus* syntax
-######################################################################################################
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-
-
-************************************
-Overview
-************************************
-
-    .. image:: ../../images/theoretical_pipeline_schematic.png
-       :scale: 50
-
-    Computational pipelines transform your data in stages until the final result is produced.
-    One easy way to understand pipelines is by imagining your data flowing across a series of
-    pipes until it reaches its final destination. Even quite complicated processes can be
-    broken into simple stages. Of course, it helps to visualise the whole process.
-
-    *Ruffus* is a way of automating the plumbing in your pipeline: You supply the python functions
-    which perform the data transformation, and tell *Ruffus* how these pipeline ``task`` functions
-    are connected up. *Ruffus* will make sure that the right data flows down your pipeline in the
-    right way at the right time.
-
-
-    .. note::
-
-        *Ruffus* refers to each stage of your pipeline as a :term:`task`.
-
-.. _new_manual.introduction.import:
-
-.. index::
-    single: importing ruffus
-
-****************************
-Importing *Ruffus*
-****************************
-
-    The most convenient way to use *Ruffus* is to import the various names directly:
-
-        .. code-block:: python
-
-            from ruffus import *
-
-    This will allow *Ruffus* terms to be used directly in your code. This is also
-    the style we have adopted for this manual.
-
-
-    If any of these clash with names in your code, you can use qualified names instead:
-        ::
-
-            import ruffus
-
-            ruffus.pipeline_printout("...")
-
-    *Ruffus* uses only standard python syntax.
-
-    There is no need to install anything extra or to have your script "preprocessed" to run
-    your pipeline.
-
-****************************************************************************************************************
-*Ruffus* `decorators <https://docs.python.org/2/glossary.html#term-decorator>`__
-****************************************************************************************************************
-
-    To let *Ruffus* know that which python functions are part of your pipeline,
-    they need to be tagged or annotated using
-    *Ruffus* `decorators <https://docs.python.org/2/glossary.html#term-decorator>`__ .
-
-    `Decorators <https://docs.python.org/2/glossary.html#term-decorator>`__ have been part of the Python language since version 2.4.
-    Common examples from the standard library include `@staticmethod  <https://docs.python.org/2/library/functions.html#staticmethod>`__ and
-    `classmethod  <https://docs.python.org/2/library/functions.html#classmethod>`__.
-
-    `decorators <https://docs.python.org/2/glossary.html#term-decorator>`__  start with a ``@``
-    prefix, and take a number of parameters in parenthesis, much like in a function call.
-
-    `decorators <https://docs.python.org/2/glossary.html#term-decorator>`__   are placed before a normal python function.
-
-        .. image:: ../../images/tutorial_step1_decorator_syntax.png
-
-
-    Multiple decorators can be stacked as necessary in whichever order:
-
-        .. code-block:: python
-
-            @follows(first_task)
-            @follows(another_task)
-            @originate(range(5))
-            def second_task():
-                ""
-
-    *Ruffus* `decorators <https://docs.python.org/2/glossary.html#term-decorator>`__ do not
-    otherwise alter the underlying function. These can still be called normally.
-
-***************************************
-Your first *Ruffus* pipeline
-***************************************
-
-==============================================================================
-1. Write down the file names
-==============================================================================
-
-    *Ruffus* is designed for data moving through a computational pipeline as a series of files.
-
-    It is also possible to use *Ruffus* pipelines without using intermediate data files but for your
-    first efforts, it is probably best not to subvert its canonical design.
-
-    The first thing when designing a new *Ruffus* pipeline is to sketch out the set of file names for
-    the pipeline on paper:
-
-        .. image:: ../../images/tutorial_ruffus_files.jpg
-           :scale: 50
-
-    Here we have a number of DNA sequence files (``*.fasta``)
-        #. mapped to a genome (``*.sam``), and
-        #. compressed (``*.bam``) before being
-        #. summarised statistically (``*.statistics``)
-
-    The first striking thing is that all of the files following the same **consistent naming scheme**.
-
-    .. note::
-
-        :highlight-red:`The most important part of a Ruffus pipeline is to have a consistent naming scheme for your files.`
-
-        This allows you to build sane pipelines.
-
-
-    In this case, each of the files at the same stage share the same file extension, e.g. (``.sam``).
-    This is usually the simplest and most sensible choice. (We shall see in later chapters
-    that *Ruffus* supports more complicated naming patterns so long as they are consistent.)
-
-
-==============================================================================
-2. Write the python functions for each stage
-==============================================================================
-
-    Next, we can sketch out the python functions which do the actual work for the pipeline.
-
-        .. note::
-
-            #. :highlight-red:`These are normal python functions with the important proviso that`
-
-                #. The first parameter contains the **Input** (file names)
-                #. The second parameter contains the **Output** (file names)
-
-                You can otherwise supply as many parameters as is required.
-
-            #. :highlight-red:`Each python function should only take a` *Single* **Input** at a time
-
-                All the parallelism in your pipeline should be handled by *Ruffus*. Make sure
-                each function analyses one thing at a time.
-
-
-    *Ruffus* refers to a pipelined function as a :term:`task`.
-
-    The code for our three task functions look something like:
-
-        .. code-block:: python
-            :emphasize-lines: 2,4,5
-
-            #
-            #   STAGE 1 fasta->sam
-            #
-            def map_dna_sequence(input_file,               # 1st parameter is Input
-                                output_file):              # 2nd parameter is Output
-                """
-                Sketch of real mapping function
-                We can do the mapping ourselves
-                    or call some other programme:
-                        os.system("stampy %s %s..." % (input_file, output_file))
-                """
-                ii = open(input_file)
-                oo = open(output_file, "w")
-
-        .. code-block:: python
-            :emphasize-lines: 2
-
-            #
-            #   STAGE 2 sam->bam
-            #
-            def compress_sam_file(input_file,              # Input  parameter
-                                  output_file):            # Output parameter
-                """
-                Sketch of real compression function
-                """
-                ii = open(input_file)
-                oo = open(output_file, "w")
-
-        .. code-block:: python
-            :emphasize-lines: 2
-
-            #
-            #   STAGE 3 bam->statistics
-            #
-            def summarise_bam_file(input_file,             # Input  parameter
-                                   output_file,            # Output parameter
-                                   extra_stats_parameter): # Any number of extra parameters as required
-                """
-                Sketch of real analysis function
-                """
-                ii = open(input_file)
-                oo = open(output_file, "w")
-
-
-    If we were calling our functions manually, without the benefit of *Ruffus*, we would need
-    the following sequence of calls:
-
-        .. code-block:: python
-
-            # STAGE 1
-            map_dna_sequence("a.fasta", "a.sam")
-            map_dna_sequence("b.fasta", "b.sam")
-            map_dna_sequence("c.fasta", "c.sam")
-
-            # STAGE 2
-            compress_sam_file("a.sam", "a.bam")
-            compress_sam_file("b.sam", "b.bam")
-            compress_sam_file("c.sam", "c.bam")
-
-            # STAGE 3
-            summarise_bam_file("a.bam", "a.statistics")
-            summarise_bam_file("b.bam", "b.statistics")
-            summarise_bam_file("c.bam", "c.statistics")
-
-==============================================================================
-3. Link the python functions into a pipeline
-==============================================================================
-
-    *Ruffus* makes exactly the same function calls on your behalf. However, first, we need to
-    tell *Ruffus* what the arguments should be for each of the function calls.
-
-    * The **Input** is easy: This is either the starting file set (``*.fasta``) or whatever is produced
-      by the previous stage.
-
-    * The **Output** file name is the same as the **Input** but with the appropriate extension.
-
-    These are specified using the *Ruffus* :ref:`@transform <decorators.transform>` decorator as follows:
-
-        .. code-block:: python
-            :emphasize-lines: 6-8,17-19,29-31
-
-            from ruffus import *
-
-            starting_files = ["a.fasta", "b.fasta", "c.fasta"]
-
-            #
-            #   STAGE 1 fasta->sam
-            #
-            @transform(starting_files,                     # Input = starting files
-                        suffix(".fasta"),                  #         suffix = .fasta
-                        ".sam")                            # Output  suffix = .sam
-            def map_dna_sequence(input_file,
-                                output_file):
-                ii = open(input_file)
-                oo = open(output_file, "w")
-
-            #
-            #   STAGE 2 sam->bam
-            #
-            @transform(map_dna_sequence,                   # Input = previous stage
-                        suffix(".sam"),                    #         suffix = .sam
-                        ".bam")                            # Output  suffix = .bam
-            def compress_sam_file(input_file,
-                                  output_file):
-                ii = open(input_file)
-                oo = open(output_file, "w")
-
-            #
-            #   STAGE 3 bam->statistics
-            #
-            @transform(compress_sam_file,                  # Input = previous stage
-                        suffix(".bam"),                    #         suffix = .bam
-                        ".statistics",                     # Output  suffix = .statistics
-                        "use_linear_model")                # Extra statistics parameter
-            def summarise_bam_file(input_file,
-                                   output_file,
-                                   extra_stats_parameter):
-                """
-                Sketch of real analysis function
-                """
-                ii = open(input_file)
-                oo = open(output_file, "w")
-
-
-==============================================================================
-4. @transform syntax
-==============================================================================
-
-    #. | The 1st parameter for :ref:`@transform <decorators.transform>` is the **Input**.
-       | This is either the set of starting data or the name of the previous pipeline function.
-       | *Ruffus* *chains* together the stages of a pipeline by linking the **Output** of the previous stage into the **Input** of the next.
-
-    #. | The 2nd parameter is the current :ref:`suffix <decorators.suffix>`
-       | (i.e. our **Input** file extensions of ``".fasta"`` or  ``".sam"`` or  ``".bam"``)
-
-    #. | The 3rd parameter is what we want our **Output** file name to be after :ref:`suffix <decorators.suffix>` string substitution (e.g. ``.fasta - > .sam``).
-       | This works because we are using a sane naming scheme for our data files.
-
-    #. Other parameters can be passed to ``@transform`` and they will be forwarded to our python
-       pipeline function.
-
-
-    The functions that do the actual work of each stage of the pipeline remain unchanged.
-    The role of *Ruffus* is to make sure each is called in the right order,
-    with the right parameters, running in parallel (using multiprocessing if desired).
-
-
-.. index::
-    pair: pipeline_run; Tutorial
-
-.. _new_manual.pipeline_run:
-
-==============================================================================
-5. Run the pipeline!
-==============================================================================
-
-    .. note ::
-
-        **Key Ruffus Terminology**:
-
-        A  :term:`task` is an annotated python function which represents a recipe or stage of your pipeline.
-
-        A  :term:`job` is each time your recipe is applied to a piece of data, i.e. each time *Ruffus* calls your function.
-
-        Each **task** or pipeline recipe can thus have many **jobs** each of which can work in parallel on different data.
-
-    Now we can run the pipeline with the *Ruffus* function :ref:`pipeline_run<pipeline_functions.pipeline_run>`:
-
-        .. code-block:: python
-
-            pipeline_run()
-
-
-
-        This produces three sets of results in parallel, as you might expect:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [a.fasta -> a.sam] completed
-                Job  = [b.fasta -> b.sam] completed
-                Job  = [c.fasta -> c.sam] completed
-            Completed Task = map_dna_sequence
-                Job  = [a.sam -> a.bam] completed
-                Job  = [b.sam -> b.bam] completed
-                Job  = [c.sam -> c.bam] completed
-            Completed Task = compress_sam_file
-                Job  = [a.bam -> a.statistics, use_linear_model] completed
-                Job  = [b.bam -> b.statistics, use_linear_model] completed
-                Job  = [c.bam -> c.statistics, use_linear_model] completed
-            Completed Task = summarise_bam_file
-
-
-
-    To work out which functions to call, :ref:`pipeline_run<pipeline_functions.pipeline_run>`
-    finds the **last** :term:`task` function of your pipeline, then
-    works out all the other functions this depends on, working backwards up the chain of
-    dependencies automatically.
-
-    We can specify this end point of your pipeline explicitly:
-
-        ::
-
-            >>> pipeline_run(target_tasks = [summarise_bam_file])
-
-
-    This allows us to only run part of the pipeline, for example:
-
-        ::
-
-            >>> pipeline_run(target_tasks = [compress_sam_file])
-
-
-.. note::
-
-    The :ref:`example code <new_manual.introduction.code>` can be copied and pasted into a python
-    command shell.
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/introduction_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/introduction_code.txt
deleted file mode 100644
index 7bdd203..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/introduction_code.txt
+++ /dev/null
@@ -1,94 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.introduction.code:
-
-##############################################################################################################
-|new_manual.introduction.chapter_num|: Python Code for An introduction to basic Ruffus syntax
-##############################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@transform syntax in detail <decorators.transform>`
-    * Back to |new_manual.introduction.chapter_num|: :ref:`An introduction to basic Ruffus syntax <new_manual.introduction>`
-
-*******************************************
-Your first Ruffus script
-*******************************************
-
-    .. code-block:: python
-
-        ::
-
-        #
-        #   The starting data files would normally exist beforehand!
-        #       We create some empty files for this example
-        #
-        starting_files = ["a.fasta", "b.fasta", "c.fasta"]
-
-        for ff in starting_files:
-            open(ff, "w")
-
-
-        from ruffus import *
-
-        #
-        #   STAGE 1 fasta->sam
-        #
-        @transform(starting_files,                     # Input = starting files
-                    suffix(".fasta"),                  #         suffix = .fasta
-                    ".sam")                            # Output  suffix = .sam
-        def map_dna_sequence(input_file,
-                            output_file):
-            ii = open(input_file)
-            oo = open(output_file, "w")
-
-        #
-        #   STAGE 2 sam->bam
-        #
-        @transform(map_dna_sequence,                   # Input = previous stage
-                    suffix(".sam"),                    #         suffix = .sam
-                    ".bam")                            # Output  suffix = .bam
-        def compress_sam_file(input_file,
-                              output_file):
-            ii = open(input_file)
-            oo = open(output_file, "w")
-
-        #
-        #   STAGE 3 bam->statistics
-        #
-        @transform(compress_sam_file,                  # Input = previous stage
-                    suffix(".bam"),                    #         suffix = .bam
-                    ".statistics",                     # Output  suffix = .statistics
-                    "use_linear_model")                # Extra statistics parameter
-        def summarise_bam_file(input_file,
-                               output_file,
-                               extra_stats_parameter):
-            """
-            Sketch of real analysis function
-            """
-            ii = open(input_file)
-            oo = open(output_file, "w")
-
-        pipeline_run()
-
-
-************************************
-Resulting Output
-************************************
-    ::
-
-            >>> pipeline_run()
-                Job  = [a.fasta -> a.sam] completed
-                Job  = [b.fasta -> b.sam] completed
-                Job  = [c.fasta -> c.sam] completed
-            Completed Task = map_dna_sequence
-                Job  = [a.sam -> a.bam] completed
-                Job  = [b.sam -> b.bam] completed
-                Job  = [c.sam -> c.bam] completed
-            Completed Task = compress_sam_file
-                Job  = [a.bam -> a.statistics, use_linear_model] completed
-                Job  = [b.bam -> b.statistics, use_linear_model] completed
-                Job  = [c.bam -> c.statistics, use_linear_model] completed
-            Completed Task = summarise_bam_file
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/list_of_ruffus_names.txt b/doc/_build/html/_sources/tutorials/new_tutorial/list_of_ruffus_names.txt
deleted file mode 100644
index aa8b66b..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/list_of_ruffus_names.txt
+++ /dev/null
@@ -1,77 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: Ruffus names list; Tutorial
-
-.. _new_manual.ruffus_names:
-
-##########################################################################################################################################################################################################################################
-|new_manual.ruffus_names.chapter_num|: Names exported from Ruffus
-##########################################################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-
-******************
-Ruffus Names
-******************
-
-    This is a list of all the names *Ruffus* makes available:
-
-
-    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
-    | Category                                                      | Manual                                                                                                                                                        |
-    +===============================================================+===============================================================================================================================================================+
-    |  **Pipeline functions**                                       | | :ref:`pipeline_printout() <pipeline_functions.pipeline_printout>` (:ref:`Manual <new_manual.pipeline_printout>`)                                            |
-    |                                                               | | :ref:`pipeline_printout() <pipeline_functions.pipeline_printout_graph>` (:ref:`Manual <new_manual.pipeline_printout_graph>`)                                |
-    |                                                               | | :ref:`pipeline_printout() <pipeline_functions.pipeline_run>` (:ref:`Manual <new_manual.pipeline_run>`)                                                      |
-    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
-    |  **Decorators**                                               |                                                                                                                                                               |
-    |                                                               | | :ref:`@active_if <decorators.active_if>` (:ref:`Manual <new_manual.active_if>`)                                                                             |
-    |                                                               | | :ref:`@check_if_uptodate <decorators.check_if_uptodate>` (:ref:`Manual <new_manual.check_if_uptodate>`)                                                     |
-    |                                                               | | :ref:`@collate <decorators.collate>` (:ref:`Manual <new_manual.collate>`)                                                                                   |
-    |                                                               | | :ref:`@files <decorators.files>` (:ref:`Manual <new_manual.deprecated_files>`)                                                                              |
-    |                                                               | | :ref:`@follows <decorators.follows>` (:ref:`Manual <new_manual.follows>`)                                                                                   |
-    |                                                               | | :ref:`@jobs_limit <decorators.jobs_limit>` (:ref:`Manual <new_manual.jobs_limit>`)                                                                          |
-    |                                                               | | :ref:`@merge <decorators.merge>` (:ref:`Manual <new_manual.merge>`)                                                                                         |
-    |                                                               | | :ref:`@mkdir <decorators.mkdir>` (:ref:`Manual <new_manual.mkdir>`)                                                                                         |
-    |                                                               | | :ref:`@originate <decorators.originate>` (:ref:`Manual <new_manual.originate>`)                                                                             |
-    |                                                               | | :ref:`@parallel <decorators.parallel>` (:ref:`Manual <new_manual.deprecated_parallel>`)                                                                     |
-    |                                                               | | :ref:`@posttask <decorators.posttask>` (:ref:`Manual <new_manual.posttask>`)                                                                                |
-    |                                                               | | :ref:`@split <decorators.split>` (:ref:`Manual <new_manual.split>`)                                                                                         |
-    |                                                               | | :ref:`@subdivide <decorators.subdivide>` (:ref:`Manual <new_manual.subdivide>`)                                                                             |
-    |                                                               | | :ref:`@transform <decorators.transform>` (:ref:`Manual <new_manual.transform>`)                                                                             |
-    |                                                               | | :ref:`@files_re <decorators.files_re>` (:ref:`Manual <new_manual.deprecated_files_re>`)                                                                     |
-    |                                                               |                                                                                                                                                               |
-    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
-    |  **Loggers**                                                  |                                                                                                                                                               |
-    |                                                               | | stderr_logger                                                                                                                                               |
-    |                                                               | | black_hole_logger                                                                                                                                           |
-    |                                                               |                                                                                                                                                               |
-    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
-    |  **Parameter disambiguating Indicators**                      | | :ref:`suffix <decorators.suffix>` (:ref:`Manual <new_manual.suffix>`)                                                                                       |
-    |                                                               | | :ref:`regex <decorators.regex>` (:ref:`Manual <new_manual.regex>`)                                                                                          |
-    |                                                               | | :ref:`formatter <decorators.formatter>` (:ref:`Manual <new_manual.formatter>`)                                                                              |
-    |                                                               | | :ref:`inputs <decorators.inputs>` (:ref:`Manual <new_manual.inputs>`)                                                                                       |
-    |                                                               | | :ref:`inputs <decorators.add_inputs>` (:ref:`Manual <new_manual.inputs>`)                                                                                   |
-    |                                                               | | :ref:`touch_file <decorators.touch_file>` (:ref:`Manual <new_manual.posttask.touch_file>`)                                                                  |
-    |                                                               | | :ref:`combine <decorators.combine>`                                                                                                                         |
-    |                                                               | | :ref:`mkdir <decorators.follows.mkdir>` (:ref:`Manual <new_manual.follows.mkdir>`)                                                                          |
-    |                                                               | | :ref:`output_from <decorators.output_from>` (:ref:`Manual <new_manual.output_from>`)                                                                        |
-    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
-    |  **Decorators in ruffus.combinatorics**                       |                                                                                                                                                               |
-    |                                                               | | :ref:`@combinations <decorators.combinations>` (:ref:`Manual <new_manual.combinations>`)                                                                    |
-    |                                                               | | :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>` (:ref:`Manual <new_manual.combinations_with_replacement>`)                 |
-    |                                                               | | :ref:`@permutations <decorators.permutations>` (:ref:`Manual <new_manual.permutations>`)                                                                    |
-    |                                                               | | :ref:`@product <decorators.product>` (:ref:`Manual <new_manual.product>`)                                                                                   |
-    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
-    |  **Decorators in ruffus.cmdline**                             |                                                                                                                                                               |
-    |                                                               | | :ref:`get_argparse <new_manual.cmdline.get_argparse>`                                                                                                       |
-    |                                                               | | :ref:`setup_logging <new_manual.cmdline.setup_logging>`                                                                                                     |
-    |                                                               | | :ref:`run <new_manual.cmdline.run>`                                                                                                                         |
-    |                                                               | | :ref:`MESSAGE <new_manual.cmdline.MESSAGE>`                                                                                                                 |
-    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/logging.txt b/doc/_build/html/_sources/tutorials/new_tutorial/logging.txt
deleted file mode 100644
index 4e42e69..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/logging.txt
+++ /dev/null
@@ -1,221 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: logging; Tutorial
-
-.. _new_manual.logging:
-
-######################################################################################################
-|new_manual.logging.chapter_num|: Logging progress through a pipeline
-######################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-
-.. note::
-
-    Remember to look at the :ref:`example code <new_manual.logging.code>`
-
-*************************
-Overview
-*************************
-
-    There are two parts to logging with **Ruffus**:
-
-    * Logging progress through the pipeline
-
-        This produces the sort of output displayed in this manual:
-
-        ::
-
-            >>> pipeline_run([parallel_io_task])
-            Task = parallel_io_task
-                Job = ["a.1" -> "a.2", "A file"] completed
-                Job = ["b.1" -> "b.2", "B file"] unnecessary: already up to date
-            Completed Task = parallel_io_task
-
-
-    * Logging your own messages from within your pipelined functions.
-
-        Because **Ruffus** may run each task function in separate process on a separate
-        CPU (multiprocessing), some attention has to be paid to how to send and
-        synchronise your log messages across process boundaries.
-
-
-    We shall deal with these in turn.
-
-
-.. _new_manual.logging.pipeline:
-
-**********************************
-Logging task/job completion
-**********************************
-    By default, *Ruffus* logs each task and each job as it is completed to
-    `sys.stderr  <http://docs.python.org/2/library/sys.html#sys.stderr>`__.
-
-    By default, Ruffus logs to ``STDERR``: :ref:`pipeline_run(logger = stderr_logger) <pipeline_functions.pipeline_run>`.
-
-    If you want to turn off all tracking messages as the pipeline runs, apart from setting ``verbose = 0``, you
-    can also use the aptly named Ruffus ``black_hole_logger``:
-
-        .. code-block:: python
-
-            pipeline_run(logger = black_hole_logger)
-
-.. index::
-    pair: pipeline_run verbosity; Tutorial
-
-=================================
-Controlling logging verbosity
-=================================
-    :ref:`pipeline_run() <pipeline_functions.pipeline_run>` currently has five levels of verbosity, set by the optional ``verbose``
-    parameter which defaults to 1:
-
-        ::
-
-                verbose = 0: nothing
-                verbose = 1: logs completed jobs/tasks;
-                verbose = 2: logs up to date jobs in incomplete tasks
-                verbose = 3: logs reason for running job
-                verbose = 4: logs messages useful only for debugging ruffus pipeline code
-
-
-        ``verbose`` > ``5`` are intended for debugging **Ruffus** by the developers and the details
-        are liable to change from release to release
-
-
-.. index::
-    pair: logging with ruffus.cmdline; Tutorial
-
-********************************************************************************
-Use :ref:`ruffus.cmdline <new_manual.cmdline>`
-********************************************************************************
-
-    As always, it is easiest to use :ref:`ruffus.cmdline <new_manual.cmdline>`.
-
-    Set your script to
-
-        * write messages to ``STDERR`` with the ``--verbose`` option and
-        * to a log file with the ``--log_file`` option.
-
-        .. code-block:: python
-           :emphasize-lines: 3
-
-            from ruffus import *
-
-            #  Python logger which can be synchronised across concurrent Ruffus tasks
-            logger, logger_mutex = cmdline.setup_logging (__name__, options.log_file, options.verbose)
-
-            @transform( ["job1.input"], suffix(".input"), ".output1"),
-            def first_task(input_file, output_file):
-                pass
-
-            pipeline_run(logger=logger)
-
-
-.. index::
-    pair: logging customising; Tutorial
-
-****************************************
-Customising logging
-****************************************
-
-    You can also specify exactly how logging works by providing a `logging <http://docs.python.org/library/logging.html>`_ object
-    to :ref:`pipeline_run() <pipeline_functions.pipeline_run>` .
-    This log object should have ``debug()`` and ``info()`` methods.
-
-    Instead of writing your own, it is usually more convenient to use the python
-    `logging <http://docs.python.org/library/logging.html>`_
-    module which provides logging classes with rich functionality.
-
-    The :ref:`example code<new_manual.logging.code>` sets up a logger to a rotating set of files
-
-
-.. index::
-    pair: logging your own message; Tutorial
-
-.. _new_manual.logging.per_job:
-
-****************************************
-Log your own messages
-****************************************
-
-    You need to take a little care when logging your custom messages *within* your pipeline.
-
-    * If your Ruffus pipeline may run in parallel, make sure that logging is synchronised.
-    * If your Ruffus pipeline may run across separate processes, send your logging object across process boundaries.
-
-
-    `logging <http://docs.python.org/library/logging.html>`_ objects can not be
-    `pickled <http://docs.python.org/library/pickle.html>`_ and shared naively across
-    processes. Instead, we need to create proxies which forward the logging to a single
-    shared log.
-
-    The :ref:`ruffus.proxy_logger <proxy-logger>` module provides an easy way to share
-    `logging <http://docs.python.org/library/logging.html>`_ objects among
-    jobs. This requires just two simple steps:
-
-
-
-
-.. note::
-
-    * This is a good template for sharing `non-picklable objects <http://docs.python.org/2/library/pickle.html#what-can-be-pickled-and-unpickled>`_
-      across processes.
-
-
-.. _new_manual.sharing_proxy_object:
-
-
-============================================================
-    1. Set up logging
-============================================================
-
-    Things are easiest if you are using ``ruffus.cmdline``:
-
-    .. code-block:: python
-
-        #  standard python logger which can be synchronised across concurrent Ruffus tasks
-        logger, logger_mutex = cmdline.setup_logging (__name__, options.log_file, options.verbose)
-
-
-    Otherwise, manually:
-
-    .. code-block:: python
-
-
-        from ruffus.proxy_logger import *
-        (logger,
-         logging_mutex) = make_shared_logger_and_proxy (setup_std_shared_logger,
-                                                        "my_logger",
-                                                        {"file_name" :"/my/lg.log"})
-
-============================================================
-    2. Share the proxy
-============================================================
-        Now, pass:
-
-            * ``logger`` (which forwards logging calls across jobs) and
-            * ``logging_mutex`` (which prevents different jobs which are logging simultaneously
-              from being jumbled up)
-
-        to each job:
-
-        .. code-block:: python
-            :emphasize-lines: 4,6,9
-
-            @transform( initial_file,
-                        suffix(".input"),
-                        ".output1",
-                        logger, logging_mutex),         # pass log and synchronisation as parameters
-            def first_task(input_file, output_file,
-                        logger, logging_mutex):         # pass log and synchronisation as parameters
-                pass
-
-                # synchronise logging
-                with logging_mutex:
-                    logger.info("Here we go logging...")
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/logging_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/logging_code.txt
deleted file mode 100644
index 69bd51b..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/logging_code.txt
+++ /dev/null
@@ -1,55 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.logging.code:
-
-######################################################################################################
-|new_manual.logging.chapter_num|: Python Code for Logging progress through a pipeline
-######################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * Back to |new_manual.logging.chapter_num|: :ref:`Logging progress through a pipeline <new_manual.logging>`
-
-****************************************
-Rotating set of file logs
-****************************************
-
-    .. code-block:: python
-        :emphasize-lines: 10,14,17,31
-
-        import logging
-        import logging.handlers
-
-        LOG_FILENAME = '/tmp/ruffus.log'
-
-        # Set up a specific logger with our desired output level
-        logger = logging.getLogger('My_Ruffus_logger')
-        logger.setLevel(logging.DEBUG)
-
-        # Rotate a set of 5 log files every 2kb
-        handler = logging.handlers.RotatingFileHandler(
-                      LOG_FILENAME, maxBytes=2000, backupCount=5)
-
-        # Add the log message handler to the logger
-        logger.addHandler(handler)
-
-        # Ruffus pipeline
-        from ruffus import *
-
-        # Start with some initial data file of yours...
-        initial_file = "job1.input"
-        open(initial_file, "w")
-
-        @transform( initial_file,
-                    suffix(".input"),
-                    ".output1"),
-        def first_task(input_file, output_file):
-            "Some detailed description"
-            pass
-
-        #   use our custom logging object
-        pipeline_run(logger=logger)
-        print open("/tmp/ruffus.log").read()
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/manual_contents.txt b/doc/_build/html/_sources/tutorials/new_tutorial/manual_contents.txt
deleted file mode 100644
index e17dbf2..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/manual_contents.txt
+++ /dev/null
@@ -1,64 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.table_of_contents:
-
-####################################################################
-**Ruffus** Manual: List of Chapters and Example code
-####################################################################
-
-    Download as :download:`pdf <../../static_data/ruffus.pdf>`.
-
-    * |new_manual.introduction.chapter_num|: :ref:`An introduction to basic Ruffus syntax <new_manual.introduction>`
-    * |new_manual.transform.chapter_num|: :ref:`Transforming data in a pipeline with @transform <new_manual.transform>`
-    * |new_manual.transform_in_parallel.chapter_num|: :ref:`More on @transform-ing data <new_manual.transform_in_parallel>`
-    * |new_manual.originate.chapter_num|: :ref:`Creating files with @originate <new_manual.originate>`
-    * |new_manual.pipeline_printout.chapter_num|: :ref:`Understanding how your pipeline works with pipeline_printout() <new_manual.pipeline_printout>`
-    * |new_manual.cmdline.chapter_num|: :ref:`Running Ruffus from the command line with ruffus.cmdline <new_manual.cmdline>`
-    * |new_manual.pipeline_printout_graph.chapter_num|: :ref:`Displaying the pipeline visually with pipeline_printout_graph() <new_manual.pipeline_printout_graph>`
-    * |new_manual.output_file_names.chapter_num|: :ref:`Specifying output file names with formatter() and regex() <new_manual.output_file_names>`
-    * |new_manual.mkdir.chapter_num|: :ref:`Preparing directories for output with @mkdir <new_manual.mkdir>`
-    * |new_manual.checkpointing.chapter_num|: :ref:`Checkpointing: Interrupted Pipelines and Exceptions <new_manual.checkpointing>`
-    * |new_manual.decorators_compendium.chapter_num|: :ref:`Pipeline topologies and a compendium of Ruffus decorators <new_manual.decorators_compendium>`
-    * |new_manual.split.chapter_num|: :ref:`Splitting up large tasks / files with @split <new_manual.split>`
-    * |new_manual.merge.chapter_num|: :ref:`@merge multiple input into a single result <new_manual.merge>`
-    * |new_manual.logging.chapter_num|: :ref:`Logging progress through a pipeline <new_manual.logging>`
-    * |new_manual.multiprocessing.chapter_num|: :ref:`Multiprocessing, drmaa and Computation Clusters <new_manual.multiprocessing>`
-    * |new_manual.subdivide_collate.chapter_num|: :ref:`@subdivide tasks to run efficiently and regroup with @collate <new_manual.subdivide_collate>`
-    * |new_manual.combinatorics.chapter_num|: :ref:`@combinations, @permutations and all versus all @product <new_manual.combinatorics>`
-    * |new_manual.active_if.chapter_num|: :ref:`Turning parts of the pipeline on and off at runtime with @active_if <new_manual.active_if>`
-    * |new_manual.inputs.chapter_num|: :ref:`Manipulating task inputs via string substitution with inputs() and add_inputs() <new_manual.inputs>`
-    * |new_manual.posttask.chapter_num|: :ref:`Signal the completion of each stage of our pipeline with @posttask <new_manual.posttask>`
-    * |new_manual.on_the_fly.chapter_num|: :ref:`Esoteric: Generating parameters on the fly with @files <new_manual.on_the_fly>`
-    * |new_manual.parallel.chapter_num|: :ref:`Esoteric: Running jobs in parallel without files using @parallel <new_manual.deprecated_parallel>`
-    * |new_manual.check_if_uptodate.chapter_num|: :ref:`Esoteric: Writing custom functions to decide which jobs are up to date with @check_if_uptodate <new_manual.check_if_uptodate>`
-    * |new_manual.flowchart_colours.chapter_num| :ref:`Flow Chart Colours with pipeline_printout_graph <new_manual.flowchart_colours>`
-    * |new_manual.dependencies.chapter_num| :ref:`Under the hood: How dependency works <new_manual.dependencies>`
-    * |new_manual.exceptions.chapter_num| :ref:`Exceptions thrown inside pipelines <new_manual.exceptions>`
-    * |new_manual.ruffus_names.chapter_num| :ref:`Names (keywords) exported from Ruffus <new_manual.ruffus_names>`
-    * |new_manual.deprecated_files.chapter_num|: :ref:`Legacy and deprecated syntax @files <new_manual.deprecated_files>`
-    * |new_manual.deprecated_files_re.chapter_num|: :ref:`Legacy and deprecated syntax @files_re <new_manual.deprecated_files_re>`
-
-
-
-**Ruffus** Manual: List of Example Code for Each Chapter:
-
-    * :ref:`new_manual.introduction.code`
-    * :ref:`new_manual.transform.code`
-    * :ref:`new_manual.transform_in_parallel.code`
-    * :ref:`new_manual.originate.code`
-    * :ref:`new_manual.pipeline_printout.code`
-    * :ref:`new_manual.pipeline_printout_graph.code`
-    * :ref:`new_manual.output_file_names.code`
-    * :ref:`new_manual.mkdir.code`
-    * :ref:`new_manual.checkpointing.code`
-    * :ref:`new_manual.split.code`
-    * :ref:`new_manual.merge.code`
-    * :ref:`new_manual.multiprocessing.code`
-    * :ref:`new_manual.logging.code`
-    * :ref:`new_manual.subdivide_collate.code`
-    * :ref:`new_manual.combinatorics.code`
-    * :ref:`new_manual.inputs.code`
-    * :ref:`new_manual.on_the_fly.code`
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/merge.txt b/doc/_build/html/_sources/tutorials/new_tutorial/merge.txt
deleted file mode 100644
index 4b8466e..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/merge.txt
+++ /dev/null
@@ -1,140 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: merge; Tutorial
-
-.. _new_manual.merge:
-
-######################################################################################################
-|new_manual.merge.chapter_num|: ``@merge`` multiple input into a single result
-######################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@merge <decorators.merge>` syntax
-   * :ref:`Example code for this chapter <new_manual.merge.code>`
-
-
-**************************************************************************************
-Overview of :ref:`@merge <decorators.merge>` 
-**************************************************************************************
-
-    The :ref:`previous chapter <new_manual.split>` explained how **Ruffus** allows large
-    jobs to be split into small pieces with :ref:`@split <decorators.split>` and analysed
-    in parallel using for example, our old friend :ref:`@transform <decorators.transform>`.
-
-    Having done this, our next task is to recombine the fragments into a seamless whole.
-
-    This is the role of the :ref:`@merge <decorators.merge>` decorator.
-
-**************************************************************************************
-:ref:`@merge <decorators.merge>`  is a many to one operator
-**************************************************************************************
-
-    :ref:`@transform <decorators.transform>` tasks multiple *inputs* and produces a single *output*, **Ruffus**
-    is again agnostic as to the sort of data contained within this single *output*. It can be a single
-    (string) file name, an arbitrary complicated nested structure with numbers, objects etc.
-    Or even a list. 
-
-    The main thing is that downstream tasks will interpret this output as a single entity leading to a single
-    job.
-
-    :ref:`@split <decorators.split>` and :ref:`@merge <decorators.merge>` are, in other words, about network topology.
-
-    Because of this :ref:`@merge <decorators.merge>` is also very useful for summarising the progress
-    in our pipeline. At key selected points, we can gather data from the multitude of data or disparate *inputs*
-    and :ref:`@merge <decorators.merge>` them to a single set of summaries.
-
-
-    
-**************************************************************************************
-Example: Combining partial solutions: Calculating variances
-**************************************************************************************
-
-    The :ref:`previous chapter <new_manual.split>` we had almost completed all the pieces of our flowchart:
-
-    .. image:: ../../images/manual_split_merge_example.jpg
-       :scale: 30 
-
-    What remains is to take the partial solutions from the different ``.sums`` files
-    and turn these into the variance as follows:
-
-        ::
-                                                                                                                             
-            variance = (sum_squared - sum * sum / N)/N                                                                   
-                                                                                                                     
-        where ``N`` is the number of values                                                                              
-
-        See the `wikipedia <http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance>`_ entry for a discussion of
-        why this is a very naive approach.
-
-    
-
-    To do this, all we have to do is iterate through all the values in ``*.sums``,
-    add up the ``sums`` and ``sum_squared``, and apply the above (naive) formula.
-    
-    
-    .. code-block:: python
-        :emphasize-lines: 2
-    
-        #
-        #   @merge files together
-        #    
-        @merge(sum_of_squares, "variance.result")
-        def calculate_variance (input_file_names, output_file_name):
-            """
-            Calculate variance naively
-            """
-            #
-            #   initialise variables
-            #
-            all_sum_squared = 0.0
-            all_sum         = 0.0
-            all_cnt_values  = 0.0
-            #
-            # added up all the sum_squared, and sum and cnt_values from all the chunks
-            #
-            for input_file_name in input_file_names:
-                sum_squared, sum, cnt_values = map(float, open(input_file_name).readlines())
-                all_sum_squared += sum_squared
-                all_sum         += sum
-                all_cnt_values  += cnt_values
-            all_mean = all_sum / all_cnt_values
-            variance = (all_sum_squared - all_sum * all_mean)/(all_cnt_values)
-            #
-            #   print output
-            #
-            open(output_file_name,  "w").write("%s\n" % variance)
-
-
-
-    This results in the following equivalent function call:
-
-        .. code-block:: python
-            :emphasize-lines: 2
-    
-    
-            calculate_variance (["1.sums", "2.sums", "3.sums", 
-                                 "4.sums", "5.sums", "6.sums", 
-                                 "7.sums", "8.sums", "9.sums, "10.sums"], "variance.result")
-
-    and the following display:
-    
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [[1.sums, 10.sums, 2.sums, 3.sums, 4.sums, 5.sums, 6.sums, 7.sums, 8.sums, 9.sums] -> variance.result] completed
-            Completed Task = calculate_variance
-            
-
-
-    The final result is in ``variance.result``
-            
-
-    Have a look at the :ref:`complete example code for this chapter <new_manual.merge.code>`.
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/merge_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/merge_code.txt
deleted file mode 100644
index cc5bd8b..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/merge_code.txt
+++ /dev/null
@@ -1,147 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.merge.code:
-
-##############################################################################################################
-|new_manual.merge.chapter_num|: Python Code for  ``@merge`` multiple input into a single result
-##############################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@merge syntax in detail <decorators.merge>`
-    * Back to |new_manual.merge.chapter_num|: :ref:`Splitting up large tasks / files with @merge <new_manual.merge>`
-
-*******************************************
-Splitting large jobs
-*******************************************
-
-        ::
-
-            from ruffus import *
-
-            NUMBER_OF_RANDOMS = 10000
-            CHUNK_SIZE = 1000
-
-
-            import random, os, glob
-
-            #---------------------------------------------------------------
-            #
-            #   Create random numbers
-            #
-            @originate("random_numbers.list")
-            def create_random_numbers(output_file_name):
-                f = open(output_file_name, "w")
-                for i in range(NUMBER_OF_RANDOMS):
-                    f.write("%g\n" % (random.random() * 100.0))
-
-            #---------------------------------------------------------------
-            #
-            #   split initial file
-            #
-            @split(create_random_numbers, "*.chunks")
-            def split_problem (input_file_names, output_files):
-                """
-                    splits random numbers file into xxx files of chunk_size each
-                """
-                #
-                #   clean up any files from previous runs
-                #
-                #for ff in glob.glob("*.chunks"):
-                for ff in input_file_names:
-                    os.unlink(ff)
-                #
-                #
-                #   create new file every chunk_size lines and
-                #       copy each line into current file
-                #
-                output_file = None
-                cnt_files = 0
-                for input_file_name in input_file_names:
-                    for i, line in enumerate(open(input_file_name)):
-                        if i % CHUNK_SIZE == 0:
-                            cnt_files += 1
-                            output_file = open("%d.chunks" % cnt_files, "w")
-                        output_file.write(line)
-
-            #---------------------------------------------------------------
-            #
-            #   Calculate sum and sum of squares for each chunk file
-            #
-            @transform(split_problem, suffix(".chunks"), ".sums")
-            def sum_of_squares (input_file_name, output_file_name):
-                output = open(output_file_name,  "w")
-                sum_squared, sum = [0.0, 0.0]
-                cnt_values = 0
-                for line in open(input_file_name):
-                    cnt_values += 1
-                    val = float(line.rstrip())
-                    sum_squared += val * val
-                    sum += val
-                output.write("%s\n%s\n%d\n" % (repr(sum_squared), repr(sum), cnt_values))
-
-            #---------------------------------------------------------------
-            #
-            #   Calculate variance from sums
-            #
-            @merge(sum_of_squares, "variance.result")
-            def calculate_variance (input_file_names, output_file_name):
-                """
-                Calculate variance naively
-                """
-                #
-                #   initialise variables
-                #
-                all_sum_squared = 0.0
-                all_sum         = 0.0
-                all_cnt_values  = 0.0
-                #
-                # added up all the sum_squared, and sum and cnt_values from all the chunks
-                #
-                for input_file_name in input_file_names:
-                    sum_squared, sum, cnt_values = map(float, open(input_file_name).readlines())
-                    all_sum_squared += sum_squared
-                    all_sum         += sum
-                    all_cnt_values  += cnt_values
-                all_mean = all_sum / all_cnt_values
-                variance = (all_sum_squared - all_sum * all_mean)/(all_cnt_values)
-                #
-                #   print output
-                #
-                open(output_file_name,  "w").write("%s\n" % variance)
-
-            #---------------------------------------------------------------
-            #
-            #       Run
-            #
-            pipeline_run()
-
-
-
-
-************************************
-Resulting Output
-************************************
-    ::
-
-        >>> pipeline_run()
-            Job  = [None -> random_numbers.list] completed
-        Completed Task = create_random_numbers
-            Job  = [[random_numbers.list] -> *.chunks] completed
-        Completed Task = split_problem
-            Job  = [1.chunks -> 1.sums] completed
-            Job  = [10.chunks -> 10.sums] completed
-            Job  = [2.chunks -> 2.sums] completed
-            Job  = [3.chunks -> 3.sums] completed
-            Job  = [4.chunks -> 4.sums] completed
-            Job  = [5.chunks -> 5.sums] completed
-            Job  = [6.chunks -> 6.sums] completed
-            Job  = [7.chunks -> 7.sums] completed
-            Job  = [8.chunks -> 8.sums] completed
-            Job  = [9.chunks -> 9.sums] completed
-        Completed Task = sum_of_squares
-            Job  = [[1.sums, 10.sums, 2.sums, 3.sums, 4.sums, 5.sums, 6.sums, 7.sums, 8.sums, 9.sums] -> variance.result] completed
-        Completed Task = calculate_variance
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/mkdir.txt b/doc/_build/html/_sources/tutorials/new_tutorial/mkdir.txt
deleted file mode 100644
index a7632c6..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/mkdir.txt
+++ /dev/null
@@ -1,152 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: mkdir; Tutorial
-
-.. _new_manual.mkdir:
-
-######################################################################################################################################################################
-|new_manual.mkdir.chapter_num|: Preparing directories for output with :ref:`@mkdir() <decorators.mkdir>`
-######################################################################################################################################################################
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@follows(mkdir()) syntax in detail <decorators.follows>`
-   * :ref:`@mkdir syntax in detail <decorators.mkdir>`
-
-.. note::
-
-    Remember to look at the example code:
-
-        * :ref:`new_manual.mkdir.code`
-
-
-***************************************
-Overview
-***************************************
-
-    In |new_manual.transform_in_parallel.chapter_num|, we saw that we could use :ref:`@follows(mkdir()) <new_manual.follows.mkdir>` to
-    ensure that output directories exist:
-
-    .. code-block:: python
-        :emphasize-lines: 4
-
-        #
-        #   create_new_files() @follows mkdir
-        #
-        @follows(mkdir("output/results/here"))
-        @originate(["output/results/here/a.start_file",
-                    "output/results/here/b.start_file"])
-        def create_new_files(output_file_pair):
-            pass
-
-
-    This ensures that the decorated task follows (:ref:`@follows <new_manual.follows.mkdir>`) the
-    making of the specified directory (``mkdir()``).
-
-    Sometimes, however, the **Output** is intended not for any single directory but a group
-    of destinations depending on the parsed contents of **Input** paths.
-
-*********************************************************************************************************************
-Creating directories after string substitution in a zoo...
-*********************************************************************************************************************
-
-    You may remember :ref:`this example <new_manual.output_file_names.formatter.zoo>` from |new_manual.output_file_names.chapter_num|:
-
-    We want to feed the denizens of a zoo. The original file names are spread over several directories and we
-    group their food supply by the *clade* of the animal in the following manner:
-
-        .. image:: ../../images/simple_tutorial_zoo_animals_formatter_example.jpg
-           :scale: 50
-
-        .. code-block:: python
-            :emphasize-lines: 13,14
-
-            #   Put different animals in different directories depending on their clade
-            @transform(create_initial_files,                                       # Input
-
-                       formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-
-                       "{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food", # Replacement
-
-                       "{subpath[0][1]}/{clade[0]}",                               # new_directory
-                       "{subdir[0][0]}",                                           # animal_name
-                       "{tame[0]}")                                                # tameness
-            def feed(input_file, output_file, new_directory, animal_name, tameness):
-                print "%40s -> %90s" % (input_file, output_file)
-                # this blows up
-                # open(output_file, "w")
-
-
-    The example code from |new_manual.output_file_names.chapter_num| is, however, incomplete. If we were to actually create the specified
-    files we would realise that we had forgotten to create the destination directories ``reptiles``, ``mammals`` first!
-
-==============================================================================
-using :ref:`formatter() <decorators.formatter>`
-==============================================================================
-
-    We could of course create directories manually.
-    However, apart from being tedious and error prone, we have already gone to some lengths
-    to parse out the diretories for :ref:`@transform <decorators.transform>`.
-    Why don't we use the same logic to make the directories?
-
-    Can you see the parallels between the syntax for :ref:`@mkdir <decorators.mkdir>` and :ref:`@transform <decorators.transform>`?
-
-        .. code-block:: python
-
-            # create directories for each clade
-            @mkdir(    create_initial_files,                                       # Input
-
-                       formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-                       "{subpath[0][1]}/{clade[0]})                                # new_directory
-
-            #   Put animals of each clade in the same directory
-            @transform(create_initial_files,                                       # Input
-
-                       formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-
-                       "{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food", # Replacement
-
-                       "{subpath[0][1]}/{clade[0]}",                               # new_directory
-                       "{subdir[0][0]}",                                           # animal_name
-                       "{tame[0]}")                                                # tameness
-            def feed(input_file, output_file, new_directory, animal_name, tameness):
-                print "%40s -> %90s" % (input_file, output_file)
-                # this works now
-                open(output_file, "w")
-
-    See the :ref:`example code <new_manual.mkdir.code>`
-
-==============================================================================
-using :ref:`regex() <decorators.regex>`
-==============================================================================
-
-    If you are particularly fond of using regular expression to parse file paths,
-    you could also use :ref:`regex() <decorators.regex>`:
-
-
-        .. code-block:: python
-
-            # create directories for each clade
-            @mkdir(    create_initial_files,                                       # Input
-
-                       regex(r"(.*?)/?(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"), # Only animals: ignore plants!
-                       r"\1/\g<clade>")                                             # new_directory
-
-            #   Put animals of each clade in the same directory
-            @transform(create_initial_files,                                       # Input
-
-                       formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-
-                       "{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food", # Replacement
-
-                       "{subpath[0][1]}/{clade[0]}",                               # new_directory
-                       "{subdir[0][0]}",                                           # animal_name
-                       "{tame[0]}")                                                # tameness
-            def feed(input_file, output_file, new_directory, animal_name, tameness):
-                print "%40s -> %90s" % (input_file, output_file)
-                # this works now
-                open(output_file, "w")
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/mkdir_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/mkdir_code.txt
deleted file mode 100644
index 91f3661..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/mkdir_code.txt
+++ /dev/null
@@ -1,113 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.mkdir.code:
-
-############################################################################################################################################################################################################
-|new_manual.mkdir.chapter_num|: Python Code for Preparing directories for output with :ref:`@mkdir() <decorators.mkdir>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`mkdir() <decorators.mkdir>` syntax
-    * :ref:`formatter() <decorators.formatter>` syntax
-    * :ref:`regex() <decorators.regex>` syntax
-    * Back to |new_manual.mkdir.chapter_num|: :ref:`Preparing directories for output with @mkdir() <new_manual.mkdir>`
-
-****************************************************************************************************************
-Code for :ref:`formatter() <decorators.formatter>` Zoo example
-****************************************************************************************************************
-
-
-    .. code-block:: python
-
-        from ruffus import *
-
-        #   Make directories
-        @mkdir(["tiger", "lion", "dog", "crocodile", "rose"])
-        @originate(
-                    #   List of animals and plants
-                    [    "tiger/mammals.wild.animals",
-                        "lion/mammals.wild.animals",
-                        "lion/mammals.handreared.animals",
-                        "dog/mammals.tame.animals",
-                        "dog/mammals.wild.animals",
-                        "crocodile/reptiles.wild.animals",
-                        "rose/flowering.handreared.plants"])
-        def create_initial_files(output_file):
-            with open(output_file, "w") as oo: pass
-
-
-        # create directories for each clade
-        @mkdir(    create_initial_files,                                       # Input
-
-                   formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-
-                   "{subpath[0][1]}/{clade[0]}")                               # new_directory
-        #   Put different animals in different directories depending on their clade
-        @transform(create_initial_files,                                       # Input
-
-                   formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-
-                   "{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food", # Replacement
-
-                   "{subpath[0][1]}/{clade[0]}",                               # new_directory
-                   "{subdir[0][0]}",                                           # animal_name
-                   "{tame[0]}")                                                # tameness
-        def feed(input_file, output_file, new_directory, animal_name, tameness):
-                print "%40s -> %90s" % (input_file, output_file)
-                # this works now
-                open(output_file, "w")
-
-
-        pipeline_run(verbose=0)
-
-
-****************************************************************************************************************
-Code for :ref:`regex() <decorators.regex>` Zoo example
-****************************************************************************************************************
-
-
-    .. code-block:: python
-
-        from ruffus import *
-
-        #   Make directories
-        @mkdir(["tiger", "lion", "dog", "crocodile", "rose"])
-        @originate(
-                    #   List of animals and plants
-                    [    "tiger/mammals.wild.animals",
-                        "lion/mammals.wild.animals",
-                        "lion/mammals.handreared.animals",
-                        "dog/mammals.tame.animals",
-                        "dog/mammals.wild.animals",
-                        "crocodile/reptiles.wild.animals",
-                        "rose/flowering.handreared.plants"])
-        def create_initial_files(output_file):
-            with open(output_file, "w") as oo: pass
-
-
-        # create directories for each clade
-        @mkdir(    create_initial_files,                                       # Input
-
-                   regex(r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"), # Only animals: ignore plants!
-                   r"\g<clade>")                                             # new_directory
-        #   Put different animals in different directories depending on their clade
-        @transform(create_initial_files,                                        # Input
-
-                   regex(r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"), # Only animals: ignore plants!
-
-                   r"\1\g<clade>/\g<tame>.\2.food",                            # Replacement
-
-                   r"\1\g<clade>",                                             # new_directory
-                   r"\2",                                                       # animal_name
-                   "\g<tame>")                                                  # tameness
-        def feed(input_file, output_file, new_directory, animal_name, tameness):
-            print "%40s -> %90s" % (input_file, output_file)
-            # this works now
-            open(output_file, "w")
-
-
-        pipeline_run(verbose=0)
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/multiprocessing.txt b/doc/_build/html/_sources/tutorials/new_tutorial/multiprocessing.txt
deleted file mode 100644
index aaf77ed..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/multiprocessing.txt
+++ /dev/null
@@ -1,293 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: multiprocessing; Tutorial
-
-.. _new_manual.multiprocessing:
-
-####################################################################################################################################################
-|new_manual.multiprocessing.chapter_num|: Multiprocessing, ``drmaa`` and Computation Clusters
-####################################################################################################################################################
-
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@jobs_limit <decorators.jobs_limit>` syntax
-    * :ref:`pipeline_run() <pipeline_functions.pipeline_run>` syntax
-    * :ref:`drmaa_wrapper.run_job() <drmaa_wrapper.run_job>` syntax
-
-.. note::
-
-    Remember to look at the example code:
-
-        * :ref:`new_manual.multiprocessing.code`
-
-***********************
-Overview
-***********************
-
-.. index::
-    pair: pipeline_run(multiprocess); Tutorial
-
-=====================
-Multi Processing
-=====================
-
-    *Ruffus* uses python `multiprocessing <http://docs.python.org/library/multiprocessing.html>`_ to run
-    each job in a separate process.
-
-    This means that jobs do *not* necessarily complete in the order of the defined parameters.
-    Task hierachies are, of course, inviolate: upstream tasks run before downstream, dependent tasks.
-
-    Tasks that are independent (i.e. do not precede each other) may be run in parallel as well.
-
-    The number of concurrent jobs can be set in :ref:`pipeline_run<pipeline_functions.pipeline_run>`:
-
-        ::
-
-            pipeline_run([parallel_task], multiprocess = 5)
-
-
-    If ``multiprocess`` is set to 1, then jobs will be run on a single process.
-
-
-
-.. index::
-    pair: data sharing across processes; Tutorial
-
-=====================
-Data sharing
-=====================
-
-    Running jobs in separate processes allows *Ruffus* to make full use of the multiple
-    processors in modern computers. However, some `multiprocessing guidelines <http://docs.python.org/library/multiprocessing.html#multiprocessing-programming>`_
-    should be borne in mind when writing *Ruffus* pipelines. In particular:
-
-    * Try not to pass large amounts of data between jobs, or at least be aware that this has to be marshalled
-      across process boundaries.
-
-    * Only data which can be `pickled <http://docs.python.org/library/pickle.html>`_ can be passed as
-      parameters to *Ruffus* task functions. Happily, that applies to almost any native Python data type.
-      The use of the rare, unpicklable object will cause python to complain (fail) loudly when *Ruffus* pipelines
-      are run.
-
-
-
-.. index::
-    pair: @jobs_limit; Tutorial
-
-.. _new_manual.jobs_limit:
-
-
-********************************************************************************************
-Restricting parallelism with :ref:`@jobs_limit <decorators.jobs_limit>`
-********************************************************************************************
-
-    Calling :ref:`pipeline_run(multiprocess = NNN)<pipeline_functions.pipeline_run>` allows
-    multiple jobs (from multiple independent tasks) to be run in parallel. However, there
-    are some operations that consume so many resources that we might want them to run
-    with less or no concurrency.
-
-    For example, we might want to download some files via FTP but the server restricts
-    requests from each IP address. Even if the rest of the pipeline is running 100 jobs in
-    parallel, the FTP downloading must be restricted to 2 files at a time. We would really
-    like to keep the pipeline running as is, but let this one operation run either serially,
-    or with little concurrency.
-
-
-    * :ref:`pipeline_run(multiprocess = NNN)<pipeline_functions.pipeline_run>` sets the pipeline-wide concurrency but
-    * :ref:`@jobs_limit(MMM)<decorators.jobs_limit>` sets concurrency at ``MMM`` only for jobs in the decorated task.
-
-    The optional name (e.g. ``@jobs_limit(3, "ftp_download_limit")``) allows the same limit to
-    be shared across multiple tasks. To be pedantic: a limit of ``3`` jobs at a time would be applied
-    across all tasks which have a ``@jobs_limit`` named ``"ftp_download_limit"``.
-
-    The :ref:`example code<new_manual.multiprocessing.code>` uses up to 10 processes across the
-    pipeline, but runs the ``stage1_big`` and ``stage1_small`` tasks 3 at a time (shared across
-    both tasks). ``stage2`` jobs run 5 at a time.
-
-
-
-.. _new_manual.ruffus.drmaa_wrapper.run_job:
-
-********************************************************************************************
-Using ``drmaa`` to dispatch work to Computational Clusters or Grid engines from Ruffus jobs
-********************************************************************************************
-
-    Ruffus has been widely used to manage work on computational clusters or grid engines. Though Ruffus
-    task functions cannot (yet!) run natively and transparently on remote cluster nodes, it is trivial
-    to dispatch work across the cluster.
-
-    From version 2.4 onwards, Ruffus includes an optional helper module which interacts with
-    `python bindings  <https://github.com/drmaa-python/drmaa-python>`__ for the widely used `drmaa  <http://en.wikipedia.org/wiki/DRMAA>`__
-    Open Grid Forum API specification. This allows jobs to dispatch work to a computational cluster and wait until it completes.
-
-
-    Here are the necessary steps
-
-==============================================================================
-1) Use a shared drmaa session:
-==============================================================================
-
-    Before your pipeline runs:
-
-    .. code-block:: python
-
-        #
-        #   start shared drmaa session for all jobs / tasks in pipeline
-        #
-        import drmaa
-        drmaa_session = drmaa.Session()
-        drmaa_session.initialize()
-
-
-    Cleanup after your pipeline completes:
-
-    .. code-block:: python
-
-        #
-        #   pipeline functions go here
-        #
-        if __name__ == '__main__':
-            drmaa_session.exit()
-
-
-==============================================================================
-2) import ``ruffus.drmaa_wrapper``
-==============================================================================
-
-    * The optional ``ruffus.drmaa_wrapper`` module needs to be imported explicitly:
-
-    .. code-block:: python
-        :emphasize-lines: 1
-
-        # imported ruffus.drmaa_wrapper explicitly
-        from ruffus.drmaa_wrapper import run_job, error_drmaa_job
-
-
-==============================================================================
-3) call :ref:`drmaa_wrapper.run_job()<drmaa_wrapper.run_job>`
-==============================================================================
-
-    :ref:`drmaa_wrapper.run_job() <drmaa_wrapper.run_job>` dispatches the work to a cluster node within a normal Ruffus job and waits for completion
-
-    This is the equivalent of `os.system  <http://docs.python.org/2/library/os.html#os.system>`__  or
-    `subprocess.check_output  <http://docs.python.org/2/library/subprocess.html#subprocess.check_call>`__ but the code will run remotely as specified:
-
-        .. code-block:: python
-            :emphasize-lines: 1
-
-                # ruffus.drmaa_wrapper.run_job
-                stdout_res, stderr_res  = run_job(cmd_str           = "touch " + output_file,
-                                                  job_name          = job_name,
-                                                  logger            = logger,
-                                                  drmaa_session     = drmaa_session,
-                                                  run_locally       = options.local_run,
-                                                  job_other_options = job_other_options)
-
-        The complete code is available :ref:`here <using_ruffus.drmaa_wrapper>`
-
-    * :ref:`drmaa_wrapper.run_job() <drmaa_wrapper.run_job>` is a convenience wrapper around the `python drmaa bindings <https://github.com/drmaa-python/drmaa-python>`__
-      `RunJob <http://drmaa-python.readthedocs.org/en/latest/tutorials.html#waiting-for-a-job>`__ function.
-      It takes care of writing drmaa *job templates* for you.
-    * Each call creates a separate drmaa *job template*.
-
-==================================================================================================
-4) Use multithread: :ref:`pipeline_run(multithread = NNN) <pipeline_functions.pipeline_run>`
-==================================================================================================
-
-    .. warning ::
-
-        :ref:`drmaa_wrapper.run_job()<drmaa_wrapper.run_job>`
-
-            **requires** ``pipeline_run`` :ref:`(multithread = NNN)<pipeline_functions.pipeline_run>`
-
-            **and will not work with**  ``pipeline_run`` :ref:`(multiprocess = NNN)<pipeline_functions.pipeline_run>`
-
-
-    Using multithreading rather than multiprocessing
-        * allows the drmaa session to be shared
-        * prevents "processing storms" which lock up the queue submission node when hundreds or thousands of grid engine / cluster commands complete at the same time.
-
-        .. code-block:: python
-
-            pipeline_run (..., multithread = NNN, ...)
-
-        or if you are using ruffus.cmdline:
-
-        .. code-block:: python
-
-            cmdline.run (options, multithread = options.jobs)
-
-
-    Normally multithreading reduces the amount of parallelism in python due to the python `Global interpreter Lock (GIL)  <http://en.wikipedia.org/wiki/Global_Interpreter_Lock>`__.
-    However, as the work load is almost entirely on another computer (i.e. a cluster / grid engine node) with a separate python interpreter, any cost benefit calculations of this sort are moot.
-
-==================================================================================================
-5) Develop locally
-==================================================================================================
-
-    :ref:`drmaa_wrapper.run_job() <drmaa_wrapper.run_job>` provides two convenience parameters for developing grid engine pipelines:
-
-    * commands can run locally, i.e. on the local machine rather than on cluster nodes:
-
-          .. code-block:: python
-
-              run_job(cmd_str, run_locally = True)
-
-    * Output files can be `touch  <http://en.wikipedia.org/wiki/Touch_(Unix)>`__\ed, i.e. given the appearance of the work having being done without actually running the commands
-
-          .. code-block:: python
-
-              run_job(cmd_str, touch_only = True)
-
-
-.. index::
-    pair: pipeline_run touch mode; Tutorial
-    pair: touch mode pipeline_run; Tutorial
-
-.. _new_manual.pipeline_run_touch:
-
-
-********************************************************************************************
-Forcing a pipeline to appear up to date
-********************************************************************************************
-
-    Sometimes, we *know* that a pipeline has run to completion, that everything is up-to-date. However, Ruffus still insists on the basis
-    of file modification times that you need to rerun.
-
-    For example, sometimes a trivial accounting modification needs to be made to a data file.
-    Even though you know that this changes nothing in practice, Ruffus will detect the modification and
-    ask to rerun everything from that point forwards.
-
-    One way to convince Ruffus that everything is fine is to manually `touch  <http://en.wikipedia.org/wiki/Touch_(Unix)>`__
-    all subsequent data files one by one in sequence so that the file timestamps follow the appropriate progression.
-
-    You can also ask *Ruffus* to do this automatically for you by running the pipeline in `touch  <http://en.wikipedia.org/wiki/Touch_(Unix)>`__
-    mode:
-
-        .. code-block:: python
-
-            pipeline_run( touch_files_only = True)
-
-
-    :ref:`pipeline_run <pipeline_functions.pipeline_run>` will run your pipeline script normally working backwards from any specified final target, or else the
-    last task in the pipeline. It works out where it should begin running, i.e. with the first out-of-date data files.
-    After that point, instead of calling your pipeline task functions, each missing or out-of-date file is
-    `touch-ed  <http://en.wikipedia.org/wiki/Touch_(Unix)>`__ in turn so that the file modification dates
-    follow on successively.
-
-
-    This turns out to be useful way to check that your pipeline runs correctly by creating a series of dummy (empty files).
-    However, *Ruffus* does not know how to read your mind to know which files to create from :ref:`@split <decorators.split>` or
-    :ref:`@subdivide <decorators.subdivide>` tasks.
-
-
-    Using :ref:`ruffus.cmdline <new_manual.cmdline>` from version 2.4, you can just specify:
-
-        .. code-block:: bash
-
-            your script --touch_files_only [--other_options_of_your_own_etc]
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/multiprocessing_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/multiprocessing_code.txt
deleted file mode 100644
index 6766bd5..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/multiprocessing_code.txt
+++ /dev/null
@@ -1,183 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.multiprocessing.code:
-
-################################################################################################################################################################
-|new_manual.multiprocessing.chapter_num|: Python Code for Multiprocessing, ``drmaa`` and Computation Clusters
-################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@jobs_limit <decorators.jobs_limit>` syntax
-    * :ref:`pipeline_run() <pipeline_functions.pipeline_run>` syntax
-    * :ref:`drmaa_wrapper.run_job() <drmaa_wrapper.run_job>` syntax
-    * Back to |new_manual.multiprocessing.chapter_num|: :ref:`Multiprocessing, drmaa and Computation Clusters <new_manual.multiprocessing>`
-
-************************************************************************************
-:ref:`@jobs_limit <decorators.jobs_limit>`
-************************************************************************************
-
-    * First 2 tasks are constrained to a parallelism of 3 shared jobs at a time
-    * Final task is constrained to a parallelism of 5 jobs at a time
-    * The entire pipeline is constrained to a (theoretical) parallelism of 10 jobs at a time
-
-    .. code-block:: python
-        :emphasize-lines: 12,17,22
-
-        from ruffus import *
-        import time
-
-        # make list of 10 files
-        @split(None, "*stage1")
-        def make_files(input_files, output_files):
-            for i in range(10):
-                if i < 5:
-                    open("%d.small_stage1" % i, "w")
-                else:
-                    open("%d.big_stage1" % i, "w")
-
-        @jobs_limit(3, "ftp_download_limit")
-        @transform(make_files, suffix(".small_stage1"), ".stage2")
-        def stage1_small(input_file, output_file):
-            print "FTP downloading %s ->Start" % input_file
-            time.sleep(2)
-            open(output_file, "w")
-            print "FTP downloading %s ->Finished" % input_file
-
-        @jobs_limit(3, "ftp_download_limit")
-        @transform(make_files, suffix(".big_stage1"), ".stage2")
-        def stage1_big(input_file, output_file):
-            print "FTP downloading %s ->Start" % input_file
-            time.sleep(2)
-            open(output_file, "w")
-            print "FTP downloading %s ->Finished" % input_file
-
-        @jobs_limit(5)
-        @transform([stage1_small, stage1_big], suffix(".stage2"), ".stage3")
-        def stage2(input_file, output_file):
-            print "Processing stage2 %s ->Start" % input_file
-            time.sleep(2)
-            open(output_file, "w")
-            print "Processing stage2 %s ->Finished" % input_file
-
-        pipeline_run(multiprocess = 10, verbose = 0)
-
-
-    Giving:
-
-    .. code-block:: pycon
-        :emphasize-lines: 3,25
-
-        >>> pipeline_run(multiprocess = 10, verbose = 0)
-
-        >>> # 3 jobs at a time, interleaved
-        FTP downloading 5.big_stage1 ->Start
-        FTP downloading 6.big_stage1 ->Start
-        FTP downloading 7.big_stage1 ->Start
-        FTP downloading 5.big_stage1 ->Finished
-        FTP downloading 8.big_stage1 ->Start
-        FTP downloading 6.big_stage1 ->Finished
-        FTP downloading 9.big_stage1 ->Start
-        FTP downloading 7.big_stage1 ->Finished
-        FTP downloading 0.small_stage1 ->Start
-        FTP downloading 8.big_stage1 ->Finished
-        FTP downloading 1.small_stage1 ->Start
-        FTP downloading 9.big_stage1 ->Finished
-        FTP downloading 2.small_stage1 ->Start
-        FTP downloading 0.small_stage1 ->Finished
-        FTP downloading 3.small_stage1 ->Start
-        FTP downloading 1.small_stage1 ->Finished
-        FTP downloading 4.small_stage1 ->Start
-        FTP downloading 2.small_stage1 ->Finished
-        FTP downloading 3.small_stage1 ->Finished
-        FTP downloading 4.small_stage1 ->Finished
-
-        >>> # 5 jobs at a time, interleaved
-        Processing stage2 0.stage2 ->Start
-        Processing stage2 1.stage2 ->Start
-        Processing stage2 2.stage2 ->Start
-        Processing stage2 3.stage2 ->Start
-        Processing stage2 4.stage2 ->Start
-        Processing stage2 0.stage2 ->Finished
-        Processing stage2 5.stage2 ->Start
-        Processing stage2 1.stage2 ->Finished
-        Processing stage2 6.stage2 ->Start
-        Processing stage2 2.stage2 ->Finished
-        Processing stage2 4.stage2 ->Finished
-        Processing stage2 7.stage2 ->Start
-        Processing stage2 8.stage2 ->Start
-        Processing stage2 3.stage2 ->Finished
-        Processing stage2 9.stage2 ->Start
-        Processing stage2 5.stage2 ->Finished
-        Processing stage2 7.stage2 ->Finished
-        Processing stage2 6.stage2 ->Finished
-        Processing stage2 8.stage2 ->Finished
-        Processing stage2 9.stage2 ->Finished
-
-.. _using_ruffus.drmaa_wrapper:
-
-************************************************************************************
-Using  ``ruffus.drmaa_wrapper``
-************************************************************************************
-
-    .. code-block:: python
-        :emphasize-lines: 17,31,53
-
-        #!/usr/bin/python
-        job_queue_name    = "YOUR_QUEUE_NAME_GOES_HERE"
-        job_other_options = "-P YOUR_PROJECT_NAME_GOES_HERE"
-
-        from ruffus import *
-        from ruffus.drmaa_wrapper import run_job, error_drmaa_job
-
-        parser = cmdline.get_argparse(description='WHAT DOES THIS PIPELINE DO?')
-
-        options = parser.parse_args()
-
-        #  logger which can be passed to multiprocessing ruffus tasks
-        logger, logger_mutex = cmdline.setup_logging (__name__, options.log_file, options.verbose)
-
-
-        #
-        #   start shared drmaa session for all jobs / tasks in pipeline
-        #
-        import drmaa
-        drmaa_session = drmaa.Session()
-        drmaa_session.initialize()
-
-        @originate(["1.chromosome", "X.chromosome"],
-                   logger, logger_mutex)
-        def create_test_files(output_file):
-            try:
-                stdout_res, stderr_res = "",""
-                job_queue_name, job_other_options = get_queue_options()
-
-                #
-                #   ruffus.drmaa_wrapper.run_job
-                #
-                stdout_res, stderr_res  = run_job(cmd_str           = "touch " + output_file,
-                                                  job_name          = job_name,
-                                                  logger            = logger,
-                                                  drmaa_session     = drmaa_session,
-                                                  run_locally       = options.local_run,
-                                                  job_queue_name    = job_queue_name,
-                                                  job_other_options = job_other_options)
-
-            # relay all the stdout, stderr, drmaa output to diagnose failures
-            except error_drmaa_job as err:
-                raise Exception("\n".join(map(str,
-                                    "Failed to run:"
-                                    cmd,
-                                    err,
-                                    stdout_res,
-                                    stderr_res)))
-
-
-        if __name__ == '__main__':
-            cmdline.run (options, multithread = options.jobs)
-            # cleanup drmaa
-            drmaa_session.exit()
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/onthefly.txt b/doc/_build/html/_sources/tutorials/new_tutorial/onthefly.txt
deleted file mode 100644
index 221b050..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/onthefly.txt
+++ /dev/null
@@ -1,192 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: on_the_fly; Tutorial
-
-.. _new_manual.on_the_fly:
-
-####################################################################################################################################################
-|new_manual.on_the_fly.chapter_num|: Esoteric: Generating parameters on the fly with :ref:`@files<decorators.files_on_the_fly>`
-####################################################################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@files on-the-fly syntax in detail <decorators.files_on_the_fly>`
-
-.. note::
-
-    Remember to look at the example code:
-
-    * :ref:`new_manual.on_the_fly.code`
-
-
-***********************
-Overview
-***********************
-
-    The different *Ruffus* :ref:`decorators <decorators>` connect up different tasks and
-    generate *Output* (file names) from your *Input* in all sorts of different ways.
-
-    However, sometimes, none of them *quite* do exactly what you need. And it becomes
-    necessary to generate your own *Input* and *Output* parameters on the fly.
-
-    Although this additional flexibility comes at the cost of a lot of extra inconvenient
-    code, you can continue to leverage the rest of *Ruffus* functionality such as
-    checking whether files are up to date or not.
-
-.. index::
-    pair: @files; Tutorial on-the-fly parameter generation
-
-
-*********************************************************************
-:ref:`@files <decorators.files_on_the_fly>` syntax
-*********************************************************************
-    To generate parameters on the fly, use the :ref:`@files <decorators.files_on_the_fly>`
-    with a :term:`generator` function which yields one list / tuple of parameters per job.
-
-    For example:
-
-    .. code-block:: python
-        :emphasize-lines: 3,16
-
-        from ruffus import *
-
-        # generator function
-        def generate_parameters_on_the_fly():
-            """
-            returns one list of parameters per job
-            """
-            parameters = [
-                                ['A.input', 'A.output', (1, 2)], # 1st job
-                                ['B.input', 'B.output', (3, 4)], # 2nd job
-                                ['C.input', 'C.output', (5, 6)], # 3rd job
-                            ]
-            for job_parameters in parameters:
-                yield job_parameters
-
-        # tell ruffus that parameters should be generated on the fly
-        @files(generate_parameters_on_the_fly)
-        def pipeline_task(input, output, extra):
-            open(output, "w").write(open(input).read())
-            sys.stderr.write("%d + %d => %d\n" % (extra[0] , extra[1], extra[0] + extra[1]))
-
-        pipeline_run()
-
-
-    Produces:
-
-        .. code-block:: pycon
-
-        Task = parallel_task
-            1 + 2 = 3
-            Job = ["A", 1, 2] completed
-            3 + 4 = 7
-            Job = ["B", 3, 4] completed
-            5 + 6 = 11
-            Job = ["C", 5, 6] completed
-
-
-    .. note::
-
-        Be aware that the parameter generating function may be invoked
-        :ref:`more than once<new_manual.dependencies.checking_multiple_times>`:
-        * The first time to check if this part of the pipeline is up-to-date.
-        * The second time when the pipeline task function is run.
-
-    The resulting custom *inputs*, *outputs* parameters per job are
-    treated normally for the purposes of checking to see if jobs are up-to-date and
-    need to be re-run.
-
-
-**********************************************
- A Cartesian Product, all vs all example
-**********************************************
-
-    The :ref:`accompanying example<new_manual.on_the_fly.code>` provides a more realistic reason why
-    you would want to generate parameters on the fly. It is a fun piece of code, which generates
-    N x M combinations from two sets of files as the *inputs* of a pipeline stage.
-
-    The *inputs* / *outputs* filenames are generated as a pair of nested for-loops to produce
-    the N (outside loop) x M (inside loop) combinations, with the appropriate parameters
-    for each job ``yield``\ed per iteration of the inner loop. The gist of this is:
-
-        .. code-block:: python
-            :emphasize-lines: 3
-
-            #_________________________________________________________________________________________
-            #
-            #   Generator function
-            #
-            #        N x M jobs
-            #_________________________________________________________________________________________
-            def generate_simulation_params ():
-                """
-                Custom function to generate
-                file names for gene/gwas simulation study
-                """
-                for sim_file in get_simulation_files():
-                    for (gene, gwas) in get_gene_gwas_file_pairs():
-                        result_file = "%s.%s.results" % (gene, sim_file)
-                        yield (gene, gwas, sim_file), result_file
-
-
-
-            @files(generate_simulation_params)
-            def gwas_simulation(input_files, output_file):
-                "..."
-
-        If ``get_gene_gwas_file_pairs()`` produces:
-            ::
-
-                ['a.sim', 'b.sim', 'c.sim']
-
-        and ``get_gene_gwas_file_pairs()`` produces:
-            ::
-
-                [('1.gene', '1.gwas'), ('2.gene', '2.gwas')]
-
-        then we would end up with ``3`` x ``2`` = ``6`` jobs and the following equivalent function calls:
-
-            ::
-
-                gwas_simulation(('1.gene', '1.gwas', 'a.sim'), "1.gene.a.sim.results")
-                gwas_simulation(('2.gene', '2.gwas', 'a.sim'), "2.gene.a.sim.results")
-                gwas_simulation(('1.gene', '1.gwas', 'b.sim'), "1.gene.b.sim.results")
-                gwas_simulation(('2.gene', '2.gwas', 'b.sim'), "2.gene.b.sim.results")
-                gwas_simulation(('1.gene', '1.gwas', 'c.sim'), "1.gene.c.sim.results")
-                gwas_simulation(('2.gene', '2.gwas', 'c.sim'), "2.gene.c.sim.results")
-
-
-    The :ref:`accompanying code<new_manual.on_the_fly.code>` looks slightly more complicated because
-    of some extra bookkeeping.
-
-
-
-    You can compare this approach with the alternative of using :ref:`@product <decorators.product>`:
-
-        .. code-block:: python
-            :emphasize-lines: 3
-
-            #_________________________________________________________________________________________
-            #
-            #        N x M jobs
-            #_________________________________________________________________________________________
-            @product(   os.path.join(simulation_data_dir, "*.simulation"),
-                        formatter(),
-
-                        os.path.join(gene_data_dir, "*.gene"),
-                        formatter(),
-
-                        # add gwas as an input: looks like *.gene but with a differnt extension
-                        add_inputs("{path[1][0]/{basename[1][0]}.gwas")
-
-                        "{basename[0][0]}.{basename[1][0]}.results")    # output file
-            def gwas_simulation(input_files, output_file):
-                "..."
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/onthefly_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/onthefly_code.txt
deleted file mode 100644
index 2ddc060..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/onthefly_code.txt
+++ /dev/null
@@ -1,328 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.on_the_fly.code:
-
-############################################################################################################################################################################################################
-|new_manual.on_the_fly.chapter_num|: Esoteric: Python Code for Generating parameters on the fly with :ref:`@files<decorators.files_on_the_fly>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@files on-the-fly syntax in detail <decorators.files_on_the_fly>`
-    * Back to |new_manual.on_the_fly.chapter_num|: :ref:`Generating parameters on the fly <new_manual.on_the_fly>`
-
-************************************
-Introduction
-************************************
-
-    | This script takes N pairs of input file pairs (with the suffices .gene and .gwas)
-    | and runs them against M sets of simulation data (with the suffix .simulation)
-    | A summary per input file pair is then produced
-
-
-    In pseudo-code:
-
-        STEP_1:
-
-        ::
-
-            for n_file in NNN_pairs_of_input_files:
-                for m_file in MMM_simulation_data:
-
-                    [n_file.gene,
-                     n_file.gwas,
-                     m_file.simulation] -> n_file.m_file.simulation_res
-
-
-        STEP_2:
-
-        ::
-
-            for n_file in NNN_pairs_of_input_files:
-
-                n_file.*.simulation_res -> n_file.mean
-
-
-        | n = CNT_GENE_GWAS_FILES
-        | m = CNT_SIMULATION_FILES
-
-************************************
-Code
-************************************
-    ::
-
-        from ruffus import *
-        import os
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #   constants
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        working_dir             = "temp_NxM"
-        simulation_data_dir     = os.path.join(working_dir, "simulation")
-        gene_data_dir           = os.path.join(working_dir, "gene")
-        CNT_GENE_GWAS_FILES     = 2
-        CNT_SIMULATION_FILES    = 3
-
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #   imports
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-        import os, sys
-        from itertools import izip
-        import glob
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #   Functions
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #_________________________________________________________________________________________
-        #
-        #   get gene gwas file pairs
-        #
-        #_________________________________________________________________________________________
-        def get_gene_gwas_file_pairs(  ):
-            """
-            Helper function to get all *.gene, *.gwas from the direction specified
-                in --gene_data_dir
-
-            Returns
-                file pairs with both .gene and .gwas extensions,
-                corresponding roots (no extension) of each file
-            """
-            gene_files = glob.glob(os.path.join(gene_data_dir, "*.gene"))
-            gwas_files = glob.glob(os.path.join(gene_data_dir, "*.gwas"))
-            #
-            common_roots = set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gene_files))
-            common_roots &=set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gwas_files))
-            common_roots = list(common_roots)
-            #
-            p = os.path; g_dir = gene_data_dir
-            file_pairs = [[p.join(g_dir, x + ".gene"), p.join(g_dir, x + ".gwas")] for x in common_roots]
-            return file_pairs, common_roots
-
-        #_________________________________________________________________________________________
-        #
-        #   get simulation files
-        #
-        #_________________________________________________________________________________________
-        def get_simulation_files(  ):
-            """
-            Helper function to get all *.simulation from the direction specified
-                in --simulation_data_dir
-                Returns
-                    file with .simulation extensions,
-                    corresponding roots (no extension) of each file
-            """
-            simulation_files = glob.glob(os.path.join(simulation_data_dir, "*.simulation"))
-            simulation_roots =map(lambda x: os.path.splitext(os.path.split(x)[1])[0], simulation_files)
-            return simulation_files, simulation_roots
-
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-        #   Main logic
-
-
-        #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-
-
-
-
-
-        #_________________________________________________________________________________________
-        #
-        #   setup_simulation_data
-        #
-        #_________________________________________________________________________________________
-
-        #
-        # mkdir: makes sure output directories exist before task
-        #
-        @follows(mkdir(gene_data_dir, simulation_data_dir))
-        def setup_simulation_data ():
-            """
-            create simulation files
-            """
-            for i in range(CNT_GENE_GWAS_FILES):
-                open(os.path.join(gene_data_dir, "%03d.gene" % i), "w")
-                open(os.path.join(gene_data_dir, "%03d.gwas" % i), "w")
-            #
-            # gene files without corresponding gwas and vice versa
-            open(os.path.join(gene_data_dir, "orphan1.gene"), "w")
-            open(os.path.join(gene_data_dir, "orphan2.gwas"), "w")
-            open(os.path.join(gene_data_dir, "orphan3.gwas"), "w")
-            #
-            for i in range(CNT_SIMULATION_FILES):
-                open(os.path.join(simulation_data_dir, "%03d.simulation" % i), "w")
-
-
-
-
-        #_________________________________________________________________________________________
-        #
-        #   cleanup_simulation_data
-        #
-        #_________________________________________________________________________________________
-        def try_rmdir (d):
-            if os.path.exists(d):
-                try:
-                    os.rmdir(d)
-                except OSError:
-                    sys.stderr.write("Warning:\t%s is not empty and will not be removed.\n" % d)
-
-
-
-        def cleanup_simulation_data ():
-            """
-            cleanup files
-            """
-            sys.stderr.write("Cleanup working directory and simulation files.\n")
-            #
-            #   cleanup gene and gwas files
-            #
-            for f in glob.glob(os.path.join(gene_data_dir, "*.gene")):
-                os.unlink(f)
-            for f in glob.glob(os.path.join(gene_data_dir, "*.gwas")):
-                os.unlink(f)
-            try_rmdir(gene_data_dir)
-            #
-            #   cleanup simulation
-            #
-            for f in glob.glob(os.path.join(simulation_data_dir, "*.simulation")):
-                os.unlink(f)
-            try_rmdir(simulation_data_dir)
-            #
-            #   cleanup working_dir
-            #
-            for f in glob.glob(os.path.join(working_dir, "simulation_results", "*.simulation_res")):
-                os.unlink(f)
-            try_rmdir(os.path.join(working_dir, "simulation_results"))
-            #
-            for f in glob.glob(os.path.join(working_dir, "*.mean")):
-                os.unlink(f)
-            try_rmdir(working_dir)
-
-
-        #_________________________________________________________________________________________
-        #
-        #   Step 1:
-        #
-        #        for n_file in NNN_pairs_of_input_files:
-        #            for m_file in MMM_simulation_data:
-        #
-        #                [n_file.gene,
-        #                 n_file.gwas,
-        #                 m_file.simulation] -> working_dir/n_file.m_file.simulation_res
-        #
-        #_________________________________________________________________________________________
-        def generate_simulation_params ():
-            """
-            Custom function to generate
-            file names for gene/gwas simulation study
-            """
-            simulation_files, simulation_file_roots    = get_simulation_files()
-            gene_gwas_file_pairs, gene_gwas_file_roots =  get_gene_gwas_file_pairs()
-            #
-            for sim_file, sim_file_root in izip(simulation_files, simulation_file_roots):
-                for (gene, gwas), gene_file_root in izip(gene_gwas_file_pairs, gene_gwas_file_roots):
-                    #
-                    result_file = "%s.%s.simulation_res" % (gene_file_root, sim_file_root)
-                    result_file_path = os.path.join(working_dir, "simulation_results", result_file)
-                    #
-                    yield [gene, gwas, sim_file], result_file_path, gene_file_root, sim_file_root, result_file
-
-
-
-        #
-        # mkdir: makes sure output directories exist before task
-        #
-        @follows(mkdir(working_dir, os.path.join(working_dir, "simulation_results")))
-        @files(generate_simulation_params)
-        def gwas_simulation(input_files, result_file_path, gene_file_root, sim_file_root, result_file):
-            """
-            Dummy calculation of gene gwas vs simulation data
-            Normally runs in parallel on a computational cluster
-            """
-            (gene_file,
-            gwas_file,
-            simulation_data_file) = input_files
-            #
-            simulation_res_file = open(result_file_path, "w")
-            simulation_res_file.write("%s + %s -> %s\n" % (gene_file_root, sim_file_root, result_file))
-
-
-        #_________________________________________________________________________________________
-        #
-        #   Step 2:
-        #
-        #       Statistical summary per gene/gwas file pair
-        #
-        #        for n_file in NNN_pairs_of_input_files:
-        #            working_dir/simulation_results/n.*.simulation_res
-        #               -> working_dir/n.mean
-        #
-        #_________________________________________________________________________________________
-
-
-        @collate(gwas_simulation, regex(r"simulation_results/(\d+).\d+.simulation_res"), r"\1.mean")
-        @posttask(lambda : sys.stdout.write("\nOK\n"))
-        def statistical_summary (result_files, summary_file):
-            """
-            Simulate statistical summary
-            """
-            summary_file = open(summary_file, "w")
-            for f in result_files:
-                summary_file.write(open(f).read())
-
-
-
-        pipeline_run([setup_simulation_data], multiprocess = 5, verbose = 2)
-        pipeline_run([statistical_summary], multiprocess = 5, verbose = 2)
-
-        # uncomment to printout flowchar
-        #
-        # pipeline_printout(sys.stdout, [statistical_summary], verbose=2)
-        # graph_printout ("flowchart.jpg", "jpg", [statistical_summary])
-        #
-
-        cleanup_simulation_data ()
-
-
-
-
-************************************
-Resulting Output
-************************************
-    ::
-
-        >>> pipeline_run([setup_simulation_data], multiprocess = 5, verbose = 2)
-            Make directories [temp_NxM/gene, temp_NxM/simulation] completed
-        Completed Task = setup_simulation_data_mkdir_1
-            Job completed
-        Completed Task = setup_simulation_data
-
-
-        >>> pipeline_run([statistical_summary], multiprocess = 5, verbose = 2)
-            Make directories [temp_NxM, temp_NxM/simulation_results] completed
-        Completed Task = gwas_simulation_mkdir_1
-            Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/000.simulation] -> temp_NxM/simulation_results/001.000.simulation_res, 001, 000, 001.000.simulation_res] completed
-            Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/000.simulation] -> temp_NxM/simulation_results/000.000.simulation_res, 000, 000, 000.000.simulation_res] completed
-            Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/001.simulation] -> temp_NxM/simulation_results/001.001.simulation_res, 001, 001, 001.001.simulation_res] completed
-            Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/001.simulation] -> temp_NxM/simulation_results/000.001.simulation_res, 000, 001, 000.001.simulation_res] completed
-            Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/002.simulation] -> temp_NxM/simulation_results/000.002.simulation_res, 000, 002, 000.002.simulation_res] completed
-            Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/002.simulation] -> temp_NxM/simulation_results/001.002.simulation_res, 001, 002, 001.002.simulation_res] completed
-        Completed Task = gwas_simulation
-            Job = [[temp_NxM/simulation_results/000.000.simulation_res, temp_NxM/simulation_results/000.001.simulation_res, temp_NxM/simulation_results/000.002.simulation_res] -> temp_NxM/000.mean] completed
-            Job = [[temp_NxM/simulation_results/001.000.simulation_res, temp_NxM/simulation_results/001.001.simulation_res, temp_NxM/simulation_results/001.002.simulation_res] -> temp_NxM/001.mean] completed
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/originate.txt b/doc/_build/html/_sources/tutorials/new_tutorial/originate.txt
deleted file mode 100644
index 0c7f0fe..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/originate.txt
+++ /dev/null
@@ -1,92 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-
-.. index::
-    pair: originate; Tutorial
-
-.. _new_manual.originate:
-
-######################################################################################################
-|new_manual.originate.chapter_num|: Creating files with ``@originate``
-######################################################################################################
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@originate syntax in detail <decorators.originate>`
-
-.. note::
-
-    Remember to look at the example code:
-
-    * :ref:`new_manual.originate.code`
-
-********************************************************************************************
-Simplifying our example with :ref:`@originate <decorators.originate>`
-********************************************************************************************
-
-    Our previous pipeline example started off with a set of files which we had to create first.
-
-    This is a common task: pipelines have to start *somewhere*.
-
-    Ideally, though, we would only want to create these starting files if they didn't already exist. In other words, we want a sort of ``@transform`` which makes files from nothing (``None``?).
-
-    This is exactly what :ref:`@originate <decorators.originate>` helps you to do.
-
-    Rewriting our pipeline with :ref:`@originate <decorators.originate>` gives the following three steps:
-
-
-    .. code-block:: python
-        :emphasize-lines: 6
-
-        from ruffus import *
-
-        #---------------------------------------------------------------
-        #   create initial files
-        #
-        @originate([   ['job1.a.start', 'job1.b.start'],
-                       ['job2.a.start', 'job2.b.start'],
-                       ['job3.a.start', 'job3.b.start']    ])
-        def create_initial_file_pairs(output_files):
-            # create both files as necessary
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-        #---------------------------------------------------------------
-        #   first task
-        @transform(create_initial_file_pairs, suffix(".start"), ".output.1")
-        def first_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-
-        #---------------------------------------------------------------
-        #   second task
-        @transform(first_task, suffix(".output.1"), ".output.2")
-        def second_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-        #
-        #       Run
-        #
-        pipeline_run([second_task])
-
-
-
-    ::
-
-            Job  = [None -> [job1.a.start, job1.b.start]] completed
-            Job  = [None -> [job2.a.start, job2.b.start]] completed
-            Job  = [None -> [job3.a.start, job3.b.start]] completed
-        Completed Task = create_initial_file_pairs
-            Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1] completed
-            Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1] completed
-            Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1] completed
-        Completed Task = first_task
-            Job  = [job1.a.output.1 -> job1.a.output.2] completed
-            Job  = [job2.a.output.1 -> job2.a.output.2] completed
-            Job  = [job3.a.output.1 -> job3.a.output.2] completed
-        Completed Task = second_task
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/originate_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/originate_code.txt
deleted file mode 100644
index 215e47a..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/originate_code.txt
+++ /dev/null
@@ -1,71 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.originate.code:
-
-######################################################################################################
-|new_manual.originate.chapter_num|: Python Code for Creating files with ``@originate``
-######################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@transform syntax in detail <decorators.transform>`
-    * Back to |new_manual.originate.chapter_num|: :ref:`@originate <new_manual.originate>`
-
-**********************************************
-Using ``@originate``
-**********************************************
-    ::
-
-        from ruffus import *
-
-        #---------------------------------------------------------------
-        #   create initial files
-        #
-        @originate([   ['job1.a.start', 'job1.b.start'],
-                       ['job2.a.start', 'job2.b.start'],
-                       ['job3.a.start', 'job3.b.start']    ])
-        def create_initial_file_pairs(output_files):
-            # create both files as necessary
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-        #---------------------------------------------------------------
-        #   first task
-        @transform(create_initial_file_pairs, suffix(".start"), ".output.1")
-        def first_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-
-        #---------------------------------------------------------------
-        #   second task
-        @transform(first_task, suffix(".output.1"), ".output.2")
-        def second_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-        #
-        #       Run
-        #
-        pipeline_run([second_task])
-
-
-************************************
-Resulting Output
-************************************
-
-    ::
-
-            Job  = [None -> [job1.a.start, job1.b.start]] completed
-            Job  = [None -> [job2.a.start, job2.b.start]] completed
-            Job  = [None -> [job3.a.start, job3.b.start]] completed
-        Completed Task = create_initial_file_pairs
-            Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1] completed
-            Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1] completed
-            Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1] completed
-        Completed Task = first_task
-            Job  = [job1.a.output.1 -> job1.a.output.2] completed
-            Job  = [job2.a.output.1 -> job2.a.output.2] completed
-            Job  = [job3.a.output.1 -> job3.a.output.2] completed
-        Completed Task = second_task
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/output_file_names.txt b/doc/_build/html/_sources/tutorials/new_tutorial/output_file_names.txt
deleted file mode 100644
index 5523794..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/output_file_names.txt
+++ /dev/null
@@ -1,560 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: formatter; Tutorial
-    pair: suffix; Tutorial
-    pair: regex; Tutorial
-    pair: output file names; Tutorial
-
-.. _new_manual.output_file_names:
-
-############################################################################################################################################################################################################
-|new_manual.output_file_names.chapter_num|: Specifying output file names with :ref:`formatter() <decorators.formatter>` and :ref:`regex() <decorators.regex>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`suffix() <decorators.suffix>` syntax
-    * :ref:`formatter() <decorators.formatter>` syntax
-    * :ref:`regex() <decorators.regex>` syntax
-
-
-.. note::
-
-    Remember to look at the example code:
-
-    * :ref:`new_manual.output_file_names.code`
-
-
-
-***************************************
-Review
-***************************************
-    .. image:: ../../images/theoretical_pipeline_schematic.png
-       :scale: 50
-
-    Computational pipelines transform your data in stages until the final result is produced.
-    The most straightforward way to use Ruffus is to hold the intermediate results after each stage
-    in a series of files with related file names.
-
-    Part of telling Ruffus how these pipeline stages or :term:`task` functions are connected
-    together is to write simple rules for how to the file names for each stage follow on from each other.
-    Ruffus helps you to specify these file naming rules.
-
-    .. note::
-
-        **The best way to design a pipeline is to:**
-
-            * **Write down the file names of the data as it flows across your pipeline.**
-              Do these file names follow a *pattern* ?
-            * **Write down the names of functions which transforms the data at each stage of the pipeline.**
-
-
-.. _new_manual.suffix:
-
-**********************************************************************************************************************************************
-A different file name :ref:`suffix() <decorators.suffix>` for each pipeline stage
-**********************************************************************************************************************************************
-
-
-    The easiest and cleanest way to write Ruffus pipelines is to use a different suffix
-    for each stage of your pipeline.
-
-    We used this approach in :ref:`new_manual.introduction`  and in :ref:`code <new_manual.transform_in_parallel.code>` from :ref:`new_manual.transform_in_parallel`:
-
-
-    .. code-block:: bash
-        :emphasize-lines: 1
-
-            #Task Name:                  File suffices
-            _________________________      ______________________
-            create_initial_file_pairs            *.start
-            first_task                           *.output.1
-            second_task                          *.output.2
-
-
-    There is a long standing convention of using file suffices to denote file type: For example, a **"compile"** task might convert **source** files of type ``*.c`` to **object** files of type ``*.o``.
-
-    We can think of Ruffus tasks comprising :
-        * recipes in ``@transform(...)`` for transforming file names: changing  ``.c`` to a ``.o`` (e.g. ``AA.c -> AA.o`` ``BB.c -> BB.o``)
-        * recipes in a task function ``def foo_bar()`` for transforming your data: from **source** ``.c`` to **object** ``.o``
-
-
-    Let us review the Ruffus syntax for doing this:
-
-        .. code-block:: bash
-            :emphasize-lines: 1,2,3
-
-            @transform( create_initial_file_pairs,  # Input:   Name of previous task(s)
-                        suffix(".start"),           # Matching suffix
-                        ".output.1")                # Replacement string
-            def first_task(input_files, output_file):
-                with open(output_file, "w"): pass
-
-
-    #. **Input**:
-
-        The first parameter for ``@transform`` can be a mixture of one or more:
-            * previous tasks (e.g. ``create_initial_file_pairs``)
-            * file names (all python strings are treated as paths)
-            * glob specifications (e.g ``*.c``, ``/my/path/*.foo``)
-
-        Each element provides an input for the task. So if the previous task ``create_initial_file_pairs`` has five outputs, the next ``@transform`` task will accept
-        these as five separate inputs leading to five independent jobs.
-
-    #. :ref:`suffix() <decorators.suffix>`:
-
-        The second parameter ``suffix(".start")`` must match the end of the first string in each input.
-        For example, ``create_initial_file_pairs`` produces the list ``['job1.a.start', 'job1.b.start']``, then ``suffix(".start")``  must matches the first string, i.e. ``'job1.a.start'``.
-        If the input is nested structure, this would be iterated through recursively to find the first string.
-
-        .. note::
-
-            Inputs which do not match the suffix are discarded altogether.
-
-    #. **Replacement**:
-
-        The third parameter is the replacement for the suffix.
-        The pair of input strings in the step3 example produces the following output parameter
-
-            ::
-
-                input_parameters   = ['job1.a.start', 'job1.b.start']
-                matching_input     = 'job1.a.start'
-                output_parameter   = 'job1.a.output.1'
-
-
-        When the pipeline is run, this results in the following equivalent call to ``first_task(...)``:
-
-            .. code-block:: python
-
-                first_task(['job1.a.start', 'job1.b.start'], 'job1.a.output.1'):
-
-        The replacement parameter can itself be a list or any arbitrary complicated structure:
-
-            .. code-block:: bash
-                :emphasize-lines: 1,2,3
-
-                @transform(create_initial_file_pairs,            # Input
-                            suffix(".a.start"),                  # Matching suffix
-                            [".output.a.1", ".output.b.1", 45])  # Replacement list
-                def first_task(input_files, output_parameters):
-                    print "input_parameters = ", input_files
-                    print "output_parameters = ", output_parameters
-
-        In which case, all the strings are used as replacements, other values are left untouched, and we obtain the following:
-
-            .. code-block:: bash
-                :emphasize-lines: 1,5,9
-
-                # job #1
-                input  =  ['job1.a.start',    'job1.b.start']
-                output =  ['job1.output.a.1', 'job1.output.b.1', 45]
-
-                # job #2
-                input  =  ['job2.a.start',    'job2.b.start']
-                output =  ['job2.output.a.1', 'job2.output.b.1', 45]
-
-                # job #3
-                input  =  ['job3.a.start',    'job3.b.start']
-                output =  ['job3.output.a.1', 'job3.output.b.1', 45]
-
-
-        Note how task function is called with the value ``45`` *verbatim* because it is not a string.
-
-
-
-.. _new_manual.formatter:
-
-************************************************************************************************************************************************************
- :ref:`formatter() <decorators.formatter>` manipulates pathnames and regular expression
-************************************************************************************************************************************************************
-
-    :ref:`suffix() <decorators.suffix>` replacement is the cleanest and easiest way to generate suitable output file names for each stage in a pipeline.
-    Often, however, we require more complicated manipulations to specify our file names.
-    For example,
-
-        * It is common to have to change directories from a *data* directory to a *working* directory as the first step of a pipeline.
-        * Data management can be simplified by separate files from each pipeline stage into their own directory.
-        * Information may have to be decoded from data file names, e.g. ``"experiment373.IBM.03March2002.txt"``
-
-
-    Though :ref:`formatter() <decorators.formatter>` is much more powerful, the principle and syntax are the same:
-    we take string elements from the **Input** and perform some replacements to generate the **Output** parameters.
-
-
-    :ref:`formatter() <decorators.formatter>`
-
-        * Allows easy manipulation of path subcomponents in the style of `os.path.split()  <http://docs.python.org/2/library/os.path.html#os.path.split>`__, and `os.path.basename  <http://docs.python.org/2/library/os.path.html#os.path.basename>`__
-        * Uses familiar python `string.format  <http://docs.python.org/2/library/string.html#string-formatting>`__ syntax (See `string.format examples  <http://docs.python.org/2/library/string.html#format-examples>`__. )
-        * Supports optional regular expression (`re   <http://docs.python.org/2/library/re.html#re.MatchObject.group>`__) matches including named captures.
-        * Can refer to any file path (i.e. python string) in each input and is not limited like :ref:`suffix() <decorators.suffix>` to the first string.
-        * Can even refer to individual letters within a match
-
-
-========================
-Path name components
-========================
-
-    :ref:`formatter() <decorators.formatter>` breaks down each input pathname into path name components which can then be recombined in whichever way by the replacement string.
-
-    Given an example string of :
-
-        .. code-block:: python
-
-            input_string = "/directory/to/a/file.name.ext"
-            formatter()
-
-        the path components are:
-
-        * ``basename``: The `base name <http://docs.python.org/2/library/os.path.html#os.path.basename>`__ *excluding* `extension  <http://docs.python.org/2/library/os.path.html#os.path.splitext>`__, ``"file.name"``
-        * ``ext``     : The `extension <http://docs.python.org/2/library/os.path.html#os.path.splitext>`__, ``".ext"``
-        * ``path``    : The `dirname <http://docs.python.org/2/library/os.path.html#os.path.dirname>`__, ``"/directory/to/a"``
-        * ``subdir``  : A list of sub-directories in the ``path`` in reverse order, ``["a", "to", "directory", "/"]``
-        * ``subpath`` : A list of descending sub-paths in reverse order, ``["/directory/to/a", "/directory/to", "/directory", "/"]``
-
-
-    The replacement string refers to these components by using python `string.format <http://docs.python.org/2/library/string.html#string-formatting>`__ style curly braces. ``"{NAME}"``
-
-    We refer to an element from the Nth input string by index, for example:
-
-       * ``"{ext[0]}"``     is the extension of the first file name string in **Input**.
-       * ``"{basename[1]}"`` is the basename of the second file name in **Input**.
-       * ``"{basename[1][0:3]}"`` are the first three letters from the basename of the second file name in **Input**.
-
-
-    ``subdir``, ``subpath`` were designed to help you navigate directory hierachies with the minimum of fuss.
-    For example, you might want to graft a hierachical path to another location:
-    ``"{subpath[0][2]}/from/{subdir[0][0]}/{basename[0]}"`` neatly replaces just one directory (``"to"``) in the path with another  (``"from"``):
-
-        .. code-block:: python
-
-            replacement_string = "{subpath[0][2]}/from/{subdir[0][0]}/{basename[0]}"
-
-            input_string    = "/directory/to/a/file.name.ext"
-            result_string   = "/directory/from/a/file.name.ext"
-
-
-.. _new_manual.formatter.regex:
-
-================================================
-Filter and parse using regular expressions
-================================================
-
-    `Regular expression   <http://docs.python.org/2/library/re.html#re.MatchObject.group>`__ matches can be used with the similar syntax.
-    Our example string can be parsed using the following regular expression:
-
-        .. code-block:: python
-
-            input_string = "/directory/to/a/file.name.ext"
-            formatter(r"/directory/(.+)/(?P<MYFILENAME>)\.ext")
-
-        We capture part of the path using ``(.+)``, and the base name using ``(?P<MYFILENAME>)``.
-        These `matching subgroups  <http://docs.python.org/2/library/re.html#re.MatchObject.group>`__ can be referred to by index
-        but for greater clarity the second named capture can also be referred to by name, i.e. ``{MYFILENAME}``.
-
-
-    The regular expression components for the first string can thus be referred to as follows:
-
-        * ``{0[0]}``          : The entire match captured by index, ``"/directory/to/a/file.name.ext"``
-        * ``{1[0]}``          : The first match captured by index, ``"to/a"``
-        * ``{2[0]}``          : The second match captured by index, ``"file.name"``
-        * ``{MYFILENAME[0]}`` : The match captured by name, ``"file.name"``
-
-
-    If each input consists of a list of paths such as ``['job1.a.start', 'job1.b.start', 'job1.c.start']``, we can match each of them separately
-    by using as many regular expressions as necessary. For example:
-
-        .. code-block:: python
-
-            input_string = ['job1.a.start', 'job1.b.start', 'job1.c.start']
-            # Regular expression matches for 1st, 2nd but not 3rd element
-            formatter(".+a.start", "b.start$")
-
-
-    Or if you only wanted regular expression matches for the second file name (string), pad with ``None``:
-
-        .. code-block:: python
-
-            input_string = ['job1.a.start', 'job1.b.start', 'job1.c.start']
-            # Regular expression matches for 2nd but not 1st or 3rd elements
-            formatter(None, "b.start$")
-
-================================================================================================
-Using :ref:`@transform() <decorators.transform>` with :ref:`formatter() <decorators.formatter>`
-================================================================================================
-
-    We can put these together in the following example:
-
-        .. code-block:: python
-            :emphasize-lines: 21,22
-
-            from ruffus import *
-
-            #   create initial files
-            @originate([   ['job1.a.start', 'job1.b.start'],
-                           ['job2.a.start', 'job2.b.start'],
-                           ['job3.a.start', 'job3.c.start']    ])
-            def create_initial_file_pairs(output_files):
-                # create both files as necessary
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-
-            #---------------------------------------------------------------
-            #
-            #   formatter
-            #
-
-            #   first task
-            @transform(create_initial_file_pairs,                               # Input
-
-                        formatter(".+/job(?P<JOBNUMBER>\d+).a.start",           # Extract job number
-                                  ".+/job[123].b.start"),                       # Match only "b" files
-
-                        ["{path[0]}/jobs{JOBNUMBER[0]}.output.a.1",             # Replacement list
-                         "{path[1]}/jobs{JOBNUMBER[0]}.output.b.1", 45])
-            def first_task(input_files, output_parameters):
-                print "input_parameters = ", input_files
-                print "output_parameters = ", output_parameters
-
-
-            #
-            #       Run
-            #
-            pipeline_run(verbose=0)
-
-
-        This produces:
-
-        .. code-block:: pycon
-
-            input_parameters  =  ['job1.a.start',
-                                  'job1.b.start']
-            output_parameters =  ['/home/lg/src/temp/jobs1.output.a.1',
-                                  '/home/lg/src/temp/jobs1.output.b.1', 45]
-
-            input_parameters  =  ['job2.a.start',
-                                  'job2.b.start']
-            output_parameters =  ['/home/lg/src/temp/jobs2.output.a.1',
-                                  '/home/lg/src/temp/jobs2.output.b.1', 45]
-
-
-
-        Notice that ``job3`` has ``'job3.c.start'`` as the second file.
-        This fails to match the regular expression and is discarded.
-
-        .. note::
-
-            Failed regular expression mismatches are ignored.
-
-            :ref:`formatter() <decorators.formatter>` regular expressions are thus very useful in filtering out all
-            files which do not match your specified criteria.
-
-            If your some of your task inputs have a mixture of different file types, a simple ``Formatter(".txt$")``, for example, will make
-            your code a lot simpler...
-
-
-
-================================================================================================
-string substitution for "extra" arguments
-================================================================================================
-
-    The first two arguments for Ruffus task functions are special because they are the **Input** and **Output**
-    parameters which link different stages of a pipeline.
-
-
-    Python strings in these arguments are names of data files whose modification times indicate whether the pipeline is up to date or not.
-
-    Other arguments to task functions are not passed down the pipeline but consumed.
-    Any python strings they contain do not need to be file names. These extra arguments are very useful
-    for passing data to pipelined tasks, such as shared values, loggers, programme options etc.
-
-    One helpful feature is that strings in these extra arguments are also subject to :ref:`formatter() <decorators.formatter>` string substitution.
-    This means you can leverage the parsing capabilities of Ruffus to decode any information about the pipeline data files,
-    These might include the directories you are running in and parts of the file name.
-
-    For example, if we would want to know which files go with which "job number" in the previous example:
-
-
-        .. code-block:: python
-            :emphasize-lines: 21,22
-
-            from ruffus import *
-
-            #   create initial files
-            @originate([   ['job1.a.start', 'job1.b.start'],
-                           ['job2.a.start', 'job2.b.start'],
-                           ['job3.a.start', 'job3.c.start']    ])
-            def create_initial_file_pairs(output_files):
-                for output_file in output_files:
-                    with open(output_file, "w") as oo: pass
-
-
-            #---------------------------------------------------------------
-            #
-            #   print job number as an extra argument
-            #
-
-            #   first task
-            @transform(create_initial_file_pairs,                               # Input
-
-                        formatter(".+/job(?P<JOBNUMBER>\d+).a.start",           # Extract job number
-                                  ".+/job[123].b.start"),                       # Match only "b" files
-
-                        ["{path[0]}/jobs{JOBNUMBER[0]}.output.a.1",             # Replacement list
-                         "{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"],
-
-                         "{JOBNUMBER[0]}"
-            def first_task(input_files, output_parameters, job_number):
-                print job_number, ":", input_files
-
-
-            pipeline_run(verbose=0)
-
-        ::
-
-            >>> pipeline_run(verbose=0)
-            1 : ['job1.a.start', 'job1.b.start']
-            2 : ['job2.a.start', 'job2.b.start']
-
-
-
-.. _new_manual.output_file_names.formatter.zoo:
-
-================================================================================================
-Changing directories using :ref:`formatter() <decorators.formatter>` in a zoo...
-================================================================================================
-
-    Here is a more fun example. We would like to feed the denizens of a zoo. Unfortunately, the file names for
-    these are spread over several directories. Ideally, we would like their food supply to be grouped more
-    sensibly. And, of course, we only want to feed the animals, not the plants.
-
-    I have colour coded the input and output files for this task to show how we would like to rearrange them:
-
-        .. image:: ../../images/simple_tutorial_zoo_animals_formatter_example.jpg
-           :scale: 50
-
-        .. code-block:: python
-            :emphasize-lines: 7,22,26,27,28
-
-            from ruffus import *
-
-            #   Make directories
-            @mkdir(["tiger", "lion", "dog", "crocodile", "rose"])
-
-            @originate(
-                        #   List of animals and plants
-                        [    "tiger/mammals.wild.animals",
-                            "lion/mammals.wild.animals",
-                            "lion/mammals.handreared.animals",
-                            "dog/mammals.tame.animals",
-                            "dog/mammals.wild.animals",
-                            "crocodile/reptiles.wild.animals",
-                            "rose/flowering.handreared.plants"])
-            def create_initial_files(output_file):
-                with open(output_file, "w") as oo: pass
-
-
-            #   Put different animals in different directories depending on their clade
-            @transform(create_initial_files,                                       # Input
-
-                       formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-
-                       "{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food", # Replacement
-
-                       "{subpath[0][1]}/{clade[0]}",                               # new_directory
-                       "{subdir[0][0]}",                                           # animal_name
-                       "{tame[0]}")                                                # tameness
-            def feed(input_file, output_file, new_directory, animal_name, tameness):
-                print "Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}".format(**locals())
-
-            pipeline_run(verbose=0)
-
-
-        .. comment **
-
-        We can see that the food for each animal are now grouped by clade in the same directory, which makes a lot more sense...
-
-        Note how we used ``subpath[0][1]`` to move down one level of the file path to build a new file name.
-
-        ::
-
-            >>> pipeline_run(verbose=0)
-            Food for the wild        crocodile = ./reptiles/wild.crocodile.food will be placed in ./reptiles
-            Food for the tame        dog       = ./mammals/tame.dog.food        will be placed in ./mammals
-            Food for the wild        dog       = ./mammals/wild.dog.food        will be placed in ./mammals
-            Food for the handreared  lion      = ./mammals/handreared.lion.food will be placed in ./mammals
-            Food for the wild        lion      = ./mammals/wild.lion.food       will be placed in ./mammals
-            Food for the wild        tiger     = ./mammals/wild.tiger.food      will be placed in ./mammals
-
-
-.. _new_manual.regex:
-
-******************************************************************************
- :ref:`regex() <decorators.regex>` manipulates via regular expressions
-******************************************************************************
-
-
-    If you are a hard core regular expressions fan, you may want to use :ref:`regex() <decorators.regex>` instead of :ref:`suffix() <decorators.suffix>` or :ref:`formatter() <decorators.formatter>`.
-
-    .. note::
-
-        :ref:`regex() <decorators.regex>` uses regular expressions like :ref:`formatter() <decorators.formatter>` but
-
-            * It only matches the first file name in the input. As described above, :ref:`formatter() <decorators.formatter>` can match any one or more of the input filename strings.
-            * It does not understand file paths so you may have to perform your own directory / file name parsing.
-            * String replacement uses syntax borrowed from `re.sub()  <http://docs.python.org/2/library/re.html#re.sub>`__, rather than building a result from parsed regular expression (and file path) components
-
-        In general :ref:`formatter() <decorators.formatter>` is more powerful and was introduced from version 2.4 is intended to be a more user friendly replacement for :ref:`regex() <decorators.regex>`.
-
-    Let us see how the previous zoo example looks with :ref:`regex() <decorators.regex>`:
-
-
-        :ref:`formatter() <decorators.formatter>` code:
-
-        .. code-block:: python
-            :emphasize-lines: 4,6
-
-            #   Put different animals in different directories depending on their clade
-            @transform(create_initial_files,                                       # Input
-
-                       formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-
-                       "{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food", # Replacement
-
-                       "{subpath[0][1]}/{clade[0]}",                               # new_directory
-                       "{subdir[0][0]}",                                           # animal_name
-                       "{tame[0]}")                                                # tameness
-            def feed(input_file, output_file, new_directory, animal_name, tameness):
-                print "Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}".format(**locals())
-
-        :ref:`regex() <decorators.regex>` code:
-
-        .. code-block:: python
-            :emphasize-lines: 4,6
-
-            #   Put different animals in different directories depending on their clade
-            @transform(create_initial_files,                                        # Input
-
-                       regex(r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"), # Only animals: ignore plants!
-
-                       r"\1/\g<clade>/\g<tame>.\2.food",                            # Replacement
-
-                       r"\1/\g<clade>",                                             # new_directory
-                       r"\2",                                                       # animal_name
-                       "\g<tame>")                                                  # tameness
-            def feed(input_file, output_file, new_directory, animal_name, tameness):
-                print "Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}".format(**locals())
-
-
-    The regular expression to parse the input file path safely was a bit hairy to write, and it is not
-    clear that it handles all edge conditions (e.g. files in the root directory). Apart from that, if the
-    limitations of :ref:`regex() <decorators.regex>` do not preclude its use, then the two approaches
-    are not so different in practice.
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/output_file_names_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/output_file_names_code.txt
deleted file mode 100644
index 7e70f58..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/output_file_names_code.txt
+++ /dev/null
@@ -1,248 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.output_file_names.code:
-
-############################################################################################################################################################################################################
-|new_manual.output_file_names.chapter_num|: Python Code for Specifying output file names with :ref:`formatter() <decorators.formatter>` and :ref:`regex() <decorators.regex>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`suffix() <decorators.suffix>` syntax
-    * :ref:`formatter() <decorators.formatter>` syntax
-    * :ref:`regex() <decorators.regex>` syntax
-    * Back to |new_manual.output_file_names.chapter_num|: :ref:`Specifying output file names <new_manual.output_file_names>`
-
-************************************************************************
-Example Code for :ref:`suffix() <decorators.suffix>`
-************************************************************************
-    .. code-block:: python
-
-        from ruffus import *
-
-        #---------------------------------------------------------------
-        #   create initial files
-        #
-        @originate([   ['job1.a.start', 'job1.b.start'],
-                       ['job2.a.start', 'job2.b.start'],
-                       ['job3.a.start', 'job3.b.start']    ])
-        def create_initial_file_pairs(output_files):
-            # create both files as necessary
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-        #---------------------------------------------------------------
-        #
-        #   suffix
-        #
-        @transform(create_initial_file_pairs,             # name of previous task(s) (or list of files, or a glob)
-                    suffix(".start"),                     # matching suffix of the "input file"
-                    [".output.a.1", 45, ".output.b.1"])   # resulting suffix
-        def first_task(input_files, output_parameters):
-            print "  input_parameters  = ", input_files
-            print "  output_parameters = ", output_parameters
-
-
-        #
-        #       Run
-        #
-        pipeline_run([first_task])
-
-
-
-************************************************************************
-Example Code for :ref:`formatter() <decorators.formatter>`
-************************************************************************
-
-    .. code-block:: python
-
-        from ruffus import *
-
-        #   create initial files
-        @originate([   ['job1.a.start', 'job1.b.start'],
-                       ['job2.a.start', 'job2.b.start'],
-                       ['job3.a.start', 'job3.c.start']    ])
-        def create_initial_file_pairs(output_files):
-            # create both files as necessary
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-
-        #---------------------------------------------------------------
-        #
-        #   formatter
-        #
-
-        #   first task
-        @transform(create_initial_file_pairs,                               # Input
-
-                    formatter(".+/job(?P<JOBNUMBER>\d+).a.start",           # Extract job number
-                              ".+/job[123].b.start"),                       # Match only "b" files
-
-                    ["{path[0]}/jobs{JOBNUMBER[0]}.output.a.1",             # Replacement list
-                     "{path[1]}/jobs{JOBNUMBER[0]}.output.b.1", 45])
-        def first_task(input_files, output_parameters):
-            print "input_parameters = ", input_files
-            print "output_parameters = ", output_parameters
-
-
-        #
-        #       Run
-        #
-        pipeline_run(verbose=0)
-
-
-****************************************************************************************************************
-Example Code for :ref:`formatter() <decorators.formatter>` with replacements in *extra* arguments
-****************************************************************************************************************
-
-
-    .. code-block:: python
-
-        from ruffus import *
-
-        #   create initial files
-        @originate([   ['job1.a.start', 'job1.b.start'],
-                       ['job2.a.start', 'job2.b.start'],
-                       ['job3.a.start', 'job3.c.start']    ])
-        def create_initial_file_pairs(output_files):
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-
-        #---------------------------------------------------------------
-        #
-        #   print job number as an extra argument
-        #
-
-        #   first task
-        @transform(create_initial_file_pairs,                               # Input
-
-                    formatter(".+/job(?P<JOBNUMBER>\d+).a.start",           # Extract job number
-                              ".+/job[123].b.start"),                       # Match only "b" files
-
-                    ["{path[0]}/jobs{JOBNUMBER[0]}.output.a.1",             # Replacement list
-                     "{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"],
-
-                     "{JOBNUMBER[0]}"
-        def first_task(input_files, output_parameters, job_number):
-            print job_number, ":", input_files
-
-
-        pipeline_run(verbose=0)
-
-
-****************************************************************************************************************
-Example Code for :ref:`formatter() <decorators.formatter>` in Zoos
-****************************************************************************************************************
-
-
-    .. code-block:: python
-
-        from ruffus import *
-
-        #   Make directories
-        @mkdir(["tiger", "lion", "dog", "crocodile", "rose"])
-
-        @originate(
-                    #   List of animals and plants
-                    [    "tiger/mammals.wild.animals",
-                        "lion/mammals.wild.animals",
-                        "lion/mammals.handreared.animals",
-                        "dog/mammals.tame.animals",
-                        "dog/mammals.wild.animals",
-                        "crocodile/reptiles.wild.animals",
-                        "rose/flowering.handreared.plants"])
-        def create_initial_files(output_file):
-            with open(output_file, "w") as oo: pass
-
-
-        #   Put different animals in different directories depending on their clade
-        @transform(create_initial_files,                                       # Input
-
-                   formatter(".+/(?P<clade>\w+).(?P<tame>\w+).animals"),       # Only animals: ignore plants!
-
-                   "{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food", # Replacement
-
-                   "{subpath[0][1]}/{clade[0]}",                               # new_directory
-                   "{subdir[0][0]}",                                           # animal_name
-                   "{tame[0]}")                                                # tameness
-        def feed(input_file, output_file, new_directory, animal_name, tameness):
-            print "Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}".format(**locals())
-
-
-        pipeline_run(verbose=0)
-
-
-        Results in:
-
-        ::
-
-            >>> pipeline_run(verbose=0)
-            Food for the wild        crocodile = ./reptiles/wild.crocodile.food will be placed in ./reptiles
-            Food for the tame        dog       = ./mammals/tame.dog.food        will be placed in ./mammals
-            Food for the wild        dog       = ./mammals/wild.dog.food        will be placed in ./mammals
-            Food for the handreared  lion      = ./mammals/handreared.lion.food will be placed in ./mammals
-            Food for the wild        lion      = ./mammals/wild.lion.food       will be placed in ./mammals
-            Food for the wild        tiger     = ./mammals/wild.tiger.food      will be placed in ./mammals
-
-
-
-****************************************************************************************************************
-Example Code for :ref:`regex() <decorators.regex>` in zoos
-****************************************************************************************************************
-
-
-    .. code-block:: python
-
-        from ruffus import *
-
-        #   Make directories
-        @mkdir(["tiger", "lion", "dog", "crocodile", "rose"])
-
-        @originate(
-                    #   List of animals and plants
-                    [    "tiger/mammals.wild.animals",
-                        "lion/mammals.wild.animals",
-                        "lion/mammals.handreared.animals",
-                        "dog/mammals.tame.animals",
-                        "dog/mammals.wild.animals",
-                        "crocodile/reptiles.wild.animals",
-                        "rose/flowering.handreared.plants"])
-        def create_initial_files(output_file):
-            with open(output_file, "w") as oo: pass
-
-
-
-        #   Put different animals in different directories depending on their clade
-        @transform(create_initial_files,                                        # Input
-
-                   regex(r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"), # Only animals: ignore plants!
-
-                   r"\1/\g<clade>/\g<tame>.\2.food",                            # Replacement
-
-                   r"\1/\g<clade>",                                             # new_directory
-                   r"\2",                                                       # animal_name
-                   "\g<tame>")                                                  # tameness
-        def feed(input_file, output_file, new_directory, animal_name, tameness):
-            print "Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}".format(**locals())
-
-
-        pipeline_run(verbose=0)
-
-
-        Results in:
-
-        ::
-
-            >>> pipeline_run(verbose=0)
-            Food for the wild        crocodile = reptiles/wild.crocodile.food will be placed in reptiles
-            Food for the tame        dog       = mammals/tame.dog.food        will be placed in mammals
-            Food for the wild        dog       = mammals/wild.dog.food        will be placed in mammals
-            Food for the handreared  lion      = mammals/handreared.lion.food will be placed in mammals
-            Food for the wild        lion      = mammals/wild.lion.food       will be placed in mammals
-            Food for the wild        tiger     = mammals/wild.tiger.food      will be placed in mammals
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/parallel.txt b/doc/_build/html/_sources/tutorials/new_tutorial/parallel.txt
deleted file mode 100644
index 90a825f..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/parallel.txt
+++ /dev/null
@@ -1,63 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: @parallel; Tutorial
-
-.. _new_manual.deprecated_parallel:
-
-####################################################################################################################################################
-|new_manual.parallel.chapter_num|: Esoteric: Running jobs in parallel without files using :ref:`@parallel<decorators.parallel>`
-####################################################################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@parallel<decorators.parallel>` syntax in detail
-
-
-
-***************************************
-**@parallel**
-***************************************
-
-    **@parallel** supplies parameters for multiple **jobs** exactly like :ref:`@files<new_manual.deprecated_files>` except that:
-
-        #. The first two parameters are not treated like *inputs* and *ouputs* parameters,
-           and strings are not assumed to be file names
-        #. Thus no checking of whether each job is up-to-date is made using *inputs* and *outputs* files
-        #. No expansions of |glob|_ patterns or *output* from previous tasks is carried out.
-
-    This syntax is most useful when a pipeline stage does not involve creating or consuming any files, and
-    you wish to forego the conveniences of :ref:`@files<new_manual.deprecated_files>`, :ref:`@transform<new_manual.transform>` etc.
-
-    The following code performs some arithmetic in parallel:
-
-        ::
-
-            import sys
-            from ruffus import *
-            parameters = [
-                             ['A', 1, 2], # 1st job
-                             ['B', 3, 4], # 2nd job
-                             ['C', 5, 6], # 3rd job
-                         ]
-            @parallel(parameters)
-            def parallel_task(name, param1, param2):
-                sys.stderr.write("    Parallel task %s: " % name)
-                sys.stderr.write("%d + %d = %d\n" % (param1, param2, param1 + param2))
-
-            pipeline_run([parallel_task])
-
-        produces the following::
-
-            Task = parallel_task
-                Parallel task A: 1 + 2 = 3
-                Job = ["A", 1, 2] completed
-                Parallel task B: 3 + 4 = 7
-                Job = ["B", 3, 4] completed
-                Parallel task C: 5 + 6 = 11
-                Job = ["C", 5, 6] completed
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout.txt b/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout.txt
deleted file mode 100644
index 02ad07d..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout.txt
+++ /dev/null
@@ -1,215 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: pipeline_printout; Tutorial
-
-.. _new_manual.pipeline_printout:
-
-############################################################################################################################################################################################################
-|new_manual.pipeline_printout.chapter_num|: Understanding how your pipeline works with :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>`
-############################################################################################################################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` syntax
-   * :ref:`Python Code for this chapter <new_manual.pipeline_printout.code>`
-
-
-.. note::
-
-    * **Whether you are learning or developing ruffus pipelines, your best friend is** :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>`
-      **This shows the exact parameters and files as they are passed through the pipeline.**
-
-    * **We also** *strongly* **recommend you use the** ``Ruffus.cmdline`` **convenience module which**
-      **will take care of all the command line arguments for you. See** :ref:`new_manual.cmdline`.
-
-
-
-=======================================
-Printing out which jobs will be run
-=======================================
-
-    :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` takes the same parameters as pipeline_run but just prints
-    the tasks which are and are not up-to-date.
-
-    The ``verbose`` parameter controls how much detail is displayed.
-
-    Let us take the pipelined code we previously wrote in
-    |new_manual.transform_in_parallel.chapter_num| :ref:`More on @transform-ing data and @originate <new_manual.transform_in_parallel.code>`
-    but call :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` instead of
-    :ref:`pipeline_run(...) <pipeline_functions.pipeline_run>`.
-    This lists the tasks which will be run in the pipeline:
-
-        ::
-
-            >>> import sys
-            >>> pipeline_printout(sys.stdout, [second_task])
-
-            ________________________________________
-            Tasks which will be run:
-
-            Task = create_initial_file_pairs
-            Task = first_task
-            Task = second_task
-            ________________________________________
-
-
-
-    To see the input and output parameters of each job in the pipeline, try increasing the verbosity from the default (``1``) to ``3``
-    (See :ref:`code  <new_manual.pipeline_printout.code>`)
-
-    This is very useful for checking that the input and output parameters have been specified correctly.
-
-=============================================
-Determining which jobs are out-of-date or not
-=============================================
-
-    It is often useful to see which tasks are or are not up-to-date. For example, if we
-    were to run the pipeline in full, and then modify one of the intermediate files, the
-    pipeline would be partially out of date.
-
-
-    Let us start by run the pipeline in full but then modify ``job1.a.output.1`` so that the second task appears out-of-date:
-
-        .. code-block:: python
-            :emphasize-lines: 3
-
-            pipeline_run([second_task])
-
-            # "touch" job1.stage1
-            open("job1.a.output.1", "w").close()
-
-
-    Run :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` with a verbosity of ``5``.
-
-    This will tell you exactly why ``second_task(...)`` needs to be re-run:
-    because ``job1.a.output.1`` has a file modification time *after* ``job1.a.output.2`` (highlighted):
-
-
-        .. code-block:: pycon
-            :emphasize-lines: 9
-
-            >>> pipeline_printout(sys.stdout, [second_task], verbose = 5)
-
-            ________________________________________
-            Tasks which are up-to-date:
-
-            Task = create_initial_file_pairs
-            Task = first_task
-
-            ________________________________________
-
-            ________________________________________
-            Tasks which will be run:
-
-            Task = second_task
-                   Job  = [job1.a.output.1
-                         -> job1.a.output.2]
-            >>> # File modification times shown for out of date files
-                     Job needs update:
-                     Input files:
-                      * 22 Jul 2014 15:29:19.33: job1.a.output.1
-                     Output files:
-                      * 22 Jul 2014 15:29:07.53: job1.a.output.2
-
-                   Job  = [job2.a.output.1
-                         -> job2.a.output.2]
-                   Job  = [job3.a.output.1
-                         -> job3.a.output.2]
-
-            ________________________________________
-
-
-    N.B. At a verbosity of 5, even jobs which are up-to-date in ``second_task`` are displayed.
-
-
-
-=============================================
-Verbosity levels
-=============================================
-
-    The verbosity levels for :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` and :ref:`pipeline_run(...) <pipeline_functions.pipeline_run>`
-    can be specified from ``verbose = 0`` (print out nothing) to the extreme verbosity of ``verbose=6``.  A verbosity of above 10 is reserved for the internal
-    debugging of Ruffus
-
-        * level **0** : *nothing*
-        * level **1** : *Out-of-date Task names*
-        * level **2** : *All Tasks (including any task function docstrings)*
-        * level **3** : *Out-of-date Jobs in Out-of-date Tasks, no explanation*
-        * level **4** : *Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings*
-        * level **5** : *All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)*
-        * level **6** : *All jobs in All Tasks whether out of date or not*
-        * level **10**: *logs messages useful only for debugging ruffus pipeline code*
-
-.. _new_manual.pipeline_printout.verbose_abbreviated_path:
-
-==========================================================================================
-Abbreviating long file paths with ``verbose_abbreviated_path``
-==========================================================================================
-
-    Pipelines often produce interminable lists of deeply nested filenames. It would be nice to be able to abbreviate this
-    to just enough information to follow the progress.
-
-    The ``verbose_abbreviated_path`` parameter specifies that   :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` and :ref:`pipeline_run(...) <pipeline_functions.pipeline_run>` only display
-
-        1) the ``NNN`` th top level sub-directories to be included, or that
-        2) the message to be truncated to a specified ```MMM`` characters (to fit onto a line, for example). ``MMM`` is specified by setting ``verbose_abbreviated_path = -MMM``, i.e. negative values.
-
-           Note that the number of characters specified is just the separate lengths of the input and output parameters,
-           not the entire indented line. You many need to specify a smaller limit that you expect (e.g. ``60`` rather than `80`)
-
-        .. code-block:: python
-
-            pipeline_printout(verbose_abbreviated_path = NNN)
-            pipeline_run(verbose_abbreviated_path = -MMM)
-
-
-
-    ``verbose_abbreviated_path`` defaults to ``2``
-
-
-    For example:
-
-        Given ``["aa/bb/cc/dddd.txt", "aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt"]``
-
-
-        .. code-block:: python
-           :emphasize-lines: 1,4,8,19
-
-            # Original relative paths
-            "[aa/bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"
-
-            # Full abspath
-            verbose_abbreviated_path = 0
-            "[/test/ruffus/src/aa/bb/cc/dddd.txt, /test/ruffus/src/aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"
-
-            # Specifed level of nested directories
-            verbose_abbreviated_path = 1
-            "[.../dddd.txt, .../gggg.txt]"
-
-            verbose_abbreviated_path = 2
-            "[.../cc/dddd.txt, .../ffff/gggg.txt]"
-
-            verbose_abbreviated_path = 3
-            "[.../bb/cc/dddd.txt, .../eeee/ffff/gggg.txt]"
-
-
-            # Truncated to MMM characters
-            verbose_abbreviated_path = -60
-            "<???> /bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"
-
-
-=============================================
-Getting a list of all tasks in a pipeline
-=============================================
-
-    If you just wanted a list of all tasks (Ruffus decorated function names), then you can
-    just run Run :ref:`pipeline_get_task_names(...) <pipeline_functions.pipeline_get_task_names>`.
-
-    This doesn't touch any pipeline code or even check to see if the pipeline is connected up properly.
-
-    However, it is sometimes useful to allow users at the command line to choose from a list of
-    possible tasks as a target.
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_code.txt
deleted file mode 100644
index f8eedf3..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_code.txt
+++ /dev/null
@@ -1,203 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.pipeline_printout.code:
-
-############################################################################################################################################################################################################
-|new_manual.pipeline_printout.chapter_num|: Python Code for Understanding how your pipeline works with :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` syntax
-    * Back to |new_manual.pipeline_printout.chapter_num|: :ref:`Understanding how your pipeline works <new_manual.pipeline_printout>`
-
-******************************************
-Display the initial state of the pipeline
-******************************************
-    ::
-
-        from ruffus import *
-        import sys
-
-        #---------------------------------------------------------------
-        #   create initial files
-        #
-        @originate([   ['job1.a.start', 'job1.b.start'],
-                       ['job2.a.start', 'job2.b.start'],
-                       ['job3.a.start', 'job3.b.start']    ])
-        def create_initial_file_pairs(output_files):
-            # create both files as necessary
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-        #---------------------------------------------------------------
-        #   first task
-        @transform(create_initial_file_pairs, suffix(".start"), ".output.1")
-        def first_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-
-        #---------------------------------------------------------------
-        #   second task
-        @transform(first_task, suffix(".output.1"), ".output.2")
-        def second_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-        pipeline_printout(sys.stdout, [second_task], verbose = 1)
-        pipeline_printout(sys.stdout, [second_task], verbose = 3)
-
-************************************
-Normal Output
-************************************
-    ::
-
-        >>> pipeline_printout(sys.stdout, [second_task], verbose = 1)
-
-        ________________________________________
-        Tasks which will be run:
-
-        Task = create_initial_file_pairs
-        Task = first_task
-        Task = second_task
-
-
-************************************
-High Verbosity Output
-************************************
-
-    ::
-
-        >>> pipeline_printout(sys.stdout, [second_task], verbose = 4)
-
-        ________________________________________
-        Tasks which will be run:
-
-        Task = create_initial_file_pairs
-               Job  = [None
-                     -> job1.a.start
-                     -> job1.b.start]
-                 Job needs update: Missing files [job1.a.start, job1.b.start]
-               Job  = [None
-                     -> job2.a.start
-                     -> job2.b.start]
-                 Job needs update: Missing files [job2.a.start, job2.b.start]
-               Job  = [None
-                     -> job3.a.start
-                     -> job3.b.start]
-                 Job needs update: Missing files [job3.a.start, job3.b.start]
-
-        Task = first_task
-               Job  = [[job1.a.start, job1.b.start]
-                     -> job1.a.output.1]
-                 Job needs update: Missing files [job1.a.start, job1.b.start, job1.a.output.1]
-               Job  = [[job2.a.start, job2.b.start]
-                     -> job2.a.output.1]
-                 Job needs update: Missing files [job2.a.start, job2.b.start, job2.a.output.1]
-               Job  = [[job3.a.start, job3.b.start]
-                     -> job3.a.output.1]
-                 Job needs update: Missing files [job3.a.start, job3.b.start, job3.a.output.1]
-
-        Task = second_task
-               Job  = [job1.a.output.1
-                     -> job1.a.output.2]
-                 Job needs update: Missing files [job1.a.output.1, job1.a.output.2]
-               Job  = [job2.a.output.1
-                     -> job2.a.output.2]
-                 Job needs update: Missing files [job2.a.output.1, job2.a.output.2]
-               Job  = [job3.a.output.1
-                     -> job3.a.output.2]
-                 Job needs update: Missing files [job3.a.output.1, job3.a.output.2]
-
-        ________________________________________
-
-******************************************
-Display the partially up-to-date pipeline
-******************************************
-    Run the pipeline, modify ``job1.stage`` so that the second task is no longer up-to-date
-    and printout the pipeline stage again::
-
-        >>> pipeline_run([second_task], verbose=3)
-        Task enters queue = create_initial_file_pairs
-            Job  = [None -> [job1.a.start, job1.b.start]]
-            Job  = [None -> [job2.a.start, job2.b.start]]
-            Job  = [None -> [job3.a.start, job3.b.start]]
-            Job  = [None -> [job1.a.start, job1.b.start]] completed
-            Job  = [None -> [job2.a.start, job2.b.start]] completed
-            Job  = [None -> [job3.a.start, job3.b.start]] completed
-        Completed Task = create_initial_file_pairs
-        Task enters queue = first_task
-            Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1]
-            Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1]
-            Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1]
-            Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1] completed
-            Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1] completed
-            Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1] completed
-        Completed Task = first_task
-        Task enters queue = second_task
-            Job  = [job1.a.output.1 -> job1.a.output.2]
-            Job  = [job2.a.output.1 -> job2.a.output.2]
-            Job  = [job3.a.output.1 -> job3.a.output.2]
-            Job  = [job1.a.output.1 -> job1.a.output.2] completed
-            Job  = [job2.a.output.1 -> job2.a.output.2] completed
-            Job  = [job3.a.output.1 -> job3.a.output.2] completed
-        Completed Task = second_task
-
-
-        # modify job1.stage1
-        >>> open("job1.a.output.1", "w").close()
-
-    At a verbosity of 6, even jobs which are up-to-date will be displayed::
-
-        >>> pipeline_printout(sys.stdout, [second_task], verbose = 6)
-
-        ________________________________________
-        Tasks which are up-to-date:
-
-        Task = create_initial_file_pairs
-               Job  = [None
-                     -> job1.a.start
-                     -> job1.b.start]
-               Job  = [None
-                     -> job2.a.start
-                     -> job2.b.start]
-               Job  = [None
-                     -> job3.a.start
-                     -> job3.b.start]
-
-        Task = first_task
-               Job  = [[job1.a.start, job1.b.start]
-                     -> job1.a.output.1]
-               Job  = [[job2.a.start, job2.b.start]
-                     -> job2.a.output.1]
-               Job  = [[job3.a.start, job3.b.start]
-                     -> job3.a.output.1]
-
-        ________________________________________
-
-
-
-        ________________________________________
-        Tasks which will be run:
-
-        Task = second_task
-               Job  = [job1.a.output.1
-                     -> job1.a.output.2]
-                 Job needs update:
-                 Input files:
-                  * 22 Jul 2014 15:29:19.33: job1.a.output.1
-                 Output files:
-                  * 22 Jul 2014 15:29:07.53: job1.a.output.2
-
-               Job  = [job2.a.output.1
-                     -> job2.a.output.2]
-               Job  = [job3.a.output.1
-                     -> job3.a.output.2]
-
-        ________________________________________
-
-
-
-    We can now see that the there is only one job in "second_task" which needs to be re-run
-    because 'job1.stage1' has been modified after 'job1.stage2'
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_graph.txt b/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_graph.txt
deleted file mode 100644
index 5076efe..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_graph.txt
+++ /dev/null
@@ -1,170 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: pipeline_printout_graph; Tutorial
-
-.. _new_manual.pipeline_printout_graph:
-
-############################################################################################################################################################################################################
-|new_manual.pipeline_printout_graph.chapter_num|: Displaying the pipeline visually with :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>` syntax
-    * :ref:`@graphviz(...) <decorators.graphviz>` syntax
-
-.. note::
-
-    Remember to look at the example code:
-
-    * :ref:`new_manual.pipeline_printout_graph.code`
-
-=============================================
-Printing out a flowchart of our pipeline
-=============================================
-
-    It is all very well being able to trace the data flow through the pipeline as text.
-    Sometimes, however, we need a bit of eye-candy!
-
-    We can see a flowchart for our fledgling pipeline by executing:
-
-        ::
-
-            pipeline_printout_graph (   'flowchart.svg',
-                                        'svg',
-                                        [second_task],
-                                        no_key_legend = False)
-
-        .. image:: ../../images/simple_tutorial_stage5_flowchart.png
-           :scale: 70
-
-
-    Flowcharts can be printed in a large number of formats including ``jpg``, ``svg``, ``png`` and ``pdf``.
-
-
-    .. note::
-
-        Flowcharts rely on the ``dot`` programme from `Graphviz <http://www.graphviz.org/>`__.
-
-        Please make sure this is installed.
-
-    There are 8 standard colour schemes, but you can further customise all the colours to your satisfaction:
-
-
-        .. image:: ../../images/flowchart_colour_schemes.png
-
-    See :ref:`here <new_manual.flowchart_colours>` for example code.
-
-================================================================
-Command line options made easier with ``ruffus.cmdline``
-================================================================
-
-
-    If you are using ``ruffus.cmdline``, then you can easily ask for a flowchart from the command line:
-
-        .. code-block:: bash
-
-            your_script.py --flowchart pipeline_flow_chart.png
-
-
-    The output format is deduced from the extension but can be specified manually:
-
-        .. code-block:: bash
-
-            # specify format. Otherwise, deduced from the extension
-            your_script.py --flowchart pipeline_flow_chart.png --flowchart_format png
-
-    Print the flow chart horizontally or vertically...
-
-        .. code-block:: bash
-
-            # flowchart proceeds from left to right , rather than from  top to bottom
-            your_script.py --flowchart pipeline_flow_chart.png --draw_graph_horizontally
-
-    ...with or without a key legend
-
-        .. code-block:: bash
-
-            # Draw key legend
-            your_script.py --flowchart pipeline_flow_chart.png --key_legend_in_graph
-
-
-=============================================
-Horribly complicated pipelines!
-=============================================
-    Flowcharts are especially useful if you have really complicated pipelines, such as
-
-        .. image:: ../../images/simple_tutorial_complex_flowchart.png
-           :scale: 70
-
-
-=============================================
-Circular dependency errors in pipelines!
-=============================================
-    Especially, if the pipeline is not set up properly, and vicious circular dependencies
-    are present:
-
-        .. image:: ../../images/simple_tutorial_complex_flowchart_error.png
-           :scale: 70
-
-==========================================================================================
-``@graphviz``: Customising the appearance of each task
-==========================================================================================
-
-    The graphic for each task can be further customised as you please by adding
-    `graphviz attributes  <http://www.graphviz.org/doc/info/attrs.html>`__ such as the URL, shape, colour
-    directly to that node using the decorator ```@graphviz``.
-
-    For example, we can customise the graphic for ``myTask()`` to look like:
-
-        .. image:: ../../images/history_html_flowchart.png
-           :scale: 30
-
-    by adding the requisite attributes as follows:
-
-
-
-    .. code-block:: python
-
-
-        @graphviz(URL='"http://cnn.com"', fillcolor = '"#FFCCCC"',
-                        color = '"#FF0000"', pencolor='"#FF0000"', fontcolor='"#4B6000"',
-                        label_suffix = "???", label_prefix = "What is this?<BR/> ",
-                        label = "<What <FONT COLOR=\"red\">is</FONT>this>",
-                        shape= "component", height = 1.5, peripheries = 5,
-                        style="dashed")
-        def Up_to_date_task2(infile, outfile):
-            pass
-
-        #   Can use dictionary if you wish...
-        graphviz_params = {"URL":"http://cnn.com", "fontcolor": '"#FF00FF"'}
-        @graphviz(**graphviz_params)
-        def myTask(input,output):
-            pass
-
-    .. **
-
-
-    You can even using HTML formatting in task names, including specifying line wraps (as in the above example),
-    using the ``label`` parameter. However, HTML labels **must** be enclosed in ``<`` and ``>``.
-
-
-          .. code-block:: python
-
-            label = "<Line <BR/> wrapped task_name()>"
-
-    Otherwise, you can also opt to keep the task name and wrap it with a prefix and suffix:
-
-          .. code-block:: python
-
-            label_suffix = "??? ", label_prefix = ": What is this?"
-
-    The ``URL`` attribute allows the generation of clickable svg, and also client / server
-          side image maps usable in web pages.
-          See `Graphviz documentation  <http://www.graphviz.org/content/output-formats#dimap>`__
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_graph_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_graph_code.txt
deleted file mode 100644
index c836b83..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/pipeline_printout_graph_code.txt
+++ /dev/null
@@ -1,109 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.pipeline_printout_graph.code:
-
-############################################################################################################################################################################################################
-|new_manual.pipeline_printout_graph.chapter_num|: Python Code for Displaying the pipeline visually with :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>`
-############################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>` syntax
-    * Back to |new_manual.pipeline_printout_graph.chapter_num|: :ref:`Displaying the pipeline visually <new_manual.pipeline_printout_graph>`
-
-************************************
-Code
-************************************
-    .. code-block:: python
-        :emphasize-lines: 28, 51
-        :linenos:
-
-        from ruffus import *
-        import sys
-
-        #---------------------------------------------------------------
-        #   create initial files
-        #
-        @originate([   ['job1.a.start', 'job1.b.start'],
-                       ['job2.a.start', 'job2.b.start'],
-                       ['job3.a.start', 'job3.b.start']    ])
-        def create_initial_file_pairs(output_files):
-            # create both files as necessary
-            for output_file in output_files:
-                with open(output_file, "w") as oo: pass
-
-        #---------------------------------------------------------------
-        #   first task
-        @transform(create_initial_file_pairs, suffix(".start"), ".output.1")
-        def first_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-
-        #---------------------------------------------------------------
-        #   second task
-        @transform(first_task, suffix(".output.1"), ".output.2")
-        def second_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-        #  Print graph before running pipeline
-
-        #---------------------------------------------------------------
-        #
-        #       Show flow chart and tasks before running the pipeline
-        #
-        print "Show flow chart and tasks before running the pipeline"
-        pipeline_printout_graph ( open("simple_tutorial_stage5_before.png", "w"),
-                                 "png",
-                                 [second_task],
-                                 minimal_key_legend=True)
-
-        #---------------------------------------------------------------
-        #
-        #       Run
-        #
-        pipeline_run([second_task])
-
-
-        # modify job1.stage1
-        open("job1.a.output.1", "w").close()
-
-
-        #  Print graph after everything apart from ``job1.a.output.1`` is update
-
-        #---------------------------------------------------------------
-        #
-        #       Show flow chart and tasks after running the pipeline
-        #
-        print "Show flow chart and tasks after running the pipeline"
-        pipeline_printout_graph ( open("simple_tutorial_stage5_after.png", "w"),
-                                 "png",
-                                 [second_task],
-                                 no_key_legend=True)
-
-
-************************************
-Resulting Flowcharts
-************************************
-   +-------------------------------------------------------------+-----------------------------------------------------------------------+
-   | .. image:: ../../images/simple_tutorial_stage5_before.png   | .. image::  ../../images/simple_tutorial_stage5_after.png             |
-   |           :alt: Before running the pipeline                 |     :alt: After running the pipeline                                  |
-   |           :scale: 95                                        |     :scale: 95                                                        |
-   |           :align: center                                    |     :align: center                                                    |
-   |                                                             |                                                                       |
-   | .. centered:: Before                                        | .. centered:: After                                                   |
-   |                                                             |                                                                       |
-   +-------------------------------------------------------------+-----------------------------------------------------------------------+
-
-   +-------------------------------------------------------------------------------------------------------------------------------------+
-   | .. image:: ../../images/tutorial_key.png                                                                                            |
-   |           :alt: Legend key                                                                                                          |
-   |           :scale: 50                                                                                                                |
-   |           :align: center                                                                                                            |
-   |                                                                                                                                     |
-   | .. centered:: Legend                                                                                                                |
-   |                                                                                                                                     |
-   +-------------------------------------------------------------------------------------------------------------------------------------+
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/posttask.txt b/doc/_build/html/_sources/tutorials/new_tutorial/posttask.txt
deleted file mode 100644
index a468a27..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/posttask.txt
+++ /dev/null
@@ -1,122 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: posttask; Tutorial
-
-.. _new_manual.posttask:
-
-####################################################################################################################################################
-|new_manual.posttask.chapter_num|: Signal the completion of each stage of our pipeline with :ref:`@posttask <decorators.posttask>`
-####################################################################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@posttask <decorators.posttask>` syntax
-
-
-***********************
-Overview
-***********************
-
-
-
-    It is often useful to signal the completion of each task by specifying a specific
-    action to be taken or function to be called. This can range from
-    printing out some message, or  `touching  <http://en.wikipedia.org/wiki/Touch_(Unix)>`__ some sentinel file,
-    to emailing the author. This is particular useful if the :term:`task` is a recipe apply to an unspecified number
-    of parameters in parallel in different :term:`job`\ s. If the task is never run, or if it
-    fails, needless-to-say no task completion action will happen.
-
-
-    *Ruffus* uses the :ref:`@posttask <decorators.posttask>` decorator for this purpose.
-
-
-=================
-**@posttask**
-=================
-
-    We can signal the completion of each task by specifying
-    one or more function(s) using :ref:`@posttask <decorators.posttask>` ::
-
-        from ruffus import *
-
-        def task_finished():
-            print "hooray"
-
-        @posttask(task_finished)
-        @originate("a.1")
-        def create_if_necessary(output_file):
-            open(output_file, "w")
-
-        pipeline_run([create_if_necessary])
-
-
-    This is such a short function, we might as well write it in-line:
-
-        ::
-
-            @posttask(lambda: sys.stdout.write("hooray\n"))
-            @originate("a.1")
-            def create_if_necessary(output_file):
-                open(output_file, "w")
-
-
-.. note::
-
-    The function(s) provided to :ref:`@posttask <decorators.posttask>` will be called if the pipeline passes
-    through a task, even if none of its jobs are run because they are up-to-date.
-    This happens when a upstream task is out-of-date, and the execution passes through
-    this point in the pipeline. See the example in :ref:`new_manual.dependencies`
-    of this manual.
-
-
-.. index::
-    single: @posttask; touchfile (Manual)
-    single: touchfile ; @posttask (Manual)
-
-
-.. _new_manual.posttask.touch_file:
-
-============================================
-:ref:`touch_file<decorators.touch_file>`
-============================================
-
-    One way to note the completion of a task is to create some sort of
-    "flag" file. Each stage in a traditional ``make`` pipeline would contain a
-    ``touch completed.flag``.
-
-    This is such a useful idiom that *Ruffus* provides the shorthand :ref:`touch_file<decorators.touch_file>`:
-
-        .. code-block:: python
-
-            from ruffus import *
-
-            @posttask(touch_file("task_completed.flag"))
-            @files(None, "a.1")
-            def create_if_necessary(input_file, output_file):
-                open(output_file, "w")
-
-            pipeline_run()
-
-=======================================
-Adding several post task actions
-=======================================
-    You can, of course, add more than one different action to be taken on completion of the
-    task, either by stacking up as many :ref:`@posttask<decorators.posttask>` decorators
-    as necessary, or by including several functions in the same :ref:`@posttask <decorators.posttask>`:
-
-        .. code-block:: python
-
-            from ruffus import *
-
-            @posttask(print_hooray, print_whoppee)
-            @posttask(print_hip_hip, touch_file("sentinel_flag"))
-            @originate("a.1")
-            def create_if_necessary(output_file):
-                open(output_file, "w")
-
-            pipeline_run()
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/split.txt b/doc/_build/html/_sources/tutorials/new_tutorial/split.txt
deleted file mode 100644
index dc866b2..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/split.txt
+++ /dev/null
@@ -1,233 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: split; Tutorial
-
-.. _new_manual.split:
-
-######################################################################################################
-|new_manual.split.chapter_num|: Splitting up large tasks / files with **@split**
-######################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@split <decorators.split>` syntax
-   * :ref:`Example code for this chapter <new_manual.split.code>`
-
-
-**************************************************************************************
-Overview
-**************************************************************************************
-
-    A common requirement in computational pipelines is to split up a large task into
-    small jobs which can be run on different processors, (or sent to a computational
-    cluster). Very often, the number of jobs depends dynamically on the size of the
-    task, and cannot be known beforehand.
-
-    *Ruffus* uses the :ref:`@split <decorators.split>` decorator to indicate that
-    the :term:`task` function will produce an indeterminate number of independent *Outputs* from a single *Input*.
-
-**************************************************************************************
-Example: Calculate variance for a large list of numbers in parallel
-**************************************************************************************
-
-    Suppose we wanted to calculate the `variance  <http://en.wikipedia.org/wiki/Variance>`__ for
-    100,000 numbers, how can we parallelise the calculation so that we can get an answer as
-    speedily as possible?
-
-    We need to
-
-        * break down the problem into manageable chunks
-        * solve these in parallel, possibly on a computational cluster and then
-        * merge the partial solutions back together for a final result.
-
-
-    To complicate things, we usually do not want to hard-code the number of parallel chunks beforehand.
-    The degree of parallelism is often only apparent as we process our data.
-
-    **Ruffus** was designed to solve such problems which are common, for example, in bioinformatics and genomics.
-
-    A flowchart for our variance problem might look like this:
-
-    .. image:: ../../images/manual_split_merge_example.jpg
-       :scale: 30
-
-    (In this toy example, we create our own starting data in ``create_random_numbers()``.)
-
-
-**************************************************************************************
-Output files for :ref:`@split <decorators.split>`
-**************************************************************************************
-
-
-    The *Ruffus* decorator :ref:`@split<decorators.split>` is designed specifically with this run-time flexibility in mind:
-
-
-    .. code-block:: python
-
-        @split(create_random_numbers, "*.chunks")
-        def split_problem (input_file_names, output_files):
-            pass
-
-
-    This will split the incoming ``input_file_names`` into ``NNN`` number of *outputs* where ``NNN`` is not predetermined:
-
-    The *output* (second) parameter of :ref:`@split<decorators.split>` often contains a |glob|_ pattern like the ``*.chunks`` above.
-
-    Only **after** the task function has completed, will Ruffus match the **Output** parameter (``*.chunks``)
-    against the files which have been created by ``split_problem()`` (e.g. ``1.chunks``, ``2.chunks``, ``3.chunks``)
-
-**************************************************************************************
-Be careful in specifying  **Output** globs
-**************************************************************************************
-
-    Note that it is your responsibility to keep the **Output** specification tight enough so that Ruffus does not
-    pick up extraneous files.
-
-    You can specify multiple |glob|_ patterns to match *all* the files which are the
-    result of the splitting task function. These can even cover different directories,
-    or groups of file names. This is a more extreme example:
-
-        ::
-
-            @split("input.file", ['a*.bits', 'b*.pieces', 'somewhere_else/c*.stuff'])
-            def split_function (input_filename, output_files):
-                "Code to split up 'input.file'"
-
-**************************************************************************************
-Clean up previous pipeline runs
-**************************************************************************************
-
-    Problem arise when the current directory contains results of previous pipeline runs.
-
-    * For example, if the previous analysis involved a large data set, there might be 3 chunks: ``1.chunks``, ``2.chunks``, ``3.chunks``.
-    * In the current analysis, there might be a smaller data set which divides into only 2 chunks, ``1.chunks`` and ``2.chunks``.
-    * Unfortunately, ``3.chunks`` from the previous run is still hanging around and will be included erroneously by the glob ``*.chunks``.
-
-
-    .. warning::
-
-        **Your first duty in** :ref:`@split <decorators.split>` **tasks functions should be to clean up**
-
-    To help you clean up thoroughly, Ruffus initialises the **output** parameter to all files which match specification.
-
-    The first order of business is thus invariably to cleanup ( delete with ``os.unlink``) all files in **Output**.
-
-    .. code-block:: python
-        :emphasize-lines: 11
-
-        #---------------------------------------------------------------
-        #
-        #   split initial file
-        #
-        @split(create_random_numbers, "*.chunks")
-        def split_problem (input_file_names, output_files):
-            """
-                splits random numbers file into xxx files of chunk_size each
-            """
-            #
-            #   clean up any files from previous runs
-            #
-            #for ff in glob.glob("*.chunks"):
-            for ff in input_file_names:
-                os.unlink(ff)
-
-    (The first time you run the example code, ``*.chunks`` will initialise ``output_files`` to an empty list. )
-
-.. _new_manual.split.one_to_many:
-
-**************************************************************************************
-1 to many
-**************************************************************************************
-
-    :ref:`@split <decorators.split>` is a one to many operator because its
-    outputs are a list of *independent* items.
-
-    If :ref:`@split <decorators.split>` generates 5 files, then this will lead to 5 jobs downstream.
-
-    This means we can just connect our old friend :ref:`@transform <decorators.transform>` to our pipeline
-    and the results of :ref:`@split <decorators.split>` will be analysed in parallel. This code should look
-    familiar:
-
-        .. code-block:: python
-
-            #---------------------------------------------------------------
-            #
-            #   Calculate sum and sum of squares for each chunk file
-            #
-            @transform(split_problem, suffix(".chunks"), ".sums")
-            def sum_of_squares (input_file_name, output_file_name):
-                pass
-
-
-    Which results in output like this:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [[random_numbers.list] -> *.chunks] completed
-            Completed Task = split_problem
-                Job  = [1.chunks -> 1.sums] completed
-                Job  = [10.chunks -> 10.sums] completed
-                Job  = [2.chunks -> 2.sums] completed
-                Job  = [3.chunks -> 3.sums] completed
-                Job  = [4.chunks -> 4.sums] completed
-                Job  = [5.chunks -> 5.sums] completed
-                Job  = [6.chunks -> 6.sums] completed
-                Job  = [7.chunks -> 7.sums] completed
-                Job  = [8.chunks -> 8.sums] completed
-                Job  = [9.chunks -> 9.sums] completed
-            Completed Task = sum_of_squares
-
-    Have a look at the :ref:`Example code for this chapter <new_manual.split.code>`
-
-.. _new_manual.split.nothing_to_many:
-
-**************************************************************************************
-Nothing to many
-**************************************************************************************
-
-
-    Normally we would use :ref:`@originate <new_manual.originate>` to create files from
-    scratch, for example at the beginning of the pipeline.
-
-    However, sometimes, it is not possible to determine ahead of time how many files you
-    will be creating from scratch. :ref:`@split<decorators.split>` can also be useful even in such cases:
-
-        .. code-block:: python
-            :emphasize-lines: 6
-
-            from random import randint
-            from ruffus import *
-            import os
-
-            # Create between 2 and 5 files
-            @split(None, "*.start")
-            def create_initial_files(no_input_file, output_files):
-                # cleanup first
-                for oo in output_files:
-                    os.unlink(oo)
-                # make new files
-                for ii in range(randint(2,5)):
-                    open("%d.start" % ii, "w")
-
-            @transform(create_initial_files, suffix(".start"), ".processed")
-            def process_files(input_file, output_file):
-                open(output_file, "w")
-
-            pipeline_run()
-
-        Giving:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [None -> *.start] completed
-            Completed Task = create_initial_files
-                Job  = [0.start -> 0.processed] completed
-                Job  = [1.start -> 1.processed] completed
-            Completed Task = process_files
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/split_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/split_code.txt
deleted file mode 100644
index eb4e725..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/split_code.txt
+++ /dev/null
@@ -1,115 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.split.code:
-
-##############################################################################################################
-|new_manual.split.chapter_num|: Python Code for Splitting up large tasks / files with **@split**
-##############################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@split syntax in detail <decorators.split>`
-    * Back to |new_manual.split.chapter_num|: :ref:`Splitting up large tasks / files with @split <new_manual.split>`
-
-*******************************************
-Splitting large jobs
-*******************************************
-
-        ::
-
-            from ruffus import *
-
-            NUMBER_OF_RANDOMS = 10000
-            CHUNK_SIZE = 1000
-
-
-            import random, os, glob
-
-            #---------------------------------------------------------------
-            #
-            #   Create random numbers
-            #
-            @originate("random_numbers.list")
-            def create_random_numbers(output_file_name):
-                f = open(output_file_name, "w")
-                for i in range(NUMBER_OF_RANDOMS):
-                    f.write("%g\n" % (random.random() * 100.0))
-
-            #---------------------------------------------------------------
-            #
-            #   split initial file
-            #
-            @split(create_random_numbers, "*.chunks")
-            def split_problem (input_file_names, output_files):
-                """
-                    splits random numbers file into xxx files of chunk_size each
-                """
-                #
-                #   clean up any files from previous runs
-                #
-                #for ff in glob.glob("*.chunks"):
-                for ff in input_file_names:
-                    os.unlink(ff)
-                #
-                #
-                #   create new file every chunk_size lines and
-                #       copy each line into current file
-                #
-                output_file = None
-                cnt_files = 0
-                for input_file_name in input_file_names:
-                    for i, line in enumerate(open(input_file_name)):
-                        if i % CHUNK_SIZE == 0:
-                            cnt_files += 1
-                            output_file = open("%d.chunks" % cnt_files, "w")
-                        output_file.write(line)
-
-            #---------------------------------------------------------------
-            #
-            #   Calculate sum and sum of squares for each chunk file
-            #
-            @transform(split_problem, suffix(".chunks"), ".sums")
-            def sum_of_squares (input_file_name, output_file_name):
-                output = open(output_file_name,  "w")
-                sum_squared, sum = [0.0, 0.0]
-                cnt_values = 0
-                for line in open(input_file_name):
-                    cnt_values += 1
-                    val = float(line.rstrip())
-                    sum_squared += val * val
-                    sum += val
-                output.write("%s\n%s\n%d\n" % (repr(sum_squared), repr(sum), cnt_values))
-
-            #---------------------------------------------------------------
-            #
-            #       Run
-            #
-            pipeline_run()
-
-
-
-
-************************************
-Resulting Output
-************************************
-    ::
-
-            >>> pipeline_run()
-                Job  = [None -> random_numbers.list] completed
-            Completed Task = create_random_numbers
-                Job  = [[random_numbers.list] -> *.chunks] completed
-            Completed Task = split_problem
-                Job  = [1.chunks -> 1.sums] completed
-                Job  = [10.chunks -> 10.sums] completed
-                Job  = [2.chunks -> 2.sums] completed
-                Job  = [3.chunks -> 3.sums] completed
-                Job  = [4.chunks -> 4.sums] completed
-                Job  = [5.chunks -> 5.sums] completed
-                Job  = [6.chunks -> 6.sums] completed
-                Job  = [7.chunks -> 7.sums] completed
-                Job  = [8.chunks -> 8.sums] completed
-                Job  = [9.chunks -> 9.sums] completed
-            Completed Task = sum_of_squares
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/subdivide_collate.txt b/doc/_build/html/_sources/tutorials/new_tutorial/subdivide_collate.txt
deleted file mode 100644
index ae913b9..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/subdivide_collate.txt
+++ /dev/null
@@ -1,234 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: @subdivide; Tutorial
-    pair: @collate; Tutorial
-
-.. _new_manual.subdivide_collate:
-
-############################################################################################################################################################################
-|new_manual.subdivide_collate.chapter_num|: :ref:`@subdivide <decorators.subdivide>` tasks to run efficiently and regroup with :ref:`@collate <decorators.collate>`
-############################################################################################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@subdivide <decorators.subdivide>` syntax
-   * :ref:`@collate <decorators.collate>` syntax
-
-
-***********************
-Overview
-***********************
-
-    In |new_manual.split.chapter_num| and |new_manual.merge.chapter_num|, we saw how a large
-    task can be :ref:`@split <new_manual.split>` into small jobs to be analysed efficiently
-    in parallel. Ruffus can then :ref:`@merge <new_manual.split>` these back together
-    to give a single, unified result.
-
-    This assumes that your pipeline is processing one item at a time. Usually, however, we
-    will have, for example, 10 large pieces of data in play, each of which has to be
-    subdivided into smaller pieces for analysis before being put back together.
-
-    This is the role of :ref:`@subdivide <decorators.subdivide>` and  :ref:`@subdivide <decorators.collate>`.
-
-    Like :ref:`@split <decorators.split>`,  the number of output files
-    :ref:`@subdivide <decorators.subdivide>` produces for *each* **Input** is not predetermined.
-
-    On the other hand, these output files should be named in such a way that they can
-    later be grouped back together later using :ref:`@subdivide <decorators.collate>`.
-
-    This will be clearer with some worked examples.
-
-
-.. _new_manual.subdivide:
-
-*********************************************************************
-:ref:`@subdivide <decorators.subdivide>` in parallel
-*********************************************************************
-
-    Let us start from 3 files with varying number of lines. We wish to process these two
-    lines at a time but we do not know ahead of time how long each file is:
-
-    .. code-block:: python
-        :emphasize-lines: 3,5
-
-        from ruffus import *
-        import os, random, sys
-
-        # Create files a random number of lines
-        @originate(["a.start",
-                    "b.start",
-                    "c.start"])
-        def create_test_files(output_file):
-            cnt_lines = random.randint(1,3) * 2
-            with open(output_file, "w") as oo:
-                for ii in range(cnt_lines):
-                    oo.write("data item = %d\n" % ii)
-                print "        %s has %d lines" % (output_file, cnt_lines)
-
-
-        #
-        #   subdivide the input files into NNN fragment files of 2 lines each
-        #
-        @subdivide( create_test_files,
-                    formatter(),
-                    "{path[0]}/{basename[0]}.*.fragment",
-                    "{path[0]}/{basename[0]}")
-        def subdivide_files(input_file, output_files, output_file_name_stem):
-            #
-            #   cleanup any previous results
-            #
-            for oo in output_files:
-                os.unlink(oo)
-            #
-            #   Output files contain two lines each
-            #       (new output files every even line)
-            #
-            cnt_output_files = 0
-            for ii, line in enumerate(open(input_file)):
-                if ii % 2 == 0:
-                    cnt_output_files += 1
-                    output_file_name = "%s.%d.fragment" % (output_file_name_stem, cnt_output_files)
-                    output_file = open(output_file_name, "w")
-                    print "        Subdivide %s -> %s" % (input_file, output_file_name)
-                output_file.write(line)
-
-
-        #
-        #   Analyse each fragment independently
-        #
-        @transform(subdivide_files, suffix(".fragment"), ".analysed")
-        def analyse_fragments(input_file, output_file):
-            print "        Analysing %s -> %s" % (input_file, output_file)
-            with open(output_file, "w") as oo:
-                for line in open(input_file):
-                    oo.write("analysed " + line)
-
-
-    This produces the following output:
-
-    .. code-block:: pycon
-        :emphasize-lines: 8,20,36
-
-        >>> pipeline_run(verbose = 1)
-                a.start has 2 lines
-            Job  = [None -> a.start] completed
-                b.start has 6 lines
-            Job  = [None -> b.start] completed
-                c.start has 6 lines
-            Job  = [None -> c.start] completed
-        Completed Task = create_test_files
-
-                Subdivide a.start -> /home/lg/temp/a.1.fragment
-            Job  = [a.start -> a.*.fragment, a] completed
-
-                Subdivide b.start -> /home/lg/temp/b.1.fragment
-                Subdivide b.start -> /home/lg/temp/b.2.fragment
-                Subdivide b.start -> /home/lg/temp/b.3.fragment
-            Job  = [b.start -> b.*.fragment, b] completed
-
-                Subdivide c.start -> /home/lg/temp/c.1.fragment
-                Subdivide c.start -> /home/lg/temp/c.2.fragment
-                Subdivide c.start -> /home/lg/temp/c.3.fragment
-            Job  = [c.start -> c.*.fragment, c] completed
-
-        Completed Task = subdivide_files
-
-                Analysing /home/lg/temp/a.1.fragment -> /home/lg/temp/a.1.analysed
-            Job  = [a.1.fragment -> a.1.analysed] completed
-                Analysing /home/lg/temp/b.1.fragment -> /home/lg/temp/b.1.analysed
-            Job  = [b.1.fragment -> b.1.analysed] completed
-
-            [ ...SEE EXAMPLE CODE FOR MORE LINES ...]
-
-        Completed Task = analyse_fragments
-
-
-    ``a.start`` has two lines and results in a single ``.fragment`` file,
-    while there are 3 ``b.*.fragment`` files because it has 6 lines.
-    Whatever their origin, all of the different fragment files are treated equally
-    in ``analyse_fragments()`` and processed (in parallel) in the same way.
-
-
-
-.. _new_manual.collate:
-
-*********************************************************************
-Grouping using :ref:`@collate <decorators.collate>`
-*********************************************************************
-
-    All that is left in our example is to reassemble the analysed fragments back together into
-    3 sets of results corresponding to the original 3 pieces of starting data.
-
-    This is straightforward by eye: the file names all have the same pattern: ``[abc].*.analysed``:
-
-        ::
-
-            a.1.analysed    ->   a.final_result
-            b.1.analysed    ->   b.final_result
-            b.2.analysed    ->   ..
-            b.3.analysed    ->   ..
-            c.1.analysed    ->   c.final_result
-            c.2.analysed    ->   ..
-
-    :ref:`@collate <decorators.collate>` does something similar:
-
-        #. Specify a string substitution e.g. ``c.??.analysed  -> c.final_result`` and
-        #. Ask *ruffus* to group together any **Input** (e.g. ``c.1.analysed``, ``c.2.analysed``)
-           that will result in the same **Output** (e.g. ``c.final_result``)
-
-
-        .. code-block:: python
-            :emphasize-lines: 3,5
-
-            #
-            #   ``XXX.??.analysed  -> XXX.final_result``
-            #   Group results using original names
-            #
-            @collate(   analyse_fragments,
-
-                        # split file name into [abc].NUMBER.analysed
-                        formatter("/(?P<NAME>[abc]+)\.\d+\.analysed$"),
-
-                        "{path[0]}/{NAME[0]}.final_result")
-            def recombine_analyses(input_file_names, output_file):
-                with open(output_file, "w") as oo:
-                    for input_file in input_file_names:
-                        print "        Recombine %s -> %s" % (input_file, output_file)
-                        for line in open(input_file):
-                            oo.write(line)
-
-        This produces the following output:
-
-        .. code-block:: pycon
-            :emphasize-lines: 11
-
-                    Recombine /home/lg/temp/a.1.analysed -> /home/lg/temp/a.final_result
-                Job  = [[a.1.analysed] -> a.final_result] completed
-                    Recombine /home/lg/temp/b.1.analysed -> /home/lg/temp/b.final_result
-                    Recombine /home/lg/temp/b.2.analysed -> /home/lg/temp/b.final_result
-                    Recombine /home/lg/temp/b.3.analysed -> /home/lg/temp/b.final_result
-                Job  = [[b.1.analysed, b.2.analysed, b.3.analysed] -> b.final_result] completed
-                    Recombine /home/lg/temp/c.1.analysed -> /home/lg/temp/c.final_result
-                    Recombine /home/lg/temp/c.2.analysed -> /home/lg/temp/c.final_result
-                    Recombine /home/lg/temp/c.3.analysed -> /home/lg/temp/c.final_result
-                Job  = [[c.1.analysed, c.2.analysed, c.3.analysed] -> c.final_result] completed
-            Completed Task = recombine_analyses
-
-
-    .. warning::
-
-        * **Input** file names are grouped together not in a guaranteed order.
-
-              For example, the fragment files may not be sent to ``recombine_analyses(input_file_names, ...)``
-              in alphabetically or any other useful order.
-
-              You may want to sort **Input** before concatenation.
-
-        * All **Input** are grouped together if they have both the same **Output** *and* **Extra**
-          parameters. If any string substitution is specified in any of the other **Extra** parameters
-          to :ref:`@subdivide <decorators.subdivide>`, they must give the same answers for **Input**
-          in the same group.
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/subdivide_collate_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/subdivide_collate_code.txt
deleted file mode 100644
index 3160181..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/subdivide_collate_code.txt
+++ /dev/null
@@ -1,155 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.subdivide_collate.code:
-
-#############################################################################################################################################################################################################################################################################################################################
-|new_manual.subdivide_collate.chapter_num|: Python Code for :ref:`@subdivide <decorators.subdivide>` tasks to run efficiently and regroup with :ref:`@collate <decorators.collate>`
-#############################################################################################################################################################################################################################################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@jobs_limit <decorators.jobs_limit>` syntax
-    * :ref:`pipeline_run() <pipeline_functions.pipeline_run>` syntax
-    * :ref:`drmaa_wrapper.run_job() <drmaa_wrapper.run_job>` syntax
-    * Back to |new_manual.subdivide_collate.chapter_num|: :ref:`:ref:`@subdivide tasks to run efficiently and regroup with @collate <new_manual.subdivide_collate>`
-
-*****************************************************************************************************************************
-:ref:`@subdivide <decorators.subdivide>` and regroup with :ref:`@collate <decorators.collate>` example
-*****************************************************************************************************************************
-
-    .. code-block:: python
-        :emphasize-lines: 17
-
-        from ruffus import *
-        import os, random, sys
-
-        # Create files a random number of lines
-        @originate(["a.start",
-                    "b.start",
-                    "c.start"])
-        def create_test_files(output_file):
-            cnt_lines = random.randint(1,3) * 2
-            with open(output_file, "w") as oo:
-                for ii in range(cnt_lines):
-                    oo.write("data item = %d\n" % ii)
-                print "        %s has %d lines" % (output_file, cnt_lines)
-
-
-        #
-        #   subdivide the input files into NNN fragment files of 2 lines each
-        #
-        @subdivide( create_test_files,
-                    formatter(),
-                    "{path[0]}/{basename[0]}.*.fragment",
-                    "{path[0]}/{basename[0]}")
-        def subdivide_files(input_file, output_files, output_file_name_stem):
-            #
-            #   cleanup any previous results
-            #
-            for oo in output_files:
-                os.unlink(oo)
-            #
-            #   Output files contain two lines each
-            #       (new output files every even line)
-            #
-            cnt_output_files = 0
-            for ii, line in enumerate(open(input_file)):
-                if ii % 2 == 0:
-                    cnt_output_files += 1
-                    output_file_name = "%s.%d.fragment" % (output_file_name_stem, cnt_output_files)
-                    output_file = open(output_file_name, "w")
-                    print "        Subdivide %s -> %s" % (input_file, output_file_name)
-                output_file.write(line)
-
-
-        #
-        #   Analyse each fragment independently
-        #
-        @transform(subdivide_files, suffix(".fragment"), ".analysed")
-        def analyse_fragments(input_file, output_file):
-            print "        Analysing %s -> %s" % (input_file, output_file)
-            with open(output_file, "w") as oo:
-                for line in open(input_file):
-                    oo.write("analysed " + line)
-
-
-        #
-        #   Group results using original names
-        #
-        @collate(   analyse_fragments,
-
-                    # split file name into [abc].NUMBER.analysed
-                    formatter("/(?P<NAME>[abc]+)\.\d+\.analysed$"),
-
-                    "{path[0]}/{NAME[0]}.final_result")
-        def recombine_analyses(input_file_names, output_file):
-            with open(output_file, "w") as oo:
-                for input_file in input_file_names:
-                    print "        Recombine %s -> %s" % (input_file, output_file)
-                    for line in open(input_file):
-                        oo.write(line)
-
-
-
-
-        #pipeline_printout(sys.stdout, verbose = 3)
-
-
-        pipeline_run(verbose = 1)
-
-    Results in
-
-    .. code-block:: pycon
-
-        >>> pipeline_run(verbose = 1)
-
-                a.start has 2 lines
-            Job  = [None -> a.start] completed
-                b.start has 6 lines
-            Job  = [None -> b.start] completed
-                c.start has 6 lines
-            Job  = [None -> c.start] completed
-        Completed Task = create_test_files
-
-                Subdivide a.start -> /home/lg/temp/a.1.fragment
-            Job  = [a.start -> a.*.fragment, a] completed
-                Subdivide b.start -> /home/lg/temp/b.1.fragment
-                Subdivide b.start -> /home/lg/temp/b.2.fragment
-                Subdivide b.start -> /home/lg/temp/b.3.fragment
-            Job  = [b.start -> b.*.fragment, b] completed
-                Subdivide c.start -> /home/lg/temp/c.1.fragment
-                Subdivide c.start -> /home/lg/temp/c.2.fragment
-                Subdivide c.start -> /home/lg/temp/c.3.fragment
-            Job  = [c.start -> c.*.fragment, c] completed
-        Completed Task = subdivide_files
-
-                Analysing /home/lg/temp/a.1.fragment -> /home/lg/temp/a.1.analysed
-            Job  = [a.1.fragment -> a.1.analysed] completed
-                Analysing /home/lg/temp/b.1.fragment -> /home/lg/temp/b.1.analysed
-            Job  = [b.1.fragment -> b.1.analysed] completed
-                Analysing /home/lg/temp/b.2.fragment -> /home/lg/temp/b.2.analysed
-            Job  = [b.2.fragment -> b.2.analysed] completed
-                Analysing /home/lg/temp/b.3.fragment -> /home/lg/temp/b.3.analysed
-            Job  = [b.3.fragment -> b.3.analysed] completed
-                Analysing /home/lg/temp/c.1.fragment -> /home/lg/temp/c.1.analysed
-            Job  = [c.1.fragment -> c.1.analysed] completed
-                Analysing /home/lg/temp/c.2.fragment -> /home/lg/temp/c.2.analysed
-            Job  = [c.2.fragment -> c.2.analysed] completed
-                Analysing /home/lg/temp/c.3.fragment -> /home/lg/temp/c.3.analysed
-            Job  = [c.3.fragment -> c.3.analysed] completed
-        Completed Task = analyse_fragments
-
-                Recombine /home/lg/temp/a.1.analysed -> /home/lg/temp/a.final_result
-            Job  = [[a.1.analysed] -> a.final_result] completed
-                Recombine /home/lg/temp/b.1.analysed -> /home/lg/temp/b.final_result
-                Recombine /home/lg/temp/b.2.analysed -> /home/lg/temp/b.final_result
-                Recombine /home/lg/temp/b.3.analysed -> /home/lg/temp/b.final_result
-            Job  = [[b.1.analysed, b.2.analysed, b.3.analysed] -> b.final_result] completed
-                Recombine /home/lg/temp/c.1.analysed -> /home/lg/temp/c.final_result
-                Recombine /home/lg/temp/c.2.analysed -> /home/lg/temp/c.final_result
-                Recombine /home/lg/temp/c.3.analysed -> /home/lg/temp/c.final_result
-            Job  = [[c.1.analysed, c.2.analysed, c.3.analysed] -> c.final_result] completed
-        Completed Task = recombine_analyses
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/transform.txt b/doc/_build/html/_sources/tutorials/new_tutorial/transform.txt
deleted file mode 100644
index 9e743c0..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/transform.txt
+++ /dev/null
@@ -1,194 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: transform; Tutorial
-
-.. _new_manual.transform:
-
-############################################################################################################################################################################################################
-|new_manual.transform.chapter_num|: Transforming data in a pipeline with :ref:`@transform <decorators.transform>`
-############################################################################################################################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@transform <decorators.transform>` syntax
-
-.. note::
-
-    Remember to look at the example code:
-
-    * :ref:`new_manual.transform.code`
-
-
-***************************************
-Review
-***************************************
-    .. image:: ../../images/theoretical_pipeline_schematic.png
-       :scale: 50
-
-    Computational pipelines transform your data in stages until the final result is produced.
-    Ruffus automates the plumbing in your pipeline. You supply the python functions which perform the data transformation,
-    and tell Ruffus how these pipeline stages or :term:`task` functions are connected together.
-
-    .. note::
-
-        **The best way to design a pipeline is to:**
-
-            * **write down the file names of the data as it flows across your pipeline**
-            * **write down the names of functions which transforms the data at each stage of the pipeline.**
-
-
-
-************************************
-Task functions as recipes
-************************************
-
-    Each :term:`task` function of the pipeline is a recipe or
-    `rule <http://www.gnu.org/software/make/manual/make.html#Rule-Introduction>`_
-    which can be applied repeatedly to our data.
-
-    For example, one can have
-
-        * a ``compile()`` *task* which will compile any number of source code files, or
-        * a ``count_lines()`` *task* which will count the number of lines in any file or
-        * an ``align_dna()`` *task* which will align the DNA of many chromosomes.
-
-
-.. index::
-    pair: one to one @transform; Tutorial
-
-******************************************************************************
-:ref:`@transform <decorators.transform>` is a 1 to 1 operation
-******************************************************************************
-
-
-    ``@transform`` is a 1:1 operation because for each input, it generates one output.
-
-    .. image:: ../../images/transform_1_to_1_example.png
-       :scale: 50
-
-
-    This is obvious when you count the number of jobs at each step. In our example pipeline, there are always
-    three jobs moving through in step at each stage (:term:`task`).
-
-    Each **Input** or **Output** is not limited, however, to a single filename. Each job can accept, for example,
-    a pair of files as its **Input**, or generate more than one file or a dictionary or numbers as its **Output**.
-
-    When each job outputs a pair of files, this does not generate two jobs downstream. It just means that the successive
-    :term:`task` in the pipeline will receive a list or tuple of files as its input parameter.
-
-    .. note::
-
-        The different sort of decorators in Ruffus determine the *topology* of your pipeline,
-        i.e. how the jobs from different tasks are linked together seamlessly.
-
-        :ref:`@transform <decorators.transform>` always generates one **Output** for one **Input**.
-
-        In the later parts of the tutorial, we will encounter more decorators which can *split up*, or *join together* or *group* inputs.
-
-        In other words, using other decorators **Input** and **Output**  can have **many to one**, **many to many** etc. relationships.
-
-=======================================
-A pair of files as the **Input**
-=======================================
-
-    Let us rewrite our previous example so that the **Input** of the first task
-    are `matching pairs  <http://en.wikipedia.org/wiki/DNA_sequencing_theory#Pairwise_end-sequencing>`__
-    of DNA sequence files, processed in tandem.
-
-
-        .. code-block:: python
-            :emphasize-lines: 6-8,17-19,29-31
-
-            from ruffus import *
-
-            starting_files = [("a.1.fastq", "a.2.fastq"),
-                              ("a.1.fastq", "a.2.fastq"),
-                              ("a.1.fastq", "a.2.fastq")]
-
-            #
-            #   STAGE 1 fasta->sam
-            #
-            @transform(starting_files,                     # Input = starting files
-                        suffix(".1.fastq"),                #         suffix = .1.fastq
-                        ".sam")                            # Output  suffix = .sam
-            def map_dna_sequence(input_files,
-                                output_file):
-                # remember there are two input files now
-                ii1 = open(input_files[0])
-                ii2 = open(input_files[1])
-                oo = open(output_file, "w")
-
-
-    The only changes are to the first task:
-
-        .. code-block:: pycon
-
-            pipeline_run()
-                Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed
-                Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed
-                Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed
-            Completed Task = map_dna_sequence
-
-
-    :ref:`suffix <decorators.suffix>` always matches only the first file name in each **Input**.
-
-.. index::
-    pair: input / output parameters; Tutorial
-
-************************************
-**Input** and **Output** parameters
-************************************
-
-    **Ruffus** chains together different tasks by taking the **Output** from one job
-    and plugging it automatically as the **Input** of the next.
-
-    The first two parameters of each job are the **Input** and **Output** parameters respectively.
-
-    In the above example, we have:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run()
-                Job  = [a.bam -> a.statistics, use_linear_model] completed
-                Job  = [b.bam -> b.statistics, use_linear_model] completed
-                Job  = [c.bam -> c.statistics, use_linear_model] completed
-            Completed Task = summarise_bam_file
-
-
-
-        .. table:: Parameters for ``summarise_bam_file()``
-
-           ================   ====================  =============================================
-           **Inputs**           **Outputs**             **Extra**
-           ================   ====================  =============================================
-           ``"a.bam"``         ``"a.statistics"``    ``"use_linear_model"``
-           ``"b.bam"``         ``"b.statistics"``    ``"use_linear_model"``
-           ``"c.bam"``         ``"c.statistics"``    ``"use_linear_model"``
-           ================   ====================  =============================================
-
-
-
-    **Extra** parameters are for the consumption of ``summarise_bam_file()`` and will not passed to the next task.
-
-    Ruffus was designed for pipelines which save intermediate data in files. This is not
-    compulsory but saving your data in files at each step provides many advantages:
-
-        #. Ruffus can use file system time stamps to check if your pipeline is up to date
-        #. Your data is persistent across runs
-        #. This is a good way to pass large amounts of data across processes and computational nodes
-
-    Nevertheless, *all* the :term:`task` parameters can include anything which suits your workflow, from lists of files, to numbers,
-    sets or tuples. *Ruffus* imposes few constraints on what *you*
-    would like to send to each stage of your pipeline.
-
-
-    *Ruffus* does, however, assume that if the **Input** and **Output** parameter contains strings, these will be interpreted as file names
-    required by and produced by that job. As we shall see, the modification times of these file names
-    indicate whether that part of the pipeline is up to date or needs to be rerun.
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/transform_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/transform_code.txt
deleted file mode 100644
index 2f2457d..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/transform_code.txt
+++ /dev/null
@@ -1,99 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.transform.code:
-
-##############################################################################################################
-|new_manual.introduction.chapter_num|: Python Code for Transforming data in a pipeline with ``@transform``
-##############################################################################################################
-
-.. seealso::
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@transform syntax in detail <decorators.transform>`
-    * Back to |new_manual.transform.chapter_num|: :ref:`Transforming data in a pipeline with @transform <new_manual.transform>`
-
-*******************************************
-Your first Ruffus script
-*******************************************
-
-    .. code-block:: python
-
-        #
-        #   The starting data files would normally exist beforehand!
-        #       We create some empty files for this example
-        #
-        starting_files = [("a.1.fastq", "a.2.fastq"),
-                          ("b.1.fastq", "b.2.fastq"),
-                          ("c.1.fastq", "c.2.fastq")]
-
-
-        for ff_pair in starting_files:
-            open(ff_pair[0], "w")
-            open(ff_pair[1], "w")
-
-
-        from ruffus import *
-
-        #
-        #   STAGE 1 fasta->sam
-        #
-        @transform(starting_files,                     # Input = starting files
-                   suffix(".1.fastq"),                 #         suffix = .1.fastq
-                   ".sam")                             # Output  suffix = .sam
-        def map_dna_sequence(input_files,
-                            output_file):
-            # remember there are two input files now
-            ii1 = open(input_files[0])
-            ii2 = open(input_files[1])
-            oo = open(output_file, "w")
-
-        #
-        #   STAGE 2 sam->bam
-        #
-        @transform(map_dna_sequence,                   # Input = previous stage
-                    suffix(".sam"),                    #         suffix = .sam
-                    ".bam")                            # Output  suffix = .bam
-        def compress_sam_file(input_file,
-                              output_file):
-            ii = open(input_file)
-            oo = open(output_file, "w")
-
-        #
-        #   STAGE 3 bam->statistics
-        #
-        @transform(compress_sam_file,                  # Input = previous stage
-                    suffix(".bam"),                    #         suffix = .bam
-                    ".statistics",                     # Output  suffix = .statistics
-                    "use_linear_model")                # Extra statistics parameter
-        def summarise_bam_file(input_file,
-                               output_file,
-                               extra_stats_parameter):
-            """
-            Sketch of real analysis function
-            """
-            ii = open(input_file)
-            oo = open(output_file, "w")
-
-        pipeline_run()
-
-
-************************************
-Resulting Output
-************************************
-    ::
-
-            >>> pipeline_run()
-                Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed
-                Job  = [[b.1.fastq, b.2.fastq] -> b.sam] completed
-                Job  = [[c.1.fastq, c.2.fastq] -> c.sam] completed
-            Completed Task = map_dna_sequence
-                Job  = [a.sam -> a.bam] completed
-                Job  = [b.sam -> b.bam] completed
-                Job  = [c.sam -> c.bam] completed
-            Completed Task = compress_sam_file
-                Job  = [a.bam -> a.statistics, use_linear_model] completed
-                Job  = [b.bam -> b.statistics, use_linear_model] completed
-                Job  = [c.bam -> c.statistics, use_linear_model] completed
-            Completed Task = summarise_bam_file
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/transform_in_parallel.txt b/doc/_build/html/_sources/tutorials/new_tutorial/transform_in_parallel.txt
deleted file mode 100644
index 57d0337..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/transform_in_parallel.txt
+++ /dev/null
@@ -1,394 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. index::
-    pair: transforming in parallel; Tutorial
-
-.. _new_manual.transform_in_parallel:
-
-######################################################################################################
-|new_manual.transform_in_parallel.chapter_num|: More on ``@transform``-ing data
-######################################################################################################
-
-
-.. seealso::
-
-   * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-   * :ref:`@transform <decorators.transform>`  syntax
-
-.. note::
-
-    Remember to look at the example code:
-
-    * :ref:`new_manual.transform_in_parallel.code`
-
-***************************************
-Review
-***************************************
-    .. image:: ../../images/theoretical_pipeline_schematic.png
-       :scale: 50
-
-    Computational pipelines transform your data in stages until the final result is produced.
-    *Ruffus* automates the plumbing in your pipeline. You supply the python functions which perform the data transformation,
-    and tell *Ruffus* how these pipeline stages or :term:`task` functions are connected together.
-
-    .. note::
-
-        **The best way to design a pipeline is to:**
-
-            * **write down the file names of the data as it flows across your pipeline**
-            * **write down the names of functions which transforms the data at each stage of the pipeline.**
-
-
-    :ref:`new_manual.introduction` described the bare bones of a simple *Ruffus* pipeline.
-
-    Using the *Ruffus* :ref:`@transform <decorators.transform>` decorator, we were able to
-    specify the data files moving through our pipeline so that our specified task functions
-    could be invoked.
-
-    This may seem like a lot of effort and complication for something so simple: a couple of
-    simple python function calls we could have invoked ourselves.
-    However, By letting *Ruffus* manage your pipeline parameters, you will get the following features
-    for free:
-
-        #. Only out-of-date parts of the pipeline will be re-run
-        #. Multiple jobs can be run in parallel (on different processors if possible)
-        #. Pipeline stages can be chained together automatically. This means you can apply your
-           pipeline just as easily to 1000 files as to 3.
-
-
-
-************************************
-Running pipelines in parallel
-************************************
-    Even though three sets of files have been specified for our initial pipeline, and they can be
-    processed completely independently, by default  *Ruffus* runs each of them serially in succession.
-
-    To ask *Ruffus* to run them in parallel, all you have to do is to add a ``multiprocess`` parameter to ``pipeline_run``:
-
-        ::
-
-            >>> pipeline_run(multiprocess = 5)
-
-    In this case, we are telling *Ruffus* to run a maximum of 5 jobs at the same time. Since we only have
-    three sets of data, that is as much parallelism as we are going to get...
-
-
-
-.. _new_manual.only_rerun_out_of_date:
-
-**************************************************
-Up-to-date jobs are not re-run unnecessarily
-**************************************************
-
-    A job will be run only if the output file timestamps are out of date.
-    If you ran our example code a second time, nothing would happen because all the work is already complete.
-
-    We can check the details by asking *Ruffus* for more ``verbose`` output
-
-        ::
-
-            >>> pipeline_run(verbose = 4)
-              Task = map_dna_sequence
-                All jobs up to date
-              Task = compress_sam_file
-                All jobs up to date
-              Task = summarise_bam_file
-                All jobs up to date
-
-
-    Nothing happens because:
-        * ``a.sam`` was created later than ``a.1.fastq`` and ``a.2.fastq``, and
-        * ``a.bam`` was created later than ``a.sam`` and
-        * ``a.statistics`` was created later than ``a.bam``.
-
-    and so on...
-
-
-    Let us see what happens if we recreated the file ``a.1.fastq`` so that it appears as if 1 out of the original data files is out of date
-        ::
-
-            open("a.1.fastq", "w")
-            pipeline_run(multiprocess = 5)
-
-
-    The up to date jobs are cleverly ignored and only the out of date files are reprocessed.
-
-        .. code-block:: pycon
-           :emphasize-lines: 3,4,7,8,11,12
-
-            >>> open("a.1.fastq", "w")
-            >>> pipeline_run(verbose=2)
-                Job  = [[b.1.fastq, b.2.fastq] -> b.sam] # unnecessary: already up to date
-                Job  = [[c.1.fastq, c.2.fastq] -> c.sam] # unnecessary: already up to date
-                Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed
-            Completed Task = map_dna_sequence
-                Job  = [b.sam -> b.bam] # unnecessary: already up to date
-                Job  = [c.sam -> c.bam] # unnecessary: already up to date
-                Job  = [a.sam -> a.bam] completed
-            Completed Task = compress_sam_file
-                Job  = [b.bam -> b.statistics, use_linear_model] # unnecessary: already up to date
-                Job  = [c.bam -> c.statistics, use_linear_model] # unnecessary: already up to date
-                Job  = [a.bam -> a.statistics, use_linear_model] completed
-            Completed Task = summarise_bam_file
-
-
-
-
-.. index::
-    pair: output_from; referring to functions before they are defined
-    pair: output_from; defining tasks out of order
-
-.. _new_manual.output_from:
-
-***************************************
-Defining pipeline tasks out of order
-***************************************
-
-    The examples so far assumes that all your pipelined tasks are defined in order.
-    (``first_task`` before ``second_task``). This is usually the most sensible way to arrange your code.
-
-    If you wish to refer to tasks which are not yet defined, you can do so by quoting the function name as a string and wrapping
-    it with the :ref:`indicator class <decorators.indicator_objects>` :ref:`output_from(...) <decorators.output_from>` so that *Ruffus*
-    knowns this is a :term:`task` name, not a file name
-
-        .. code-block:: python
-           :emphasize-lines: 5
-
-            #---------------------------------------------------------------
-            #
-            #   second task
-            #
-            #   task name string wrapped in output_from(...)
-            @transform(output_from("first_task"), suffix(".output.1"), ".output2")
-            def second_task(input_files, output_file):
-                with open(output_file, "w"): pass
-
-
-            #---------------------------------------------------------------
-            #
-            #   first task
-            #
-            @transform(first_task_params, suffix(".start"),
-                                    [".output.1",
-                                     ".output.extra.1"],
-                                   "some_extra.string.for_example", 14)
-            def first_task(input_files, output_file_pair,
-                            extra_parameter_str, extra_parameter_num):
-                for output_file in output_file_pair:
-                    with open(output_file, "w"):
-                        pass
-
-
-            #---------------------------------------------------------------
-            #
-            #       Run
-            #
-            pipeline_run([second_task])
-
-    You can also refer to tasks (functions) in other modules, in which case the full
-    qualified name must be used:
-
-        ::
-
-            @transform(output_from("other_module.first_task"), suffix(".output.1"), ".output2")
-            def second_task(input_files, output_file):
-                pass
-
-
-
-.. index::
-    pair: @transform; multiple dependencies
-
-.. _new_manual.transform.multiple_dependencies:
-
-***************************************
-Multiple dependencies
-***************************************
-
-    Each task can depend on more than one antecedent simply by chaining to a list in :ref:`@transform <decorators.transform>`
-
-        .. code-block:: python
-           :emphasize-lines: 2
-
-            #
-            # third_task depends on both first_task() and second_task()
-            #
-            @transform([first_task, second_task], suffix(".output.1"), ".output2")
-            def third_task(input_files, output_file):
-                with open(output_file, "w"): pass
-
-
-    ``third_task()`` depends on and follows both ``first_task()`` and ``second_task()``. However, these latter two tasks are independent of each other
-    and can and will run in parallel. This can be clearly shown for our example if we added a little randomness to the run time of each job:
-
-        .. code-block:: python
-
-            time.sleep(random.random())
-
-    The execution of ``first_task()`` and ``second_task()`` jobs will be interleaved and they finish in no particular order:
-
-        .. code-block:: pycon
-
-            >>> pipeline_run([third_task], multiprocess = 6)
-                Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Completed Task = second_task
-                Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
-
-
-    .. note::
-
-        See the :ref:`example code <new_manual.transform.multiple_dependencies.code>`
-
-
-.. index::
-    pair: @follow; imposing order with
-
-.. _new_manual.follows:
-
-***************************************
-:ref:`@follows <decorators.follows>`
-***************************************
-
-    If there is some extrinsic reason one non-dependent task has to precede the other, then this can be specified explicitly using :ref:`@follows <decorators.follows>`:
-
-
-        .. code-block:: python
-           :emphasize-lines: 2
-
-            #
-            #   @follows specifies a preceding task
-            #
-            @follows("first_task")
-            @transform(second_task_params, suffix(".start"),
-                                    [".output.1",
-                                     ".output.extra.1"],
-                                   "some_extra.string.for_example", 14)
-            def second_task(input_files, output_file_pair,
-                            extra_parameter_str, extra_parameter_num):
-
-
-    :ref:`@follows <decorators.follows>` specifies either a preceding task (e.g. ``first_task``), or if
-    it has not yet been defined, the name (as a string) of a task function (e.g. ``"first_task"``).
-
-    With the addition of :ref:`@follows <decorators.follows>`, all the jobs
-    of ``second_task()`` start *after* those from ``first_task()`` have finished:
-
-        .. code-block:: pycon
-
-
-            >>> pipeline_run([third_task], multiprocess = 6)
-                Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Completed Task = first_task
-                Job  = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Completed Task = second_task
-
-
-
-.. index::
-    single: @follows; mkdir (Manual)
-    single: mkdir; @follows (Manual)
-
-.. _new_manual.follows.mkdir:
-
-************************************************************************************************************************************************************
-Making directories automatically with :ref:`@follows <decorators.follows>` and  :ref:`mkdir <decorators.mkdir>`
-************************************************************************************************************************************************************
-
-    :ref:`@follows <decorators.follows>` is also useful for making sure one or more destination directories
-    exist before a task is run.
-
-    *Ruffus* provides special syntax to support this, using the special
-    :ref:`mkdir <decorators.mkdir>` indicator class. For example:
-
-        .. code-block:: python
-            :emphasize-lines: 2
-
-            #
-            #   @follows specifies both a preceding task and a directory name
-            #
-            @follows("first_task", mkdir("output/results/here"))
-            @transform(second_task_params, suffix(".start"),
-                                    [".output.1",
-                                     ".output.extra.1"],
-                                   "some_extra.string.for_example", 14)
-            def second_task(input_files, output_file_pair,
-                            extra_parameter_str, extra_parameter_num):
-
-    Before ``second_task()`` is run, the ``output/results/here`` directory will be created if necessary.
-
-
-.. index::
-    pair: inputs parameters; globs
-    pair: globs in input parameters; Tutorial
-
-.. _new_manual.globs_as_input:
-
-
-******************************************************************************
-Globs in the **Input** parameter
-******************************************************************************
-
-    * As a syntactic convenience, *Ruffus* also allows you to specify a |glob|_ pattern (e.g. ``*.txt``) in the
-      **Input** parameter.
-    * |glob|_ patterns will be automatically specify all matching file names as the **Input**.
-    * Any strings within **Input** which contain the letters: ``*?[]`` will be treated as a |glob|_ pattern.
-
-    The first function in our initial *Ruffus* pipeline example could have been written as:
-
-        .. code-block:: python
-            :emphasize-lines: 4
-
-            #
-            #   STAGE 1 fasta->sam
-            #
-            @transform("*.fasta",                          # Input = glob
-                        suffix(".fasta"),                  #         suffix = .fasta
-                        ".sam")                            # Output  suffix = .sam
-            def map_dna_sequence(input_file,
-                                output_file):
-                ""
-
-
-.. index::
-    pair: Mixing tasks, globs and file names; Tutorial
-
-
-******************************************************************************
-Mixing Tasks and Globs in the **Input** parameter
-******************************************************************************
-
-    |glob|_ patterns, references to tasks and file names strings
-    can be mixed freely in (nested) python lists and tuples in the **Input** parameter.
-
-    For example, a task function can chain to the **Output** from multiple upstream tasks:
-
-        .. code-block:: python
-
-            @transform([task1, task2,                      # Input = multiple tasks
-                        "aa*.fasta",                               + all files matching glob
-                        "zz.fasta"]                                + file name
-                        suffix(".fasta"),                  #         suffix = .fasta
-                        ".sam")                            # Output  suffix = .sam
-            def map_dna_sequence(input_file,
-                                output_file):
-                ""
-
-    In all cases, *Ruffus* tries to do the right thing, and to make the simple or
-    obvious case require the simplest, least onerous syntax.
-
-    If sometimes *Ruffus* does not behave the way you expect, please write to the authors:
-    it may be a bug!
-
-    :ref:`new_manual.pipeline_printout`  and
-    :ref:`new_manual.cmdline` will show you how to
-    to make sure that your intentions are reflected in *Ruffus* code.
-
diff --git a/doc/_build/html/_sources/tutorials/new_tutorial/transform_in_parallel_code.txt b/doc/_build/html/_sources/tutorials/new_tutorial/transform_in_parallel_code.txt
deleted file mode 100644
index 3160e2e..0000000
--- a/doc/_build/html/_sources/tutorials/new_tutorial/transform_in_parallel_code.txt
+++ /dev/null
@@ -1,366 +0,0 @@
-.. include:: ../../global.inc
-.. include:: manual_chapter_numbers.inc
-
-.. _new_manual.transform_in_parallel.code:
-
-######################################################################################################
-|new_manual.transform_in_parallel.chapter_num|: Python Code for More on ``@transform``-ing data
-######################################################################################################
-
-.. seealso::
-
-
-    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`
-    * :ref:`@transform syntax in detail <decorators.transform>`
-    * Back to |new_manual.transform_in_parallel.chapter_num|: :ref:`More on @transform-ing data and @originate <new_manual.transform_in_parallel>`
-
-*******************************************
-Producing several items / files per job
-*******************************************
-
-    ::
-
-        from ruffus import *
-
-        #---------------------------------------------------------------
-        #   Create pairs of input files
-        #
-        first_task_params = [
-                             ['job1.a.start', 'job1.b.start'],
-                             ['job2.a.start', 'job2.b.start'],
-                             ['job3.a.start', 'job3.b.start'],
-                            ]
-
-        for input_file_pairs in first_task_params:
-            for input_file in input_file_pairs:
-                open(input_file, "w")
-
-
-        #---------------------------------------------------------------
-        #
-        #   first task
-        #
-        @transform(first_task_params, suffix(".start"),
-                                [".output.1",
-                                 ".output.extra.1"],
-                               "some_extra.string.for_example", 14)
-        def first_task(input_files, output_file_pair,
-                        extra_parameter_str, extra_parameter_num):
-            for output_file in output_file_pair:
-                with open(output_file, "w"):
-                    pass
-
-
-        #---------------------------------------------------------------
-        #
-        #   second task
-        #
-        @transform(first_task, suffix(".output.1"), ".output2")
-        def second_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-
-        #---------------------------------------------------------------
-        #
-        #       Run
-        #
-        pipeline_run([second_task])
-
-=============================
-Resulting Output
-=============================
-
-        ::
-
-            >>> pipeline_run([second_task])
-                Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Completed Task = first_task
-                Job  = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed
-                Job  = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed
-                Job  = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed
-            Completed Task = second_task
-
-
-
-*******************************************
-Defining tasks function out of order
-*******************************************
-
-    .. code-block:: python
-       :emphasize-lines: 22
-
-        from ruffus import *
-
-        #---------------------------------------------------------------
-        #   Create pairs of input files
-        #
-        first_task_params = [
-                             ['job1.a.start', 'job1.b.start'],
-                             ['job2.a.start', 'job2.b.start'],
-                             ['job3.a.start', 'job3.b.start'],
-                            ]
-
-        for input_file_pairs in first_task_params:
-            for input_file in input_file_pairs:
-                open(input_file, "w")
-
-
-
-        #---------------------------------------------------------------
-        #
-        #   second task defined first
-        #
-        #   task name string wrapped in output_from(...)
-        @transform(output_from("first_task"), suffix(".output.1"), ".output2")
-        def second_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-
-        #---------------------------------------------------------------
-        #
-        #   first task
-        #
-        @transform(first_task_params, suffix(".start"),
-                                [".output.1",
-                                 ".output.extra.1"],
-                               "some_extra.string.for_example", 14)
-        def first_task(input_files, output_file_pair,
-                        extra_parameter_str, extra_parameter_num):
-            for output_file in output_file_pair:
-                with open(output_file, "w"):
-                    pass
-
-
-        #---------------------------------------------------------------
-        #
-        #       Run
-        #
-        pipeline_run([second_task])
-
-
-=============================
-Resulting Output
-=============================
-
-        .. code-block:: pycon
-
-            >>> pipeline_run([second_task])
-                Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
-                Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Completed Task = first_task
-                Job  = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed
-                Job  = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed
-                Job  = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed
-            Completed Task = second_task
-
-.. _new_manual.transform.multiple_dependencies.code:
-
-*******************************************
-Multiple dependencies
-*******************************************
-
-    .. code-block:: python
-       :emphasize-lines: 58
-
-        from ruffus import *
-        import time
-        import random
-
-        #---------------------------------------------------------------
-        #   Create pairs of input files
-        #
-        first_task_params = [
-                             ['job1.a.start', 'job1.b.start'],
-                             ['job2.a.start', 'job2.b.start'],
-                             ['job3.a.start', 'job3.b.start'],
-                            ]
-        second_task_params = [
-                             ['job4.a.start', 'job4.b.start'],
-                             ['job5.a.start', 'job5.b.start'],
-                             ['job6.a.start', 'job6.b.start'],
-                            ]
-
-        for input_file_pairs in first_task_params + second_task_params:
-            for input_file in input_file_pairs:
-                open(input_file, "w")
-
-
-
-        #---------------------------------------------------------------
-        #
-        #   first task
-        #
-        @transform(first_task_params, suffix(".start"),
-                                [".output.1",
-                                 ".output.extra.1"],
-                               "some_extra.string.for_example", 14)
-        def first_task(input_files, output_file_pair,
-                        extra_parameter_str, extra_parameter_num):
-            for output_file in output_file_pair:
-                with open(output_file, "w"):
-                    pass
-            time.sleep(random.random())
-
-
-
-        #---------------------------------------------------------------
-        #
-        #   second task
-        #
-        @transform(second_task_params, suffix(".start"),
-                                [".output.1",
-                                 ".output.extra.1"],
-                               "some_extra.string.for_example", 14)
-        def second_task(input_files, output_file_pair,
-                        extra_parameter_str, extra_parameter_num):
-            for output_file in output_file_pair:
-                with open(output_file, "w"):
-                    pass
-            time.sleep(random.random())
-
-
-        #---------------------------------------------------------------
-        #
-        #   third task
-        #
-        #       depends on both first_task() and second_task()
-        @transform([first_task, second_task], suffix(".output.1"), ".output2")
-        def third_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-
-        #---------------------------------------------------------------
-        #
-        #       Run
-        #
-        pipeline_run([third_task], multiprocess = 6)
-
-=============================
-Resulting Output
-=============================
-
-    .. code-block:: pycon
-
-        >>> pipeline_run([third_task], multiprocess = 6)
-            Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Job  = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Job  = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Job  = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed
-        Completed Task = second_task
-            Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
-        Completed Task = first_task
-            Job  = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed
-            Job  = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed
-            Job  = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed
-            Job  = [[job4.a.output.1, job4.a.output.extra.1] -> job4.a.output2] completed
-            Job  = [[job5.a.output.1, job5.a.output.extra.1] -> job5.a.output2] completed
-            Job  = [[job6.a.output.1, job6.a.output.extra.1] -> job6.a.output2] completed
-        Completed Task = third_task
-
-
-*******************************************
-Multiple dependencies after @follows
-*******************************************
-
-    .. code-block:: python
-        :emphasize-lines: 31
-
-        from ruffus import *
-        import time
-        import random
-
-        #---------------------------------------------------------------
-        #   Create pairs of input files
-        #
-        first_task_params = [
-                             ['job1.a.start', 'job1.b.start'],
-                             ['job2.a.start', 'job2.b.start'],
-                             ['job3.a.start', 'job3.b.start'],
-                            ]
-        second_task_params = [
-                             ['job4.a.start', 'job4.b.start'],
-                             ['job5.a.start', 'job5.b.start'],
-                             ['job6.a.start', 'job6.b.start'],
-                            ]
-
-        for input_file_pairs in first_task_params + second_task_params:
-            for input_file in input_file_pairs:
-                open(input_file, "w")
-
-
-
-        #---------------------------------------------------------------
-        #
-        #   first task
-        #
-        @transform(first_task_params, suffix(".start"),
-                                [".output.1",
-                                 ".output.extra.1"],
-                               "some_extra.string.for_example", 14)
-        def first_task(input_files, output_file_pair,
-                        extra_parameter_str, extra_parameter_num):
-            for output_file in output_file_pair:
-                with open(output_file, "w"):
-                    pass
-            time.sleep(random.random())
-
-
-
-        #---------------------------------------------------------------
-        #
-        #   second task
-        #
-        @follows("first_task")
-        @transform(second_task_params, suffix(".start"),
-                                [".output.1",
-                                 ".output.extra.1"],
-                               "some_extra.string.for_example", 14)
-        def second_task(input_files, output_file_pair,
-                        extra_parameter_str, extra_parameter_num):
-            for output_file in output_file_pair:
-                with open(output_file, "w"):
-                    pass
-            time.sleep(random.random())
-
-
-        #---------------------------------------------------------------
-        #
-        #   third task
-        #
-        #       depends on both first_task() and second_task()
-        @transform([first_task, second_task], suffix(".output.1"), ".output2")
-        def third_task(input_files, output_file):
-            with open(output_file, "w"): pass
-
-
-        #---------------------------------------------------------------
-        #
-        #       Run
-        #
-        pipeline_run([third_task], multiprocess = 6)
-
-=======================================================================================
-Resulting Output: ``first_task`` completes before ``second_task``
-=======================================================================================
-
-    .. code-block:: pycon
-
-        >>> pipeline_run([third_task], multiprocess = 6)
-            Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
-        Completed Task = first_task
-            Job  = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Job  = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed
-            Job  = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed
-        Completed Task = second_task
-            Job  = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed
-            Job  = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed
-            Job  = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed
-            Job  = [[job4.a.output.1, job4.a.output.extra.1] -> job4.a.output2] completed
-            Job  = [[job5.a.output.1, job5.a.output.extra.1] -> job5.a.output2] completed
-            Job  = [[job6.a.output.1, job6.a.output.extra.1] -> job6.a.output2] completed
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/simple_tutorial.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/simple_tutorial.txt
deleted file mode 100644
index 113e126..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/simple_tutorial.txt
+++ /dev/null
@@ -1,71 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial:
-
-
-############################################################
-A simple tutorial: 8 steps to *Ruffus*
-############################################################
-
-***************************************
-Table of Contents
-***************************************
-
-============
-Features
-============
-
-The **Ruffus** provides automatic support for
-
-        * Managing dependencies
-        * Parallel jobs
-        * Re-starting from arbitrary points, especially after errors
-        * Display of the pipeline as a flowchart
-        * Reporting
-
-
-    | This tutorial has seven steps which cover all the core functionality of *Ruffus*.
-    | Don't worry if steps 1 and 2 seem a bit slow: Once you get used to **Ruffus**
-      steps 4-8 will be a breeze.
-
-    You can click on "previous" and "next" at the top and bottom of each page to
-    navigate through the tutorial.
-
-
-============================
-The first steps (1-4)
-============================
-
-    The first half of the tutorial will show you how to:
-
-    1. :ref:`Chain tasks (functions) together into a pipeline <Simple_Tutorial_1st_step>`
-    2. :ref:`Provide parameters to run jobs in parallel <Simple_Tutorial_2nd_step>`
-    3. :ref:`Tracing through your new pipeline <Simple_Tutorial_3rd_step>`
-    4. :ref:`Using flowcharts <Simple_Tutorial_4th_step_graphical>`
-
-============================
-A worked example (steps 5-8)
-============================
-
-    The second half of the tutorial is a worked example to calculate
-    the sample variance of 10,000 random numbers. This shows you how to:
-
-    5. :ref:`Split up a large problem into smaller chunks <Simple_Tutorial_5th_step>`
-    6. :ref:`Calculate partial solutions in parallel <Simple_Tutorial_6th_step>`
-    7. :ref:`Re-combine the partial solutions into the final result <Simple_Tutorial_7th_step>`
-    8. :ref:`Automatically signal the completion of each step of our pipeline <Simple_Tutorial_8th_step>`
-
-
-    This covers the core functionality of *Ruffus*.
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/simple_tutorial_code.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/simple_tutorial_code.txt
deleted file mode 100644
index b562cd7..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/simple_tutorial_code.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_code:
-
-
-############################################################
-Code for the simple tutorial: 8 steps to *Ruffus*
-############################################################
-
-    * :ref:`A simple tutorial<Simple_Tutorial>`
-
-
-***************************************
-Table of Contents
-***************************************
-
-
-   :ref:`Chain tasks (functions) together into a pipeline <Simple_Tutorial_1st_step>`
-   :ref:`Provide parameters to run jobs in parallel <Simple_Tutorial_2nd_step>`
-   :ref:`Tracing through your new pipeline <Simple_Tutorial_3rd_step>`
-   :ref:`Using flowcharts  <Simple_Tutorial_4th_step_graphical>`
-   :ref:`Split up a large problem into smaller chunks <Simple_Tutorial_5th_step>`
-   :ref:`Calculate partial solutions in parallel <Simple_Tutorial_6th_step>`
-   :ref:`Re-combine the partial solutions into the final result <Simple_Tutorial_7th_step>`
-   :ref:`Automatically signal the completion of each step of our pipeline <Simple_Tutorial_8th_step>`
-
-
-
-
-
-
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step1_follows.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step1_follows.txt
deleted file mode 100644
index 21a4ae1..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step1_follows.txt
+++ /dev/null
@@ -1,258 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_1st_step:
-    
-    * :ref:`Simple tutorial overview <Simple_Tutorial>` 
-
-###################################################################
-Step 1: An introduction to Ruffus pipelines
-###################################################################
-
-************************************
-Overview
-************************************
-
-    .. raw:: html
-
-        <svg version="1.0" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0" y="0"
-            width="731.3pt"
-            height="83pt"
-            viewBox="0 0 731.3 83">
-          <defs id="defs3287">
-            <marker refX="0" refY="0" orient="auto" id="Arrow2Mend" style="overflow:visible">
-              <path d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z" transform="scale(-0.6,-0.6)" id="path4124" style="fill-rule:evenodd;stroke-width:0.625;stroke-linejoin:round" />
-            </marker>
-            <marker refX="0" refY="0" orient="auto" id="Arrow2Lend" style="overflow:visible">
-              <path d="M 8.7185878,4.0337352 -2.2072895,0.01601326 8.7185884,-4.0017078 c -1.7454984,2.3720609 -1.7354408,5.6174519 -6e-7,8.035443 z" transform="matrix(-1.1,0,0,-1.1,-1.1,0)" id="path4118" style="fill-rule:evenodd;stroke-width:0.625;stroke-linejoin:round" />
-            </marker>
-            <marker refX="0" refY="0" orient="auto" id="Arrow1Lend" style="overflow:visible">
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-
-    Computational pipelines transform your data in stages until the final result is produced. One easy way to understand pipelines is by imagining your data flowing across a series of pipes until it reaches its final destination. Even quite complicated processes can be simplified if we broke things down into simple stages. Of course, it helps if we can visualise the whole process.
-
-    Ruffus is a way of automating the plumbing in your pipeline: You supply the python functions which perform the data transformation, and tell Ruffus how these pipeline ``task`` functions are connected up. Ruffus will make sure that the right data flows down your pipeline in the right way at the right time.
-
-    
-    .. note::
-        
-        Ruffus refers to each stage of your pipeline as a :term:`task`.
-
-***************************************
-A gentle introduction to Ruffus syntax
-***************************************
-
-    | Let us start with the usual "Hello World" programme.
-    | We have the following two python functions which
-      we would like to turn into an automatic pipeline:
-      
-    
-        ::
-        
-            def first_task():
-                print "Hello "
-        
-            def second_task():
-                print "world"
-
-    
-    The simplest **Ruffus** pipeline would look like this:
-    
-        .. ::
-        
-            from ruffus import *
-            
-            def first_task():
-                print "Hello "
-        
-            @follows(first_task)
-            def second_task():
-                print "world"
-    
-            pipeline_run([second_task])
-
-
-    .. raw:: html
-
-        <svg version="1.0" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0" y="0"
-            width="411pt"
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-        <text x="0" y="33" id="text6715" xml:space="preserve" />
-        <text x="0" y="52" id="text6717" xml:space="preserve"><tspan id="tspan6719" style="font-weight:bold;fill:#008000">def</tspan> <tspan id="tspan6721" style="font-weight:bold;fill:#0060b0">first_task</tspan>():</text>
-        <text x="0" y="71" id="text6723" xml:space="preserve">    <tspan id="tspan6725" style="font-weight:bold;fill:#008000">print</tspan> "Hello "</text>
-        <text x="0" y="90" id="text6727" xml:space="preserve" />
-        <text x="0" y="109" id="text6729" xml:space="preserve"><tspan id="tspan6731" style="font-weight:bold;fill:#505050">@follows</tspan>(first_task)</text>
-        <text x="0" y="128" id="text6733" xml:space="preserve"><tspan id="tspan6735" style="font-weight:bold;fill:#008000">def</tspan> <tspan id="tspan6737" style="font-weight:bold;fill:#0060b0">second_task</tspan>():</text>
-        <text x="0" y="147" id="text6739" xml:space="preserve">    <tspan id="tspan6741" style="font-weight:bold;fill:#008000">print</tspan> "world"</text>
-        <text x="0" y="166" id="text6743" xml:space="preserve" />
-        <text x="0" y="185" id="text6745" xml:space="preserve">pipeline_run([second_task])</text>
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-
-    
-    The functions which do the actual work of each stage of the pipeline remain unchanged.
-    The role of **Ruffus** is to make sure these functions are called in the right order, 
-    with the right parameters, running in parallel using multiprocessing if desired.
-        
-    There are three simple parts to building a **ruffus** pipeline
-
-        #. importing ruffus
-        #. "Decorating" functions which are part of the pipeline
-        #. Running the pipeline!
-    
-.. index:: 
-    pair: decorators; Tutorial
-    
-
-****************************
-"Decorators"
-****************************
-
-    You need to tag or :term:`decorator` existing code to tell **Ruffus** that they are part
-    of the pipeline.
-    
-    .. note::
-        
-        python :term:`decorator`\ s are ways to tag or mark out functions. 
-
-        They start with a ``@`` prefix and take a number of parameters in parenthesis.
-
-        .. :: .. image:: ../../images/simple_tutorial_decorator_syntax.png
-
-        .. raw:: html
-
-            <svg version="1.0" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0" y="0"
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-                <text transform="matrix(1 0 0 1 14.5 33.6177)"><tspan x="0" y="0" font-family="'Courier'" font-weight="bold"  font-size="12">@follows</tspan><tspan x="57.609" y="0" font-family="'Courier'" font-size="12">(first_task)</tspan><tspan x="0" y="14.4" fill="#006838" font-family="'Courier'" font-weight="bold"  font-size="12">def</tspan><tspan x="21.604" y="14.4" font-family="'Courier'" font-size="12"> second_task():</tspan><tspan x="0" y="28.8" font-family="'Courier'" font-size= [...]
-                <path fill="none" stroke="#ED1C24" stroke-miterlimit="10" d="M73.25,29.762c0,4.688-3.731,8.488-8.333,8.488H18.083
-                	c-4.602,0-8.333-3.8-8.333-8.488l0,0c0-4.688,3.731-8.488,8.333-8.488h46.834C69.519,21.274,73.25,25.075,73.25,29.762L73.25,29.762
-                	z"/>
-                <g>
-                	<g>
-                		<line fill="none" stroke="#FF0000" stroke-miterlimit="10" x1="74.775" y1="20.142" x2="106" y2="7.5"/>
-                		<g>
-                			<path fill="#ED1C24" d="M71.978,21.274c1.514-0.044,3.484,0.127,4.854,0.6l-1.689-1.881l-0.095-2.526
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-                		</g>
-                	</g>
-                </g>
-                <text transform="matrix(1 0 0 1 107.75 11.5)" fill="#FF0000" " font-size="12">Decorator</text>
-                <text transform="matrix(1 0 0 1 170.75 50.75)"><tspan x="0" y="0" fill="#0000FF" font-size="12">Normal Python </tspan><tspan x="0" y="14.4" fill="#0000FF" font-size="12">Function</tspan></text>
-                <g>
-                	<line fill="#0000FF" x1="166.5" y1="46.5" x2="147" y2="46.5"/>
-                	<g>
-                		<line fill="none" stroke="#0000FF" stroke-miterlimit="10" x1="166.5" y1="46.5" x2="150.018" y2="46.5"/>
-                		<g>
-                			<path fill="#0000FF" d="M147,46.5c1.42-0.527,3.182-1.426,4.273-2.378l-0.86,2.378l0.86,2.377
-                				C150.182,47.925,148.42,47.026,147,46.5z"/>
-                		</g>
-                	</g>
-                </g>
-            </g>
-            </svg>
-                
-    The **ruffus** decorator :ref:`@follows <decorators.follows>` makes sure that
-    ``second_task`` follows ``first_task``.
-    
-
-    | Multiple :term:`decorator`\ s can be used for each :term:`task` function to add functionality
-      to *Ruffus* pipeline functions. 
-    | However, the decorated python functions can still be
-      called normally, outside of *Ruffus*.
-    | *Ruffus* :term:`decorator`\ s can be added to (stacked on top of) any function in any order.
-
-    * :ref:`More on @follows in the in the Ruffus `Manual <manual.follows>`
-    * :ref:`@follows syntax in detail <decorators.follows>`
-
-
-.. index:: 
-    pair: pipeline_run; Tutorial
-
-****************************
-Running the pipeline
-****************************
-
-    We run the pipeline by specifying the **last** stage (:term:`task` function) of your pipeline.
-    Ruffus will know what other functions this depends on, following the appropriate chain of
-    dependencies automatically, making sure that the entire pipeline is up-to-date.
-
-    Because ``second_task`` depends on ``first_task``, both functions are executed in order.
-
-        ::
-            
-            >>> pipeline_run([second_task], verbose = 1)
-        
-    Ruffus by default prints out the ``verbose`` progress through the pipelined code, 
-    interleaved with the **Hello** printed by ``first_task`` and **World** printed
-    by ``second_task``.
-    
-            
-    
-        .. ::
-            
-            >>> pipeline_run([second_task], verbose = 1)
-            Start Task = first_task
-            Hello
-                Job completed
-            Completed Task = first_task
-            Start Task = second_task
-            world
-                Job completed
-            Completed Task = second_task
-
-
-        .. raw:: html
-
-            <svg version="1.0" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0" y="0"
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-            </svg>
-    
-    
-    
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step2.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step2.txt
deleted file mode 100644
index 06c8f3b..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step2.txt
+++ /dev/null
@@ -1,517 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_2nd_step:
-
-.. index::
-    pair: @transform; Tutorial
-
-###################################################################
-Step 2: ``@transform``-ing data in a pipeline
-###################################################################
-
-   * :ref:`Simple tutorial overview <Simple_Tutorial>`
-   * :ref:`@transform syntax in detail <decorators.transform>`
-
-.. note::
-
-    Remember to look at the example code:
-
-    * :ref:`Python Code for step 2 <Simple_Tutorial_2nd_step_code>`
-
-***************************************
-Overview
-***************************************
-    .. raw:: html
-
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-
-
-    Computational pipelines transform your data in stages until the final result is produced.
-    Ruffus automates the plumbing in your pipeline. You supply the python functions which perform the data transformation,
-    and tell Ruffus how these pipeline stages or :term:`task` functions are connected together.
-
-    .. note::
-
-        **The best way to design a pipeline is to:**
-
-            * **write down the file names of the data as it flows across your pipeline**
-            * **write down the names of functions which transforms the data at each stage of the pipeline.**
-
-
-    By letting **Ruffus** manage your pipeline parameters, you will get the following features
-    for free:
-
-        #. only out-of-date parts of the pipeline will be re-run
-        #. multiple jobs can be run in parallel (on different processors if possible)
-        #. pipeline stages can be chained together automatically
-
-
-
-
-************************************
- at transform
-************************************
-    Let us start with the simplest pipeline with a single *input* data file **transform**\ed
-    into a single *output* file. We will add some arbitrary extra parameters as well.
-
-    The :ref:`@transform <decorators.transform>` decorator tells Ruffus that this
-    task function **transforms** each and every piece of input data into a corresponding output.
-
-        In other words, inputs and outputs have a **1 to 1** relationship.
-
-    .. note::
-
-        In the second part of the tutorial, we will encounter more decorators which can *split up*, or *join together* or *group* inputs.
-
-            In other words, inputs and output can have **many to one**, **many to many** etc. relationships.
-
-
-
-    Let us provide **input**\s and **output**\s to our new pipeline:
-
-        .. raw:: html
-
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-              <text x="4.0742145" y="13.589844" id="text3629" style="font-size:12px;fill:#ff0000;font-family:ArialMT">Decorator</text>
-              <text x="114.1965" y="15.776917" id="text3643" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Inputs</text>
-              <text x="207.08836" y="15.776917" id="text3657" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Extra parameters</text>
-              <text x="313.42374" y="15.776917" id="text3673" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Outputs</text>
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-              <text x="22.156881" y="126.48013" transform="scale(1.0042467,0.99577126)" id="text3311" xml:space="preserve" style="font-size:9.89657974px;font-family:monospace">               extra_parameter_str, extra_parameter_num):</text>
-              <text x="22.156881" y="139.91115" transform="scale(1.0042467,0.99577126)" id="text3313" xml:space="preserve" style="font-size:9.89657974px;font-family:monospace">    <tspan id="tspan3315" style="font-weight:bold;fill:#008000">pass</tspan></text>
-              <text x="22.156881" y="166.77328" transform="scale(1.0042467,0.99577126)" id="text3319" xml:space="preserve" style="font-size:9.89657974px;font-family:monospace"><tspan id="tspan3321" style="fill:#808080">#   make sure the input file is there</tspan></text>
-              <text x="22.156881" y="180.20436" transform="scale(1.0042467,0.99577126)" id="text3323" xml:space="preserve" style="font-size:9.89657974px;font-family:monospace"><tspan id="tspan3325" style="fill:#007020">open</tspan>('job1.input', "w")</text>
-              <text x="22.156881" y="199.1844" transform="scale(1.0042467,0.99577126)" id="text3329" xml:space="preserve" style="font-size:9.89657974px;font-family:monospace">pipeline_run([first_task])</text>
-              <path d="m 11.798134,17.75418 0,40.879392 11.506636,16.489166" id="path3696" style="fill:none;stroke:#ff0000;stroke-width:1.25536001;stroke-linecap:butt;stroke-linejoin:bevel;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-end:url(#Arrow2Mend)" />
-            </svg>
-
-
-        The ``@transform`` decorator tells Ruffus to generate the appropriate arguments for our python function:
-
-            * The input file name is as given: ``job1.input``
-            * The output file name is the input file name with its **suffix** of ``.input`` replaced with ``.output1``
-            * There are two extra parameters, a string and a number.
-
-        This is exactly equivalent to the following function call:
-
-            ::
-
-                first_task('job1.input', 'job1.output1', "some_extra.string.for_example", 14)
-
-
-        Even though this (empty) function doesn't do anything just yet, the output from **Ruffus** ``pipeline_run`` will show that that this part of the pipeline completed successfully:
-
-            .. raw:: html
-
-                <svg version="1.0" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0" y="0" width="374.86499pt" height="92.02504pt" viewBox="0 0 374.86498 92.025041">
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-                                <polygon points="128.888,48.153 125.897,53.333 122.905,48.153 " id="polygon3655" style="fill:#00a651" />
-                            </g>
-                        </g>
-                    </g>
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-                        <g id="g3663">
-                            <line stroke-miterlimit="10" x1="267.23001" y1="66.361" x2="267.23001" y2="15.667" id="line3665" style="fill:none;stroke:#00a651;stroke-miterlimit:10" />
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-                                <polygon points="267.23,70.667 264.238,65.486 270.222,65.486 " id="polygon3669" style="fill:#00a651" />
-                            </g>
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-                    </g>
-                    <path d="m 153.04485,51.262472 c 0,3.583 -4.15868,6.488 -9.28879,6.488 H 91.550787 c -5.130114,0 -9.288794,-2.905 -9.288794,-6.488 l 0,0 c 0,-3.583 4.15868,-6.488 9.288794,-6.488 h 52.204323 c 5.13012,0 9.28974,2.905 9.28974,6.488 l 0,0 z" id="path3671" style="opacity:0.2;fill:#00a14b" />
-                    <g transform="matrix(1,0,0,0.72872639,-103.64072,4.6212592)" id="g3675">
-                        <line x1="313.56299" y1="53.333" x2="313.56299" y2="15.667" id="line3677" style="fill:#00ff00" />
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-                            <line stroke-miterlimit="10" x1="313.56299" y1="49.028" x2="313.56299" y2="15.667" id="line3681" style="fill:none;stroke:#00a651;stroke-miterlimit:10" />
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-                                <polygon points="316.556,48.153 313.564,53.333 310.572,48.153 " id="polygon3685" style="fill:#00a651" />
-                            </g>
-                        </g>
-                    </g>
-                    <path d="m 250.58388,51.262472 c 0,3.583 -4.83746,6.488 -10.80388,6.488 h -60.72201 c -5.96757,0 -10.80503,-2.905 -10.80503,-6.488 l 0,0 c 0,-3.583 4.83746,-6.488 10.80503,-6.488 H 239.78 c 5.96642,0 10.80388,2.905 10.80388,6.488 l 0,0 z" id="path3687" style="opacity:0.2;fill:#00a14b" />
-                    <path d="m 295.61399,65.440811 c 0,3.406 -2.537,6.167 -5.667,6.167 H 85.280993 c -3.129,0 -5.667,-2.761 -5.667,-6.167 l 0,0 c 0,-3.406 2.537,-6.167 5.667,-6.167 H 289.94799 c 3.129,10e-4 5.666,2.762 5.666,6.167 l 0,0 z" id="path3689" style="opacity:0.2;fill:#00a14b" />
-                    <text x="92.396126" y="13.742188" id="text3643" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Inputs</text>
-                    <text x="193.83928" y="13.742188" id="text3673" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Outputs</text>
-                    <text x="256.93237" y="13.742188" id="text3657" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Extra parameters</text>
-                    <text x="9.3237839" y="40.037392" id="text3040" xml:space="preserve" style="font-size:10.32079887px;font-family:monospace"><tspan id="tspan3042" style="font-weight:bold;fill:#ff0000">>>></tspan> pipeline_run([first_task])</text>
-                    <text x="9.3237839" y="54.044189" id="text3046" xml:space="preserve" style="font-size:10.32079887px;font-family:monospace">    Job  <tspan id="tspan3048" style="fill:#666666">=</tspan> [job1<tspan id="tspan3050" style="fill:#666666">.</tspan>input <tspan id="tspan3052" style="fill:#666666">-></tspan> job1<tspan id="tspan3056" style="fill:#666666">.</tspan>output1,</text>
-                    <text x="58.633194" y="67.193367" id="text3160" xml:space="preserve" style="font-size:10.32079887px;font-family:monospace">    some_extra.string.for_example, 14] completed</text>
-                    <text x="9.3237839" y="82.432899" id="text3058" xml:space="preserve" style="font-size:10.32079887px;font-family:monospace">Completed Task <tspan id="tspan3060" style="fill:#666666">=</tspan> first_task</text>
-                    </svg>
-
-
-
-************************************
-Task functions as recipes
-************************************
-    This may seem like a lot of effort and complication for something so simple: a normal python function call.
-    However, now that we have annotated a task, we can start using it as part of our computational pipeline:
-
-
-    Each :term:`task` function of the pipeline is a recipe or
-    `rule <http://www.gnu.org/software/make/manual/make.html#Rule-Introduction>`_
-    which can be applied repeatedly to our data.
-
-    For example, one can have
-
-        * a ``compile()`` *task* which will compile any number of source code files, or
-        * a ``count_lines()`` *task* which will count the number of lines in any file or
-        * an ``align_dna()`` *task* which will align the DNA of many chromosomes.
-
-    .. note ::
-
-        **Key Ruffus Terminology**:
-
-        A  :term:`task` is an annotated python function which represents a recipe or stage of your pipeline.
-
-        A  :term:`job` is each time your recipe is applied to a piece of data, i.e. each time Ruffus calls your function.
-
-        Each **task** or pipeline recipe can thus have many **jobs** each of which can work in parallel on different data.
-
-    In the original example, we have made a single output file by supplying a single input parameter.
-    We shall use much the same syntax to apply the same recipe to *multiple* input files.
-    Instead of providing a single *input*, and a single *output*, we are going to specify
-    the parameters for *three* jobs at once:
-
-        ::
-
-            # previously,
-            # first_task_params = 'job1.input'
-            first_task_params = [
-                                'job1.input',
-                                'job2.input'
-                                'job3.input'
-                                ]
-
-            # make sure the input files are there
-            open('job1.input', "w")
-            open('job2.input', "w")
-            open('job3.input', "w")
-
-            pipeline_run([first_task])
-
-
-    .. :: .. image:: ../../images/simple_tutorial_files3.png
-
-
-
-    Just by changing the inputs from a single file to a list of three files, we now have a pipeline which runs independently on three pieces of data.
-    The results should look familiar:
-
-        ::
-
-            >>> pipeline_run([first_task])
-                Job  = [job1.input -> job1.output1,
-                        some_extra.string.for_example, 14] completed
-                Job  = [job2.input -> job2.output1,
-                        some_extra.string.for_example, 14] completed
-                Job  = [job3.input -> job3.output1,
-                        some_extra.string.for_example, 14] completed
-            Completed Task = first_task
-
-
-************************************
-Multiple steps
-************************************
-
-    Best of all, it is easy to add another step to our initial pipeline.
-
-    We have to
-
-        * add another ``@transform`` decorated function (``second_task()``),
-        * specify ``first_task()`` as the source:
-        * use a ``suffix`` which matches the output from ``first_task()``
-
-
-        ::
-
-            @transform(first_task, suffix(".output1"), ".output2")
-            def second_task(input_file, output_file):
-                # make output file
-                open(output_file, "w")
-
-        * call ``pipeline_run()`` with the correct final task (``second_task()``)
-
-
-    The full source code can be found :ref:`here <Simple_Tutorial_2nd_step_code>`
-
-    With very little effort, we now have three independent pieces of information coursing through our pipeline.
-    Because ``second_task()`` *transforms* the output from ``first_task()``, it magically knows its dependencies and
-    that it too has to work on three jobs.
-
-
-************************************
-Multi-tasking
-************************************
-
-    Though, three jobs have been specified in parallel, **Ruffus** defaults to running
-    each of them successively. With modern CPUs, it is often a lot faster to run parts
-    of your pipeline in parallel, all at the same time.
-
-    To do this, all you have to do is to add a multiprocess parameter to pipeline_run:
-
-        ::
-
-            >>> pipeline_run([second_task], multiprocess = 5)
-
-    In this case, ruffus will try to run up to 5 jobs at the same time. Since our second
-    task only has three jobs, these will be started simultaneously.
-
-
-
-**************************************************
-Up-to-date jobs are not re-run unnecessarily
-**************************************************
-
-    A job will be run only if the output file timestamps are out of date.
-    If you ran the same code a second time,
-
-        ::
-
-            >>> pipeline_run([second_task])
-
-
-    Nothing would happen because:
-        * ``job1.output2`` is more recent than ``job1.output1`` and
-        * ``job2.output2`` is more recent than ``job2.output1`` and
-        * ``job3.output2`` is more recent than ``job3.output1``.
-
-    Let us see what happens when just 1 out of 3 pieces of data is modified
-        ::
-
-            open("job1.input1", "w")
-            pipeline_run([second_task], verbose =2, multiprocess = 5)
-
-
-    You would see that only the out of date jobs (highlighted) have been re-run:
-
-        .. code-block:: pycon
-           :emphasize-lines: 2,6
-
-           >>> pipeline_run([second_task], verbose =2, multiprocess = 5)
-               Job  = [job1.input -> job1.output1, some_extra.string.for_example, 14] completed
-               Job  = [job3.input -> job3.output1, some_extra.string.for_example, 14] unnecessary: already up to date
-               Job  = [job2.input -> job2.output1, some_extra.string.for_example, 14] unnecessary: already up to date
-           Completed Task = first_task
-               Job  = [job1.output1 -> job1.output2] completed
-               Job  = [job2.output1 -> job2.output2] unnecessary: already up to date
-               Job  = [job3.output1 -> job3.output2] unnecessary: already up to date
-           Completed Task = second_task
-
-
-.. index::
-    pair: input / output parameters; Tutorial
-
-***************************************
-Intermediate files
-***************************************
-
-    In the above examples, the *input* and *output* parameters are file names.
-    Ruffus was designed for pipelines which save intermediate data in files. This is not
-    compulsory but saving your data in files at each step provides a few advantages:
-
-        #) Ruffus can use file system time stamps to check if your pipeline is up to date
-        #) Your data is persistent across runs
-        #) This is a good way to pass large amounts of data across processes and computational nodes
-
-    Otherwise, task parameters could be all sorts of data, from lists of files, to numbers,
-    sets or tuples. Ruffus imposes few constraints on what *you*
-    would like to send to each stage of your pipeline.
-
-    **Ruffus** does, however, assume that all strings in your *input* and *output*
-    parameters represent file names.
-
-    *input* parameters which contains a |glob|_ pattern (e.g. ``*.txt``) are expanded to the matching file names.
-
-
-***************************************
- at transform is a 1 to 1 operation
-***************************************
-
-
-    ``@transform`` is a 1:1 operation because it keeps the number of jobs constant
-    entering and leaving the task. Each job can accept, for example, a pair of files as its input,
-    or generate more than one output files.
-
-    Let us see this in action using the previous example:
-        * ``first_task_params`` is changed to 3 *pairs* of file names
-        * ``@transform`` for ``first_task`` is modified to produce *pairs* of file names
-            * ``.output.1``
-            * ``.output.extra.1``
-
-
-        ::
-
-            from ruffus import *
-
-            #---------------------------------------------------------------
-            #   Create pairs of input files
-            #
-            first_task_params = [
-                                 ['job1.a.input', 'job1.b.input'],
-                                 ['job2.a.input', 'job2.b.input'],
-                                 ['job3.a.input', 'job3.b.input'],
-                                ]
-
-            for input_file_pairs in first_task_params:
-                for input_file in input_file_pairs:
-                    open(input_file, "w")
-
-
-            #---------------------------------------------------------------
-            #
-            #   first task
-            #
-            @transform(first_task_params, suffix(".input"),
-                                    [".output.1",
-                                     ".output.extra.1"],
-                                   "some_extra.string.for_example", 14)
-            def first_task(input_files, output_file_pairs,
-                            extra_parameter_str, extra_parameter_num):
-                # make both pairs of output files
-                for output_file in output_file_pairs:
-                    open(output_file, "w")
-
-
-            #---------------------------------------------------------------
-            #
-            #   second task
-            #
-            @transform(first_task, suffix(".output.1"), ".output2")
-            def second_task(input_files, output_file):
-                # make output file
-                open(output_file, "w")
-
-            #---------------------------------------------------------------
-            #
-            #       Run
-            #
-            pipeline_run([second_task])
-
-        This gives the following results:
-
-        ::
-
-            >>> pipeline_run([pipeline_task])
-
-
-        We see that apart from having a file pair where previously there was a single file,
-        little else has changed. We still have three pieces of data going through the
-        pipeline in three parallel jobs.
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step2_code.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step2_code.txt
deleted file mode 100644
index 6325cc7..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step2_code.txt
+++ /dev/null
@@ -1,72 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_2nd_step_code:
-
-###################################################################
-Code for Step 2: Passing parameters to the pipeline
-###################################################################
-* :ref:`Up <Simple_Tutorial>` 
-* :ref:`Back <Simple_Tutorial_2nd_step>` 
-* :ref:`@transform syntax <decorators.transform>` in detail
-
-************************************
-Code
-************************************
-::
-
-    from ruffus import *
-
-    #---------------------------------------------------------------
-    #   Create input files
-    #
-    first_task_params = [
-                        'job1.input', 
-                        'job2.input',
-                        'job3.input'
-                        ]
-
-    for input_file in first_task_params:
-        open(input_file, "w")
-
-
-    #---------------------------------------------------------------
-    #
-    #   first task
-    #
-    @transform(first_task_params, suffix(".input"), ".output1",
-                           "some_extra.string.for_example", 14)
-    def first_task(input_file, output_file,
-                    extra_parameter_str, extra_parameter_num):
-        # make output file
-        open(output_file, "w")
-
-
-    #---------------------------------------------------------------
-    #
-    #   second task
-    #
-    @transform(first_task, suffix(".output1"), ".output2")
-    def second_task(input_file, output_file):
-        # make output file
-        open(output_file, "w")
-
-    #---------------------------------------------------------------
-    #
-    #       Run
-    #
-    pipeline_run([second_task])
-
-
-************************************
-Resulting Output
-************************************
-    ::
-
-        >>> pipeline_run([second_task])
-            Job  = [job1.input -> job1.output1, some_extra.string.for_example, 14] completed
-            Job  = [job2.input -> job2.output1, some_extra.string.for_example, 14] completed
-            Job  = [job3.input -> job3.output1, some_extra.string.for_example, 14] completed
-        Completed Task = first_task
-            Job  = [job1.output1 -> job1.output2] completed
-            Job  = [job2.output1 -> job2.output2] completed
-            Job  = [job3.output1 -> job3.output2] completed
-        Completed Task = second_task
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step3_run_pipeline.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step3_run_pipeline.txt
deleted file mode 100644
index 5d31ab2..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step3_run_pipeline.txt
+++ /dev/null
@@ -1,161 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_3rd_step:
-
-
-
-###################################################################
-Step 3: Understanding how your pipeline works
-###################################################################
-    * :ref:`Simple tutorial overview <Simple_Tutorial>`
-    * :ref:`pipeline functions <pipeline_functions>` in detail
-
-
-.. note::
-    Remember to look at the example code:
-
-    * :ref:`Python Code for step 3 <Simple_Tutorial_3nd_step_code>`
-
-.. index::
-    pair: pipeline_printout; Tutorial
-
-
-
-The trickiest part of developing pipelines is understanding how your
-data flows through the pipeline.
-
-Parameters and files are passed from one task to another down the chain
-of pipelined functions.
-
-Whether you are learning how to use **ruffus**, or trying out a new
-feature in **ruffus**, or just have a horrendously complicated pipeline
-to debug (we have colleagues with >100 criss-crossing pipelined stages),
-your best friend is :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>`
-
-
-
-=======================================
-Printing out which jobs will be run
-=======================================
-
-    :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` takes the same parameters as pipeline_run but just prints
-    the tasks which are and are not up-to-date.
-
-    The ``verbose`` parameter controls how much detail is displayed.
-
-    Let us take the two step :ref:`pipelined code<Simple_Tutorial_3nd_step_code>` we have previously written,
-    but call :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` instead of
-    :ref:`pipeline_run(...) <pipeline_functions.pipeline_run>`.
-    This lists the tasks which will be run in the pipeline:
-
-
-        .. image:: ../../images/simple_tutorial_pipeline_printout1.png
-
-    .. ::
-
-        ::
-
-            >>> pipeline_printout(sys.stdout, [second_task])
-
-            ________________________________________
-            Tasks which will be run:
-
-            Task = first_task
-            Task = second_task
-            ________________________________________
-
-
-
-    To see the input and output parameters of each job in the pipeline, we can increase the verbosity from the default (1) to 3:
-
-        .. image:: ../../images/simple_tutorial_pipeline_printout2.png
-
-    .. ::
-
-        >>> pipeline_printout(sys.stdout, [second_task], verbose = 3)
-
-        ________________________________________
-        Tasks which will be run:
-
-        Task = first_task
-               Job = [None
-                     ->job1.stage1]
-                 Job needs update: Missing file job1.stage1
-               Job = [None
-                     ->job2.stage1]
-                 Job needs update: Missing file job2.stage1
-
-        Task = second_task
-               Job = [job1.stage1
-                     ->job1.stage2,     1st_job]
-                 Job needs update: Missing file job1.stage1
-               Job = [job2.stage1
-                     ->job2.stage2,     2nd_job]
-                 Job needs update: Missing file job2.stage1
-
-        ________________________________________
-
-
-    This is very useful for checking that the input and output parameters have been specified
-        correctly.
-
-=============================================
-Determining which jobs are out-of-date or not
-=============================================
-
-    It is often useful to see which tasks are or are not up-to-date. For example, if we
-    were to run the pipeline in full, and then modify one of the intermediate files, the
-    pipeline would be partially out of date.
-
-
-    Let us start by run the pipeline in full but then modify ``job1.stage`` so that the second task is no longer up-to-date::
-
-        pipeline_run([second_task])
-
-        # modify job1.stage1
-        open("job1.stage1", "w").close()
-
-
-    At a verbosity of 5, even jobs which are up-to-date will be displayed.
-    We can now see that the there is only one job in ``second_task(...)`` which needs to be re-run
-    because ``job1.stage1`` has been modified after ``job1.stage2`` (highlighted in blue):
-
-
-        .. image:: ../../images/simple_tutorial_pipeline_printout3.png
-
-    .. ::
-
-        ::
-
-            >>> pipeline_printout(sys.stdout, [second_task], verbose = 5)
-            ________________________________________
-            Tasks which are up-to-date:
-
-            Task = first_task
-                   Job = [None
-                         ->job1.stage1]
-                     Job up-to-date
-                   Job = [None
-                         ->job2.stage1]
-                     Job up-to-date
-
-
-            ________________________________________
-            Tasks which will be run:
-
-            Task = second_task
-                   Job = [job1.stage1
-                         ->job1.stage2,     1st_job]
-                     Job needs update:
-                            Need update file times= [
-                                       [(1269025787.0, 'job1.stage1')],
-                                       [(1269025785.0, 'job1.stage2')] ]
-                   Job = [job2.stage1
-                         ->job2.stage2,     2nd_job]
-                     Job up-to-date
-
-            ________________________________________
-
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step3_run_pipeline_code.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step3_run_pipeline_code.txt
deleted file mode 100644
index 3a8ec01..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step3_run_pipeline_code.txt
+++ /dev/null
@@ -1,112 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_3nd_step_code:
-
-
-###################################################################
-Code for Step 3: Displaying the pipeline visually
-###################################################################
-* :ref:`Simple tutorial overview <Simple_Tutorial>` 
-* :ref:`pipeline functions <pipeline_functions>` in detail
-* :ref:`Back to Step 3 <Simple_Tutorial_3rd_step>` 
-
-******************************************
-Display the initial state of the pipeline
-******************************************
-    ::
-        
-        from ruffus import *
-        import sys
-        
-        #---------------------------------------------------------------
-        #
-        #   first task
-        #
-        task1_param = [
-                            [ None, 'job1.stage1'], # 1st job
-                            [ None, 'job2.stage1'], # 2nd job
-                      ]
-                                            
-        @files(task1_param)
-        def first_task(no_input_file, output_file):
-            open(output_file, "w")
-            #
-            # pretend we have worked hard
-
-
-        #---------------------------------------------------------------
-        #
-        #   second task
-        #
-        task2_param = [
-                            [ 'job1.stage1', "job1.stage2", "    1st_job"], # 1st job
-                            [ 'job2.stage1', "job2.stage2", "    2nd_job"], # 2nd job
-                      ]
-        
-        @follows(first_task)
-        @files(task2_param)
-        def second_task(input_file, output_file, extra_parameter):
-            open(output_file, "w")
-            print extra_parameter
-        
-        pipeline_printout(sys.stdout, [second_task], verbose = 3)
-        
-************************************
-Resulting Output
-************************************
-    ::
-
-        >>> pipeline_printout(sys.stdout, [second_task])
-
-            Task = first_task
-                   Job = [None -> job1.stage1]
-                   Job = [None -> job2.stage1]
-            
-            Task = second_task
-                   Job = [job1.stage1 -> job1.stage2,     1st_job]
-                   Job = [job2.stage1 -> job2.stage2,     2nd_job]
-            
-******************************************
-Display the partially up-to-date pipeline
-******************************************
-    Run the pipeline, modify ``job1.stage`` so that the second task is no longer up-to-date
-    and printout the pipeline stage again::
-        
-        pipeline_run([second_task])
-   
-        # modify job1.stage1
-        open("job1.stage1", "w").close()
-   
-
-    At a verbosity of 5, even jobs which are up-to-date will be displayed::
-    
-        >>> pipeline_printout(sys.stdout, [second_task], verbose = 5)
-        ________________________________________
-        Tasks which are up-to-date:
-        
-        Task = first_task
-               Job = [None
-                     ->job1.stage1]
-                 Job up-to-date
-               Job = [None
-                     ->job2.stage1]
-                 Job up-to-date
-        
-        
-        ________________________________________
-        Tasks which will be run:
-        
-        Task = second_task
-               Job = [job1.stage1
-                     ->job1.stage2,     1st_job]
-                 Job needs update: Need update file times= [[(1269025787.0, 'job1.stage1')], [(1269025785.0,
-                       'job1.stage2')]]
-               Job = [job2.stage1
-                     ->job2.stage2,     2nd_job]
-                 Job up-to-date
-        
-        ________________________________________
-
-    We can now see that the there is only one job in "second_task" which needs to be re-run
-    because 'job1.stage1' has been modified after 'job1.stage2'
-
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step4_run_pipeline_graphically.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step4_run_pipeline_graphically.txt
deleted file mode 100644
index a5b652e..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step4_run_pipeline_graphically.txt
+++ /dev/null
@@ -1,71 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_4th_step_graphical:
-
-
-
-###################################################################
-Step 4: Displaying the pipeline visually
-###################################################################
-    * :ref:`Simple tutorial overview <Simple_Tutorial>` 
-    * :ref:`pipeline functions <pipeline_functions>` in detail
-
-.. note::
-    Remember to look at the example code:
-
-    * :ref:`Python Code for step 4 <Simple_Tutorial_4th_step_graphical_code>` 
-    
-.. index:: 
-    pair: pipeline_printout; Tutorial
-
-
-
-.. index:: 
-    pair: pipeline_printout_graph; Tutorial
-
-=============================================
-Printing out a flowchart of our pipeline
-=============================================
-
-    It is all very well being able to trace the data flow through the pipeline.
-    Sometimes, however, we need a bit of eye-candy.
-
-    .. csv-table:: 
-        :widths: 1,99
-        :class: borderless
-
-        ".. image:: ../../images/simple_tutorial_step4.png", "
-            We can see this flowchart of our fledgling pipeline by executing:
-                ::
-                
-                    pipeline_printout_graph (   'flowchart.svg', 
-                                                'svg', 
-                                                [second_task], 
-                                                no_key_legend = False)
-            
-            Flowcharts can be printed in a large number of formats including jpg, svg, 
-            png and pdf provided that the ``dot`` programme from 
-            `Graphviz <http://www.graphviz.org/>`_ is installed.
-
-            For this simple case, we have ommitted the legend key which distinguishes between the
-            different states of the various tasks. (See below for the legend key.)
-            "
-            
-            
-
-=============================================
-Horribly complicated pipelines!
-=============================================
-    Flowcharts are especially useful if you have really complicated pipelines, such as
-    
-        .. image:: ../../images/simple_tutorial_complex_flowchart.png
-        
-
-=============================================
-Circular dependency errors in pipelines!
-=============================================
-    Especially, if the pipeline is not set up properly, and vicious circular dependencies
-    are present:
-    
-                    
-        .. image:: ../../images/simple_tutorial_complex_flowchart_error.png
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step4_run_pipeline_graphically_code.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step4_run_pipeline_graphically_code.txt
deleted file mode 100644
index 8fb1018..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step4_run_pipeline_graphically_code.txt
+++ /dev/null
@@ -1,104 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_4th_step_graphical_code:
-
-
-###################################################################
-Code for Step 4: Displaying the pipeline visually
-###################################################################
-* :ref:`Simple tutorial overview <Simple_Tutorial>` 
-* :ref:`pipeline functions <pipeline_functions>` in detail
-* :ref:`Back to Step 4 <Simple_Tutorial_4th_step_graphical>` 
-
-************************************
-Code
-************************************
-    ::
-        
-        from ruffus import *
-        import time
-        
-        #---------------------------------------------------------------
-        #
-        #   first task
-        #
-        task1_param = [
-                            [ None, 'job1.stage1'], # 1st job
-                            [ None, 'job2.stage1'], # 2nd job
-                      ]
-                                            
-        @files(task1_param)
-        def first_task(no_input_file, output_file):
-            open(output_file, "w")
-
-
-        #---------------------------------------------------------------
-        #
-        #   second task
-        #
-        task2_param = [
-                            [ 'job1.stage1', "job1.stage2", "    1st_job"], # 1st job
-                            [ 'job2.stage1', "job2.stage2", "    2nd_job"], # 2nd job
-                      ]
-        
-        @follows(first_task)
-        @files(task2_param)
-        def second_task(input_file, output_file, extra_parameter):
-            open(output_file, "w")
-            print extra_parameter
-        
-        #---------------------------------------------------------------
-        #
-        #       Show flow chart and tasks before running the pipeline
-        #
-        print "Show flow chart and tasks before running the pipeline"
-        pipeline_printout_graph ( open("flowchart_before.png", "w"),
-                                 "png",
-                                 [second_task],
-                                 no_key_legend=True)
-        
-        #---------------------------------------------------------------
-        #
-        #       Run
-        #
-        pipeline_run([second_task])
-    
-   
-        # modify job1.stage1
-        open("job1.stage1", "w").close()
-   
-       
-        #---------------------------------------------------------------
-        #
-        #       Show flow chart and tasks after running the pipeline
-        #
-        print "Show flow chart and tasks after running the pipeline"
-        pipeline_printout_graph ( open("flowchart_after.png", "w"),
-                                 "png",
-                                 [second_task],
-                                 no_key_legend=True)
-        
-        
-************************************
-Resulting Flowcharts
-************************************
-   +-------------------------------------------------------------+-----------------------------------------------------------------------+
-   | .. image:: ../../images/simple_tutorial_stage4_before.png   | .. image::  ../../images/simple_tutorial_stage4_after.png             |
-   |           :alt: Before running the pipeline                 |     :alt: After running the pipeline                                  |                           
-   |           :scale: 50                                        |     :scale: 50                                                        |                           
-   |           :align: center                                    |     :align: center                                                    |                           
-   |                                                             |                                                                       |                           
-   | .. centered:: Before                                        | .. centered:: After                                                   |                           
-   |                                                             |                                                                       |                           
-   +-------------------------------------------------------------+-----------------------------------------------------------------------+
-
-   +-------------------------------------------------------------------------------------------------------------------------------------+
-   | .. image:: ../../images/tutorial_key.jpg                                                                                            |
-   |           :alt: Legend key                                                                                                          |                           
-   |           :scale: 75                                                                                                                |                           
-   |           :align: center                                                                                                            |                           
-   |                                                                                                                                     |                           
-   | .. centered:: Legend                                                                                                                |                           
-   |                                                                                                                                     |                           
-   +-------------------------------------------------------------------------------------------------------------------------------------+
-
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step5_split.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step5_split.txt
deleted file mode 100644
index 8dec152..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step5_split.txt
+++ /dev/null
@@ -1,112 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_5th_step:
-.. _tutorial.split:
-.. index::
-    pair: @split; Tutorial
-
-
-###################################################################
-Step 5: Splitting up large tasks / files
-###################################################################
-    * :ref:`Simple tutorial overview <Simple_Tutorial>`
-    * :ref:`@split in detail <decorators.split>`
-
-    .. note::
-        Remember to look at the example code:
-
-        * :ref:`Python Code for step 5 <Simple_Tutorial_5th_step_code>`
-
-    | The second half of this tutorial is a worked example to calculate
-      the sample variance of 10,000 random numbers.
-    | This is similar to many computational projects: we are tackling a big problem
-      by splitting it up into many tiny problems solved in parallel. We can then
-      merge our piecemeal solutions into our final answer. These
-      `embarassingly parallel <http://en.wikipedia.org/wiki/Embarrassingly_parallel>`_
-      problems motivated the original design of **Ruffus**.
-
-    **Ruffus** has three dedicated decorators to handle these problems with ease:
-
-        * :ref:`@split<decorators.split>` to break up the big problem
-        * :ref:`@transfrom<decorators.split>` to solve the parts in parallel
-        * :ref:`@merge<decorators.split>` to merge our piecemeal solutions into the final answer.
-
-
-**************************************************************************************
-Splitting up a long list of random numbers to calculate their variance
-**************************************************************************************
-
-    .. csv-table::
-        :widths: 1,99
-        :class: borderless
-
-        ".. centered::
-            Step 5 from:
-
-        .. image:: ../../images/simple_tutorial_step5.png", "
-            Suppose we had a list of 100,000 random numbers in the file ``random_numbers.list``:
-
-                ::
-
-                    import random
-                    f = open('random_numbers.list', 'w')
-                    for i in range(NUMBER_OF_RANDOMS):
-                        f.write('%g\n' % (random.random() * 100.0))
-
-
-            We might want to calculate the sample variance more quickly by splitting them
-            into ``NNN`` parcels of 1000 numbers each and working on them in parallel.
-            In this case we known that ``NNN == 100`` but usually the number of resulting files
-            is only apparent after we have finished processing our starting file."
-
-
-    Our pipeline function needs to take the random numbers file ``random_numbers.list``,
-    read the random numbers from it, and write to a new file every 100 lines.
-
-    The *Ruffus* decorator :ref:`@split<decorators.split>` is designed specifically for
-    splitting up input into an indeterminate ``NNN`` number of output files:
-
-        .. image:: ../../images/simple_tutorial_split.png
-
-    .. ::
-
-        ::
-
-            @split("random_numbers.list", "*.chunks")
-            def step_5_split_numbers_into_chunks (input_file_name, output_files):
-                #
-                """code goes here"""
-
-
-    Ruffus will set
-
-        | ``input_file_name`` to ``"random_numbers.list"``
-        | ``output_files`` to all files which match ``*.chunks`` (i.e. ``"1.chunks"``, ``"2.chunks"`` etc.).
-
-    The first time you run this function ``*.chunks`` will return an empty list because
-    no ``.chunks`` files have been created, resulting in the following:
-
-        ::
-
-            step_5_split_numbers_into_chunks ("random_numbers.list", [])
-
-    After that ``*.chunks`` will match the list of current ``.chunks`` files created by
-    the previous pipeline run. Some of these files will be out of date or superfluous.
-    These file names are usually only useful for removing detritus from previous runs
-    (have a look at :ref:`step_5_split_numbers_into_chunks(...) <Simple_Tutorial_5th_step_code>`).
-
-    .. note ::
-
-        The great value of specifying correctly the list of *output* files will become apparent in the next
-        step of this tutorial when we shall see how pipeline tasks can be "chained" together conveniently.
-
-        Remember to specify ``globs`` patterns which match *all* the files you are splitting up. You can
-        cover different directories, or groups of file names by using a list of ``globs``:
-        e.g.   ::
-
-                @split("input.file", ['a*.bits', 'b*.pieces', 'somewhere_else/c*.stuff'])
-                def split_function (input_filename, output_files):
-                    "Code to split up 'input.file'"
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step5_split_code.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step5_split_code.txt
deleted file mode 100644
index 9afe18c..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step5_split_code.txt
+++ /dev/null
@@ -1,81 +0,0 @@
-.. _Simple_Tutorial_5th_step_code:
-.. include:: ../../global.inc
-
-###################################################################
-Code for Step 5: Splitting up large tasks / files
-###################################################################
-    * :ref:`Simple tutorial overview <Simple_Tutorial>` 
-    * :ref:`@split in detail <decorators.split>`
-    * :ref:`back to step 5 <Simple_Tutorial_5th_step>`
-
-************************************
-Code
-************************************
-    ::
-        
-        NUMBER_OF_RANDOMS = 10000
-        CHUNK_SIZE = 1000
-        
-        
-        from ruffus import *
-        import time
-        
-        import random
-        
-        #---------------------------------------------------------------
-        #
-        #   Create random numbers 
-        #
-        @files(None, "random_numbers.list")
-        def create_random_numbers(input_file_name, output_file_name):
-            f = open(output_file_name, "w")
-            for i in range(NUMBER_OF_RANDOMS):
-                f.write("%g\n" % (random.random() * 100.0))
-        
-        #---------------------------------------------------------------
-        #
-        #   Split initial file
-        #
-        @follows(create_random_numbers)        
-        @split("random_numbers.list", "*.chunks")
-        def step_5_split_numbers_into_chunks (input_file_name, output_files):
-            """
-                Splits random numbers file into XXX files of CHUNK_SIZE each
-            """
-            #
-            #   clean up files from previous runs
-            # 
-            for f in glob.glob("*.chunks"):
-                os.unlink(f)
-            #
-            #   create new file every CHUNK_SIZE lines and 
-            #       copy each line into current file
-            # 
-            output_file = None
-            cnt_files = 0
-            for i, line in enumerate(open(input_file_name)):
-                if i % CHUNK_SIZE == 0:
-                    cnt_files += 1
-                    output_file = open("%d.chunks" % cnt_files, "w")
-                output_file.write(line)
-
-        pipeline_run([step_5_split_numbers_into_chunks], verbose = 2)
-
-************************************
-Resulting Output
-************************************
-    ::
-                           
-        >>> pipeline_run([step_5_split_numbers_into_chunks], verbose = 2)
-        
-            Start Task = create_random_numbers
-            
-                Job = [None -> random_numbers.list] Missing file random_numbers.list
-                Job = [None -> random_numbers.list] completed
-            Completed Task = create_random_numbers
-            Start Task = step_5_split_numbers_into_chunks
-            Splits random numbers file into XXX files of CHUNK_SIZE each
-                Job = [random_numbers.list -> *.chunks] Missing output file
-                Job = [random_numbers.list -> *.chunks] completed
-            Completed Task = step_5_split_numbers_into_chunks
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step6_transform.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step6_transform.txt
deleted file mode 100644
index 7845c62..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step6_transform.txt
+++ /dev/null
@@ -1,89 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_6th_step:
-.. _tutorial.transform:
-
-.. index:: 
-    pair: @transform; Tutorial
-
-
-
-###################################################################
-Step 6: Running jobs in parallel
-###################################################################
-* :ref:`Simple tutorial overview <Simple_Tutorial>` 
-* :ref:`@transform in detail <decorators.transform>`
-
-.. note::
-    Remember to look at the example code:
-
-    * :ref:`Python Code for step 6 <Simple_Tutorial_6th_step_code>` 
-
-**************************************************************************************
-Calculating sums and sum of squares in parallel
-**************************************************************************************
-    Now that we have many smaller lists of numbers in separate files, we can calculate their sums and 
-    sum of squares in parallel.
-    
-    All we need is a function which takes a ``*.chunk`` file, reads the numbers, calculates
-    the answers and writes them back out to a corresponding ``*.sums`` file.
-    
-    *Ruffus* magically takes care of applying this task function to all the different
-    data files in parallel.
-    
-        .. image:: ../../images/simple_tutorial_transform.png
-      
-    .. ::
-        ::
-            
-            #---------------------------------------------------------------
-            #
-            #   Calculate sum and sum of squares for each chunk file
-            #
-            @transform(step_5_split_numbers_into_chunks, suffix(".chunks"), ".sums")
-            def step_6_calculate_sum_of_squares (input_file_name, output_file_name):
-                #
-                #   calculate sums and sums of squares for all values in the input_file_name
-                #       writing to output_file_name
-                ""
-
-       
-
-    | The first thing to note about this example is that the *input* files are not specified
-      as a |glob|_  (e.g. ``*.chunk``) but as the preceding task. 
-    | *Ruffus* will take all
-      the files produced by ``step_5_split_numbers_into_chunks()`` and feed them as the *input*
-      into step 6. 
-    
-    This handy shortcut also means that **Ruffus** knows that ``step_6_calculate_sum_of_squares``
-    depends on ``step_5_split_numbers_into_chunks`` and an additional ``@follows`` directive
-    is unnecessary.
-    
-    The use of :ref:`suffix<decorators.transform.suffix_string>` within the decorator tells 
-    *Ruffus* to take all *input* files with the ``.chunks`` suffix and substitute a ``.sums`` 
-    suffix to generate the corresponding *output* file name.
-    
-    
-    Thus if ``step_5_split_numbers_into_chunks`` created
-        ::
-        
-            "1.chunks"
-            "2.chunks"
-            "3.chunks"
-        
-    This would result in the following function calls:
-    
-        ::
-        
-            step_6_calculate_sum_of_squares ("1.chunk", "1.sums")
-            step_6_calculate_sum_of_squares ("2.chunk", "2.sums")
-            step_6_calculate_sum_of_squares ("3.chunk", "3.sums")
-            
-            # etc...
-            
-
-
-    .. note::    
-
-        It is possible to generate *output* filenames using more powerful regular expressions
-        as well. See the :ref:`@transform <decorators.transform>` syntax documentation for more details.
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step6_transform_code.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step6_transform_code.txt
deleted file mode 100644
index 2521c87..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step6_transform_code.txt
+++ /dev/null
@@ -1,104 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_6th_step_code:
-
-###################################################################
-Code for Step 6: Running jobs in parallel
-###################################################################
-* :ref:`Simple tutorial overview <Simple_Tutorial>` 
-* :ref:`@transform in detail <decorators.transform>`
-* :ref:`back to step 6 <Simple_Tutorial_6th_step>`
-
-************************************
-Code
-************************************
-    ::
-        
-        NUMBER_OF_RANDOMS = 10000
-        CHUNK_SIZE = 1000
-        
-        
-        from ruffus import *
-        import time
-        
-        import random
-        import glob
-        
-        #---------------------------------------------------------------
-        #
-        #   Create random numbers 
-        #
-        @files(None, "random_numbers.list")
-        def create_random_numbers(input_file_name, output_file_name):
-            f = open(output_file_name, "w")
-            for i in range(NUMBER_OF_RANDOMS):
-                f.write("%g\n" % (random.random() * 100.0))
-        
-        #---------------------------------------------------------------
-        #
-        #   Split initial file
-        #
-        @follows(create_random_numbers)        
-        @split("random_numbers.list", "*.chunks")
-        def step_5_split_numbers_into_chunks (input_file_name, output_files):
-            """
-                Splits random numbers file into XXX files of CHUNK_SIZE each
-            """
-            #
-            #   clean up files from previous runs
-            # 
-            for f in glob.glob("*.chunks"):
-                os.unlink(f)
-            #
-            #
-            #   create new file every CHUNK_SIZE lines and 
-            #       copy each line into current file
-            # 
-            output_file = None
-            cnt_files = 0
-            for i, line in enumerate(open(input_file_name)):
-                if i % CHUNK_SIZE == 0:
-                    cnt_files += 1
-                    output_file = open("%d.chunks" % cnt_files, "w")
-                output_file.write(line)
-        
-        #---------------------------------------------------------------
-        #
-        #   Calculate sum and sum of squares for each chunk file
-        #
-        @transform(step_5_split_numbers_into_chunks, suffix(".chunks"), ".sums")
-        def step_6_calculate_sum_of_squares (input_file_name, output_file_name):
-            output = open(output_file_name,  "w")
-            sum_squared, sum = [0.0, 0.0]
-            cnt_values = 0
-            for line in open(input_file_name):
-                cnt_values += 1
-                val = float(line.rstrip())
-                sum_squared += val * val
-                sum += val
-            output.write("%s\n%s\n%d\n" % (repr(sum_squared), repr(sum), cnt_values))
-
-        pipeline_run([step_6_calculate_sum_of_squares], verbose = 1)
-
-                                                                   
-************************************
-Resulting Output
-************************************
-    ::
-
-        >>> pipeline_run([step_6_calculate_sum_of_squares], verbose = 1)
-            Job = [None -> random_numbers.list] unnecessary: already up to date
-        Completed Task = create_random_numbers
-            Job = [random_numbers.list -> *.chunks] unnecessary: already up to date
-        Completed Task = step_5_split_numbers_into_chunks
-            Job = [6.chunks -> 6.sums] completed
-            Job = [1.chunks -> 1.sums] completed
-            Job = [4.chunks -> 4.sums] completed
-            Job = [7.chunks -> 7.sums] completed
-            Job = [2.chunks -> 2.sums] completed
-            Job = [9.chunks -> 9.sums] completed
-            Job = [10.chunks -> 10.sums] completed
-            Job = [3.chunks -> 3.sums] completed
-            Job = [5.chunks -> 5.sums] completed
-            Job = [8.chunks -> 8.sums] completed
-        Completed Task = step_6_calculate_sum_of_squares
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step7_merge.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step7_merge.txt
deleted file mode 100644
index d2752f5..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step7_merge.txt
+++ /dev/null
@@ -1,80 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_7th_step:
-
-.. index:: 
-    pair: @merge; Tutorial
-
-
-###################################################################
-Step 7: Merging results back together
-###################################################################
-* :ref:`Simple tutorial overview <Simple_Tutorial>` 
-* :ref:`@merge in detail <decorators.merge>`
-
-.. note::
-    Remember to look at the example code:
-
-    * :ref:`Python Code for step 7 <Simple_Tutorial_7th_step_code>` 
-
-
-Now that we have all the partial solutions in ``*.sums``, we can merge them
-together to generate the final answer: the variance of all 100,000 random
-numbers.
-
-**************************************************************************************
-Calculating variances from the sums and sum of squares of all chunks
-**************************************************************************************
-
-    If we add up all the sums, and sum of squares we calculated previously, we can
-    obtain the variance as follows::
-    
-        variance = (sum_squared - sum * sum / N)/N
-        
-    where ``N`` is the number of values
-
-    See the `wikipedia <http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance>`_ entry for a discussion of 
-    why this is a very naive approach!
-    
-    To do this, all we have to do is merge together all the values in ``*.sums``, i.e.
-    add up the ``sums`` and ``sum_squared`` for each chunk. We can then apply the above (naive) formula.
-    
-    Merging files is straightforward in **Ruffus**:
-    
-        .. image:: ../../images/simple_tutorial_merge1.png
-    
-    .. ::
-        
-        ::
-
-            @merge(step_6_calculate_sum_of_squares, "variance.result")
-            def step_7_calculate_variance (input_file_names, output_file_name):
-                #
-                #   add together sums and sums of squares from each input_file_name
-                #       calculate variance and write to output_file_name
-                ""
-
-
-    The :ref:`@merge <decorators.merge>` decorator tells *Ruffus* to take all the files from the step 6 task (i.e. ``*.sums``),
-    and produced a merged file in the form of ``"variance.result"``.
-    
-    Thus if ``step_6_calculate_sum_of_squares`` created
-        | ``1.sums`` and 
-        | ``2.sums`` etc.
-        
-    This would result in the following function call:
-    
-        .. image:: ../../images/simple_tutorial_merge2.png
-
-    .. ::
-
-        ::
-        
-            step_7_calculate_variance (["1.sums", "2.sums"], "variance.result")
-            
-
-    The final result is, of course, in ``"variance.result"``.
-            
-
-
-
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step7_merge_code.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step7_merge_code.txt
deleted file mode 100644
index 279919f..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step7_merge_code.txt
+++ /dev/null
@@ -1,138 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_7th_step_code:
-
-###################################################################
-Code for Step 7: Merging results back together
-###################################################################
-* :ref:`Simple tutorial overview <Simple_Tutorial>` 
-* :ref:`@merge in detail <decorators.merge>`
-* :ref:`back to step 7 <Simple_Tutorial_7th_step>`
-
-************************************
-Code
-************************************
-    ::
-        
-        NUMBER_OF_RANDOMS = 10000
-        CHUNK_SIZE = 1000
-        
-        
-        from ruffus import *
-        import time
-        
-        import random
-        import glob
-        
-        #---------------------------------------------------------------
-        #
-        #   Create random numbers 
-        #
-        @files(None, "random_numbers.list")
-        def create_random_numbers(input_file_name, output_file_name):
-            f = open(output_file_name, "w")
-            for i in range(NUMBER_OF_RANDOMS):
-                f.write("%g\n" % (random.random() * 100.0))
-        
-        #---------------------------------------------------------------
-        #
-        #   Split initial file
-        #
-        @follows(create_random_numbers)        
-        @split("random_numbers.list", "*.chunks")
-        def step_5_split_numbers_into_chunks (input_file_name, output_files):
-            """
-                Splits random numbers file into XXX files of CHUNK_SIZE each
-            """
-            #
-            #   clean up files from previous runs
-            # 
-            for f in glob.glob("*.chunks"):
-                os.unlink(f)
-            #
-            #   create new file every CHUNK_SIZE lines and 
-            #       copy each line into current file
-            # 
-            output_file = None
-            cnt_files = 0
-            for i, line in enumerate(open(input_file_name)):
-                if i % CHUNK_SIZE == 0:
-                    cnt_files += 1
-                    output_file = open("%d.chunks" % cnt_files, "w")
-                output_file.write(line)
-        
-        #---------------------------------------------------------------
-        #
-        #   Calculate sum and sum of squares for each chunk file
-        #
-        @transform(step_5_split_numbers_into_chunks, suffix(".chunks"), ".sums")
-        def step_6_calculate_sum_of_squares (input_file_name, output_file_name):
-            output = open(output_file_name,  "w")
-            sum_squared, sum = [0.0, 0.0]
-            cnt_values = 0
-            for line in open(input_file_name):
-                cnt_values += 1
-                val = float(line.rstrip())
-                sum_squared += val * val
-                sum += val
-            output.write("%s\n%s\n%d\n" % (repr(sum_squared), repr(sum), cnt_values))
-        
-        #---------------------------------------------------------------
-        #
-        #   Calculate sum and sum of squares for each chunk
-        #
-        @merge(step_6_calculate_sum_of_squares, "variance.result")
-        def step_7_calculate_variance (input_file_names, output_file_name):
-            """
-            Calculate variance naively
-            """
-            output = open(output_file_name,  "w")
-            # 
-            #   initialise variables            
-            #
-            all_sum_squared = 0.0
-            all_sum         = 0.0
-            all_cnt_values  = 0.0 
-            # 
-            # added up all the sum_squared, and sum and cnt_values from all the chunks
-            # 
-            for input_file_name in input_file_names:
-                sum_squared, sum, cnt_values = map(float, open(input_file_name).readlines())
-                all_sum_squared += sum_squared
-                all_sum         += sum        
-                all_cnt_values  += cnt_values 
-            all_mean = all_sum / all_cnt_values
-            variance = (all_sum_squared - all_sum * all_mean)/(all_cnt_values)
-            # 
-            #   print output
-            #
-            print >>output, variance
-        
-        #---------------------------------------------------------------
-        #
-        #       Run
-        #
-        pipeline_run([step_7_calculate_variance], [create_random_numbers], verbose = 1)
-
-************************************
-Resulting Output
-************************************
-    ::
-
-        pipeline_run([step_7_calculate_variance], [create_random_numbers], verbose = 1)
-            Job = [None -> random_numbers.list] completed
-        Completed Task = create_random_numbers
-            Job = [random_numbers.list -> *.chunks] completed
-        Completed Task = step_5_split_numbers_into_chunks
-            Job = [6.chunks -> 6.sums] completed
-            Job = [1.chunks -> 1.sums] completed
-            Job = [4.chunks -> 4.sums] completed
-            Job = [7.chunks -> 7.sums] completed
-            Job = [2.chunks -> 2.sums] completed
-            Job = [9.chunks -> 9.sums] completed
-            Job = [10.chunks -> 10.sums] completed
-            Job = [3.chunks -> 3.sums] completed
-            Job = [5.chunks -> 5.sums] completed
-            Job = [8.chunks -> 8.sums] completed
-        Completed Task = step_6_calculate_sum_of_squares
-            Job = [[6.sums, 5.sums, 1.sums, 4.sums, 3.sums, 2.sums, 8.sums, 7.sums, 10.sums, 9.sums] -> variance.result] completed
-        Completed Task = step_7_calculate_variance
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step8_posttask.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step8_posttask.txt
deleted file mode 100644
index ff98bbf..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step8_posttask.txt
+++ /dev/null
@@ -1,119 +0,0 @@
-.. include:: ../../global.inc
-.. index:: 
-    pair: @posttask; Tutorial
-
-.. _Simple_Tutorial_8th_step:
-
-
-###################################################################
-Step 8: Signal the completion of each stage of our pipeline
-###################################################################
-* :ref:`Simple tutorial overview <Simple_Tutorial>` 
-* :ref:`@posttask<decorators.posttask>` in detail
-
-.. note::
-    Remember to look at the example code:
-
-    * :ref:`Python Code for step 8 <Simple_Tutorial_8th_step_code>` 
-    
-Let us finish by celebrating the success of our modest pipeline example.
-
-**************************************************************************************
-Running some code to show that a stage of the pipeline has finished
-**************************************************************************************
-
-    A common requirement is to take some extra action when a particular 
-    :term:`task` or stage of a pipeline is complete.
-    
-    This can range from printing out some message, or ``touching`` some sentinel file,
-    to emailing the author.
-    
-    This is particular useful if the :term:`task` is a recipe apply to an unspecified number
-    of parameters in parallel in different :term:`job`\s
-    
-    The "extra action" can be added to a *Ruffus* pipeline using the :ref:`@posttask<decorators.posttask>`
-    decorator.
-    
-    Let us print a "hooray" message to show that we have finished calculating variances.
-    
-        .. image:: ../../images/simple_tutorial_posttask.png
-
-    .. ::
-    
-        ::
-        
-            def print_hooray():
-                sys.stdout.write("hooray\n")
-        
-            @posttask(print_hooray)
-            @merge(step_6_calculate_sum_of_squares, "variance.result")
-            def step_7_calculate_variance (input_file_names, output_file_name):
-                ""
-    
-    This is such a short function, we can even write it in-line:
-    
-        ::
-        
-            @posttask(lambda: sys.stdout.write("hooray\n"))
-            @merge(step_6_calculate_sum_of_squares, "variance.result")
-            def step_7_calculate_variance (input_file_names, output_file_name):
-                ""
-    
-.. index:: 
-    single: @posttask; touchfile (Tutorial)
-    single: touchfile ; @posttask (Tutorial)
-
-**************************************************************************************
-*Touching* a sentinel file after finishing a pipeline stage
-**************************************************************************************
-    | Very often we would like to mark the competion of a pipeline stage by using the
-      date/time stamp of a "sentinel" file.
-    | This is such a common requirement that *Ruffus* even has special syntax for this
-      in the form of :ref:`touch_file<decorators.touch_file>`.
-      
-    
-        ::
-        
-            @posttask(touch_file("sentinel_flag"))
-            def your_pipeline_function (input_file_names, output_file_name):
-                ""
-                
-    The file ``sentinel_flag`` will be created (if it did not exist) or its
-    date/time stamp changed to the current time whenever this stage of the pipeline is
-    completed.
-    
-
-**************************************************************************************
-Adding several post task actions
-**************************************************************************************
-    You can, of course, add more than one different action to be taken on completion of the 
-    task, either by stacking up :ref:`@posttask<decorators.posttask>` decorators or by including
-    several functions in the same **@posttask**:
-    
-        ::
-        
-            @posttask(print_hooray, print_whopee)
-            @posttask(touch_file("sentinel_flag"))
-            def your_pipeline_function (input_file_names, output_file_name):
-                ""
-                
-**************************************************************************************
-Finding out more about **Ruffus**
-**************************************************************************************
-
-    This wraps up our short tutorial on the **Ruffus**. 
-    
-    Here are a few useful topics you may be interested in:
-    
-        * :ref:`How to summarise disparate input by category <manual.collate>`
-        * :ref:`How to log pipeline progress <manual.logging>`
-        * :ref:`How exceptions are handled <manual.exceptions>`
-
-    To find out more about **Ruffus**, you can read the :ref:`manual<manual.introduction>`
-    or just start using **Ruffus**.
-    
-    Email the authors at ruffus_lib at llew.org.uk if you have any comments or suggestions.
-    
-    Happy pipelining!
-    
-
diff --git a/doc/_build/html/_sources/tutorials/simple_tutorial/step8_posttask_code.txt b/doc/_build/html/_sources/tutorials/simple_tutorial/step8_posttask_code.txt
deleted file mode 100644
index fbecb00..0000000
--- a/doc/_build/html/_sources/tutorials/simple_tutorial/step8_posttask_code.txt
+++ /dev/null
@@ -1,162 +0,0 @@
-.. include:: ../../global.inc
-.. _Simple_Tutorial_8th_step_code:
-
-#########################################################################
-Code for Step 8: Signal the completion of each stage of our pipeline
-#########################################################################
-* :ref:`Simple tutorial overview <Simple_Tutorial>` 
-* :ref:`@posttask in detail <decorators.posttask>`
-* :ref:`back to step 8 <Simple_Tutorial_8th_step>`
-
-************************************
-Code
-************************************
-    ::
-    
-        NUMBER_OF_RANDOMS = 10000
-        CHUNK_SIZE = 1000
-        working_dir = "temp_tutorial8/"
-        
-        
-        
-        import time, sys, os
-        from ruffus import *
-        
-        import random
-        import glob
-        
-        
-        
-        
-        #---------------------------------------------------------------
-        #
-        #   Create random numbers
-        #
-        @follows(mkdir(working_dir))
-        @files(None, working_dir + "random_numbers.list")
-        def create_random_numbers(input_file_name, output_file_name):
-            f = open(output_file_name, "w")
-            for i in range(NUMBER_OF_RANDOMS):
-                f.write("%g\n" % (random.random() * 100.0))
-        
-        #---------------------------------------------------------------
-        #
-        #   Split initial file
-        #
-        @follows(create_random_numbers)
-        @split(working_dir + "random_numbers.list", working_dir + "*.chunks")
-        def step_5_split_numbers_into_chunks (input_file_name, output_files):
-            """
-                Splits random numbers file into XXX files of CHUNK_SIZE each
-            """
-            #
-            #   clean up files from previous runs
-            #
-            for f in glob.glob("*.chunks"):
-                os.unlink(f)
-            #
-            #   create new file every CHUNK_SIZE lines and
-            #       copy each line into current file
-            #
-            output_file = None
-            cnt_files = 0
-            for i, line in enumerate(open(input_file_name)):
-                if i % CHUNK_SIZE == 0:
-                    cnt_files += 1
-                    output_file = open(working_dir + "%d.chunks" % cnt_files, "w")
-                output_file.write(line)
-        
-        #---------------------------------------------------------------
-        #
-        #   Calculate sum and sum of squares for each chunk file
-        #
-        @transform(step_5_split_numbers_into_chunks, suffix(".chunks"), ".sums")
-        def step_6_calculate_sum_of_squares (input_file_name, output_file_name):
-            output = open(output_file_name,  "w")
-            sum_squared, sum = [0.0, 0.0]
-            cnt_values = 0
-            for line in open(input_file_name):
-                cnt_values += 1
-                val = float(line.rstrip())
-                sum_squared += val * val
-                sum += val
-            output.write("%s\n%s\n%d\n" % (repr(sum_squared), repr(sum), cnt_values))
-        
-        
-        def print_hooray_again():
-            print "hooray again"
-        
-        def print_whoppee_again():
-            print "whoppee again"
-        
-        
-        #---------------------------------------------------------------
-        #
-        #   Calculate sum and sum of squares for each chunk
-        #
-        @posttask(lambda: sys.stdout.write("hooray\n"))
-        @posttask(print_hooray_again, print_whoppee_again, touch_file("done"))
-        @merge(step_6_calculate_sum_of_squares, "variance.result")
-        def step_7_calculate_variance (input_file_names, output_file_name):
-            """
-            Calculate variance naively
-            """
-            output = open(output_file_name,  "w")
-            #
-            #   initialise variables
-            #
-            all_sum_squared = 0.0
-            all_sum         = 0.0
-            all_cnt_values  = 0.0
-            #
-            # added up all the sum_squared, and sum and cnt_values from all the chunks
-            #
-            for input_file_name in input_file_names:
-                sum_squared, sum, cnt_values = map(float, open(input_file_name).readlines())
-                all_sum_squared += sum_squared
-                all_sum         += sum
-                all_cnt_values  += cnt_values
-            all_mean = all_sum / all_cnt_values
-            variance = (all_sum_squared - all_sum * all_mean)/(all_cnt_values)
-            #
-            #   print output
-            #
-            print >>output, variance
-        
-        #---------------------------------------------------------------
-        #
-        #       Run
-        #
-        pipeline_run([step_7_calculate_variance], verbose = 1)
-
-        
-
-************************************
-Resulting Output
-************************************
-    ::
-
-        >> pipeline_run([step_7_calculate_variance], verbose = 1)
-            Make directories [temp_tutorial8/] completed
-        Completed Task = create_random_numbers_mkdir_1
-            Job = [None -> temp_tutorial8/random_numbers.list] completed
-        Completed Task = create_random_numbers
-            Job = [temp_tutorial8/random_numbers.list -> temp_tutorial8/*.chunks] completed
-        Completed Task = step_5_split_numbers_into_chunks
-            Job = [temp_tutorial8/1.chunks -> temp_tutorial8/1.sums] completed
-            Job = [temp_tutorial8/10.chunks -> temp_tutorial8/10.sums] completed
-            Job = [temp_tutorial8/2.chunks -> temp_tutorial8/2.sums] completed
-            Job = [temp_tutorial8/3.chunks -> temp_tutorial8/3.sums] completed
-            Job = [temp_tutorial8/4.chunks -> temp_tutorial8/4.sums] completed
-            Job = [temp_tutorial8/5.chunks -> temp_tutorial8/5.sums] completed
-            Job = [temp_tutorial8/6.chunks -> temp_tutorial8/6.sums] completed
-            Job = [temp_tutorial8/7.chunks -> temp_tutorial8/7.sums] completed
-            Job = [temp_tutorial8/8.chunks -> temp_tutorial8/8.sums] completed
-            Job = [temp_tutorial8/9.chunks -> temp_tutorial8/9.sums] completed
-        Completed Task = step_6_calculate_sum_of_squares
-            Job = [[temp_tutorial8/1.sums, temp_tutorial8/10.sums, temp_tutorial8/2.sums, temp_tutorial8/3.sums, temp_tutorial8/4.sums, temp_tutorial8/5.sums, temp_tutorial8/6.sums, temp_tutorial8/7.sums, temp_tutorial8/8.sums, temp_tutorial8/9.sums] -> variance.result] completed
-        hooray again
-        whoppee again
-        hooray
-        Completed Task = step_7_calculate_variance
-        
diff --git a/doc/_build/html/_sources/why_ruffus.txt b/doc/_build/html/_sources/why_ruffus.txt
deleted file mode 100644
index 3e26396..0000000
--- a/doc/_build/html/_sources/why_ruffus.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-.. Design:
-
-.. include:: global.inc
-
-.. index::
-    pair: Ruffus; Etymology
-    pair: Ruffus; Name origins
-
-.. _design.why_ruffus:
-
-###############################
-Why *Ruffus*?
-###############################
-
-**Cylindrophis ruffus** is the name of the
-`red-tailed pipe snake <http://en.wikipedia.org/wiki/Cylindrophis_ruffus>`_ (bad python-y pun)
-which can be found in `Hong Kong <http://www.discoverhongkong.com/eng/index.html>`_ where the original author comes from.
-
-
-*Ruffus* is a shy creature, and pretends to be a cobra or a `banded krait  <http://en.wikipedia.org/wiki/File:Bandedkrait.jpg>`__ by putting up its red tail and ducking its
-head in its coils when startled.
-
-+------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-|   .. image:: images/wikimedia_cyl_ruffus.jpg                           |    .. image:: images/wikimedia_bandedkrait.jpg                                                                                                                                       |
-|                                                                        |        :scale: 77                                                                                                                                                                    |
-+------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| * Not venomous                                                         |  * Deadly poisonous                                                                                                                                                                  |
-| * `Mostly Harmless <http://en.wikipedia.org/wiki/Mostly_Harmless>`_    |  * `Seriously unfriendly  <http://en.wikipedia.org/wiki/List_of_races_and_species_in_The_Hitchhiker's_Guide_to_the_Galaxy#Ravenous_Bugblatter_Beast_of_Traal>`_                      |
-+------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-
-
-Be careful not to step on one when running down country park lanes at full speed
-in Hong Kong: this snake is a `rare breed <http://www.hkras.org/eng/info/hkspp.htm>`_!
-
-*Ruffus* does most of its work at night and sleeps during the day: typical of many (but alas not all) python programmers!
-
-The original `red-tail pipe  <http://upload.wikimedia.org/wikipedia/commons/a/a1/Cyl_ruffus_061212_2025_tdp.jpg>`__ and `banded krait  <http://en.wikipedia.org/wiki/File:AB_054_Banded_Krait.JPG>`__ images are from wikimedia.
diff --git a/doc/_build/html/_static/ajax-loader.gif b/doc/_build/html/_static/ajax-loader.gif
deleted file mode 100644
index 61faf8c..0000000
Binary files a/doc/_build/html/_static/ajax-loader.gif and /dev/null differ
diff --git a/doc/_build/html/_static/basic.css b/doc/_build/html/_static/basic.css
deleted file mode 100644
index a04c8e1..0000000
--- a/doc/_build/html/_static/basic.css
+++ /dev/null
@@ -1,540 +0,0 @@
-/*
- * basic.css
- * ~~~~~~~~~
- *
- * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-/* -- main layout ----------------------------------------------------------- */
-
-div.clearer {
-    clear: both;
-}
-
-/* -- relbar ---------------------------------------------------------------- */
-
-div.related {
-    width: 100%;
-    font-size: 90%;
-}
-
-div.related h3 {
-    display: none;
-}
-
-div.related ul {
-    margin: 0;
-    padding: 0 0 0 10px;
-    list-style: none;
-}
-
-div.related li {
-    display: inline;
-}
-
-div.related li.right {
-    float: right;
-    margin-right: 5px;
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index 8614442..0000000
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-        });
-      }, 10);
-      $('<p class="highlight-link"><a href="javascript:Documentation.' +
-        'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
-          .appendTo($('#searchbox'));
-    }
-  },
-
-  /**
-   * init the domain index toggle buttons
-   */
-  initIndexTable : function() {
-    var togglers = $('img.toggler').click(function() {
-      var src = $(this).attr('src');
-      var idnum = $(this).attr('id').substr(7);
-      $('tr.cg-' + idnum).toggle();
-      if (src.substr(-9) == 'minus.png')
-        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
-      else
-        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
-    }).css('display', '');
-    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
-        togglers.click();
-    }
-  },
-
-  /**
-   * helper function to hide the search marks again
-   */
-  hideSearchWords : function() {
-    $('#searchbox .highlight-link').fadeOut(300);
-    $('span.highlighted').removeClass('highlighted');
-  },
-
-  /**
-   * make the url absolute
-   */
-  makeURL : function(relativeURL) {
-    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
-  },
-
-  /**
-   * get the current relative url
-   */
-  getCurrentURL : function() {
-    var path = document.location.pathname;
-    var parts = path.split(/\//);
-    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
-      if (this == '..')
-        parts.pop();
-    });
-    var url = parts.join('/');
-    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
-  }
-};
-
-// quick alias for translations
-_ = Documentation.gettext;
-
-$(document).ready(function() {
-  Documentation.init();
-});
diff --git a/doc/_build/html/_static/down-pressed.png b/doc/_build/html/_static/down-pressed.png
deleted file mode 100644
index 6f7ad78..0000000
Binary files a/doc/_build/html/_static/down-pressed.png and /dev/null differ
diff --git a/doc/_build/html/_static/down.png b/doc/_build/html/_static/down.png
deleted file mode 100644
index 3003a88..0000000
Binary files a/doc/_build/html/_static/down.png and /dev/null differ
diff --git a/doc/_build/html/_static/example_scripts/complicated_example.py b/doc/_build/html/_static/example_scripts/complicated_example.py
deleted file mode 100755
index 3c626a8..0000000
--- a/doc/_build/html/_static/example_scripts/complicated_example.py
+++ /dev/null
@@ -1,527 +0,0 @@
-#!/usr/bin/env python
-"""
-
-    complicated_example.py
-
-"""
-
-import os, sys
-exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
-sys.path.append(os.path.abspath(os.path.join(exe_path,"..", "..")))
-from ruffus import *
-from time import sleep
-import random
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   options        
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-from optparse import OptionParser
-parser = OptionParser(version="%prog 1.0")
-parser.add_option("-t", "--target_tasks", dest="target_tasks",
-                  action="append",
-                  default = ["summarise_all"],
-                  metavar="JOBNAME", 
-                  type="string",
-                  help="Target task(s) of pipeline.")
-parser.add_option("-f", "--forced_tasks", dest="forced_tasks",
-                  action="append",
-                  default = list(),
-                  metavar="JOBNAME", 
-                  type="string",
-                  help="Pipeline task(s) which will be included even if they are up to date.")
-parser.add_option("-j", "--jobs", dest="jobs",
-                  default=5,
-                  metavar="jobs", 
-                  type="int",
-                  help="Specifies the number of jobs (commands) to run simultaneously.")
-
-parser.add_option("-d", "--data_dir", dest="data_dir",
-                  default="%s/data_for_complicated_example" % exe_path,
-                  metavar="PATH", 
-                  type="string",
-                  help="Directory with starting data [*.fa].")
-parser.add_option("-w", "--working_dir", dest="working_dir",
-                  default="/working_dir",
-                  metavar="PATH", 
-                  type="string",
-                  help="Working directory.")
-
-
-parser.add_option("-v", "--verbose", dest = "verbose",
-                  action="store_true", default=False,
-                  help="Do not echo to shell but only print to log.")
-parser.add_option("-D", "--dependency", dest="dependency_file",
-                  metavar="FILE", 
-                  type="string",
-                  help="Print a dependency graph of the pipeline that would be executed "
-                        "to FILE, but do not execute it.")
-parser.add_option("-F", "--dependency_graph_format", dest="dependency_graph_format",
-                  metavar="FORMAT", 
-                  type="string",
-                  default = 'svg',
-                  help="format of dependency graph file. Can be 'ps' (PostScript), "+
-                  "'svg' 'svgz' (Structured Vector Graphics), " +
-                  "'png' 'gif' (bitmap  graphics) etc ")
-parser.add_option("-n", "--just_print", dest="just_print",
-                    action="store_true", default=False,
-                    help="Print a description of the jobs that would be executed, "
-                        "but do not execute them.")
-
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   imports        
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-import StringIO
-import re
-import operator
-import sys
-from collections import defaultdict
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Functions
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#_________________________________________________________________________________________
-#
-#   Helper function:
-# 
-#       split_gene_files 
-#
-#_________________________________________________________________________________________
-def split_gene_files (  gene_file_name, 
-                        job_completion_flag_file_name,
-                        split_output_dir):
-    """
-    Helper function to simulate splitting gene files into "chunks" suitable for
-        parallel jobs on a computational cluster       
-
-    The number of output files is only known at runtime
-        because the number of "chunks" depend on the size    
-        of starting the gene sets                            
-
-    We simulate this using a random number from 20->50 
-    """
-
-    #
-    #   make output directory
-    #    
-    if not os.path.exists(split_output_dir):
-        os.makedirs(split_output_dir)
-
-    # save number of chunks for later tasks
-    number_of_output_files = int(random.uniform(20, 50))
-
-    for index in range(number_of_output_files):
-        open("%s/%d.fa" % (split_output_dir, index), "w")
-    open(job_completion_flag_file_name, "w")
-
-
-#_________________________________________________________________________________________
-#
-#   get_unknown_gene_set_names
-#   get_species_names
-#   
-#   
-#   functions for getting unknown gene set names and species names
-#
-#_________________________________________________________________________________________
-import glob, re
-def get_chunked_gene_file_names (dir_name):
-    """
-    Get list of gene file names
-    Helper function for getting unknown gene set names, and species names
-    """
-    regex = re.compile(r".+/(.+).genes.fa")
-    gene_set_names = []
-    for file_name in glob.glob("%s/%s/*.genes.fa"   % (d_dir, dir_name)):
-        m = regex.search(file_name)
-        gene_set_names.append(m.group(1))
-    return gene_set_names
-def get_unknown_gene_set_names ():
-    return get_chunked_gene_file_names("unknown_genes")
-def get_species_names ():
-    return get_chunked_gene_file_names("all_genes_in_each_species")
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Main logic
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-
-
-
-# get help string
-f =StringIO.StringIO()
-parser.print_help(f)
-helpstr = f.getvalue()
-(options, remaining_args) = parser.parse_args()
-
-
-d_dir = options.data_dir
-w_dir = options.working_dir
-
-
-
-
-#_________________________________________________________________________________________
-#
-#   Step 1:
-#       
-#       split_unknown_gene_set
-#       
-#           data_dir/unknown_genes/XXX.genes.fa
-#               ->working_dir/XXX/split_gene_sets.completed
-#               ->working_dir/XXX/NNN.fa
-#       
-#_________________________________________________________________________________________
- at follows(mkdir(w_dir))
- at files_re("%s/unknown_genes/*.genes.fa"      % d_dir,
-          r"(.*/)(.*)(\.genes.fa)",                    
-          r"\1\2\3",                                   # unknown_gene_set file name
-          r"%s/\2/split_gene_sets.completed" % w_dir,  # job_completion_flag
-          r"%s/\2"                           % w_dir)  # split_output_dir
-def split_unknown_gene_set( starting_gene_set, 
-                            job_completion_flag,
-                            split_output_dir):
-    """
-    Simulate splitting gene files for unknown gene set into "chunks" suitable for
-        parallel jobs on a computational cluster       
-    """
-    split_gene_files (  starting_gene_set, 
-                        job_completion_flag,
-                        split_output_dir)
-    sleep(1)
-    
-    
-#_________________________________________________________________________________________
-#
-#   Step 2:
-#       
-#       split_per_species_gene_sets
-
-#           data_dir/all_genes_in_each_species/YYY.genes.fa
-#               ->working_dir/species_YYY/split_gene_sets.completed
-#               ->working_dir/species_YYY/MMM.fa
-#       
-#_________________________________________________________________________________________
- at follows(mkdir(w_dir))
- at files_re("%s/all_genes_in_each_species/*.genes.fa"  % d_dir,
-          r"(.*/)(.*)(\.genes.fa)",                    
-          r"\1\2\3",                                           # all_genes_in_species
-          r"%s/species_\2/split_gene_sets.completed" % w_dir,  # job_completion_flag
-          r"%s/species_\2"                           % w_dir)  # split_output_dir
-def split_per_species_gene_sets(all_genes_in_species, 
-                                job_completion_flag,
-                                split_output_dir):
-    """
-    Simulate splitting gene files for each species into "chunks" suitable for
-        parallel jobs on a computational cluster       
-    """
-    split_gene_files (  all_genes_in_species, 
-                        job_completion_flag,
-                        split_output_dir)
-    sleep(1)
-
-
-
-#_________________________________________________________________________________________
-#
-#   Step 3:
-#       
-#       all_vs_all_comparisons
-#                 working_dir/species_YYY/MMM.fa
-#                 working_dir/XXX/NNN.fa
-#                                 -> compare/x/y.n.m.comparison_res
-#                                 -> compare/x/y.n.m.complete
-#       
-#_________________________________________________________________________________________
-#
-#           function for generating custom parameters
-#
-def generate_all_vs_all_params ():
-    """
-    Custom function to generate 
-    all vs. all file names for the various "chunks"
-    """
-
-    chunk_index_regex = re.compile(r".+/(.+).fa")
-    def parse_index_from_chunk_filename (chunk_filename):
-        match = chunk_index_regex.search(chunk_filename)
-        return int(match.group(1))
-       
-    species_names = get_species_names()
-    gene_set_names = get_unknown_gene_set_names()
-    for x in gene_set_names:
-        for y in species_names:
-            y = "species_" + y
-            
-            m_files = glob.glob("%s/%s/*.fa" % (w_dir, x))
-            n_files = glob.glob("%s/%s/*.fa" % (w_dir, y))
-
-            #
-            #    for each species chunk vs for each unknown chunk
-            # 
-            for m_file in m_files:
-                for n_file in n_files:
-                    input_files = [m_file, n_file]
-                    output_dir  = "%s/compare/%s" % (w_dir, x)
-
-                    m = parse_index_from_chunk_filename(m_file)
-                    n = parse_index_from_chunk_filename(n_file)
-
-                    job_completion_flag  = output_dir + "/%s.%d.%d.complete" % (y, m, n)
-                    result_file          = output_dir + "/%s.%d.%d.comparison_res" % (y, m, n)
-                    name                 = "%s -> %d vs %d\n" % (y, m, n)
-                    yield input_files, job_completion_flag, output_dir, result_file, name
-    
-
-    
- at follows(split_unknown_gene_set, split_per_species_gene_sets)
- at files(generate_all_vs_all_params)
-def all_vs_all_comparisons(file_chunks, 
-                           job_completion_flag,
-                           output_dir,
-                           result_file,
-                           name):
-    """
-    Simulate comparison of gene chunks against each  other
-    Normally runs in parallel on a computational cluster       
-    """
-
-    #
-    #   make output directory
-    #    
-    try:
-        os.makedirs(output_dir)
-    except OSError:
-        pass
-    
-    open(job_completion_flag, "w")
-    open(result_file, "w").write(name)
-
-
-#_________________________________________________________________________________________
-#
-#   Step 4:
-#       
-#       Recombine: alignment results to make gene families
-#            compare/x/*.comparison_res
-#               -> multiple_alignment/x/x.gene_families
-#       
-#_________________________________________________________________________________________
-
-#
-#   generate_params_for_making_gene_families
-#       
-#           function for generating custom parameters
-#
-def generate_params_for_making_gene_families ():
-    """
-    Custom function to combining comparison files into gene families
-    """
-    gene_set_names = get_unknown_gene_set_names()
-    for x in gene_set_names:
-        results_files = glob.glob("%s/compare/%s/*.comparison_res" % (w_dir, x))
-        output_dir = "%s/multiple_alignment/%s" % (w_dir, x)
-        family_file = "%s/gene.families" % output_dir
-        yield results_files, family_file, output_dir
-
-
- at follows(all_vs_all_comparisons)
- at files(generate_params_for_making_gene_families)
-def combine_into_gene_familes (results_files, family_file_name, output_dir):
-    """
-    Simulate making gene families by concatenating comparison results :-)
-    """
-    #
-    #   make output directory
-    #    
-    if not os.path.exists(output_dir):
-        os.makedirs(output_dir)
-
-    family_file = open(family_file_name, "w")
-    for f in results_files:
-        family_file.write(open(f).read())
-    sleep(1)
-
-#_________________________________________________________________________________________
-#
-#   Step 5:
-#       
-#       split_gene_family_for_evolutionary_analysis
-#           multiple_alignment/x/x.gene_families
-#               -> multiple_alignment/x/NNN.aln
-#               -> multiple_alignment/x/split.completed
-#       
-#_________________________________________________________________________________________
- at follows(combine_into_gene_familes)
- at files_re("%s/multiple_alignment/*/gene.families"      % w_dir,
-          r"(.+)/(gene.families)",                    
-          r"\1/\2",                                   
-          r"\1/split.completed",
-          r"\1")
-def split_gene_family_for_evolutionary_analysis( family_file, 
-                                                 job_completion_flag_file, split_output_dir):
-    """
-    Simulate splitting family of genes into "chunks" suitable for
-        parallel jobs on a computational cluster       
-    """
-
-    # save number of chunks for later tasks
-    number_of_output_files = int(random.uniform(20, 50))
-    
-    for index in range(number_of_output_files):
-        open("%s/%d.aln" % (split_output_dir, index), "w").write("chunk %d" % index)
-    open(job_completion_flag_file, "w")
-    sleep(1)
-
-
-#_________________________________________________________________________________________
-#
-#   Step 6:
-#       
-#       evolution_analysis
-#           multiple_alignment/x/NNN.aln
-#               -> multiple_alignment/x/NNN.evo_res
-#       
-#_________________________________________________________________________________________
- at follows(split_gene_family_for_evolutionary_analysis)
- at files_re("%s/multiple_alignment/*/*.aln"      % w_dir,
-          r"(.+).aln",                    
-          r"\1.evo_res")
-def evolution_analysis( family_file, result_file_name):
-    """
-    Simulate evolutionary analysis
-    """
-
-    result_file = open(result_file_name, "w")
-    result_file.write(family_file + "\n")
-    sleep(1)
-
-    
-#_________________________________________________________________________________________
-#
-#   Step 7:
-#       
-#       combine_evolution_analysis
-#           multiple_alignment/x/NNN.evo_res
-#               -> evolutionary_analysis/x.results
-#       
-#_________________________________________________________________________________________
-    
-#
-#   generate_params_for_combining_evolutionary_analyses
-#       
-#           function for generating custom parameters
-#
-def generate_params_for_combining_evolutionary_analyses ():
-    """
-    Custom function to combining evolutionary analyses per unknown gene set
-    """
-    gene_set_names = get_unknown_gene_set_names()
-    for x in gene_set_names:
-        results_files = glob.glob("%s/multiple_alignment/%s/*.evo_res" % (w_dir, x))
-        combined_file = "%s/evolutionary_analysis/%s.results" % (w_dir, x)
-        yield results_files, combined_file
-        
- at follows(evolution_analysis, mkdir("%s/evolutionary_analysis" % w_dir))
- at files(generate_params_for_combining_evolutionary_analyses)
-def combine_evolution_analysis (results_files, combined_file_name):
-    """
-    Simular combining evolutionary analyses
-    """
-    combined_file = open(combined_file_name, "w")
-    for f  in results_files:
-        combined_file.write(open(f).read())
-    sleep(1)
-    
-    
-
-#_________________________________________________________________________________________
-#
-#   Step 8:
-#       
-#       summarise_evolution_analysis
-#           evolutionary_analysis/x.results
-#                -> evolutionary_analysis/x.summary
-#       
-#_________________________________________________________________________________________
- at follows(combine_evolution_analysis)
- at files_re("%s/evolutionary_analysis/*.results"      % w_dir,
-          r"(.+).results",                    
-          r"\1.summary")
-def summarise_evolution_analysis( results_file, summary_file_name):
-    """
-    Simulate summary of evolutionary analysis
-    """
-    summary_file = open(summary_file_name, "w")
-    summary_file.write("summary of " + open(results_file).read())
-    sleep(1)
-
-
-#_________________________________________________________________________________________
-#
-#   Step 9:
-#       
-#       summarise_all
-#       evolutionary_analysis/x.summary
-#           -> all.total_summary
-#       
-#_________________________________________________________________________________________
-summary_file_names = ["%s/evolutionary_analysis/%s.summary" % (w_dir, n) 
-                        for n in get_unknown_gene_set_names()]
-total_summary_file_name = "%s/all.total_summary" % w_dir
-
- at follows(summarise_evolution_analysis)
- at files(summary_file_names, total_summary_file_name)
-def summarise_all( summary_files, total_summary_file_name):
-    """
-    Simulate summarize all
-    """
-    total_summary_file = open(total_summary_file_name, "w")
-    total_summary_file.write("Over all Summary:\n")
-    for f in summary_files:
-        total_summary_file.write(open(f).read())
-    sleep(1)
-
-
-
-    
-    
-    
-    
-#888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888    
-#
-#   print pipeline or run pipeline
-# 
-
-if options.just_print:
-    pipeline_printout(sys.stdout, options.target_tasks, options.forced_tasks, long_winded=True)
-
-elif options.dependency_file:
-    graph_printout (     open(options.dependency_file, "w"),
-                         options.dependency_graph_format,
-                         options.target_tasks, 
-                         options.forced_tasks)
-else:    
-    pipeline_run(options.target_tasks, options.forced_tasks, multiprocess = options.jobs)
-    
diff --git a/doc/_build/html/_static/example_scripts/intermediate_example.py b/doc/_build/html/_static/example_scripts/intermediate_example.py
deleted file mode 100755
index 8128903..0000000
--- a/doc/_build/html/_static/example_scripts/intermediate_example.py
+++ /dev/null
@@ -1,313 +0,0 @@
-#!/usr/bin/env python
-"""
-
-    intermediate_example.py
-    
-        This script takes N pairs of input file pairs
-                                (with the suffices .gene and .gwas)
-                          and runs them against M sets of simulation data
-                                (with the suffix .simulation)
-        A summary per input file pair is then produced
-                    
-        
-    In pseudo-code:
-        
-        STEP_1:
-        
-        for n_file in NNN_pairs_of_input_files:
-            for m_file in MMM_simulation_data:
-
-                [n_file.gene,
-                 n_file.gwas,
-                 m_file.simulation] -> n_file.m_file.simulation_res
-                 
-
-        STEP_2:
-        
-        for n_file in NNN_pairs_of_input_files:
-            
-            n_file.*.simulation_res -> n_file.mean
-            
-        
-
-"""
-
-import os, sys
-exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
-from ruffus import *
-from time import sleep
-import random
-from itertools import izip
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   options        
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-from optparse import OptionParser
-parser = OptionParser(version="%prog 1.0")
-parser.add_option("-t", "--target_tasks", dest="target_tasks",
-                  action="append",
-                  default = ["statistical_summary"],
-                  metavar="JOBNAME", 
-                  type="string",
-                  help="Target task(s) of pipeline.")
-parser.add_option("-f", "--forced_tasks", dest="forced_tasks",
-                  action="append",
-                  default = list(),
-                  metavar="JOBNAME", 
-                  type="string",
-                  help="Pipeline task(s) which will be included even if they are up to date.")
-parser.add_option("-j", "--jobs", dest="jobs",
-                  default=5,
-                  metavar="jobs", 
-                  type="int",
-                  help="Specifies the number of jobs (commands) to run simultaneously.")
-
-parser.add_option("-g", "--gene_data_dir", dest="gene_data_dir",
-                  default="%s/data_for_intermediate_example/genes" % exe_path,
-                  metavar="PATH", 
-                  type="string",
-                  help="Directory with gene data [*.genes / *.gwas].")
-parser.add_option("-s", "--simulation_data_dir", dest="simulation_data_dir",
-                  default="%s/data_for_intermediate_example/simulation" % exe_path,
-                  metavar="PATH", 
-                  type="string",
-                  help="Directory with simulation data [*.simulation].")
-parser.add_option("-w", "--working_dir", dest="working_dir",
-                  default="/working_dir",
-                  metavar="PATH", 
-                  type="string",
-                  help="Working directory.")
-
-
-parser.add_option("-v", "--verbose", dest = "verbose",
-                  action="store_true", default=False,
-                  help="Do not echo to shell but only print to log.")
-parser.add_option("-D", "--dependency", dest="dependency_file",
-                  metavar="FILE", 
-                  type="string",
-                  help="Print a dependency graph of the pipeline that would be executed "
-                        "to FILE, but do not execute it.")
-parser.add_option("-F", "--dependency_graph_format", dest="dependency_graph_format",
-                  metavar="FORMAT", 
-                  type="string",
-                  default = 'svg',
-                  help="format of dependency graph file. Can be 'ps' (PostScript), "+
-                  "'svg' 'svgz' (Structured Vector Graphics), " +
-                  "'png' 'gif' (bitmap  graphics) etc ")
-parser.add_option("-n", "--just_print", dest="just_print",
-                    action="store_true", default=False,
-                    help="Print a description of the jobs that would be executed, "
-                        "but do not execute them.")
-
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   imports        
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-import StringIO
-import re
-import operator
-import sys
-from collections import defaultdict
-import glob
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Functions
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-#_________________________________________________________________________________________
-#
-#   get gene gwas file pairs
-#
-#_________________________________________________________________________________________
-def get_gene_gwas_file_pairs(  ):
-    """
-    Helper function to get all *.gene, *.gwas from the direction specified
-        in --gene_data_dir
-        
-    Returns 
-        file pairs with both .gene and .gwas extensions, 
-        corresponding roots (no extension) of each file
-    """
-    
-
-    gene_files = glob.glob(os.path.join(options.gene_data_dir, "*.gene"))
-    gwas_files = glob.glob(os.path.join(options.gene_data_dir, "*.gwas"))
-    
-    common_roots = set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gene_files))
-    common_roots &=set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gwas_files))
-    common_roots = list(common_roots)
-        
-    p = os.path; g_dir = options.gene_data_dir
-    
-    file_pairs = [[p.join(g_dir, x + ".gene"), p.join(g_dir, x + ".gwas")] for x in common_roots]
-    
-    return file_pairs, common_roots
-
-#_________________________________________________________________________________________
-#
-#   get simulation files
-#
-#_________________________________________________________________________________________
-def get_simulation_files(  ):
-    """
-    Helper function to get all *.simulation from the direction specified
-        in --simulation_data_dir
-        Returns 
-            file with .simulation extensions, 
-            corresponding roots (no extension) of each file
-    """
-    simulation_files = glob.glob(os.path.join(options.simulation_data_dir, "*.simulation"))
-    simulation_roots =map(lambda x: os.path.splitext(os.path.split(x)[1])[0], simulation_files)
-    return simulation_files, simulation_roots
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Main logic
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-
-
-
-# get help string
-f =StringIO.StringIO()
-parser.print_help(f)
-helpstr = f.getvalue()
-(options, remaining_args) = parser.parse_args()
-
-
-working_dir = options.working_dir
-
-
-
-
-#_________________________________________________________________________________________
-#
-#   Step 1:
-#       
-#        for n_file in NNN_pairs_of_input_files:
-#            for m_file in MMM_simulation_data:
-#
-#                [n_file.gene,
-#                 n_file.gwas,
-#                 m_file.simulation] -> working_dir/n_file.m_file.simulation_res
-#
-#_________________________________________________________________________________________
-def generate_simulation_params ():
-    """
-    Custom function to generate 
-    file names for gene/gwas simulation study
-    """
-
-    simulation_files, simulation_file_roots    = get_simulation_files()
-    gene_gwas_file_pairs, gene_gwas_file_roots =  get_gene_gwas_file_pairs()
-    
-    for sim_file, sim_file_root in izip(simulation_files, simulation_file_roots):
-        for (gene, gwas), gene_file_root in izip(gene_gwas_file_pairs, gene_gwas_file_roots):
-            
-            result_file = "%s.%s.simulation_res" % (gene_file_root, sim_file_root)
-            result_file_path = os.path.join(working_dir, "simulation_results", result_file)
-            
-            yield [gene, gwas, sim_file], result_file_path, gene_file_root, sim_file_root, result_file
-
-# 
-# mkdir: makes sure output directories exist before task    
-#
- at follows(mkdir(options.working_dir, os.path.join(working_dir, "simulation_results")))
- at files(generate_simulation_params)
-def gwas_simulation(input_files, result_file_path, gene_file_root, sim_file_root, result_file):
-    """
-    Dummy calculation of gene gwas vs simulation data
-    Normally runs in parallel on a computational cluster       
-    """
-    (gene_file,
-    gwas_file,
-    simulation_data_file) = input_files
-
-    simulation_res_file = open(result_file_path, "w")
-    simulation_res_file.write("%s + %s -> %s\n" % (gene_file_root, sim_file_root, result_file))
-
-
-#_________________________________________________________________________________________
-#
-#   Step 2:
-#       
-#       Statistical summary per gene/gwas file pair
-# 
-#        for n_file in NNN_pairs_of_input_files:
-#            working_dir/simulation_results/n.*.simulation_res
-#               -> working_dir/n.mean
-#       
-#_________________________________________________________________________________________
-def generate_statistical_summary_params():
-    """
-    Custom function to summarising simulation results files per gene / gwas file pair
-    """
-    gene_gwas_file_pairs, gene_gwas_file_roots =  get_gene_gwas_file_pairs()
-
-    for (gene, gwas), gene_file_root in izip(gene_gwas_file_pairs, gene_gwas_file_roots):
-            result_glob_spec = "%s.*.simulation_res" % (gene_file_root)
-            result_files     = glob.glob(os.path.join(working_dir, "simulation_results", result_glob_spec))
-            summary_file     = os.path.join(working_dir, gene_file_root + ".mean")
-                
-            yield result_files, summary_file
-                
-
-
- at follows(gwas_simulation)
- at files(generate_statistical_summary_params)
- at posttask(lambda : sys.stdout.write("\nAll finished: hooray!!!\n"))
-def statistical_summary (result_files, summary_file):
-    """
-    Simulate statistical summary
-    """
-
-    summary_file = open(summary_file, "w")
-    for f in result_files:
-        summary_file.write(open(f).read())
-    sleep(1)
-    
-
-
-
-
-
-    
-    
-    
-    
-#888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888    
-#
-#   print pipeline or run pipeline
-# 
-
-if options.just_print:
-    pipeline_printout(sys.stdout, options.target_tasks, options.forced_tasks, long_winded=True)
-
-elif options.dependency_file:
-    graph_printout (     open(options.dependency_file, "w"),
-                         options.dependency_graph_format,
-                         options.target_tasks, 
-                         options.forced_tasks)
-else:    
-    pipeline_run(options.target_tasks, options.forced_tasks, multiprocess = options.jobs)
-    
diff --git a/doc/_build/html/_static/example_scripts/play_with_colours.py b/doc/_build/html/_static/example_scripts/play_with_colours.py
deleted file mode 100644
index 5054aa4..0000000
--- a/doc/_build/html/_static/example_scripts/play_with_colours.py
+++ /dev/null
@@ -1,268 +0,0 @@
-#!/usr/bin/env python
-"""
-
-    play_with_colours.py
-    [--log_file PATH]
-    [--verbose]
-
-"""
-
-################################################################################
-#
-#   test
-#
-#
-#   Copyright (c) 7/13/2010 Leo Goodstadt
-#
-#   Permission is hereby granted, free of charge, to any person obtaining a copy
-#   of this software and associated documentation files (the "Software"), to deal
-#   in the Software without restriction, including without limitation the rights
-#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-#   copies of the Software, and to permit persons to whom the Software is
-#   furnished to do so, subject to the following conditions:
-#
-#   The above copyright notice and this permission notice shall be included in
-#   all copies or substantial portions of the Software.
-#
-#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-#   THE SOFTWARE.
-#################################################################################
-
-import sys, os
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   options
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-from optparse import OptionParser
-import StringIO
-
-parser = OptionParser(version="%play_with_colours 1.0",
-                      usage = "\n\n    play_with_colours "
-                                "--flowchart FILE [options] "
-                                "[--colour_scheme_index INT ] "
-                                "[--key_legend_in_graph]")
-
-#
-#   pipeline
-#
-parser.add_option("--flowchart", dest="flowchart",
-                    metavar="FILE",
-                    type="string",
-                    help="Don't actually run any commands; just print the pipeline "
-                         "as a flowchart.")
-parser.add_option("--colour_scheme_index", dest="colour_scheme_index",
-                    metavar="INTEGER",
-                    type="int",
-                    help="Index of colour scheme for flow chart.")
-parser.add_option("--key_legend_in_graph", dest="key_legend_in_graph",
-                    action="store_true", default=False,
-                    help="Print out legend and key for dependency graph.")
-
-(options, remaining_args) = parser.parse_args()
-if not options.flowchart:
-    raise Exception("Missing mandatory parameter: --flowchart.\n")
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   imports
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-from ruffus import *
-from ruffus.ruffus_exceptions import JobSignalledBreak
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Pipeline
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-#
-# up to date tasks
-#
- at check_if_uptodate (lambda : (False, ""))
-def Up_to_date_task1(infile, outfile):
-    pass
-
- at check_if_uptodate (lambda : (False, ""))
- at follows(Up_to_date_task1)
-def Up_to_date_task2(infile, outfile):
-    pass
-
- at check_if_uptodate (lambda : (False, ""))
- at follows(Up_to_date_task2)
-def Up_to_date_task3(infile, outfile):
-    pass
-
-
- at check_if_uptodate (lambda : (False, ""))
- at follows(Up_to_date_task3)
-def Up_to_date_final_target(infile, outfile):
-    pass
-
-
-#
-# Explicitly specified
-#
- at check_if_uptodate (lambda : (False, ""))
- at follows(Up_to_date_task1)
-def Explicitly_specified_task(infile, outfile):
-    pass
-
-
-
-#
-# Tasks to run
-#
- at follows(Explicitly_specified_task)
-def Task_to_run1(infile, outfile):
-    pass
-
-
- at follows(Task_to_run1)
-def Task_to_run2(infile, outfile):
-    pass
-
- at follows(Task_to_run2)
-def Task_to_run3(infile, outfile):
-    pass
-
- at check_if_uptodate (lambda : (False, ""))
- at follows(Task_to_run2)
-def Up_to_date_task_forced_to_rerun(infile, outfile):
-    pass
-
-
-#
-# Final target
-#
- at follows(Up_to_date_task_forced_to_rerun, Task_to_run3)
-def Final_target(infile, outfile):
-    pass
-
-#
-# Ignored downstream
-#
- at follows(Final_target)
-def Downstream_task1_ignored(infile, outfile):
-    pass
-
- at follows(Final_target)
-def Downstream_task2_ignored(infile, outfile):
-    pass
-
-
-
-
-
-
-
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Main logic
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-from collections import defaultdict
-custom_flow_chart_colour_scheme = defaultdict(dict)
-
-#
-#   Base chart on this overall colour scheme index
-#
-custom_flow_chart_colour_scheme["colour_scheme_index"] = options.colour_scheme_index
-
-#
-#   Overriding colours
-#
-if options.colour_scheme_index == None:
-    custom_flow_chart_colour_scheme["Vicious cycle"]["linecolor"]                        = '"#FF3232"'
-    custom_flow_chart_colour_scheme["Pipeline"]["fontcolor"]                             = '"#FF3232"'
-    custom_flow_chart_colour_scheme["Key"]["fontcolor"]                                  = "black"
-    custom_flow_chart_colour_scheme["Key"]["fillcolor"]                                  = '"#F6F4F4"'
-    custom_flow_chart_colour_scheme["Task to run"]["linecolor"]                          = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Up-to-date"]["linecolor"]                           = "gray"
-    custom_flow_chart_colour_scheme["Final target"]["fillcolor"]                         = '"#EFA03B"'
-    custom_flow_chart_colour_scheme["Final target"]["fontcolor"]                         = "black"
-    custom_flow_chart_colour_scheme["Final target"]["color"]                             = "black"
-    custom_flow_chart_colour_scheme["Final target"]["dashed"]                            = 0
-    custom_flow_chart_colour_scheme["Vicious cycle"]["fillcolor"]                        = '"#FF3232"'
-    custom_flow_chart_colour_scheme["Vicious cycle"]["fontcolor"]                        = 'white'
-    custom_flow_chart_colour_scheme["Vicious cycle"]["color"]                            = "white"
-    custom_flow_chart_colour_scheme["Vicious cycle"]["dashed"]                           = 0
-    custom_flow_chart_colour_scheme["Up-to-date task"]["fillcolor"]                      = '"#B8CC6E"'
-    custom_flow_chart_colour_scheme["Up-to-date task"]["fontcolor"]                      = '"#006000"'
-    custom_flow_chart_colour_scheme["Up-to-date task"]["color"]                          = '"#006000"'
-    custom_flow_chart_colour_scheme["Up-to-date task"]["dashed"]                         = 0
-    custom_flow_chart_colour_scheme["Down stream"]["fillcolor"]                          = "white"
-    custom_flow_chart_colour_scheme["Down stream"]["fontcolor"]                          = "gray"
-    custom_flow_chart_colour_scheme["Down stream"]["color"]                              = "gray"
-    custom_flow_chart_colour_scheme["Down stream"]["dashed"]                             = 0
-    custom_flow_chart_colour_scheme["Explicitly specified task"]["fillcolor"]            = "transparent"
-    custom_flow_chart_colour_scheme["Explicitly specified task"]["fontcolor"]            = "black"
-    custom_flow_chart_colour_scheme["Explicitly specified task"]["color"]                = "black"
-    custom_flow_chart_colour_scheme["Explicitly specified task"]["dashed"]               = 0
-    custom_flow_chart_colour_scheme["Task to run"]["fillcolor"]                          = '"#EBF3FF"'
-    custom_flow_chart_colour_scheme["Task to run"]["fontcolor"]                          = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Task to run"]["color"]                              = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Task to run"]["dashed"]                             = 0
-    custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["fillcolor"]      = 'transparent'
-    custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["fontcolor"]      = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["color"]          = '"#0044A0"'
-    custom_flow_chart_colour_scheme["Up-to-date task forced to rerun"]["dashed"]         = 1
-    custom_flow_chart_colour_scheme["Up-to-date Final target"]["fillcolor"]              = '"#EFA03B"'
-    custom_flow_chart_colour_scheme["Up-to-date Final target"]["fontcolor"]              = '"#006000"'
-    custom_flow_chart_colour_scheme["Up-to-date Final target"]["color"]                  = '"#006000"'
-    custom_flow_chart_colour_scheme["Up-to-date Final target"]["dashed"]                 = 0
-
-if __name__ == '__main__':
-    pipeline_printout_graph (
-
-                                    open(options.flowchart, "w"),
-                                    # use flowchart file name extension to decide flowchart format
-                                    #   e.g. svg, jpg etc.
-                                    os.path.splitext(options.flowchart)[1][1:],
-
-                                    # final targets
-                                    [Final_target, Up_to_date_final_target],
-
-                                    # Explicitly specified tasks
-                                    [Explicitly_specified_task],
-
-                                    # Do we want key legend
-                                    no_key_legend   = not options.key_legend_in_graph,
-
-                                    # Print all the task types whether used or not
-                                    minimal_key_legend             = False,
-
-                                    user_colour_scheme = custom_flow_chart_colour_scheme,
-                                    pipeline_name = "Colour schemes")
-
-
-
-
-
-
-
-
diff --git a/doc/_build/html/_static/example_scripts/ruffus_template.py b/doc/_build/html/_static/example_scripts/ruffus_template.py
deleted file mode 100644
index 69a082d..0000000
--- a/doc/_build/html/_static/example_scripts/ruffus_template.py
+++ /dev/null
@@ -1,270 +0,0 @@
-#!/usr/bin/env python
-"""
-
-    ruffus_template.py
-                        [--log_file PATH]
-                        [--verbose]
-                        [--target_tasks]
-                        [--jobs]
-                        [--just_print]
-                        [--flowchart]
-                        [--key_legend_in_graph]
-                        [--forced_tasks]
-
-"""
-import sys, os
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   options
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-if __name__ == '__main__':
-    from optparse import OptionParser
-    import StringIO
-
-    parser = OptionParser(version="%prog 1.0", usage = "\n\n    %progs [options]")
-
-
-
-    #
-    #   general options: verbosity / logging
-    #
-    parser.add_option("-v", "--verbose", dest = "verbose",
-                      action="count", default=0,
-                      help="Print more verbose messages for each additional verbose level.")
-    parser.add_option("-L", "--log_file", dest="log_file",
-                      metavar="FILE",
-                      type="string",
-                      help="Name and path of log file")
-
-
-
-
-    #
-    #   pipeline
-    #
-    parser.add_option("-t", "--target_tasks", dest="target_tasks",
-                        action="append",
-                        default = list(),
-                        metavar="JOBNAME",
-                        type="string",
-                        help="Target task(s) of pipeline.")
-    parser.add_option("-j", "--jobs", dest="jobs",
-                        default=1,
-                        metavar="N",
-                        type="int",
-                        help="Allow N jobs (commands) to run simultaneously.")
-    parser.add_option("-n", "--just_print", dest="just_print",
-                        action="store_true", default=False,
-                        help="Don't actually run any commands; just print the pipeline.")
-    parser.add_option("--flowchart", dest="flowchart",
-                        metavar="FILE",
-                        type="string",
-                        help="Don't actually run any commands; just print the pipeline "
-                             "as a flowchart.")
-
-    #
-    #   Less common pipeline options
-    #
-    parser.add_option("--key_legend_in_graph", dest="key_legend_in_graph",
-                        action="store_true", default=False,
-                        help="Print out legend and key for dependency graph.")
-    parser.add_option("--forced_tasks", dest="forced_tasks",
-                        action="append",
-                        default = list(),
-                        metavar="JOBNAME",
-                        type="string",
-                        help="Pipeline task(s) which will be included even if they are up to date.")
-
-    # get help string
-    f =StringIO.StringIO()
-    parser.print_help(f)
-    helpstr = f.getvalue()
-    (options, remaining_args) = parser.parse_args()
-
-
-    #vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
-    #                                             #
-    #   Change this if necessary                  #
-    #                                             #
-    #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-    #
-    #   Add names of mandatory options,
-    #       strings corresponding to the "dest" parameter
-    #       in the options defined above
-    #
-    mandatory_options = [ ]
-
-    #vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
-    #                                             #
-    #   Change this if necessary                  #
-    #                                             #
-    #^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-    def check_mandatory_options (options, mandatory_options, helpstr):
-        """
-        Check if specified mandatory options have b een defined
-        """
-        missing_options = []
-        for o in mandatory_options:
-            if not getattr(options, o):
-                missing_options.append("--" + o)
-
-        if not len(missing_options):
-            return
-
-        raise Exception("Missing mandatory parameter%s: %s.\n\n%s\n\n" %
-                        ("s" if len(missing_options) > 1 else "",
-                         ", ".join(missing_options),
-                         helpstr))
-    check_mandatory_options (options, mandatory_options, helpstr)
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   imports
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-from ruffus import *
-from ruffus.ruffus_exceptions import JobSignalledBreak
-
-#from json import dumps
-#from collections import defaultdict
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Functions
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Logger
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-if __name__ == '__main__':
-    import logging
-    import logging.handlers
-
-    MESSAGE = 15
-    logging.addLevelName(MESSAGE, "MESSAGE")
-
-    def setup_std_logging (logger, log_file, verbose):
-        """
-        set up logging using programme options
-        """
-        class debug_filter(logging.Filter):
-            """
-            Ignore INFO messages
-            """
-            def filter(self, record):
-                return logging.INFO != record.levelno
-
-        class NullHandler(logging.Handler):
-            """
-            for when there is no logging
-            """
-            def emit(self, record):
-                pass
-
-        # We are interesting in all messages
-        logger.setLevel(logging.DEBUG)
-        has_handler = False
-
-        # log to file if that is specified
-        if log_file:
-            handler = logging.FileHandler(log_file, delay=False)
-            handler.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)6s - %(message)s"))
-            handler.setLevel(MESSAGE)
-            logger.addHandler(handler)
-            has_handler = True
-
-        # log to stderr if verbose
-        if verbose:
-            stderrhandler = logging.StreamHandler(sys.stderr)
-            stderrhandler.setFormatter(logging.Formatter("    %(message)s"))
-            stderrhandler.setLevel(logging.DEBUG)
-            if log_file:
-                stderrhandler.addFilter(debug_filter())
-            logger.addHandler(stderrhandler)
-            has_handler = True
-
-        # no logging
-        if not has_handler:
-            logger.addHandler(NullHandler())
-
-
-    #
-    #   set up log
-    #
-    logger = logging.getLogger(module_name)
-    setup_std_logging(logger, options.log_file, options.verbose)
-
-    #
-    #   Allow logging across Ruffus pipeline
-    #
-    def get_logger (logger_name, args):
-        return logger
-
-    from ruffus.proxy_logger import *
-    (logger_proxy,
-     logging_mutex) = make_shared_logger_and_proxy (get_logger,
-                                                    module_name,
-                                                    {})
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Pipeline
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#       Put pipeline code here
-
-
-
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Main logic
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-if __name__ == '__main__':
-    if options.just_print:
-        pipeline_printout(sys.stdout, options.target_tasks, options.forced_tasks,
-                            verbose=options.verbose)
-
-    elif options.flowchart:
-        pipeline_printout_graph (   open(options.flowchart, "w"),
-                                    # use flowchart file name extension to decide flowchart format
-                                    #   e.g. svg, jpg etc.
-                                    os.path.splitext(options.flowchart)[1][1:],
-                                    options.target_tasks,
-                                    options.forced_tasks,
-                                    no_key_legend   = not options.key_legend_in_graph)
-    else:
-        pipeline_run(options.target_tasks, options.forced_tasks,
-                            multiprocess    = options.jobs,
-                            logger          = stderr_logger,
-                            verbose         = options.verbose)
-
diff --git a/doc/_build/html/_static/example_scripts/simpler.py b/doc/_build/html/_static/example_scripts/simpler.py
deleted file mode 100644
index c858130..0000000
--- a/doc/_build/html/_static/example_scripts/simpler.py
+++ /dev/null
@@ -1,260 +0,0 @@
-#!/usr/bin/env python2.5
-"""
-
-    test_tasks.py
-
-"""
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   options        
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-from optparse import OptionParser
-import sys, os
-import os.path
-import StringIO
-
-# add self to search path for testing
-exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
-if __name__ == '__main__':
-    module_name = os.path.split(sys.argv[0])[1]
-    module_name = os.path.splitext(module_name)[0];
-else:
-    module_name = __name__
-
-
-
-
-parser = OptionParser(version="%prog 1.0")
-parser.add_option("-t", "--target_tasks", dest="target_tasks",
-                  action="append",
-                  default = list(),
-                  metavar="JOBNAME", 
-                  type="string",
-                  help="Target task(s) of pipeline.")
-parser.add_option("-f", "--forced_tasks", dest="forced_tasks",
-                  action="append",
-                  default = list(),
-                  metavar="JOBNAME", 
-                  type="string",
-                  help="Pipeline task(s) which will be included even if they are up to date.")
-parser.add_option("-j", "--jobs", dest="jobs",
-                  default=5,
-                  metavar="jobs", 
-                  type="int",
-                  help="Specifies  the number of jobs (commands) to run simultaneously.")
-parser.add_option("-v", "--verbose", dest = "verbose",
-                  action="store_true", default=False,
-                  help="Do not echo to shell but only print to log.")
-parser.add_option("-d", "--dependency", dest="dependency_file",
-                  default="simple.svg",
-                  metavar="FILE", 
-                  type="string",
-                  help="Print a dependency graph of the pipeline that would be executed "
-                        "to FILE, but do not execute it.")
-parser.add_option("-F", "--dependency_graph_format", dest="dependency_graph_format",
-                  metavar="FORMAT", 
-                  type="string",
-                  default = 'svg',
-                  help="format of dependency graph file. Can be 'ps' (PostScript), "+
-                  "'svg' 'svgz' (Structured Vector Graphics), " +
-                  "'png' 'gif' (bitmap  graphics) etc ")
-parser.add_option("-n", "--just_print", dest="just_print",
-                    action="store_true", default=False,
-                    help="Print a description of the jobs that would be executed, "
-                        "but do not execute them.")
-parser.add_option("-M", "--minimal_rebuild_mode", dest="minimal_rebuild_mode",
-                    action="store_true", default=False,
-                    help="Rebuild a minimum of tasks necessary for the target. "
-                    "Ignore upstream out of date tasks if intervening tasks are fine.")
-parser.add_option("-K", "--no_key_legend_in_graph", dest="no_key_legend_in_graph",
-                    action="store_true", default=False,
-                    help="Do not print out legend and key for dependency graph.")
-parser.add_option("-H", "--draw_graph_horizontally", dest="draw_horizontally",
-                    action="store_true", default=False,
-                    help="Draw horizontal dependency graph.")
-
-parameters = [  
-                ]
-
-
-
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   imports        
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-import StringIO
-import re
-import operator
-import sys
-from collections import defaultdict
-
-sys.path.append(os.path.abspath(os.path.join(exe_path,"..", "..")))
-from ruffus import *
-import json
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Functions
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-def create_custom_file_func(params):
-    """
-    creates function which can be used as input to @files_func
-    """
-    def cust_func ():
-        for job_param in params:
-            yield job_param
-    return cust_func
-    
-    
-def is_job_uptodate (infiles, outfiles, *extra_params):
-    """
-    assumes first two parameters are files, checks if they are up to date
-    """
-    return task.needs_update_check_modify_time (infiles, outfiles, *extra_params)
-    
-    
-    
-def test_post_task_function ():
-    print "Hooray"
-
-import time
-def test_job_io(infiles, outfiles, extra_params):
-    """
-    cat input files content to output files
-        after writing out job parameters
-    """
-    # dump parameters
-    params = (infiles, outfiles) + extra_params
-    sys.stdout.write('    job = %s\n' % json.dumps(params))
-
-    
-        
-    if isinstance(infiles, str):
-        infiles = [infiles]
-    elif infiles == None:
-        infiles = []
-    if isinstance(outfiles, str):
-        outfiles = [outfiles]
-    output_text = list()
-    for f in infiles:
-        output_text.append(open(f).read())
-    output_text = "".join(sorted(output_text))
-    output_text += json.dumps(infiles) + " -> " + json.dumps(outfiles) + "\n"
-    for f in outfiles:
-        open(f, "w").write(output_text)
-    time.sleep(1)
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Main logic
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-
-
-
-# get help string
-f =StringIO.StringIO()
-parser.print_help(f)
-helpstr = f.getvalue()
-(options, remaining_args) = parser.parse_args()
-
-
-
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-#   Tasks
-
-
-#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
-
-
-#
-#    task1
-#
- at files(None, 'a.1')
-def task1(infiles, outfiles, *extra_params):
-    """
-    First task
-    """
-    test_job_io(infiles, outfiles, extra_params)
-
-
-
-#
-#    task2
-#
- at files_re('*.1', '(.*).1', r'\1.1', r'\1.2')
- at follows(task1)
-def task2(infiles, outfiles, *extra_params):
-    """
-    Second task
-    """
-    test_job_io(infiles, outfiles, extra_params)
-
-
-
-#
-#    task3
-#
- at files_re('*.1', '(.*).1', r'\1.2', r'\1.3')
- at follows(task2)
-def task3(infiles, outfiles, *extra_params):
-    """
-    Third task
-    """
-    test_job_io(infiles, outfiles, extra_params)
-
-
-
-#
-#    task4
-#
- at files_re('*.1', '(.*).1', r'\1.3', r'\1.4')
- at follows(task3)
-def task4(infiles, outfiles, *extra_params):
-    """
-    Fourth task
-    """
-    test_job_io(infiles, outfiles, extra_params)
-
-
-
-        
-if options.just_print:
-    pipeline_printout(sys.stdout, options.target_tasks, options.forced_tasks, 
-                        long_winded=True, 
-                        gnu_make_maximal_rebuild_mode = not options.minimal_rebuild_mode)
-
-elif options.dependency_file:
-    pipeline_printout_graph (     open(options.dependency_file, "w"),
-                         options.dependency_graph_format,
-                         options.target_tasks, 
-                         options.forced_tasks,
-                         draw_vertically = not options.draw_horizontally,
-                         gnu_make_maximal_rebuild_mode  = not options.minimal_rebuild_mode,
-                         no_key_legend  = options.no_key_legend_in_graph)
-else:    
-    pipeline_run(options.target_tasks, options.forced_tasks, multiprocess = options.jobs, 
-                    gnu_make_maximal_rebuild_mode  = not options.minimal_rebuild_mode)
-    
diff --git a/doc/_build/html/_static/file.png b/doc/_build/html/_static/file.png
deleted file mode 100644
index d18082e..0000000
Binary files a/doc/_build/html/_static/file.png and /dev/null differ
diff --git a/doc/_build/html/_static/minus.png b/doc/_build/html/_static/minus.png
deleted file mode 100644
index da1c562..0000000
Binary files a/doc/_build/html/_static/minus.png and /dev/null differ
diff --git a/doc/_build/html/_static/plus.png b/doc/_build/html/_static/plus.png
deleted file mode 100644
index b3cb374..0000000
Binary files a/doc/_build/html/_static/plus.png and /dev/null differ
diff --git a/doc/_build/html/_static/pygments.css b/doc/_build/html/_static/pygments.css
deleted file mode 100644
index d79caa1..0000000
--- a/doc/_build/html/_static/pygments.css
+++ /dev/null
@@ -1,62 +0,0 @@
-.highlight .hll { background-color: #ffffcc }
-.highlight  { background: #eeffcc; }
-.highlight .c { color: #408090; font-style: italic } /* Comment */
-.highlight .err { border: 1px solid #FF0000 } /* Error */
-.highlight .k { color: #007020; font-weight: bold } /* Keyword */
-.highlight .o { color: #666666 } /* Operator */
-.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
-.highlight .cp { color: #007020 } /* Comment.Preproc */
-.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
-.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
-.highlight .gd { color: #A00000 } /* Generic.Deleted */
-.highlight .ge { font-style: italic } /* Generic.Emph */
-.highlight .gr { color: #FF0000 } /* Generic.Error */
-.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
-.highlight .gi { color: #00A000 } /* Generic.Inserted */
-.highlight .go { color: #333333 } /* Generic.Output */
-.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
-.highlight .gs { font-weight: bold } /* Generic.Strong */
-.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
-.highlight .gt { color: #0044DD } /* Generic.Traceback */
-.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
-.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
-.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
-.highlight .kp { color: #007020 } /* Keyword.Pseudo */
-.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
-.highlight .kt { color: #902000 } /* Keyword.Type */
-.highlight .m { color: #208050 } /* Literal.Number */
-.highlight .s { color: #4070a0 } /* Literal.String */
-.highlight .na { color: #4070a0 } /* Name.Attribute */
-.highlight .nb { color: #007020 } /* Name.Builtin */
-.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
-.highlight .no { color: #60add5 } /* Name.Constant */
-.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
-.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
-.highlight .ne { color: #007020 } /* Name.Exception */
-.highlight .nf { color: #06287e } /* Name.Function */
-.highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
-.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
-.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
-.highlight .nv { color: #bb60d5 } /* Name.Variable */
-.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
-.highlight .w { color: #bbbbbb } /* Text.Whitespace */
-.highlight .mf { color: #208050 } /* Literal.Number.Float */
-.highlight .mh { color: #208050 } /* Literal.Number.Hex */
-.highlight .mi { color: #208050 } /* Literal.Number.Integer */
-.highlight .mo { color: #208050 } /* Literal.Number.Oct */
-.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
-.highlight .sc { color: #4070a0 } /* Literal.String.Char */
-.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
-.highlight .s2 { color: #4070a0 } /* Literal.String.Double */
-.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
-.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
-.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
-.highlight .sx { color: #c65d09 } /* Literal.String.Other */
-.highlight .sr { color: #235388 } /* Literal.String.Regex */
-.highlight .s1 { color: #4070a0 } /* Literal.String.Single */
-.highlight .ss { color: #517918 } /* Literal.String.Symbol */
-.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
-.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
-.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
-.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
-.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
\ No newline at end of file
diff --git a/doc/_build/html/_static/ruffus.css b/doc/_build/html/_static/ruffus.css
deleted file mode 100644
index 4734d47..0000000
--- a/doc/_build/html/_static/ruffus.css
+++ /dev/null
@@ -1,327 +0,0 @@
-/*
- * Sphinx stylesheet -- default theme
- * ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- */
-
- at import url("basic.css");
-
-/* -- page layout ----------------------------------------------------------- */
-
-body {
-    font-family: sans-serif;
-    font-size: 100%;
-    background-color: #11303d;
-    color: #000;
-    margin: 0;
-    padding: 0;
-}
-
-div.document {
-    background-color: #1c4e63;
-}
-
-div.documentwrapper {
-    float: left;
-    width: 100%;
-}
-
-div.bodywrapper {
-    margin: 0 0 0 230px;
-}
-
-div.body {
-    background-color: #ffffff;
-    color: #000000;
-    padding: 0 20px 30px 20px;
-}
-
-div.footer {
-    color: #ffffff;
-    width: 100%;
-    padding: 9px 0 9px 0;
-    text-align: center;
-    font-size: 75%;
-}
-
-div.footer a {
-    color: #ffffff;
-    text-decoration: underline;
-}
-
-div.related {
-    background-color: #133f52;
-    line-height: 30px;
-    color: #ffffff;
-}
-
-div.related a {
-    font-size: 120%;    /* new */
-    color: #c0c0FF;     /* new */
-    /*color: #ffffff;     /* orig */
-}
-
-div.sphinxsidebar {
-}
-
-div.sphinxsidebar h3 {
-    font-family: 'Trebuchet MS', sans-serif;
-    color: #ffffff;
-    font-size: 1.4em;
-    font-weight: normal;
-    margin: 0;
-    padding: 0;
-}
-
-div.sphinxsidebar h3 a {
-    color: #98dbcc;
-    margin: 0;
-    padding: 0;
-/*    margin: 0px 0px 0px 0px;
-    padding: 0px 0px 0px 0px;*/
-}
-
-
-
-div.sphinxsidebar h4 {
-    font-family: 'Trebuchet MS', sans-serif;
-    color: #ffffff;
-    font-size: 1.3em;
-    font-weight: normal;
-    margin: 5px 0 0 0;
-    padding: 0;
-}
-
-div.sphinxsidebar p {
-    color: #ffffff;
-}
-
-div.sphinxsidebar p.topless {
-    margin: 5px 10px 10px 10px;
-}
-
-div.sphinxsidebar ul {
-    font-size: 100%;    /* NEW */
-    margin: 10px;
-    padding: 0;
-    color: #ffffff;
-}
-
-div.sphinxsidebar a {
-    color: #98dbcc;
-}
-
-div.sphinxsidebar a em{
-    color: #98dbcc;
-}
-
-div.sphinxsidebar input {
-    border: 1px solid #98dbcc;
-    font-family: sans-serif;
-    font-size: 1em;
-}
-
-/* -- body styles ----------------------------------------------------------- */
-
-a {
-    color: #355f7c;
-    text-decoration: none;
-}
-
-a:hover {
-    text-decoration: underline;
-}
-
-div.body p, div.body dd, div.body li {
-    text-align: justify;
-    line-height: 130%;
-}
-
-div.body h1,
-div.body h2,
-div.body h3,
-div.body h4,
-div.body h5,
-div.body h6 {
-    font-family: 'Trebuchet MS', sans-serif;
-    background-color: #f2f2f2;
-    font-weight: normal;
-    color: #20435c;
-    border-bottom: 1px solid #ccc;
-    margin: 20px -20px 10px -20px;
-    padding: 3px 0 3px 10px;
-}
-
-div.body h1 { margin-top: 0; font-size: 200%; color: #0088FF }
-div.body h2 { font-size: 200%; color: #000000 }
-div.body h3 { font-size: 140%; color: #800080; margin-left: 0px; margin-top: 40px ;font-style:italic;}        
-div.body h4 { font-size: 110%; color: #008000; margin-left: 10px; margin-top: 40px;background-color: #F0F0F0;} 
-div.body h5 { font-size: 90%; }
-div.body h6 { font-size: 80%; }
-
-div.body h3 cite
-{
-    font-family: monospace;
-    font-weight: normal;
-    color: #0000ff;
-    font-style: normal;
-    font-size: 90%; 
-}
-
-div.body h3 em
-{
-    font-weight: normal;
-    color: #000000;
-    font-style: normal;
-    font-size: 80%; 
-}
-
-div.body h2 em
-{
-    font-family: monospace;
-    font-weight: normal;
-    color: #800080;
-    font-style: normal;
-    font-size: 100%; 
-}
-
-div.body h2 cite
-{
-    font-family: monospace;
-    font-weight: normal;
-    color: #0000ff;
-    font-style: italic;
-    font-size: 80%; 
-}
-
-div.body h2 a
-{
-    font-family: monospace;
-    font-weight: normal;
-    color: #0000ff;
-    font-style: italic;
-    font-size: 80%; 
-}
-
-div.body h1 em
-{
-    font-family: monospace;
-    font-weight: normal;
-    color: #0088FF;
-    font-size: 100%; 
-}
-
-dt em
-{
-    font-family: monospace;
-    color: #0000ff;
-    font-style: italic;
-    font-size: 120%; 
-}
-
-
-a.headerlink {
-    color: #c60f0f;
-    font-size: 0.8em;
-    padding: 0 4px 0 4px;
-    text-decoration: none;
-}
-
-a.headerlink:hover {
-    background-color: #c60f0f;
-    color: white;
-}
-
-div.body p, div.body dd, div.body li {
-    text-align: justify;
-    line-height: 130%;
-}
-
-div.admonition p.admonition-title + p {
-    display: inline;
-}
-
-div.note {
-    background-color: #eee;
-    border: 1px solid #ccc;
-}
-
-div.seealso {
-    background-color: #ffc;
-    border: 1px solid #ff6;
-}
-
-div.topic {
-    background-color: #eee;
-}
-
-div.warning {
-    background-color: #ffe4e4;
-    border: 1px solid #f66;
-}
-
-p.admonition-title {
-    display: inline;
-}
-
-p.admonition-title:after {
-    content: ":";
-}
-
-pre {
-    padding: 5px;
-    background-color: #eeffcc;
-    color: #333333;
-    line-height: 120%;
-    border: 1px solid #ac9;
-    border-left: none;
-    border-right: none;
-}
-
-tt {
-    background-color: #ecf0f3;
-    padding: 0 1px 0 1px;
-    font-size: 0.95em;
-}
-
-
-/*
-div.sphinxsidebar h3 {
-    font-family: 'Trebuchet MS', sans-serif;
-    color: #ffffff;
-    font-size: 1.4em;
-    font-weight: normal;
-    margin: 0 0 0 0;
-    padding: 0 0 0 0;
-}
-
-div.sphinxsidebar h3 a{
-    color: #98dbcc;
-    margin: 0px 0px 0px 0px;
-    padding: 0px 0px 0px 0px;
-}
-
-*/
-
-
-
-/*
-
-    Override Pygment style so that I can annotate the code
-
-    The key style are comments within highlighted sections. I have set these to have a
-    white background with big bold red text, so that it stands out from and does not appear
-    to be part of the surrounding code. This way I don't have to screen shot and highlight
-    manually the code in photoshop, and the embedded bitmapped code doesn't get out of date,...
-    and the code is selectable, and it fits into a sane workflow etc. etc.
-
-    I use :nth-of-type(n) pseudo class (but one which matches everything)
-        so that this is a specialisation of the css .hll class style in pygments.css
-
-    Nasty hack but this way I don't have to modify pygments.css by hand each time, and I don't have
-    to create my own pygments style.
-
-*/
-
-.highlight .nd:nth-of-type(n)   { background-color: #ffff88; color: red; font-weight: bold; outline:red dotted thin}/**/
-.highlight .hll:nth-of-type(n)   { background-color: #eeffcc; font-weight: bold}
-.highlight .hll .c:nth-of-type(n)    { background-color: #ffffff; color: red; font-weight: bold; font-style: normal;font-size:120%} /* Comment */
diff --git a/doc/_build/html/_static/ruffus.pdf b/doc/_build/html/_static/ruffus.pdf
deleted file mode 100644
index 68836b8..0000000
Binary files a/doc/_build/html/_static/ruffus.pdf and /dev/null differ
diff --git a/doc/_build/html/_static/searchtools.js b/doc/_build/html/_static/searchtools.js
deleted file mode 100644
index 56676b2..0000000
--- a/doc/_build/html/_static/searchtools.js
+++ /dev/null
@@ -1,622 +0,0 @@
-/*
- * searchtools.js_t
- * ~~~~~~~~~~~~~~~~
- *
- * Sphinx JavaScript utilties for the full-text search.
- *
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-
-/**
- * Porter Stemmer
- */
-var Stemmer = function() {
-
-  var step2list = {
-    ational: 'ate',
-    tional: 'tion',
-    enci: 'ence',
-    anci: 'ance',
-    izer: 'ize',
-    bli: 'ble',
-    alli: 'al',
-    entli: 'ent',
-    eli: 'e',
-    ousli: 'ous',
-    ization: 'ize',
-    ation: 'ate',
-    ator: 'ate',
-    alism: 'al',
-    iveness: 'ive',
-    fulness: 'ful',
-    ousness: 'ous',
-    aliti: 'al',
-    iviti: 'ive',
-    biliti: 'ble',
-    logi: 'log'
-  };
-
-  var step3list = {
-    icate: 'ic',
-    ative: '',
-    alize: 'al',
-    iciti: 'ic',
-    ical: 'ic',
-    ful: '',
-    ness: ''
-  };
-
-  var c = "[^aeiou]";          // consonant
-  var v = "[aeiouy]";          // vowel
-  var C = c + "[^aeiouy]*";    // consonant sequence
-  var V = v + "[aeiou]*";      // vowel sequence
-
-  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
-  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
-  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
-  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
-
-  this.stemWord = function (w) {
-    var stem;
-    var suffix;
-    var firstch;
-    var origword = w;
-
-    if (w.length < 3)
-      return w;
-
-    var re;
-    var re2;
-    var re3;
-    var re4;
-
-    firstch = w.substr(0,1);
-    if (firstch == "y")
-      w = firstch.toUpperCase() + w.substr(1);
-
-    // Step 1a
-    re = /^(.+?)(ss|i)es$/;
-    re2 = /^(.+?)([^s])s$/;
-
-    if (re.test(w))
-      w = w.replace(re,"$1$2");
-    else if (re2.test(w))
-      w = w.replace(re2,"$1$2");
-
-    // Step 1b
-    re = /^(.+?)eed$/;
-    re2 = /^(.+?)(ed|ing)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      re = new RegExp(mgr0);
-      if (re.test(fp[1])) {
-        re = /.$/;
-        w = w.replace(re,"");
-      }
-    }
-    else if (re2.test(w)) {
-      var fp = re2.exec(w);
-      stem = fp[1];
-      re2 = new RegExp(s_v);
-      if (re2.test(stem)) {
-        w = stem;
-        re2 = /(at|bl|iz)$/;
-        re3 = new RegExp("([^aeiouylsz])\\1$");
-        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
-        if (re2.test(w))
-          w = w + "e";
-        else if (re3.test(w)) {
-          re = /.$/;
-          w = w.replace(re,"");
-        }
-        else if (re4.test(w))
-          w = w + "e";
-      }
-    }
-
-    // Step 1c
-    re = /^(.+?)y$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(s_v);
-      if (re.test(stem))
-        w = stem + "i";
-    }
-
-    // Step 2
-    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      suffix = fp[2];
-      re = new RegExp(mgr0);
-      if (re.test(stem))
-        w = stem + step2list[suffix];
-    }
-
-    // Step 3
-    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      suffix = fp[2];
-      re = new RegExp(mgr0);
-      if (re.test(stem))
-        w = stem + step3list[suffix];
-    }
-
-    // Step 4
-    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
-    re2 = /^(.+?)(s|t)(ion)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(mgr1);
-      if (re.test(stem))
-        w = stem;
-    }
-    else if (re2.test(w)) {
-      var fp = re2.exec(w);
-      stem = fp[1] + fp[2];
-      re2 = new RegExp(mgr1);
-      if (re2.test(stem))
-        w = stem;
-    }
-
-    // Step 5
-    re = /^(.+?)e$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(mgr1);
-      re2 = new RegExp(meq1);
-      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
-      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
-        w = stem;
-    }
-    re = /ll$/;
-    re2 = new RegExp(mgr1);
-    if (re.test(w) && re2.test(w)) {
-      re = /.$/;
-      w = w.replace(re,"");
-    }
-
-    // and turn initial Y back to y
-    if (firstch == "y")
-      w = firstch.toLowerCase() + w.substr(1);
-    return w;
-  }
-}
-
-
-
-/**
- * Simple result scoring code.
- */
-var Scorer = {
-  // Implement the following function to further tweak the score for each result
-  // The function takes a result array [filename, title, anchor, descr, score]
-  // and returns the new score.
-  /*
-  score: function(result) {
-    return result[4];
-  },
-  */
-
-  // query matches the full name of an object
-  objNameMatch: 11,
-  // or matches in the last dotted part of the object name
-  objPartialMatch: 6,
-  // Additive scores depending on the priority of the object
-  objPrio: {0:  15,   // used to be importantResults
-            1:  5,   // used to be objectResults
-            2: -5},  // used to be unimportantResults
-  //  Used when the priority is not in the mapping.
-  objPrioDefault: 0,
-
-  // query found in title
-  title: 15,
-  // query found in terms
-  term: 5
-};
-
-
-/**
- * Search Module
- */
-var Search = {
-
-  _index : null,
-  _queued_query : null,
-  _pulse_status : -1,
-
-  init : function() {
-      var params = $.getQueryParameters();
-      if (params.q) {
-          var query = params.q[0];
-          $('input[name="q"]')[0].value = query;
-          this.performSearch(query);
-      }
-  },
-
-  loadIndex : function(url) {
-    $.ajax({type: "GET", url: url, data: null,
-            dataType: "script", cache: true,
-            complete: function(jqxhr, textstatus) {
-              if (textstatus != "success") {
-                document.getElementById("searchindexloader").src = url;
-              }
-            }});
-  },
-
-  setIndex : function(index) {
-    var q;
-    this._index = index;
-    if ((q = this._queued_query) !== null) {
-      this._queued_query = null;
-      Search.query(q);
-    }
-  },
-
-  hasIndex : function() {
-      return this._index !== null;
-  },
-
-  deferQuery : function(query) {
-      this._queued_query = query;
-  },
-
-  stopPulse : function() {
-      this._pulse_status = 0;
-  },
-
-  startPulse : function() {
-    if (this._pulse_status >= 0)
-        return;
-    function pulse() {
-      var i;
-      Search._pulse_status = (Search._pulse_status + 1) % 4;
-      var dotString = '';
-      for (i = 0; i < Search._pulse_status; i++)
-        dotString += '.';
-      Search.dots.text(dotString);
-      if (Search._pulse_status > -1)
-        window.setTimeout(pulse, 500);
-    }
-    pulse();
-  },
-
-  /**
-   * perform a search for something (or wait until index is loaded)
-   */
-  performSearch : function(query) {
-    // create the required interface elements
-    this.out = $('#search-results');
-    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
-    this.dots = $('<span></span>').appendTo(this.title);
-    this.status = $('<p style="display: none"></p>').appendTo(this.out);
-    this.output = $('<ul class="search"/>').appendTo(this.out);
-
-    $('#search-progress').text(_('Preparing search...'));
-    this.startPulse();
-
-    // index already loaded, the browser was quick!
-    if (this.hasIndex())
-      this.query(query);
-    else
-      this.deferQuery(query);
-  },
-
-  /**
-   * execute search (requires search index to be loaded)
-   */
-  query : function(query) {
-    var i;
-    var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
-
-    // stem the searchterms and add them to the correct list
-    var stemmer = new Stemmer();
-    var searchterms = [];
-    var excluded = [];
-    var hlterms = [];
-    var tmp = query.split(/\s+/);
-    var objectterms = [];
-    for (i = 0; i < tmp.length; i++) {
-      if (tmp[i] !== "") {
-          objectterms.push(tmp[i].toLowerCase());
-      }
-
-      if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
-          tmp[i] === "") {
-        // skip this "word"
-        continue;
-      }
-      // stem the word
-      var word = stemmer.stemWord(tmp[i]).toLowerCase();
-      var toAppend;
-      // select the correct list
-      if (word[0] == '-') {
-        toAppend = excluded;
-        word = word.substr(1);
-      }
-      else {
-        toAppend = searchterms;
-        hlterms.push(tmp[i].toLowerCase());
-      }
-      // only add if not already in the list
-      if (!$u.contains(toAppend, word))
-        toAppend.push(word);
-    }
-    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
-    // console.debug('SEARCH: searching for:');
-    // console.info('required: ', searchterms);
-    // console.info('excluded: ', excluded);
-
-    // prepare search
-    var terms = this._index.terms;
-    var titleterms = this._index.titleterms;
-
-    // array of [filename, title, anchor, descr, score]
-    var results = [];
-    $('#search-progress').empty();
-
-    // lookup as object
-    for (i = 0; i < objectterms.length; i++) {
-      var others = [].concat(objectterms.slice(0, i),
-                             objectterms.slice(i+1, objectterms.length));
-      results = results.concat(this.performObjectSearch(objectterms[i], others));
-    }
-
-    // lookup as search terms in fulltext
-    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
-                     .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
-
-    // let the scorer override scores with a custom scoring function
-    if (Scorer.score) {
-      for (i = 0; i < results.length; i++)
-        results[i][4] = Scorer.score(results[i]);
-    }
-
-    // now sort the results by score (in opposite order of appearance, since the
-    // display function below uses pop() to retrieve items) and then
-    // alphabetically
-    results.sort(function(a, b) {
-      var left = a[4];
-      var right = b[4];
-      if (left > right) {
-        return 1;
-      } else if (left < right) {
-        return -1;
-      } else {
-        // same score: sort alphabetically
-        left = a[1].toLowerCase();
-        right = b[1].toLowerCase();
-        return (left > right) ? -1 : ((left < right) ? 1 : 0);
-      }
-    });
-
-    // for debugging
-    //Search.lastresults = results.slice();  // a copy
-    //console.info('search results:', Search.lastresults);
-
-    // print the results
-    var resultCount = results.length;
-    function displayNextItem() {
-      // results left, load the summary and display it
-      if (results.length) {
-        var item = results.pop();
-        var listItem = $('<li style="display:none"></li>');
-        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
-          // dirhtml builder
-          var dirname = item[0] + '/';
-          if (dirname.match(/\/index\/$/)) {
-            dirname = dirname.substring(0, dirname.length-6);
-          } else if (dirname == 'index/') {
-            dirname = '';
-          }
-          listItem.append($('<a/>').attr('href',
-            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
-            highlightstring + item[2]).html(item[1]));
-        } else {
-          // normal html builders
-          listItem.append($('<a/>').attr('href',
-            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
-            highlightstring + item[2]).html(item[1]));
-        }
-        if (item[3]) {
-          listItem.append($('<span> (' + item[3] + ')</span>'));
-          Search.output.append(listItem);
-          listItem.slideDown(5, function() {
-            displayNextItem();
-          });
-        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
-          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
-                  dataType: "text",
-                  complete: function(jqxhr, textstatus) {
-                    var data = jqxhr.responseText;
-                    if (data !== '') {
-                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
-                    }
-                    Search.output.append(listItem);
-                    listItem.slideDown(5, function() {
-                      displayNextItem();
-                    });
-                  }});
-        } else {
-          // no source available, just display title
-          Search.output.append(listItem);
-          listItem.slideDown(5, function() {
-            displayNextItem();
-          });
-        }
-      }
-      // search finished, update title and status message
-      else {
-        Search.stopPulse();
-        Search.title.text(_('Search Results'));
-        if (!resultCount)
-          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
-        else
-            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
-        Search.status.fadeIn(500);
-      }
-    }
-    displayNextItem();
-  },
-
-  /**
-   * search for object names
-   */
-  performObjectSearch : function(object, otherterms) {
-    var filenames = this._index.filenames;
-    var objects = this._index.objects;
-    var objnames = this._index.objnames;
-    var titles = this._index.titles;
-
-    var i;
-    var results = [];
-
-    for (var prefix in objects) {
-      for (var name in objects[prefix]) {
-        var fullname = (prefix ? prefix + '.' : '') + name;
-        if (fullname.toLowerCase().indexOf(object) > -1) {
-          var score = 0;
-          var parts = fullname.split('.');
-          // check for different match types: exact matches of full name or
-          // "last name" (i.e. last dotted part)
-          if (fullname == object || parts[parts.length - 1] == object) {
-            score += Scorer.objNameMatch;
-          // matches in last name
-          } else if (parts[parts.length - 1].indexOf(object) > -1) {
-            score += Scorer.objPartialMatch;
-          }
-          var match = objects[prefix][name];
-          var objname = objnames[match[1]][2];
-          var title = titles[match[0]];
-          // If more than one term searched for, we require other words to be
-          // found in the name/title/description
-          if (otherterms.length > 0) {
-            var haystack = (prefix + ' ' + name + ' ' +
-                            objname + ' ' + title).toLowerCase();
-            var allfound = true;
-            for (i = 0; i < otherterms.length; i++) {
-              if (haystack.indexOf(otherterms[i]) == -1) {
-                allfound = false;
-                break;
-              }
-            }
-            if (!allfound) {
-              continue;
-            }
-          }
-          var descr = objname + _(', in ') + title;
-
-          var anchor = match[3];
-          if (anchor === '')
-            anchor = fullname;
-          else if (anchor == '-')
-            anchor = objnames[match[1]][1] + '-' + fullname;
-          // add custom score for some objects according to scorer
-          if (Scorer.objPrio.hasOwnProperty(match[2])) {
-            score += Scorer.objPrio[match[2]];
-          } else {
-            score += Scorer.objPrioDefault;
-          }
-          results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
-        }
-      }
-    }
-
-    return results;
-  },
-
-  /**
-   * search for full-text terms in the index
-   */
-  performTermsSearch : function(searchterms, excluded, terms, score) {
-    var filenames = this._index.filenames;
-    var titles = this._index.titles;
-
-    var i, j, file, files;
-    var fileMap = {};
-    var results = [];
-
-    // perform the search on the required terms
-    for (i = 0; i < searchterms.length; i++) {
-      var word = searchterms[i];
-      // no match but word was a required one
-      if (!(files = terms[word]))
-        break;
-      if (files.length === undefined) {
-        files = [files];
-      }
-      // create the mapping
-      for (j = 0; j < files.length; j++) {
-        file = files[j];
-        if (file in fileMap)
-          fileMap[file].push(word);
-        else
-          fileMap[file] = [word];
-      }
-    }
-
-    // now check if the files don't contain excluded terms
-    for (file in fileMap) {
-      var valid = true;
-
-      // check if all requirements are matched
-      if (fileMap[file].length != searchterms.length)
-          continue;
-
-      // ensure that none of the excluded terms is in the search result
-      for (i = 0; i < excluded.length; i++) {
-        if (terms[excluded[i]] == file ||
-          $u.contains(terms[excluded[i]] || [], file)) {
-          valid = false;
-          break;
-        }
-      }
-
-      // if we have still a valid result we can add it to the result list
-      if (valid) {
-        results.push([filenames[file], titles[file], '', null, score]);
-      }
-    }
-    return results;
-  },
-
-  /**
-   * helper function to return a node containing the
-   * search summary for a given text. keywords is a list
-   * of stemmed words, hlwords is the list of normal, unstemmed
-   * words. the first one is used to find the occurance, the
-   * latter for highlighting it.
-   */
-  makeSearchSummary : function(text, keywords, hlwords) {
-    var textLower = text.toLowerCase();
-    var start = 0;
-    $.each(keywords, function() {
-      var i = textLower.indexOf(this.toLowerCase());
-      if (i > -1)
-        start = i;
-    });
-    start = Math.max(start - 120, 0);
-    var excerpt = ((start > 0) ? '...' : '') +
-      $.trim(text.substr(start, 240)) +
-      ((start + 240 - text.length) ? '...' : '');
-    var rv = $('<div class="context"></div>').text(excerpt);
-    $.each(hlwords, function() {
-      rv = rv.highlightText(this, 'highlighted');
-    });
-    return rv;
-  }
-};
-
-$(document).ready(function() {
-  Search.init();
-});
\ No newline at end of file
diff --git a/doc/_build/html/_static/sidebar.js b/doc/_build/html/_static/sidebar.js
deleted file mode 100644
index 5adf895..0000000
--- a/doc/_build/html/_static/sidebar.js
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
- * sidebar.js
- * ~~~~~~~~~~
- *
- * This script makes the Sphinx sidebar collapsible.
- *
- * .sphinxsidebar contains .sphinxsidebarwrapper.  This script adds
- * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton
- * used to collapse and expand the sidebar.
- *
- * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden
- * and the width of the sidebar and the margin-left of the document
- * are decreased. When the sidebar is expanded the opposite happens.
- * This script saves a per-browser/per-session cookie used to
- * remember the position of the sidebar among the pages.
- * Once the browser is closed the cookie is deleted and the position
- * reset to the default (expanded).
- *
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-$(function() {
-  
-  
-  
-  
-  
-  
-  
-
-  // global elements used by the functions.
-  // the 'sidebarbutton' element is defined as global after its
-  // creation, in the add_sidebar_button function
-  var bodywrapper = $('.bodywrapper');
-  var sidebar = $('.sphinxsidebar');
-  var sidebarwrapper = $('.sphinxsidebarwrapper');
-
-  // for some reason, the document has no sidebar; do not run into errors
-  if (!sidebar.length) return;
-
-  // original margin-left of the bodywrapper and width of the sidebar
-  // with the sidebar expanded
-  var bw_margin_expanded = bodywrapper.css('margin-left');
-  var ssb_width_expanded = sidebar.width();
-
-  // margin-left of the bodywrapper and width of the sidebar
-  // with the sidebar collapsed
-  var bw_margin_collapsed = '.8em';
-  var ssb_width_collapsed = '.8em';
-
-  // colors used by the current theme
-  var dark_color = $('.related').css('background-color');
-  var light_color = $('.document').css('background-color');
-
-  function sidebar_is_collapsed() {
-    return sidebarwrapper.is(':not(:visible)');
-  }
-
-  function toggle_sidebar() {
-    if (sidebar_is_collapsed())
-      expand_sidebar();
-    else
-      collapse_sidebar();
-  }
-
-  function collapse_sidebar() {
-    sidebarwrapper.hide();
-    sidebar.css('width', ssb_width_collapsed);
-    bodywrapper.css('margin-left', bw_margin_collapsed);
-    sidebarbutton.css({
-        'margin-left': '0',
-        'height': bodywrapper.height()
-    });
-    sidebarbutton.find('span').text('»');
-    sidebarbutton.attr('title', _('Expand sidebar'));
-    document.cookie = 'sidebar=collapsed';
-  }
-
-  function expand_sidebar() {
-    bodywrapper.css('margin-left', bw_margin_expanded);
-    sidebar.css('width', ssb_width_expanded);
-    sidebarwrapper.show();
-    sidebarbutton.css({
-        'margin-left': ssb_width_expanded-12,
-        'height': bodywrapper.height()
-    });
-    sidebarbutton.find('span').text('«');
-    sidebarbutton.attr('title', _('Collapse sidebar'));
-    document.cookie = 'sidebar=expanded';
-  }
-
-  function add_sidebar_button() {
-    sidebarwrapper.css({
-        'float': 'left',
-        'margin-right': '0',
-        'width': ssb_width_expanded - 28
-    });
-    // create the button
-    sidebar.append(
-        '<div id="sidebarbutton"><span>«</span></div>'
-    );
-    var sidebarbutton = $('#sidebarbutton');
-    light_color = sidebarbutton.css('background-color');
-    // find the height of the viewport to center the '<<' in the page
-    var viewport_height;
-    if (window.innerHeight)
- 	  viewport_height = window.innerHeight;
-    else
-	  viewport_height = $(window).height();
-    sidebarbutton.find('span').css({
-        'display': 'block',
-        'margin-top': (viewport_height - sidebar.position().top - 20) / 2
-    });
-
-    sidebarbutton.click(toggle_sidebar);
-    sidebarbutton.attr('title', _('Collapse sidebar'));
-    sidebarbutton.css({
-        'color': '#FFFFFF',
-        'border-left': '1px solid ' + dark_color,
-        'font-size': '1.2em',
-        'cursor': 'pointer',
-        'height': bodywrapper.height(),
-        'padding-top': '1px',
-        'margin-left': ssb_width_expanded - 12
-    });
-
-    sidebarbutton.hover(
-      function () {
-          $(this).css('background-color', dark_color);
-      },
-      function () {
-          $(this).css('background-color', light_color);
-      }
-    );
-  }
-
-  function set_position_from_cookie() {
-    if (!document.cookie)
-      return;
-    var items = document.cookie.split(';');
-    for(var k=0; k<items.length; k++) {
-      var key_val = items[k].split('=');
-      var key = key_val[0];
-      if (key == 'sidebar') {
-        var value = key_val[1];
-        if ((value == 'collapsed') && (!sidebar_is_collapsed()))
-          collapse_sidebar();
-        else if ((value == 'expanded') && (sidebar_is_collapsed()))
-          expand_sidebar();
-      }
-    }
-  }
-
-  add_sidebar_button();
-  var sidebarbutton = $('#sidebarbutton');
-  set_position_from_cookie();
-});
\ No newline at end of file
diff --git a/doc/_build/html/_static/up-pressed.png b/doc/_build/html/_static/up-pressed.png
deleted file mode 100644
index 8bd587a..0000000
Binary files a/doc/_build/html/_static/up-pressed.png and /dev/null differ
diff --git a/doc/_build/html/_static/up.png b/doc/_build/html/_static/up.png
deleted file mode 100644
index b946256..0000000
Binary files a/doc/_build/html/_static/up.png and /dev/null differ
diff --git a/doc/_build/html/_static/websupport.js b/doc/_build/html/_static/websupport.js
deleted file mode 100644
index 19fcda5..0000000
--- a/doc/_build/html/_static/websupport.js
+++ /dev/null
@@ -1,808 +0,0 @@
-/*
- * websupport.js
- * ~~~~~~~~~~~~~
- *
- * sphinx.websupport utilties for all documentation.
- *
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-(function($) {
-  $.fn.autogrow = function() {
-    return this.each(function() {
-    var textarea = this;
-
-    $.fn.autogrow.resize(textarea);
-
-    $(textarea)
-      .focus(function() {
-        textarea.interval = setInterval(function() {
-          $.fn.autogrow.resize(textarea);
-        }, 500);
-      })
-      .blur(function() {
-        clearInterval(textarea.interval);
-      });
-    });
-  };
-
-  $.fn.autogrow.resize = function(textarea) {
-    var lineHeight = parseInt($(textarea).css('line-height'), 10);
-    var lines = textarea.value.split('\n');
-    var columns = textarea.cols;
-    var lineCount = 0;
-    $.each(lines, function() {
-      lineCount += Math.ceil(this.length / columns) || 1;
-    });
-    var height = lineHeight * (lineCount + 1);
-    $(textarea).css('height', height);
-  };
-})(jQuery);
-
-(function($) {
-  var comp, by;
-
-  function init() {
-    initEvents();
-    initComparator();
-  }
-
-  function initEvents() {
-    $('a.comment-close').live("click", function(event) {
-      event.preventDefault();
-      hide($(this).attr('id').substring(2));
-    });
-    $('a.vote').live("click", function(event) {
-      event.preventDefault();
-      handleVote($(this));
-    });
-    $('a.reply').live("click", function(event) {
-      event.preventDefault();
-      openReply($(this).attr('id').substring(2));
-    });
-    $('a.close-reply').live("click", function(event) {
-      event.preventDefault();
-      closeReply($(this).attr('id').substring(2));
-    });
-    $('a.sort-option').live("click", function(event) {
-      event.preventDefault();
-      handleReSort($(this));
-    });
-    $('a.show-proposal').live("click", function(event) {
-      event.preventDefault();
-      showProposal($(this).attr('id').substring(2));
-    });
-    $('a.hide-proposal').live("click", function(event) {
-      event.preventDefault();
-      hideProposal($(this).attr('id').substring(2));
-    });
-    $('a.show-propose-change').live("click", function(event) {
-      event.preventDefault();
-      showProposeChange($(this).attr('id').substring(2));
-    });
-    $('a.hide-propose-change').live("click", function(event) {
-      event.preventDefault();
-      hideProposeChange($(this).attr('id').substring(2));
-    });
-    $('a.accept-comment').live("click", function(event) {
-      event.preventDefault();
-      acceptComment($(this).attr('id').substring(2));
-    });
-    $('a.delete-comment').live("click", function(event) {
-      event.preventDefault();
-      deleteComment($(this).attr('id').substring(2));
-    });
-    $('a.comment-markup').live("click", function(event) {
-      event.preventDefault();
-      toggleCommentMarkupBox($(this).attr('id').substring(2));
-    });
-  }
-
-  /**
-   * Set comp, which is a comparator function used for sorting and
-   * inserting comments into the list.
-   */
-  function setComparator() {
-    // If the first three letters are "asc", sort in ascending order
-    // and remove the prefix.
-    if (by.substring(0,3) == 'asc') {
-      var i = by.substring(3);
-      comp = function(a, b) { return a[i] - b[i]; };
-    } else {
-      // Otherwise sort in descending order.
-      comp = function(a, b) { return b[by] - a[by]; };
-    }
-
-    // Reset link styles and format the selected sort option.
-    $('a.sel').attr('href', '#').removeClass('sel');
-    $('a.by' + by).removeAttr('href').addClass('sel');
-  }
-
-  /**
-   * Create a comp function. If the user has preferences stored in
-   * the sortBy cookie, use those, otherwise use the default.
-   */
-  function initComparator() {
-    by = 'rating'; // Default to sort by rating.
-    // If the sortBy cookie is set, use that instead.
-    if (document.cookie.length > 0) {
-      var start = document.cookie.indexOf('sortBy=');
-      if (start != -1) {
-        start = start + 7;
-        var end = document.cookie.indexOf(";", start);
-        if (end == -1) {
-          end = document.cookie.length;
-          by = unescape(document.cookie.substring(start, end));
-        }
-      }
-    }
-    setComparator();
-  }
-
-  /**
-   * Show a comment div.
-   */
-  function show(id) {
-    $('#ao' + id).hide();
-    $('#ah' + id).show();
-    var context = $.extend({id: id}, opts);
-    var popup = $(renderTemplate(popupTemplate, context)).hide();
-    popup.find('textarea[name="proposal"]').hide();
-    popup.find('a.by' + by).addClass('sel');
-    var form = popup.find('#cf' + id);
-    form.submit(function(event) {
-      event.preventDefault();
-      addComment(form);
-    });
-    $('#s' + id).after(popup);
-    popup.slideDown('fast', function() {
-      getComments(id);
-    });
-  }
-
-  /**
-   * Hide a comment div.
-   */
-  function hide(id) {
-    $('#ah' + id).hide();
-    $('#ao' + id).show();
-    var div = $('#sc' + id);
-    div.slideUp('fast', function() {
-      div.remove();
-    });
-  }
-
-  /**
-   * Perform an ajax request to get comments for a node
-   * and insert the comments into the comments tree.
-   */
-  function getComments(id) {
-    $.ajax({
-     type: 'GET',
-     url: opts.getCommentsURL,
-     data: {node: id},
-     success: function(data, textStatus, request) {
-       var ul = $('#cl' + id);
-       var speed = 100;
-       $('#cf' + id)
-         .find('textarea[name="proposal"]')
-         .data('source', data.source);
-
-       if (data.comments.length === 0) {
-         ul.html('<li>No comments yet.</li>');
-         ul.data('empty', true);
-       } else {
-         // If there are comments, sort them and put them in the list.
-         var comments = sortComments(data.comments);
-         speed = data.comments.length * 100;
-         appendComments(comments, ul);
-         ul.data('empty', false);
-       }
-       $('#cn' + id).slideUp(speed + 200);
-       ul.slideDown(speed);
-     },
-     error: function(request, textStatus, error) {
-       showError('Oops, there was a problem retrieving the comments.');
-     },
-     dataType: 'json'
-    });
-  }
-
-  /**
-   * Add a comment via ajax and insert the comment into the comment tree.
-   */
-  function addComment(form) {
-    var node_id = form.find('input[name="node"]').val();
-    var parent_id = form.find('input[name="parent"]').val();
-    var text = form.find('textarea[name="comment"]').val();
-    var proposal = form.find('textarea[name="proposal"]').val();
-
-    if (text == '') {
-      showError('Please enter a comment.');
-      return;
-    }
-
-    // Disable the form that is being submitted.
-    form.find('textarea,input').attr('disabled', 'disabled');
-
-    // Send the comment to the server.
-    $.ajax({
-      type: "POST",
-      url: opts.addCommentURL,
-      dataType: 'json',
-      data: {
-        node: node_id,
-        parent: parent_id,
-        text: text,
-        proposal: proposal
-      },
-      success: function(data, textStatus, error) {
-        // Reset the form.
-        if (node_id) {
-          hideProposeChange(node_id);
-        }
-        form.find('textarea')
-          .val('')
-          .add(form.find('input'))
-          .removeAttr('disabled');
-	var ul = $('#cl' + (node_id || parent_id));
-        if (ul.data('empty')) {
-          $(ul).empty();
-          ul.data('empty', false);
-        }
-        insertComment(data.comment);
-        var ao = $('#ao' + node_id);
-        ao.find('img').attr({'src': opts.commentBrightImage});
-        if (node_id) {
-          // if this was a "root" comment, remove the commenting box
-          // (the user can get it back by reopening the comment popup)
-          $('#ca' + node_id).slideUp();
-        }
-      },
-      error: function(request, textStatus, error) {
-        form.find('textarea,input').removeAttr('disabled');
-        showError('Oops, there was a problem adding the comment.');
-      }
-    });
-  }
-
-  /**
-   * Recursively append comments to the main comment list and children
-   * lists, creating the comment tree.
-   */
-  function appendComments(comments, ul) {
-    $.each(comments, function() {
-      var div = createCommentDiv(this);
-      ul.append($(document.createElement('li')).html(div));
-      appendComments(this.children, div.find('ul.comment-children'));
-      // To avoid stagnating data, don't store the comments children in data.
-      this.children = null;
-      div.data('comment', this);
-    });
-  }
-
-  /**
-   * After adding a new comment, it must be inserted in the correct
-   * location in the comment tree.
-   */
-  function insertComment(comment) {
-    var div = createCommentDiv(comment);
-
-    // To avoid stagnating data, don't store the comments children in data.
-    comment.children = null;
-    div.data('comment', comment);
-
-    var ul = $('#cl' + (comment.node || comment.parent));
-    var siblings = getChildren(ul);
-
-    var li = $(document.createElement('li'));
-    li.hide();
-
-    // Determine where in the parents children list to insert this comment.
-    for(i=0; i < siblings.length; i++) {
-      if (comp(comment, siblings[i]) <= 0) {
-        $('#cd' + siblings[i].id)
-          .parent()
-          .before(li.html(div));
-        li.slideDown('fast');
-        return;
-      }
-    }
-
-    // If we get here, this comment rates lower than all the others,
-    // or it is the only comment in the list.
-    ul.append(li.html(div));
-    li.slideDown('fast');
-  }
-
-  function acceptComment(id) {
-    $.ajax({
-      type: 'POST',
-      url: opts.acceptCommentURL,
-      data: {id: id},
-      success: function(data, textStatus, request) {
-        $('#cm' + id).fadeOut('fast');
-        $('#cd' + id).removeClass('moderate');
-      },
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem accepting the comment.');
-      }
-    });
-  }
-
-  function deleteComment(id) {
-    $.ajax({
-      type: 'POST',
-      url: opts.deleteCommentURL,
-      data: {id: id},
-      success: function(data, textStatus, request) {
-        var div = $('#cd' + id);
-        if (data == 'delete') {
-          // Moderator mode: remove the comment and all children immediately
-          div.slideUp('fast', function() {
-            div.remove();
-          });
-          return;
-        }
-        // User mode: only mark the comment as deleted
-        div
-          .find('span.user-id:first')
-          .text('[deleted]').end()
-          .find('div.comment-text:first')
-          .text('[deleted]').end()
-          .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
-                ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
-          .remove();
-        var comment = div.data('comment');
-        comment.username = '[deleted]';
-        comment.text = '[deleted]';
-        div.data('comment', comment);
-      },
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem deleting the comment.');
-      }
-    });
-  }
-
-  function showProposal(id) {
-    $('#sp' + id).hide();
-    $('#hp' + id).show();
-    $('#pr' + id).slideDown('fast');
-  }
-
-  function hideProposal(id) {
-    $('#hp' + id).hide();
-    $('#sp' + id).show();
-    $('#pr' + id).slideUp('fast');
-  }
-
-  function showProposeChange(id) {
-    $('#pc' + id).hide();
-    $('#hc' + id).show();
-    var textarea = $('#pt' + id);
-    textarea.val(textarea.data('source'));
-    $.fn.autogrow.resize(textarea[0]);
-    textarea.slideDown('fast');
-  }
-
-  function hideProposeChange(id) {
-    $('#hc' + id).hide();
-    $('#pc' + id).show();
-    var textarea = $('#pt' + id);
-    textarea.val('').removeAttr('disabled');
-    textarea.slideUp('fast');
-  }
-
-  function toggleCommentMarkupBox(id) {
-    $('#mb' + id).toggle();
-  }
-
-  /** Handle when the user clicks on a sort by link. */
-  function handleReSort(link) {
-    var classes = link.attr('class').split(/\s+/);
-    for (var i=0; i<classes.length; i++) {
-      if (classes[i] != 'sort-option') {
-	by = classes[i].substring(2);
-      }
-    }
-    setComparator();
-    // Save/update the sortBy cookie.
-    var expiration = new Date();
-    expiration.setDate(expiration.getDate() + 365);
-    document.cookie= 'sortBy=' + escape(by) +
-                     ';expires=' + expiration.toUTCString();
-    $('ul.comment-ul').each(function(index, ul) {
-      var comments = getChildren($(ul), true);
-      comments = sortComments(comments);
-      appendComments(comments, $(ul).empty());
-    });
-  }
-
-  /**
-   * Function to process a vote when a user clicks an arrow.
-   */
-  function handleVote(link) {
-    if (!opts.voting) {
-      showError("You'll need to login to vote.");
-      return;
-    }
-
-    var id = link.attr('id');
-    if (!id) {
-      // Didn't click on one of the voting arrows.
-      return;
-    }
-    // If it is an unvote, the new vote value is 0,
-    // Otherwise it's 1 for an upvote, or -1 for a downvote.
-    var value = 0;
-    if (id.charAt(1) != 'u') {
-      value = id.charAt(0) == 'u' ? 1 : -1;
-    }
-    // The data to be sent to the server.
-    var d = {
-      comment_id: id.substring(2),
-      value: value
-    };
-
-    // Swap the vote and unvote links.
-    link.hide();
-    $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
-      .show();
-
-    // The div the comment is displayed in.
-    var div = $('div#cd' + d.comment_id);
-    var data = div.data('comment');
-
-    // If this is not an unvote, and the other vote arrow has
-    // already been pressed, unpress it.
-    if ((d.value !== 0) && (data.vote === d.value * -1)) {
-      $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
-      $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
-    }
-
-    // Update the comments rating in the local data.
-    data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
-    data.vote = d.value;
-    div.data('comment', data);
-
-    // Change the rating text.
-    div.find('.rating:first')
-      .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
-    // Send the vote information to the server.
-    $.ajax({
-      type: "POST",
-      url: opts.processVoteURL,
-      data: d,
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem casting that vote.');
-      }
-    });
-  }
-
-  /**
-   * Open a reply form used to reply to an existing comment.
-   */
-  function openReply(id) {
-    // Swap out the reply link for the hide link
-    $('#rl' + id).hide();
-    $('#cr' + id).show();
-
-    // Add the reply li to the children ul.
-    var div = $(renderTemplate(replyTemplate, {id: id})).hide();
-    $('#cl' + id)
-      .prepend(div)
-      // Setup the submit handler for the reply form.
-      .find('#rf' + id)
-      .submit(function(event) {
-        event.preventDefault();
-        addComment($('#rf' + id));
-        closeReply(id);
-      })
-      .find('input[type=button]')
-      .click(function() {
-        closeReply(id);
-      });
-    div.slideDown('fast', function() {
-      $('#rf' + id).find('textarea').focus();
-    });
-  }
-
-  /**
-   * Close the reply form opened with openReply.
-   */
-  function closeReply(id) {
-    // Remove the reply div from the DOM.
-    $('#rd' + id).slideUp('fast', function() {
-      $(this).remove();
-    });
-
-    // Swap out the hide link for the reply link
-    $('#cr' + id).hide();
-    $('#rl' + id).show();
-  }
-
-  /**
-   * Recursively sort a tree of comments using the comp comparator.
-   */
-  function sortComments(comments) {
-    comments.sort(comp);
-    $.each(comments, function() {
-      this.children = sortComments(this.children);
-    });
-    return comments;
-  }
-
-  /**
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diff --git a/doc/_build/html/cheatsheet.html b/doc/_build/html/cheatsheet.html
deleted file mode 100644
index 0d48a19..0000000
--- a/doc/_build/html/cheatsheet.html
+++ /dev/null
@@ -1,283 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>Cheat Sheet — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-    
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-  </head>
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-             accesskey="I">index</a></li>
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-            
-  <div class="section" id="cheat-sheet">
-<span id="id1"></span><h1>Cheat Sheet<a class="headerlink" href="#cheat-sheet" title="Permalink to this headline">¶</a></h1>
-<p>The <tt class="docutils literal"><span class="pre">ruffus</span></tt> module is a lightweight way to add support
-for running computational pipelines.</p>
-<div class="line-block">
-<div class="line">Each stage or <strong>task</strong> in a computational pipeline is represented by a python function</div>
-<div class="line">Each python function can be called in parallel to run multiple <strong>jobs</strong>.</div>
-</div>
-<div class="section" id="annotate-functions-with-ruffus-decorators">
-<h2>1. Annotate functions with <strong>Ruffus</strong> decorators<a class="headerlink" href="#annotate-functions-with-ruffus-decorators" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="core">
-<h3>Core<a class="headerlink" href="#core" title="Permalink to this headline">¶</a></h3>
-<table border="1" class="docutils">
-<colgroup>
-<col width="14%" />
-<col width="86%" />
-<col width="0%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">Decorator</th>
-<th class="head">Syntax</th>
-<th class="head"> </th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td>@originate (<a class="reference internal" href="tutorials/new_tutorial/originate.html#new-manual-originate"><em>Manual</em></a>)</td>
-<td><a class="reference internal" href="decorators/originate.html#decorators-originate"><em>@originate</em></a> ( <tt class="docutils literal"><span class="pre">output_files</span></tt>, [<tt class="docutils literal"><span class="pre">extra_parameters</span></tt>,...] )</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td>@split (<a class="reference internal" href="tutorials/new_tutorial/split.html#new-manual-split"><em>Manual</em></a>)</td>
-<td><a class="reference internal" href="decorators/split.html#decorators-split"><em>@split</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <tt class="docutils literal"><span class="pre">output_files</span></tt>, [<tt class="docutils literal"><span class="pre">extra_parameters</span></tt>,...] )</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td>@transform (<a class="reference internal" href="tutorials/new_tutorial/transform.html#new-manual-transform"><em>Manual</em></a>)</td>
-<td><div class="first last line-block">
-<div class="line"><a class="reference internal" href="decorators/transform.html#decorators-transform"><em>@transform</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="decorators/transform_ex.html#decorators-transform-suffix-string"><em>suffix</em></a><em>(</em><tt class="docutils literal"><span class="pre">suffix_string</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</spa [...]
-<div class="line"><a class="reference internal" href="decorators/transform.html#decorators-transform"><em>@transform</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="decorators/transform_ex.html#decorators-transform-matching-regex"><em>regex</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</spa [...]
-</div>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td>@merge (<a class="reference internal" href="tutorials/new_tutorial/merge.html#new-manual-merge"><em>Manual</em></a>)</td>
-<td><a class="reference internal" href="decorators/merge.html#decorators-merge"><em>@merge</em></a> (<tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <tt class="docutils literal"><span class="pre">output</span></tt>, [<tt class="docutils literal"><span class="pre">extra_parameters</span></tt>,...] )</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td>@posttask (<a class="reference internal" href="tutorials/new_tutorial/posttask.html#new-manual-posttask"><em>Manual</em></a>)</td>
-<td><div class="first last line-block">
-<div class="line"><a class="reference internal" href="decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> ( <tt class="docutils literal"><span class="pre">signal_task_completion_function</span></tt> )</div>
-<div class="line"><a class="reference internal" href="decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> (<a class="reference internal" href="decorators/indicator_objects.html#decorators-touch-file"><em>touch_file</em></a>( <tt class="docutils literal"><span class="pre">'task1.completed'</span></tt> ))</div>
-</div>
-</td>
-<td> </td>
-</tr>
-</tbody>
-</table>
-</div>
-<div class="section" id="see-decorators-for-a-complete-list-of-decorators">
-<h3>See <a class="reference internal" href="decorators/decorators.html#decorators"><em>Decorators</em></a> for a complete list of decorators<a class="headerlink" href="#see-decorators-for-a-complete-list-of-decorators" title="Permalink to this headline">¶</a></h3>
-</div>
-</div>
-<div class="section" id="print-dependency-graph-if-necessary">
-<h2>2. Print dependency graph if necessary<a class="headerlink" href="#print-dependency-graph-if-necessary" title="Permalink to this headline">¶</a></h2>
-<ul>
-<li><p class="first">For a graphical flowchart in <tt class="docutils literal"><span class="pre">jpg</span></tt>, <tt class="docutils literal"><span class="pre">svg</span></tt>, <tt class="docutils literal"><span class="pre">dot</span></tt>, <tt class="docutils literal"><span class="pre">png</span></tt>, <tt class="docutils literal"><span class="pre">ps</span></tt>, <tt class="docutils literal"><span class="pre">gif</span></tt> formats:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span> <span class="p">(</span> <span class="s">"flowchart.svg"</span><span class="p">)</span>
-</pre></div>
-</div>
-</li>
-</ul>
-<ul>
-<li><p class="first">For a text printout of all jobs</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout</span><span class="p">()</span>
-</pre></div>
-</div>
-</li>
-</ul>
-</div>
-<div class="section" id="run-the-pipeline">
-<h2>3. Run the pipeline<a class="headerlink" href="#run-the-pipeline" title="Permalink to this headline">¶</a></h2>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="n">multiprocess</span> <span class="o">=</span> <span class="n">N_PARALLEL_JOBS</span><span class="p">)</span>
-</pre></div>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Cheat Sheet</a><ul>
-<li><a class="reference internal" href="#annotate-functions-with-ruffus-decorators">1. Annotate functions with <strong>Ruffus</strong> decorators</a><ul>
-<li><a class="reference internal" href="#core">Core</a></li>
-<li><a class="reference internal" href="#see-decorators-for-a-complete-list-of-decorators">See <tt class="docutils literal"><span class="pre">Decorators</span></tt> for a complete list of decorators</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#print-dependency-graph-if-necessary">2. Print dependency graph if necessary</a></li>
-<li><a class="reference internal" href="#run-the-pipeline">3. Run the pipeline</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="tutorials/new_tutorial/flowchart_colours_code.html"
-                        title="previous chapter"><strong>Appendix 1</strong>: Python code for Flow Chart Colours with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="pipeline_functions.html"
-                        title="next chapter">Pipeline functions</a></p>
-  <h3>This Page</h3>
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-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
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-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
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-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
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-<h1><strong>Ruffus</strong> documentation<a class="headerlink" href="#ruffus-documentation" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="start-here">
-<h2>Start Here:<a class="headerlink" href="#start-here" title="Permalink to this headline">¶</a></h2>
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-<ul>
-<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#the-easy-way">The easy way</a></li>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#the-most-up-to-date-code">The most up-to-date code:</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/manual_contents.html"><strong>Ruffus</strong> Manual: List of Chapters and Example code</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/introduction.html"><strong>Chapter 1</strong>: An introduction to basic <em>Ruffus</em> syntax</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/introduction.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/introduction.html#importing-ruffus">Importing <em>Ruffus</em></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/introduction.html#ruffus-decorators"><em>Ruffus</em> decorators</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/introduction.html#your-first-ruffus-pipeline">Your first <em>Ruffus</em> pipeline</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/transform.html"><strong>Chapter 2</strong>: Transforming data in a pipeline with <tt class="docutils literal"><span class="pre">@transform</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform.html#review">Review</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform.html#task-functions-as-recipes">Task functions as recipes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform.html#transform-is-a-1-to-1-operation"><tt class="docutils literal"><span class="pre">@transform</span></tt> is a 1 to 1 operation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform.html#input-and-output-parameters"><strong>Input</strong> and <strong>Output</strong> parameters</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html"><strong>Chapter 3</strong>: More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#review">Review</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#running-pipelines-in-parallel">Running pipelines in parallel</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#up-to-date-jobs-are-not-re-run-unnecessarily">Up-to-date jobs are not re-run unnecessarily</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#defining-pipeline-tasks-out-of-order">Defining pipeline tasks out of order</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#multiple-dependencies">Multiple dependencies</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#follows"><tt class="docutils literal"><span class="pre">@follows</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#making-directories-automatically-with-follows-and-mkdir">Making directories automatically with <tt class="docutils literal"><span class="pre">@follows</span></tt> and  <tt class="docutils literal"><span class="pre">mkdir</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#globs-in-the-input-parameter">Globs in the <strong>Input</strong> parameter</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel.html#mixing-tasks-and-globs-in-the-input-parameter">Mixing Tasks and Globs in the <strong>Input</strong> parameter</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/originate.html"><strong>Chapter 4</strong>: Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/originate.html#simplifying-our-example-with-originate">Simplifying our example with <tt class="docutils literal"><span class="pre">@originate</span></tt></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout.html"><strong>Chapter 5</strong>: Understanding how your pipeline works with <tt class="docutils literal"><span class="pre">pipeline_printout(...)</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout.html#printing-out-which-jobs-will-be-run">Printing out which jobs will be run</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout.html#determining-which-jobs-are-out-of-date-or-not">Determining which jobs are out-of-date or not</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout.html#verbosity-levels">Verbosity levels</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout.html#abbreviating-long-file-paths-with-verbose-abbreviated-path">Abbreviating long file paths with <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout.html#getting-a-list-of-all-tasks-in-a-pipeline">Getting a list of all tasks in a pipeline</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/command_line.html"><strong>Chapter 6</strong>: Running <em>Ruffus</em> from the command line with ruffus.cmdline</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#template-for-argparse">Template for argparse</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#command-line-arguments">Command Line Arguments</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#logging">1) Logging</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#tracing-pipeline-progress">2) Tracing pipeline progress</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#printing-a-flowchart">3) Printing a flowchart</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#running-in-parallel-on-multiple-processors">4) Running in parallel on multiple processors</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#setup-checkpointing-so-that-ruffus-knows-which-files-are-out-of-date">5) Setup checkpointing so that <em>Ruffus</em> knows which files are out of date</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#skipping-specified-options">6) Skipping specified options</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#specifying-verbosity-and-abbreviating-long-paths">7) Specifying verbosity and abbreviating long paths</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#displaying-the-version">8) Displaying the version</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/command_line.html#template-for-optparse">Template for optparse</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout_graph.html"><strong>Chapter 7</strong>: Displaying the pipeline visually with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout_graph.html#printing-out-a-flowchart-of-our-pipeline">Printing out a flowchart of our pipeline</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout_graph.html#command-line-options-made-easier-with-ruffus-cmdline">Command line options made easier with <tt class="docutils literal"><span class="pre">ruffus.cmdline</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout_graph.html#horribly-complicated-pipelines">Horribly complicated pipelines!</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout_graph.html#circular-dependency-errors-in-pipelines">Circular dependency errors in pipelines!</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout_graph.html#graphviz-customising-the-appearance-of-each-task"><tt class="docutils literal"><span class="pre">@graphviz</span></tt>: Customising the appearance of each task</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/output_file_names.html"><strong>Chapter 8</strong>: Specifying output file names with <tt class="docutils literal"><span class="pre">formatter()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/output_file_names.html#review">Review</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/output_file_names.html#a-different-file-name-suffix-for-each-pipeline-stage">A different file name <tt class="docutils literal"><span class="pre">suffix()</span></tt> for each pipeline stage</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/output_file_names.html#formatter-manipulates-pathnames-and-regular-expression"><tt class="docutils literal"><span class="pre">formatter()</span></tt> manipulates pathnames and regular expression</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/output_file_names.html#regex-manipulates-via-regular-expressions"><tt class="docutils literal"><span class="pre">regex()</span></tt> manipulates via regular expressions</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/mkdir.html"><strong>Chapter 9</strong>: Preparing directories for output with <tt class="docutils literal"><span class="pre">@mkdir()</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/mkdir.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/mkdir.html#creating-directories-after-string-substitution-in-a-zoo">Creating directories after string substitution in a zoo...</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html"><strong>Chapter 10</strong>: Checkpointing: Interrupted Pipelines and Exceptions</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#interrupting-tasks">Interrupting tasks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#checkpointing-only-log-completed-jobs">Checkpointing: only log completed jobs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#do-not-share-the-same-checkpoint-file-across-for-multiple-pipelines">Do not share the same checkpoint file across for multiple pipelines!</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#setting-checkpoint-file-names">Setting checkpoint file names</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#useful-checkpoint-file-name-policies-default-ruffus-history-file">Useful checkpoint file name policies <tt class="docutils literal"><span class="pre">DEFAULT_RUFFUS_HISTORY_FILE</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#regenerating-the-checkpoint-file">Regenerating the checkpoint file</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#rules-for-determining-if-files-are-up-to-date">Rules for determining if files are up to date</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#missing-files-generate-exceptions">Missing files generate exceptions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#caveats-coarse-timestamp-resolution">Caveats: Coarse Timestamp resolution</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#flag-files-checkpointing-for-the-paranoid">Flag files: Checkpointing for the paranoid</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html"><strong>Chapter 11</strong>: Pipeline topologies and a compendium of <em>Ruffus</em> decorators</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#transform"><tt class="docutils literal"><span class="pre">@transform</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#a-bestiary-of-ruffus-decorators">A bestiary of <em>Ruffus</em> decorators</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#originate"><tt class="docutils literal"><span class="pre">@originate</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#merge"><tt class="docutils literal"><span class="pre">@merge</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#split"><tt class="docutils literal"><span class="pre">@split</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#subdivide"><tt class="docutils literal"><span class="pre">@subdivide</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#collate"><tt class="docutils literal"><span class="pre">@collate</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#combinatorics">Combinatorics</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#product"><tt class="docutils literal"><span class="pre">@product</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#combinations"><tt class="docutils literal"><span class="pre">@combinations</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#combinations-with-replacement"><tt class="docutils literal"><span class="pre">@combinations_with_replacement</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/decorators_compendium.html#permutations"><tt class="docutils literal"><span class="pre">@permutations</span></tt></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/split.html"><strong>Chapter 12</strong>: Splitting up large tasks / files with <strong>@split</strong></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/split.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/split.html#example-calculate-variance-for-a-large-list-of-numbers-in-parallel">Example: Calculate variance for a large list of numbers in parallel</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/split.html#output-files-for-split">Output files for <tt class="docutils literal"><span class="pre">@split</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/split.html#be-careful-in-specifying-output-globs">Be careful in specifying  <strong>Output</strong> globs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/split.html#clean-up-previous-pipeline-runs">Clean up previous pipeline runs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/split.html#to-many">1 to many</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/split.html#nothing-to-many">Nothing to many</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/merge.html"><strong>Chapter 13</strong>: <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/merge.html#overview-of-merge">Overview of <tt class="docutils literal"><span class="pre">@merge</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/merge.html#merge-is-a-many-to-one-operator"><tt class="docutils literal"><span class="pre">@merge</span></tt>  is a many to one operator</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/merge.html#example-combining-partial-solutions-calculating-variances">Example: Combining partial solutions: Calculating variances</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/multiprocessing.html"><strong>Chapter 14</strong>: Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/multiprocessing.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/multiprocessing.html#restricting-parallelism-with-jobs-limit">Restricting parallelism with <tt class="docutils literal"><span class="pre">@jobs_limit</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/multiprocessing.html#using-drmaa-to-dispatch-work-to-computational-clusters-or-grid-engines-from-ruffus-jobs">Using <tt class="docutils literal"><span class="pre">drmaa</span></tt> to dispatch work to Computational Clusters or Grid engines from Ruffus jobs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/multiprocessing.html#forcing-a-pipeline-to-appear-up-to-date">Forcing a pipeline to appear up to date</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/logging.html"><strong>Chapter 15</strong>: Logging progress through a pipeline</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/logging.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/logging.html#logging-task-job-completion">Logging task/job completion</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/logging.html#use-ruffus-cmdline">Use <tt class="docutils literal"><span class="pre">ruffus.cmdline</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/logging.html#customising-logging">Customising logging</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/logging.html#log-your-own-messages">Log your own messages</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/subdivide_collate.html"><strong>Chapter 16</strong>: <tt class="docutils literal"><span class="pre">@subdivide</span></tt> tasks to run efficiently and regroup with <tt class="docutils literal"><span class="pre">@collate</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/subdivide_collate.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/subdivide_collate.html#subdivide-in-parallel"><tt class="docutils literal"><span class="pre">@subdivide</span></tt> in parallel</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/subdivide_collate.html#grouping-using-collate">Grouping using <tt class="docutils literal"><span class="pre">@collate</span></tt></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html"><strong>Chapter 17</strong>: <tt class="docutils literal"><span class="pre">@combinations</span></tt>, <tt class="docutils literal"><span class="pre">@permutations</span></tt> and all versus all <tt class="docutils literal"><span class="pre">@product</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#generating-output-with-formatter">Generating output with <tt class="docutils literal"><span class="pre">formatter()</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#all-vs-all-comparisons-with-product">All vs all comparisons with <tt class="docutils literal"><span class="pre">@product</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#permute-all-k-tuple-orderings-of-inputs-without-repeats-using-permutations">Permute all k-tuple orderings of inputs without repeats using <tt class="docutils literal"><span class="pre">@permutations</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#select-unordered-k-tuples-within-inputs-excluding-repeated-elements-using-combinations">Select unordered k-tuples within inputs excluding repeated elements using <tt class="docutils literal"><span class="pre">@combinations</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#select-unordered-k-tuples-within-inputs-including-repeated-elements-with-combinations-with-replacement">Select unordered k-tuples within inputs <em>including</em> repeated elements with <tt class="docutils literal"><span class="pre">@combinations_with_replacement</span></tt></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/active_if.html"><strong>Chapter 18</strong>: Turning parts of the pipeline on and off at runtime with <tt class="docutils literal"><span class="pre">@active_if</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/active_if.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/active_if.html#active-if-controls-the-state-of-tasks"><tt class="docutils literal"><span class="pre">@active_if</span></tt>  controls the state of tasks</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/posttask.html"><strong>Chapter 19</strong>: Signal the completion of each stage of our pipeline with <tt class="docutils literal"><span class="pre">@posttask</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/posttask.html#overview">Overview</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/inputs.html"><strong>Chapter 20</strong>: Manipulating task inputs via string substitution using <tt class="docutils literal"><span class="pre">inputs()</span></tt> and  <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/inputs.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/inputs.html#adding-additional-input-prerequisites-per-job-with-add-inputs">Adding additional <em>input</em> prerequisites per job with <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/inputs.html#replacing-all-input-parameters-with-inputs">Replacing all input parameters with <tt class="docutils literal"><span class="pre">inputs()</span></tt></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/onthefly.html"><strong>Chapter 21</strong>: Esoteric: Generating parameters on the fly with <tt class="docutils literal"><span class="pre">@files</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/onthefly.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/onthefly.html#files-syntax"><tt class="docutils literal"><span class="pre">@files</span></tt> syntax</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/onthefly.html#a-cartesian-product-all-vs-all-example">A Cartesian Product, all vs all example</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/parallel.html"><strong>Chapter 22</strong>: Esoteric: Running jobs in parallel without files using <tt class="docutils literal"><span class="pre">@parallel</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/parallel.html#parallel"><strong>@parallel</strong></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/check_if_uptodate.html"><strong>Chapter 23</strong>: Esoteric: Writing custom functions to decide which jobs are up to date with <tt class="docutils literal"><span class="pre">@check_if_uptodate</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/check_if_uptodate.html#check-if-uptodate-manual-dependency-checking"><strong>@check_if_uptodate</strong> : Manual dependency checking</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/flowchart_colours.html"><strong>Appendix 1</strong>: Flow Chart Colours with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/flowchart_colours.html#flowchart-colours">Flowchart colours</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/dependencies.html"><strong>Appendix 2</strong>: How dependency is checked</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/dependencies.html#overview">Overview</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/exceptions.html"><strong>Appendix 3</strong>: Exceptions thrown inside pipelines</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/exceptions.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/exceptions.html#pipelines-running-in-parallel-accumulate-exceptions">Pipelines running in parallel accumulate Exceptions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/exceptions.html#terminate-pipeline-immediately-upon-exceptions">Terminate pipeline immediately upon Exceptions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/exceptions.html#display-exceptions-as-they-occur">Display exceptions as they occur</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/list_of_ruffus_names.html"><strong>Appendix 4</strong>: Names exported from Ruffus</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/list_of_ruffus_names.html#ruffus-names">Ruffus Names</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/deprecated_files.html"><strong>Appendix 5</strong>: <strong>@files</strong>: Deprecated syntax</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/deprecated_files.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/deprecated_files.html#files"><strong>@files</strong></a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/deprecated_files.html#running-the-same-code-on-different-parameters-in-parallel">Running the same code on different parameters in parallel</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/deprecated_files_re.html"><strong>Appendix 6</strong>: <strong>@files_re</strong>: Deprecated <cite>syntax using regular expressions</cite></a><ul>
-<li class="toctree-l2"><a class="reference internal" href="tutorials/new_tutorial/deprecated_files_re.html#overview">Overview</a></li>
-</ul>
-</li>
-</ul>
-</div>
-<p>Example code for:</p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/introduction_code.html"><strong>Chapter 1</strong>: Python Code for An introduction to basic Ruffus syntax</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/transform_code.html"><strong>Chapter 1</strong>: Python Code for Transforming data in a pipeline with <tt class="docutils literal"><span class="pre">@transform</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/transform_in_parallel_code.html"><strong>Chapter 3</strong>: Python Code for More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/originate_code.html"><strong>Chapter 4</strong>: Python Code for Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout_code.html"><strong>Chapter 5</strong>: Python Code for Understanding how your pipeline works with <tt class="docutils literal"><span class="pre">pipeline_printout(...)</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/pipeline_printout_graph_code.html"><strong>Chapter 7</strong>: Python Code for Displaying the pipeline visually with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/output_file_names_code.html"><strong>Chapter 8</strong>: Python Code for Specifying output file names with <tt class="docutils literal"><span class="pre">formatter()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/mkdir_code.html"><strong>Chapter 9</strong>: Python Code for Preparing directories for output with <tt class="docutils literal"><span class="pre">@mkdir()</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/checkpointing_code.html"><strong>Chapter 10</strong>: Python Code for Checkpointing: Interrupted Pipelines and Exceptions</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/split_code.html"><strong>Chapter 12</strong>: Python Code for Splitting up large tasks / files with <strong>@split</strong></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/merge_code.html"><strong>Chapter 13</strong>: Python Code for  <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/multiprocessing_code.html"><strong>Chapter 14</strong>: Python Code for Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/logging_code.html"><strong>Chapter 15</strong>: Python Code for Logging progress through a pipeline</a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/subdivide_collate_code.html"><strong>Chapter 16</strong>: Python Code for <tt class="docutils literal"><span class="pre">@subdivide</span></tt> tasks to run efficiently and regroup with <tt class="docutils literal"><span class="pre">@collate</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/combinatorics_code.html"><strong>Chapter 17</strong>: Python Code for <tt class="docutils literal"><span class="pre">@combinations</span></tt>, <tt class="docutils literal"><span class="pre">@permutations</span></tt> and all versus all <tt class="docutils literal"><span class="pre">@product</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/inputs_code.html"><strong>Chapter 20</strong>: Python Code for Manipulating task inputs via string substitution using <tt class="docutils literal"><span class="pre">inputs()</span></tt>  and  <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/onthefly_code.html"><strong>Chapter 21</strong>: Esoteric: Python Code for Generating parameters on the fly with <tt class="docutils literal"><span class="pre">@files</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="tutorials/new_tutorial/flowchart_colours_code.html"><strong>Appendix 1</strong>: Python code for Flow Chart Colours with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></li>
-</ul>
-</div>
-</div>
-<div class="section" id="overview">
-<h2>Overview:<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="cheatsheet.html">Cheat Sheet</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="cheatsheet.html#annotate-functions-with-ruffus-decorators">1. Annotate functions with <strong>Ruffus</strong> decorators</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cheatsheet.html#print-dependency-graph-if-necessary">2. Print dependency graph if necessary</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cheatsheet.html#run-the-pipeline">3. Run the pipeline</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="pipeline_functions.html">Pipeline functions</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="pipeline_functions.html#index-0"><em>pipeline_run</em></a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline_functions.html#index-1"><em>pipeline_printout</em></a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline_functions.html#index-2"><em>pipeline_printout_graph</em></a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline_functions.html#index-3"><em>pipeline_get_task_names</em></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="drmaa_wrapper_functions.html">drmaa functions</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="drmaa_wrapper_functions.html#index-0"><em>run_job</em></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#the-easy-way">The easy way</a></li>
-<li class="toctree-l2"><a class="reference internal" href="installation.html#the-most-up-to-date-code">The most up-to-date code:</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="design.html">Design & Architecture</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="design.html#gnu-make"><cite>GNU Make</cite></a></li>
-<li class="toctree-l2"><a class="reference internal" href="design.html#scons-rake-and-other-make-alternatives"><cite>Scons</cite>, <cite>Rake</cite> and other <cite>Make</cite> alternatives</a></li>
-<li class="toctree-l2"><a class="reference internal" href="design.html#managing-pipelines-stage-by-stage-using-ruffus">Managing pipelines stage-by-stage using <strong>Ruffus</strong></a></li>
-<li class="toctree-l2"><a class="reference internal" href="design.html#alternatives-to-ruffus">Alternatives to <strong>Ruffus</strong></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="history.html">Major Features added to Ruffus</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-5rc">version 2.5RC</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-4-1">version 2.4.1</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-4">version 2.4</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-3">version 2.3</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-2">version 2.2</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-1-1">version 2.1.1</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-1-0">version 2.1.0</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-0-10">version 2.0.10</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-0-9">version 2.0.9</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-0-8">version 2.0.8</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-0-2">version 2.0.2</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-2-0">version 2.0</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-1-1-4">version 1.1.4</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-1-0-7">version 1.0.7</a></li>
-<li class="toctree-l2"><a class="reference internal" href="history.html#version-1-0">version 1.0</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="history.html#fixed-bugs">Fixed Bugs</a></li>
-<li class="toctree-l1"><a class="reference internal" href="todo.html">Future Changes to Ruffus</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#todo-pipeline-printout-graph-should-print-inactive-tasks">Todo: pipeline_printout_graph should print inactive tasks</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#todo-mark-input-strings-as-non-file-names-and-add-support-for-dynamically-returned-parameters">Todo: Mark input strings as non-file names, and add support for dynamically returned parameters</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#todo-allow-extra-parameters-to-be-used-in-output-substitution">Todo: Allow “extra” parameters to be used in output substitution</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#todo-extra-signalling-before-and-after-each-task-and-job">Todo: Extra signalling before and after each task and job</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#todo-split-subdivide-returns-the-actual-output-created">Todo: <tt class="docutils literal"><span class="pre">@split</span></tt> / <tt class="docutils literal"><span class="pre">@subdivide</span></tt> returns the actual output created</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#id1">Todo: New decorators</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#todo-named-parameters-in-decorators-for-clarity">Todo: Named parameters in decorators for clarity</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#todo-bioinformatics-example-to-end-all-examples">Todo: Bioinformatics example to end all examples</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#todo-allow-the-next-task-to-start-before-all-jobs-in-the-previous-task-have-finished">Todo: Allow the next task to start before all jobs in the previous task have finished</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="todo.html#planned-improvements-to-ruffus">Planned Improvements to Ruffus</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#planned-running-python-code-task-functions-transparently-on-remote-cluster-nodes">Planned: Running python code (task functions) transparently on remote cluster nodes</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#planned-custom-parameter-generator">Planned: Custom parameter generator</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#planned-ruffus-gui-interface">Planned: Ruffus GUI interface.</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#planned-non-decorator-function-interface-to-ruffus">Planned: Non-decorator / Function interface to Ruffus</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#planned-remove-intermediate-files">Planned: Remove intermediate files</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#planned-retry-on-error-num-of-retries">Planned: @retry_on_error(NUM_OF_RETRIES)</a></li>
-<li class="toctree-l2"><a class="reference internal" href="todo.html#planned-clean-up">Planned: Clean up</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="implementation_notes.html">Implementation Tips</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#release">Release</a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#dbdict-py">dbdict.py</a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#how-to-write-new-decorators">how to write new decorators</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="implementation_notes.html#implementation-notes">Implementation notes</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#ctrl-c-handling"><tt class="docutils literal"><span class="pre">Ctrl-C</span></tt> handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#python3-compatability">Python3 compatability</a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#refactoring-parameter-handling">Refactoring: parameter handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#formatter"><tt class="docutils literal"><span class="pre">formatter</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#product">@product()</a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#permutations-combinations-combinations-with-replacement"><tt class="docutils literal"><span class="pre">@permutations(...),</span></tt> <tt class="docutils literal"><span class="pre">@combinations(...),</span></tt> <tt class="docutils literal"><span class="pre">@combinations_with_replacement(...)</span></tt></a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#drmaa-alternatives">drmaa alternatives</a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#task-completion-monitoring">Task completion monitoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="implementation_notes.html#mkdir"><tt class="docutils literal"><span class="pre">@mkdir(...),</span></tt></a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="faq.html">FAQ</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="faq.html#citations">Citations</a></li>
-<li class="toctree-l2"><a class="reference internal" href="faq.html#good-practices">Good practices</a></li>
-<li class="toctree-l2"><a class="reference internal" href="faq.html#general">General</a></li>
-<li class="toctree-l2"><a class="reference internal" href="faq.html#windows">Windows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="faq.html#sun-grid-engine-pbs-slurm-etc">Sun Grid Engine / PBS / SLURM etc</a></li>
-<li class="toctree-l2"><a class="reference internal" href="faq.html#sharing-python-objects-between-ruffus-processes-running-concurrently">Sharing python objects between Ruffus processes running concurrently</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="glossary.html">Glossary</a></li>
-<li class="toctree-l1"><a class="reference internal" href="gallery.html">Hall of Fame: User contributed flowcharts</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="gallery.html#rnaseq-pipeline">RNASeq pipeline</a></li>
-<li class="toctree-l2"><a class="reference internal" href="gallery.html#non-coding-evolutionary-constraints">non-coding evolutionary constraints</a></li>
-<li class="toctree-l2"><a class="reference internal" href="gallery.html#snp-annotation">SNP annotation</a></li>
-<li class="toctree-l2"><a class="reference internal" href="gallery.html#chip-seq-analysis">Chip-Seq analysis</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="why_ruffus.html">Why <em>Ruffus</em>?</a></li>
-</ul>
-</div>
-</div>
-<div class="section" id="examples">
-<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="examples/bioinformatics/index.html">Construction of a simple pipeline to run BLAST jobs</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#prerequisites">Prerequisites</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#code">Code</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#step-1-splitting-up-the-query-sequences">Step 1. Splitting up the query sequences</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#step-2-run-blast-jobs-in-parallel">Step 2. Run BLAST jobs in parallel</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#step-3-combining-blast-results">Step 3. Combining BLAST results</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#step-4-running-the-pipeline">Step 4. Running the pipeline</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#step-5-testing-dependencies">Step 5. Testing dependencies</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/index.html#what-is-next">What is next?</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="examples/bioinformatics/part2.html">Part 2: A slightly more practical pipeline to run blasts jobs</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/part2.html#overview">Overview</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/part2.html#step-1-cleaning-up-any-leftover-junk-from-previous-pipeline-runs">Step 1. Cleaning up any leftover junk from previous pipeline runs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/part2.html#step-2-adding-a-flag-file-to-mark-successful-completion">Step 2. Adding a “flag” file to mark successful completion</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/part2.html#step-3-allowing-the-script-to-be-invoked-on-the-command-line">Step 3. Allowing the script to be invoked on the command line</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/part2.html#step-4-printing-out-a-flowchart-for-the-pipeline">Step 4. Printing out a flowchart for the pipeline</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/part2.html#step-5-errors">Step 5. Errors</a></li>
-<li class="toctree-l2"><a class="reference internal" href="examples/bioinformatics/part2.html#step-6-will-it-run">Step 6. Will it run?</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="examples/bioinformatics/part1_code.html">Ruffus code</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples/bioinformatics/part2_code.html">Ruffus code</a></li>
-<li class="toctree-l1"><a class="reference internal" href="examples/paired_end_data.py.html">Example code for <tt class="docutils literal"><span class="pre">FAQ</span> <span class="pre">Good</span> <span class="pre">practices:</span> <span class="pre">"What</span> <span class="pre">is</span> <span class="pre">the</span> <span class="pre">best</span> <span class="pre">way</span> <span class="pre">of</span> <span class="pre">handling</span> <span class="pre">data</span> <span class="p [...]
-</ul>
-</div>
-</div>
-<div class="section" id="reference">
-<h2>Reference:<a class="headerlink" href="#reference" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="decorators">
-<h3>Decorators<a class="headerlink" href="#decorators" title="Permalink to this headline">¶</a></h3>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="decorators/decorators.html">Ruffus Decorators</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/indicator_objects.html">Indicator Objects</a></li>
-</ul>
-</div>
-<div class="topic">
-<p class="topic-title first">Core</p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="decorators/originate.html">@originate</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/split.html">@split</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/split.html#split-with-regex-add-inputs-and-inputs">@split with <tt class="docutils literal"><span class="pre">regex(...)</span></tt>, <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/transform.html">@transform</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/merge.html">@merge</a></li>
-</ul>
-</div>
-</div>
-<div class="topic">
-<p class="topic-title first">For advanced users</p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="decorators/subdivide.html">@subdivide</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/transform_ex.html">@transform  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/collate.html">@collate</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/collate_ex.html">@collate  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/graphviz.html">@graphviz</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/mkdir.html">@mkdir</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/jobs_limit.html">@jobs_limit</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/posttask.html">@posttask</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/active_if.html">@active_if</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/follows.html">@follows</a></li>
-</ul>
-</div>
-</div>
-<div class="topic">
-<p class="topic-title first">Combinatorics</p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="decorators/product.html">@product</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/permutations.html">@permutations</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/combinations.html">@combinations</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/combinations_with_replacement.html">@combinations_with_replacement</a></li>
-</ul>
-</div>
-</div>
-<div class="topic">
-<p class="topic-title first">Esoteric</p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="decorators/files_ex.html">Generating parameters on the fly for @files</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/check_if_uptodate.html">@check_if_uptodate</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/parallel.html">@parallel</a></li>
-</ul>
-</div>
-</div>
-<div class="topic">
-<p class="topic-title first">Deprecated</p>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="decorators/files.html">@files</a></li>
-<li class="toctree-l1"><a class="reference internal" href="decorators/files_re.html">@files_re</a></li>
-</ul>
-</div>
-</div>
-</div>
-<div class="section" id="modules">
-<h3>Modules:<a class="headerlink" href="#modules" title="Permalink to this headline">¶</a></h3>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="task.html">ruffus.Task</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="task.html#decorators">Decorators</a></li>
-<li class="toctree-l2"><a class="reference internal" href="task.html#pipeline-functions">Pipeline functions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="task.html#id1">Logging</a></li>
-<li class="toctree-l2"><a class="reference internal" href="task.html#implementation">Implementation:</a></li>
-<li class="toctree-l2"><a class="reference internal" href="task.html#exceptions-and-errors">Exceptions and Errors</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="proxy_logger.html">ruffus.proxy_logger</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="proxy_logger.html#create-proxy-for-logging-for-use-with-multiprocessing">Create proxy for logging for use with multiprocessing</a></li>
-<li class="toctree-l2"><a class="reference internal" href="proxy_logger.html#proxies-for-a-log">Proxies for a log:</a></li>
-<li class="toctree-l2"><a class="reference internal" href="proxy_logger.html#create-a-logging-object">Create a logging object</a></li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-</div>
-<div class="section" id="indices-and-tables">
-<h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h2>
-<ul class="simple">
-<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li>
-<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li>
-<li><a class="reference internal" href="search.html"><em>Search Page</em></a></li>
-</ul>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="#">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Ruffus</strong> documentation</a><ul>
-<li><a class="reference internal" href="#start-here">Start Here:</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#overview">Overview:</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#examples">Examples</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#reference">Reference:</a><ul>
-<li><a class="reference internal" href="#decorators">Decorators</a><ul>
-</ul>
-</li>
-<li><a class="reference internal" href="#modules">Modules:</a><ul>
-</ul>
-</li>
-</ul>
-</li>
-<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Next topic</h4>
-  <p class="topless"><a href="installation.html"
-                        title="next chapter">Installation</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="_sources/contents.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
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-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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diff --git a/doc/_build/html/decorators/active_if.html b/doc/_build/html/decorators/active_if.html
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-            
-  <span class="target" id="decorators-active-if"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-<li>More on @active_if in the <tt class="docutils literal"><span class="pre">Ruffus</span></tt> <a class="reference internal" href="../tutorials/new_tutorial/active_if.html#new-manual-active-if"><em>Manual</em></a></li>
-</ul>
-</div>
-<div class="section" id="active-if">
-<h1>@active_if<a class="headerlink" href="#active-if" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="active-if-on-or-off1-on-or-off2">
-<h2><em>@active_if</em>(on_or_off1, [on_or_off2,...])<a class="headerlink" href="#active-if-on-or-off1-on-or-off2" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><ul class="simple">
-<li>Switches tasks on and off at run time depending on its parameters</li>
-<li>Evaluated each time <tt class="docutils literal"><span class="pre">pipeline_run</span></tt>, <tt class="docutils literal"><span class="pre">pipeline_printout</span></tt> or <tt class="docutils literal"><span class="pre">pipeline_printout_graph</span></tt> is called.</li>
-<li>The Design and initial implementation were contributed by Jacob Biesinger</li>
-<li>Dormant tasks behave as if they are up to date and have no output.</li>
-</ul>
-</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">run_if_true_1</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="n">run_if_true_2</span> <span class="o">=</span> <span class="bp">False</span>
-<span class="n">run_if_true_3</span> <span class="o">=</span> <span class="bp">True</span>
-
-
-<span class="c">#</span>
-<span class="c">#    task1</span>
-<span class="c">#</span>
-<span class="nd">@originate</span><span class="p">([</span><span class="s">'a.foo'</span><span class="p">,</span> <span class="s">'b.foo'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_files</span><span class="p">(</span><span class="n">outfile</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    create_files</span>
-<span class="sd">    """</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">outfile</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   Only runs if all three run_if_true conditions are met</span>
-<span class="c">#</span>
-<span class="hll"><span class="c">#   @active_if determines if task is active</span>
-</span><span class="nd">@active_if</span><span class="p">(</span><span class="n">run_if_true_1</span><span class="p">,</span> <span class="k">lambda</span><span class="p">:</span> <span class="n">run_if_true_2</span><span class="p">)</span>
-<span class="nd">@active_if</span><span class="p">(</span><span class="n">run_if_true_3</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".foo"</span><span class="p">),</span> <span class="s">".bar"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">this_task_might_be_inactive</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">infile</span> [...]
-
-
-<span class="c"># @active_if switches off task because run_if_true_2 == False</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="c"># @active_if switches on task because all run_if_true conditions are met</span>
-<span class="n">run_if_true_2</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>Produces the following output:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="hll"><span class="gp">>>> </span><span class="c"># @active_if switches off task "this_task_might_be_inactive" because run_if_true_2 == False</span>
-</span><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="go">Task enters queue = create_files</span>
-<span class="go">create_files</span>
-<span class="go">    Job  = [None -> a.foo] Missing file [a.foo]</span>
-<span class="go">    Job  = [None -> b.foo] Missing file [b.foo]</span>
-<span class="go">    Job  = [None -> a.foo] completed</span>
-<span class="go">    Job  = [None -> b.foo] completed</span>
-<span class="go">Completed Task = create_files</span>
-<span class="go">Inactive Task = this_task_might_be_inactive</span>
-
-<span class="hll"><span class="gp">>>> </span><span class="c"># @active_if switches on task "this_task_might_be_inactive" because all run_if_true conditions are met</span>
-</span><span class="gp">>>> </span><span class="n">run_if_true_2</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="go">Task enters queue = this_task_might_be_inactive</span>
-
-<span class="go">    Job  = [a.foo -> a.bar] Missing file [a.bar]</span>
-<span class="go">    Job  = [b.foo -> b.bar] Missing file [b.bar]</span>
-<span class="go">    Job  = [a.foo -> a.bar] completed</span>
-<span class="go">    Job  = [b.foo -> b.bar] completed</span>
-<span class="go">Completed Task = this_task_might_be_inactive</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-active-if-on-or-off">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>on_or_off</em>:</dt>
-<dd><p class="first">A comma separated list of boolean conditions. These can be values, functions or callable objects which return True / False</p>
-<p class="last">Multiple <tt class="docutils literal"><span class="pre">@active_if</span></tt> decorators can be stacked for clarity as in the example</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
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-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@active_if</a><ul>
-<li><a class="reference internal" href="#active-if-on-or-off1-on-or-off2"><em>@active_if</em>(on_or_off1, [on_or_off2,...])</a></li>
-</ul>
-</li>
-</ul>
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diff --git a/doc/_build/html/decorators/check_if_uptodate.html b/doc/_build/html/decorators/check_if_uptodate.html
deleted file mode 100644
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-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <span class="target" id="decorators-check-if-uptodate"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="check-if-uptodate">
-<h1>@check_if_uptodate<a class="headerlink" href="#check-if-uptodate" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="check-if-uptodate-dependency-checking-function">
-<h2><em>@check_if_uptodate</em> (<a class="reference internal" href="#decorators-check-if-uptodate-dependency-checking-function"><cite>dependency_checking_function</cite></a>)<a class="headerlink" href="#check-if-uptodate-dependency-checking-function" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">Checks to see if a job is up to date, and needs to be run.</p>
-<p class="last">Usually used in conjunction with <a class="reference internal" href="parallel.html#decorators-parallel"><em>@parallel()</em></a></p>
-</dd>
-</dl>
-<p><strong>Example</strong>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">os</span>
-<span class="k">def</span> <span class="nf">check_file_exists</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">True</span><span class="p">,</span> <span class="s">"Missing file </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">output_file</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">False</span><span class="p">,</span> <span class="s">"File </span><span class="si">%s</span><span class="s"> exists"</span> <span class="o">%</span> <span class="n">output_file</span>
-
-<span class="nd">@parallel</span><span class="p">([[</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">]])</span>
-<span class="nd">@check_if_uptodate</span><span class="p">(</span><span class="n">check_file_exists</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>Is equivalent to:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>Both produce the same output:</p>
-<div class="highlight-python"><pre>Task = create_if_necessary
-    Job = [null, "a.1"] completed</pre>
-</div>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-check-if-uptodate-dependency-checking-function">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>dependency_checking_function</em>:</dt>
-<dd><p class="first">returns two parameters: if job needs to be run, and a message explaining why</p>
-<p class="last">dependency_checking_func() needs to handle the same number of parameters as the
-task function e.g. <tt class="docutils literal"><span class="pre">input_file</span></tt> and <tt class="docutils literal"><span class="pre">output_file</span></tt> above.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@check_if_uptodate</a><ul>
-<li><a class="reference internal" href="#check-if-uptodate-dependency-checking-function"><em>@check_if_uptodate</em> (<cite>dependency_checking_function</cite>)</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="files_ex.html"
-                        title="previous chapter">Generating parameters on the fly for @files</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="parallel.html"
-                        title="next chapter">@parallel</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/check_if_uptodate.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="#">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
-
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-      <div class="clearer"></div>
-    </div>
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diff --git a/doc/_build/html/decorators/collate.html b/doc/_build/html/decorators/collate.html
deleted file mode 100644
index 3b3b5d7..0000000
--- a/doc/_build/html/decorators/collate.html
+++ /dev/null
@@ -1,362 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>@collate — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="../_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
-        VERSION:     '2.5',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true
-      };
-    </script>
-    <script type="text/javascript" src="../_static/jquery.js"></script>
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-    <link rel="top" title="ruffus 2.5 documentation" href="../index.html" />
-    <link rel="next" title="@collate with add_inputs and inputs" href="collate_ex.html" />
-    <link rel="prev" title="@transform with add_inputs and inputs" href="transform_ex.html" /> 
-  </head>
-  <body>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="collate_ex.html" title="@collate with add_inputs and inputs"
-             accesskey="N">next</a> |</li>
-        <li class="right" >
-          <a href="transform_ex.html" title="@transform with add_inputs and inputs"
-             accesskey="P">previous</a> |</li>
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-            <li><a href="../installation.html">Install</a>  | </li>
-            <li><a href="../tutorials/new_tutorial/introduction.html">Manual</a>  / </li>
-            <li><a href="../tutorials/new_tutorial/manual_contents.html">(TOC)</a>  | </li>
-            <li><a href="../faq.html">FAQ</a>  | </li>
-            <li><a href="../cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="../tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="../gallery.html">Gallery</a> |  </li>
-            <li><a href="../history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <span class="target" id="decorators-collate"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="collate">
-<h1>@collate<a class="headerlink" href="#collate" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="collate-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-output-pattern-extra-parameters">
-<h2><em>@collate</em> ( <a class="reference internal" href="#decorators-collate-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a><em>(</em><a class="reference internal" href="#decorators-collate-matching-regex"><cite>matching_regex</cite></a><em>)</em> |  <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a><em>(</em><a class="refe [...]
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">Groups / collates sets of input files, each into a separate summary.</p>
-<p>Only out of date tasks (comparing input and output files) will be run</p>
-<p>Output file names and strings in the extra parameters
-are determined from <a class="reference internal" href="#decorators-collate-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of up stream tasks, or a list of file names.</p>
-<p>String replacement occurs either through suffix matches via <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a> or
-the <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> or <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicators.</p>
-<p><tt class="docutils literal"><span class="pre">@collate</span></tt> groups together all <strong>Input</strong> which result in identical <strong>Output</strong> and <strong>extra</strong>
-parameters.</p>
-<p class="last">It is a <strong>many to fewer</strong> operation.</p>
-</dd>
-<dt><strong>Example</strong>:</dt>
-<dd><p class="first"><tt class="docutils literal"><span class="pre">regex(r".*(\..+)"),</span> <span class="pre">"\1.summary"</span></tt> creates a separate summary file for each suffix:</p>
-<div class="last highlight-python"><div class="highlight"><pre><span class="n">animal_files</span> <span class="o">=</span> <span class="s">"a.fish"</span><span class="p">,</span> <span class="s">"b.fish"</span><span class="p">,</span> <span class="s">"c.mammals"</span><span class="p">,</span> <span class="s">"d.mammals"</span>
-<span class="c"># summarise by file suffix:</span>
-<span class="nd">@collate</span><span class="p">(</span><span class="n">animal_files</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"\.(.+)$"</span><span class="p">),</span>  <span class="s">r'\1.summary'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">summary_file</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-collate-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-matching-regex">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_regex</em></dt>
-<dd><p class="first last">is a python regular expression string, which must be wrapped in
-a <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicator object
-See python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>
-documentation for details of regular expression syntax</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s).</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">Any extra parameters are passed verbatim to the task function</p>
-</dd>
-</dl>
-</li>
-</ul>
-<ol class="arabic simple">
-<li><em>outputs</em> and optional extra parameters are passed to the functions after string
-substitution in any strings. Non-string values are passed through unchanged.</li>
-<li>Each collate job consists of input files which are aggregated by string substitution
-to a single set of output / extra parameter matches</li>
-<li>In the above cases, <tt class="docutils literal"><span class="pre">a.fish</span></tt> and <tt class="docutils literal"><span class="pre">b.fish</span></tt> both produce <tt class="docutils literal"><span class="pre">fish.summary</span></tt> after regular
-expression subsitution, and are collated into a single job:
-<tt class="docutils literal"><span class="pre">["a.fish",</span> <span class="pre">"b.fish"</span> <span class="pre">-></span> <span class="pre">"fish.summary"]</span></tt>
-while <tt class="docutils literal"><span class="pre">c.mammals</span></tt>, <tt class="docutils literal"><span class="pre">d.mammals</span></tt> both produce <tt class="docutils literal"><span class="pre">mammals.summary</span></tt>, are collated in a separate job:
-<tt class="docutils literal"><span class="pre">["c.mammals",</span> <span class="pre">"d.mammals"</span> <span class="pre">-></span> <span class="pre">"mammals.summary"]</span></tt></li>
-</ol>
-<p><strong>Example2</strong>:</p>
-<blockquote>
-<div><p>Suppose we had the following files:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">cows</span><span class="o">.</span><span class="n">mammals</span><span class="o">.</span><span class="n">animal</span>
-<span class="n">horses</span><span class="o">.</span><span class="n">mammals</span><span class="o">.</span><span class="n">animal</span>
-<span class="n">sheep</span><span class="o">.</span><span class="n">mammals</span><span class="o">.</span><span class="n">animal</span>
-
-<span class="n">snake</span><span class="o">.</span><span class="n">reptile</span><span class="o">.</span><span class="n">animal</span>
-<span class="n">lizard</span><span class="o">.</span><span class="n">reptile</span><span class="o">.</span><span class="n">animal</span>
-<span class="n">crocodile</span><span class="o">.</span><span class="n">reptile</span><span class="o">.</span><span class="n">animal</span>
-
-<span class="n">pufferfish</span><span class="o">.</span><span class="n">fish</span><span class="o">.</span><span class="n">animal</span>
-</pre></div>
-</div>
-<p>and we wanted to end up with three different resulting output:</p>
-<div class="highlight-python"><pre>cow.mammals.animal
-horse.mammals.animal
-sheep.mammals.animal
-    -> mammals.results
-
-snake.reptile.animal
-lizard.reptile.animal
-crocodile.reptile.animal
-    -> reptile.results
-
-pufferfish.fish.animal
-    -> fish.results</pre>
-</div>
-<p>This is the <tt class="docutils literal"><span class="pre">@collate</span></tt> code required:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">animals</span> <span class="o">=</span> <span class="p">[</span>     <span class="s">"cows.mammals.animal"</span><span class="p">,</span>
-                <span class="s">"horses.mammals.animal"</span><span class="p">,</span>
-                <span class="s">"sheep.mammals.animal"</span><span class="p">,</span>
-                <span class="s">"snake.reptile.animal"</span><span class="p">,</span>
-                <span class="s">"lizard.reptile.animal"</span><span class="p">,</span>
-                <span class="s">"crocodile.reptile.animal"</span><span class="p">,</span>
-                <span class="s">"pufferfish.fish.animal"</span><span class="p">]</span>
-
-<span class="nd">@collate</span><span class="p">(</span><span class="n">animals</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"(.+)\.(.+)\.animal"</span><span class="p">),</span>  <span class="s">r"\2.results"</span><span class="p">)</span>
-<span class="c"># \1 = species [cow, horse]</span>
-<span class="c"># \2 = phylogenetics group [mammals, reptile, fish]</span>
-<span class="k">def</span> <span class="nf">summarize_animals_into_groups</span><span class="p">(</span><span class="n">species_file</span><span class="p">,</span> <span class="n">result_file</span><span class="p">):</span>
-    <span class="s">" ... more code here"</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<p>See <a class="reference internal" href="merge.html#decorators-merge"><em>@merge</em></a> for an alternative way to summarise files.</p>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@collate</a><ul>
-<li><a class="reference internal" href="#collate-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-output-pattern-extra-parameters"><em>@collate</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">regex</span></tt><em>(</em><cite>matching_regex</cite><em>)</em> |  <tt class="docutils literal"><span class="pre">formatter</span></tt><em>(</em><cite>matching_formatter</cite><em>)</em>, <cite>output_pattern</cite>, [<cite>extra_para [...]
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="transform_ex.html"
-                        title="previous chapter">@transform  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="collate_ex.html"
-                        title="next chapter">@collate  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
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-            <li><a href="#">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
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-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
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-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
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-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-         <a href="../todo.html">Future plans</a>
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-          <div class="body">
-            
-  <span class="target" id="decorators-collate-ex"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="collate-with-add-inputs-and-inputs">
-<h1>@collate  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt><a class="headerlink" href="#collate-with-add-inputs-and-inputs" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="collate-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-inputs-input-pattern-or-glob-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters">
-<h2><em>@collate</em> ( <a class="reference internal" href="#decorators-collate-ex-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a><em>(</em><a class="reference internal" href="#decorators-collate-ex-matching-regex"><cite>matching_regex</cite></a><em>)</em> |  <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a><em>(</em><a class [...]
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">Groups / collates sets of input files, each into a separate summary.</p>
-<p>This variant of <tt class="docutils literal"><span class="pre">@collate</span></tt> allows additional inputs or dependencies to be added
-dynamically to the task.</p>
-<p>Output file names are determined from <a class="reference internal" href="#decorators-collate-ex-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of up stream tasks, or a list of file names.</p>
-<p>This variant of <tt class="docutils literal"><span class="pre">@collate</span></tt> allows input file names to be derived in the same way.</p>
-<p><a class="reference internal" href="indicator_objects.html#decorators-add-inputs"><em>add_inputs</em></a> nests the the original input parameters in a list before adding additional dependencies.</p>
-<p><a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a> replaces the original input parameters wholescale.</p>
-<p class="last">Only out of date tasks (comparing input and output files) will be run</p>
-</dd>
-</dl>
-<p><strong>Example of</strong> <a class="reference internal" href="indicator_objects.html#decorators-add-inputs"><em>add_inputs</em></a></p>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">regex(r".*(\..+)"),</span> <span class="pre">"\1.summary"</span></tt> creates a separate summary file for each suffix.
-But we also add date of birth data for each species:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">animal_files</span> <span class="o">=</span> <span class="s">"tuna.fish"</span><span class="p">,</span> <span class="s">"shark.fish"</span><span class="p">,</span> <span class="s">"dog.mammals"</span><span class="p">,</span> <span class="s">"cat.mammals"</span>
-<span class="c"># summarise by file suffix:</span>
-<span class="nd">@collate</span><span class="p">(</span><span class="n">animal_files</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r".+\.(.+)$"</span><span class="p">),</span>  <span class="n">add_inputs</span><span class="p">(</span><span class="s">r"\1.date_of_birth"</span><span class="p">),</span> <span class="s">r'\1.summary'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">summary_file</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>This results in the following equivalent function calls:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">summarize</span><span class="p">([</span> <span class="p">[</span><span class="s">"shark.fish"</span><span class="p">,</span>  <span class="s">"fish.date_of_birth"</span>   <span class="p">],</span>
-            <span class="p">[</span><span class="s">"tuna.fish"</span><span class="p">,</span>   <span class="s">"fish.date_of_birth"</span>   <span class="p">]</span> <span class="p">],</span> <span class="s">"fish.summary"</span><span class="p">)</span>
-<span class="n">summarize</span><span class="p">([</span> <span class="p">[</span><span class="s">"cat.mammals"</span><span class="p">,</span> <span class="s">"mammals.date_of_birth"</span><span class="p">],</span>
-            <span class="p">[</span><span class="s">"dog.mammals"</span><span class="p">,</span> <span class="s">"mammals.date_of_birth"</span><span class="p">]</span> <span class="p">],</span> <span class="s">"mammals.summary"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Example of</strong> <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>add_inputs</em></a></p>
-<blockquote>
-<div><p>using <tt class="docutils literal"><span class="pre">inputs(...)</span></tt> will summarise only the dates of births for each species group:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">animal_files</span> <span class="o">=</span> <span class="s">"tuna.fish"</span><span class="p">,</span> <span class="s">"shark.fish"</span><span class="p">,</span> <span class="s">"dog.mammals"</span><span class="p">,</span> <span class="s">"cat.mammals"</span>
-<span class="c"># summarise by file suffix:</span>
-<span class="nd">@collate</span><span class="p">(</span><span class="n">animal_files</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r".+\.(.+)$"</span><span class="p">),</span>  <span class="n">inputs</span><span class="p">(</span><span class="s">r"\1.date_of_birth"</span><span class="p">),</span> <span class="s">r'\1.summary'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">summary_file</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>This results in the following equivalent function calls:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">summarize</span><span class="p">([</span><span class="s">"fish.date_of_birth"</span>   <span class="p">],</span> <span class="s">"fish.summary"</span><span class="p">)</span>
-<span class="n">summarize</span><span class="p">([</span><span class="s">"mammals.date_of_birth"</span><span class="p">],</span> <span class="s">"mammals.summary"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-collate-ex-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-ex-matching-regex">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_regex</em></dt>
-<dd><p class="first last">is a python regular expression string, which must be wrapped in
-a <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicator object
-See python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>
-documentation for details of regular expression syntax</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-ex-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-ex-input-pattern-or-glob">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>input_pattern</em></dt>
-<dd><p class="first">Specifies the resulting input(s) to each job.
-Must be wrapped in an <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a> or an <a class="reference internal" href="indicator_objects.html#decorators-add-inputs"><em>inputs</em></a> indicator object.</p>
-<p>Can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><p class="first last">Strings will be subject to substitution.
-File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.
-E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-ex-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s).</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-collate-ex-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">Any extra parameters are passed verbatim to the task function</p>
-</dd>
-</dl>
-</li>
-</ul>
-<ol class="arabic simple">
-<li><em>outputs</em> and optional extra parameters are passed to the functions after string
-substitution in any strings. Non-string values are passed through unchanged.</li>
-<li>Each collate job consists of input files which are aggregated by string substitution
-to a single set of output / extra parameter matches</li>
-</ol>
-</div></blockquote>
-<p>See <a class="reference internal" href="collate.html#decorators-collate"><em>@collate</em></a> for more straightforward ways to use collate.</p>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@collate  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a><ul>
-<li><a class="reference internal" href="#collate-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-inputs-input-pattern-or-glob-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters"><em>@collate</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">regex</span></tt><em>(</em><cite>matching_regex</cite><em>)</em> |  <tt class="docutils literal"><span class="pre">formatter</span></tt><em>(</em><cite>matching_formatter</c [...]
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="collate.html"
-                        title="previous chapter">@collate</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="graphviz.html"
-                        title="next chapter">@graphviz</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/collate_ex.txt"
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
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-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
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-            
-  <span class="target" id="decorators-combinations"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="combinations">
-<h1>@combinations<a class="headerlink" href="#combinations" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="combinations-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters">
-<h2><em>@combinations</em> ( <a class="reference internal" href="#decorators-combinations-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a><em>(</em><a class="reference internal" href="#decorators-combinations-matching-formatter"><cite>matching_formatter</cite></a><em>)</em>, <a class="reference internal" href="#decorators-combinations-output-pattern"><cite>output_pattern< [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>Generates the <strong>combinations</strong>, between all the elements of a set of <strong>Input</strong> (e.g. <strong>A B C D</strong>),
-i.e. r-length tuples of <em>input</em> elements with no repeated elements (<strong>A A</strong>)
-and where order of the tuples is irrelevant (either <strong>A B</strong> or  <strong>B A</strong>, not both).</p>
-<p>The effect is analogous to the python <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.combinations">itertools</a>
-function of the same name:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">combinations</span>
-<span class="hll"><span class="gp">>>> </span><span class="c"># combinations('ABCD', 3) --> ABC ABD ACD BCD</span>
-</span><span class="gp">>>> </span><span class="p">[</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">combinations</span><span class="p">(</span><span class="s">"ABCD"</span><span class="p">,</span> <span class="mi">3</span><span class="p">)]</span>
-<span class="go">['ABC', 'ABD', 'ACD', 'BCD']</span>
-</pre></div>
-</div>
-<p>Only out of date tasks (comparing input and output files) will be run</p>
-<p>Output file names and strings in the extra parameters
-are determined from <a class="reference internal" href="#decorators-combinations-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of up stream tasks, or a list of file names, after string replacement via
-<a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a>.</p>
-<p>The replacement strings require an extra level of indirection to refer to
-parsed components:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>The first level refers to which <em>set</em> in each tuple of inputs.</li>
-<li>The second level refers to which input file in any particular <em>set</em> of inputs.</li>
-</ol>
-</div></blockquote>
-</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><p>Calculates the <strong>@combinations</strong> of <strong>A,B,C,D</strong> files</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @combinations</span>
-</span><span class="nd">@combinations</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>      <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                    <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 3 at a time</span>
-</span>              <span class="mi">3</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}_vs_"</span>
-              <span class="s">"{basename[2][1]}.combinations"</span><span class="p">,</span>
-<span class="hll">
-</span>              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-<span class="hll">
-</span><span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span>               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#              2nd</span>
-               <span class="s">"{basename[2][0]}"</span><span class="p">,</span>  <span class="c">#              3rd</span>
-               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">combinations_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">A - B - C</span>
-<span class="go">A - B - D</span>
-<span class="go">A - C - D</span>
-<span class="go">B - C - D</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-combinations-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-combinations-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-combinations-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s) after string
-substitution</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-combinations-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">Optional extra parameters are passed to the functions after string
-substitution</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@combinations</a><ul>
-<li><a class="reference internal" href="#combinations-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters"><em>@combinations</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">formatter</span></tt><em>(</em><cite>matching_formatter</cite><em>)</em>, <cite>output_pattern</cite>, [<cite>extra_parameters</cite>,...] )</a></li>
-</ul>
-</li>
-</ul>
-
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-  <span class="target" id="decorators-combinations-with-replacement"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="combinations-with-replacement">
-<h1>@combinations_with_replacement<a class="headerlink" href="#combinations-with-replacement" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="combinations-with-replacement-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters">
-<h2><em>@combinations_with_replacement</em> ( <a class="reference internal" href="#decorators-combinations-with-replacement-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a><em>(</em><a class="reference internal" href="#decorators-combinations-with-replacement-matching-formatter"><cite>matching_formatter</cite></a><em>)</em>, <a class="reference internal" href="#decorators [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>Generates the <strong>combinations_with_replacement</strong>, between all the elements of a set of <strong>Input</strong> (e.g. <strong>A B C D</strong>),
-i.e. r-length tuples of <em>input</em> elements included repeated elements (<strong>A A</strong>)
-and where order of the tuples is irrelevant (either <strong>A B</strong> or  <strong>B A</strong>, not both).</p>
-<p>The effect is analogous to the python <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.combinations_with_replacement">itertools</a>
-function of the same name:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">combinations_with_replacement</span>
-<span class="hll"><span class="gp">>>> </span><span class="c"># combinations_with_replacement('ABCD', 2) --> AA AB AC AD BB BC BD CC CD DD</span>
-</span><span class="gp">>>> </span><span class="p">[</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">combinations_with_replacement</span><span class="p">(</span><span class="s">'ABCD'</span><span class="p">,</span> <span class="mi">2</span><span class="p">)]</span>
-<span class="go">['AA', 'AB', 'AC', 'AD', 'BB', 'BC', 'BD', 'CC', 'CD', 'DD']</span>
-</pre></div>
-</div>
-<p>Only out of date tasks (comparing input and output files) will be run</p>
-<p>Output file names and strings in the extra parameters
-are determined from <a class="reference internal" href="#decorators-combinations-with-replacement-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of up stream tasks, or a list of file names, after string replacement via
-<a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a>.</p>
-<p>The replacement strings require an extra level of indirection to refer to
-parsed components:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>The first level refers to which <em>set</em> in each tuple of inputs.</li>
-<li>The second level refers to which input file in any particular <em>set</em> of inputs.</li>
-</ol>
-</div></blockquote>
-</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><p>Calculates the <strong>@combinations_with_replacement</strong> of <strong>A,B,C,D</strong> files</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @combinations_with_replacement</span>
-</span><span class="nd">@combinations_with_replacement</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>   <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                                  <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 2 at a time</span>
-</span>              <span class="mi">2</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}.combinations_with_replacement"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-</span>              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span><span class="hll">               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#              2rd</span>
-</span>               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">combinations_with_replacement_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">A - A</span>
-<span class="go">A - B</span>
-<span class="go">A - C</span>
-<span class="go">A - D</span>
-<span class="go">B - B</span>
-<span class="go">B - C</span>
-<span class="go">B - D</span>
-<span class="go">C - C</span>
-<span class="go">C - D</span>
-<span class="go">D - D</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-combinations-with-replacement-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-combinations-with-replacement-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-combinations-with-replacement-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s) after string
-substitution</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-combinations-with-replacement-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">Optional extra parameters are passed to the functions after string
-substitution</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@combinations_with_replacement</a><ul>
-<li><a class="reference internal" href="#combinations-with-replacement-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters"><em>@combinations_with_replacement</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">formatter</span></tt><em>(</em><cite>matching_formatter</cite><em>)</em>, <cite>output_pattern</cite>, [<cite>extra_parameters</cite>,...] )</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="combinations.html"
-                        title="previous chapter">@combinations</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="files_ex.html"
-                        title="next chapter">Generating parameters on the fly for @files</a></p>
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-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
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-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
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-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
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-            <li><a href="#">@combinations_ _with_replacement </a>                    </li>
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-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
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-
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-        <h4 >Pipeline functions</h4>
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-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-  <div class="section" id="ruffus-decorators">
-<h1>Ruffus Decorators<a class="headerlink" href="#ruffus-decorators" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="indicator_objects.html#decorators-indicator-objects"><em>Indicator objects</em></a></p>
-</div>
-<div class="section" id="core">
-<span id="decorators"></span><h2><em>Core</em><a class="headerlink" href="#core" title="Permalink to this headline">¶</a></h2>
-<table border="1" class="docutils">
-<colgroup>
-<col width="40%" />
-<col width="60%" />
-<col width="0%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">Decorator</th>
-<th class="head">Examples</th>
-<th class="head"> </th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td><p class="first"><strong>@originate</strong> (<a class="reference internal" href="originate.html#decorators-originate"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/originate.html#new-manual-originate"><em>Manual</em></a>)</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>Creates (originates) a set of starting file without dependencies from scratch  (<em>ex nihilo</em>!)</li>
-<li>Only called to create files which do not exist.</li>
-<li>Invoked onces (a job created) per item in the <tt class="docutils literal"><span class="pre">output_files</span></tt> list.</li>
-</ul>
-</div></blockquote>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="originate.html#decorators-originate"><em>@originate</em></a> ( <tt class="docutils literal"><span class="pre">output_files</span></tt>, [<tt class="docutils literal"><span class="pre">extra_parameters</span></tt>,...] )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@split</strong> (<a class="reference internal" href="split.html#decorators-split"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/split.html#new-manual-split"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Splits a single input into multiple output</li>
-<li>Globs in <tt class="docutils literal"><span class="pre">output</span></tt> can specify an indeterminate number of files.</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="split.html#decorators-split"><em>@split</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <tt class="docutils literal"><span class="pre">output_files</span></tt>, [<tt class="docutils literal"><span class="pre">extra_parameters</span></tt>,...] )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td><p class="first"><strong>@transform</strong> (<a class="reference internal" href="transform.html#decorators-transform"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/transform.html#new-manual-transform"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Applies the task function to transform input data to output.</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="transform_ex.html#decorators-transform-suffix-string"><em>suffix</em></a><em>(</em><tt class="docutils literal"><span class="pre">suffix_string</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</span></tt>, [<tt class="docutils litera [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="transform_ex.html#decorators-transform-matching-regex"><em>regex</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</span></tt>, [<tt class="docutils litera [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="transform_ex.html#decorators-transform-matching-formatter"><em>formatter</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</span></tt>, [<tt class="docutil [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@merge</strong> (<a class="reference internal" href="merge.html#decorators-merge"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/merge.html#new-manual-merge"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Merges multiple input files into a single output.</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="merge.html#decorators-merge"><em>@merge</em></a> (<tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <tt class="docutils literal"><span class="pre">output</span></tt>, [<tt class="docutils literal"><span class="pre">extra_parameters</span></tt>,...] )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-</tbody>
-</table>
-</div>
-<div class="section" id="combinatorics">
-<span id="decorators-combinatorics"></span><h2><em>Combinatorics</em><a class="headerlink" href="#combinatorics" title="Permalink to this headline">¶</a></h2>
-<table border="1" class="docutils">
-<colgroup>
-<col width="40%" />
-<col width="60%" />
-<col width="0%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">Decorator</th>
-<th class="head">Examples</th>
-<th class="head"> </th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td><p class="first"><strong>@product</strong> (<a class="reference internal" href="product.html#decorators-product"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/combinatorics.html#new-manual-product"><em>Manual</em></a>)</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>Generates the <strong>product</strong>, i.e. all vs all comparisons, between sets of input files.</li>
-</ul>
-</div></blockquote>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="product.html#decorators-product"><em>@product</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="product.html#decorators-product-matching-formatter"><em>formatter</em></a> <em>([</em> <tt class="docutils literal"><span class="pre">regex_pattern</span></tt> <em>])</em> ,*[* <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="referenc [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@permutations</strong> (<a class="reference internal" href="permutations.html#decorators-permutations"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/combinatorics.html#new-manual-permutations"><em>Manual</em></a>)</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>Generates the <strong>permutations</strong>, between all the elements of a set of <strong>Input</strong></li>
-<li>Analogous to the python <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.permutations">itertools.permutations</a></li>
-<li>permutations(‘ABCD’, 2) –> AB AC AD BA BC BD CA CB CD DA DB DC</li>
-</ul>
-</div></blockquote>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="permutations.html#decorators-permutations"><em>@permutations</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="product.html#decorators-product-matching-formatter"><em>formatter</em></a> <em>([</em> <tt class="docutils literal"><span class="pre">regex_pattern</span></tt> <em>])</em>, <tt class="docutils literal"><span class="pre">tuple_size</span></tt>, <tt class="docut [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td><p class="first"><strong>@combinations</strong> (<a class="reference internal" href="combinations.html#decorators-combinations"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/combinatorics.html#new-manual-combinations"><em>Manual</em></a>)</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>Generates the <strong>permutations</strong>, between all the elements of a set of <strong>Input</strong></li>
-<li>Analogous to the python <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.permutations">itertools.combinations</a></li>
-<li>combinations(‘ABCD’, 3) –> ABC ABD ACD BCD</li>
-<li>Generates the <strong>combinations</strong>, between all the elements of a set of <strong>Input</strong>:
-i.e. r-length tuples of <em>input</em> elements with no repeated elements (<strong>A A</strong>)
-and where order of the tuples is irrelevant (either <strong>A B</strong> or  <strong>B A</strong>, not both).</li>
-</ul>
-</div></blockquote>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="permutations.html#decorators-permutations"><em>@combinations</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="product.html#decorators-product-matching-formatter"><em>formatter</em></a> <em>([</em> <tt class="docutils literal"><span class="pre">regex_pattern</span></tt> <em>])</em>, <tt class="docutils literal"><span class="pre">tuple_size</span></tt>, <tt class="docut [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@combinations_with_replacement</strong> (<a class="reference internal" href="combinations_with_replacement.html#decorators-combinations-with-replacement"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/combinatorics.html#new-manual-combinations-with-replacement"><em>Manual</em></a>)</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>Generates the <strong>permutations</strong>, between all the elements of a set of <strong>Input</strong></li>
-<li>Analogous to the python <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.permutations">itertools.permutations</a></li>
-<li>combinations(‘ABCD’, 3) –> ABC ABD ACD BCD</li>
-<li>Generates the <strong>combinations_with_replacement</strong>, between all the elements of a set of <strong>Input</strong>:
-i.e. r-length tuples of <em>input</em> elements with no repeated elements (<strong>A A</strong>)
-and where order of the tuples is irrelevant (either <strong>A B</strong> or  <strong>B A</strong>, not both).</li>
-</ul>
-</div></blockquote>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="permutations.html#decorators-permutations"><em>@combinations_with_replacement</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="product.html#decorators-product-matching-formatter"><em>formatter</em></a> <em>([</em> <tt class="docutils literal"><span class="pre">regex_pattern</span></tt> <em>])</em>, <tt class="docutils literal"><span class="pre">tuple_size</span></tt>, [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-</tbody>
-</table>
-</div>
-<div class="section" id="advanced">
-<h2><em>Advanced</em><a class="headerlink" href="#advanced" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><table border="1" class="docutils">
-<colgroup>
-<col width="40%" />
-<col width="60%" />
-<col width="0%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">Decorator</th>
-<th class="head">Examples</th>
-<th class="head"> </th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td><strong>@subdivide</strong> (<a class="reference internal" href="subdivide.html#decorators-subdivide"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/subdivide_collate.html#new-manual-subdivide"><em>Manual</em></a>)
-- Subdivides a set of <em>Inputs</em> each further into multiple <em>Outputs</em>.
-- The number of files in each <em>Output</em> can be set at runtime by the use of globs.
-- <strong>Many to Even More</strong> operator.
-- The use of <strong>split</strong> is a synonym for subdivide is deprecated.</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="subdivide.html#decorators-subdivide"><em>@subdivide</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="subdivide.html#decorators-subdivide-matching-regex"><em>regex</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, [ <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a> | <a  [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="subdivide.html#decorators-subdivide"><em>@subdivide</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="subdivide.html#decorators-subdivide-matching-formatter"><em>formatter</em></a><em>(</em>[<tt class="docutils literal"><span class="pre">regex_pattern</span></tt>] <em>)</em>, [ <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@transform</strong> (<a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/inputs.html#new-manual-inputs"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Infers input as well as output from regular expression substitutions</li>
-<li>Useful for adding additional file dependencies</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>@transform</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="transform_ex.html#decorators-transform-matching-regex"><em>regex</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, [ <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em>< [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>@transform</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="transform_ex.html#decorators-transform-matching-formatter"><em>formatter</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, [ <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inpu [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td><p class="first"><strong>@collate</strong> (<a class="reference internal" href="collate.html#decorators-collate"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/subdivide_collate.html#new-manual-collate"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Groups multiple input files using regular expression matching</li>
-<li>Input resulting in the same output after substitution will be collated together.</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="collate.html#decorators-collate"><em>@collate</em></a> (<tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="collate.html#decorators-collate-matching-regex"><em>regex</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</span></tt>, [<tt class="docutils literal"><span class [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="collate_ex.html#decorators-collate-ex"><em>@collate</em></a> (<tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="collate_ex.html#decorators-collate-ex-matching-regex"><em>regex</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a> | <a c [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="collate.html#decorators-collate"><em>@collate</em></a> (<tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="collate.html#decorators-collate-matching-formatter"><em>formatter</em></a><em>(</em><tt class="docutils literal"><span class="pre">formatter_pattern</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</span></tt>, [<tt class="docutils literal" [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="collate_ex.html#decorators-collate-ex"><em>@collate</em></a> (<tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="collate_ex.html#decorators-collate-ex-matching-formatter"><em>formatter</em></a><em>(</em><tt class="docutils literal"><span class="pre">formatter_pattern</span></tt><em>)</em>, <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em [...]
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@follows</strong> (<a class="reference internal" href="follows.html#decorators-follows"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/transform_in_parallel.html#new-manual-follows"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Indicates task dependency</li>
-<li>optional <a class="reference internal" href="follows.html#decorators-follows-directory-name"><em>mkdir</em></a> prerequisite (<a class="reference internal" href="../tutorials/new_tutorial/transform_in_parallel.html#new-manual-follows-mkdir"><em>see Manual</em></a>)</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="follows.html#decorators-follows"><em>@follows</em></a> ( <tt class="docutils literal"><span class="pre">task1</span></tt>, <tt class="docutils literal"><span class="pre">'task2'</span></tt> ))</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="follows.html#decorators-follows"><em>@follows</em></a> ( <tt class="docutils literal"><span class="pre">task1</span></tt>,  <a class="reference internal" href="follows.html#decorators-follows-directory-name"><em>mkdir</em></a>( <tt class="docutils literal"><span class="pre">'my/directory/'</span></tt> ))</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td><p class="first"><strong>@posttask</strong> (<a class="reference internal" href="posttask.html#decorators-posttask"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/posttask.html#new-manual-posttask"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Calls function after task completes</li>
-<li>Optional <a class="reference internal" href="posttask.html#decorators-posttask-file-name"><em>touch_file</em></a> indicator (<a class="reference internal" href="../tutorials/new_tutorial/posttask.html#new-manual-posttask-touch-file"><em>Manual</em></a>)</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="posttask.html#decorators-posttask"><em>@posttask</em></a> ( <tt class="docutils literal"><span class="pre">signal_task_completion_function</span></tt> )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="posttask.html#decorators-posttask"><em>@posttask</em></a> (<a class="reference internal" href="indicator_objects.html#decorators-touch-file"><em>touch_file</em></a>( <tt class="docutils literal"><span class="pre">'task1.completed'</span></tt> ))</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@active_if</strong> (<a class="reference internal" href="active_if.html#decorators-active-if"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/active_if.html#new-manual-active-if"><em>Manual</em></a>)</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>Switches tasks on and off at run time depending on its parameters</li>
-<li>Evaluated each time <a class="reference internal" href="../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(...)</em></a>, <a class="reference internal" href="../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> or <a class="reference internal" href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a> is called.</li>
-<li>Dormant tasks behave as if they are up to date and have no output.</li>
-</ul>
-</div></blockquote>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="active_if.html#decorators-active-if"><em>@active_if</em></a> ( <tt class="docutils literal"><span class="pre">on_or_off1,</span> <span class="pre">[on_or_off2,</span> <span class="pre">...]</span></tt> )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td><p class="first"><strong>@jobs_limit</strong> (<a class="reference internal" href="jobs_limit.html#decorators-jobs-limit"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/multiprocessing.html#new-manual-jobs-limit"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Limits the amount of multiprocessing for the specified task</li>
-<li>Ensures that fewer than N jobs for this task are run in parallel</li>
-<li>Overrides <tt class="docutils literal"><span class="pre">multiprocess</span></tt> parameter in <a class="reference internal" href="../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(...)</em></a></li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit</em></a> ( <tt class="docutils literal"><span class="pre">NUMBER_OF_JOBS_RUNNING_CONCURRENTLY</span></tt> )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@mkdir</strong> (<a class="reference internal" href="mkdir.html#decorators-mkdir"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/mkdir.html#new-manual-mkdir"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Generates paths for <a class="reference external" href="http://docs.python.org/2/library/os.html#os.makedirs">os.makedirs</a></li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="mkdir.html#decorators-mkdir"><em>@mkdir</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="mkdir.html#decorators-mkdir-suffix-string"><em>suffix</em></a><em>(</em><tt class="docutils literal"><span class="pre">suffix_string</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</span></tt> )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="mkdir.html#decorators-mkdir"><em>@mkdir</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="mkdir.html#decorators-mkdir-matching-regex"><em>regex</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</span></tt> )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="mkdir.html#decorators-mkdir"><em>@mkdir</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <a class="reference internal" href="mkdir.html#decorators-mkdir-matching-formatter"><em>formatter</em></a><em>(</em><tt class="docutils literal"><span class="pre">regex_pattern</span></tt><em>)</em>, <tt class="docutils literal"><span class="pre">output_pattern</span></tt>)</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td><p class="first"><strong>@graphviz</strong> (<a class="reference internal" href="graphviz.html#decorators-graphviz"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/pipeline_printout_graph.html#new-manual-pipeline-printout-graph"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Customise the graphic for each task in printed flowcharts</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="graphviz.html#decorators-graphviz"><em>@graphviz</em></a> ( <tt class="docutils literal"><span class="pre">graphviz_parameter</span> <span class="pre">=</span> <span class="pre">XXX</span></tt>, <tt class="docutils literal"><span class="pre">[graphviz_parameter2</span> <span class="pre">=</span> <span class="pre">YYY</span> <span class="pre">...]</span></tt>)</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-</tbody>
-</table>
-</div></blockquote>
-</div>
-<div class="section" id="esoteric">
-<h2><em>Esoteric!</em><a class="headerlink" href="#esoteric" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><table border="1" class="docutils">
-<colgroup>
-<col width="40%" />
-<col width="60%" />
-<col width="0%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">Decorator</th>
-<th class="head">Examples</th>
-<th class="head"> </th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td><p class="first"><strong>@files</strong> (<a class="reference internal" href="files.html#decorators-files"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/deprecated_files.html#new-manual-deprecated-files"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>I/O parameters</li>
-<li>skips up-to-date jobs</li>
-<li>Should use <a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a> etc instead</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="files.html#decorators-files"><em>@files</em></a>( <tt class="docutils literal"><span class="pre">parameter_list</span></tt> )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="files.html#decorators-files"><em>@files</em></a>( <tt class="docutils literal"><span class="pre">parameter_generating_function</span></tt> )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="files.html#decorators-files"><em>@files</em></a> ( <tt class="docutils literal"><span class="pre">input_file</span></tt>, <tt class="docutils literal"><span class="pre">output_file</span></tt>, <tt class="docutils literal"><span class="pre">other_params</span></tt>, ... )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><p class="first"><strong>@parallel</strong> (<a class="reference internal" href="parallel.html#decorators-parallel"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/parallel.html#new-manual-deprecated-parallel"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>By default, does not check if jobs are up to date</li>
-<li>Best used in conjuction with <a class="reference internal" href="check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate</em></a></li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="parallel.html#decorators-parallel"><em>@parallel</em></a> ( <tt class="docutils literal"><span class="pre">parameter_list</span></tt> ) (<a class="reference internal" href="../tutorials/new_tutorial/parallel.html#new-manual-deprecated-parallel"><em>see Manual</em></a>)</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="parallel.html#decorators-parallel"><em>@parallel</em></a> ( <tt class="docutils literal"><span class="pre">parameter_generating_function</span></tt> ) (<a class="reference internal" href="../tutorials/new_tutorial/onthefly.html#new-manual-on-the-fly"><em>see Manual</em></a>)</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-even"><td><p class="first"><strong>@check_if_uptodate</strong> (<a class="reference internal" href="check_if_uptodate.html#decorators-check-if-uptodate"><em>Summary</em></a> / <a class="reference internal" href="../tutorials/new_tutorial/check_if_uptodate.html#new-manual-check-if-uptodate"><em>Manual</em></a>)</p>
-<ul class="last simple">
-<li>Custom function to determine if jobs need to be run</li>
-</ul>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate</em></a> ( <tt class="docutils literal"><span class="pre">is_task_up_to_date_function</span></tt> )</dt>
-<dd><p class="first last"></p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><div class="first last admonition tip">
-<p class="first admonition-title">Tip</p>
-<dl class="last docutils">
-<dt>The use of this overly complicated function is discouraged.</dt>
-<dd><p class="first"><strong>@files_re</strong> (<a class="reference internal" href="files_re.html#decorators-files-re"><em>Summary</em></a>)</p>
-<ul class="last simple">
-<li>I/O file names via regular
-expressions</li>
-<li>start from lists of file names
-or <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> results</li>
-<li>skips up-to-date jobs</li>
-</ul>
-</dd>
-</dl>
-</div>
-</td>
-<td><ul class="first last">
-<li><dl class="first docutils">
-<dt><a class="reference internal" href="files_re.html#decorators-files-re"><em>@files_re</em></a> ( <tt class="docutils literal"><span class="pre">tasks_or_file_names</span></tt>, <tt class="docutils literal"><span class="pre">matching_regex</span></tt>, [<tt class="docutils literal"><span class="pre">input_pattern</span></tt>,] <tt class="docutils literal"><span class="pre">output_pattern</span></tt>, <tt class="docutils literal"><span class="pre">...</span></tt> )</dt>
-<dd><p class="first last"><tt class="docutils literal"><span class="pre">input_pattern</span></tt>/<tt class="docutils literal"><span class="pre">output_pattern</span></tt> are regex patterns
-used to create input/output file names from the starting
-list of either glob_str or file names</p>
-</dd>
-</dl>
-</li>
-</ul>
-</td>
-<td> </td>
-</tr>
-</tbody>
-</table>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Ruffus Decorators</a><ul>
-<li><a class="reference internal" href="#core"><em>Core</em></a></li>
-<li><a class="reference internal" href="#combinatorics"><em>Combinatorics</em></a></li>
-<li><a class="reference internal" href="#advanced"><em>Advanced</em></a></li>
-<li><a class="reference internal" href="#esoteric"><em>Esoteric!</em></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="../examples/paired_end_data.py.html"
-                        title="previous chapter">Example code for <tt class="docutils literal"><span class="pre">FAQ</span> <span class="pre">Good</span> <span class="pre">practices:</span> <span class="pre">"What</span> <span class="pre">is</span> <span class="pre">the</span> <span class="pre">best</span> <span class="pre">way</span> <span class="pre">of</span> <span class="pre">handling</span> <span class="pre">data</span> <span class="pre">in</span> <span class="pre">file</span>  [...]
-  <h4>Next topic</h4>
-  <p class="topless"><a href="indicator_objects.html"
-                        title="next chapter">Indicator Objects</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-           rel="nofollow">Show Source</a></li>
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-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../search.html" method="get">
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="##core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="##advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="##combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="##esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
-
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-      </div>
-      <div class="clearer"></div>
-    </div>
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diff --git a/doc/_build/html/decorators/files.html b/doc/_build/html/decorators/files.html
deleted file mode 100644
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--- a/doc/_build/html/decorators/files.html
+++ /dev/null
@@ -1,364 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>@files — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="../_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
-        VERSION:     '2.5',
-        COLLAPSE_INDEX: false,
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-        HAS_SOURCE:  true
-      };
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-    <link rel="top" title="ruffus 2.5 documentation" href="../index.html" />
-    <link rel="next" title="@files_re" href="files_re.html" />
-    <link rel="prev" title="@parallel" href="parallel.html" /> 
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-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
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-        <li class="right" >
-          <a href="files_re.html" title="@files_re"
-             accesskey="N">next</a> |</li>
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- 
-      </ul>
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-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <span class="target" id="decorators-files"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="files">
-<h1>@files<a class="headerlink" href="#files" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="files-input1-output1-extra-parameters1">
-<h2><em>@files</em> (<a class="reference internal" href="#decorators-files-input1"><cite>input1</cite></a>, <a class="reference internal" href="#decorators-files-output1"><cite>output1</cite></a>, [<a class="reference internal" href="#decorators-files-extra-parameters1"><cite>extra_parameters1</cite></a>, ...])<a class="headerlink" href="#files-input1-output1-extra-parameters1" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="files-for-single-jobs">
-<h3>@files for single jobs<a class="headerlink" href="#files-for-single-jobs" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">Provides parameters to run a task.</p>
-<p>The first two parameters in each set represent the input and output which are
-used to see if the job is out of date and needs to be (re-)run.</p>
-<p class="last">By default, out of date checking uses input/output file timestamps.
-(On some file systems, timestamps have a resolution in seconds.)
-See <a class="reference internal" href="check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate()</em></a> for alternatives.</p>
-</dd>
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="nd">@files</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="s">'a.2'</span><span class="p">,</span> <span class="s">'A file'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">transform_files</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">text</span><span class="p">):</span>
-    <span class="k">pass</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">transform_files</span><span class="p">])</span>
-</pre></div>
-</div>
-</dd>
-<dt>If <tt class="docutils literal"><span class="pre">a.2</span></tt> is missing or was created before <tt class="docutils literal"><span class="pre">a.1</span></tt>, then the following will be called:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">transform_files</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="s">'a.2'</span><span class="p">,</span> <span class="s">'A file'</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-files-input1">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>input</em></dt>
-<dd><p class="first last">Input file names</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-output1">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output</em></dt>
-<dd><p class="first last">Output file names</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-extra-parameters1">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">optional <tt class="docutils literal"><span class="pre">extra_parameters</span></tt> are passed verbatim to each job.</p>
-</dd>
-</dl>
-</li>
-</ul>
-<dl class="docutils">
-<dt><strong>Checking if jobs are up to date:</strong></dt>
-<dd><p class="first">Strings in <tt class="docutils literal"><span class="pre">input</span></tt> and <tt class="docutils literal"><span class="pre">output</span></tt> (including in nested sequences) are interpreted as file names and
-used to check if jobs are up-to-date.</p>
-<p class="last">See <a class="reference internal" href="#decorators-files-check-up-to-date"><em>above</em></a> for more details</p>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="files-input-output-extra-parameters">
-<h2><em>@files</em> ( <em>((</em> <a class="reference internal" href="#decorators-files-input"><cite>input</cite></a>, <a class="reference internal" href="#decorators-files-output"><cite>output</cite></a>, [<a class="reference internal" href="#decorators-files-extra-parameters"><cite>extra_parameters</cite></a>,...] <em>), (...), ...)</em> )<a class="headerlink" href="#files-input-output-extra-parameters" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="files-in-parallel">
-<h3>@files in parallel<a class="headerlink" href="#files-in-parallel" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>Passes each set of parameters to separate jobs which can run in parallel</p>
-<p>The first two parameters in each set represent the input and output which are
-used to see if the job is out of date and needs to be (re-)run.</p>
-<p>By default, out of date checking uses input/output file timestamps.
-(On some file systems, timestamps have a resolution in seconds.)
-See <a class="reference internal" href="check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate()</em></a> for alternatives.</p>
-</div></blockquote>
-<dl class="docutils">
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="s">'a.1'</span><span class="p">,</span> <span class="s">'a.2'</span><span class="p">,</span> <span class="s">'A file'</span><span class="p">],</span> <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="s">'b.1'</span><span class="p">,</span> <span class="s">'b.2'</span><span class="p">,</span> <span class="s">'B file'</span><span class="p">],</span> <span class="c"># 2nd job</span>
-              <span class="p">]</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">parallel_io_task</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">text</span><span class="p">):</span>
-    <span class="k">pass</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_io_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</dd>
-<dt>is the equivalent of calling:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">parallel_io_task</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="s">'a.2'</span><span class="p">,</span> <span class="s">'A file'</span><span class="p">)</span>
-<span class="n">parallel_io_task</span><span class="p">(</span><span class="s">'b.1'</span><span class="p">,</span> <span class="s">'b.2'</span><span class="p">,</span> <span class="s">'B file'</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-files-input">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>input</em></dt>
-<dd><p class="first last">Input file names</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-output">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output</em></dt>
-<dd><p class="first last">Output file names</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">optional <tt class="docutils literal"><span class="pre">extra_parameters</span></tt> are passed verbatim to each job.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-check-up-to-date">
-<div><dl class="docutils">
-<dt><strong>Checking if jobs are up to date:</strong></dt>
-<dd><ol class="first last arabic simple">
-<li>Strings in <tt class="docutils literal"><span class="pre">input</span></tt> and <tt class="docutils literal"><span class="pre">output</span></tt> (including in nested sequences) are interpreted as file names and
-used to check if jobs are up-to-date.</li>
-<li>In the absence of input files (e.g. <tt class="docutils literal"><span class="pre">input</span> <span class="pre">==</span> <span class="pre">None</span></tt>), the job will run if any output file is missing.</li>
-<li>In the absence of output files (e.g. <tt class="docutils literal"><span class="pre">output</span> <span class="pre">==</span> <span class="pre">None</span></tt>), the job will always run.</li>
-<li>If any of the output files is missing, the job will run.</li>
-<li>If any of the input files is missing when the job is run, a
-<tt class="docutils literal"><span class="pre">MissingInputFileError</span></tt> exception will be raised.</li>
-</ol>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@files</a><ul>
-<li><a class="reference internal" href="#files-input1-output1-extra-parameters1"><em>@files</em> (<cite>input1</cite>, <cite>output1</cite>, [<cite>extra_parameters1</cite>, ...])</a><ul>
-<li><a class="reference internal" href="#files-for-single-jobs">@files for single jobs</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#files-input-output-extra-parameters"><em>@files</em> ( <em>((</em> <cite>input</cite>, <cite>output</cite>, [<cite>extra_parameters</cite>,...] <em>), (...), ...)</em> )</a><ul>
-<li><a class="reference internal" href="#files-in-parallel">@files in parallel</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="parallel.html"
-                        title="previous chapter">@parallel</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="files_re.html"
-                        title="next chapter">@files_re</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/files.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
-
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-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
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-             >index</a></li>
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-             >next</a> |</li>
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diff --git a/doc/_build/html/decorators/files_ex.html b/doc/_build/html/decorators/files_ex.html
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-            
-  <span class="target" id="decorators-files-on-the-fly"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="generating-parameters-on-the-fly-for-files">
-<h1>Generating parameters on the fly for @files<a class="headerlink" href="#generating-parameters-on-the-fly-for-files" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="files-custom-function">
-<h2><em>@files</em> (<a class="reference internal" href="#decorators-files-custom-function"><cite>custom_function</cite></a>)<a class="headerlink" href="#files-custom-function" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>Uses a custom function to generate sets of parameters to separate jobs which can run in parallel.</p>
-<p>The first two parameters in each set represent the input and output which are
-used to see if the job is out of date and needs to be (re-)run.</p>
-<p>By default, out of date checking uses input/output file timestamps.
-(On some file systems, timestamps have a resolution in seconds.)
-See <a class="reference internal" href="check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate()</em></a> for alternatives.</p>
-</div></blockquote>
-<dl class="docutils">
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="k">def</span> <span class="nf">generate_parameters_on_the_fly</span><span class="p">():</span>
-    <span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                        <span class="p">[</span><span class="s">'input_file1'</span><span class="p">,</span> <span class="s">'output_file1'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="c"># 1st job</span>
-                        <span class="p">[</span><span class="s">'input_file2'</span><span class="p">,</span> <span class="s">'output_file2'</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="c"># 2nd job</span>
-                        <span class="p">[</span><span class="s">'input_file3'</span><span class="p">,</span> <span class="s">'output_file3'</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span> <span class="c"># 3rd job</span>
-                 <span class="p">]</span>
-    <span class="k">for</span> <span class="n">job_parameters</span> <span class="ow">in</span> <span class="n">parameters</span><span class="p">:</span>
-        <span class="k">yield</span> <span class="n">job_parameters</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">generate_parameters_on_the_fly</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">parallel_io_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">param1</span><span class="p">,</span> <span class="n">param2</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</dd>
-<dt>is the equivalent of calling:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">parallel_io_task</span><span class="p">(</span><span class="s">'input_file1'</span><span class="p">,</span> <span class="s">'output_file1'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
-<span class="n">parallel_io_task</span><span class="p">(</span><span class="s">'input_file2'</span><span class="p">,</span> <span class="s">'output_file2'</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
-<span class="n">parallel_io_task</span><span class="p">(</span><span class="s">'input_file3'</span><span class="p">,</span> <span class="s">'output_file3'</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-files-custom-function">
-<div><blockquote>
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>custom_function</em>:</dt>
-<dd><p class="first last">Generator function which yields each time a complete set of parameters for one job</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<dl class="docutils">
-<dt><strong>Checking if jobs are up to date:</strong></dt>
-<dd><p class="first">Strings in <tt class="docutils literal"><span class="pre">input</span></tt> and <tt class="docutils literal"><span class="pre">output</span></tt> (including in nested sequences) are interpreted as file names and
-used to check if jobs are up-to-date.</p>
-<p class="last">See <a class="reference internal" href="files.html#decorators-files-check-up-to-date"><em>above</em></a> for more details</p>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Generating parameters on the fly for @files</a><ul>
-<li><a class="reference internal" href="#files-custom-function"><em>@files</em> (<cite>custom_function</cite>)</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="combinations_with_replacement.html"
-                        title="previous chapter">@combinations_with_replacement</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="check_if_uptodate.html"
-                        title="next chapter">@check_if_uptodate</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/files_ex.txt"
-           rel="nofollow">Show Source</a></li>
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="#">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
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diff --git a/doc/_build/html/decorators/files_re.html b/doc/_build/html/decorators/files_re.html
deleted file mode 100644
index 17ee9a5..0000000
--- a/doc/_build/html/decorators/files_re.html
+++ /dev/null
@@ -1,344 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>@files_re — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="../_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
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-        HAS_SOURCE:  true
-      };
-    </script>
-    <script type="text/javascript" src="../_static/jquery.js"></script>
-    <script type="text/javascript" src="../_static/underscore.js"></script>
-    <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <link rel="top" title="ruffus 2.5 documentation" href="../index.html" />
-    <link rel="next" title="ruffus.Task" href="../task.html" />
-    <link rel="prev" title="@files" href="files.html" /> 
-  </head>
-  <body>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="../task.html" title="ruffus.Task"
-             accesskey="N">next</a> |</li>
-        <li class="right" >
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-            <li><a href="../cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="../tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="../gallery.html">Gallery</a> |  </li>
-            <li><a href="../history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <span class="target" id="decorators-files-re"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="files-re">
-<h1>@files_re<a class="headerlink" href="#files-re" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="files-re-tasks-or-file-names-matching-regex-input-pattern-output-pattern-extra-parameters">
-<h2><em>@files_re</em> (<a class="reference internal" href="#decorators-files-re-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="#decorators-files-re-matching-regex"><cite>matching_regex</cite></a>, [<a class="reference internal" href="#decorators-files-re-input-pattern"><cite>input_pattern</cite></a>], <a class="reference internal" href="#decorators-files-re-output-pattern"><cite>output_pattern</cite></a>, [<a class="reference internal" [...]
-<div class="section" id="legacy-design-now-deprecated-we-suggest-using-transform-instead">
-<h3>Legacy design now deprecated. We suggest using <a class="reference internal" href="transform.html#decorators-transform"><em>@transform()</em></a> instead<a class="headerlink" href="#legacy-design-now-deprecated-we-suggest-using-transform-instead" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>All singing, all dancing decorator which can do everything that <a class="reference internal" href="merge.html#decorators-merge"><em>@merge()</em></a> and
-<a class="reference internal" href="transform.html#decorators-transform"><em>@transform()</em></a> can do.</p>
-<p>Applies the task function to transform data from input to output files.</p>
-<p>Output file names are determined from <a class="reference internal" href="#decorators-files-re-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of specified tasks, or a list of file names, using regular expression pattern substitutions.</p>
-<p>Only out of date tasks (comparing input and output files) will be run.</p>
-</div></blockquote>
-<dl class="docutils">
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="c">#</span>
-<span class="c">#   convert all files ending in ".1" into files ending in ".2"</span>
-<span class="c">#</span>
-<span class="nd">@files_re</span><span class="p">(</span><span class="s">'*.1'</span><span class="p">,</span> <span class="s">'(.*).1'</span><span class="p">,</span> <span class="s">r'\1.2'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">transform_func</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> <span class="o">+</span> <span class="s">"</span><span cla [...]
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">task_re</span><span class="p">])</span>
-</pre></div>
-</div>
-</dd>
-<dt>If the following files are present <tt class="docutils literal"><span class="pre">a.1</span></tt>, <tt class="docutils literal"><span class="pre">b.1</span></tt>, <tt class="docutils literal"><span class="pre">c.1</span></tt>, this will result in the following function calls:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">transform_func</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">,</span> <span class="s">"a.2"</span><span class="p">)</span>
-<span class="n">transform_func</span><span class="p">(</span><span class="s">"b.1"</span><span class="p">,</span> <span class="s">"b.2"</span><span class="p">)</span>
-<span class="n">transform_func</span><span class="p">(</span><span class="s">"c.1"</span><span class="p">,</span> <span class="s">"c.2"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-files-re-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> .</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-re-matching-regex">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_regex</em></dt>
-<dd><p class="first">a python regular expression string.</p>
-<div class="last line-block">
-<div class="line">See python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a> documentation for details of regular expression syntax</div>
-<div class="line">Each output file name is created using regular expression substitution with <a class="reference internal" href="#decorators-files-re-output-pattern"><cite>output_pattern</cite></a></div>
-</div>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-re-input-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>input_pattern</em></dt>
-<dd><p class="first last">Optionally specifies the resulting input file name(s).</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-re-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s).</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-files-re-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt>[<em>extra_parameters, ...</em>]</dt>
-<dd><p class="first">Any extra parameters are passed to the task function.</p>
-<div class="line-block">
-<div class="line">Regular expression substitution is first applied to (even nested) string parameters.</div>
-<div class="line">Other data types are passed verbatim.</div>
-</div>
-<dl class="last docutils">
-<dt>For example:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="c">#</span>
-<span class="c">#   convert all files ending in ".1" into files ending in ".2"</span>
-<span class="c">#</span>
-<span class="nd">@files_re</span><span class="p">(</span><span class="s">'*.1'</span><span class="p">,</span> <span class="s">'(.*).1'</span><span class="p">,</span> <span class="s">r'\1.2'</span><span class="p">,</span> <span class="p">[</span><span class="s">r'\1'</span><span class="p">,</span> <span class="mi">55</span><span class="p">],</span> <span class="mi">17</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">transform_func</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">extras</span><span class="p">,</span> <span class="n">extra3</span><span class="p">):</span>
-    <span class="n">extra1</span><span class="p">,</span> <span class="n">extra2</span> <span class="o">=</span> <span class="n">extras</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> <span class="o">+</span> <span class="s">"</span><span cla [...]
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">transform_func</span><span class="p">])</span>
-</pre></div>
-</div>
-</dd>
-<dt>If the following files are present <tt class="docutils literal"><span class="pre">a.1</span></tt>, <tt class="docutils literal"><span class="pre">b.1</span></tt>, <tt class="docutils literal"><span class="pre">c.1</span></tt>, this will result in the following function calls:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">transform_func</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">,</span> <span class="s">"a.2"</span><span class="p">,</span> <span class="p">[</span><span class="s">"a"</span><span class="p">,</span> <span class="mi">55</span><span class="p">],</span> <span class="mi">17</span><span class="p">)</span>
-<span class="n">transform_func</span><span class="p">(</span><span class="s">"b.1"</span><span class="p">,</span> <span class="s">"b.2"</span><span class="p">,</span> <span class="p">[</span><span class="s">"b"</span><span class="p">,</span> <span class="mi">55</span><span class="p">],</span> <span class="mi">17</span><span class="p">)</span>
-<span class="n">transform_func</span><span class="p">(</span><span class="s">"c.1"</span><span class="p">,</span> <span class="s">"c.2"</span><span class="p">,</span> <span class="p">[</span><span class="s">"c"</span><span class="p">,</span> <span class="mi">55</span><span class="p">],</span> <span class="mi">17</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@files_re</a><ul>
-<li><a class="reference internal" href="#files-re-tasks-or-file-names-matching-regex-input-pattern-output-pattern-extra-parameters"><em>@files_re</em> (<cite>tasks_or_file_names</cite>, <cite>matching_regex</cite>, [<cite>input_pattern</cite>], <cite>output_pattern</cite>, [<cite>extra_parameters</cite>,...])</a><ul>
-<li><a class="reference internal" href="#legacy-design-now-deprecated-we-suggest-using-transform-instead">Legacy design now deprecated. We suggest using <tt class="docutils literal"><span class="pre">@transform()</span></tt> instead</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="files.html"
-                        title="previous chapter">@files</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="../task.html"
-                        title="next chapter">ruffus.Task</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/files_re.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             >index</a></li>
-        <li class="right" >
-          <a href="../task.html" title="ruffus.Task"
-             >next</a> |</li>
-        <li class="right" >
-          <a href="files.html" title="@files"
-             >previous</a> |</li>
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-  </body>
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\ No newline at end of file
diff --git a/doc/_build/html/decorators/follows.html b/doc/_build/html/decorators/follows.html
deleted file mode 100644
index 696ebea..0000000
--- a/doc/_build/html/decorators/follows.html
+++ /dev/null
@@ -1,274 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>@follows — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="../_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
-        VERSION:     '2.5',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true
-      };
-    </script>
-    <script type="text/javascript" src="../_static/jquery.js"></script>
-    <script type="text/javascript" src="../_static/underscore.js"></script>
-    <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <link rel="top" title="ruffus 2.5 documentation" href="../index.html" />
-    <link rel="next" title="@product" href="product.html" />
-    <link rel="prev" title="@active_if" href="active_if.html" /> 
-  </head>
-  <body>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="product.html" title="@product"
-             accesskey="N">next</a> |</li>
-        <li class="right" >
-          <a href="active_if.html" title="@active_if"
-             accesskey="P">previous</a> |</li>
-        Ruffus v. 2.5
-            <li><a href="../index.html">Home</a> | </li>
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-            <li><a href="../installation.html">Install</a>  | </li>
-            <li><a href="../tutorials/new_tutorial/introduction.html">Manual</a>  / </li>
-            <li><a href="../tutorials/new_tutorial/manual_contents.html">(TOC)</a>  | </li>
-            <li><a href="../faq.html">FAQ</a>  | </li>
-            <li><a href="../cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="../tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="../gallery.html">Gallery</a> |  </li>
-            <li><a href="../history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <span class="target" id="decorators-follows"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-<li>More on @follows in the <tt class="docutils literal"><span class="pre">Ruffus</span></tt> <a class="reference internal" href="../tutorials/new_tutorial/transform_in_parallel.html#new-manual-follows"><em>Manual</em></a></li>
-</ul>
-<div class="last admonition note">
-<p class="first admonition-title">Note</p>
-<p>Only missing directories are created.</p>
-<p class="last">In other words, the same directory can be specified multiple times safely without, for example, being recreated repeatedly.
-Sometimes, for pipelines with multiple entry points, this is the only way to make sure that certain working or output
-directories are always created or available <em>before</em> the pipeline runs.</p>
-</div>
-</div>
-<div class="section" id="follows">
-<h1>@follows<a class="headerlink" href="#follows" title="Permalink to this headline">¶</a></h1>
-<span class="target" id="decorators-follows-mkdir"></span><div class="section" id="follows-task-task-name-mkdir-directory-name-more-tasks">
-<h2><em>@follows</em>(<a class="reference internal" href="#decorators-follows-task"><cite>task</cite></a> | <a class="reference internal" href="#decorators-follows-task-name"><cite>“task_name”</cite></a> | <a class="reference internal" href="mkdir.html#decorators-mkdir"><em>mkdir</em></a> (<a class="reference internal" href="#decorators-follows-directory-name"><cite>directory_name</cite></a>), [more_tasks, ...])<a class="headerlink" href="#follows-task-task-name-mkdir-dir [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>Indicates either</p>
-<blockquote>
-<div><ul class="simple">
-<li>task dependencies</li>
-<li>that the task requires a directory to be created first <em>if necessary</em>. (Existing directories will not be overwritten)</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-<p><strong>Example</strong>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">def</span> <span class="nf">task1</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"doing task 1"</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">task1</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"doing task 2"</span>
-</pre></div>
-</div>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-follows-task">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>task</em>:</dt>
-<dd><p class="first last">a list of tasks which have to be run <strong>before</strong> this function</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-follows-task-name">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>“task_name”</em>:</dt>
-<dd><p class="first">Dependencies can be quoted function names.
-Quoted function names allow dependencies to be added before the function is defined.</p>
-<p class="last">Functions in other modules need to be fully qualified.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-follows-directory-name">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>directory_name</em>:</dt>
-<dd><p class="first">Directories which need to be created (<em>only if they don’t exist</em>) before
-the task is run can be specified via a <tt class="docutils literal"><span class="pre">mkdir</span></tt> indicator object:</p>
-<blockquote class="last">
-<div><div class="highlight-python"><pre>@follows(task_x, mkdir("/output/directory") ...)
-def task():
-    pass</pre>
-</div>
-</div></blockquote>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@follows</a><ul>
-<li><a class="reference internal" href="#follows-task-task-name-mkdir-directory-name-more-tasks"><em>@follows</em>(<cite>task</cite> | <cite>“task_name”</cite> | <tt class="docutils literal"><span class="pre">mkdir</span></tt> (<cite>directory_name</cite>), [more_tasks, ...])</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="active_if.html"
-                        title="previous chapter">@active_if</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="product.html"
-                        title="next chapter">@product</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/follows.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="#">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
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diff --git a/doc/_build/html/decorators/graphviz.html b/doc/_build/html/decorators/graphviz.html
deleted file mode 100644
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--- a/doc/_build/html/decorators/graphviz.html
+++ /dev/null
@@ -1,278 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-          <div class="body">
-            
-  <span class="target" id="decorators-graphviz"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="graphviz">
-<h1>@graphviz<a class="headerlink" href="#graphviz" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="graphviz-graphviz-parameters">
-<h2><em>@graphviz</em> ( <a class="reference internal" href="#decorators-graphviz-graphviz-parameters"><cite>graphviz_parameters</cite></a>,...] )<a class="headerlink" href="#graphviz-graphviz-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><em>Contributed by Sean Davis, with improved syntax via Jake Biesinger</em></p>
-<dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">Customise the graphic for each task in printed flowcharts by adding
-<a class="reference external" href="http://www.graphviz.org/doc/info/attrs.html">graphviz attributes</a>,
-(URL, shape, colour) to that node.</p>
-<ul class="last">
-<li><p class="first">This allows HTML formatting in the task names (using the <tt class="docutils literal"><span class="pre">label</span></tt> parameter as in the following example).
-HTML labels <strong>must</strong> be enclosed in <tt class="docutils literal"><span class="pre"><</span></tt> and <tt class="docutils literal"><span class="pre">></span></tt>. E.g.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">label</span> <span class="o">=</span> <span class="s">"<Line <BR/> wrapped task_name()>"</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">You can also opt to keep the task name and wrap it with a prefix and suffix:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">label_suffix</span> <span class="o">=</span> <span class="s">"??? "</span><span class="p">,</span> <span class="n">label_prefix</span> <span class="o">=</span> <span class="s">": What is this?"</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">The <tt class="docutils literal"><span class="pre">URL</span></tt> attribute allows the generation of clickable svg, and also client / server
-side image maps usable in web pages.
-See <a class="reference external" href="http://www.graphviz.org/content/output-formats#dimap">Graphviz documentation</a></p>
-</li>
-</ul>
-</dd>
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first highlight-python"><div class="highlight"><pre><span class="nd">@graphviz</span><span class="p">(</span><span class="n">URL</span><span class="o">=</span><span class="s">'"http://cnn.com"'</span><span class="p">,</span> <span class="n">fillcolor</span> <span class="o">=</span> <span class="s">'"#FFCCCC"'</span><span class="p">,</span>
-                <span class="n">color</span> <span class="o">=</span> <span class="s">'"#FF0000"'</span><span class="p">,</span> <span class="n">pencolor</span><span class="o">=</span><span class="s">'"#FF0000"'</span><span class="p">,</span> <span class="n">fontcolor</span><span class="o">=</span><span class="s">'"#4B6000"'</span><span class="p">,</span>
-                <span class="n">label_suffix</span> <span class="o">=</span> <span class="s">"???"</span><span class="p">,</span> <span class="n">label_prefix</span> <span class="o">=</span> <span class="s">"What is this?<BR/> "</span><span class="p">,</span>
-                <span class="n">label</span> <span class="o">=</span> <span class="s">"<What <FONT COLOR=</span><span class="se">\"</span><span class="s">red</span><span class="se">\"</span><span class="s">>is</FONT>this>"</span><span class="p">,</span>
-                <span class="n">shape</span><span class="o">=</span> <span class="s">"component"</span><span class="p">,</span> <span class="n">height</span> <span class="o">=</span> <span class="mf">1.5</span><span class="p">,</span> <span class="n">peripheries</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span>
-                <span class="n">style</span><span class="o">=</span><span class="s">"dashed"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Up_to_date_task2</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="c">#   Can use dictionary if you wish...</span>
-<span class="n">graphviz_params</span> <span class="o">=</span> <span class="p">{</span><span class="s">"URL"</span><span class="p">:</span><span class="s">"http://cnn.com"</span><span class="p">,</span> <span class="s">"fontcolor"</span><span class="p">:</span> <span class="s">'"#FF00FF"'</span><span class="p">}</span>
-<span class="nd">@graphviz</span><span class="p">(</span><span class="o">**</span><span class="n">graphviz_params</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">myTask</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span><span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<a class="last reference internal image-reference" href="../_images/history_html_flowchart1.png"><img alt="../_images/history_html_flowchart1.png" src="../_images/history_html_flowchart1.png" style="width: 336.6px; height: 316.5px;" /></a>
-</dd>
-</dl>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-graphviz-graphviz-parameters">
-<div><ul>
-<li><p class="first">named <em>graphviz_parameters</em></p>
-<blockquote>
-<div><p>Including among others:</p>
-<blockquote>
-<div><ul class="simple">
-<li>URL (e.g. <tt class="docutils literal"><span class="pre">"www.ruffus.org.uk"</span></tt>)</li>
-<li>fillcolor</li>
-<li>color</li>
-<li>pencolor</li>
-<li>fontcolor</li>
-<li>label_suffix (appended to task name)</li>
-<li>label_prefix (precedes task name)</li>
-<li>label (replaces task name)</li>
-<li>shape (e.g. <tt class="docutils literal"><span class="pre">"component",</span> <span class="pre">"box",</span> <span class="pre">"diamond",</span> <span class="pre">"doubleoctagon"</span></tt> etc., see <a class="reference external" href="http://www.graphviz.org/doc/info/shapes.html">graphviz</a> )</li>
-<li>height</li>
-<li>peripheries (Number of borders)</li>
-<li>style (e.g. <tt class="docutils literal"><span class="pre">"solid",</span> <span class="pre">"wedged",</span> <span class="pre">"dashed"</span></tt>  etc., see <a class="reference external" href="http://www.graphviz.org/doc/info/attrs.html#k:style">graphviz</a> )</li>
-</ul>
-</div></blockquote>
-<p>Colours may specified as <tt class="docutils literal"><span class="pre">'"#FFCCCC"',</span> <span class="pre">'red',</span> <span class="pre">'red:blue',</span> <span class="pre">'/bugn9/7'</span></tt> etc. see  <a class="reference external" href="http://www.graphviz.org/doc/info/attrs.html#k:color">color names</a> and <a class="reference external" href="http://www.graphviz.org/doc/info/colors.html">colour schemes</a></p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
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-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@graphviz</a><ul>
-<li><a class="reference internal" href="#graphviz-graphviz-parameters"><em>@graphviz</em> ( <cite>graphviz_parameters</cite>,...] )</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="collate_ex.html"
-                        title="previous chapter">@collate  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a></p>
-  <h4>Next topic</h4>
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-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
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-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="#">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
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-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
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-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
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-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
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-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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diff --git a/doc/_build/html/decorators/indicator_objects.html b/doc/_build/html/decorators/indicator_objects.html
deleted file mode 100644
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+++ /dev/null
@@ -1,688 +0,0 @@
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-  <div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<p class="last"><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a></p>
-</div>
-<div class="section" id="indicator-objects">
-<span id="decorators-indicator-objects"></span><span id="index-0"></span><h1>Indicator Objects<a class="headerlink" href="#indicator-objects" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><p>How <em>ruffus</em> disambiguates certain parameters to decorators.</p>
-<p>They are like <a class="reference external" href="http://docs.python.org/tutorial/controlflow.html#keyword-arguments">keyword arguments</a> in python, a little more verbose but they make the syntax much simpler.</p>
-<p>Indicator objects are also “self-documenting” so you can see
-exactly what is happening clearly.</p>
-</div></blockquote>
-<div class="section" id="formatter">
-<span id="decorators-formatter"></span><span id="index-1"></span><h2><em>formatter</em><a class="headerlink" href="#formatter" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>formatter([</strong> <tt class="docutils literal"><span class="pre">regex</span> <span class="pre">|</span> <span class="pre">None</span></tt> <strong>, regex | None...])</strong></p>
-<ul class="simple">
-<li>The optional enclosed parameters are a python regular expression strings</li>
-<li>Each regular expression matches a corresponding <em>Input</em> file name string</li>
-<li><em>formatter</em> parses each file name string into path and regular expression components</li>
-<li>Parsing fails altogether if the regular expression is not matched</li>
-</ul>
-<p>Path components include:</p>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">basename</span></tt>: The <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.basename">base name</a> <em>excluding</em> <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.splitext">extension</a>, <tt class="docutils literal"><span class="pre">"file.name"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">ext</span></tt>     : The <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.splitext">extension</a>, <tt class="docutils literal"><span class="pre">".ext"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">path</span></tt>    : The <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.dirname">dirname</a>, <tt class="docutils literal"><span class="pre">"/directory/to/a"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">subdir</span></tt>  : A list of sub-directories in the <tt class="docutils literal"><span class="pre">path</span></tt> in reverse order, <tt class="docutils literal"><span class="pre">["a",</span> <span class="pre">"to",</span> <span class="pre">"directory",</span> <span class="pre">"/"]</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">subpath</span></tt> : A list of descending sub-paths in reverse order, <tt class="docutils literal"><span class="pre">["/directory/to/a",</span> <span class="pre">"/directory/to",</span> <span class="pre">"/directory",</span> <span class="pre">"/"]</span></tt></li>
-</ul>
-</div></blockquote>
-<p>The replacement string refers to these components using python <a class="reference external" href="http://docs.python.org/2/library/string.html#string-formatting">string.format</a> style curly braces. <tt class="docutils literal"><span class="pre">{NAME}</span></tt></p>
-<p>We refer to an element from the Nth input string by index, for example:</p>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">"{ext[0]}"</span></tt>     is the extension of the first input string.</li>
-<li><tt class="docutils literal"><span class="pre">"{basename[1]}"</span></tt> is the basename of the second input string.</li>
-<li><tt class="docutils literal"><span class="pre">"{basename[1][0:3]}"</span></tt> are the first three letters from the basename of the second input string.</li>
-</ul>
-</div></blockquote>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="split.html#decorators-split"><em>@split</em></a></li>
-<li><a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a></li>
-<li><a class="reference internal" href="merge.html#decorators-merge"><em>@merge</em></a></li>
-<li><a class="reference internal" href="subdivide.html#decorators-subdivide"><em>@subdivide</em></a></li>
-<li><a class="reference internal" href="collate.html#decorators-collate"><em>@collate</em></a></li>
-<li><a class="reference internal" href="product.html#decorators-product"><em>@product</em></a></li>
-<li><a class="reference internal" href="permutations.html#decorators-permutations"><em>@permutations</em></a></li>
-<li><a class="reference internal" href="combinations.html#decorators-combinations"><em>@combinations</em></a></li>
-<li><a class="reference internal" href="combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a></li>
-</ul>
-</dd>
-</dl>
-<p><strong>@transform example</strong>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   create initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.c.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="hll"><span class="c">#   formatter</span>
-</span><span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span>                               <span class="c"># Input</span>
-
-<span class="hll">            <span class="n">formatter</span><span class="p">(</span><span class="s">".+/job(?P<JOBNUMBER>\d+).a.start"</span><span class="p">,</span>           <span class="c"># Extract job number</span>
-</span><span class="hll">                      <span class="s">".+/job[123].b.start"</span><span class="p">),</span>                       <span class="c"># Match only "b" files</span>
-</span>
-            <span class="p">[</span><span class="s">"{path[0]}/jobs{JOBNUMBER[0]}.output.a.1"</span><span class="p">,</span>             <span class="c"># Replacement list</span>
-             <span class="s">"{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_parameters</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"input_parameters = "</span><span class="p">,</span> <span class="n">input_files</span>
-    <span class="k">print</span> <span class="s">"output_parameters = "</span><span class="p">,</span> <span class="n">output_parameters</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This produces:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="go">input_parameters  =  ['job1.a.start',</span>
-<span class="go">                      'job1.b.start']</span>
-<span class="go">output_parameters =  ['/home/lg/src/temp/jobs1.output.a.1',</span>
-<span class="go">                      '/home/lg/src/temp/jobs1.output.b.1', 45]</span>
-
-<span class="go">input_parameters  =  ['job2.a.start',</span>
-<span class="go">                      'job2.b.start']</span>
-<span class="go">output_parameters =  ['/home/lg/src/temp/jobs2.output.a.1',</span>
-<span class="go">                      '/home/lg/src/temp/jobs2.output.b.1', 45]</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>@permutations example</strong>:</p>
-<blockquote>
-<div><p>Combinatoric decorators such as <a class="reference internal" href="product.html#decorators-product"><em>@product</em></a> or
-<a class="reference internal" href="permutations.html#decorators-permutations"><em>@product</em></a> behave much
-like nested for loops in enumerating, combining, and permutating the original sets
-of inputs.</p>
-<p>The replacement strings require an extra level of indirection to refer to
-parsed components:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   create initial files</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="s">'a.start'</span><span class="p">,</span> <span class="s">'b.start'</span><span class="p">,</span> <span class="s">'c.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   formatter</span>
-<span class="c">#</span>
-<span class="hll"><span class="nd">@permutations</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                           <span class="c"># Input</span>
-</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>                                           <span class="c"># match input file in permutations</span>
-            <span class="mi">2</span><span class="p">,</span>
-<span class="hll">
-</span><span class="hll">            <span class="s">"{path[0][0]}/{basename[0][0]}_vs_{basename[1][0]}.product"</span><span class="p">,</span>    <span class="c"># Output Replacement string</span>
-</span>            <span class="s">"{path[0][0]}"</span><span class="p">,</span>                                                 <span class="c"># path for 1st set of files, 1st file name</span>
-            <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>                                            <span class="c"># basename for 1st set of files, 1st file name</span>
-             <span class="s">"{basename[1][0]}"</span><span class="p">])</span>                                           <span class="c"># basename for 2nd set of files, 1st file name</span>
-<span class="k">def</span> <span class="nf">product_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"input_parameter  = "</span><span class="p">,</span> <span class="n">input_file</span>
-    <span class="k">print</span> <span class="s">"output_parameter = "</span><span class="p">,</span> <span class="n">output_parameter</span>
-    <span class="k">print</span> <span class="s">"shared_path      = "</span><span class="p">,</span> <span class="n">shared_path</span>
-    <span class="k">print</span> <span class="s">"basenames        = "</span><span class="p">,</span> <span class="n">basenames</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This produces:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">input_parameter  =  ('a.start', 'b.start')</span>
-<span class="go">output_parameter =  /home/lg/src/oss/ruffus/a_vs_b.product</span>
-<span class="go">shared_path      =  /home/lg/src/oss/ruffus</span>
-<span class="go">basenames        =  ['a', 'b']</span>
-
-<span class="go">input_parameter  =  ('a.start', 'c.start')</span>
-<span class="go">output_parameter =  /home/lg/src/oss/ruffus/a_vs_c.product</span>
-<span class="go">shared_path      =  /home/lg/src/oss/ruffus</span>
-<span class="go">basenames        =  ['a', 'c']</span>
-
-<span class="go">input_parameter  =  ('b.start', 'a.start')</span>
-<span class="go">output_parameter =  /home/lg/src/oss/ruffus/b_vs_a.product</span>
-<span class="go">shared_path      =  /home/lg/src/oss/ruffus</span>
-<span class="go">basenames        =  ['b', 'a']</span>
-
-<span class="go">input_parameter  =  ('b.start', 'c.start')</span>
-<span class="go">output_parameter =  /home/lg/src/oss/ruffus/b_vs_c.product</span>
-<span class="go">shared_path      =  /home/lg/src/oss/ruffus</span>
-<span class="go">basenames        =  ['b', 'c']</span>
-
-<span class="go">input_parameter  =  ('c.start', 'a.start')</span>
-<span class="go">output_parameter =  /home/lg/src/oss/ruffus/c_vs_a.product</span>
-<span class="go">shared_path      =  /home/lg/src/oss/ruffus</span>
-<span class="go">basenames        =  ['c', 'a']</span>
-
-<span class="go">input_parameter  =  ('c.start', 'b.start')</span>
-<span class="go">output_parameter =  /home/lg/src/oss/ruffus/c_vs_b.product</span>
-<span class="go">shared_path      =  /home/lg/src/oss/ruffus</span>
-<span class="go">basenames        =  ['c', 'b']</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="suffix">
-<span id="decorators-suffix"></span><span id="index-2"></span><h2><em>suffix</em><a class="headerlink" href="#suffix" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>suffix(</strong> <tt class="docutils literal"><span class="pre">string</span></tt> <strong>)</strong></p>
-<p>The enclosed parameter is a string which must match <em>exactly</em> to the end
-of a file name.</p>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a></li>
-</ul>
-</dd>
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   Transforms ``*.c`` to ``*.o``::</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">previous_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="regex">
-<span id="decorators-regex"></span><span id="index-3"></span><h2><em>regex</em><a class="headerlink" href="#regex" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>regex(</strong> <tt class="docutils literal"><span class="pre">regular_expression</span></tt> <strong>)</strong></p>
-<p>The enclosed parameter is a python regular expression string,
-which must be wrapped in a <tt class="docutils literal"><span class="pre">regex</span></tt> indicator object.</p>
-<p>See python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>
-documentation for details of regular expression syntax</p>
-<p><strong>Used by:</strong></p>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a></li>
-<li><a class="reference internal" href="subdivide.html#decorators-subdivide"><em>@subdivide</em></a></li>
-<li><a class="reference internal" href="collate.html#decorators-collate"><em>@collate</em></a></li>
-<li>The deprecated <a class="reference internal" href="files_re.html#decorators-files-re"><em>@files_re</em></a></li>
-</ul>
-</div></blockquote>
-<dl class="docutils">
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">previous_task</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r".c$"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="add-inputs">
-<span id="decorators-add-inputs"></span><span id="index-4"></span><h2><em>add_inputs</em><a class="headerlink" href="#add-inputs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>add_inputs(</strong> <tt class="docutils literal"><span class="pre">input_file_pattern</span></tt> <strong>)</strong></p>
-<p>The enclosed parameter(s) are pattern strings or a nested structure which is added to the
-input for each job.</p>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>@transform</em></a></li>
-<li><a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>@collate</em></a></li>
-<li><a class="reference internal" href="subdivide.html#decorators-subdivide"><em>@subdivide</em></a></li>
-</ul>
-</dd>
-</dl>
-<p><strong>Example @transform with suffix(...)</strong></p>
-<blockquote>
-<div><p>A common task in compiling C code is to include the corresponding header file for the source.
-To compile <tt class="docutils literal"><span class="pre">*.c</span></tt> to <tt class="docutils literal"><span class="pre">*.o</span></tt>, adding <tt class="docutils literal"><span class="pre">*.h</span></tt> and the common header <tt class="docutils literal"><span class="pre">universal.h</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="n">add_inputs</span><span class="p">([</span><span class="s">r"\1.h"</span><span class="p">,</span> <spa [...]
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="c"># do something here</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="line-block">
-<div class="line">The starting files names are <tt class="docutils literal"><span class="pre">1.c</span></tt> and <tt class="docutils literal"><span class="pre">2.c</span></tt>.</div>
-<div class="line"><tt class="docutils literal"><span class="pre">suffix(".c")</span></tt> matches ”.c” so <tt class="docutils literal"><span class="pre">\1</span></tt> stands for the unmatched prefices  <tt class="docutils literal"><span class="pre">"1"</span></tt> and <tt class="docutils literal"><span class="pre">"2"</span></tt></div>
-</div>
-<dl class="docutils">
-<dt>This will result in the following functional calls:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"1.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">],</span> <span class="s">"1.o"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">([</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"2.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">],</span> <span class="s">"2.o"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>A string like <tt class="docutils literal"><span class="pre">universal.h</span></tt> in <tt class="docutils literal"><span class="pre">add_inputs</span></tt> will added <em>as is</em>.
-<tt class="docutils literal"><span class="pre">r"\1.h"</span></tt>, however, performs suffix substitution, with the special form <tt class="docutils literal"><span class="pre">r"\1"</span></tt> matching everything up to the suffix.
-Remember to ‘escape’ <tt class="docutils literal"><span class="pre">r"\1"</span></tt> otherwise Ruffus will complain and throw an <tt class="docutils literal"><span class="pre">Exception</span></tt> to remind you.
-The most convenient way is to use a python “raw” string.</p>
-</div></blockquote>
-<p><strong>Example of add_inputs(...) with regex(...)</strong></p>
-<blockquote>
-<div><dl class="docutils">
-<dt>The suffix match (<tt class="docutils literal"><span class="pre">suffix(...)</span></tt>) is exactly equivalent to the following code using regular expression (<tt class="docutils literal"><span class="pre">regex(...)</span></tt>):</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"^(.+)\.c$"</span><span class="p">),</span> <span class="n">add_inputs</span><span class="p">([</span><span class="s">r"\1.h"</span><span class= [...]
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="c"># do something here</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>The <tt class="docutils literal"><span class="pre">suffix(..)</span></tt> code is much simpler but the regular expression allows more complex substitutions.</p>
-</div></blockquote>
-<p><strong>add_inputs(...) preserves original inputs</strong></p>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">add_inputs</span></tt> nests the the original input parameters in a list before adding additional dependencies.</p>
-<dl class="docutils">
-<dt>This can be seen in the following example:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span>    <span class="p">[</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"A.c"</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
-                <span class="p">[</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"B.c"</span><span class="p">,</span> <span class="s">"C.c"</span><span class="p">,</span> <span class="mi">3</span><span class="p">]],</span>
-                <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="n">add_inputs</span><span class="p">([</span><span class="s">r"\1.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">]),</span>  <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="c"># do something here</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-<dt>This will result in the following functional calls:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">([[</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"A.c"</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span>        <span class="s">"1.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">],</span> <span class="s">"1.o"</span><span [...]
-<span class="nb">compile</span><span class="p">([[</span><span class="s">"3.c"</span><span class="p">,</span> <span class="s">"B.c"</span><span class="p">,</span> <span class="s">"C.c"</span><span class="p">,</span> <span class="mi">3</span><span class="p">],</span> <span class="s">"2.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">],</span> <span class="s">"2.o"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>The original parameters are retained unchanged as the first item in a list</p>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="inputs">
-<span id="decorators-inputs"></span><span id="index-5"></span><h2><em>inputs</em><a class="headerlink" href="#inputs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>inputs(</strong> <tt class="docutils literal"><span class="pre">input_file_pattern</span></tt> <strong>)</strong></p>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>@transform</em></a></li>
-<li><a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>@collate</em></a></li>
-<li><a class="reference internal" href="subdivide.html#decorators-subdivide"><em>@subdivide</em></a></li>
-</ul>
-</dd>
-</dl>
-<p>The enclosed single parameter is a pattern string or a nested structure which is
-used to construct the input for each job.</p>
-<p>If more than one argument is supplied to inputs, an exception will be raised.</p>
-<p>Use a tuple or list (as in the following example) to send multiple input arguments to each job.</p>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li>The advanced form of <a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>@transform</em></a></li>
-</ul>
-</dd>
-</dl>
-<p><strong>inputs(...) replaces original inputs</strong></p>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">inputs(...)</span></tt> allows the original input parameters to be replaced wholescale.</p>
-<dl class="docutils">
-<dt>This can be seen in the following example:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span>    <span class="p">[</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"A.c"</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
-                <span class="p">[</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"B.c"</span><span class="p">,</span> <span class="s">"C.c"</span><span class="p">,</span> <span class="mi">3</span><span class="p">]],</span>
-                <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="n">inputs</span><span class="p">([</span><span class="s">r"\1.py"</span><span class="p">,</span> <span class="s">"docs.rst"</span><span class="p">]),</span>  <span class="s">".pyc"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="c"># do something here</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-<dt>This will result in the following functional calls:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">([</span><span class="s">"1.py"</span><span class="p">,</span> <span class="s">"docs.rst"</span><span class="p">],</span> <span class="s">"1.pyc"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">([</span><span class="s">"2.py"</span><span class="p">,</span> <span class="s">"docs.rst"</span><span class="p">],</span> <span class="s">"2.pyc"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>In this example, the corresponding python files have been sneakily substituted
-without trace in the place of the C source files.</p>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="mkdir">
-<span id="decorators-indicator-objects-mkdir"></span><span id="index-6"></span><h2><em>mkdir</em><a class="headerlink" href="#mkdir" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>mkdir(</strong> <tt class="docutils literal"><span class="pre">directory_name1</span></tt> <strong>, [</strong> <tt class="docutils literal"><span class="pre">directory_name2</span></tt> <strong>, ...] )</strong></p>
-<p>The enclosed parameter is a directory name or a sequence of directory names.
-These directories will be created as part of the prerequisites of running a task.</p>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="follows.html#decorators-follows"><em>@follows</em></a></li>
-</ul>
-</dd>
-<dt><strong>Example:</strong></dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="n">mkdir</span><span class="p">(</span><span class="s">"/output/directory"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">task</span><span class="p">():</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="touch-file">
-<span id="decorators-touch-file"></span><span id="index-7"></span><h2><em>touch_file</em><a class="headerlink" href="#touch-file" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>touch_file(</strong> <tt class="docutils literal"><span class="pre">file_name</span></tt> <strong>)</strong></p>
-<p>The enclosed parameter is a file name. This file will be <tt class="docutils literal"><span class="pre">touch</span></tt>-ed after a
-task is executed.</p>
-<p>This will change the date/time stamp of the <tt class="docutils literal"><span class="pre">file_name</span></tt> to the current date/time.
-If the file does not exist, an empty file will be created.</p>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="posttask.html#decorators-posttask"><em>@posttask</em></a></li>
-</ul>
-</dd>
-<dt><strong>Example:</strong></dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@posttask</span><span class="p">(</span><span class="n">touch_file</span><span class="p">(</span><span class="s">"task_completed.flag"</span><span class="p">))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">do_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="output-from">
-<span id="decorators-output-from"></span><span id="index-8"></span><h2><em>output_from</em><a class="headerlink" href="#output-from" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>output_from (</strong> <tt class="docutils literal"><span class="pre">file_name_string1</span></tt> <strong>[,</strong> <tt class="docutils literal"><span class="pre">file_name_string1</span></tt> <strong>, ...] )</strong></p>
-<p>Indicates that any enclosed strings are not file names but refer to task functions.</p>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="split.html#decorators-split"><em>@split</em></a></li>
-<li><a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a></li>
-<li><a class="reference internal" href="merge.html#decorators-merge"><em>@merge</em></a></li>
-<li><a class="reference internal" href="collate.html#decorators-collate"><em>@collate</em></a></li>
-<li><a class="reference internal" href="subdivide.html#decorators-subdivide"><em>@subdivide</em></a></li>
-<li><a class="reference internal" href="product.html#decorators-product"><em>@product</em></a></li>
-<li><a class="reference internal" href="permutations.html#decorators-permutations"><em>@permutations</em></a></li>
-<li><a class="reference internal" href="combinations.html#decorators-combinations"><em>@combinations</em></a></li>
-<li><a class="reference internal" href="combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a></li>
-<li><a class="reference internal" href="files.html#decorators-files"><em>@files</em></a></li>
-</ul>
-</dd>
-<dt><strong>Example:</strong></dt>
-<dd><div class="first highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">([</span><span class="s">"a.file"</span><span class="p">,</span> <span class="p">(</span><span class="s">"b.file"</span><span class="p">,</span> <span class="n">output_from</span><span class="p">(</span><span class="s">"task1"</span><span class="p">,</span> <span class="mi">76</span><span class="p">,</span> <span class="s">"task2"</span [...]
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>is equivalent to:</p>
-<div class="last highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">([</span><span class="s">"a.file"</span><span class="p">,</span> <span class="p">(</span><span class="s">"b.file"</span><span class="p">,</span> <span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="mi">76</span><span class="p">,</span> <span class="n">task2</span><span class="p">))],</span> <span class="s">"*.split&quot [...]
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="combine">
-<span id="decorators-combine"></span><span id="index-9"></span><h2><em>combine</em><a class="headerlink" href="#combine" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>combine(</strong> <tt class="docutils literal"><span class="pre">arguments</span></tt> <strong>)</strong></p>
-<div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<p>This is deprecated syntax.</p>
-<p>Please do not use!</p>
-<p class="last"><a class="reference internal" href="merge.html#decorators-merge"><em>@merge</em></a> and <a class="reference internal" href="collate.html#decorators-collate"><em>@collate</em></a> are more powerful
-and have straightforward syntax.</p>
-</div>
-<p>Indicates that the <em>inputs</em> of <a class="reference internal" href="files_re.html#decorators-files-re"><em>@files_re</em></a> will be collated
-or summarised into <em>outputs</em> by category. See the <a class="reference internal" href="../tutorials/new_tutorial/deprecated_files_re.html#new-manual-files-re-combine"><em>Manual</em></a>  or
-:ref:` @collate <new_manual.collate>` for examples.</p>
-<dl class="docutils">
-<dt><strong>Used by:</strong></dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="../tutorials/new_tutorial/deprecated_files_re.html#new-manual-files-re-combine"><em>@files_re</em></a></li>
-</ul>
-</dd>
-<dt><strong>Example:</strong></dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@files_re</span><span class="p">(</span><span class="s">'*.animals'</span><span class="p">,</span>                           <span class="c"># inputs = all *.animal files</span>
-            <span class="s">r'mammals.([^.]+)'</span><span class="p">,</span>                  <span class="c"># regular expression</span>
-            <span class="n">combine</span><span class="p">(</span><span class="s">r'\1/animals.in_my_zoo'</span><span class="p">),</span>    <span class="c"># single output file per species</span>
-            <span class="s">r'\1'</span> <span class="p">)</span>                              <span class="c"># species name</span>
-<span class="k">def</span> <span class="nf">capture_mammals</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>
-    <span class="c"># summarise all animals of this species</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Indicator Objects</a><ul>
-<li><a class="reference internal" href="#formatter"><em>formatter</em></a></li>
-<li><a class="reference internal" href="#suffix"><em>suffix</em></a></li>
-<li><a class="reference internal" href="#regex"><em>regex</em></a></li>
-<li><a class="reference internal" href="#add-inputs"><em>add_inputs</em></a></li>
-<li><a class="reference internal" href="#inputs"><em>inputs</em></a></li>
-<li><a class="reference internal" href="#mkdir"><em>mkdir</em></a></li>
-<li><a class="reference internal" href="#touch-file"><em>touch_file</em></a></li>
-<li><a class="reference internal" href="#output-from"><em>output_from</em></a></li>
-<li><a class="reference internal" href="#combine"><em>combine</em></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="decorators.html"
-                        title="previous chapter">Ruffus Decorators</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="originate.html"
-                        title="next chapter">@originate</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/indicator_objects.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="#">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
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diff --git a/doc/_build/html/decorators/jobs_limit.html b/doc/_build/html/decorators/jobs_limit.html
deleted file mode 100644
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--- a/doc/_build/html/decorators/jobs_limit.html
+++ /dev/null
@@ -1,267 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-            
-  <span class="target" id="decorators-jobs-limit"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="jobs-limit">
-<h1>@jobs_limit<a class="headerlink" href="#jobs-limit" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="jobs-limit-maximum-num-of-jobs-name">
-<h2><em>@jobs_limit</em> ( <a class="reference internal" href="#decorators-jobs-limit-maximum-num-of-jobs"><cite>maximum_num_of_jobs</cite></a>, [ <a class="reference internal" href="#decorators-jobs-limit-name"><cite>name</cite></a> ])<a class="headerlink" href="#jobs-limit-maximum-num-of-jobs-name" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><div class="first last line-block">
-<div class="line">Manages the resources available for a task.</div>
-<div class="line">Limits the number of concurrent jobs which can be run in parallel for this task</div>
-<div class="line">Overrides the value for <tt class="docutils literal"><span class="pre">multiprocess</span></tt> in <a class="reference internal" href="../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a></div>
-<div class="line">If an optional <tt class="docutils literal"><span class="pre">name</span></tt> is given, the same limit is shared across all tasks with the same @job_limit name.</div>
-</div>
-</dd>
-</dl>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-jobs-limit-maximum-num-of-jobs">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>maximum_num_of_jobs</em></dt>
-<dd><p class="first last">The maximum number of concurrent jobs for this task. Must be an integer number
-greater than or equal to 1.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-jobs-limit-name">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>name</em></dt>
-<dd><p class="first last">Optional name for the limit. All tasks with the same name share the same limit if they
-are running concurrently.</p>
-</dd>
-</dl>
-</li>
-</ul>
-<dl class="docutils">
-<dt><strong>Example</strong></dt>
-<dd><div class="first highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c"># make list of 10 files</span>
-<span class="nd">@split</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"*.stage1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">make_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">):</span>
-        <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.stage1"</span> <span class="o">%</span> <span class="n">i</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">make_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".stage1"</span><span class="p">),</span> <span class="s">".stage2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage1</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">stage1</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".stage2"</span><span class="p">),</span> <span class="s">".stage3"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage2</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">stage2</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>will run the 10 jobs of <tt class="docutils literal"><span class="pre">stage1</span></tt> 2 at a time, while `` stage2`` will
-run 5 at a time (from <tt class="docutils literal"><span class="pre">multiprocess</span> <span class="pre">=</span> <span class="pre">5</span></tt>):</p>
-<img alt="../_images/jobs_limit.png" class="last" src="../_images/jobs_limit.png" />
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@jobs_limit</a><ul>
-<li><a class="reference internal" href="#jobs-limit-maximum-num-of-jobs-name"><em>@jobs_limit</em> ( <cite>maximum_num_of_jobs</cite>, [ <cite>name</cite> ])</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="mkdir.html"
-                        title="previous chapter">@mkdir</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="posttask.html"
-                        title="next chapter">@posttask</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/jobs_limit.txt"
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-    Enter search terms or a module, class or function name.
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="decorators.html#core">Core:</a></h4>   
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-            <li><a href="collate.html">@collate</a>                               </li>
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-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="#">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
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-        <h4 >Pipeline functions</h4>
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-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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diff --git a/doc/_build/html/decorators/merge.html b/doc/_build/html/decorators/merge.html
deleted file mode 100644
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--- a/doc/_build/html/decorators/merge.html
+++ /dev/null
@@ -1,269 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
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-    
-    <title>@merge — ruffus 2.5 documentation</title>
-    
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-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
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-        URL_ROOT:    '../',
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-        HAS_SOURCE:  true
-      };
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-    <link rel="top" title="ruffus 2.5 documentation" href="../index.html" />
-    <link rel="next" title="@subdivide" href="subdivide.html" />
-    <link rel="prev" title="@transform" href="transform.html" /> 
-  </head>
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-    <div class="related">
-      <h3>Navigation</h3>
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- 
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-          <div class="body">
-            
-  <span class="target" id="decorators-merge"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="merge">
-<h1>@merge<a class="headerlink" href="#merge" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="merge-tasks-or-file-names-output-file-extra-parameters">
-<h2><em>@merge</em> ( <a class="reference internal" href="#decorators-merge-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="#decorators-merge-output-file"><cite>output_file</cite></a>, [<a class="reference internal" href="#decorators-merge-extra-parameters"><cite>extra_parameters</cite></a>,...] )<a class="headerlink" href="#merge-tasks-or-file-names-output-file-extra-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">Merges multiple input files into a single output.</p>
-<p class="last">Only out of date tasks (comparing input and output files) will be run</p>
-</dd>
-</dl>
-<p><strong>Example</strong>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@merge</span><span class="p">(</span><span class="n">previous_task</span><span class="p">,</span> <span class="s">'all.summary'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">summarize</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">summary_file</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-merge-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-merge-output-file">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_file</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s).</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-merge-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters, ...</em></dt>
-<dd><p class="first last">Any optional extra parameters are passed verbatim to the task function</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<p>See <a class="reference internal" href="collate.html#decorators-collate"><em>here</em></a> for more advanced uses of merging.</p>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@merge</a><ul>
-<li><a class="reference internal" href="#merge-tasks-or-file-names-output-file-extra-parameters"><em>@merge</em> ( <cite>tasks_or_file_names</cite>, <cite>output_file</cite>, [<cite>extra_parameters</cite>,...] )</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="transform.html"
-                        title="previous chapter">@transform</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="subdivide.html"
-                        title="next chapter">@subdivide</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/merge.txt"
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-    Enter search terms or a module, class or function name.
-    </p>
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-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="#">@merge</a>                                   </li>
-        </ul>
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-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
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diff --git a/doc/_build/html/decorators/mkdir.html b/doc/_build/html/decorators/mkdir.html
deleted file mode 100644
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--- a/doc/_build/html/decorators/mkdir.html
+++ /dev/null
@@ -1,422 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
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-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
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-    
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-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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-            
-  <span class="target" id="decorators-mkdir"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-<li>More on @mkdir in the <tt class="docutils literal"><span class="pre">Ruffus</span></tt> <a class="reference internal" href="../tutorials/new_tutorial/mkdir.html#new-manual-mkdir"><em>Manual</em></a></li>
-<li><a class="reference internal" href="follows.html#decorators-follows"><em>@follows(mkdir(“dir”))</em></a> specifies the creation of a <em>single</em> directory as a task pre-requisite.</li>
-</ul>
-</div>
-<div class="section" id="mkdir">
-<h1>@mkdir<a class="headerlink" href="#mkdir" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="mkdir-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-output-pattern">
-<h2><em>@mkdir</em> ( <a class="reference internal" href="#decorators-mkdir-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a><em>(</em><a class="reference internal" href="#decorators-mkdir-suffix-string"><cite>suffix_string</cite></a><em>)</em>| <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a><em>(</em><a class="reference internal"  [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><ul class="simple">
-<li>Prepares directories to receive <em>Output</em> files</li>
-<li>Used when <em>Output</em> path names are generated at runtime from <em>Inputs</em>. <strong>mkdir</strong> can make sure these runtime specified paths exist.</li>
-<li>Directory names are generated from <strong>Input</strong> using string substitution via <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter()</em></a>,  <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix()</em></a> or  <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex()</em></a>.</li>
-<li>Behaves essentially like <tt class="docutils literal"><span class="pre">@transform</span></tt> but with its own (internal) function which does the actual work of making a directory</li>
-<li>Does <em>not</em> invoke the host task function to which it is attached</li>
-<li>Makes specified directories using <a class="reference external" href="http://docs.python.org/2/library/os.html#os.makedirs">os.makedirs</a></li>
-<li>Multiple directories can be created in a list</li>
-</ul>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Only missing directories are created.</p>
-<p>In other words, the same directory can be specified multiple times safely without, for example, being recreated repeatedly.</p>
-<p class="last">Sometimes, for pipelines with multiple entry points, this is the only way to make sure that certain working or output
-directories are always created or available <em>before</em> the pipeline runs.</p>
-</div>
-</div></blockquote>
-<p><strong>Simple Example</strong></p>
-<blockquote>
-<div><p>Creates multiple directories per job to hold the results of <a class="reference internal" href="transform.html#decorators-transform"><em>@transform</em></a></p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial files</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="s">'A.start'</span><span class="p">,</span>
-             <span class="s">'B.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="hll"><span class="c"># create files without making directories -> ERROR</span>
-</span><span class="nd">@transform</span><span class="p">(</span> <span class="n">create_initial_files</span><span class="p">,</span>
-            <span class="n">formatter</span><span class="p">(),</span>
-            <span class="p">[</span><span class="s">"{path[0]}/{basename[0]}/processed.txt"</span><span class="p">,</span>
-             <span class="s">"{path[0]}/{basename[0]}.tmp/tmp.processed.txt"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_files_without_mkdir</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_files</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_files</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="hll"><span class="c"># create files after making corresponding directories</span>
-</span><span class="nd">@mkdir</span><span class="p">(</span> <span class="n">create_initial_files</span><span class="p">,</span>
-        <span class="n">formatter</span><span class="p">(),</span>
-        <span class="p">[</span><span class="s">"{path[0]}/{basename[0]}"</span><span class="p">,</span>         <span class="c"># create directory</span>
-         <span class="s">"{path[0]}/{basename[0]}.tmp"</span><span class="p">])</span>    <span class="c"># create directory.tmp</span>
-<span class="nd">@transform</span><span class="p">(</span> <span class="n">create_initial_files</span><span class="p">,</span>
-            <span class="n">formatter</span><span class="p">(),</span>
-            <span class="p">[</span><span class="s">"{path[0]}/{basename[0]}/processed.txt"</span><span class="p">,</span>
-             <span class="s">"{path[0]}/{basename[0]}.tmp/tmp.processed.txt"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_files_with_mkdir</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_files</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_files</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_files_without_mkdir</span><span class="p">])</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_files_with_mkdir</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Running without making the directories first gives errors:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_files_without_mkdir</span><span class="p">])</span>
-<span class="go">    Job  = [None -> A.start] completed</span>
-<span class="go">    Job  = [None -> B.start] completed</span>
-<span class="go">Completed Task = create_initial_files</span>
-
-<span class="go">    Traceback (most recent call last):</span>
-<span class="go">      File "<stdin>", line 1, in <module></span>
-<span class="go">      File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 3738, in pipeline_run</span>
-<span class="go">        raise job_errors</span>
-<span class="go">    ruffus.ruffus_exceptions.RethrownJobError:</span>
-
-<span class="go">    Original exception:</span>
-
-<span class="hll"><span class="gp">>>> </span><span class="c">#    Exception #1</span>
-</span><span class="hll"><span class="gp">>>> </span><span class="c">#      'exceptions.IOError([Errno 2] No such file or directory: 'A/processed.txt')' raised in ...</span>
-</span><span class="hll"><span class="gp">>>> </span><span class="c">#       Task = def create_files_without_mkdir(...):</span>
-</span><span class="hll"><span class="gp">>>> </span><span class="c">#       Job  = [A.start -> [processed.txt, tmp.processed.txt]]</span>
-</span></pre></div>
-</div>
-</div></blockquote>
-<p>Running after making the directories first:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_files_with_mkdir</span><span class="p">])</span>
-<span class="go">    Job  = [None -> A.start] completed</span>
-<span class="go">    Job  = [None -> B.start] completed</span>
-<span class="go">Completed Task = create_initial_files</span>
-<span class="go">    Make directories [A, A.tmp] completed</span>
-<span class="go">    Make directories [B, B.tmp] completed</span>
-<span class="go">Completed Task = (mkdir 1) before create_files_with_mkdir</span>
-<span class="go">    Job  = [A.start -> [processed.txt, tmp.processed.txt]] completed</span>
-<span class="go">    Job  = [B.start -> [processed.txt, tmp.processed.txt]] completed</span>
-<span class="go">Completed Task = create_files_with_mkdir</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<p><strong>Escaping regular expression patterns</strong></p>
-<blockquote>
-<div>A string like <tt class="docutils literal"><span class="pre">universal.h</span></tt> in <tt class="docutils literal"><span class="pre">add_inputs</span></tt> will added <em>as is</em>.
-<tt class="docutils literal"><span class="pre">r"\1.h"</span></tt>, however, performs suffix substitution, with the special form <tt class="docutils literal"><span class="pre">r"\1"</span></tt> matching everything up to the suffix.
-Remember to ‘escape’ <tt class="docutils literal"><span class="pre">r"\1"</span></tt> otherwise Ruffus will complain and throw an Exception to remind you.
-The most convenient way is to use a python “raw” string.</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-mkdir-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-mkdir-suffix-string">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>suffix_string</em></dt>
-<dd><p class="first">must be wrapped in a <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a> indicator object.
-The end of each input file name which matches <tt class="docutils literal"><span class="pre">suffix_string</span></tt> will be replaced by <tt class="docutils literal"><span class="pre">output_pattern</span></tt>.</p>
-<p>Input file names which do not match suffix_string will be ignored</p>
-<p>The non-suffix part of the match can be referred to using the <tt class="docutils literal"><span class="pre">"\1"</span></tt> pattern. This
-can be useful for putting the output in different directory, for example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@mkdir</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="s">r"my_path/\1.o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>This results in the following function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># 1.c -> my_path/1.o</span>
-<span class="c"># 2.c -> my_path/2.o</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"my_path/1.o"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"my_path/2.o"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>For convenience and visual clarity, the  <tt class="docutils literal"><span class="pre">"\1"</span></tt> can be omitted from the output parameter.
-However, the <tt class="docutils literal"><span class="pre">"\1"</span></tt> is mandatory for string substitutions in additional parameters,</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@mkdir</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="p">[</span><span class="s">r"\1.o"</span><span class="p">,</span> <span class="s">".o"</span><span clas [...]
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>Results in the following function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">(</span><span class="s">"1.c"</span><span class="p">,</span> <span class="p">[</span><span class="s">"1.o"</span><span class="p">,</span> <span class="s">"1.o"</span><span class="p">],</span> <span class="s">"Compiling 1"</span><span class="p">,</span> <span class="s">"verbatim"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"2.c"</span><span class="p">,</span> <span class="p">[</span><span class="s">"2.o"</span><span class="p">,</span> <span class="s">"2.o"</span><span class="p">],</span> <span class="s">"Compiling 2"</span><span class="p">,</span> <span class="s">"verbatim"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p class="last">Since r”1” is optional for the output parameter, <tt class="docutils literal"><span class="pre">"\1.o"</span></tt> and <tt class="docutils literal"><span class="pre">".o"</span></tt> are equivalent.
-However, strings in other parameters which do not contain r”1” will be included verbatim, much
-like the string <tt class="docutils literal"><span class="pre">"verbatim"</span></tt> in the above example.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-mkdir-matching-regex">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_regex</em></dt>
-<dd><p class="first last">is a python regular expression string, which must be wrapped in
-a <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicator object
-See python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>
-documentation for details of regular expression syntax
-Each output file name is created using regular expression substitution with <tt class="docutils literal"><span class="pre">output_pattern</span></tt></p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-mkdir-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-mkdir-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s).</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@mkdir</a><ul>
-<li><a class="reference internal" href="#mkdir-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-output-pattern"><em>@mkdir</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">suffix</span></tt><em>(</em><cite>suffix_string</cite><em>)</em>| <tt class="docutils literal"><span class="pre">regex</span></tt><em>(</em><cite>matching_regex</cite><em>)</em> |  <tt class="docutils literal"><span class="pre">formatt [...]
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="graphviz.html"
-                        title="previous chapter">@graphviz</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="jobs_limit.html"
-                        title="next chapter">@jobs_limit</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/mkdir.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="#">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             >index</a></li>
-        <li class="right" >
-          <a href="jobs_limit.html" title="@jobs_limit"
-             >next</a> |</li>
-        <li class="right" >
-          <a href="graphviz.html" title="@graphviz"
-             >previous</a> |</li>
-        Ruffus v. 2.5
-            <li><a href="../index.html">Home</a> | </li>
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-            <li><a href="../installation.html">Install</a>  | </li>
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-            <li><a href="../cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="../tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="../gallery.html">Gallery</a> |  </li>
-            <li><a href="../history.html">Latest Changes</a> » </li>
- 
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-    <div class="footer">
-        © Copyright 2009-2013 Leo Goodstadt.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
-    </div>
-  </body>
-</html>
\ No newline at end of file
diff --git a/doc/_build/html/decorators/originate.html b/doc/_build/html/decorators/originate.html
deleted file mode 100644
index d6e08fc..0000000
--- a/doc/_build/html/decorators/originate.html
+++ /dev/null
@@ -1,275 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>@originate — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="../_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
-        VERSION:     '2.5',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true
-      };
-    </script>
-    <script type="text/javascript" src="../_static/jquery.js"></script>
-    <script type="text/javascript" src="../_static/underscore.js"></script>
-    <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <link rel="top" title="ruffus 2.5 documentation" href="../index.html" />
-    <link rel="next" title="@split" href="split.html" />
-    <link rel="prev" title="Indicator Objects" href="indicator_objects.html" /> 
-  </head>
-  <body>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="split.html" title="@split"
-             accesskey="N">next</a> |</li>
-        <li class="right" >
-          <a href="indicator_objects.html" title="Indicator Objects"
-             accesskey="P">previous</a> |</li>
-        Ruffus v. 2.5
-            <li><a href="../index.html">Home</a> | </li>
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-            <li><a href="../installation.html">Install</a>  | </li>
-            <li><a href="../tutorials/new_tutorial/introduction.html">Manual</a>  / </li>
-            <li><a href="../tutorials/new_tutorial/manual_contents.html">(TOC)</a>  | </li>
-            <li><a href="../faq.html">FAQ</a>  | </li>
-            <li><a href="../cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="../tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="../gallery.html">Gallery</a> |  </li>
-            <li><a href="../history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <span class="target" id="decorators-originate"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="originate">
-<h1>@originate<a class="headerlink" href="#originate" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="originate-output-files-extra-parameters">
-<h2><em>@originate</em> ( <a class="reference internal" href="#decorators-originate-output-files"><cite>output_files</cite></a>, [<a class="reference internal" href="#decorators-originate-extra-parameters"><cite>extra_parameters</cite></a>,...] )<a class="headerlink" href="#originate-output-files-extra-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><ul class="first simple">
-<li>Creates (originates) a set of starting file without dependencies from scratch  (<em>ex nihilo</em>!)</li>
-<li>Only called to create files which do not exist.</li>
-<li>Invoked onces (a job created) per item in the <tt class="docutils literal"><span class="pre">output_files</span></tt> list.</li>
-</ul>
-<div class="last admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The first argument for the task function is the <em>Output</em>. There is by definition no
-<em>Input</em> for <tt class="docutils literal"><span class="pre">@originate</span></tt></p>
-</div>
-</dd>
-</dl>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="nd">@originate</span><span class="p">([</span><span class="s">"a"</span><span class="p">,</span> <span class="s">"b"</span><span class="p">,</span> <span class="s">"c"</span><span class="p">,</span> <span class="s">"d"</span><span class="p">],</span> <span class="s">"extra"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">test</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="n">extra</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [None -> a, extra] completed</span>
-<span class="go">    Job  = [None -> b, extra] completed</span>
-<span class="go">    Job  = [None -> c, extra] completed</span>
-<span class="go">    Job  = [None -> d, extra] completed</span>
-<span class="go">Completed Task = test</span>
-
-<span class="hll"><span class="gp">>>> </span><span class="c"># all files exist: nothing to do</span>
-</span><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-
-<span class="hll"><span class="gp">>>> </span><span class="c"># delete 'a' so that it is missing</span>
-</span><span class="gp">>>> </span><span class="kn">import</span> <span class="nn">os</span>
-<span class="gp">>>> </span><span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="s">"a"</span><span class="p">)</span>
-
-<span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [None -> a, extra] completed</span>
-<span class="go">Completed Task = test</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-originate-output-files">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_files</em></dt>
-<dd><ul class="first last simple">
-<li>Can be a single file name or a list of files</li>
-<li>Each item in the list is treated as the <em>Output</em> of a separate job</li>
-</ul>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-originate-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">Any extra parameters are passed verbatim to the task function</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@originate</a><ul>
-<li><a class="reference internal" href="#originate-output-files-extra-parameters"><em>@originate</em> ( <cite>output_files</cite>, [<cite>extra_parameters</cite>,...] )</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="indicator_objects.html"
-                        title="previous chapter">Indicator Objects</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="split.html"
-                        title="next chapter">@split</a></p>
-  <h3>This Page</h3>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="decorators.html#core">Core:</a></h4>   
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-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
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diff --git a/doc/_build/html/decorators/parallel.html b/doc/_build/html/decorators/parallel.html
deleted file mode 100644
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-            
-  <span class="target" id="decorators-parallel"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="parallel">
-<h1>@parallel<a class="headerlink" href="#parallel" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="parallel-job-params-job-params-parameter-generating-function">
-<h2><em>@parallel</em> ( [ [<a class="reference internal" href="#decorators-parallel-job-params"><cite>job_params</cite></a>, ...], [<a class="reference internal" href="#decorators-parallel-job-params"><cite>job_params</cite></a>, ...]...] | <a class="reference internal" href="#decorators-parallel-parameter-generating-function"><cite>parameter_generating_function</cite></a>)<a class="headerlink" href="#parallel-job-params-job-params-parameter-generating-function" title="Permalink to  [...]
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">To apply the (task) function to a set of parameters in parallel without file dependency checking.</p>
-<p class="last">Most useful allied to <a class="reference internal" href="check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate()</em></a></p>
-</dd>
-</dl>
-<p><strong>Example</strong>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                 <span class="p">[</span><span class="s">'A'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="c"># 1st job</span>
-                 <span class="p">[</span><span class="s">'B'</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="c"># 2nd job</span>
-                 <span class="p">[</span><span class="s">'C'</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span> <span class="c"># 3rd job</span>
-             <span class="p">]</span>
-<span class="nd">@parallel</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">parallel_task</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">param1</span><span class="p">,</span> <span class="n">param2</span><span class="p">):</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"    Parallel task </span><span class="si">%s</span><span class="s">: "</span> <span class="o">%</span> <span class="n">name</span><span class="p">)</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s"> + </span><span class="si">%d</span><span class="s"> = </span><span class="si">%d</span><span class="se">\\</span><span class="s">n"</span> <span class="o">%</span> <span class="p">(</span><span class="n">param1</span><span class="p">,</span> <span class="n [...]
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_task</span><span class="p">])</span>
-</pre></div>
-</div>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-parallel-job-params">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>job_params</em>:</dt>
-<dd><p class="first">Requires a sequence of parameters, one set for each job.</p>
-<p>Each set of parameters can be one or more items in a sequence which will be passed to
-the decorated task function iteratively (or in parallel)</p>
-<p>For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                 <span class="p">[</span><span class="s">'A'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="c"># 1st job</span>
-                 <span class="p">[</span><span class="s">'B'</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="c"># 2nd job</span>
-                 <span class="p">[</span><span class="s">'C'</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span> <span class="c"># 3rd job</span>
-             <span class="p">]</span>
-<span class="nd">@parallel</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">parallel_task</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">param1</span><span class="p">,</span> <span class="n">param2</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>Will result in the following function calls:</p>
-<div class="last highlight-python"><div class="highlight"><pre><span class="n">parallel_task</span><span class="p">(</span><span class="s">'A'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
-<span class="n">parallel_task</span><span class="p">(</span><span class="s">'B'</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
-<span class="n">parallel_task</span><span class="p">(</span><span class="s">'C'</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-parallel-parameter-generating-function">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>parameter_generating_function</em></dt>
-<dd><ol class="first last arabic simple">
-<li>A generator yielding  set of parameters (as above) in turn and on the fly</li>
-<li>A function returning a sequence of parameter sets, as above</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@parallel</a><ul>
-<li><a class="reference internal" href="#parallel-job-params-job-params-parameter-generating-function"><em>@parallel</em> ( [ [<cite>job_params</cite>, ...], [<cite>job_params</cite>, ...]...] | <cite>parameter_generating_function</cite>)</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="check_if_uptodate.html"
-                        title="previous chapter">@check_if_uptodate</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="files.html"
-                        title="next chapter">@files</a></p>
-  <h3>This Page</h3>
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-    Enter search terms or a module, class or function name.
-    </p>
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-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
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-            <li><a href="merge.html">@merge</a>                                   </li>
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-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="#">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
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-      <h3>Navigation</h3>
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-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
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-  </body>
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diff --git a/doc/_build/html/decorators/permutations.html b/doc/_build/html/decorators/permutations.html
deleted file mode 100644
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+++ /dev/null
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-  <span class="target" id="decorators-permutations"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="permutations">
-<h1>@permutations<a class="headerlink" href="#permutations" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="permutations-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters">
-<h2><em>@permutations</em> ( <a class="reference internal" href="#decorators-permutations-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a><em>(</em><a class="reference internal" href="#decorators-permutations-matching-formatter"><cite>matching_formatter</cite></a><em>)</em>, <a class="reference internal" href="#decorators-permutations-output-pattern"><cite>output_pattern< [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>Generates the <strong>permutations</strong>, between all the elements of a set of <strong>Input</strong></p>
-<p>The effect is analogous to the python <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.permutations">itertools</a>
-function of the same name:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">permutations</span>
-<span class="hll"><span class="gp">>>> </span><span class="c"># permutations('ABCD', 2) --> AB AC AD BA BC BD CA CB CD DA DB DC</span>
-</span><span class="gp">>>> </span><span class="p">[</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">permutations</span><span class="p">(</span><span class="s">"ABCD"</span><span class="p">,</span> <span class="mi">2</span><span class="p">)]</span>
-<span class="go">['AB', 'AC', 'AD', 'BA', 'BC', 'BD', 'CA', 'CB', 'CD', 'DA', 'DB', 'DC']</span>
-</pre></div>
-</div>
-<p>Only out of date tasks (comparing input and output files) will be run</p>
-<p>Output file names and strings in the extra parameters
-are determined from <a class="reference internal" href="#decorators-permutations-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of up stream tasks, or a list of file names, after string replacement via
-<a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a>.</p>
-<p>The replacement strings require an extra level of indirection to refer to
-parsed components:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>The first level refers to which <em>set</em> in each tuple of inputs.</li>
-<li>The second level refers to which input file in any particular <em>set</em> of inputs.</li>
-</ol>
-</div></blockquote>
-</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><p>Calculates the <strong>@permutations</strong> of <strong>A,B,C,D</strong> files</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @permutations</span>
-</span><span class="nd">@permutations</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>      <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                    <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 2 at a time</span>
-</span>              <span class="mi">2</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}.permutations"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-</span>              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span><span class="hll">               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#                                2nd</span>
-</span>               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">permutations_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-
-<span class="go">A - B</span>
-<span class="go">A - C</span>
-<span class="go">A - D</span>
-<span class="go">B - A</span>
-<span class="go">B - C</span>
-<span class="go">B - D</span>
-<span class="go">C - A</span>
-<span class="go">C - B</span>
-<span class="go">C - D</span>
-<span class="go">D - A</span>
-<span class="go">D - B</span>
-<span class="go">D - C</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-permutations-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-permutations-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-permutations-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s) after string
-substitution</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-permutations-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">Optional extra parameters are passed to the functions after string
-substitution</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
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-<li><a class="reference internal" href="#">@permutations</a><ul>
-<li><a class="reference internal" href="#permutations-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters"><em>@permutations</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">formatter</span></tt><em>(</em><cite>matching_formatter</cite><em>)</em>, <cite>output_pattern</cite>, [<cite>extra_parameters</cite>,...] )</a></li>
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-                        title="next chapter">@combinations</a></p>
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-</div>
-<div class="section" id="posttask">
-<h1>@posttask<a class="headerlink" href="#posttask" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="posttask-function-touch-file-file-name">
-<h2><em>@posttask</em> (<a class="reference internal" href="#decorators-posttask-function"><cite>function</cite></a> | <a class="reference internal" href="indicator_objects.html#decorators-touch-file"><em>touch_file</em></a><em>(</em><a class="reference internal" href="#decorators-posttask-file-name"><cite>file_name</cite></a><em>)</em>)<a class="headerlink" href="#posttask-function-touch-file-file-name" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd>Calls functions to signal the completion of each task</dd>
-</dl>
-<p><strong>Example</strong>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="k">def</span> <span class="nf">task_finished</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"hooray"</span>
-
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">task_finished</span><span class="p">)</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-posttask-function">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>function</em>:</dt>
-<dd><p class="first"><tt class="docutils literal"><span class="pre">function()</span></tt> will be called when the ruffus passes through a task.</p>
-<p class="last">This may happen even if all of the jobs are up-to-date:
-when a upstream task is out-of-date, and the execution passes through
-this point in the pipeline</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-posttask-file-name">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>file_name</em></dt>
-<dd><p class="first">Files to be <tt class="docutils literal"><span class="pre">touch</span></tt>-ed after the task is executed.</p>
-<p>This will change the date/time stamp of the <tt class="docutils literal"><span class="pre">file_name</span></tt> to the current date/time.
-If the file does not exist, an empty file will be created.</p>
-<p>Requires to be wrapped in a <a class="reference internal" href="indicator_objects.html#decorators-touch-file"><em>touch_file</em></a> indicator object:</p>
-<div class="last highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">touch_file</span><span class="p">(</span><span class="s">"task_completed.flag"</span><span class="p">))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@posttask</a><ul>
-<li><a class="reference internal" href="#posttask-function-touch-file-file-name"><em>@posttask</em> (<cite>function</cite> | <tt class="docutils literal"><span class="pre">touch_file</span></tt><em>(</em><cite>file_name</cite><em>)</em>)</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="jobs_limit.html"
-                        title="previous chapter">@jobs_limit</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="active_if.html"
-                        title="next chapter">@active_if</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/posttask.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="#">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             >index</a></li>
-        <li class="right" >
-          <a href="active_if.html" title="@active_if"
-             >next</a> |</li>
-        <li class="right" >
-          <a href="jobs_limit.html" title="@jobs_limit"
-             >previous</a> |</li>
-        Ruffus v. 2.5
-            <li><a href="../index.html">Home</a> | </li>
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-            <li><a href="../installation.html">Install</a>  | </li>
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-            <li><a href="../history.html">Latest Changes</a> » </li>
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-    <div class="footer">
-        © Copyright 2009-2013 Leo Goodstadt.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
-    </div>
-  </body>
-</html>
\ No newline at end of file
diff --git a/doc/_build/html/decorators/product.html b/doc/_build/html/decorators/product.html
deleted file mode 100644
index 098d430..0000000
--- a/doc/_build/html/decorators/product.html
+++ /dev/null
@@ -1,393 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>@product — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="../_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
-        VERSION:     '2.5',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true
-      };
-    </script>
-    <script type="text/javascript" src="../_static/jquery.js"></script>
-    <script type="text/javascript" src="../_static/underscore.js"></script>
-    <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <link rel="top" title="ruffus 2.5 documentation" href="../index.html" />
-    <link rel="next" title="@permutations" href="permutations.html" />
-    <link rel="prev" title="@follows" href="follows.html" /> 
-  </head>
-  <body>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="permutations.html" title="@permutations"
-             accesskey="N">next</a> |</li>
-        <li class="right" >
-          <a href="follows.html" title="@follows"
-             accesskey="P">previous</a> |</li>
-        Ruffus v. 2.5
-            <li><a href="../index.html">Home</a> | </li>
-            <li><a href="../contents.html">Contents</a> | </li>
-            <li><a href="../installation.html">Install</a>  | </li>
-            <li><a href="../tutorials/new_tutorial/introduction.html">Manual</a>  / </li>
-            <li><a href="../tutorials/new_tutorial/manual_contents.html">(TOC)</a>  | </li>
-            <li><a href="../faq.html">FAQ</a>  | </li>
-            <li><a href="../cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="../tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="../gallery.html">Gallery</a> |  </li>
-            <li><a href="../history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <span class="target" id="decorators-product"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="product">
-<h1>@product<a class="headerlink" href="#product" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="product-tasks-or-file-names-formatter-matching-formatter-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters">
-<h2><em>@product</em> ( <a class="reference internal" href="#decorators-product-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a><em>(</em><a class="reference internal" href="#decorators-product-matching-formatter"><cite>matching_formatter</cite></a><em>)</em>, [<a class="reference internal" href="#decorators-product-tasks-or-file-names"><cite>tasks_or_file_names</cite></a [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>Generates the Cartesian <strong>product</strong>, i.e. all vs all comparisons, between sets of input files.</p>
-<p>The effect is analogous to the python <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.product">itertools</a>
-function of the same name, i.e. a nested for loop.</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">product</span>
-<span class="hll"><span class="gp">>>> </span><span class="c"># product('ABC', 'XYZ') --> AX AY AZ BX BY BZ CX CY CZ</span>
-</span><span class="gp">>>> </span><span class="p">[</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">product</span><span class="p">(</span><span class="s">'ABC'</span><span class="p">,</span> <span class="s">'XYZ'</span><span class="p">)]</span>
-<span class="go">['AX', 'AY', 'AZ', 'BX', 'BY', 'BZ', 'CX', 'CY', 'CZ']</span>
-</pre></div>
-</div>
-<p>Only out of date tasks (comparing input and output files) will be run</p>
-<p>Output file names and strings in the extra parameters
-are determined from <a class="reference internal" href="#decorators-product-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of up stream tasks, or a list of file names, after string replacement via
-<a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a>.</p>
-<p>The replacement strings require an extra level of indirection to refer to
-parsed components:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>The first level refers to which <em>set</em> of inputs (e.g. <strong>A,B</strong> or <strong>P,Q</strong> or <strong>X,Y</strong>
-in the following example.)</li>
-<li>The second level refers to which input file in any particular <em>set</em> of inputs.</li>
-</ol>
-</div></blockquote>
-<dl class="docutils">
-<dt>For example, <tt class="docutils literal"><span class="pre">'{basename[2][0]}'</span></tt> is the <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.basename">basename</a> for</dt>
-<dd><ul class="first last simple">
-<li>the third set of inputs (<strong>X,Y</strong>) and</li>
-<li>the first file name string in each <strong>Input</strong> of that set (<tt class="docutils literal"><span class="pre">"x.1_start"</span></tt> and <tt class="docutils literal"><span class="pre">"y.1_start"</span></tt>)</li>
-</ul>
-</dd>
-</dl>
-</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><p>Calculates the <strong>@product</strong> of <strong>A,B</strong> and <strong>P,Q</strong> and <strong>X, Y</strong> files</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="hll"><span class="c">#   Three sets of initial files</span>
-</span><span class="nd">@originate</span><span class="p">([</span> <span class="s">'a.start'</span><span class="p">,</span> <span class="s">'b.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ab</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="nd">@originate</span><span class="p">([</span> <span class="s">'p.start'</span><span class="p">,</span> <span class="s">'q.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_pq</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'x.1_start'</span><span class="p">,</span> <span class="s">'x.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'y.1_start'</span><span class="p">,</span> <span class="s">'y.2_start'</span><span class="p">]</span> <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_xy</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-<span class="hll">
-</span><span class="c">#   @product</span>
-<span class="hll"><span class="nd">@product</span><span class="p">(</span>   <span class="n">create_initial_files_ab</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 1</span>
-
-<span class="hll">            <span class="n">create_initial_files_pq</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 2</span>
-
-<span class="hll">            <span class="n">create_initial_files_xy</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 3</span>
-<span class="hll">
-</span><span class="hll">            <span class="s">"{path[0][0]}/"</span>                 <span class="c"># Output Replacement string</span>
-</span><span class="hll">            <span class="s">"{basename[0][0]}_vs_"</span>          <span class="c">#</span>
-</span><span class="hll">            <span class="s">"{basename[1][0]}_vs_"</span>          <span class="c">#</span>
-</span>            <span class="s">"{basename[2][0]}.product"</span><span class="p">,</span>     <span class="c">#</span>
-<span class="hll">
-</span>            <span class="s">"{path[0][0]}"</span><span class="p">,</span>                 <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-<span class="hll">
-</span><span class="hll">            <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>            <span class="c"># Extra parameter: basename for 1st set of files, 1st file name</span>
-</span><span class="hll">             <span class="s">"{basename[1][0]}"</span><span class="p">,</span>            <span class="c">#                               2nd</span>
-</span>             <span class="s">"{basename[2][0]}"</span><span class="p">,</span>            <span class="c">#                               3rd</span>
-             <span class="p">])</span>
-<span class="k">def</span> <span class="nf">product_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"# basenames      = "</span><span class="p">,</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-    <span class="k">print</span> <span class="s">"input_parameter  = "</span><span class="p">,</span> <span class="n">input_file</span>
-    <span class="k">print</span> <span class="s">"output_parameter = "</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a p x</span>
-<span class="go">input_parameter  =  ('a.start', 'p.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_p_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a p y</span>
-<span class="go">input_parameter  =  ('a.start', 'p.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_p_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a q x</span>
-<span class="go">input_parameter  =  ('a.start', 'q.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_q_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a q y</span>
-<span class="go">input_parameter  =  ('a.start', 'q.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_q_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b p x</span>
-<span class="go">input_parameter  =  ('b.start', 'p.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_p_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b p y</span>
-<span class="go">input_parameter  =  ('b.start', 'p.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_p_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b q x</span>
-<span class="go">input_parameter  =  ('b.start', 'q.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_q_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b q y</span>
-<span class="go">input_parameter  =  ('b.start', 'q.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_q_vs_y.product</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-product-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-product-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-product-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s) after string
-substitution</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-product-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">Optional extra parameters are passed to the functions after string
-substitution</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@product</a><ul>
-<li><a class="reference internal" href="#product-tasks-or-file-names-formatter-matching-formatter-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters"><em>@product</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">formatter</span></tt><em>(</em><cite>matching_formatter</cite><em>)</em>, [<cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">formatter</span></tt><em>(</em><cite>matching_forma [...]
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="follows.html"
-                        title="previous chapter">@follows</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="permutations.html"
-                        title="next chapter">@permutations</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../_sources/decorators/product.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
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-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
-            <li><a href="transform.html">@transform</a>                           </li>
-            <li><a href="merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="subdivide.html">@subdivide</a>                           </li>
-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="#">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
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-             >index</a></li>
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-             >next</a> |</li>
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-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
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-  </body>
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\ No newline at end of file
diff --git a/doc/_build/html/decorators/split.html b/doc/_build/html/decorators/split.html
deleted file mode 100644
index f2928ea..0000000
--- a/doc/_build/html/decorators/split.html
+++ /dev/null
@@ -1,295 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>@split — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="../_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    '../',
-        VERSION:     '2.5',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true
-      };
-    </script>
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-    <script type="text/javascript" src="../_static/underscore.js"></script>
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-    <link rel="top" title="ruffus 2.5 documentation" href="../index.html" />
-    <link rel="next" title="@transform" href="transform.html" />
-    <link rel="prev" title="@originate" href="originate.html" /> 
-  </head>
-  <body>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="transform.html" title="@transform"
-             accesskey="N">next</a> |</li>
-        <li class="right" >
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-        Ruffus v. 2.5
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-            <li><a href="../tutorials/new_tutorial/manual_contents.html">(TOC)</a>  | </li>
-            <li><a href="../faq.html">FAQ</a>  | </li>
-            <li><a href="../cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="../tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="../gallery.html">Gallery</a> |  </li>
-            <li><a href="../history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <span class="target" id="decorators-split"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="split">
-<h1>@split<a class="headerlink" href="#split" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="split-tasks-or-file-names-output-files-extra-parameters">
-<h2><em>@split</em> ( <a class="reference internal" href="#decorators-split-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="#decorators-split-output-files"><cite>output_files</cite></a>, [<a class="reference internal" href="#decorators-split-extra-parameters"><cite>extra_parameters</cite></a>,...]  )<a class="headerlink" href="#split-tasks-or-file-names-output-files-extra-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><div class="first last line-block">
-<div class="line">Splits a single set of input files into multiple output file names, where the number of
-output files may not be known beforehand.</div>
-<div class="line">Only out of date tasks (comparing input and output files) will be run</div>
-</div>
-</dd>
-</dl>
-<p><strong>Example</strong>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="s">"big_file"</span><span class="p">,</span> <span class="s">'*.little_files'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">split_big_to_small</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"input_file = </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">input_file</span>
-    <span class="k">print</span> <span class="s">"output_file = </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">output_file</span>
-</pre></div>
-</div>
-<p>.</p>
-<blockquote>
-<div><p>will produce:</p>
-<div class="highlight-python"><pre>input_file = big_file
-output_file = *.little_files</pre>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-split-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><p class="first">(Nested) list of file name strings (as in the example above).</p>
-<blockquote>
-<div><div class="line-block">
-<div class="line">File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</div>
-<div class="line">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></div>
-</div>
-</div></blockquote>
-</li>
-<li><p class="first">Task / list of tasks.</p>
-<blockquote>
-<div><p>File names are taken from the output of the specified task(s)</p>
-</div></blockquote>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-split-output-files">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_files</em></dt>
-<dd><p class="first">Specifies the resulting output file name(s).</p>
-<div class="line-block">
-<div class="line">These are used <strong>only</strong> to check if the task is up to date.</div>
-<div class="line">Normally you would use either a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> (e.g. <tt class="docutils literal"><span class="pre">*.little_files</span></tt> as above) or  a “sentinel file”
-to indicate that the task has completed successfully.</div>
-<div class="line">You can of course do both:</div>
-</div>
-<blockquote class="last">
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="s">"big_file"</span><span class="p">,</span> <span class="p">[</span><span class="s">"sentinel.file"</span><span class="p">,</span> <span class="s">"*.little_files"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">split_big_to_small</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-split-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt>[<em>extra_parameters, ...</em>]</dt>
-<dd><p class="first last">Any extra parameters are passed verbatim to the task function</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="split-with-regex-add-inputs-and-inputs">
-<h1>@split with <tt class="docutils literal"><span class="pre">regex(...)</span></tt>, <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt><a class="headerlink" href="#split-with-regex-add-inputs-and-inputs" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div>This deprecated syntax is a synonym for <a class="reference internal" href="subdivide.html#decorators-subdivide"><em>@subdivide</em></a>.</div></blockquote>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@split</a><ul>
-<li><a class="reference internal" href="#split-tasks-or-file-names-output-files-extra-parameters"><em>@split</em> ( <cite>tasks_or_file_names</cite>, <cite>output_files</cite>, [<cite>extra_parameters</cite>,...]  )</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#split-with-regex-add-inputs-and-inputs">@split with <tt class="docutils literal"><span class="pre">regex(...)</span></tt>, <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a></li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="originate.html"
-                        title="previous chapter">@originate</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="transform.html"
-                        title="next chapter">@transform</a></p>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
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-            <li><a href="subdivide.html">@subdivide</a>                           </li>
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-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
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-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
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-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../todo.html">Future plans</a>
-    </ul>
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-          <div class="body">
-            
-  <span class="target" id="decorators-subdivide"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="subdivide">
-<h1>@subdivide<a class="headerlink" href="#subdivide" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="subdivide-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-inputs-input-pattern-or-glob-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters">
-<h2><em>@subdivide</em> ( <a class="reference internal" href="#decorators-subdivide-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a><em>(</em><a class="reference internal" href="#decorators-subdivide-matching-regex"><cite>matching_regex</cite></a><em>)</em> |  <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a><em>(</em><a class [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><ul>
-<li><p class="first">Subdivides a set of <em>Inputs</em> each further into multiple <em>Outputs</em>.</p>
-</li>
-<li><p class="first"><strong>Many to Even More</strong> operator</p>
-</li>
-<li><p class="first">The number of files in each <em>Output</em> can be set at runtime by the use of globs</p>
-</li>
-<li><p class="first">Output file names are specified using the <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> or <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicators from <a class="reference internal" href="#decorators-subdivide-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of specified tasks, or a list of file names, or a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> matching pattern.</p>
-</li>
-<li><dl class="first docutils">
-<dt>Additional inputs or dependencies can be added dynamically to the task:</dt>
-<dd><p class="first"><a class="reference internal" href="indicator_objects.html#decorators-add-inputs"><em>add_inputs</em></a> nests the the original input parameters in a list before adding additional dependencies.</p>
-<p class="last"><a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a> replaces the original input parameters wholescale.</p>
-</dd>
-</dl>
-</li>
-<li><p class="first">Only out of date tasks (comparing input and output files) will be run.</p>
-</li>
-</ul>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The use of <strong>split</strong> is a synonym for subdivide is deprecated.</p>
-</div>
-</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">random</span> <span class="kn">import</span> <span class="n">randint</span>
-<span class="kn">from</span> <span class="nn">random</span> <span class="kn">import</span> <span class="n">os</span>
-
-<span class="nd">@originate</span><span class="p">([</span><span class="s">'0.start'</span><span class="p">,</span> <span class="s">'1.start'</span><span class="p">,</span> <span class="s">'2.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-        <span class="k">pass</span>
-
-
-<span class="c">#</span>
-<span class="hll"><span class="c">#   Subdivide each of 3 start files further into [NNN1, NNN2, NNN3] number of files</span>
-</span><span class="hll"><span class="c">#      where NNN1, NNN2, NNN3 are determined at run time</span>
-</span><span class="c">#</span>
-<span class="nd">@subdivide</span><span class="p">(</span><span class="n">create_files</span><span class="p">,</span> <span class="n">formatter</span><span class="p">(),</span>
-            <span class="s">"{path[0]}/{basename[0]}.*.step1"</span><span class="p">,</span>  <span class="c"># Output parameter: Glob matches any number of output file names</span>
-            <span class="s">"{path[0]}/{basename[0]}"</span><span class="p">)</span>          <span class="c"># Extra parameter:  Append to this for output file names</span>
-<span class="k">def</span> <span class="nf">subdivide_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">,</span> <span class="n">output_file_name_root</span><span class="p">):</span>
-    <span class="c">#</span>
-<span class="hll">    <span class="c">#   IMPORTANT: cleanup rubbish from previous run first</span>
-</span>    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">oo</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">oo</span><span class="p">)</span>
-    <span class="c">#   The number of output files is decided at run time</span>
-    <span class="n">number_of_output_files</span> <span class="o">=</span> <span class="n">randint</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span><span class="mi">4</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">ii</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">number_of_output_files</span><span class="p">):</span>
-        <span class="n">output_file_name</span> <span class="o">=</span> <span class="s">"{output_file_name_root}.{ii}.step1"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-            <span class="k">pass</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Each output of subdivide_files results in a separate job for downstream tasks</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">subdivide_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".step1"</span><span class="p">),</span> <span class="s">".step2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">analyse_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-        <span class="k">pass</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [None -> 0.start] completed</span>
-<span class="go">    Job  = [None -> 1.start] completed</span>
-<span class="go">    Job  = [None -> 2.start] completed</span>
-<span class="go">Completed Task = create_files</span>
-<span class="go">    Job  = [0.start -> 0.*.step1, 0] completed</span>
-<span class="go">    Job  = [1.start -> 1.*.step1, 1] completed</span>
-<span class="go">    Job  = [2.start -> 2.*.step1, 2] completed</span>
-<span class="go">Completed Task = subdivide_files</span>
-<span class="go">    Job  = [0.0.step1 -> 0.0.step2] completed</span>
-<span class="go">    Job  = [0.1.step1 -> 0.1.step2] completed</span>
-<span class="go">    Job  = [0.2.step1 -> 0.2.step2] completed</span>
-<span class="go">    Job  = [1.0.step1 -> 1.0.step2] completed</span>
-<span class="go">    Job  = [1.1.step1 -> 1.1.step2] completed</span>
-<span class="go">    Job  = [1.2.step1 -> 1.2.step2] completed</span>
-<span class="go">    Job  = [1.3.step1 -> 1.3.step2] completed</span>
-<span class="go">    Job  = [2.0.step1 -> 2.0.step2] completed</span>
-<span class="go">    Job  = [2.1.step1 -> 2.1.step2] completed</span>
-<span class="go">    Job  = [2.2.step1 -> 2.2.step2] completed</span>
-<span class="go">    Job  = [2.3.step1 -> 2.3.step2] completed</span>
-<span class="go">Completed Task = analyse_files</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-subdivide-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-subdivide-matching-regex">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_regex</em></dt>
-<dd><p class="first last">is a python regular expression string, which must be wrapped in
-a <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicator object
-See python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>
-documentation for details of regular expression syntax</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-subdivide-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-subdivide-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s). Can include glob patterns.
-Strings are subject to <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> or <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a>
-substitution.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-subdivide-input-pattern-or-glob">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>input_pattern</em></dt>
-<dd><p class="first">Specifies the resulting input(s) to each job.
-Must be wrapped in an <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a> or an <a class="reference internal" href="indicator_objects.html#decorators-add-inputs"><em>inputs</em></a> indicator object.</p>
-<p>Can be a:</p>
-<ol class="arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><p class="first">(Nested) list of file name strings.</p>
-</li>
-</ol>
-<p class="last">Strings are subject to <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> or <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> substitution.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-subdivide-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>extra_parameters</em></dt>
-<dd><p class="first last">Any extra parameters are consumed by the task function and not forwarded further down the pipeline.
-Strings are subject to <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> or <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a>
-substitution.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
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-
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-          </div>
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-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@subdivide</a><ul>
-<li><a class="reference internal" href="#subdivide-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-inputs-input-pattern-or-glob-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters"><em>@subdivide</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">regex</span></tt><em>(</em><cite>matching_regex</cite><em>)</em> |  <tt class="docutils literal"><span class="pre">formatter</span></tt><em>(</em><cite>matching_formatte [...]
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="merge.html"
-                        title="previous chapter">@merge</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="transform_ex.html"
-                        title="next chapter">@transform  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a></p>
-  <h3>This Page</h3>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
-            <li><a href="split.html">@split</a>                                   </li>
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-            <li><a href="transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="graphviz.html">@graphviz</a>                             </li>
-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="active_if.html">@active_if</a>                           </li>
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-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
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-
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-        <h4 >Pipeline functions</h4>
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-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
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-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-            
-  <span class="target" id="decorators-transform"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="transform">
-<h1>@transform<a class="headerlink" href="#transform" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="transform-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-output-pattern-extra-parameters">
-<h2><em>@transform</em> ( <a class="reference internal" href="#decorators-transform-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a><em>(</em><a class="reference internal" href="#decorators-transform-suffix-string"><cite>suffix_string</cite></a><em>)</em>| <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a><em>(</em><a class="referenc [...]
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">Applies the task function to transform data from input to output files.</p>
-<p>Output file names are specified from <a class="reference internal" href="#decorators-transform-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of specified tasks, or a list of file names, or a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> matching pattern.</p>
-<p>String replacement occurs either through suffix matches via <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a> or
-the <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> or <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicators.</p>
-<p class="last">Only out of date tasks (comparing input and output files) will be run</p>
-</dd>
-</dl>
-<p><strong>Simple Example</strong></p>
-<blockquote>
-<div><p>Transforms <tt class="docutils literal"><span class="pre">*.c</span></tt> to <tt class="docutils literal"><span class="pre">*.o</span></tt>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>Same example with a regular expression:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">regex</span><span class="p">(</span><span class="s">r".c$"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>Both result in the following function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># 1.c -> 1.o</span>
-<span class="c"># 2.c -> 2.o</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"1.o"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"2.o"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<p><strong>Escaping regular expression patterns</strong></p>
-<blockquote>
-<div>A string like <tt class="docutils literal"><span class="pre">universal.h</span></tt> in <tt class="docutils literal"><span class="pre">add_inputs</span></tt> will added <em>as is</em>.
-<tt class="docutils literal"><span class="pre">r"\1.h"</span></tt>, however, performs suffix substitution, with the special form <tt class="docutils literal"><span class="pre">r"\1"</span></tt> matching everything up to the suffix.
-Remember to ‘escape’ <tt class="docutils literal"><span class="pre">r"\1"</span></tt> otherwise Ruffus will complain and throw an Exception to remind you.
-The most convenient way is to use a python “raw” string.</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-transform-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-suffix-string">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>suffix_string</em></dt>
-<dd><p class="first">must be wrapped in a <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a> indicator object.
-The end of each input file name which matches <tt class="docutils literal"><span class="pre">suffix_string</span></tt> will be replaced by <tt class="docutils literal"><span class="pre">output_pattern</span></tt>.</p>
-<p>Input file names which do not match suffix_string will be ignored</p>
-<p>The non-suffix part of the match can be referred to using the <tt class="docutils literal"><span class="pre">"\1"</span></tt> pattern. This
-can be useful for putting the output in different directory, for example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="s">r"my_path/\1.o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>This results in the following function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># 1.c -> my_path/1.o</span>
-<span class="c"># 2.c -> my_path/2.o</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"my_path/1.o"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"my_path/2.o"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>For convenience and visual clarity, the  <tt class="docutils literal"><span class="pre">"\1"</span></tt> can be omitted from the output parameter.
-However, the <tt class="docutils literal"><span class="pre">"\1"</span></tt> is mandatory for string substitutions in additional parameters,</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="p">[</span><span class="s">r"\1.o"</span><span class="p">,</span> <span class="s">".o"</span><span  [...]
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>Results in the following function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">(</span><span class="s">"1.c"</span><span class="p">,</span> <span class="p">[</span><span class="s">"1.o"</span><span class="p">,</span> <span class="s">"1.o"</span><span class="p">],</span> <span class="s">"Compiling 1"</span><span class="p">,</span> <span class="s">"verbatim"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"2.c"</span><span class="p">,</span> <span class="p">[</span><span class="s">"2.o"</span><span class="p">,</span> <span class="s">"2.o"</span><span class="p">],</span> <span class="s">"Compiling 2"</span><span class="p">,</span> <span class="s">"verbatim"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p class="last">Since r”1” is optional for the output parameter, <tt class="docutils literal"><span class="pre">"\1.o"</span></tt> and <tt class="docutils literal"><span class="pre">".o"</span></tt> are equivalent.
-However, strings in other parameters which do not contain r”1” will be included verbatim, much
-like the string <tt class="docutils literal"><span class="pre">"verbatim"</span></tt> in the above example.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-matching-regex">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_regex</em></dt>
-<dd><p class="first last">is a python regular expression string, which must be wrapped in
-a <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicator object
-See python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>
-documentation for details of regular expression syntax
-Each output file name is created using regular expression substitution with <tt class="docutils literal"><span class="pre">output_pattern</span></tt></p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s).</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt>[<em>extra_parameters, ...</em>]</dt>
-<dd><p class="first">Any extra parameters are passed to the task function.</p>
-<p>If <tt class="docutils literal"><span class="pre">regex(matching_regex)</span></tt> or <tt class="docutils literal"><span class="pre">formatter(...)`</span></tt> is used, then substitution
-is first applied to (even nested) string parameters. Other data types are passed
-verbatim.</p>
-<p>For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"a.c"</span><span class="p">,</span> <span class="s">"b.c"</span><span class="p">],</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*).c"</span><span class="p">),</span> <span class="s">r"\1.o"</span><span class="p">,</span> <span class="s">r"\1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>will result in the following function calls:</p>
-<div class="last highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">(</span><span class="s">"a.c"</span><span class="p">,</span> <span class="s">"a.o"</span><span class="p">,</span> <span class="s">"a"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"b.c"</span><span class="p">,</span> <span class="s">"b.o"</span><span class="p">,</span> <span class="s">"b"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<p>See <a class="reference internal" href="transform_ex.html#decorators-transform-ex"><em>here</em></a> for more advanced uses of transform.</p>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@transform</a><ul>
-<li><a class="reference internal" href="#transform-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-output-pattern-extra-parameters"><em>@transform</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">suffix</span></tt><em>(</em><cite>suffix_string</cite><em>)</em>| <tt class="docutils literal"><span class="pre">regex</span></tt><em>(</em><cite>matching_regex</cite><em>)</em> |  <tt class="docutils literal"> [...]
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="split.html"
-                        title="previous chapter">@split</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="merge.html"
-                        title="next chapter">@merge</a></p>
-  <h3>This Page</h3>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
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-            <li><a href="subdivide.html">@subdivide</a>                           </li>
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-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
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-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="product.html">@product </a>                              </li>
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-        <h4 >Pipeline functions</h4>
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-            
-  <span class="target" id="decorators-transform-ex"></span><div class="admonition seealso" id="index-0">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="decorators.html#decorators"><em>Decorators</em></a> for more decorators</li>
-</ul>
-</div>
-<div class="section" id="transform-with-add-inputs-and-inputs">
-<h1>@transform  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt><a class="headerlink" href="#transform-with-add-inputs-and-inputs" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="transform-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-inputs-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters">
-<h2><em>@transform</em> ( <a class="reference internal" href="#decorators-transform-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a><em>(</em><a class="reference internal" href="#decorators-transform-suffix-string"><cite>suffix_string</cite></a><em>)</em>| <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a><em>(</em><a class="referenc [...]
-<blockquote>
-<div><dl class="docutils">
-<dt><strong>Purpose:</strong></dt>
-<dd><p class="first">This variant of <tt class="docutils literal"><span class="pre">@transform</span></tt> allows additional inputs or dependencies to be added
-dynamically to the task.</p>
-<p>Output file names and strings in the extra parameters
-are determined from <a class="reference internal" href="#decorators-transform-tasks-or-file-names"><cite>tasks_or_file_names</cite></a>, i.e. from the output
-of up stream tasks, or a list of file names.</p>
-<p>This variant of <tt class="docutils literal"><span class="pre">@transform</span></tt> allows input file names to be derived in the same way.</p>
-<p>String replacement occurs either through suffix matches via <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a> or
-the <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> or <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicators.</p>
-<p><tt class="docutils literal"><span class="pre">@collate</span></tt> groups together all <strong>Input</strong> which result in identical <strong>Output</strong> and <strong>extra</strong>
-parameters.</p>
-<p>It is a <strong>many to fewer</strong> operation.</p>
-<p><a class="reference internal" href="indicator_objects.html#decorators-add-inputs"><em>add_inputs</em></a> nests the the original input parameters in a list before adding additional dependencies.</p>
-<p><a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a> replaces the original input parameters wholescale.</p>
-<p class="last">Only out of date tasks (comparing input and output files) will be run</p>
-</dd>
-</dl>
-<p><strong>Example of</strong> <a class="reference internal" href="indicator_objects.html#decorators-add-inputs"><em>add_inputs</em></a></p>
-<blockquote>
-<div><p>A common task in compiling C code is to include the corresponding header file for the source.</p>
-<dl class="docutils">
-<dt>To compile <tt class="docutils literal"><span class="pre">*.c</span></tt> to <tt class="docutils literal"><span class="pre">*.o</span></tt>, adding <tt class="docutils literal"><span class="pre">*.h</span></tt> and the common header <tt class="docutils literal"><span class="pre">universal.h</span></tt>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"2.c"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="n">add_inputs</span><span class="p">([</span><span class="s">r"\1.h"</span><span class="p">,</ [...]
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-<dt>This will result in the following functional calls:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"1.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">],</span> <span class="s">"1.o"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">([</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"2.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">],</span> <span class="s">"2.o"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-<p><strong>Example of</strong> <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a></p>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">inputs(...)</span></tt> allows the original input parameters to be replaced wholescale.</p>
-<dl class="docutils">
-<dt>This can be seen in the following example:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span>    <span class="p">[</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"A.c"</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
-                <span class="p">[</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"B.c"</span><span class="p">,</span> <span class="s">"C.c"</span><span class="p">,</span> <span class="mi">3</span><span class="p">]],</span>
-                <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="n">inputs</span><span class="p">([</span><span class="s">r"\1.py"</span><span class="p">,</span> <span class="s">"docs.rst"</span><span class="p">]),</span>  <span class="s">".pyc"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</dd>
-<dt>This will result in the following functional calls:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">([</span><span class="s">"1.py"</span><span class="p">,</span> <span class="s">"docs.rst"</span><span class="p">],</span> <span class="s">"1.pyc"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">([</span><span class="s">"2.py"</span><span class="p">,</span> <span class="s">"docs.rst"</span><span class="p">],</span> <span class="s">"2.pyc"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="decorators-transform-tasks-or-file-names">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>tasks_or_file_names</em></dt>
-<dd><p class="first">can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><dl class="first last docutils">
-<dt>File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.</dt>
-<dd><p class="first last">E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-suffix-string">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>suffix_string</em></dt>
-<dd><p class="first">must be wrapped in a <a class="reference internal" href="indicator_objects.html#decorators-suffix"><em>suffix</em></a> indicator object.
-The end of each file name which matches suffix_string will be replaced by <cite>output_pattern</cite>.
-Thus:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"a.c"</span><span class="p">,</span> <span class="s">"b.c"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>will result in the following function calls:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">(</span><span class="s">"a.c"</span><span class="p">,</span> <span class="s">"a.o"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">(</span><span class="s">"b.c"</span><span class="p">,</span> <span class="s">"b.o"</span><span class="p">)</span>
-</pre></div>
-</div>
-<p class="last">File names which do not match suffix_string will be ignored</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-matching-regex">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_regex</em></dt>
-<dd><p class="first last">is a python regular expression string, which must be wrapped in
-a <a class="reference internal" href="indicator_objects.html#decorators-regex"><em>regex</em></a> indicator object
-See python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>
-documentation for details of regular expression syntax
-Each output file name is created using regular expression substitution with <tt class="docutils literal"><span class="pre">output_pattern</span></tt></p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-matching-formatter">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>matching_formatter</em></dt>
-<dd><p class="first last">a <a class="reference internal" href="indicator_objects.html#decorators-formatter"><em>formatter</em></a> indicator object containing optionally
-a  python <a class="reference external" href="http://docs.python.org/library/re.html">regular expression (re)</a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-input-pattern-or-glob">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>input_pattern</em></dt>
-<dd><p class="first">Specifies the resulting input(s) to each job.
-Must be wrapped in an <a class="reference internal" href="indicator_objects.html#decorators-inputs"><em>inputs</em></a> or an <a class="reference internal" href="indicator_objects.html#decorators-add-inputs"><em>inputs</em></a> indicator object.</p>
-<p>Can be a:</p>
-<ol class="last arabic">
-<li><dl class="first docutils">
-<dt>Task / list of tasks (as in the example above).</dt>
-<dd><p class="first last">File names are taken from the output of the specified task(s)</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>(Nested) list of file name strings.</dt>
-<dd><p class="first last">Strings will be subject to substitution.
-File names containing <tt class="docutils literal"><span class="pre">*[]?</span></tt> will be expanded as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>.
-E.g.:<tt class="docutils literal"><span class="pre">"a.*"</span> <span class="pre">=></span> <span class="pre">"a.1",</span> <span class="pre">"a.2"</span></tt></p>
-</dd>
-</dl>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-output-pattern">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_pattern</em></dt>
-<dd><p class="first last">Specifies the resulting output file name(s).</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="decorators-transform-extra-parameters">
-<div><ul>
-<li><dl class="first docutils">
-<dt>[<em>extra_parameters, ...</em>]</dt>
-<dd><p class="first">Any extra parameters are passed to the task function.</p>
-<p>If the <tt class="docutils literal"><span class="pre">regex(...)</span></tt> or <tt class="docutils literal"><span class="pre">formatter(...)</span></tt> parameter is used, then substitution
-is first applied to (even nested) string parameters. Other data types are passed
-verbatim.</p>
-<p>For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"a.c"</span><span class="p">,</span> <span class="s">"b.c"</span><span class="p">],</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*).c"</span><span class="p">),</span> <span class="n">inputs</span><span class="p">(</span><span class="s">r"\1.c"</span><span class="p">,</span> <span clas [...]
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">file_name_root</span><span class="p">):</span>
-    <span class="c"># do something here</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>will result in the following function calls:</p>
-<div class="last highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">([</span><span class="s">"1.c"</span><span class="p">,</span> <span class="s">"1.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">],</span> <span class="s">"1.o"</span><span class="p">,</span> <span class="s">"1"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">([</span><span class="s">"2.c"</span><span class="p">,</span> <span class="s">"2.h"</span><span class="p">,</span> <span class="s">"universal.h"</span><span class="p">],</span> <span class="s">"2.o"</span><span class="p">,</span> <span class="s">"2"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<p>See <a class="reference internal" href="transform.html#decorators-transform"><em>here</em></a> for more straightforward ways to use transform.</p>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">@transform  with <tt class="docutils literal"><span class="pre">add_inputs</span></tt> and <tt class="docutils literal"><span class="pre">inputs</span></tt></a><ul>
-<li><a class="reference internal" href="#transform-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-inputs-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters"><em>@transform</em> ( <cite>tasks_or_file_names</cite>, <tt class="docutils literal"><span class="pre">suffix</span></tt><em>(</em><cite>suffix_string</cite><em>)</em>| <tt class="docutils literal"><span class="pre">regex</span></tt><em>(</em><cite>matching_regex</cite><em [...]
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="subdivide.html"
-                        title="previous chapter">@subdivide</a></p>
-  <h4>Next topic</h4>
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-                        title="next chapter">@collate</a></p>
-  <h3>This Page</h3>
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-           rel="nofollow">Show Source</a></li>
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-    Enter search terms or a module, class or function name.
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="originate.html">@originate</a>                           </li>
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-            <li><a href="collate.html">@collate</a>                               </li>
-            <li><a href="collate_ex.html">@collate (add_inputs)</a>               </li>
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-            <li><a href="mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="posttask.html">@posttask touch_file</a>                  </li>
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-            <li><a href="jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="product.html">@product </a>                              </li>
-            <li><a href="permutations.html">@permutations </a>                    </li>
-            <li><a href="combinations.html">@combinations </a>                    </li>
-            <li><a href="combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="parallel.html">@parallel</a>                             </li>
-            <li><a href="check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
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-        <h4 ><a href="indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
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-            
-  <div class="section" id="design-architecture">
-<span id="index-0"></span><h1>Design & Architecture<a class="headerlink" href="#design-architecture" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><p>The <em>ruffus</em> module has the following design goals:</p>
-<blockquote>
-<div><ul class="simple">
-<li>Simplicity.</li>
-<li>Intuitive</li>
-<li>Lightweight</li>
-<li>Unintrusive</li>
-<li>Flexible/Powerful</li>
-</ul>
-</div></blockquote>
-<p>Computational pipelines, especially in science, are best thought of in terms of data
-flowing through successive, dependent stages (<strong>ruffus</strong> calls these <a class="reference internal" href="glossary.html#term-task"><em class="xref std std-term">task</em></a>s).
-Traditionally, files have been used to
-link pipelined stages together. This means that computational pipelines can be managed
-using traditional software construction (<cite>build</cite>) systems.</p>
-</div></blockquote>
-<div class="section" id="gnu-make">
-<h2><cite>GNU Make</cite><a class="headerlink" href="#gnu-make" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The grand-daddy of these is UNIX <a class="reference external" href="http://en.wikipedia.org/wiki/Make_(software)">make</a>.
-<a class="reference external" href="http://www.gnu.org/software/make/">GNU make</a> is ubiquitous in the linux world for
-installing and compiling software.
-It has been widely used to build computational pipelines because it supports:</p>
-<ul class="simple">
-<li>Stopping and restarting computational processes</li>
-<li>Running multiple, even thousands of jobs in parallel</li>
-</ul>
-</div></blockquote>
-<div class="section" id="deficiencies-of-make-gmake">
-<span id="design-make-syntax-ugly"></span><h3>Deficiencies of <cite>make</cite> / <cite>gmake</cite><a class="headerlink" href="#deficiencies-of-make-gmake" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div>However, make and <a class="reference external" href="http://www.gnu.org/software/make/">GNU make</a> use a specialised (domain-specific)
-language, which has is been much criticised because of poor support for modern
-programming languages features, such as variable scope, pattern matching, debugging.
-Make scripts require large amounts of often obscure shell scripting
-and makefiles can quickly become unmaintainable.</div></blockquote>
-</div>
-</div>
-<div class="section" id="scons-rake-and-other-make-alternatives">
-<span id="design-scons-and-rake"></span><h2><cite>Scons</cite>, <cite>Rake</cite> and other <cite>Make</cite> alternatives<a class="headerlink" href="#scons-rake-and-other-make-alternatives" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Many attempts have been made to produce a more modern version of make, with less of its
-historical baggage. These include the Java-based <a class="reference external" href="http://ant.apache.org/">Apache ant</a> which is specified in xml.</p>
-<p>More interesting are a new breed of build systems whose scripts are written in modern programming
-languages, rather than a specially-invented “build” specificiation syntax.
-These include the Python <a class="reference external" href="http://www.scons.org/">scons</a>, Ruby <a class="reference external" href="http://rake.rubyforge.org/">rake</a> and
-its python port <a class="reference external" href="http://packages.python.org/Smithy/">Smithy</a>.</p>
-<p>The great advantages are that computation pipelines do not need to be artificially parcelled out
-between (the often second-class) workflow management code, and the logic which does the real computation
-in the pipeline. It also means that workflow management can use all the standard language and library
-features, for example, to read in directories, match file names using regular expressions and so on.</p>
-<p><strong>Ruffus</strong> is much like scons in that the modern dynamic programming language python is used seamlessly
-throughout its pipeline scripts.</p>
-</div></blockquote>
-<div class="section" id="implicit-dependencies-disadvantages-of-make-scons-rake">
-<span id="design-implicit-dependencies"></span><h3>Implicit dependencies: disadvantages of <cite>make</cite> / <cite>scons</cite> / <cite>rake</cite><a class="headerlink" href="#implicit-dependencies-disadvantages-of-make-scons-rake" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Although Python <a class="reference external" href="http://www.scons.org/">scons</a> and Ruby <a class="reference external" href="http://rake.rubyforge.org/">rake</a>
-are in many ways more powerful and easier to use for building software, they are still an
-imperfect fit to the world of computational pipelines.</p>
-<p>This is a result of the way dependencies are specified, an essential part of their design inherited
-from <a class="reference external" href="http://www.gnu.org/software/make/">GNU make</a>.</p>
-<p>The order of operations in all of these tools is specified in a <em>declarative</em> rather than
-<em>imperative</em> manner. This means that the sequence of steps that a build should take are
-not spelled out explicity and directly. Instead recipes are provided for turning input files
-of each type to another.</p>
-<p>So, for example, knowing that <tt class="docutils literal"><span class="pre">a->b</span></tt>, <tt class="docutils literal"><span class="pre">b->c</span></tt>, <tt class="docutils literal"><span class="pre">c->d</span></tt>, the build
-system can infer how to get from <tt class="docutils literal"><span class="pre">a</span></tt> to <tt class="docutils literal"><span class="pre">d</span></tt> by performing the necessary operations in the correct order.</p>
-<dl class="docutils">
-<dt>This is immensely powerful for three reasons:</dt>
-<dd><ol class="first last arabic">
-<li><p class="first">The plumbing, such as dependency checking, passing output
-from one stage to another, are handled automatically by the build system. (This is the whole point!)</p>
-</li>
-<li><p class="first">The same <em>recipe</em> can be re-used at different points in the build.</p>
-</li>
-<li><div class="first line-block">
-<div class="line">Intermediate files do not need to be retained.</div>
-<div class="line">Given the automatic inference that <tt class="docutils literal"><span class="pre">a->b->c->d</span></tt>,
-we don’t need to keep <tt class="docutils literal"><span class="pre">b</span></tt> and <tt class="docutils literal"><span class="pre">c</span></tt> files around once <tt class="docutils literal"><span class="pre">d</span></tt> has been produced.</div>
-<div class="line"><br /></div>
-</div>
-</li>
-</ol>
-</dd>
-</dl>
-<p>The disadvantage is that because stages are specified only indirectly, in terms of
-file name matches, the flow through a complex build or a pipeline can be difficult to trace, and nigh
-impossible to debug when there are problems.</p>
-</div></blockquote>
-</div>
-<div class="section" id="explicit-dependencies-in-ruffus">
-<span id="design-explicit-dependencies-in-ruffus"></span><h3>Explicit dependencies in <cite>Ruffus</cite><a class="headerlink" href="#explicit-dependencies-in-ruffus" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><strong>Ruffus</strong> takes a different approach. The order of operations is specified explicitly rather than inferred
-indirectly from the input and output types. So, for example, we would explicitly specify three successive and
-linked operations <tt class="docutils literal"><span class="pre">a->b</span></tt>, <tt class="docutils literal"><span class="pre">b->c</span></tt>, <tt class="docutils literal"><span class="pre">c->d</span></tt>. The build system knows that the operations always proceed in
-this order.</p>
-<p>Looking at a <strong>Ruffus</strong> script, it is always clear immediately what is the succession of computational steps
-which will be taken.</p>
-<p><strong>Ruffus</strong> values clarity over syntactic cleverness.</p>
-</div></blockquote>
-</div>
-<div class="section" id="static-dependencies-what-make-scons-rake-can-t-do-easily">
-<span id="design-static-dependencies"></span><h3>Static dependencies: What <cite>make</cite> / <cite>scons</cite> / <cite>rake</cite> can’t do (easily)<a class="headerlink" href="#static-dependencies-what-make-scons-rake-can-t-do-easily" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><a class="reference external" href="http://www.gnu.org/software/make/">GNU make</a>, <a class="reference external" href="http://www.scons.org/">scons</a> and <a class="reference external" href="http://rake.rubyforge.org/">rake</a>
-work by infer a static dependency (diacyclic) graph between all the files which
-are used by a computational pipeline. These tools locate the target that they are supposed
-to build and work backward through the dependency graph from that target,
-rebuilding anything that is out of date.This is perfect for building software,
-where the list of files data files can be computed <strong>statically</strong> at the beginning of the build.</p>
-<p>This is not ideal matches for scientific computational pipelines because:</p>
-<blockquote>
-<div><ul>
-<li><div class="first line-block">
-<div class="line">Though the <em>stages</em> of a pipeline (i.e. <cite>compile</cite> or <cite>DNA alignment</cite>) are
-invariably well-specified in advance, the number of
-operations (<em>job</em>s) involved at each stage may not be.</div>
-<div class="line"><br /></div>
-</div>
-</li>
-<li><div class="first line-block">
-<div class="line">A common approach is to break up large data sets into manageable chunks which
-can be operated on in parallel in computational clusters or farms
-(See <a class="reference external" href="http://en.wikipedia.org/wiki/Embarrassingly_parallel">embarassingly parallel problems</a>).</div>
-<div class="line">This means that the number of parallel operations or jobs varies with the data (the number of manageable chunks),
-and dependency trees cannot be calculated statically beforehand.</div>
-<div class="line"><br /></div>
-</div>
-</li>
-</ul>
-</div></blockquote>
-<p>Computational pipelines require <strong>dynamic</strong> dependencies which are not calculated up-front, but
-at each stage of the pipeline</p>
-<p>This is a <em>known</em> issue with traditional build systems each of which has partial strategies to work around
-this problem:</p>
-<blockquote>
-<div><ul class="simple">
-<li>gmake always builds the dependencies when first invoked, so dynamic dependencies require (complex!) recursive calls to gmake</li>
-<li><a class="reference external" href="http://objectmix.com/ruby/759716-rake-dependencies-unknown-prior-running-tasks-2.html">Rake dependencies unknown prior to running tasks</a>.</li>
-<li><a class="reference external" href="http://www.scons.org/wiki/DynamicSourceGenerator">Scons: Using a Source Generator to Add Targets Dynamically</a></li>
-</ul>
-</div></blockquote>
-<p><strong>Ruffus</strong> explicitly and straightforwardly handles tasks which produce an indeterminate (i.e. runtime dependent)
-number of output, using its <strong>@split</strong>, <strong>@transform</strong>, <strong>merge</strong> function annotations.</p>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="managing-pipelines-stage-by-stage-using-ruffus">
-<h2>Managing pipelines stage-by-stage using <strong>Ruffus</strong><a class="headerlink" href="#managing-pipelines-stage-by-stage-using-ruffus" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>Ruffus</strong> manages pipeline stages directly.</p>
-<blockquote>
-<div><ol class="arabic">
-<li><div class="first line-block">
-<div class="line">The computational operations for each stage of the pipeline are written by you, in
-separate python functions.</div>
-<div class="line">(These correspond to <a class="reference external" href="http://www.gnu.org/software/make/manual/make.html#Pattern-Rules">gmake pattern rules</a>)</div>
-<div class="line"><br /></div>
-</div>
-</li>
-<li><div class="first line-block">
-<div class="line">The dependencies between pipeline stages (python functions) are specified up-front.</div>
-<div class="line">These can be displayed as a flow chart.</div>
-</div>
-<img alt="_images/front_page_flowchart.png" src="_images/front_page_flowchart.png" />
-</li>
-<li><p class="first"><strong>Ruffus</strong> makes sure pipeline stage functions are called in the right order,
-with the right parameters, running in parallel using multiprocessing if necessary.</p>
-</li>
-<li><p class="first">Data file timestamps can be used to automatically determine if all or any parts
-of the pipeline are out-of-date and need to be rerun.</p>
-</li>
-<li><p class="first">Separate pipeline stages, and operations within each pipeline stage,
-can be run in parallel provided they are not inter-dependent.</p>
-</li>
-</ol>
-</div></blockquote>
-<p>Another way of looking at this is that <strong>ruffus</strong> re-constructs datafile dependencies dynamically
-on-the-fly when it gets to each stage of the pipeline, giving much more flexibility.</p>
-</div></blockquote>
-<div class="section" id="disadvantages-of-the-ruffus-design">
-<h3>Disadvantages of the Ruffus design<a class="headerlink" href="#disadvantages-of-the-ruffus-design" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Are there any disadvantages to this trade-off for additional clarity?</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Each pipeline stage needs to take the right input and output. For example if we specified the
-steps in the wrong order: <tt class="docutils literal"><span class="pre">a->b</span></tt>, <tt class="docutils literal"><span class="pre">c->d</span></tt>, <tt class="docutils literal"><span class="pre">b->c</span></tt>, then no useful output would be produced.</li>
-<li>We cannot re-use the same recipes in different parts of the pipeline</li>
-<li>Intermediate files need to be retained.</li>
-</ol>
-</div></blockquote>
-<p>In our experience, it is always obvious when pipeline operations are in the wrong order, precisely because the
-order of computation is the very essense of the design of each pipeline. Ruffus produces extra diagnostics when
-no output is created in a pipeline stage (usually happens for incorrectly specified regular expressions.)</p>
-<p>Re-use of recipes is as simple as an extra call to common function code.</p>
-<p>Finally, some users have proposed future enhancements to <strong>Ruffus</strong> to handle unnecessary temporary / intermediate files.</p>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="alternatives-to-ruffus">
-<span id="index-1"></span><h2>Alternatives to <strong>Ruffus</strong><a class="headerlink" href="#alternatives-to-ruffus" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>A comparison of more make-like tools is available from <a class="reference external" href="http://biowiki.org/MakeComparison">Ian Holmes’ group</a>.</p>
-<p>Build systems include:</p>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference external" href="http://www.gnu.org/software/make/">GNU make</a></li>
-<li><a class="reference external" href="http://www.scons.org/">scons</a></li>
-<li><a class="reference external" href="http://ant.apache.org/">ant</a></li>
-<li><a class="reference external" href="http://rake.rubyforge.org/">rake</a></li>
-</ul>
-</div></blockquote>
-<p>There are also complete workload managements systems such as Condor.
-Various bioinformatics pipelines are also available, including that used by the
-leading genome annotation website Ensembl, Pegasys, GPIPE, Taverna, Wildfire, MOWserv,
-Triana, Cyrille2 etc. These all are either hardwired to specific databases, and tasks,
-or have steep learning curves for both the scientist/developer and the IT system
-administrators.</p>
-<p><strong>Ruffus</strong> is designed to be lightweight and unintrusive enough to use for writing pipelines
-with just 10 lines of code.</p>
-</div></blockquote>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<p><strong>Bioinformatics workload managements systems</strong></p>
-<blockquote class="last">
-<div><dl class="docutils">
-<dt>Condor:</dt>
-<dd><a class="reference external" href="http://www.cs.wisc.edu/condor/description.html">http://www.cs.wisc.edu/condor/description.html</a></dd>
-<dt>Ensembl Analysis pipeline:</dt>
-<dd><a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/15123589">http://www.ncbi.nlm.nih.gov/pubmed/15123589</a></dd>
-<dt>Pegasys:</dt>
-<dd><a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/15096276">http://www.ncbi.nlm.nih.gov/pubmed/15096276</a></dd>
-<dt>GPIPE:</dt>
-<dd><a class="reference external" href="http://www.biomedcentral.com/pubmed/15096276">http://www.biomedcentral.com/pubmed/15096276</a></dd>
-<dt>Taverna:</dt>
-<dd><a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/15201187">http://www.ncbi.nlm.nih.gov/pubmed/15201187</a></dd>
-<dt>Wildfire:</dt>
-<dd><a class="reference external" href="http://www.biomedcentral.com/pubmed/15788106">http://www.biomedcentral.com/pubmed/15788106</a></dd>
-<dt>MOWserv:</dt>
-<dd><a class="reference external" href="http://www.biomedcentral.com/pubmed/16257987">http://www.biomedcentral.com/pubmed/16257987</a></dd>
-<dt>Triana:</dt>
-<dd><a class="reference external" href="http://dx.doi.org/10.1007/s10723-005-9007-3">http://dx.doi.org/10.1007/s10723-005-9007-3</a></dd>
-<dt>Cyrille2:</dt>
-<dd><a class="reference external" href="http://www.biomedcentral.com/1471-2105/9/96">http://www.biomedcentral.com/1471-2105/9/96</a></dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="acknowledgements">
-<span id="index-2"></span><h3>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul>
-<li><p class="first">Bruce Eckel’s insightful article on
-<a class="reference external" href="http://www.artima.com/weblogs/viewpost.jsp?thread=241209">A Decorator Based Build System</a>
-was the obvious inspiration for the use of decorators in <em>Ruffus</em>.</p>
-<dl class="docutils">
-<dt>The rest of the <em>Ruffus</em> takes uses a different approach. In particular:</dt>
-<dd><ol class="first last arabic">
-<li><p class="first"><em>Ruffus</em> uses task-based not file-based dependencies</p>
-</li>
-<li><p class="first"><em>Ruffus</em> tries to have minimal impact on the functions it decorates.</p>
-<p>Bruce Eckel’s design wraps functions in “rule” objects.</p>
-<p><em>Ruffus</em> tasks are added as attributes of the functions which can be still be
-called normally. This is how <em>Ruffus</em> decorators can be layered in any order
-onto the same task.</p>
-</li>
-</ol>
-</dd>
-</dl>
-</li>
-<li><p class="first">Languages like c++ and Java would probably use a “mixin” approach.
-Python’s easy support for reflection and function references,
-as well as the necessity of marshalling over process boundaries, dictated the
-internal architecture of <em>Ruffus</em>.</p>
-</li>
-<li><p class="first">The <a class="reference external" href="http://www.boost.org">Boost Graph library</a> for text book implementations of directed
-graph traversals.</p>
-</li>
-<li><p class="first"><a class="reference external" href="http://www.graphviz.org/">Graphviz</a>. Just works. Wonderful.</p>
-</li>
-<li><p class="first">Andreas Heger, Christoffer Nellåker and Grant Belgard for driving Ruffus towards
-ever simpler syntax.</p>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Design & Architecture</a><ul>
-<li><a class="reference internal" href="#gnu-make"><cite>GNU Make</cite></a><ul>
-<li><a class="reference internal" href="#deficiencies-of-make-gmake">Deficiencies of <cite>make</cite> / <cite>gmake</cite></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#scons-rake-and-other-make-alternatives"><cite>Scons</cite>, <cite>Rake</cite> and other <cite>Make</cite> alternatives</a><ul>
-<li><a class="reference internal" href="#implicit-dependencies-disadvantages-of-make-scons-rake">Implicit dependencies: disadvantages of <cite>make</cite> / <cite>scons</cite> / <cite>rake</cite></a></li>
-<li><a class="reference internal" href="#explicit-dependencies-in-ruffus">Explicit dependencies in <cite>Ruffus</cite></a></li>
-<li><a class="reference internal" href="#static-dependencies-what-make-scons-rake-can-t-do-easily">Static dependencies: What <cite>make</cite> / <cite>scons</cite> / <cite>rake</cite> can’t do (easily)</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#managing-pipelines-stage-by-stage-using-ruffus">Managing pipelines stage-by-stage using <strong>Ruffus</strong></a><ul>
-<li><a class="reference internal" href="#disadvantages-of-the-ruffus-design">Disadvantages of the Ruffus design</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#alternatives-to-ruffus">Alternatives to <strong>Ruffus</strong></a><ul>
-<li><a class="reference internal" href="#acknowledgements">Acknowledgements</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
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-                        title="previous chapter">Installation</a></p>
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-                        title="next chapter">Major Features added to Ruffus</a></p>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
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-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
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-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
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-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
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-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
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-            
-  <span class="target" id="drmaa-functions"></span><div class="section" id="id1">
-<h1>drmaa functions<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">drmaa_wrapper</span></tt> is not exported automatically by ruffus and must be specified explicitly:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="hll"><span class="c"># imported ruffus.drmaa_wrapper explicitly</span>
-</span><span class="kn">from</span> <span class="nn">ruffus.drmaa_wrapper</span> <span class="kn">import</span> <span class="n">run_job</span><span class="p">,</span> <span class="n">error_drmaa_job</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<span class="target" id="drmaa-wrapper-run-job"></span><div class="section" id="index-0">
-<span id="id2"></span><h2><em>run_job</em><a class="headerlink" href="#index-0" title="Permalink to this headline">¶</a></h2>
-<p><strong>run_job</strong> (<a class="reference internal" href="#drmaa-wrapper-run-job-cmd-str"><cite>cmd_str</cite></a>, <a class="reference internal" href="#drmaa-wrapper-run-job-job-name"><cite>job_name</cite></a> = None, <a class="reference internal" href="#drmaa-wrapper-run-job-job-other-options"><cite>job_other_options</cite></a> = None, <a class="reference internal" href="#drmaa-wrapper-run-job-job-script-directory"><cite>job_script_directory</cite></a> = None, <a class="referenc [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">ruffus.drmaa_wrapper.run_job</span></tt> dispatches a command with arguments to a cluster or Grid Engine node and waits for the command to complete.</p>
-<p>It is the semantic equivalent of calling <a class="reference external" href="http://docs.python.org/2/library/os.html#os.system">os.system</a>  or
-<a class="reference external" href="http://docs.python.org/2/library/subprocess.html#subprocess.check_call">subprocess.check_output</a>.</p>
-</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus.drmaa_wrapper</span> <span class="kn">import</span> <span class="n">run_job</span><span class="p">,</span> <span class="n">error_drmaa_job</span>
-<span class="kn">import</span> <span class="nn">drmaa</span>
-<span class="n">my_drmaa_session</span> <span class="o">=</span> <span class="n">drmaa</span><span class="o">.</span><span class="n">Session</span><span class="p">()</span>
-<span class="n">my_drmaa_session</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
-
-<span class="n">run_job</span><span class="p">(</span><span class="s">"ls"</span><span class="p">,</span>
-        <span class="n">job_name</span> <span class="o">=</span> <span class="s">"test"</span><span class="p">,</span>
-        <span class="n">job_other_options</span><span class="o">=</span><span class="s">"-P mott-flint.prja -q short.qa"</span><span class="p">,</span>
-        <span class="n">job_script_directory</span> <span class="o">=</span> <span class="s">"test_dir"</span><span class="p">,</span>
-        <span class="n">job_environment</span><span class="o">=</span><span class="p">{</span> <span class="s">'BASH_ENV'</span> <span class="p">:</span> <span class="s">'~/.bashrc'</span> <span class="p">},</span>
-        <span class="n">retain_job_scripts</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">drmaa_session</span><span class="o">=</span><span class="n">my_drmaa_session</span><span class="p">)</span>
-<span class="n">run_job</span><span class="p">(</span><span class="s">"ls"</span><span class="p">,</span>
-        <span class="n">job_name</span> <span class="o">=</span> <span class="s">"test"</span><span class="p">,</span>
-        <span class="n">job_other_options</span><span class="o">=</span><span class="s">"-P mott-flint.prja -q short.qa"</span><span class="p">,</span>
-        <span class="n">job_script_directory</span> <span class="o">=</span> <span class="s">"test_dir"</span><span class="p">,</span>
-        <span class="n">job_environment</span><span class="o">=</span><span class="p">{</span> <span class="s">'BASH_ENV'</span> <span class="p">:</span> <span class="s">'~/.bashrc'</span> <span class="p">},</span>
-        <span class="n">retain_job_scripts</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
-        <span class="n">drmaa_session</span><span class="o">=</span><span class="n">my_drmaa_session</span><span class="p">,</span>
-        <span class="n">working_directory</span> <span class="o">=</span> <span class="s">"/gpfs1/well/mott-flint/lg/src/oss/ruffus/doc"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   catch exceptions</span>
-<span class="c">#</span>
-<span class="k">try</span><span class="p">:</span>
-    <span class="n">stdout_res</span><span class="p">,</span> <span class="n">stderr_res</span>  <span class="o">=</span> <span class="n">run_job</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span>
-                                      <span class="n">job_name</span>          <span class="o">=</span> <span class="n">job_name</span><span class="p">,</span>
-                                      <span class="n">logger</span>            <span class="o">=</span> <span class="n">logger</span><span class="p">,</span>
-                                      <span class="n">drmaa_session</span>     <span class="o">=</span> <span class="n">drmaa_session</span><span class="p">,</span>
-                                      <span class="n">run_locally</span>       <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">local_run</span><span class="p">,</span>
-                                      <span class="n">job_other_options</span> <span class="o">=</span> <span class="n">get_queue_name</span><span class="p">())</span>
-
-<span class="c"># relay all the stdout, stderr, drmaa output to diagnose failures</span>
-<span class="k">except</span> <span class="n">error_drmaa_job</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
-    <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span>
-                        <span class="p">[</span><span class="s">"Failed to run:"</span><span class="p">,</span>
-                         <span class="n">cmd</span><span class="p">,</span>
-                         <span class="n">err</span><span class="p">,</span>
-                         <span class="n">stdout_res</span><span class="p">,</span>
-                         <span class="n">stderr_res</span><span class="p">])))</span>
-
-<span class="n">my_drmaa_session</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-cmd-str">
-<div><ul>
-<li><p class="first"><em>cmd_str</em></p>
-<blockquote>
-<div><p>The command which will be run remotely including all parameters</p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-job-name">
-<div><ul>
-<li><p class="first"><em>job_name</em></p>
-<blockquote>
-<div><p>A descriptive name for the command. This will be displayed by <a class="reference external" href="http://gridscheduler.sourceforge.net/htmlman/htmlman1/qstat.html">SGE qstat</a>, for example.
-Defaults to “ruffus_job”</p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-job-other-options">
-<div><ul>
-<li><p class="first"><em>job_other_options</em></p>
-<blockquote>
-<div><p>Other drmaa parameters can be passed verbatim as a string.</p>
-<p>Examples for SGE include project name (<tt class="docutils literal"><span class="pre">-P</span> <span class="pre">project_name</span></tt>), parallel environment (<tt class="docutils literal"><span class="pre">-pe</span> <span class="pre">parallel_environ</span></tt>), account (<tt class="docutils literal"><span class="pre">-A</span> <span class="pre">account_string</span></tt>), resource (<tt class="docutils literal"><span class="pre">-l</span> <span class="pre">resource=expression</ [...]
-queue name (<tt class="docutils literal"><span class="pre">-q</span> <span class="pre">a_queue_name</span></tt>), queue priority (<tt class="docutils literal"><span class="pre">-p</span> <span class="pre">15</span></tt>).</p>
-<p>These are parameters which you normally need to include when submitting jobs interactively, for example via
-<a class="reference external" href="http://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html">SGE qsub</a>
-or <a class="reference external" href="http://apps.man.poznan.pl/trac/slurm-drmaa/wiki/WikiStart#Nativespecification">SLURM</a> (<a class="reference external" href="https://computing.llnl.gov/linux/slurm/srun.html">srun</a>)</p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-job-script-directory">
-<div><ul>
-<li><p class="first"><em>job_script_directory</em></p>
-<blockquote>
-<div><p>The directory where drmaa temporary script files will be found. Defaults to the current working directory.</p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-job-environment">
-<div><ul>
-<li><p class="first"><em>job_environment</em></p>
-<blockquote>
-<div><p>A dictionary of key / values with environment variables. E.g. <tt class="docutils literal"><span class="pre">"{'BASH_ENV':</span> <span class="pre">'~/.bashrc'}"</span></tt></p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-working-directory">
-<div><ul>
-<li><p class="first"><em>working_directory</em></p>
-<blockquote>
-<div><ul class="simple">
-<li>Sets the working directory.</li>
-<li>Should be a fully qualified path.</li>
-<li>Defaults to the current working directory.</li>
-</ul>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-retain-job-scripts">
-<div><ul>
-<li><p class="first"><em>retain_job_scripts</em></p>
-<blockquote>
-<div><p>Do not delete temporary script files containg drmaa commands. Useful for
-debugging, running on the command line directly, and can provide a useful record of the commands.</p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-logger">
-<div><ul>
-<li><p class="first"><em>logger</em></p>
-<blockquote>
-<div><p>For logging messages indicating the progress of the pipeline in terms of tasks and jobs. Takes objects with the standard python
-<a class="reference external" href="https://docs.python.org/2/library/logging.html">logging</a> module interface.</p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-drmaa-session">
-<div><ul>
-<li><p class="first"><em>drmaa_session</em></p>
-<blockquote>
-<div><p>A shared drmaa session created and managed separately.</p>
-<p>In the main part of your <strong>Ruffus</strong> pipeline script somewhere there should be code looking like this:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   start shared drmaa session for all jobs / tasks in pipeline</span>
-<span class="c">#</span>
-<span class="kn">import</span> <span class="nn">drmaa</span>
-<span class="n">drmaa_session</span> <span class="o">=</span> <span class="n">drmaa</span><span class="o">.</span><span class="n">Session</span><span class="p">()</span>
-<span class="n">drmaa_session</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
-
-
-<span class="c">#</span>
-<span class="c">#   pipeline functions</span>
-<span class="c">#</span>
-
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
-    <span class="n">cmdline</span><span class="o">.</span><span class="n">run</span> <span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">multithread</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">jobs</span><span class="p">)</span>
-    <span class="n">drmaa_session</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-run-locally">
-<div><ul>
-<li><p class="first"><em>run_locally</em></p>
-<blockquote>
-<div><p>Runs commands locally using the standard python <a class="reference external" href="https://docs.python.org/2/library/subprocess.html">subprocess</a> module
-rather than dispatching remotely. This allows scripts to be debugged easily</p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-touch-only">
-<div><ul>
-<li><p class="first"><em>touch_only</em></p>
-<blockquote>
-<div><p>Create or update <a class="reference internal" href="#drmaa-wrapper-run-job-output-files"><em>Output files</em></a>
-only to simulate the running of the pipeline.
-Does not dispatch commands remotely or locally. This is most useful to force a
-pipeline to acknowledge that a particular part is now up-to-date.</p>
-<p>See also: <a class="reference internal" href="pipeline_functions.html#pipeline-functions-pipeline-run-touch-files-only"><em>pipeline_run(touch_files_only=True)</em></a></p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="drmaa-wrapper-run-job-output-files">
-<div><ul>
-<li><p class="first"><em>output_files</em></p>
-<blockquote>
-<div><p>Output files which will be created or updated if  <a class="reference internal" href="#drmaa-wrapper-run-job-touch-only"><em>touch_only</em></a> <tt class="docutils literal"><span class="pre">=True</span></tt></p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">drmaa functions</a><ul>
-<li><a class="reference internal" href="#index-0"><em>run_job</em></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="pipeline_functions.html"
-                        title="previous chapter">Pipeline functions</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="installation.html"
-                        title="next chapter">Installation</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="_sources/drmaa_wrapper_functions.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="##drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
-
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-      </div>
-      <div class="clearer"></div>
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-            
-  <div class="section" id="construction-of-a-simple-pipeline-to-run-blast-jobs">
-<span id="examples-bioinformatics-part1"></span><h1>Construction of a simple pipeline to run BLAST jobs<a class="headerlink" href="#construction-of-a-simple-pipeline-to-run-blast-jobs" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>This is a simple example to illustrate the convenience <strong>Ruffus</strong>
-brings to simple tasks in bioinformatics.</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li><strong>Split</strong> a problem into multiple fragments that can be</li>
-<li><strong>Run in parallel</strong> giving partial solutions that can be</li>
-<li><strong>Recombined</strong> into the complete solution.</li>
-</ol>
-</div></blockquote>
-<p>The example code runs a <a class="reference external" href="http://blast.ncbi.nlm.nih.gov/">ncbi</a>
-<a class="reference external" href="http://en.wikipedia.org/wiki/BLAST">blast</a> search for four sequences
-against the human <a class="reference external" href="http://en.wikipedia.org/wiki/RefSeq">refseq</a> protein sequence database.</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li><strong>Split</strong> each of the four sequences into a separate file.</li>
-<li><strong>Run in parallel</strong> Blastall on each sequence file</li>
-<li><strong>Recombine</strong> the BLAST results by simple concatenation.</li>
-</ol>
-</div></blockquote>
-<p>In real life,</p>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference external" href="http://blast.ncbi.nlm.nih.gov/">BLAST</a> already provides support for multiprocessing</li>
-<li>Sequence files would be split in much larger chunks, with many sequences</li>
-<li>The jobs would be submitted to large computational farms (in our case, using the SunGrid Engine).</li>
-<li>The High Scoring Pairs (HSPs) would be parsed / filtered / stored in your own formats.</li>
-</ul>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>This bioinformatics example is intended to showcase <em>some</em> of the features of Ruffus.</p>
-<blockquote class="last">
-<div><ol class="arabic simple">
-<li>See the <a class="reference internal" href="../../tutorials/new_tutorial/introduction.html#new-manual-introduction"><em>manual</em></a> to learn about the various features in Ruffus.</li>
-</ol>
-</div></blockquote>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="prerequisites">
-<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="ruffus">
-<h3>1. Ruffus<a class="headerlink" href="#ruffus" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>To install Ruffus on most systems with python installed:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>easy_install -U ruffus</pre>
-</div>
-</div></blockquote>
-<p>Otherwise, <a class="reference external" href="http://code.google.com/p/ruffus/downloads/list">download</a> Ruffus and run:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>tar -xvzf ruffus-xxx.tar.gz
-cd ruffus-xxx
-./setup install</pre>
-</div>
-</div></blockquote>
-<p>where xxx is the latest Ruffus version.</p>
-</div></blockquote>
-</div>
-<div class="section" id="blast">
-<h3>2. BLAST<a class="headerlink" href="#blast" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div>This example assumes that the <a class="reference external" href="http://blast.ncbi.nlm.nih.gov/">BLAST</a> <tt class="docutils literal"><span class="pre">blastall</span></tt> and <tt class="docutils literal"><span class="pre">formatdb</span></tt> executables are
-installed and on the search path. Otherwise download from <a class="reference external" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download">here</a>.</div></blockquote>
-</div>
-<div class="section" id="human-refseq-sequence-database">
-<h3>3. human refseq sequence database<a class="headerlink" href="#human-refseq-sequence-database" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>We also need to download the human refseq sequence file and format the ncbi database:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>wget ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz
-gunzip human.protein.faa.gz
-
-formatdb -i human.protein.faa</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="test-sequences">
-<h3>4. test sequences<a class="headerlink" href="#test-sequences" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div>Query sequences in FASTA format can be found in <a class="reference external" href="../../_static/examples/bioinformatics/original.fa">original.fa</a></div></blockquote>
-</div>
-</div>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>The code for this example can be found <a class="reference internal" href="part1_code.html#examples-bioinformatics-part1-code"><em>here</em></a>  and
-pasted into the python command shell.</div></blockquote>
-</div>
-<div class="section" id="step-1-splitting-up-the-query-sequences">
-<h2>Step 1. Splitting up the query sequences<a class="headerlink" href="#step-1-splitting-up-the-query-sequences" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>We want each of our sequences in the query file <a class="reference external" href="../../_static/examples/bioinformatics/original.fa">original.fa</a> to be placed
-in a separate files named <tt class="docutils literal"><span class="pre">XXX.segment</span></tt> where <tt class="docutils literal"><span class="pre">XXX</span></tt> = 1 -> the number of sequences.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">current_file_index</span> <span class="o">=</span> <span class="mi">0</span>
-<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="s">"original.fa"</span><span class="p">):</span>
-    <span class="c"># start a new file for each accession line</span>
-    <span class="k">if</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'>'</span><span class="p">:</span>
-        <span class="n">current_file_index</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="n">current_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.segment"</span> <span class="o">%</span> <span class="n">current_file_index</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="n">current_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>To use this in a pipeline, we only need to wrap this in a function, “decorated” with the Ruffus
-keyword <a class="reference internal" href="../../tutorials/new_tutorial/split.html#new-manual-split"><em>@split</em></a>:</p>
-<blockquote>
-<div><img alt="../../_images/examples_bioinformatics_split.jpg" src="../../_images/examples_bioinformatics_split.jpg" />
-</div></blockquote>
-<div class="line-block">
-<div class="line">This indicates that we are splitting up the input file <a class="reference external" href="../../_static/examples/bioinformatics/original.fa">original.fa</a> into however many
-<tt class="docutils literal"><span class="pre">*.segment</span></tt> files as it takes.</div>
-<div class="line">The pipelined function itself takes two arguments, for the input and output.</div>
-</div>
-<p>We shall see later this simple <a class="reference internal" href="../../tutorials/new_tutorial/split.html#new-manual-split"><em>@split</em></a> decorator already gives all the benefits of:</p>
-<blockquote>
-<div><ul class="simple">
-<li>Dependency checking</li>
-<li>Flowchart printing</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="step-2-run-blast-jobs-in-parallel">
-<h2>Step 2. Run BLAST jobs in parallel<a class="headerlink" href="#step-2-run-blast-jobs-in-parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Assuming that blast is already installed, sequence matches can be found with this python
-code:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">os</span><span class="o">.</span><span class="n">system</span><span class="p">(</span><span class="s">"blastall -p blastp -d human.protein.faa -i 1.segment > 1.blastResult"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>To pipeline this, we need to simply wrap in a function, decorated with the <strong>Ruffus</strong>
-keyword <a class="reference internal" href="../../tutorials/new_tutorial/transform.html#new-manual-transform"><em>@transform</em></a>.</p>
-<blockquote>
-<div><img alt="../../_images/examples_bioinformatics_transform.jpg" src="../../_images/examples_bioinformatics_transform.jpg" />
-</div></blockquote>
-<p>This indicates that we are taking all the output files from the previous <tt class="docutils literal"><span class="pre">splitFasta</span></tt>
-operation (<tt class="docutils literal"><span class="pre">*.segment</span></tt>) and <a class="reference internal" href="../../tutorials/new_tutorial/transform.html#new-manual-transform"><em>@transform</em></a>-ing each to a new file with the <tt class="docutils literal"><span class="pre">.blastResult</span></tt>
-suffix. Each of these transformation operations can run in parallel if specified.</p>
-</div></blockquote>
-</div>
-<div class="section" id="step-3-combining-blast-results">
-<h2>Step 3. Combining BLAST results<a class="headerlink" href="#step-3-combining-blast-results" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt>The following python code will concatenate the results together</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"final.blast_results"</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">glob</span><span class="p">(</span><span class="s">"*.blastResults"</span><span class="p">):</span>
-    <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>To pipeline this, we need again to decorate with the <strong>Ruffus</strong> keyword <a class="reference internal" href="../../tutorials/new_tutorial/merge.html#new-manual-merge"><em>@merge</em></a>.</p>
-<blockquote>
-<div><img alt="../../_images/examples_bioinformatics_merge.jpg" src="../../_images/examples_bioinformatics_merge.jpg" />
-</div></blockquote>
-<p>This indicates that we are taking all the output files from the previous <tt class="docutils literal"><span class="pre">runBlast</span></tt>
-operation (<tt class="docutils literal"><span class="pre">*.blastResults</span></tt>) and <a class="reference internal" href="../../tutorials/new_tutorial/merge.html#new-manual-merge"><em>@merge</em></a>-ing them to the new file <tt class="docutils literal"><span class="pre">final.blast_results</span></tt>.</p>
-</div></blockquote>
-</div>
-<div class="section" id="step-4-running-the-pipeline">
-<h2>Step 4. Running the pipeline<a class="headerlink" href="#step-4-running-the-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>We can run the completed pipeline using a maximum of 4 parallel processes by calling
-<a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a> :</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">combineBlastResults</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Though we have only asked Ruffus to run <tt class="docutils literal"><span class="pre">combineBlastResults</span></tt>, it traces all the dependencies
-of this task and runs all the necessary parts of the pipeline.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The full code for this example can be found  <a class="reference internal" href="part1_code.html#examples-bioinformatics-part1-code"><em>here</em></a>
-suitable for pasting into the python command shell.</p>
-</div>
-<p>The <tt class="docutils literal"><span class="pre">verbose</span></tt> parameter causes the following output to be printed to stderr as the pipeline
-runs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">combineBlastResults</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-<span class="go">    Job = [original.fa -> *.segment] completed</span>
-<span class="go">Completed Task = splitFasta</span>
-<span class="go">    Job = [1.segment -> 1.blastResult] completed</span>
-<span class="go">    Job = [3.segment -> 3.blastResult] completed</span>
-<span class="go">    Job = [2.segment -> 2.blastResult] completed</span>
-<span class="go">    Job = [4.segment -> 4.blastResult] completed</span>
-<span class="go">Completed Task = runBlast</span>
-<span class="go">    Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult] -> final.blast_results] completed</span>
-<span class="go">Completed Task = combineBlastResults</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="step-5-testing-dependencies">
-<h2>Step 5. Testing dependencies<a class="headerlink" href="#step-5-testing-dependencies" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If we invoked <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a> again, nothing
-further would happen because the
-pipeline is now up-to-date. But what if the pipeline had not run to completion?</p>
-<p>We can simulate the failure of one of the <tt class="docutils literal"><span class="pre">blastall</span></tt> jobs by deleting its results:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="s">"4.blastResult"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Let us use the <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout</em></a>
-function to print out the dependencies of the pipeline at a high <tt class="docutils literal"><span class="pre">verbose</span></tt> level which
-will show both complete and incomplete jobs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">import</span> <span class="nn">sys</span>
-<span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">combineBlastResults</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which are up-to-date:</span>
-
-<span class="go">Task = splitFasta</span>
-<span class="go">    "Split sequence file into as many fragments as appropriate depending on the size of</span>
-<span class="go">               original_fasta"</span>
-
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which will be run:</span>
-
-<span class="go">Task = runBlast</span>
-<span class="go">    "Run blast"</span>
-<span class="go">       Job = [4.segment</span>
-<span class="go">             ->4.blastResult]</span>
-<span class="go">         Job needs update: Missing file 4.blastResult</span>
-
-<span class="go">Task = combineBlastResults</span>
-<span class="go">    "Combine blast results"</span>
-<span class="go">       Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult]</span>
-<span class="go">             ->final.blast_results]</span>
-<span class="go">         Job needs update: Missing file 4.blastResult</span>
-
-<span class="go">________________________________________</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Only the parts of the pipeline which involve the missing BLAST result will be rerun.
-We can confirm this by invoking the pipeline.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">combineBlastResults</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-
-<span class="go">    Job = [1.segment -> 1.blastResult] unnecessary: already up to date</span>
-<span class="go">    Job = [2.segment -> 2.blastResult] unnecessary: already up to date</span>
-<span class="go">    Job = [3.segment -> 3.blastResult] unnecessary: already up to date</span>
-<span class="go">    Job = [4.segment -> 4.blastResult] completed</span>
-<span class="go">Completed Task = runBlast</span>
-<span class="go">    Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult] -> final.blast_results] completed</span>
-<span class="go">Completed Task = combineBlastResults</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="what-is-next">
-<h2>What is next?<a class="headerlink" href="#what-is-next" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>In the <a class="reference internal" href="part2.html#examples-bioinformatics-part2"><em>next (short) part</em></a>,
-we shall add some standard (boilerplate) code to
-turn this BLAST pipeline into a (slightly more) useful python program.</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Construction of a simple pipeline to run BLAST jobs</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#prerequisites">Prerequisites</a><ul>
-<li><a class="reference internal" href="#ruffus">1. Ruffus</a></li>
-<li><a class="reference internal" href="#blast">2. BLAST</a></li>
-<li><a class="reference internal" href="#human-refseq-sequence-database">3. human refseq sequence database</a></li>
-<li><a class="reference internal" href="#test-sequences">4. test sequences</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#step-1-splitting-up-the-query-sequences">Step 1. Splitting up the query sequences</a></li>
-<li><a class="reference internal" href="#step-2-run-blast-jobs-in-parallel">Step 2. Run BLAST jobs in parallel</a></li>
-<li><a class="reference internal" href="#step-3-combining-blast-results">Step 3. Combining BLAST results</a></li>
-<li><a class="reference internal" href="#step-4-running-the-pipeline">Step 4. Running the pipeline</a></li>
-<li><a class="reference internal" href="#step-5-testing-dependencies">Step 5. Testing dependencies</a></li>
-<li><a class="reference internal" href="#what-is-next">What is next?</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="../../why_ruffus.html"
-                        title="previous chapter">Why <em>Ruffus</em>?</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="part2.html"
-                        title="next chapter">Part 2: A slightly more practical pipeline to run blasts jobs</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/examples/bioinformatics/index.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
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-  <div class="section" id="ruffus-code">
-<span id="examples-bioinformatics-part1-code"></span><h1>Ruffus code<a class="headerlink" href="#ruffus-code" title="Permalink to this headline">¶</a></h1>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
-
-<span class="n">exe_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">0</span><sp [...]
-<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span c [...]
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-
-<span class="n">original_fasta</span> <span class="o">=</span> <span class="s">"original.fa"</span>
-<span class="n">database_file</span>  <span class="o">=</span> <span class="s">"human.protein.faa"</span>
-
-<span class="nd">@split</span><span class="p">(</span><span class="n">original_fasta</span><span class="p">,</span> <span class="s">"*.segment"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">splitFasta</span> <span class="p">(</span><span class="n">seqFile</span><span class="p">,</span> <span class="n">segments</span><span class="p">):</span>
-    <span class="sd">"""Split sequence file into</span>
-<span class="sd">       as many fragments as appropriate</span>
-<span class="sd">       depending on the size of original_fasta"""</span>
-    <span class="n">current_file_index</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">original_fasta</span><span class="p">):</span>
-        <span class="c">#</span>
-        <span class="c"># start a new file for each accession line</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'>'</span><span class="p">:</span>
-            <span class="n">current_file_index</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">current_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.segment"</span> <span class="o">%</span> <span class="n">current_file_index</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="n">current_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">splitFasta</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".segment"</span><span class="p">),</span> <span class="s">".blastResult"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">runBlast</span><span class="p">(</span><span class="n">seqFile</span><span class="p">,</span>  <span class="n">blastResultFile</span><span class="p">):</span>
-    <span class="sd">"""Run blast"""</span>
-    <span class="n">os</span><span class="o">.</span><span class="n">system</span><span class="p">(</span><span class="s">"blastall -p blastp -d </span><span class="si">%s</span><span class="s"> -i </span><span class="si">%s</span><span class="s"> > </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span>
-                <span class="p">(</span><span class="n">database_file</span><span class="p">,</span> <span class="n">seqFile</span><span class="p">,</span> <span class="n">blastResultFile</span><span class="p">))</span>
-
-
-<span class="nd">@merge</span><span class="p">(</span><span class="n">runBlast</span><span class="p">,</span> <span class="s">"final.blast_results"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">combineBlastResults</span> <span class="p">(</span><span class="n">blastResultFiles</span><span class="p">,</span> <span class="n">combinedBlastResultFile</span><span class="p">):</span>
-    <span class="sd">"""Combine blast results"""</span>
-    <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">combinedBlastResultFile</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">blastResultFiles</span><span class="p">:</span>
-        <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
-
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">combineBlastResults</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Simulate interuption of the pipeline by</span>
-<span class="c">#        deleting the output of one of the BLAST jobs</span>
-<span class="c">#</span>
-<span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="s">"4.blastResult"</span><span class="p">)</span>
-
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">combineBlastResults</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Re-running the pipeline</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">combineBlastResults</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-</pre></div>
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-
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
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-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
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-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
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-<span id="examples-bioinformatics-part2"></span><h1>Part 2: A slightly more practical pipeline to run blasts jobs<a class="headerlink" href="#part-2-a-slightly-more-practical-pipeline-to-run-blasts-jobs" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="index.html#examples-bioinformatics-part1"><em>Previously</em></a>, we had built
-a simple pipeline to split up a FASTA file of query sequences so
-that these can be matched against a sequence database in parallel.</p>
-<p>We shall wrap this code so that</p>
-<blockquote>
-<div><ul class="simple">
-<li>It is more robust to interruptions</li>
-<li>We can specify the file names on the command line</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="step-1-cleaning-up-any-leftover-junk-from-previous-pipeline-runs">
-<h2>Step 1. Cleaning up any leftover junk from previous pipeline runs<a class="headerlink" href="#step-1-cleaning-up-any-leftover-junk-from-previous-pipeline-runs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="line-block">
-<div class="line">We split up each of our sequences in the query file <a class="reference external" href="../../_static/examples/bioinformatics/original.fa">original.fa</a>
-into a separate files named <tt class="docutils literal"><span class="pre">XXX.segment</span></tt> where <tt class="docutils literal"><span class="pre">XXX</span></tt> is the number of sequences in
-the FASTA file.</div>
-</div>
-<div class="line-block">
-<div class="line">However, if we start with 6 sequences (giving <tt class="docutils literal"><span class="pre">1.segment</span></tt> ... <tt class="docutils literal"><span class="pre">6.segment</span></tt>), and we
-then edited <a class="reference external" href="../../_static/examples/bioinformatics/original.fa">original.fa</a>
-so that only 5 were left, the file <tt class="docutils literal"><span class="pre">6.segment</span></tt> would still be left
-hanging around as an unwanted, extraneous and confusing orphan.</div>
-</div>
-<p>As a general rule, it is a good idea to clean up the results of a previous run in
-a <em class="xref std std-ref">@split</em> operation:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="s">"original.fa"</span><span class="p">,</span> <span class="s">"*.segment"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">splitFasta</span> <span class="p">(</span><span class="n">seqFile</span><span class="p">,</span> <span class="n">segments</span><span class="p">):</span>
-
-    <span class="c">#</span>
-    <span class="c">#   Clean up any segment files from previous runs before creating new one</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s">"*.segment"</span><span class="p">):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
-
-    <span class="c"># code as before...</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="step-2-adding-a-flag-file-to-mark-successful-completion">
-<span id="examples-bioinformatics-part2-step2"></span><h2>Step 2. Adding a “flag” file to mark successful completion<a class="headerlink" href="#step-2-adding-a-flag-file-to-mark-successful-completion" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>When pipelined tasks are interrupted half way through an operation, the output may
-only contain part of the results in an incomplete or inconsistent state.
-There are three general options to deal with this:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Catch any interrupting conditions and delete the incomplete output</li>
-<li>Tag successfully completed output with a special marker at the end of the file</li>
-<li>Create an empty “flag” file whose only point is to signal success</li>
-</ol>
-</div></blockquote>
-<p>Option (3) is the most reliable way and involves the least amount of work in Ruffus.
-We add flag files with the suffix <tt class="docutils literal"><span class="pre">.blastSuccess</span></tt> for our parallel BLAST jobs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">splitFasta</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".segment"</span><span class="p">),</span> <span class="p">[</span><span class="s">".blastResult"</span><span class="p">,</span> <span class="s">".blastSuccess"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">runBlast</span><span class="p">(</span><span class="n">seqFile</span><span class="p">,</span>  <span class="n">output_files</span><span class="p">):</span>
-
-    <span class="n">blastResultFile</span><span class="p">,</span> <span class="n">flag_file</span> <span class="o">=</span> <span class="n">output_files</span>
-
-    <span class="c">#</span>
-    <span class="c">#   Existing code unchanged</span>
-    <span class="c">#</span>
-    <span class="n">os</span><span class="o">.</span><span class="n">system</span><span class="p">(</span><span class="s">"blastall -p blastp -d human.protein.faa "</span><span class="o">+</span>
-                <span class="s">"-i </span><span class="si">%s</span><span class="s"> > </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">seqFile</span><span class="p">,</span> <span class="n">blastResultFile</span><span class="p">))</span>
-
-    <span class="c">#</span>
-    <span class="c">#   "touch" flag file to indicate success</span>
-    <span class="c">#</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">flag_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="step-3-allowing-the-script-to-be-invoked-on-the-command-line">
-<h2>Step 3. Allowing the script to be invoked on the command line<a class="headerlink" href="#step-3-allowing-the-script-to-be-invoked-on-the-command-line" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>We allow the query sequence file, as well as the sequence database and end results
-to be specified at runtime using the standard python <a class="reference external" href="http://docs.python.org/library/optparse.html">optparse</a> module.
-We find this approach to run time arguments generally useful for many Ruffus scripts.
-The full code can be <a class="reference internal" href="part2_code.html#examples-bioinformatics-part2-code"><em>viewed here</em></a> and
-<a class="reference external" href="../../_static/examples/bioinformatics/run_parallel_blast.py">downloaded from run_parallel_blast.py</a>.</p>
-<p>The different options can be inspected by running the script with the <tt class="docutils literal"><span class="pre">--help</span></tt> or <tt class="docutils literal"><span class="pre">-h</span></tt>
-argument.</p>
-<p>The following options are useful for developing Ruffus scripts:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>--verbose | -v    :  Print more detailed messages for each additional verbose level.
-                     E.g. run_parallel_blast --verbose --verbose --verbose ... (or -vvv)
-
---jobs | -j       :  Specifies the number of jobs (operations) to run in parallel.
-
---flowchart FILE  :  Print flowchart of the pipeline to FILE. Flowchart format
-                     depends on extension. Alternatives include (".dot", ".jpg",
-                     "*.svg", "*.png" etc). Formats other than ".dot" require
-                     the dot program to be installed (http://www.graphviz.org/).
-
---just_print | -n    Only print a trace (description) of the pipeline.
-                     The level of detail is set by --verbose.</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="step-4-printing-out-a-flowchart-for-the-pipeline">
-<h2>Step 4. Printing out a flowchart for the pipeline<a class="headerlink" href="#step-4-printing-out-a-flowchart-for-the-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <tt class="docutils literal"><span class="pre">--flowchart</span></tt> argument results in a call to <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt>
-This prints out a flowchart of the pipeline. Valid formats include ”.dot”, ”.jpg”, ”.svg”, ”.png”
-but all except for the first require the <tt class="docutils literal"><span class="pre">dot</span></tt> program to be installed
-(<a class="reference external" href="http://www.graphviz.org/">http://www.graphviz.org/</a>).</p>
-<p>The state of the pipeline is reflected in the flowchart:</p>
-<img alt="../../_images/examples_bioinformatics_pipeline.jpg" src="../../_images/examples_bioinformatics_pipeline.jpg" />
-</div></blockquote>
-</div>
-<div class="section" id="step-5-errors">
-<h2>Step 5. Errors<a class="headerlink" href="#step-5-errors" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Because Ruffus scripts are just normal python functions, you can debug them using
-your usual tools, or jump to the offending line(s) even when the pipeline is running in
-parallel.</p>
-<p>For example, these are the what the error messages would look like if we had mis-spelt <tt class="docutils literal"><span class="pre">blastal</span></tt>.
-In <a class="reference internal" href="part2_code.html#examples-bioinformatics-part2-code"><em>run_parallel_blast.py</em></a>,
-python exceptions are raised if the <tt class="docutils literal"><span class="pre">blastall</span></tt> command fails.</p>
-<p>Each of the exceptions for the parallel operations are printed out with the
-offending lines (line 204), and problems (<tt class="docutils literal"><span class="pre">blastal</span></tt> not found)
-highlighted in red.</p>
-<blockquote>
-<div><img alt="../../_images/examples_bioinformatics_error.png" src="../../_images/examples_bioinformatics_error.png" />
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="step-6-will-it-run">
-<h2>Step 6. Will it run?<a class="headerlink" href="#step-6-will-it-run" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>The full code can be <a class="reference internal" href="part2_code.html#examples-bioinformatics-part2-code"><em>viewed here</em></a> and
-<a class="reference external" href="../../_static/examples/bioinformatics/run_parallel_blast.py">downloaded from run_parallel_blast.py</a>.</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Part 2: A slightly more practical pipeline to run blasts jobs</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#step-1-cleaning-up-any-leftover-junk-from-previous-pipeline-runs">Step 1. Cleaning up any leftover junk from previous pipeline runs</a></li>
-<li><a class="reference internal" href="#step-2-adding-a-flag-file-to-mark-successful-completion">Step 2. Adding a “flag” file to mark successful completion</a></li>
-<li><a class="reference internal" href="#step-3-allowing-the-script-to-be-invoked-on-the-command-line">Step 3. Allowing the script to be invoked on the command line</a></li>
-<li><a class="reference internal" href="#step-4-printing-out-a-flowchart-for-the-pipeline">Step 4. Printing out a flowchart for the pipeline</a></li>
-<li><a class="reference internal" href="#step-5-errors">Step 5. Errors</a></li>
-<li><a class="reference internal" href="#step-6-will-it-run">Step 6. Will it run?</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="index.html"
-                        title="previous chapter">Construction of a simple pipeline to run BLAST jobs</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="part1_code.html"
-                        title="next chapter">Ruffus code</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/examples/bioinformatics/part2.txt"
-           rel="nofollow">Show Source</a></li>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
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-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-         <a href="../../todo.html">Future plans</a>
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-            
-  <div class="section" id="ruffus-code">
-<span id="examples-bioinformatics-part2-code"></span><h1>Ruffus code<a class="headerlink" href="#ruffus-code" title="Permalink to this headline">¶</a></h1>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#!/usr/bin/env python</span>
-<span class="sd">"""</span>
-
-<span class="sd">    run_parallel_blast.py</span>
-<span class="sd">    [--log_file PATH]</span>
-<span class="sd">    [--quiet]</span>
-
-<span class="sd">"""</span>
-
-<span class="c">################################################################################</span>
-<span class="c">#</span>
-<span class="c">#   run_parallel_blast</span>
-<span class="c">#</span>
-<span class="c">#</span>
-<span class="c">#   Copyright (c) 4/21/2010 Leo Goodstadt</span>
-<span class="c">#</span>
-<span class="c">#   Permission is hereby granted, free of charge, to any person obtaining a copy</span>
-<span class="c">#   of this software and associated documentation files (the "Software"), to deal</span>
-<span class="c">#   in the Software without restriction, including without limitation the rights</span>
-<span class="c">#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
-<span class="c">#   copies of the Software, and to permit persons to whom the Software is</span>
-<span class="c">#   furnished to do so, subject to the following conditions:</span>
-<span class="c">#</span>
-<span class="c">#   The above copyright notice and this permission notice shall be included in</span>
-<span class="c">#   all copies or substantial portions of the Software.</span>
-<span class="c">#</span>
-<span class="c">#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
-<span class="c">#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
-<span class="c">#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
-<span class="c">#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
-<span class="c">#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
-<span class="c">#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN</span>
-<span class="c">#   THE SOFTWARE.</span>
-<span class="c">#################################################################################</span>
-<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
-<span class="n">exe_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">0</span><sp [...]
-<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span cl [...]
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   options</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="kn">from</span> <span class="nn">optparse</span> <span class="kn">import</span> <span class="n">OptionParser</span>
-<span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">os</span>
-
-<span class="n">exe_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">0</span><sp [...]
-
-
-<span class="n">parser</span> <span class="o">=</span> <span class="n">OptionParser</span><span class="p">(</span><span class="n">version</span><span class="o">=</span><span class="s">"%prog 1.0"</span><span class="p">,</span> <span class="n">usage</span> <span class="o">=</span> <span class="s">"</span><span class="se">\n\n</span><span class="s">    %prog --input_file QUERY_FASTA --database_file FASTA_DATABASE [more_options]"</span><span class="p">)</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"-i"</span><span class="p">,</span> <span class="s">"--input_file"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"input_file"</span><span class="p">,</span>
-                  <span class="n">metavar</span><span class="o">=</span><span class="s">"FILE"</span><span class="p">,</span>
-                  <span class="nb">type</span><span class="o">=</span><span class="s">"string"</span><span class="p">,</span>
-                  <span class="n">help</span><span class="o">=</span><span class="s">"Name and path of query sequence file in FASTA format. "</span><span class="p">)</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"-d"</span><span class="p">,</span> <span class="s">"--database_file"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"database_file"</span><span class="p">,</span>
-                  <span class="n">metavar</span><span class="o">=</span><span class="s">"FILE"</span><span class="p">,</span>
-                  <span class="nb">type</span><span class="o">=</span><span class="s">"string"</span><span class="p">,</span>
-                  <span class="n">help</span><span class="o">=</span><span class="s">"Name and path of FASTA database to search. "</span><span class="p">)</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"--result_file"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"result_file"</span><span class="p">,</span>
-                  <span class="n">metavar</span><span class="o">=</span><span class="s">"FILE"</span><span class="p">,</span>
-                  <span class="nb">type</span><span class="o">=</span><span class="s">"string"</span><span class="p">,</span>
-                  <span class="n">default</span><span class="o">=</span><span class="s">"final.blast_results"</span><span class="p">,</span>
-                  <span class="n">help</span><span class="o">=</span><span class="s">"Name and path of where the files should end up. "</span><span class="p">)</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"-t"</span><span class="p">,</span> <span class="s">"--temp_directory"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"temp_directory"</span><span class="p">,</span>
-                  <span class="n">metavar</span><span class="o">=</span><span class="s">"PATH"</span><span class="p">,</span>
-                  <span class="nb">type</span><span class="o">=</span><span class="s">"string"</span><span class="p">,</span>
-                  <span class="n">default</span><span class="o">=</span><span class="s">"tmp"</span><span class="p">,</span>
-                  <span class="n">help</span><span class="o">=</span><span class="s">"Name and path of temporary directory where calculations "</span>
-                            <span class="s">"should take place. "</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   general options: verbosity / logging</span>
-<span class="c">#</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"-v"</span><span class="p">,</span> <span class="s">"--verbose"</span><span class="p">,</span> <span class="n">dest</span> <span class="o">=</span> <span class="s">"verbose"</span><span class="p">,</span>
-                  <span class="n">action</span><span class="o">=</span><span class="s">"count"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
-                  <span class="n">help</span><span class="o">=</span><span class="s">"Print more detailed messages for each additional verbose level."</span>
-                       <span class="s">" E.g. run_parallel_blast --verbose --verbose --verbose ... (or -vvv)"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   pipeline</span>
-<span class="c">#</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"-j"</span><span class="p">,</span> <span class="s">"--jobs"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"jobs"</span><span class="p">,</span>
-                  <span class="n">default</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
-                  <span class="n">metavar</span><span class="o">=</span><span class="s">"jobs"</span><span class="p">,</span>
-                  <span class="nb">type</span><span class="o">=</span><span class="s">"int"</span><span class="p">,</span>
-                  <span class="n">help</span><span class="o">=</span><span class="s">"Specifies the number of jobs (operations) to run in parallel."</span><span class="p">)</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"--flowchart"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"flowchart"</span><span class="p">,</span>
-                  <span class="n">metavar</span><span class="o">=</span><span class="s">"FILE"</span><span class="p">,</span>
-                  <span class="nb">type</span><span class="o">=</span><span class="s">"string"</span><span class="p">,</span>
-                  <span class="n">help</span><span class="o">=</span><span class="s">"Print flowchart of the pipeline to FILE. Flowchart format "</span>
-                       <span class="s">"depends on extension. Alternatives include ('.dot', '.jpg', "</span>
-                       <span class="s">"'*.svg', '*.png' etc). Formats other than '.dot' require "</span>
-                       <span class="s">"the dot program to be installed (http://www.graphviz.org/)."</span><span class="p">)</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"-n"</span><span class="p">,</span> <span class="s">"--just_print"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"just_print"</span><span class="p">,</span>
-                    <span class="n">action</span><span class="o">=</span><span class="s">"store_true"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
-                    <span class="n">help</span><span class="o">=</span><span class="s">"Only print a trace (description) of the pipeline. "</span>
-                         <span class="s">" The level of detail is set by --verbose."</span><span class="p">)</span>
-
-<span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">remaining_args</span><span class="p">)</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
-
-
-<span class="k">if</span> <span class="ow">not</span> <span class="n">options</span><span class="o">.</span><span class="n">flowchart</span><span class="p">:</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">options</span><span class="o">.</span><span class="n">database_file</span><span class="p">:</span>
-        <span class="n">parser</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s">"</span><span class="se">\n\n\t</span><span class="s">Missing parameter --database_file FILE</span><span class="se">\n\n</span><span class="s">"</span><span class="p">)</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">options</span><span class="o">.</span><span class="n">input_file</span><span class="p">:</span>
-        <span class="n">parser</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s">"</span><span class="se">\n\n\t</span><span class="s">Missing parameter --input_file FILE</span><span class="se">\n\n</span><span class="s">"</span><span class="p">)</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   imports</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">subprocess</span>
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Functions</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="k">def</span> <span class="nf">run_cmd</span><span class="p">(</span><span class="n">cmd_str</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Throw exception if run command fails</span>
-<span class="sd">    """</span>
-    <span class="n">process</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">(</span><span class="n">cmd_str</span><span class="p">,</span> <span class="n">stdout</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span>
-                                <span class="n">stderr</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">shell</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-    <span class="n">stdout_str</span><span class="p">,</span> <span class="n">stderr_str</span> <span class="o">=</span> <span class="n">process</span><span class="o">.</span><span class="n">communicate</span><span class="p">()</span>
-    <span class="k">if</span> <span class="n">process</span><span class="o">.</span><span class="n">returncode</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Failed to run '</span><span class="si">%s</span><span class="s">'</span><span class="se">\n</span><span class="si">%s%s</span><span class="s">Non-zero exit status </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span>
-                            <span class="p">(</span><span class="n">cmd_str</span><span class="p">,</span> <span class="n">stdout_str</span><span class="p">,</span> <span class="n">stderr_str</span><span class="p">,</span> <span class="n">process</span><span class="o">.</span><span class="n">returncode</span><span class="p">))</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Logger</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="kn">import</span> <span class="nn">logging</span>
-<span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s">"run_parallel_blast"</span><span class="p">)</span>
-<span class="c">#</span>
-<span class="c"># We are interesting in all messages</span>
-<span class="c">#</span>
-<span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
-    <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
-    <span class="n">stderrhandler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span>
-    <span class="n">stderrhandler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s">"    </span><span class="si">%(message)s</span><span class="s">"</span><span class="p">))</span>
-    <span class="n">stderrhandler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
-    <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">stderrhandler</span><span class="p">)</span>
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Pipeline tasks</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="n">original_fasta</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">input_file</span>
-<span class="n">database_file</span>  <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">database_file</span>
-<span class="n">temp_directory</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">temp_directory</span>
-<span class="n">result_file</span>    <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">result_file</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">mkdir</span><span class="p">(</span><span class="n">temp_directory</span><span class="p">))</span>
-
-<span class="nd">@split</span><span class="p">(</span><span class="n">original_fasta</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_directory</span><span class="p">,</span> <span class="s">"*.segment"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">splitFasta</span> <span class="p">(</span><span class="n">seqFile</span><span class="p">,</span> <span class="n">segments</span><span class="p">):</span>
-    <span class="sd">"""Split sequence file into</span>
-<span class="sd">       as many fragments as appropriate</span>
-<span class="sd">       depending on the size of original_fasta"""</span>
-    <span class="c">#</span>
-    <span class="c">#   Clean up any segment files from previous runs before creating new one</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">segments</span><span class="p">:</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="n">current_file_index</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">original_fasta</span><span class="p">):</span>
-        <span class="c">#</span>
-        <span class="c"># start a new file for each accession line</span>
-        <span class="c">#</span>
-        <span class="k">if</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'>'</span><span class="p">:</span>
-            <span class="n">current_file_index</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">file_name</span> <span class="o">=</span> <span class="s">"</span><span class="si">%d</span><span class="s">.segment"</span> <span class="o">%</span> <span class="n">current_file_index</span>
-            <span class="n">file_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">temp_directory</span><span class="p">,</span> <span class="n">file_name</span><span class="p">)</span>
-            <span class="n">current_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="n">current_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">splitFasta</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".segment"</span><span class="p">),</span> <span class="p">[</span><span class="s">".blastResult"</span><span class="p">,</span> <span class="s">".blastSuccess"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">runBlast</span><span class="p">(</span><span class="n">seqFile</span><span class="p">,</span>  <span class="n">output_files</span><span class="p">):</span>
-    <span class="c">#</span>
-    <span class="n">blastResultFile</span><span class="p">,</span> <span class="n">flag_file</span> <span class="o">=</span> <span class="n">output_files</span>
-    <span class="c">#</span>
-    <span class="n">run_cmd</span><span class="p">(</span><span class="s">"blastall -p blastp -d human.protein.faa -i </span><span class="si">%s</span><span class="s"> > </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">seqFile</span><span class="p">,</span> <span class="n">blastResultFile</span><span class="p">))</span>
-    <span class="c">#</span>
-    <span class="c">#   "touch" flag file to indicate success</span>
-    <span class="c">#</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">flag_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="nd">@merge</span><span class="p">(</span><span class="n">runBlast</span><span class="p">,</span> <span class="n">result_file</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">combineBlastResults</span> <span class="p">(</span><span class="n">blastResult_and_flag_Files</span><span class="p">,</span> <span class="n">combinedBlastResultFile</span><span class="p">):</span>
-    <span class="sd">"""Combine blast results"""</span>
-    <span class="c">#</span>
-    <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">combinedBlastResultFile</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">blastResult_file</span><span class="p">,</span> <span class="n">flag_file</span> <span class="ow">in</span> <span class="n">blastResult_and_flag_Files</span><span class="p">:</span>
-        <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">blastResult_file</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
-
-
-
-
-
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Print list of tasks</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">just_print</span><span class="p">:</span>
-    <span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">combineBlastResults</span><span class="p">],</span> <span class="n">verbose</span><span class="o">=</span><span class="n">options</span><span class="o">.</span><span class="n">verbose</span><span class="p">)</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Print flowchart</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="k">elif</span> <span class="n">options</span><span class="o">.</span><span class="n">flowchart</span><span class="p">:</span>
-    <span class="c"># use file extension for output format</span>
-    <span class="n">output_format</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">options</span><span class="o">.</span><span class="n">flowchart</span><span class="p">)[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span>
-    <span class="n">pipeline_printout_graph</span> <span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">options</span><span class="o">.</span><span class="n">flowchart</span><span class="p">,</span> <span class="s">"w"</span><span class="p">),</span>
-                             <span class="n">output_format</span><span class="p">,</span>
-                             <span class="p">[</span><span class="n">combineBlastResults</span><span class="p">],</span>
-                             <span class="n">no_key_legend</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Run Pipeline</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="k">else</span><span class="p">:</span>
-    <span class="n">pipeline_run</span><span class="p">([</span><span class="n">combineBlastResults</span><span class="p">],</span>  <span class="n">multiprocess</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">jobs</span><span class="p">,</span>
-                        <span class="n">logger</span> <span class="o">=</span> <span class="n">logger</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="n">options</span><span class="o">.</span><span class="n">verbose</span><span class="p">)</span>
-</pre></div>
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-                        title="previous chapter">Ruffus code</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="../paired_end_data.py.html"
-                        title="next chapter">Example code for <tt class="docutils literal"><span class="pre">FAQ</span> <span class="pre">Good</span> <span class="pre">practices:</span> <span class="pre">"What</span> <span class="pre">is</span> <span class="pre">the</span> <span class="pre">best</span> <span class="pre">way</span> <span class="pre">of</span> <span class="pre">handling</span> <span class="pre">data</span> <span class="pre">in</span> <span class="pre">file</span> <spa [...]
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-  <div class="section" id="example-code-for-faq-good-practices-what-is-the-best-way-of-handling-data-in-file-pairs-or-triplets-etc">
-<span id="faq-paired-files-code"></span><h1>Example code for <a class="reference internal" href="../faq.html#faq-paired-files"><em>FAQ Good practices: “What is the best way of handling data in file pairs (or triplets etc.)?”</em></a><a class="headerlink" href="#example-code-for-faq-good-practices-what-is-the-best-way-of-handling-data-in-file-pairs-or-triplets-etc" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="../tutorials/new_tutorial/subdivide_collate.html#new-manual-collate"><em>@collate</em></a></li>
-</ul>
-</div>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#!/usr/bin/env python</span>
-<span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">os</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">ruffus.cmdline</span> <span class="kn">as</span> <span class="nn">cmdline</span>
-<span class="kn">from</span> <span class="nn">subprocess</span> <span class="kn">import</span> <span class="n">check_call</span>
-
-<span class="n">parser</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">get_argparse</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s">"Parimala's pipeline?"</span><span class="p">)</span>
-
-<span class="hll"><span class="c">#                                                                                 .</span>
-</span><span class="hll"><span class="c">#   Very flexible handling of input files                                         .</span>
-</span><span class="hll"><span class="c">#                                                                                 .</span>
-</span><span class="hll"><span class="c">#      input files can be specified flexibly as:                                  .</span>
-</span><span class="hll"><span class="c">#                 --input a.fastq b.fastq                                         .</span>
-</span><span class="hll"><span class="c">#                 --input a.fastq --input b.fastq                                 .</span>
-</span><span class="hll"><span class="c">#                 --input *.fastq --input other/*.fastq                           .</span>
-</span><span class="hll"><span class="c">#                 --input "*.fastq"                                               .</span>
-</span><span class="hll"><span class="c">#                                                                                 .</span>
-</span><span class="hll"><span class="c">#       The last form is expanded in the script and avoids limitations on command .</span>
-</span><span class="hll"><span class="c">#           line lengths                                                          .</span>
-</span><span class="hll"><span class="c">#                                                                                 .</span>
-</span><span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'-i'</span><span class="p">,</span> <span class="s">'--input'</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s">'+'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s">"FILE"</span><span class="p">,</span> <span class="n">act [...]
-
-<span class="n">options</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
-
-<span class="c">#  standard python logger which can be synchronised across concurrent Ruffus tasks</span>
-<span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">setup_logging</span> <span class="p">(</span><span class="s">"PARIMALA"</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">log_file</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">verbose</span> [...]
-
-<span class="hll"><span class="c">#                                                                                .</span>
-</span><span class="hll"><span class="c">#   Useful code to turn input files into a flat list                             .</span>
-</span><span class="hll"><span class="c">#                                                                                .</span>
-</span><span class="kn">from</span> <span class="nn">glob</span> <span class="kn">import</span> <span class="n">glob</span>
-<span class="n">original_data_files</span> <span class="o">=</span> <span class="p">[</span><span class="n">fn</span> <span class="k">for</span> <span class="n">grouped</span> <span class="ow">in</span> <span class="n">options</span><span class="o">.</span><span class="n">input</span> <span class="k">for</span> <span class="n">glob_spec</span> <span class="ow">in</span> <span class="n">grouped</span> <span class="k">for</span> <span class="n">fn</span> <span class="ow">in</span> <span cl [...]
-<span class="k">if</span> <span class="ow">not</span> <span class="n">original_data_files</span><span class="p">:</span>
-    <span class="n">original_data_files</span> <span class="o">=</span> <span class="p">[[</span><span class="s">"C1W1_R1.fastq.gz"</span><span class="p">,</span> <span class="s">"C1W1_R2.fastq.gz"</span><span class="p">]]</span>
-    <span class="c">#raise Exception ("No matching files specified with --input.")</span>
-
-<span class="c">#   <<<----  pipelined functions go here</span>
-
-<span class="hll"><span class="c">#_________________________________________________________________________________</span>
-</span><span class="hll"><span class="c">#                                                                                .</span>
-</span><span class="hll"><span class="c">#   Group together file pairs                                                    .</span>
-</span><span class="hll"><span class="c">#_________________________________________________________________________________</span>
-</span><span class="nd">@collate</span><span class="p">(</span><span class="n">original_data_files</span><span class="p">,</span>
-            <span class="c"># match file name up to the "R1.fastq.gz"</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">"([^/]+)R[12].fastq.gz$"</span><span class="p">),</span>
-            <span class="c"># Create output parameter supplied to next task</span>
-            <span class="p">[</span><span class="s">"{path[0]}/{1[0]}paired.R1.fastq.gz"</span><span class="p">,</span>  <span class="c"># paired file 1</span>
-             <span class="s">"{path[0]}/{1[0]}paired.R2.fastq.gz"</span><span class="p">],</span> <span class="c"># paired file 2</span>
-            <span class="c"># Extra parameters for our own convenience and use</span>
-            <span class="p">[</span><span class="s">"{path[0]}/{1[0]}unpaired.R1.fastq.gz"</span><span class="p">,</span>  <span class="c"># unpaired file 1</span>
-             <span class="s">"{path[0]}/{1[0]}unpaired.R2.fastq.gz"</span><span class="p">],</span> <span class="c"># unpaired file 2</span>
-            <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">trim_fastq</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_paired_files</span><span class="p">,</span> <span class="n">discarded_unpaired_files</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">):</span>
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">input_files</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">2</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"One of read pairs </span><span class="si">%s</span><span class="s"> missing"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_files</span><span class="p">,))</span>
-    <span class="n">cmd</span> <span class="o">=</span> <span class="p">(</span><span class="s">"java -jar ~/SPRING-SUMMER_2014/Softwares/Trimmomatic/Trimmomatic-0.32/trimmomatic-0.32.jar "</span>
-           <span class="s">" PE -phred33  "</span>
-           <span class="s">" {input_files[0]} {input_files[1]} "</span>
-           <span class="s">" {output_paired_files[0]} {output_paired_files[1]} "</span>
-           <span class="s">" {discarded_unpaired_files[0]} {discarded_unpaired_files[1]} "</span>
-           <span class="s">" LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:50 "</span>
-        <span class="p">)</span>
-
-    <span class="n">check_call</span><span class="p">(</span><span class="n">cmd</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">()))</span>
-
-    <span class="k">with</span> <span class="n">logger_mutex</span><span class="p">:</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">"Hooray trim_fastq worked"</span><span class="p">)</span>
-
-<span class="hll"><span class="c">#_________________________________________________________________________________</span>
-</span><span class="hll"><span class="c">#                                                                                .</span>
-</span><span class="hll"><span class="c">#   Each file pair now makes its way down the rest of the pipeline as            .</span>
-</span><span class="hll"><span class="c">#       a couple                                                                 .</span>
-</span><span class="hll"><span class="c">#_________________________________________________________________________________</span>
-</span><span class="nd">@transform</span><span class="p">(</span><span class="n">trim_fastq</span><span class="p">,</span>
-            <span class="c"># regular expression match on first of pe files</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">"([^/]+)paired.R1.fastq.gz$"</span><span class="p">),</span>
-            <span class="c"># Output parameter supplied to next task</span>
-            <span class="s">"{path[0]}/{1[0]}.sam"</span>
-
-           <span class="c"># Extra parameters for our own convenience and use</span>
-            <span class="s">"{path[0]}/{1[0]}.pe_soap_pe"</span><span class="p">,</span>        <span class="c"># soap intermediate file</span>
-            <span class="s">"{path[0]}/{1[0]}.pe_soap_se"</span><span class="p">,</span>        <span class="c"># soap intermediate file</span>
-            <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">align_seq</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">soap_pe_output_file</span><span class="p">,</span> <span class="n">soap_se_output_file</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">):</span>
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">input_files</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">2</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"One of read pairs </span><span class="si">%s</span><span class="s"> missing"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_files</span><span class="p">,))</span>
-    <span class="n">cmd</span> <span class="o">=</span> <span class="p">(</span><span class="s">"~/SPRING-SUMMER_2014/Softwares/soap2.21release/soap "</span>
-            <span class="s">" -a {input_files[0]} "</span>
-            <span class="s">" -b {input_files[1]} "</span>
-            <span class="s">" -D Y55_genome.fa.index* "</span>
-            <span class="s">" -o {soap_pe_output_file} -2 {soap_se_output_file} -m 400 -x 600"</span><span class="p">)</span>
-
-    <span class="n">check_call</span><span class="p">(</span><span class="n">cmd</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">()))</span>
-
-
-    <span class="c">#Soap_to_sam</span>
-    <span class="n">cmd</span> <span class="o">=</span> <span class="s">" perl ~/SPRING-SUMMER_2014/Softwares/soap2sam.pl -p {soap_pe_output_file} > {output_file}"</span>
-
-    <span class="n">check_call</span><span class="p">(</span><span class="n">cmd</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">()))</span>
-
-
-    <span class="k">with</span> <span class="n">logger_mutex</span><span class="p">:</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">"Hooray align_seq worked"</span><span class="p">)</span>
-
-
-<span class="n">cmdline</span><span class="o">.</span><span class="n">run</span> <span class="p">(</span><span class="n">options</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-
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-                        title="previous chapter">Ruffus code</a></p>
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-                        title="next chapter">Ruffus Decorators</a></p>
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-        <h4><a href="../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
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-        </ul>
-
-
-        <h4 ><a href="../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
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diff --git a/doc/_build/html/faq.html b/doc/_build/html/faq.html
deleted file mode 100644
index 3f93593..0000000
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>FAQ — ruffus 2.5 documentation</title>
-    
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-      <h3>Navigation</h3>
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-        <li class="right" >
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-            <li><a href="cheatsheet.html">Cheat sheet</a> | </li>
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-            <li><a href="history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <div class="section" id="faq">
-<h1>FAQ<a class="headerlink" href="#faq" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="citations">
-<h2>Citations<a class="headerlink" href="#citations" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="q-how-should-ruffus-be-cited-in-academic-publications">
-<h3>Q. How should <em>Ruffus</em> be cited in academic publications?<a class="headerlink" href="#q-how-should-ruffus-be-cited-in-academic-publications" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The official publication describing the original version of <em>Ruffus</em> is:</p>
-<blockquote>
-<div><a class="reference external" href="http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524">Leo Goodstadt (2010)</a> : <strong>Ruffus: a lightweight Python library for computational pipelines.</strong> <em>Bioinformatics</em> 26(21): 2778-2779</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="good-practices">
-<h2>Good practices<a class="headerlink" href="#good-practices" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="q-what-is-the-best-way-of-keeping-my-data-and-workings-separate">
-<h3>Q. What is the best way of keeping my data and workings separate?<a class="headerlink" href="#q-what-is-the-best-way-of-keeping-my-data-and-workings-separate" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>It is good practice to run your pipeline in a temporary, “working” directory away from your original data.</p>
-<p>The first step of your pipeline might be to make softlinks to your original data in your working directory.
-This is example (relatively paranoid) code to do just this:</p>
-<div class="highlight-python"><div class="highlight"><pre>    <span class="k">def</span> <span class="nf">re_symlink</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">soft_link_name</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="hll"><span class="sd">        Helper function: relinks soft symbolic link if necessary</span>
-</span><span class="sd">        """</span>
-<span class="hll">        <span class="c"># Guard agains soft linking to oneself: Disastrous consequences of deleting the original files!!</span>
-</span>        <span class="k">if</span> <span class="n">input_file</span> <span class="o">==</span> <span class="n">soft_link_name</span><span class="p">:</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">"Warning: No symbolic link made. You are using the original data directory as the working directory."</span><span class="p">)</span>
-            <span class="k">return</span>
-        <span class="c"># Soft link already exists: delete for relink?</span>
-        <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">lexists</span><span class="p">(</span><span class="n">soft_link_name</span><span class="p">):</span>
-            <span class="c"># do not delete or overwrite real (non-soft link) file</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">islink</span><span class="p">(</span><span class="n">soft_link_name</span><span class="p">):</span>
-                <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> exists and is not a link"</span> <span class="o">%</span> <span class="n">soft_link_name</span><span class="p">)</span>
-            <span class="k">try</span><span class="p">:</span>
-                <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">soft_link_name</span><span class="p">)</span>
-            <span class="k">except</span><span class="p">:</span>
-                <span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-                    <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">"Can't unlink </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">soft_link_name</span><span class="p">))</span>
-        <span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">"os.symlink(</span><span class="si">%s</span><span class="s">, </span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">soft_link_name</span><span class="p">))</span>
-        <span class="c">#</span>
-        <span class="c">#   symbolic link relative to original directory so that the entire path</span>
-        <span class="c">#       can be moved around with breaking everything</span>
-        <span class="c">#</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">symlink</span><span class="p">(</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">relpath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">input_file</span><span class="p">),</span>
-                    <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">soft_link_name</span><span class="p">))),</span> <span class="n">soft_link_name</span><span class="p">)</span>
-
-    <span class="c">#</span>
-    <span class="c">#   First task should soft link data to working directory</span>
-    <span class="c">#</span>
-    <span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-    <span class="nd">@mkdir</span><span class="p">(</span><span class="n">options</span><span class="o">.</span><span class="n">working_dir</span><span class="p">)</span>
-    <span class="nd">@transform</span><span class="p">(</span> <span class="n">input_files</span><span class="p">,</span>
-                <span class="n">formatter</span><span class="p">(),</span>
-                <span class="c"># move to working directory</span>
-                <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">options</span><span class="o">.</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"{basename[0]}{ext[0]}"</span><span class="p">),</span>
-                <span class="n">logger</span><span class="p">,</span> <span class="n">logging_mutex</span>
-               <span class="p">)</span>
-    <span class="k">def</span> <span class="nf">soft_link_inputs_to_working_directory</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">soft_link_name</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">):</span>
-        <span class="sd">"""</span>
-<span class="sd">        Make soft link in working directory</span>
-<span class="sd">        """</span>
-        <span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-            <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"Linking files </span><span class="si">%(input_file)s</span><span class="s"> -> </span><span class="si">%(soft_link_name)s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="nb">locals</span><span class="p">())</span>
-        <span class="n">re_symlink</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">soft_link_name</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="q-what-is-the-best-way-of-handling-data-in-file-pairs-or-triplets-etc">
-<span id="faq-paired-files"></span><h3>Q. What is the best way of handling data in file pairs (or triplets etc.)<a class="headerlink" href="#q-what-is-the-best-way-of-handling-data-in-file-pairs-or-triplets-etc" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>In Bioinformatics, DNA data often consists of only the nucleotide sequence at the two ends of larger fragments.
-The <a class="reference external" href="http://www.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.ilmn">paired_end</a> or
-<a class="reference external" href="http://en.wikipedia.org/wiki/Shotgun_sequencing#Whole_genome_shotgun_sequencing">mate pair</a> data frequently
-consists of of file pairs with conveniently related names such as “<em>.R1.fastq” and “</em>.R2.fastq”.</p>
-<p>At some point in data pipeline, these file pairs or triplets must find each other and be analysed in the same job.</p>
-<p>Provided these file pairs or triplets are named consistently, an easiest way to regroup them is to use the
-Ruffus <a class="reference internal" href="tutorials/new_tutorial/subdivide_collate.html#new-manual-collate"><em>@collate</em></a> decorator. For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@collate</span><span class="p">(</span><span class="n">original_data_files</span><span class="p">,</span>
-
-            <span class="c"># match file name up to the "R1.fastq.gz"</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">"([^/]+)R[12].fastq.gz$"</span><span class="p">),</span>
-
-            <span class="c"># Create output parameter supplied to next task</span>
-            <span class="s">"{path[0]}/{1[0]}.sam"</span><span class="p">,</span>
-            <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">handle_paired_end</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_paired_files</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">):</span>
-    <span class="c"># check that we really have a pair of two files not an orphaned singleton</span>
-    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">input_files</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">2</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"One of read pairs </span><span class="si">%s</span><span class="s"> missing"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_files</span><span class="p">,))</span>
-
-    <span class="c"># do stuff here</span>
-</pre></div>
-</div>
-<p>This (incomplete, untested) <a class="reference internal" href="examples/paired_end_data.py.html#faq-paired-files-code"><em>example code</em></a> shows what this would look like <em>in vivo</em>.</p>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="general">
-<h2>General<a class="headerlink" href="#general" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="q-ruffus-won-t-create-dependency-graphs">
-<h3>Q. <em>Ruffus</em> won’t create dependency graphs<a class="headerlink" href="#q-ruffus-won-t-create-dependency-graphs" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>A. You need to have installed <tt class="docutils literal"><span class="pre">dot</span></tt> from <a class="reference external" href="http://www.graphviz.org/">Graphviz</a> to produce
-pretty flowcharts likes this:</p>
-<blockquote>
-<div><img alt="_images/pretty_flowchart.png" src="_images/pretty_flowchart.png" />
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="q-ruffus-seems-to-be-hanging-in-the-same-place">
-<h3>Q. <em>Ruffus</em> seems to be hanging in the same place<a class="headerlink" href="#q-ruffus-seems-to-be-hanging-in-the-same-place" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>A. If <em>ruffus</em> is interrupted, for example, by a Ctrl-C,
-you will often find the following lines of code highlighted:</p>
-<div class="highlight-python"><pre>File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 1904, in pipeline_run
-File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 1380, in run_all_jobs_in_task
-File "/xxxx/python2.6/multiprocessing/pool.py", line 507, in next
-  self._cond.wait(timeout)
-File "/xxxxx/python2.6/threading.py", line 237, in wait
-  waiter.acquire()</pre>
-</div>
-<p>This is <em>not</em> where <em>ruffus</em> is hanging but the boundary between the main programme process
-and the sub-processes which run <em>ruffus</em> jobs in parallel.</p>
-<p>This is naturally where broken execution threads get washed up onto.</p>
-</div></blockquote>
-</div>
-<div class="section" id="q-regular-expression-substitutions-don-t-work">
-<h3>Q. Regular expression substitutions don’t work<a class="headerlink" href="#q-regular-expression-substitutions-don-t-work" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>A. If you are using the special regular expression forms <tt class="docutils literal"><span class="pre">"\1"</span></tt>, <tt class="docutils literal"><span class="pre">"\2"</span></tt> etc.
-to refer to matching groups, remember to ‘escape’ the subsitution pattern string.
-The best option is to use <a class="reference external" href="http://docs.python.org/library/re.html">‘raw’ python strings</a>.
-For example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="s">r"\1_substitutes\2correctly\3four\4times"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Ruffus will throw an exception if it sees an unescaped <tt class="docutils literal"><span class="pre">"\1"</span></tt> or <tt class="docutils literal"><span class="pre">"\2"</span></tt> in a file name.</p>
-</div></blockquote>
-</div>
-<div class="section" id="q-how-to-force-a-pipeline-to-appear-up-to-date">
-<h3>Q. How to force a pipeline to appear up to date?<a class="headerlink" href="#q-how-to-force-a-pipeline-to-appear-up-to-date" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><em>I have made a trivial modification to one of my data files and now Ruffus wants to rerun my month long pipeline. How can I convince Ruffus that everything is fine and to leave things as they are?</em></p>
-<p>The standard way to do what you are trying to do is to touch all the files downstream...
-That way the modification times of your analysis files would postdate your existing files.
-You can do this manually but Ruffus also provides direct support:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span> <span class="p">(</span><span class="n">touch_files_only</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>pipeline_run will run your script normally stepping over up-to-date tasks and starting
-with jobs which look out of date. However, after that, none of your pipeline task functions
-will be called, instead, each non-up-to-date file is <a class="reference external" href="https://en.wikipedia.org/wiki/Touch_(Unix)">touch</a>-ed in
-turn so that the file modification dates follow on successively.</p>
-<p>See the documentation for <a class="reference internal" href="pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a></p>
-<p>It is even simpler if you are using the new Ruffus.cmdline support from version 2.4. You can just type</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>your script --touch_files_only <span class="o">[</span>--other_options_of_your_own_etc<span class="o">]</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>See <a class="reference internal" href="tutorials/new_tutorial/command_line.html#new-manual-cmdline"><em>command line</em></a> documentation.</p>
-</div></blockquote>
-</div>
-<div class="section" id="q-how-can-i-use-my-own-decorators-with-ruffus">
-<h3>Q. How can I use my own decorators with Ruffus?<a class="headerlink" href="#q-how-can-i-use-my-own-decorators-with-ruffus" title="Permalink to this headline">¶</a></h3>
-<p>(Thanks to Radhouane Aniba for contributing to this answer.)</p>
-<ol class="upperalpha simple">
-<li>With care! If the following two points are observed:</li>
-</ol>
-<div class="section" id="use-wraps-from-functools-or-michele-simionato-s-decorator-module">
-<h4>1. Use <a class="reference external" href="https://docs.python.org/2/library/functools.html#functools.wraps">@wraps</a>  from <tt class="docutils literal"><span class="pre">functools</span></tt> or Michele Simionato’s <a class="reference external" href="https://pypi.python.org/pypi/decorator">decorator</a> module<a class="headerlink" href="#use-wraps-from-functools-or-michele-simionato-s-decorator-module" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><p>These will automatically forward attributes from the task function correctly:</p>
-<ul class="simple">
-<li><tt class="docutils literal"><span class="pre">__name__</span></tt> and <tt class="docutils literal"><span class="pre">__module__</span></tt> is used to identify functions uniquely in a Ruffus pipeline, and</li>
-<li><tt class="docutils literal"><span class="pre">pipeline_task</span></tt> is used to hold per task data</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="always-call-ruffus-decorators-first-before-your-own-decorators">
-<h4>2. Always call Ruffus decorators first before your own decorators.<a class="headerlink" href="#always-call-ruffus-decorators-first-before-your-own-decorators" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><p>Otherwise, your decorator will be ignored.</p>
-<p>So this works:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="n">prev_task</span><span class="p">)</span>
-<span class="nd">@custom_decorator</span><span class="p">(</span><span class="n">something</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">test</span><span class="p">():</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>This is a bit futile</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c"># ignore @custom_decorator</span>
-<span class="nd">@custom_decorator</span><span class="p">(</span><span class="n">something</span><span class="p">)</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">prev_task</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">test</span><span class="p">():</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>This order dependency is an unfortunate quirk of how python decorators work. The last (rather futile)
-piece of code is equivalent to:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">test</span> <span class="o">=</span> <span class="n">custom_decorator</span><span class="p">(</span><span class="n">something</span><span class="p">)(</span><span class="n">ruffus</span><span class="o">.</span><span class="n">follows</span><span class="p">(</span><span class="n">prev_task</span><span class="p">)(</span><span class="n">test</span><span class="p">))</span>
-</pre></div>
-</div>
-<p>Unfortunately, Ruffus has no idea that someone else (<tt class="docutils literal"><span class="pre">custom_decorator</span></tt>) is also modifying the <tt class="docutils literal"><span class="pre">test()</span></tt> function
-after it (<tt class="docutils literal"><span class="pre">ruffus.follows</span></tt>) has had its go.</p>
-</div></blockquote>
-</div>
-<div class="section" id="example-decorator">
-<h4>Example decorator:<a class="headerlink" href="#example-decorator" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><p>Let us look at a decorator to time jobs:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">time</span>
-<span class="k">def</span> <span class="nf">time_func_call</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">stream</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-    <span class="sd">"""prints elapsed time to standard out, or any other file-like object with a .write() method.</span>
-<span class="sd">    """</span>
-   <span class="n">start</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
-   <span class="c"># Run the decorated function.</span>
-   <span class="n">ret</span> <span class="o">=</span> <span class="n">func</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-   <span class="c"># Stop the timer.</span>
-   <span class="n">end</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">()</span>
-   <span class="n">elapsed</span> <span class="o">=</span> <span class="n">end</span> <span class="o">-</span> <span class="n">start</span>
-   <span class="n">stream</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"{} took {} seconds</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">func</span><span class="o">.</span><span class="n">__name__</span><span class="p">,</span> <span class="n">elapsed</span><span class="p">))</span>
-   <span class="k">return</span> <span class="n">ret</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-<span class="kn">import</span> <span class="nn">time</span>
-
-<span class="nd">@time_job</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"First task"</span>
-
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">first_task</span><span class="p">)</span>
-<span class="nd">@time_job</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"Second task"</span>
-
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">second_task</span><span class="p">)</span>
-<span class="nd">@time_job</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">final_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"Final task"</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>What would <tt class="docutils literal"><span class="pre">@time_job</span></tt> look like?</p>
-</div></blockquote>
-</div>
-<div class="section" id="using-functools-wraps">
-<h4>1. Using functools <a class="reference external" href="https://docs.python.org/2/library/functools.html#functools.wraps">@wraps</a><a class="headerlink" href="#using-functools-wraps" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">functools</span>
-<span class="k">def</span> <span class="nf">time_job</span><span class="p">(</span><span class="n">stream</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">actual_time_job</span><span class="p">(</span><span class="n">func</span><span class="p">):</span>
-        <span class="nd">@functools.wraps</span><span class="p">(</span><span class="n">func</span><span class="p">)</span>
-        <span class="k">def</span> <span class="nf">wrapper</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-            <span class="k">return</span> <span class="n">time_func_call</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">stream</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-        <span class="k">return</span> <span class="n">wrapper</span>
-    <span class="k">return</span> <span class="n">actual_time_job</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="using-michele-simionato-s-decorator-module">
-<h4>2. Using Michele Simionato’s <a class="reference external" href="https://pypi.python.org/pypi/decorator">decorator</a> module<a class="headerlink" href="#using-michele-simionato-s-decorator-module" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">decorator</span>
-<span class="k">def</span> <span class="nf">time_job</span><span class="p">(</span><span class="n">stream</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">time_job</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">time_func_call</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">stream</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">decorator</span><span class="o">.</span><span class="n">decorator</span><span class="p">(</span><span class="n">time_job</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="by-hand-using-a-callable-object">
-<h4>2. By hand, using a <a class="reference external" href="https://docs.python.org/2/reference/datamodel.html#emulating-callable-objects">callable object</a><a class="headerlink" href="#by-hand-using-a-callable-object" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="k">class</span> <span class="nc">time_job</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">stream</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">stream</span> <span class="o">=</span> <span class="n">stream</span>
-    <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">func</span><span class="p">):</span>
-        <span class="k">def</span> <span class="nf">inner</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-            <span class="k">return</span> <span class="n">time_func_call</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">stream</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-        <span class="c"># remember to forward __name__</span>
-        <span class="n">inner</span><span class="o">.</span><span class="n">__name__</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">__name__</span>
-        <span class="n">inner</span><span class="o">.</span><span class="n">__module__</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">__module__</span>
-        <span class="n">inner</span><span class="o">.</span><span class="n">__doc__</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">__doc__</span>
-        <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="s">"pipeline_task"</span><span class="p">):</span>
-            <span class="n">inner</span><span class="o">.</span><span class="n">pipeline_task</span> <span class="o">=</span> <span class="n">func</span><span class="o">.</span><span class="n">pipeline_task</span>
-        <span class="k">return</span> <span class="n">inner</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="q-can-a-task-function-in-a-ruffus-pipeline-be-called-normally-outside-of-ruffus">
-<h3>Q. Can a task function in a <em>Ruffus</em> pipeline be called normally outside of Ruffus?<a class="headerlink" href="#q-can-a-task-function-in-a-ruffus-pipeline-be-called-normally-outside-of-ruffus" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>A. Yes. Most python decorators wrap themselves around a function. However, <em>Ruffus</em> leaves the
-original function untouched and unwrapped. Instead, <em>Ruffus</em> adds a <tt class="docutils literal"><span class="pre">pipeline_task</span></tt> attribute
-to the task function to signal that this is a pipelined function.</p>
-<p>This means the original task function can be called just like any other python function.</p>
-</div></blockquote>
-</div>
-<div class="section" id="q-my-ruffus-tasks-create-two-files-at-a-time-why-is-the-second-one-ignored-in-successive-stages-of-my-pipeline">
-<h3>Q. My  <em>Ruffus</em> tasks create two files at a time. Why is the second one ignored in successive stages of my pipeline?<a class="headerlink" href="#q-my-ruffus-tasks-create-two-files-at-a-time-why-is-the-second-one-ignored-in-successive-stages-of-my-pipeline" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><em>This is my code:</em></p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="s">"start.input"</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">".+"</span><span class="p">),</span> <span class="p">(</span><span class="s">"first_output.txt"</span><span class="p">,</span> <span class="s">"second_output.txt"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">task1</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">o</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".txt"</span><span class="p">),</span> <span class="s">".result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">task2</span><span class="p">],</span> <span class="n">verbose</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-<div class="highlight-python"><pre>________________________________________
-Tasks which will be run:
-
-Task = task1
-       Job = [start.input
-             ->[first_output.txt, second_output.txt]]
-
-Task = task2
-       Job = [[first_output.txt, second_output.txt]
-             ->first_output.result]
-
-________________________________________</pre>
-</div>
-</div></blockquote>
-<p>A: This code produces a single output of a tuple of 2 files. In fact, you want two
-outputs, each consisting of 1 file.</p>
-<p>You want a single job (single input) to be produce multiple outputs (multiple jobs
-in downstream tasks). This is a one-to-many operation which calls for
-<a class="reference internal" href="decorators/split.html#decorators-split"><em>@split</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-<span class="nd">@split</span><span class="p">(</span><span class="s">"start.input"</span><span class="p">,</span> <span class="p">(</span><span class="s">"first_output.txt"</span><span class="p">,</span> <span class="s">"second_output.txt"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">task1</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">o</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".txt"</span><span class="p">),</span> <span class="s">".result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">task2</span><span class="p">],</span> <span class="n">verbose</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-<div class="highlight-python"><pre>________________________________________
-Tasks which will be run:
-
-Task = task1
-       Job = [start.input
-             ->[first_output.txt, second_output.txt]]
-
-Task = task2
-       Job = [first_output.txt
-             ->first_output.result]
-       Job = [second_output.txt
-             ->second_output.result]
-
-________________________________________</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="q-how-can-a-ruffus-task-produce-output-which-goes-off-in-different-directions">
-<h3>Q. How can a <em>Ruffus</em> task produce output which goes off in different directions?<a class="headerlink" href="#q-how-can-a-ruffus-task-produce-output-which-goes-off-in-different-directions" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>A. As above, anytime there is a situation which requires a one-to-many operation, you should reach
-for <a class="reference internal" href="decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a>. The advanced form takes a regular expression, making
-it easier to produce multiple derivatives of the input file. The following example subdivides
-<em>2</em> jobs each into <em>3</em>, so that the subsequence task will run <em>2</em> x <em>3</em> = <em>6</em> jobs.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-<span class="nd">@subdivide</span><span class="p">([</span><span class="s">"1.input_file"</span><span class="p">,</span>
-            <span class="s">"2.input_file"</span><span class="p">],</span>
-            <span class="n">regex</span><span class="p">(</span><span class="s">r"(.+).input_file"</span><span class="p">),</span>      <span class="c"># match file prefix</span>
-           <span class="p">[</span><span class="s">r"\1.file_type1"</span><span class="p">,</span>
-            <span class="s">r"\1.file_type2"</span><span class="p">,</span>
-            <span class="s">r"\1.file_type3"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">split_task</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-   <span class="k">pass</span>
-
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">split_task</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">"(.+)"</span><span class="p">),</span> <span class="s">r"\1.test"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">test_split_output</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
-   <span class="k">pass</span>
-
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">test_split_output</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>Each of the original 2 files have been split in three so that test_split_output will run
-6 jobs simultaneously.</p>
-<blockquote>
-<div><div class="highlight-python"><pre>________________________________________
-Tasks which will be run:
-
-Task = split_task
-       Job = [1.input_file ->[1.file_type1, 1.file_type2, 1.file_type3]]
-       Job = [2.input_file ->[2.file_type1, 2.file_type2, 2.file_type3]]
-
-Task = test_split_output
-       Job = [1.file_type1 ->1.file_type1.test]
-       Job = [1.file_type2 ->1.file_type2.test]
-       Job = [1.file_type3 ->1.file_type3.test]
-       Job = [2.file_type1 ->2.file_type1.test]
-       Job = [2.file_type2 ->2.file_type2.test]
-       Job = [2.file_type3 ->2.file_type3.test]
-________________________________________</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="q-can-i-call-extra-code-before-each-job">
-<h3>Q. Can I call extra code before each job?<a class="headerlink" href="#q-can-i-call-extra-code-before-each-job" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>A. This is easily accomplished by hijacking the process
-for checking if jobs are up to date or not (<a class="reference internal" href="decorators/check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate</em></a>):</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-
-<span class="k">def</span> <span class="nf">run_this_before_each_job</span> <span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"Calling function before each job using these args"</span><span class="p">,</span> <span class="n">args</span>
-    <span class="c"># Remember to delegate to the default *Ruffus* code for checking if</span>
-    <span class="c">#   jobs need to run.</span>
-    <span class="k">return</span> <span class="n">needs_update_check_modify_time</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span>
-
-<span class="nd">@check_if_uptodate</span><span class="p">(</span><span class="n">run_this_before_each_job</span><span class="p">)</span>
-<span class="nd">@files</span><span class="p">([[</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">],</span> <span class="p">[</span><span class="bp">None</span><span class="p">,</span> <span class="s">"b.1"</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">task_func</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">task_func</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<div class="highlight-python"><pre>________________________________________
->>> pipeline_run([task_func])
-Calling function before each job using these args (None, 'a.1')
-Calling function before each job using these args (None, 'a.1')
-Calling function before each job using these args (None, 'b.1')
-    Job = [None -> a.1] completed
-    Job = [None -> b.1] completed
-Completed Task = task_func</pre>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Because <tt class="docutils literal"><span class="pre">run_this_before_each_job(...)</span></tt> is called whenever <em>Ruffus</em> checks to see if
-a job is up to date or not, the function may be called twice for some jobs
-(e.g. <tt class="docutils literal"><span class="pre">(None,</span> <span class="pre">'a.1')</span></tt> above).</p>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="q-does-ruffus-allow-checkpointing-to-distinguish-interrupted-and-completed-results">
-<h3>Q. Does <em>Ruffus</em> allow checkpointing: to distinguish interrupted and completed results?<a class="headerlink" href="#q-does-ruffus-allow-checkpointing-to-distinguish-interrupted-and-completed-results" title="Permalink to this headline">¶</a></h3>
-<div class="section" id="a-use-the-builtin-sqlite-checkpointing">
-<h4>A. Use the builtin sqlite checkpointing<a class="headerlink" href="#a-use-the-builtin-sqlite-checkpointing" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><p>By default, <tt class="docutils literal"><span class="pre">pipeline_run(...)</span></tt> will save the timestamps for output files from successfully run jobs to an sqlite database file (<tt class="docutils literal"><span class="pre">.ruffus_history.sqlite</span></tt>) in the current directory .</p>
-<ul class="simple">
-<li>If you are using <tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt>, you can change the checksum / timestamp database file name on the command line using  <tt class="docutils literal"><span class="pre">--checksum_file_name</span> <span class="pre">NNNN</span></tt></li>
-<li></li>
-</ul>
-<p>The level of timestamping / checksumming can be set via the <tt class="docutils literal"><span class="pre">checksum_level</span></tt> parameter:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="o">...</span><span class="p">,</span> <span class="n">checksum_level</span> <span class="o">=</span> <span class="n">N</span><span class="p">,</span> <span class="o">...</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>where the default is 1:</p>
-<div class="highlight-python"><pre>level 0 : Use only file timestamps
-level 1 : above, plus timestamp of successful job completion
-level 2 : above, plus a checksum of the pipeline function body
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</pre>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="a-use-a-flag-file">
-<h4>A. Use a flag file<a class="headerlink" href="#a-use-a-flag-file" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><p>When gmake is interrupted, it will delete the target file it is updating so that the target is
-remade from scratch when make is next run. Ruffus, by design, does not do this because, more often than
-not, the partial / incomplete file may be usefully if only to reveal, for example, what might have caused an interrupting error
-or exception. It also seems a bit too clever and underhand to go around the programmer’s back to delete files...</p>
-<p>A common <em>Ruffus</em> convention is create an empty checkpoint or “flag” file whose sole purpose
-is to record a modification-time and the successful completion of a job.</p>
-<p>This would be task with a completion flag:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   Assuming a pipelined task function named "stage1"</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">stage1</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".stage1"</span><span class="p">),</span> <span class="p">[</span><span class="s">".stage2"</span><span class="p">,</span> <span class="s">".stage2_finished"</span><span class="p">]</span> <span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage2</span> <span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="n">task_output_file</span><span class="p">,</span> <span class="n">flag_file</span> <span class="o">=</span> <span class="n">output_files</span>
-    <span class="n">cmd</span> <span class="o">=</span> <span class="p">(</span><span class="s">"do_something2 </span><span class="si">%(input_file)s</span><span class="s"> >| </span><span class="si">%(task_output_file)s</span><span class="s"> "</span><span class="p">)</span>
-    <span class="n">cmd</span> <span class="o">=</span> <span class="n">cmd</span> <span class="o">%</span> <span class="p">{</span>
-                    <span class="s">"input_file"</span><span class="p">:</span>               <span class="n">input_files</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
-                    <span class="s">"task_output_file"</span><span class="p">:</span>         <span class="n">task_output_file</span>
-                <span class="p">}</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">system</span><span class="p">(</span> <span class="n">cmd</span> <span class="p">):</span>
-        <span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-        <span class="c">#</span>
-        <span class="c">#   It worked: Create completion flag_file</span>
-        <span class="c">#</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">flag_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="c">#</span>
-        <span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-</pre></div>
-</div>
-<p>The flag_files <tt class="docutils literal"><span class="pre">xxx.stage2_finished</span></tt> indicate that each job is finished. If this is missing,
-<tt class="docutils literal"><span class="pre">xxx.stage2</span></tt> is only a partial, interrupted result.</p>
-<p>The only thing to be aware of is that the flag file will appear in the list of inputs of the
-downstream task, which should accordingly look like this:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">stage2</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".stage2"</span><span class="p">),</span> <span class="p">[</span><span class="s">".stage3"</span><span class="p">,</span> <span class="s">".stage3_finished"</span><span class="p">]</span> <span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage3</span> <span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-
-    <span class="c">#888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-    <span class="c">#</span>
-    <span class="c">#   Note that the first parameter is a LIST of input files, the last of which</span>
-    <span class="c">#       is the flag file from the previous task which we can ignore</span>
-    <span class="c">#</span>
-    <span class="n">input_file</span><span class="p">,</span> <span class="n">previous_flag_file</span>  <span class="o">=</span> <span class="n">input_files</span>
-    <span class="c">#</span>
-    <span class="c">#888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-    <span class="n">task_output_file</span><span class="p">,</span> <span class="n">flag_file</span>     <span class="o">=</span> <span class="n">output_files</span>
-    <span class="n">cmd</span> <span class="o">=</span> <span class="p">(</span><span class="s">"do_something3 </span><span class="si">%(input_file)s</span><span class="s"> >| </span><span class="si">%(task_output_file)s</span><span class="s"> "</span><span class="p">)</span>
-    <span class="n">cmd</span> <span class="o">=</span> <span class="n">cmd</span> <span class="o">%</span> <span class="p">{</span>
-                    <span class="s">"input_file"</span><span class="p">:</span>               <span class="n">input_file</span><span class="p">,</span>
-                    <span class="s">"task_output_file"</span><span class="p">:</span>         <span class="n">task_output_file</span>
-                <span class="p">}</span>
-    <span class="c"># completion flag file for this task</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">system</span><span class="p">(</span> <span class="n">cmd</span> <span class="p">):</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">flag_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>The <a class="reference internal" href="examples/bioinformatics/part2.html#examples-bioinformatics-part2-step2"><em>Bioinformatics example</em></a> contains <a class="reference internal" href="examples/bioinformatics/part2_code.html#examples-bioinformatics-part2-code"><em>code</em></a> for checkpointing.</p>
-</div></blockquote>
-</div>
-<div class="section" id="a-use-a-temp-file">
-<h4>A. Use a temp file<a class="headerlink" href="#a-use-a-temp-file" title="Permalink to this headline">¶</a></h4>
-<blockquote>
-<div><p>Thanks to Martin Goodson for suggesting this and providing an example. In his words:</p>
-<p>“I normally use a decorator to create a temporary file which is only renamed after the task has completed without any problems. This seems a more elegant solution to the problem:”</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="k">def</span> <span class="nf">usetemp</span><span class="p">(</span><span class="n">task_func</span><span class="p">):</span>
-    <span class="sd">""" Decorate a function to write to a tmp file and then rename it. So half finished tasks cannot create up to date targets.</span>
-<span class="sd">    """</span>
-    <span class="nd">@wraps</span><span class="p">(</span><span class="n">task_func</span><span class="p">)</span>
-    <span class="k">def</span> <span class="nf">wrapper_function</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="n">args</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
-        <span class="n">outnames</span><span class="o">=</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">outnames</span><span class="p">,</span> <span class="nb">basestring</span><span class="p">)</span> <span class="ow">and</span>  <span class="nb">hasattr</span><span class="p">(</span><span class="n">outnames</span><span class="p">,</span> <span class="s">'__getitem__'</span><span class="p">):</span>
-            <span class="n">tmpnames</span><span class="o">=</span><span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="o">+</span><span class="s">".tmp"</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">outnames</span><span class="p">]</span>
-            <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">=</span><span class="n">tmpnames</span>
-            <span class="n">task_func</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-            <span class="k">try</span><span class="p">:</span>
-                <span class="k">for</span> <span class="n">tmp</span><span class="p">,</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">tmpnames</span><span class="p">,</span> <span class="n">outnames</span><span class="p">):</span>
-                    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">tmp</span><span class="p">):</span>
-                        <span class="n">os</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">tmp</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">name</span><span class="p">))</span>
-            <span class="k">except</span> <span class="ne">BaseException</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
-                <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">outnames</span><span class="p">:</span>
-                    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">name</span><span class="p">):</span>
-                        <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">name</span><span class="p">)</span>
-                <span class="k">raise</span> <span class="p">(</span><span class="n">e</span><span class="p">)</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">tmp</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">outnames</span><span class="p">)</span><span class="o">+</span><span class="s">'.tmp'</span>
-            <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">=</span><span class="n">tmp</span>
-            <span class="n">task_func</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-            <span class="n">os</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">tmp</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">outnames</span><span class="p">))</span>
-<span class="k">return</span> <span class="n">wrapper_function</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Use like this:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">'client1.price'</span><span class="p">)</span>
-<span class="nd">@usetemp</span>
-<span class="k">def</span> <span class="nf">getusers</span><span class="p">(</span><span class="n">inputfile</span><span class="p">,</span> <span class="n">outputname</span><span class="p">):</span>
-    <span class="c">#**************************************************</span>
-    <span class="c"># code goes here</span>
-    <span class="c"># outputname now refers to temporary file</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-</div>
-<div class="section" id="windows">
-<h2>Windows<a class="headerlink" href="#windows" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="q-windows-seems-to-spawn-ruffus-processes-recursively">
-<h3>Q. Windows seems to spawn <em>ruffus</em> processes recursively<a class="headerlink" href="#q-windows-seems-to-spawn-ruffus-processes-recursively" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>A. It is necessary to protect the “entry point” of the program under windows.
-Otherwise, a new process will be started each time the main module is imported
-by a new Python interpreter as an unintended side effects. Causing a cascade
-of new processes.</p>
-<p>See: <a class="reference external" href="http://docs.python.org/library/multiprocessing.html#multiprocessing-programming">http://docs.python.org/library/multiprocessing.html#multiprocessing-programming</a></p>
-<p>This code works:</p>
-<div class="highlight-python"><pre>if __name__ == '__main__':
-    try:
-        pipeline_run([parallel_task], multiprocess = 5)
-except Exception, e:
-    print e.args</pre>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="sun-grid-engine-pbs-slurm-etc">
-<h2>Sun Grid Engine / PBS / SLURM etc<a class="headerlink" href="#sun-grid-engine-pbs-slurm-etc" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="q-can-ruffus-be-used-to-manage-a-cluster-or-grid-based-pipeline">
-<h3>Q. Can Ruffus be used to manage a cluster or grid based pipeline?<a class="headerlink" href="#q-can-ruffus-be-used-to-manage-a-cluster-or-grid-based-pipeline" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ol class="upperalpha simple">
-<li>Some minimum modifications have to be made to your <em>Ruffus</em> script to allow it to submit jobs to a cluster</li>
-</ol>
-<p>See <a class="reference internal" href="tutorials/new_tutorial/multiprocessing.html#new-manual-ruffus-drmaa-wrapper-run-job"><em>ruffus.drmaa_wrapper</em></a></p>
-<p>Thanks to Andreas Heger and others at CGAT and Bernie Pope for contributing ideas and code.</p>
-</div></blockquote>
-</div>
-<div class="section" id="q-when-i-submit-lots-of-jobs-via-sun-grid-engine-sge-the-head-node-occassionally-freezes-and-dies">
-<h3>Q. When I submit lots of jobs via Sun Grid Engine (SGE), the head node occassionally freezes and dies<a class="headerlink" href="#q-when-i-submit-lots-of-jobs-via-sun-grid-engine-sge-the-head-node-occassionally-freezes-and-dies" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ol class="upperalpha simple">
-<li>You need to use multithreading rather than multiprocessing. See <a class="reference internal" href="tutorials/new_tutorial/multiprocessing.html#new-manual-ruffus-drmaa-wrapper-run-job"><em>ruffus.drmaa_wrapper</em></a></li>
-</ol>
-</div></blockquote>
-</div>
-<div class="section" id="q-keeping-large-intermediate-files">
-<h3>Q. Keeping Large intermediate files<a class="headerlink" href="#q-keeping-large-intermediate-files" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Sometimes pipelines create a large number of intermediate files which might not be needed later.</p>
-<p>Unfortunately, the current design of <em>Ruffus</em> requires these files to hang around otherwise the pipeline
-will not know that it ran successfully.</p>
-<p>We have some tentative plans to get around this but in the meantime, Bernie Pope suggests
-truncating intermediate files in place, preserving timestamps:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c"># truncate a file to zero bytes, and preserve its original modification time</span>
-<span class="k">def</span> <span class="nf">zeroFile</span><span class="p">(</span><span class="nb">file</span><span class="p">):</span>
-    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="nb">file</span><span class="p">):</span>
-        <span class="c"># save the current time of the file</span>
-        <span class="n">timeInfo</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">stat</span><span class="p">(</span><span class="nb">file</span><span class="p">)</span>
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="nb">file</span><span class="p">,</span><span class="s">'w'</span><span class="p">)</span>
-        <span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
-            <span class="k">pass</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">truncate</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-            <span class="c"># change the time of the file back to what it was</span>
-            <span class="n">os</span><span class="o">.</span><span class="n">utime</span><span class="p">(</span><span class="nb">file</span><span class="p">,(</span><span class="n">timeInfo</span><span class="o">.</span><span class="n">st_atime</span><span class="p">,</span> <span class="n">timeInfo</span><span class="o">.</span><span class="n">st_mtime</span><span class="p">))</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="sharing-python-objects-between-ruffus-processes-running-concurrently">
-<h2>Sharing python objects between Ruffus processes running concurrently<a class="headerlink" href="#sharing-python-objects-between-ruffus-processes-running-concurrently" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The design of Ruffus envisages that much of the data flow in pipelines occurs in files but it is also possible to pass python objects in memory.</p>
-<p>Ruffus uses the <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html">multiprocessing</a> module and much of the following is a summary of what is covered
-in depth in the Python Standard Library <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#sharing-state-between-processes">Documentation</a>.</p>
-<p>Running Ruffus using <tt class="docutils literal"><span class="pre">pipeline_run(...,</span> <span class="pre">multiprocess</span> <span class="pre">=</span> <span class="pre">NNN)</span></tt> where <tt class="docutils literal"><span class="pre">NNN</span></tt> > 1 runs each job concurrently on up to <tt class="docutils literal"><span class="pre">NNN</span></tt> separate local processes.
-Each task function runs independently in a different python intepreter, possibly on a different CPU, in the most efficient way.
-However, this does mean we have to pay some attention to how data is sent across process boundaries (unlike the situation with <tt class="docutils literal"><span class="pre">pipeline_run(...,</span> <span class="pre">multithread</span> <span class="pre">=</span> <span class="pre">NNN)</span></tt> ).</p>
-<p>The python code and data which comprises your multitasking Ruffus job is sent to a separate process in three ways:</p>
-<ol class="arabic simple">
-<li>The python function code and data objects are <a class="reference external" href="http://docs.python.org/2/library/pickle.html">pickled</a>, i.e. converting into a byte stream, by the master process, sent to the remote process
-before being converted back into normal python (unpickling).</li>
-<li>The parameters for your jobs, i.e. what Ruffus calls your task functions with, are separately <a class="reference external" href="http://docs.python.org/2/library/pickle.html">pickled</a> and sent to the remote process via
-<a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Queue">multiprocessing.Queue</a></li>
-<li>You can share and synchronise other data yourselves. The canonical example is the logger provided by <tt class="docutils literal"><span class="pre">Ruffus.cmdline.setup_logging</span></tt></li>
-</ol>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Check that your function code and data can be <a class="reference external" href="http://docs.python.org/2/library/pickle.html#what-can-be-pickled-and-unpickled">pickled</a>.</p>
-<p class="last">Only functions, built-in functions and classes defined at the top level of a module are picklable.</p>
-</div>
-<p>The following answers are a short “how-to” for sharing and synchronising data yourselves.</p>
-</div></blockquote>
-<div class="section" id="can-ordinary-python-objects-be-shared-between-processes">
-<h3>Can ordinary python objects be shared between processes?<a class="headerlink" href="#can-ordinary-python-objects-be-shared-between-processes" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ol class="upperalpha">
-<li><p class="first">Objects which can be <a class="reference external" href="http://docs.python.org/2/library/pickle.html">pickled</a> can be shared as is. These include</p>
-<blockquote>
-<div><ul class="simple">
-<li>numbers</li>
-<li>strings</li>
-<li>tuples, lists, sets, and dictionaries containing only objects which can be <a class="reference external" href="http://docs.python.org/2/library/pickle.html">pickled</a>.</li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">If these do not change during your pipeline, you can just use them without any further effort in your task.</p>
-</li>
-<li><p class="first">If you need to use the value at the point when the task function is <em>called</em>, then you need to pass the python object as parameters to your task.
-For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="hll"> <span class="c"># changing_list changes...</span>
-</span> <span class="nd">@transform</span><span class="p">(</span><span class="n">previous_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".foo"</span><span class="p">),</span> <span class="s">".bar"</span><span class="p">,</span> <span class="n">changing_list</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">next_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">changing_list</span><span class="p">):</span>
-     <span class="k">pass</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">If you need to use the value when the task function is <em>run</em> then see <a class="reference internal" href="#how-about-synchronising-python-objects-in-real-time"><em>the following answer.</em></a>.</p>
-</li>
-</ol>
-</div></blockquote>
-</div>
-<div class="section" id="why-am-i-getting-picklingerror">
-<h3>Why am I getting <tt class="docutils literal"><span class="pre">PicklingError</span></tt>?<a class="headerlink" href="#why-am-i-getting-picklingerror" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>What is happening? Didn’t <a class="reference external" href="https://en.wikipedia.org/wiki/Battle_of_the_Herrings">Joan of Arc</a> solve this once and for all?</p>
-<ol class="upperalpha">
-<li><p class="first">Some of the data or code in your function cannot be <a class="reference external" href="http://docs.python.org/2/library/pickle.html">pickled</a> and is being asked to be sent by python <tt class="docutils literal"><span class="pre">mulitprocessing</span></tt> across process boundaries.</p>
-<blockquote>
-<div><p>When you run your pipeline using multiprocess:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">logger</span> <span class="o">=</span> <span class="n">ruffusLoggerProxy</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>You will get the following errors:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="ne">Exception</span> <span class="ow">in</span> <span class="n">thread</span> <span class="n">Thread</span><span class="o">-</span><span class="mi">2</span><span class="p">:</span>
-<span class="n">Traceback</span> <span class="p">(</span><span class="n">most</span> <span class="n">recent</span> <span class="n">call</span> <span class="n">last</span><span class="p">):</span>
-  <span class="n">File</span> <span class="s">"/path/to/python/python2.7/threading.py"</span><span class="p">,</span> <span class="n">line</span> <span class="mi">808</span><span class="p">,</span> <span class="ow">in</span> <span class="n">__bootstrap_inner</span>
-    <span class="bp">self</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
-  <span class="n">File</span> <span class="s">"/path/to/python/python2.7/threading.py"</span><span class="p">,</span> <span class="n">line</span> <span class="mi">761</span><span class="p">,</span> <span class="ow">in</span> <span class="n">run</span>
-    <span class="bp">self</span><span class="o">.</span><span class="n">__target</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">__args</span><span class="p">,</span> <span class="o">*</span> <span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">__kwargs</span><span class="p">)</span>
-  <span class="n">File</span> <span class="s">"/path/to/python/python2.7/multiprocessing/pool.py"</span><span class="p">,</span> <span class="n">line</span> <span class="mi">342</span><span class="p">,</span> <span class="ow">in</span> <span class="n">_handle_tasks</span>
-    <span class="n">put</span><span class="p">(</span><span class="n">task</span><span class="p">)</span>
-<span class="n">PicklingError</span><span class="p">:</span> <span class="n">Can</span><span class="s">'t pickle <type '</span><span class="n">function</span><span class="s">'>: attribute lookup __builtin__.function failed</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>which go away when you set <tt class="docutils literal"><span class="pre">pipeline_run([],</span> <span class="pre">multiprocess</span> <span class="pre">=</span> <span class="pre">1,</span> <span class="pre">...)</span></tt></p>
-</div></blockquote>
-</li>
-</ol>
-<p>Unfortunately, pickling errors are particularly ill-served by standard python error messages. The only really good advice is to take the offending
-code and try and <a class="reference external" href="http://docs.python.org/2/library/pickle.html">pickle</a> it yourself and narrow down the errors. Check your objects against the list
-in the <a class="reference external" href="http://docs.python.org/2/library/pickle.html#what-can-be-pickled-and-unpickled">pickle</a> module.
-Watch out especially for nested functions. These will have to be moved to file scope.
-Other objects may have to be passed in proxy (see below).</p>
-</div></blockquote>
-</div>
-<div class="section" id="how-about-synchronising-python-objects-in-real-time">
-<span id="id1"></span><h3>How about synchronising python objects in real time?<a class="headerlink" href="#how-about-synchronising-python-objects-in-real-time" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ol class="upperalpha simple">
-<li>You can use managers and proxy objects from the <a class="reference external" href="http://docs.python.org/library/multiprocessing.html">multiprocessing</a> module.</li>
-</ol>
-<p>The underlying python object would be owned and managed by a (hidden) server process. Other processes can access the shared objects transparently by using proxies. This is how the logger provided by
-<tt class="docutils literal"><span class="pre">Ruffus.cmdline.setup_logging</span></tt> works:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#  optional logger which can be passed to ruffus tasks</span>
-<span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">setup_logging</span> <span class="p">(</span><span class="n">__name__</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">log_file</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">verbose</span><span class= [...]
-</pre></div>
-</div>
-<p><tt class="docutils literal"><span class="pre">logger</span></tt> is a proxy for the underlying python <a class="reference external" href="http://docs.python.org/2/library/logging.html">logger</a> object, and it can be shared freely between processes.</p>
-<p>The best course is to pass <tt class="docutils literal"><span class="pre">logger</span></tt> as a parameter to a <em>Ruffus</em> task.</p>
-<p>The only caveat is that we should make sure multiple jobs are not writting to the log at the same time. To synchronise logging, we use proxy to a non-reentrant <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Lock">multiprocessing.lock</a>.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">setup_logging</span> <span class="p">(</span><span class="n">__name__</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">log_file</span><span class="p">,</span> <span class="n">options</span><span cl [...]
-
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">previous_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".foo"</span><span class="p">),</span> <span class="s">".bar"</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">next_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">):</span>
-    <span class="k">with</span> <span class="n">logger_mutex</span><span class="p">:</span>
-        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"We are in the middle of next_task: </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">))</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="can-i-share-and-synchronise-my-own-python-classes-via-proxies">
-<h3>Can I  share and synchronise my own python classes via proxies?<a class="headerlink" href="#can-i-share-and-synchronise-my-own-python-classes-via-proxies" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ol class="upperalpha">
-<li><p class="first"><a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.managers.SyncManager">multiprocessing.managers.SyncManager</a> provides out of the box support for lists, arrays and dicts etc.</p>
-<blockquote>
-<div><p>Most of the time, we can use a “vanilla” manager provided by <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.sharedctypes.multiprocessing.Manager">multiprocessing.Manager()</a>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">multiprocessing</span>
-<span class="n">manager</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Manager</span><span class="p">()</span>
-
-<span class="n">list_proxy</span> <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">list</span><span class="p">()</span>
-<span class="n">dict_proxy</span> <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">dict</span><span class="p">()</span>
-<span class="n">lock_proxy</span>          <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Lock</span><span class="p">()</span>
-<span class="n">namespace_proxy</span>     <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Namespace</span><span class="p">()</span>
-<span class="n">queue_proxy</span>         <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Queue</span><span class="p">([</span><span class="n">maxsize</span><span class="p">])</span>
-<span class="n">rentrant_lock_proxy</span> <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">RLock</span><span class="p">()</span>
-<span class="n">semaphore_proxy</span>     <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Semaphore</span><span class="p">([</span><span class="n">value</span><span class="p">])</span>
-<span class="n">char_array_proxy</span>    <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Array</span><span class="p">(</span><span class="s">'c'</span><span class="p">)</span>
-<span class="n">integer_proxy</span>       <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Value</span><span class="p">(</span><span class="s">'i'</span><span class="p">,</span> <span class="mi">6</span><span class="p">)</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">previous_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".foo"</span><span class="p">),</span> <span class="s">".bar"</span><span class="p">,</span> <span class="n">lock_proxy</span><span class="p">,</span> <span class="n">dict_proxy</span><span class="p">,</span> <span class="n">list_proxy</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">next_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">lock_proxy</span><span class="p">,</span> <span class="n">dict_proxy</span><span class="p">,</span> <span class="n">list_proxy</span><span class="p">):</span>
-    <span class="k">with</span> <span class="n">lock_proxy</span><span class="p">:</span>
-        <span class="n">list_proxy</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
-        <span class="n">dict_proxy</span><span class="p">[</span><span class="s">'a'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">5</span>
-</pre></div>
-</div>
-</div></blockquote>
-</li>
-</ol>
-<p>However, you can also create proxy custom classes for your own objects.</p>
-<p>In this case you may need to derive from  <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.managers.SyncManager">multiprocessing.managers.SyncManager</a>
-and register proxy functions. See <tt class="docutils literal"><span class="pre">Ruffus.proxy_logger</span></tt> for an example of how to do this.</p>
-</div></blockquote>
-</div>
-<div class="section" id="how-do-i-send-python-objects-back-and-forth-without-tangling-myself-in-horrible-synchronisation-code">
-<h3>How do I send python objects back and forth without tangling myself in horrible synchronisation code?<a class="headerlink" href="#how-do-i-send-python-objects-back-and-forth-without-tangling-myself-in-horrible-synchronisation-code" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ol class="upperalpha simple">
-<li>Sharing python objects by passing messages is a much more modern and safer way to coordinate multitasking than using synchronization primitives like locks.</li>
-</ol>
-<p>The python <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#pipes-and-queues">multiprocessing</a> module provides support for passing python objects as messages between processes.
-You can either use <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Pipe">pipes</a>
-or <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Queue">queues</a>.
-The idea is that one process pushes and object onto a <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Pipe">pipe</a> or <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Queue">queue</a>
-and the other processes pops it out at the other end. <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Pipe">Pipes</a> are
-only two ended so <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Queue">queues</a> are usually a better fit for sending data to multiple Ruffus jobs.</p>
-<p>Proxies for <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.managers.SyncManager.Queue">queues</a> can be passed between processes as in the previous section</p>
-</div></blockquote>
-</div>
-<div class="section" id="how-do-i-share-large-amounts-of-data-efficiently-across-processes">
-<h3>How do I share large amounts of data efficiently across processes?<a class="headerlink" href="#how-do-i-share-large-amounts-of-data-efficiently-across-processes" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ol class="upperalpha simple">
-<li>If it is really impractical to use data files on disk, you can put the data in shared memory.</li>
-</ol>
-<p>It is possible to create shared objects using shared memory which can be inherited by child processes or passed as Ruffus parameters.
-This is probably most efficently done via the <a class="reference external" href="http://docs.python.org/2/library/multiprocessing.html#multiprocessing.Array">array</a>
-interface. Again, it is easy to create locks and proxies for synchronised access:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">multiprocessing</span> <span class="kn">import</span> <span class="n">Process</span><span class="p">,</span> <span class="n">Lock</span>
-<span class="kn">from</span> <span class="nn">multiprocessing.sharedctypes</span> <span class="kn">import</span> <span class="n">Value</span><span class="p">,</span> <span class="n">Array</span>
-<span class="kn">from</span> <span class="nn">ctypes</span> <span class="kn">import</span> <span class="n">Structure</span><span class="p">,</span> <span class="n">c_double</span>
-
-<span class="n">manager</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">Manager</span><span class="p">()</span>
-
-<span class="n">lock_proxy</span>          <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Lock</span><span class="p">()</span>
-<span class="n">int_array_proxy</span>     <span class="o">=</span> <span class="n">manager</span><span class="o">.</span><span class="n">Array</span><span class="p">(</span><span class="s">'i'</span><span class="p">,</span> <span class="p">[</span><span class="mi">123</span><span class="p">]</span> <span class="o">*</span> <span class="mi">100</span><span class="p">)</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">previous_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".foo"</span><span class="p">),</span> <span class="s">".bar"</span><span class="p">,</span> <span class="n">lock_proxy</span><span class="p">,</span> <span class="n">int_array_proxy</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">next_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">lock_proxy</span><span class="p">,</span> <span class="n">int_array_proxy</span><span class="p">):</span>
-    <span class="k">with</span> <span class="n">lock_proxy</span><span class="p">:</span>
-        <span class="n">int_array_proxy</span><span class="p">[</span><span class="mi">23</span><span class="p">]</span> <span class="o">=</span> <span class="mi">71</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">FAQ</a><ul>
-<li><a class="reference internal" href="#citations">Citations</a><ul>
-<li><a class="reference internal" href="#q-how-should-ruffus-be-cited-in-academic-publications">Q. How should <em>Ruffus</em> be cited in academic publications?</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#good-practices">Good practices</a><ul>
-<li><a class="reference internal" href="#q-what-is-the-best-way-of-keeping-my-data-and-workings-separate">Q. What is the best way of keeping my data and workings separate?</a></li>
-<li><a class="reference internal" href="#q-what-is-the-best-way-of-handling-data-in-file-pairs-or-triplets-etc">Q. What is the best way of handling data in file pairs (or triplets etc.)</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#general">General</a><ul>
-<li><a class="reference internal" href="#q-ruffus-won-t-create-dependency-graphs">Q. <em>Ruffus</em> won’t create dependency graphs</a></li>
-<li><a class="reference internal" href="#q-ruffus-seems-to-be-hanging-in-the-same-place">Q. <em>Ruffus</em> seems to be hanging in the same place</a></li>
-<li><a class="reference internal" href="#q-regular-expression-substitutions-don-t-work">Q. Regular expression substitutions don’t work</a></li>
-<li><a class="reference internal" href="#q-how-to-force-a-pipeline-to-appear-up-to-date">Q. How to force a pipeline to appear up to date?</a></li>
-<li><a class="reference internal" href="#q-how-can-i-use-my-own-decorators-with-ruffus">Q. How can I use my own decorators with Ruffus?</a><ul>
-<li><a class="reference internal" href="#use-wraps-from-functools-or-michele-simionato-s-decorator-module">1. Use @wraps  from <tt class="docutils literal"><span class="pre">functools</span></tt> or Michele Simionato’s decorator module</a></li>
-<li><a class="reference internal" href="#always-call-ruffus-decorators-first-before-your-own-decorators">2. Always call Ruffus decorators first before your own decorators.</a></li>
-<li><a class="reference internal" href="#example-decorator">Example decorator:</a></li>
-<li><a class="reference internal" href="#using-functools-wraps">1. Using functools @wraps</a></li>
-<li><a class="reference internal" href="#using-michele-simionato-s-decorator-module">2. Using Michele Simionato’s decorator module</a></li>
-<li><a class="reference internal" href="#by-hand-using-a-callable-object">2. By hand, using a callable object</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#q-can-a-task-function-in-a-ruffus-pipeline-be-called-normally-outside-of-ruffus">Q. Can a task function in a <em>Ruffus</em> pipeline be called normally outside of Ruffus?</a></li>
-<li><a class="reference internal" href="#q-my-ruffus-tasks-create-two-files-at-a-time-why-is-the-second-one-ignored-in-successive-stages-of-my-pipeline">Q. My  <em>Ruffus</em> tasks create two files at a time. Why is the second one ignored in successive stages of my pipeline?</a></li>
-<li><a class="reference internal" href="#q-how-can-a-ruffus-task-produce-output-which-goes-off-in-different-directions">Q. How can a <em>Ruffus</em> task produce output which goes off in different directions?</a></li>
-<li><a class="reference internal" href="#q-can-i-call-extra-code-before-each-job">Q. Can I call extra code before each job?</a></li>
-<li><a class="reference internal" href="#q-does-ruffus-allow-checkpointing-to-distinguish-interrupted-and-completed-results">Q. Does <em>Ruffus</em> allow checkpointing: to distinguish interrupted and completed results?</a><ul>
-<li><a class="reference internal" href="#a-use-the-builtin-sqlite-checkpointing">A. Use the builtin sqlite checkpointing</a></li>
-<li><a class="reference internal" href="#a-use-a-flag-file">A. Use a flag file</a></li>
-<li><a class="reference internal" href="#a-use-a-temp-file">A. Use a temp file</a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li><a class="reference internal" href="#windows">Windows</a><ul>
-<li><a class="reference internal" href="#q-windows-seems-to-spawn-ruffus-processes-recursively">Q. Windows seems to spawn <em>ruffus</em> processes recursively</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#sun-grid-engine-pbs-slurm-etc">Sun Grid Engine / PBS / SLURM etc</a><ul>
-<li><a class="reference internal" href="#q-can-ruffus-be-used-to-manage-a-cluster-or-grid-based-pipeline">Q. Can Ruffus be used to manage a cluster or grid based pipeline?</a></li>
-<li><a class="reference internal" href="#q-when-i-submit-lots-of-jobs-via-sun-grid-engine-sge-the-head-node-occassionally-freezes-and-dies">Q. When I submit lots of jobs via Sun Grid Engine (SGE), the head node occassionally freezes and dies</a></li>
-<li><a class="reference internal" href="#q-keeping-large-intermediate-files">Q. Keeping Large intermediate files</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#sharing-python-objects-between-ruffus-processes-running-concurrently">Sharing python objects between Ruffus processes running concurrently</a><ul>
-<li><a class="reference internal" href="#can-ordinary-python-objects-be-shared-between-processes">Can ordinary python objects be shared between processes?</a></li>
-<li><a class="reference internal" href="#why-am-i-getting-picklingerror">Why am I getting <tt class="docutils literal"><span class="pre">PicklingError</span></tt>?</a></li>
-<li><a class="reference internal" href="#how-about-synchronising-python-objects-in-real-time">How about synchronising python objects in real time?</a></li>
-<li><a class="reference internal" href="#can-i-share-and-synchronise-my-own-python-classes-via-proxies">Can I  share and synchronise my own python classes via proxies?</a></li>
-<li><a class="reference internal" href="#how-do-i-send-python-objects-back-and-forth-without-tangling-myself-in-horrible-synchronisation-code">How do I send python objects back and forth without tangling myself in horrible synchronisation code?</a></li>
-<li><a class="reference internal" href="#how-do-i-share-large-amounts-of-data-efficiently-across-processes">How do I share large amounts of data efficiently across processes?</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="implementation_notes.html"
-                        title="previous chapter">Implementation Tips</a></p>
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-                        title="next chapter">Glossary</a></p>
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-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
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-            <li><a href="decorators/product.html">@product </a>                              </li>
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-        </ul>
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-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
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diff --git a/doc/_build/html/gallery.html b/doc/_build/html/gallery.html
deleted file mode 100644
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+++ /dev/null
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-    <title>Hall of Fame: User contributed flowcharts — ruffus 2.5 documentation</title>
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-            
-  <img alt="_images/logo.jpg" src="_images/logo.jpg" />
-<div class="section" id="hall-of-fame-user-contributed-flowcharts">
-<h1>Hall of Fame: User contributed flowcharts<a class="headerlink" href="#hall-of-fame-user-contributed-flowcharts" title="Permalink to this headline">¶</a></h1>
-<p>Please contribute your own work flows in your favourite colours with (an optional) short description
-to email: ruffus_lib at llew.org.uk</p>
-<div class="section" id="rnaseq-pipeline">
-<h2>RNASeq pipeline<a class="headerlink" href="#rnaseq-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference external" href="http://en.wikipedia.org/wiki/RNA-Seq">http://en.wikipedia.org/wiki/RNA-Seq</a></p>
-<p>Mapping transcripts onto genomes using high-throughput sequencing technologies (<a class="reference download internal" href="_downloads/gallery_rna_seq.svg"><tt class="xref download docutils literal"><span class="pre">svg</span></tt></a>).</p>
-<a class="reference external image-reference" href="_downloads/gallery_rna_seq.svg"><img alt="_images/gallery_rna_seq.png" src="_images/gallery_rna_seq.png" /></a>
-</div></blockquote>
-</div>
-<div class="section" id="non-coding-evolutionary-constraints">
-<h2>non-coding evolutionary constraints<a class="headerlink" href="#non-coding-evolutionary-constraints" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference external" href="http://en.wikipedia.org/wiki/Noncoding_DNA">http://en.wikipedia.org/wiki/Noncoding_DNA</a></p>
-<p>Non-protein coding evolutionary constraints in different species (<a class="reference download internal" href="_downloads/gallery_dless.svg"><tt class="xref download docutils literal"><span class="pre">svg</span></tt></a>).</p>
-<a class="reference external image-reference" href="_downloads/gallery_dless.svg"><img alt="_images/gallery_dless.png" src="_images/gallery_dless.png" /></a>
-</div></blockquote>
-</div>
-<div class="section" id="snp-annotation">
-<h2>SNP annotation<a class="headerlink" href="#snp-annotation" title="Permalink to this headline">¶</a></h2>
-<p>Predicting impact of different Single Nucleotide Polymorphisms</p>
-<p><a class="reference external" href="http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism">http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism</a></p>
-<p>Population variation across genomes (<a class="reference download internal" href="_downloads/gallery_snp_annotation.svg"><tt class="xref download docutils literal"><span class="pre">svg</span></tt></a>).</p>
-<a class="reference external image-reference" href="_downloads/gallery_snp_annotation.svg"><img alt="_images/gallery_snp_annotation.png" src="_images/gallery_snp_annotation.png" /></a>
-<p>Using “pseudo” targets to run only part of the pipeline (<a class="reference download internal" href="_downloads/gallery_snp_annotation_consequences.svg"><tt class="xref download docutils literal"><span class="pre">svg</span></tt></a>).</p>
-<a class="reference external image-reference" href="_downloads/gallery_snp_annotation_consequences.svg"><img alt="_images/gallery_snp_annotation_consequences.png" src="_images/gallery_snp_annotation_consequences.png" /></a>
-</div>
-<div class="section" id="chip-seq-analysis">
-<h2>Chip-Seq analysis<a class="headerlink" href="#chip-seq-analysis" title="Permalink to this headline">¶</a></h2>
-<p>Analysing DNA binding sites with Chip-Seq
-<a class="reference external" href="http://en.wikipedia.org/wiki/Chip-Sequencing">http://en.wikipedia.org/wiki/Chip-Sequencing</a></p>
-<blockquote>
-<div><p>(<a class="reference download internal" href="_downloads/gallery_big_pipeline.svg"><tt class="xref download docutils literal"><span class="pre">svg</span></tt></a>)</p>
-<a class="reference external image-reference" href="_downloads/gallery_big_pipeline.svg"><img alt="_images/gallery_big_pipeline.png" src="_images/gallery_big_pipeline.png" /></a>
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-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Hall of Fame: User contributed flowcharts</a><ul>
-<li><a class="reference internal" href="#rnaseq-pipeline">RNASeq pipeline</a></li>
-<li><a class="reference internal" href="#non-coding-evolutionary-constraints">non-coding evolutionary constraints</a></li>
-<li><a class="reference internal" href="#snp-annotation">SNP annotation</a></li>
-<li><a class="reference internal" href="#chip-seq-analysis">Chip-Seq analysis</a></li>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
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-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
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-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
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diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html
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-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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- <a href="#Symbols"><strong>Symbols</strong></a>
- | <a href="#A"><strong>A</strong></a>
- | <a href="#B"><strong>B</strong></a>
- | <a href="#C"><strong>C</strong></a>
- | <a href="#D"><strong>D</strong></a>
- | <a href="#E"><strong>E</strong></a>
- | <a href="#F"><strong>F</strong></a>
- | <a href="#G"><strong>G</strong></a>
- | <a href="#I"><strong>I</strong></a>
- | <a href="#J"><strong>J</strong></a>
- | <a href="#L"><strong>L</strong></a>
- | <a href="#M"><strong>M</strong></a>
- | <a href="#N"><strong>N</strong></a>
- | <a href="#O"><strong>O</strong></a>
- | <a href="#P"><strong>P</strong></a>
- | <a href="#R"><strong>R</strong></a>
- | <a href="#S"><strong>S</strong></a>
- | <a href="#T"><strong>T</strong></a>
- | <a href="#U"><strong>U</strong></a>
- 
-</div>
-<h2 id="Symbols">Symbols</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    @active_if
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/active_if.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/active_if.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @check_if_uptodate
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/check_if_uptodate.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @collate
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/collate.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/subdivide_collate.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @collate (Advanced Usage)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/collate_ex.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @collate, add_inputs(...)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/collate_ex.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @collate, inputs(...)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/collate_ex.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @combinations
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/combinations.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @combinations_with_replacement
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/combinations_with_replacement.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @files
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files.html#index-1">Manual</a>
-  </dt>
-
-        
-  <dt><a href="decorators/files.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/onthefly.html#index-1">Tutorial on-the-fly parameter generation</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files.html#index-3">check if up to date</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files.html#index-2">in parallel</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @files (on-the-fly parameter generation)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/files_ex.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @files_re
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/files_re.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-9">combine (Deprecated Syntax)</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @follow
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-3">imposing order with</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @follows
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/follows.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-4">mkdir (Manual)</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-6">mkdir (Syntax)</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @graphviz
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/graphviz.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    @jobs_limit
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/jobs_limit.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/multiprocessing.html#index-3">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @merge
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/merge.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @mkdir
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/mkdir.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @originate
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/originate.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @parallel
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/parallel.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/parallel.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @permutations
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/permutations.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @posttask
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/posttask.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-7">touch_file (Syntax)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/posttask.html#index-1">touchfile (Manual)</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @product
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/product.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @split
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/split.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @subdivide
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/subdivide.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/subdivide_collate.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @transform
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/transform.html#index-0">Syntax</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-2">multiple dependencies</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @transform, add_inputs(...)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/transform_ex.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    @transform, inputs(...)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/transform_ex.html#index-0">Syntax</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="A">A</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="design.html#index-2">Acknowledgements</a>
-  </dt>
-
-      
-  <dt>
-    add_inputs
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-4">Indicator Object (Adding additional input parameters)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/inputs.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="task.html#ruffus.task.args_param_factory">args_param_factory() (in module ruffus.task)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="B">B</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="tutorials/new_tutorial/exceptions.html#index-1">break</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="C">C</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    check if up to date
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files.html#index-3">@files</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    check_if_uptodate
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/check_if_uptodate.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Checking dependencies
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/dependencies.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="task.html#ruffus.task.collate_param_factory">collate_param_factory() (in module ruffus.task)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    combinatorics
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/combinatorics.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    combine
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-9">@follows (Deprecated Syntax)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files_re.html#index-1">Manual</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    command line
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/command_line.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Comparison of Ruffus with alternatives
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="design.html#index-1">Design</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="D">D</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    data sharing across processes
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/multiprocessing.html#index-2">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="glossary.html#term-decorator"><strong>decorator</strong></a>
-  </dt>
-
-      
-  <dt>
-    decorators_compendium
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/decorators_compendium.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    defining tasks out of order
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-1">output_from</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    deprecated @files
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    deprecated @files_re
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files_re.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Design
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="design.html#index-1">Comparison of Ruffus with alternatives</a>
-  </dt>
-
-        
-  <dt><a href="design.html#index-0">Ruffus</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    drmaa
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="drmaa_wrapper_functions.html#index-0">run_job</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="E">E</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="tutorials/new_tutorial/exceptions.html#index-1">errors</a>
-  </dt>
-
-      
-  <dt>
-    Etymology
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="why_ruffus.html#index-0">Ruffus</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Exception
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-4">Missing input files</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    Exceptions
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="tutorials/new_tutorial/exceptions.html#index-1">exceptions</a>
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/exceptions.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="F">F</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="task.html#ruffus.task.files_param_factory">files_param_factory() (in module ruffus.task)</a>
-  </dt>
-
-      
-  <dt>
-    flag files
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-6">Manual</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    flowchart colours
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/flowchart_colours.html#index-0">Tutorial</a>, <a href="tutorials/new_tutorial/flowchart_colours_code.html#index-0">[1]</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    for rerunning jobs
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-3">rules</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    formatter
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-1">Indicator Object (Disambiguating parameters)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/output_file_names.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="G">G</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="glossary.html#term-generator"><strong>generator</strong></a>
-  </dt>
-
-      
-  <dt>
-    globs
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-5">inputs parameters</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    globs in input parameters
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-5">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="I">I</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="tutorials/new_tutorial/introduction.html#index-1">importing ruffus</a>
-  </dt>
-
-      
-  <dt>
-    imposing order with
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-3">@follow</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    in parallel
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files.html#index-2">@files</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Indicator Object (Adding additional input parameters)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-4">add_inputs</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="decorators/indicator_objects.html#index-0">Indicator Object (Disambiguating parameters)</a>
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-9">combine</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-1">formatter</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-6">mkdir</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-8">output_from</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-3">regex</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-2">suffix</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-7">touch_file</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Indicator Object (Replacing input parameters)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-5">inputs</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    input / output parameters
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform.html#index-2">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    inputs
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-5">Indicator Object (Replacing input parameters)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/inputs.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    inputs parameters
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-5">globs</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Interrupted Pipeline
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    interrupting tasks
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-1">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="tutorials/new_tutorial/exceptions.html#index-1">interrupts</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="J">J</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="glossary.html#term-job"><strong>job</strong></a>
-  </dt>
-
-      
-  <dt><a href="task.html#ruffus.task.job_wrapper_generic">job_wrapper_generic() (in module ruffus.task)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="task.html#ruffus.task.job_wrapper_io_files">job_wrapper_io_files() (in module ruffus.task)</a>
-  </dt>
-
-      
-  <dt><a href="task.html#ruffus.task.job_wrapper_mkdir">job_wrapper_mkdir() (in module ruffus.task)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="L">L</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    logging
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/logging.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    logging customising
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/logging.html#index-3">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    logging with ruffus.cmdline
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/logging.html#index-2">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    logging your own message
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/logging.html#index-4">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="M">M</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="proxy_logger.html#ruffus.proxy_logger.make_shared_logger_and_proxy">make_shared_logger_and_proxy() (in module ruffus.proxy_logger)</a>
-  </dt>
-
-      
-  <dt>
-    Manual
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files.html#index-1">@files</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-5">Timestamp resolution</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/deprecated_files_re.html#index-1">combine</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-6">flag files</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    merge
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/merge.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="task.html#ruffus.task.merge_param_factory">merge_param_factory() (in module ruffus.task)</a>
-  </dt>
-
-      
-  <dt>
-    Missing input files
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-4">Exception</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    Mixing tasks, globs and file names
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-6">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    mkdir
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-4">@follows (Manual)</a>
-  </dt>
-
-        
-  <dt><a href="decorators/indicator_objects.html#index-6">@follows (Syntax)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/mkdir.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    multiple dependencies
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-2">@transform</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="tutorials/new_tutorial/exceptions.html#index-1">multiple errors</a>
-  </dt>
-
-      
-  <dt>
-    multiprocessing
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/multiprocessing.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="N">N</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    Name origins
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="why_ruffus.html#index-0">Ruffus</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="task.html#ruffus.task.needs_update_check_directory_missing">needs_update_check_directory_missing() (in module ruffus.task)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="task.html#ruffus.task.needs_update_check_modify_time">needs_update_check_modify_time() (in module ruffus.task)</a>
-  </dt>
-
-  </dl></td>
-</tr></table>
-
-<h2 id="O">O</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    on_the_fly
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/onthefly.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    one to one @transform
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform.html#index-1">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    originate
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/originate.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    output file names
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/output_file_names.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    output_from
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-8">Indicator Object (Disambiguating parameters)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-1">defining tasks out of order</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-1">referring to functions before they are defined</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    overview
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/introduction.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="P">P</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    pipeline functions
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="pipeline_functions.html#index-3">pipeline_get_task_names</a>
-  </dt>
-
-        
-  <dt><a href="pipeline_functions.html#index-2">pipeline_printout_graph</a>
-  </dt>
-
-        
-  <dt><a href="pipeline_functions.html#index-0">pipeline_run</a>, <a href="pipeline_functions.html#index-1">[1]</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    pipeline_get_task_names
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="pipeline_functions.html#index-3">print list of task names without running the pipeline</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    pipeline_printout
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="pipeline_functions.html#index-1">Printout simulated run of the pipeline</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/pipeline_printout.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="task.html#ruffus.task.pipeline_printout">pipeline_printout() (in module ruffus.task)</a>
-  </dt>
-
-      
-  <dt>
-    pipeline_printout_graph
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/pipeline_printout_graph.html#index-0">Tutorial</a>
-  </dt>
-
-        
-  <dt><a href="pipeline_functions.html#index-2">print flowchart representation of pipeline functions</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="task.html#ruffus.task.pipeline_printout_graph">pipeline_printout_graph() (in module ruffus.task)</a>
-  </dt>
-
-      
-  <dt>
-    pipeline_run
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="pipeline_functions.html#index-0">Run pipeline</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/introduction.html#index-2">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    pipeline_run touch mode
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/multiprocessing.html#index-4">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    pipeline_run verbosity
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/logging.html#index-1">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="task.html#ruffus.task.pipeline_run">pipeline_run() (in module ruffus.task)</a>
-  </dt>
-
-      
-  <dt>
-    pipeline_run(multiprocess)
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/multiprocessing.html#index-1">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    posttask
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/posttask.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    print flowchart representation of pipeline functions
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="pipeline_functions.html#index-2">pipeline_printout_graph</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    print list of task names without running the pipeline
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="pipeline_functions.html#index-3">pipeline_get_task_names</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Printout simulated run of the pipeline
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="pipeline_functions.html#index-1">pipeline_printout</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="R">R</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    referring to functions before they are defined
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-1">output_from</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Regenerating the checkpoint file
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-2">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    regex
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-3">Indicator Object (Disambiguating parameters)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/output_file_names.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Ruffus
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="design.html#index-0">Design</a>
-  </dt>
-
-        
-  <dt><a href="why_ruffus.html#index-0">Etymology</a>
-  </dt>
-
-        
-  <dt><a href="why_ruffus.html#index-0">Name origins</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Ruffus names list
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/list_of_ruffus_names.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="proxy_logger.html#module-ruffus.proxy_logger">ruffus.proxy_logger (module)</a>
-  </dt>
-
-      
-  <dt>
-    rules
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-3">for rerunning jobs</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Run drmaa
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="drmaa_wrapper_functions.html#index-0">run_job</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Run pipeline
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="pipeline_functions.html#index-0">pipeline_run</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    run_job
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="drmaa_wrapper_functions.html#index-0">Run drmaa</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="S">S</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="proxy_logger.html#ruffus.proxy_logger.setup_std_shared_logger">setup_std_shared_logger() (in module ruffus.proxy_logger)</a>
-  </dt>
-
-      
-  <dt><a href="tutorials/new_tutorial/exceptions.html#index-1">signalling</a>
-  </dt>
-
-      
-  <dt>
-    split
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/split.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="task.html#ruffus.task.split_param_factory">split_param_factory() (in module ruffus.task)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    string substiution for inputs
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/inputs.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    suffix
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-2">Indicator Object (Disambiguating parameters)</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/output_file_names.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Syntax
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/active_if.html#index-0">@active_if</a>
-  </dt>
-
-        
-  <dt><a href="decorators/check_if_uptodate.html#index-0">@check_if_uptodate</a>
-  </dt>
-
-        
-  <dt><a href="decorators/collate.html#index-0">@collate</a>
-  </dt>
-
-        
-  <dt><a href="decorators/collate_ex.html#index-0">@collate (Advanced Usage)</a>
-  </dt>
-
-        
-  <dt><a href="decorators/collate_ex.html#index-0">@collate, add_inputs(...)</a>
-  </dt>
-
-        
-  <dt><a href="decorators/collate_ex.html#index-0">@collate, inputs(...)</a>
-  </dt>
-
-        
-  <dt><a href="decorators/combinations.html#index-0">@combinations</a>
-  </dt>
-
-        
-  <dt><a href="decorators/combinations_with_replacement.html#index-0">@combinations_with_replacement</a>
-  </dt>
-
-        
-  <dt><a href="decorators/files.html#index-0">@files</a>
-  </dt>
-
-        
-  <dt><a href="decorators/files_ex.html#index-0">@files (on-the-fly parameter generation)</a>
-  </dt>
-
-        
-  <dt><a href="decorators/files_re.html#index-0">@files_re</a>
-  </dt>
-
-        
-  <dt><a href="decorators/follows.html#index-0">@follows</a>
-  </dt>
-
-        
-  <dt><a href="decorators/graphviz.html#index-0">@graphviz</a>
-  </dt>
-
-        
-  <dt><a href="decorators/jobs_limit.html#index-0">@jobs_limit</a>
-  </dt>
-
-        
-  <dt><a href="decorators/merge.html#index-0">@merge</a>
-  </dt>
-
-        
-  <dt><a href="decorators/mkdir.html#index-0">@mkdir</a>
-  </dt>
-
-        
-  <dt><a href="decorators/originate.html#index-0">@originate</a>
-  </dt>
-
-        
-  <dt><a href="decorators/parallel.html#index-0">@parallel</a>
-  </dt>
-
-        
-  <dt><a href="decorators/permutations.html#index-0">@permutations</a>
-  </dt>
-
-        
-  <dt><a href="decorators/posttask.html#index-0">@posttask</a>
-  </dt>
-
-        
-  <dt><a href="decorators/product.html#index-0">@product</a>
-  </dt>
-
-        
-  <dt><a href="decorators/split.html#index-0">@split</a>
-  </dt>
-
-        
-  <dt><a href="decorators/subdivide.html#index-0">@subdivide</a>
-  </dt>
-
-        
-  <dt><a href="decorators/transform.html#index-0">@transform</a>
-  </dt>
-
-        
-  <dt><a href="decorators/transform_ex.html#index-0">@transform, add_inputs(...)</a>
-  </dt>
-
-        
-  <dt><a href="decorators/transform_ex.html#index-0">@transform, inputs(...)</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-</tr></table>
-
-<h2 id="T">T</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt><a href="task.html#ruffus.task.t_black_hole_logger">t_black_hole_logger (class in ruffus.task)</a>
-  </dt>
-
-      
-  <dt><a href="task.html#ruffus.task.t_stderr_logger">t_stderr_logger (class in ruffus.task)</a>
-  </dt>
-
-      
-  <dt><a href="glossary.html#term-task"><strong>task</strong></a>
-  </dt>
-
-      
-  <dt>
-    Task completion
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Timestamp resolution
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-5">Manual</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    touch mode pipeline_run
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/multiprocessing.html#index-4">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    touch_file
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="decorators/indicator_objects.html#index-7">@posttask (Syntax)</a>
-  </dt>
-
-      </dl></dd>
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-      
-  <dt>
-    touchfile
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/posttask.html#index-1">@posttask (Manual)</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    transform
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt><a href="task.html#ruffus.task.transform_param_factory">transform_param_factory() (in module ruffus.task)</a>
-  </dt>
-
-      
-  <dt>
-    transforming in parallel
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-0">Tutorial</a>
-  </dt>
-
-      </dl></dd>
-      
-  <dt>
-    Tutorial
-  </dt>
-
-      <dd><dl>
-        
-  <dt><a href="tutorials/new_tutorial/active_if.html#index-0">@active_if</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/subdivide_collate.html#index-0">@collate</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/multiprocessing.html#index-3">@jobs_limit</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/parallel.html#index-0">@parallel</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/subdivide_collate.html#index-0">@subdivide</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/dependencies.html#index-0">Checking dependencies</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-0">Exceptions</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-0">Interrupted Pipeline</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/transform_in_parallel.html#index-6">Mixing tasks, globs and file names</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-2">Regenerating the checkpoint file</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/list_of_ruffus_names.html#index-0">Ruffus names list</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-0">Task completion</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/checkpointing.html#index-0">Up to date</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/inputs.html#index-0">add_inputs</a>
-  </dt>
-
-        
-  <dt><a href="tutorials/new_tutorial/check_if_uptodate.html#index-0">check_if_uptodate</a>
-  </dt>
-
-        
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-  </dt>
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-  </dt>
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-  </dt>
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-  </dt>
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-  </dt>
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-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
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-            <li><a href="decorators/product.html">@product </a>                              </li>
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-        <h4 >Pipeline functions</h4>
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-  <div class="section" id="glossary">
-<h1>Glossary<a class="headerlink" href="#glossary" title="Permalink to this headline">¶</a></h1>
-<dl class="glossary docutils">
-<dt id="term-task">task</dt>
-<dd><p class="first">A stage in a computational pipeline.</p>
-<p>Each <strong>task</strong> in <em>ruffus</em> is represented by a python function.</p>
-<p>For example, a task might be to find the products of a sets of two numbers:</p>
-<div class="last highlight-python"><pre>4 x 5 = 20
-5 x 6 = 30
-2 x 7 = 14</pre>
-</div>
-</dd>
-<dt id="term-job">job</dt>
-<dd><p class="first">Any number of operations which can be run in parallel and make up
-the work in a stage of a computional pipeline.</p>
-<p>Each <strong>task</strong> in <em>ruffus</em> is a separate call to the <strong>task</strong> function.</p>
-<p>For example, if a task is to find products of numbers, each of these will be a separate job.</p>
-<blockquote>
-<div><p>Job1:</p>
-<div class="highlight-python"><pre>4 x 5 = 20</pre>
-</div>
-<p>Job2:</p>
-<div class="highlight-python"><pre>5 x 6 = 30</pre>
-</div>
-<p>Job3:</p>
-<div class="highlight-python"><pre>2 x 7 = 14</pre>
-</div>
-</div></blockquote>
-<p class="last">Jobs need not complete in order.</p>
-</dd>
-<dt id="term-decorator">decorator</dt>
-<dd><p class="first">Ruffus decorators allow functions to be incorporated into a computational
-pipeline, with automatic generation of parameters, dependency checking etc.,
-without modifying any code within the function.
-Quoting from the <a class="reference external" href="http://wiki.python.org/moin/PythonDecorators">python wiki</a>:</p>
-<blockquote class="last">
-<div><p>A Python decorator is a specific change to the Python syntax that
-allows us to more conveniently alter functions and methods.</p>
-<p>Decorators dynamically alter the functionality of a function, method, or
-class without having to directly use subclasses or change the source code
-of the function being decorated.</p>
-</div></blockquote>
-</dd>
-<dt id="term-generator">generator</dt>
-<dd><p class="first">python generators are new to python 2.2
-(see <a class="reference external" href="http://www.ibm.com/developerworks/library/l-pycon.html">Charming Python: Iterators and simple generators</a>).
-They allow iterable data to be generated on the fly.</p>
-<p>Ruffus asks for generators when you want to generate <strong>job</strong> parameters dynamically.</p>
-<p>Each set of job parameters is returned by the <tt class="docutils literal"><span class="pre">yield</span></tt> keyword for
-greater clarity. For example,:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">def</span> <span class="nf">generate_job_parameters</span><span class="p">():</span>
-
-    <span class="k">for</span> <span class="n">file_index</span><span class="p">,</span> <span class="n">file_name</span> <span class="ow">in</span> <span class="n">iterate</span><span class="p">(</span><span class="n">all_file_names</span><span class="p">):</span>
-
-        <span class="c"># parameter for each job</span>
-        <span class="k">yield</span> <span class="n">file_index</span><span class="p">,</span> <span class="n">file_name</span>
-</pre></div>
-</div>
-<p class="last">Each job takes the parameters <tt class="docutils literal"><span class="pre">file_index</span></tt> and <tt class="docutils literal"><span class="pre">file_name</span></tt></p>
-</dd>
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-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-        <h4 >Pipeline functions</h4>
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-  <div class="section" id="major-features-added-to-ruffus">
-<h1>Major Features added to Ruffus<a class="headerlink" href="#major-features-added-to-ruffus" title="Permalink to this headline">¶</a></h1>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">See <a class="reference internal" href="todo.html#todo"><em>To do list</em></a> for future enhancements to Ruffus</p>
-</div>
-<div class="section" id="version-2-5rc">
-<h2>version 2.5RC<a class="headerlink" href="#version-2-5rc" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>31st July 2014: Release Candidate</p>
-<p>5th August 2014: Release</p>
-</div></blockquote>
-<div class="section" id="python3-compatability-but-at-least-python-2-6-is-now-required">
-<h3>1) Python3 compatability (but at least python 2.6 is now required)<a class="headerlink" href="#python3-compatability-but-at-least-python-2-6-is-now-required" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Ruffus v2.5 is now python3 compatible. This has required surprisingly many changes to the codebase. Please report any bugs to me.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><strong>Ruffus now requires at least python 2.6</strong></p>
-<p class="last">It proved to be impossible to support python 2.5 and python 3.x at the same time.</p>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="ctrl-c-interrupts">
-<h3>2) Ctrl-C interrupts<a class="headerlink" href="#ctrl-c-interrupts" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Ruffus now mostly(!) terminates gracefully when interrupted by Ctrl-C .</p>
-<p>Please send me bug reports for when this doesn’t work with a minimally reproducible case.</p>
-<p>This means that, in general, if an <tt class="docutils literal"><span class="pre">Exception</span></tt> is thrown during your pipeline but you don’t want to wait for the rest of the jobs to complete, you can still press Ctrl-C at any point.
-Note that you may still need to clean up spawned processes, for example, using <tt class="docutils literal"><span class="pre">qdel</span></tt> if you are using <tt class="docutils literal"><span class="pre">Ruffus.drmaa_wrapper</span></tt></p>
-</div></blockquote>
-</div>
-<div class="section" id="customising-flowcharts-in-pipeline-printout-graph-with-graphviz">
-<h3>3) Customising flowcharts in pipeline_printout_graph() with <tt class="docutils literal"><span class="pre">@graphviz</span></tt><a class="headerlink" href="#customising-flowcharts-in-pipeline-printout-graph-with-graphviz" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><em>Contributed by Sean Davis, with improved syntax via Jake Biesinger</em></p>
-<p>The graphics for each task can have its own attributes (URL, shape, colour) etc. by adding
-<a class="reference external" href="http://www.graphviz.org/doc/info/attrs.html">graphviz attributes</a>
-using the <tt class="docutils literal"><span class="pre">@graphviz</span></tt> decorator.</p>
-<ul>
-<li><p class="first">This allows HTML formatting in the task names (using the <tt class="docutils literal"><span class="pre">label</span></tt> parameter as in the following example).
-HTML labels <strong>must</strong> be enclosed in <tt class="docutils literal"><span class="pre"><</span></tt> and <tt class="docutils literal"><span class="pre">></span></tt>. E.g.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">label</span> <span class="o">=</span> <span class="s">"<Line <BR/> wrapped task_name()>"</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">You can also opt to keep the task name and wrap it with a prefix and suffix:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">label_suffix</span> <span class="o">=</span> <span class="s">"??? "</span><span class="p">,</span> <span class="n">label_prefix</span> <span class="o">=</span> <span class="s">": What is this?"</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">The <tt class="docutils literal"><span class="pre">URL</span></tt> attribute allows the generation of clickable svg, and also client / server
-side image maps usable in web pages.
-See <a class="reference external" href="http://www.graphviz.org/content/output-formats#dimap">Graphviz documentation</a></p>
-</li>
-</ul>
-<p>Example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@graphviz</span><span class="p">(</span><span class="n">URL</span><span class="o">=</span><span class="s">'"http://cnn.com"'</span><span class="p">,</span> <span class="n">fillcolor</span> <span class="o">=</span> <span class="s">'"#FFCCCC"'</span><span class="p">,</span>
-                <span class="n">color</span> <span class="o">=</span> <span class="s">'"#FF0000"'</span><span class="p">,</span> <span class="n">pencolor</span><span class="o">=</span><span class="s">'"#FF0000"'</span><span class="p">,</span> <span class="n">fontcolor</span><span class="o">=</span><span class="s">'"#4B6000"'</span><span class="p">,</span>
-                <span class="n">label_suffix</span> <span class="o">=</span> <span class="s">"???"</span><span class="p">,</span> <span class="n">label_prefix</span> <span class="o">=</span> <span class="s">"What is this?<BR/> "</span><span class="p">,</span>
-                <span class="n">label</span> <span class="o">=</span> <span class="s">"<What <FONT COLOR=</span><span class="se">\"</span><span class="s">red</span><span class="se">\"</span><span class="s">>is</FONT>this>"</span><span class="p">,</span>
-                <span class="n">shape</span><span class="o">=</span> <span class="s">"component"</span><span class="p">,</span> <span class="n">height</span> <span class="o">=</span> <span class="mf">1.5</span><span class="p">,</span> <span class="n">peripheries</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span>
-                <span class="n">style</span><span class="o">=</span><span class="s">"dashed"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Up_to_date_task2</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="c">#   Can use dictionary if you wish...</span>
-<span class="n">graphviz_params</span> <span class="o">=</span> <span class="p">{</span><span class="s">"URL"</span><span class="p">:</span><span class="s">"http://cnn.com"</span><span class="p">,</span> <span class="s">"fontcolor"</span><span class="p">:</span> <span class="s">'"#FF00FF"'</span><span class="p">}</span>
-<span class="nd">@graphviz</span><span class="p">(</span><span class="o">**</span><span class="n">graphviz_params</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">myTask</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span><span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<a class="reference internal image-reference" href="_images/history_html_flowchart.png"><img alt="_images/history_html_flowchart.png" src="_images/history_html_flowchart.png" style="width: 336.6px; height: 316.5px;" /></a>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="consistent-verbosity-levels">
-<h3>4. Consistent verbosity levels<a class="headerlink" href="#consistent-verbosity-levels" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The verbosity levels are now more fine-grained and consistent between pipeline_printout and pipeline_run.
-Note that At verbosity > 2, <tt class="docutils literal"><span class="pre">pipeline_run</span></tt>  outputs lists of up-to-date tasks before running the pipeline.
-Many users who defaulted to using a verbosity of 3 may want to move up to <tt class="docutils literal"><span class="pre">verbose</span> <span class="pre">=</span> <span class="pre">4</span></tt>.</p>
-<blockquote>
-<div><ul class="simple">
-<li><strong>level 0</strong> : <em>Nothing</em></li>
-<li><strong>level 1</strong> : <em>Out-of-date Task names</em></li>
-<li><strong>level 2</strong> : <em>All Tasks (including any task function docstrings)</em></li>
-<li><strong>level 3</strong> : <em>Out-of-date Jobs in Out-of-date Tasks, no explanation</em></li>
-<li><strong>level 4</strong> : <em>Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings</em></li>
-<li><strong>level 5</strong> : <em>All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)</em></li>
-<li><strong>level 6</strong> : <em>All jobs in All Tasks whether out of date or not</em></li>
-<li><strong>level 10</strong>: <em>Logs messages useful only for debugging ruffus pipeline code</em></li>
-</ul>
-</div></blockquote>
-<ul class="simple">
-<li>Defaults to <strong>level 4</strong> for pipeline_printout: <em>Out of date jobs, with explanations and warnings</em></li>
-<li>Defaults to <strong>level 1</strong> for pipeline_run: <em>Out-of-date Task names</em></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="allow-abbreviated-paths-from-pipeline-run-or-pipeline-printout">
-<h3>5. Allow abbreviated paths from <tt class="docutils literal"><span class="pre">pipeline_run</span></tt> or <tt class="docutils literal"><span class="pre">pipeline_printout</span></tt><a class="headerlink" href="#allow-abbreviated-paths-from-pipeline-run-or-pipeline-printout" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Please contact me with suggestions if you find the abbreviations useful but “aesthetically challenged”!</p>
-</div>
-<p>Some pipelines produce interminable lists of long filenames. It would be nice to be able to abbreviate this
-to just enough information to follow the progress.</p>
-<dl class="docutils">
-<dt>Ruffus now allows either</dt>
-<dd><ol class="first arabic">
-<li><p class="first">Only the nth top level sub-directories to be included</p>
-</li>
-<li><p class="first">The message to be truncated to a specified number of characters (to fit on a line, for example)</p>
-<p>Note that the number of characters specified is the separate length of the input and output parameters,
-not the entire message. You many need to specify a smaller limit that you expect (e.g. <tt class="docutils literal"><span class="pre">60</span></tt> rather than <cite>80</cite>)</p>
-</li>
-</ol>
-<div class="last highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="n">NNN</span><span class="p">)</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="o">-</span><span class="n">MMM</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>The <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span></tt> parameter restricts the length of input / output file paths to either</p>
-<blockquote>
-<div><ul class="simple">
-<li>NNN levels of nested paths</li>
-<li>A total of MMM characters, MMM is specified by setting <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span></tt> to -MMM (i.e. negative values)</li>
-</ul>
-<p><tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span></tt> defaults to <tt class="docutils literal"><span class="pre">2</span></tt></p>
-</div></blockquote>
-<p>For example:</p>
-<blockquote>
-<div><p>Given <tt class="docutils literal"><span class="pre">["aa/bb/cc/dddd.txt",</span> <span class="pre">"aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt"]</span></tt></p>
-<div class="highlight-python"><div class="highlight"><pre><span class="hll"> <span class="c"># Original relative paths</span>
-</span> <span class="s">"[aa/bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"</span>
-
-<span class="hll"> <span class="c"># Full abspath</span>
-</span> <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="s">"[/test/ruffus/src/aa/bb/cc/dddd.txt, /test/ruffus/src/aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"</span>
-
-<span class="hll"> <span class="c"># Specifed level of nested directories</span>
-</span> <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="mi">1</span>
- <span class="s">"[.../dddd.txt, .../gggg.txt]"</span>
-
- <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="mi">2</span>
- <span class="s">"[.../cc/dddd.txt, .../ffff/gggg.txt]"</span>
-
- <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="mi">3</span>
- <span class="s">"[.../bb/cc/dddd.txt, .../eeee/ffff/gggg.txt]"</span>
-
-
-<span class="hll"> <span class="c"># Truncated to MMM characters</span>
-</span> <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="o">-</span><span class="mi">60</span>
- <span class="s">"<???> /bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>If you are using <tt class="docutils literal"><span class="pre">ruffus.cmdline</span></tt>, the abbreviated path lengths can be specified on
-the command line as an extension to the verbosity:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre> <span class="c"># verbosity of 4</span>
- yourscript.py --verbose 4
-
-<span class="hll"> <span class="c"># display three levels of nested directories</span>
-</span> yourscript.py --verbose 4:3
-
-<span class="hll"> <span class="c"># restrict input and output parameters to 60 letters</span>
-</span> yourscript.py --verbose 4:-60
-</pre></div>
-</div>
-<p>The number after the colon is the abbreviated path length</p>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="other-changes">
-<h3>Other changes<a class="headerlink" href="#other-changes" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li>BUG FIX: Output producing wild cards was not saved in the checksum files!!!</li>
-<li>BUG FIX: @mkdir bug under Windows. Thanks to Sean Turley. (Aargh! Different exceptions are thrown in Windows vs. Linux for the same condition!)</li>
-<li>Added <a class="reference internal" href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names"><em>pipeline_get_task_names(...)</em></a> which returns all task name as a list of strings. Thanks to Clare Sloggett</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="version-2-4-1">
-<h2>version 2.4.1<a class="headerlink" href="#version-2-4-1" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>26th April 2014</p>
-<ul class="simple">
-<li>Breaking changes to drmaa API suggested by Bernie Pope to ensure portability across different drmaa implementations (SGE, SLURM etc.)</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-4">
-<h2>version 2.4<a class="headerlink" href="#version-2-4" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>4th April 2014</div></blockquote>
-<div class="section" id="additions-to-ruffus-namespace">
-<h3>Additions to <tt class="docutils literal"><span class="pre">ruffus</span></tt> namespace<a class="headerlink" href="#additions-to-ruffus-namespace" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="tutorials/new_tutorial/output_file_names.html#new-manual-formatter"><em>formatter()</em></a> (<a class="reference internal" href="decorators/indicator_objects.html#decorators-formatter"><em>syntax</em></a>)</li>
-<li><a class="reference internal" href="tutorials/new_tutorial/originate.html#new-manual-originate"><em>originate()</em></a> (<a class="reference internal" href="decorators/originate.html#decorators-originate"><em>syntax</em></a>)</li>
-<li><a class="reference internal" href="tutorials/new_tutorial/subdivide_collate.html#new-manual-subdivide"><em>subdivide()</em></a> (<a class="reference internal" href="decorators/subdivide.html#decorators-subdivide"><em>syntax</em></a>)</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="installation-use-pip">
-<h3>Installation: use pip<a class="headerlink" href="#installation-use-pip" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><pre>sudo pip install ruffus --upgrade</pre>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="command-line-support">
-<h3>1) Command Line support<a class="headerlink" href="#command-line-support" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div>The optional <tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt> module provides support for a set of common command
-line arguments which make writing <em>Ruffus</em> pipelines much more pleasant.
-See <a class="reference internal" href="tutorials/new_tutorial/command_line.html#new-manual-cmdline"><em>manual</em></a></div></blockquote>
-</div>
-<div class="section" id="check-pointing">
-<h3>2) Check pointing<a class="headerlink" href="#check-pointing" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul>
-<li><p class="first">Contributed by <strong>Jake Biesinger</strong></p>
-</li>
-<li><p class="first">See <a class="reference internal" href="tutorials/new_tutorial/checkpointing.html#new-manual-checkpointing"><em>Manual</em></a></p>
-</li>
-<li><p class="first">Uses a fault resistant sqlite database file to log i/o files, and additional checksums</p>
-</li>
-<li><p class="first">defaults to checking file timestamps stored in the current directory (<tt class="docutils literal"><span class="pre">ruffus_utilility.RUFFUS_HISTORY_FILE</span> <span class="pre">=</span> <span class="pre">'.ruffus_history.sqlite'</span></tt>)</p>
-</li>
-<li><p class="first"><a class="reference internal" href="pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(..., checksum_level = N, ...)</em></a></p>
-<blockquote>
-<div><ul class="simple">
-<li>level 0 = CHECKSUM_FILE_TIMESTAMPS      : Classic mode. Use only file timestamps (no checksum file will be created)</li>
-<li>level 1 = CHECKSUM_HISTORY_TIMESTAMPS   : Also store timestamps in a database after successful job completion</li>
-<li>level 2 = CHECKSUM_FUNCTIONS            : As above, plus a checksum of the pipeline function body</li>
-<li>level 3 = CHECKSUM_FUNCTIONS_AND_PARAMS : As above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</li>
-<li>defaults to level 1</li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">Can speed up trivial tasks: Previously Ruffus always added an extra 1 second pause between tasks
-to guard against file systems (Ext3, FAT, some NFS) with low timestamp granularity.</p>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="subdivide-syntax">
-<h3>3) <a class="reference internal" href="tutorials/new_tutorial/subdivide_collate.html#new-manual-subdivide"><em>subdivide()</em></a> (<a class="reference internal" href="decorators/subdivide.html#decorators-subdivide"><em>syntax</em></a>)<a class="headerlink" href="#subdivide-syntax" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li>Take a list of input jobs (like <a class="reference internal" href="decorators/transform.html#decorators-transform"><em>@transform</em></a>) but further splits each into multiple jobs, i.e. it is a <strong>many->even more</strong> relationship</li>
-<li>synonym for the deprecated <tt class="docutils literal"><span class="pre">@split(...,</span> <span class="pre">regex(),</span> <span class="pre">...)</span></tt></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="mkdir-syntax-with-formatter-suffix-and-regex">
-<h3>4) <a class="reference internal" href="tutorials/new_tutorial/mkdir.html#new-manual-mkdir"><em>mkdir()</em></a> (<a class="reference internal" href="decorators/mkdir.html#decorators-mkdir"><em>syntax</em></a>) with <a class="reference internal" href="tutorials/new_tutorial/output_file_names.html#new-manual-formatter"><em>formatter()</em></a>, <a class="reference internal" href="decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a>  and <a class="reference interna [...]
-<blockquote>
-<div><ul class="simple">
-<li>allows directories to be created depending on runtime parameters or the output of previous tasks</li>
-<li>behaves just like <a class="reference internal" href="decorators/transform.html#decorators-transform"><em>@transform</em></a> but with its own (internal) function which does the actual work of making a directory</li>
-<li>Previous behavior is retained:<tt class="docutils literal"><span class="pre">mkdir</span></tt> continues to work seamlessly inside <a class="reference internal" href="decorators/follows.html#decorators-follows"><em>@follows</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="originate-syntax">
-<h3>5) <a class="reference internal" href="tutorials/new_tutorial/originate.html#new-manual-originate"><em>originate()</em></a> (<a class="reference internal" href="decorators/originate.html#decorators-originate"><em>syntax</em></a>)<a class="headerlink" href="#originate-syntax" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li>Generates output files without dependencies from scratch  (<em>ex nihilo</em>!)</li>
-<li>For first step in a pipeline</li>
-<li>Task function obviously only takes output and not input parameters. (There <em>are</em> no inputs!)</li>
-<li>synonym for <a class="reference internal" href="decorators/split.html#decorators-split"><em>@split(None,...)</em></a></li>
-<li>See <a class="reference internal" href="decorators/originate.html#decorators-originate"><em>Summary</em></a> / <a class="reference internal" href="tutorials/new_tutorial/originate.html#new-manual-originate"><em>Manual</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="new-flexible-formatter-syntax-alternative-to-regex-suffix">
-<h3>6) New flexible <a class="reference internal" href="tutorials/new_tutorial/output_file_names.html#new-manual-formatter"><em>formatter()</em></a> (<a class="reference internal" href="decorators/indicator_objects.html#decorators-formatter"><em>syntax</em></a>) alternative to <a class="reference internal" href="decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a>  & <a class="reference internal" href="decorators/indicator_objects.html#decorators-suffix"><em>suffi [...]
-<blockquote>
-<div><ul class="simple">
-<li>Easy manipulation of path subcomponents in the style of <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.split">os.path.split()</a></li>
-<li>Regular expressions are no longer necessary for path manipulation</li>
-<li>Familiar python syntax</li>
-<li>Optional regular expression matches</li>
-<li>Can refer to any in the list of N input files (not only the first file as for <tt class="docutils literal"><span class="pre">regex(...)</span></tt>)</li>
-<li>Can even refer to individual letters within a match</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="combinatorics-all-vs-all-decorators">
-<h3>7) Combinatorics (all vs. all decorators)<a class="headerlink" href="#combinatorics-all-vs-all-decorators" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#new-manual-product"><em>@product</em></a>  (See <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.product">itertools.product</a>)</li>
-<li><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#new-manual-permutations"><em>@permutations</em></a>  (See <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.permutations">itertools.permutations</a>)</li>
-<li><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#new-manual-combinations"><em>@combinations</em></a> (See <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.combinations">itertools.combinations</a>)</li>
-<li><a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#new-manual-combinations-with-replacement"><em>@combinations_with_replacement</em></a> (See <a class="reference external" href="http://docs.python.org/2/library/itertools.html#itertools.combinations_with_replacement">itertools.combinations_with_replacement</a>)</li>
-<li>in optional <a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#new-manual-combinatorics"><em>combinatorics</em></a> module</li>
-<li>Only <a class="reference internal" href="tutorials/new_tutorial/output_file_names.html#new-manual-formatter"><em>formatter()</em></a> provides the necessary flexibility to construct the output. (<a class="reference internal" href="decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a> and <a class="reference internal" href="decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> are not supported.)</li>
-<li>See <a class="reference internal" href="decorators/decorators.html#decorators-combinatorics"><em>Summary</em></a> / <a class="reference internal" href="tutorials/new_tutorial/combinatorics.html#new-manual-combinatorics"><em>Manual</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="drmaa-support-and-multithreading">
-<h3>8) drmaa support and multithreading:<a class="headerlink" href="#drmaa-support-and-multithreading" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="tutorials/new_tutorial/multiprocessing.html#new-manual-ruffus-drmaa-wrapper-run-job"><em>ruffus.drmaa_wrapper.run_job()</em></a> (<a class="reference internal" href="drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>syntax</em></a>)</li>
-<li>Optional helper module allows jobs to dispatch work to a computational cluster and wait until it completes.</li>
-<li>Requires <tt class="docutils literal"><span class="pre">multithread</span></tt> rather than <tt class="docutils literal"><span class="pre">multiprocess</span></tt></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="pipeline-run-and-exceptions">
-<h3>9) <tt class="docutils literal"><span class="pre">pipeline_run(...)</span></tt> and exceptions<a class="headerlink" href="#pipeline-run-and-exceptions" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>See <a class="reference internal" href="tutorials/new_tutorial/exceptions.html#new-manual-exceptions"><em>Manual</em></a></p>
-<ul class="simple">
-<li>Optionally terminate pipeline after first exception</li>
-<li>Display exceptions without delay</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="miscellaneous">
-<h3>10) Miscellaneous<a class="headerlink" href="#miscellaneous" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><dl class="docutils">
-<dt>Better error messages for <tt class="docutils literal"><span class="pre">formatter()</span></tt>, <tt class="docutils literal"><span class="pre">suffix()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt> for <tt class="docutils literal"><span class="pre">pipeline_printout(...,</span> <span class="pre">verbose</span> <span class="pre">>=</span> <span class="pre">3,</span> <span class="pre">...)</span></tt></dt>
-<dd><ul class="first last simple">
-<li>Error messages for showing mismatching regular expression and offending file name</li>
-<li>Wrong capture group names or out of range indices will raise informative Exception</li>
-</ul>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="version-2-3">
-<h2>version 2.3<a class="headerlink" href="#version-2-3" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>1st September, 2013</p>
-<ul>
-<li><dl class="first docutils">
-<dt><tt class="docutils literal"><span class="pre">@active_if</span></tt> turns off tasks at runtime</dt>
-<dd><p class="first">The Design and initial implementation were contributed by Jacob Biesinger</p>
-<p>Takes one or more parameters which can be either booleans or functions or callable objects which return True / False:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">run_if_true_1</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="n">run_if_true_2</span> <span class="o">=</span> <span class="bp">False</span>
-
-<span class="nd">@active_if</span><span class="p">(</span><span class="n">run_if_true</span><span class="p">,</span> <span class="k">lambda</span><span class="p">:</span> <span class="n">run_if_true_2</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">this_task_might_be_inactive</span><span class="p">():</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>The expressions inside @active_if are evaluated each time
-<tt class="docutils literal"><span class="pre">pipeline_run</span></tt>, <tt class="docutils literal"><span class="pre">pipeline_printout</span></tt> or <tt class="docutils literal"><span class="pre">pipeline_printout_graph</span></tt> is called.</p>
-<p class="last">Dormant tasks behave as if they are up to date and have no output.</p>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>Command line parsing</dt>
-<dd><ul class="first last simple">
-<li>Supports both argparse (python 2.7) and optparse (python 2.6):</li>
-<li><tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt> module is optional.</li>
-<li>See <a class="reference internal" href="tutorials/new_tutorial/command_line.html#new-manual-cmdline"><em>manual</em></a></li>
-</ul>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>Optionally terminate pipeline after first exception</dt>
-<dd><p class="first">To have all exceptions interrupt immediately:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="o">...</span><span class="p">,</span> <span class="n">exceptions_terminate_immediately</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>By default ruffus accumulates <tt class="docutils literal"><span class="pre">NN</span></tt> errors before interrupting the pipeline prematurely. <tt class="docutils literal"><span class="pre">NN</span></tt> is the specified parallelism for <tt class="docutils literal"><span class="pre">pipeline_run(...,</span> <span class="pre">multiprocess</span> <span class="pre">=</span> <span class="pre">NN)</span></tt>.</p>
-<p class="last">Otherwise, a pipeline will only be interrupted immediately if exceptions of type <tt class="docutils literal"><span class="pre">ruffus.JobSignalledBreak</span></tt> are thrown.</p>
-</dd>
-</dl>
-</li>
-<li><p class="first">Display exceptions without delay</p>
-<blockquote>
-<div><p>By default, Ruffus re-throws exceptions in ensemble after pipeline termination.</p>
-<p>To see exceptions as they occur:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="o">...</span><span class="p">,</span> <span class="n">log_exceptions</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-<p><tt class="docutils literal"><span class="pre">logger.error(...)</span></tt> will be invoked with the string representation of the each exception, and associated stack trace.</p>
-<p>The default logger prints to sys.stderr, but this can be changed to any class from the logging module or compatible object via <tt class="docutils literal"><span class="pre">pipeline_run(...,</span> <span class="pre">logger</span> <span class="pre">=</span> <span class="pre">???)</span></tt></p>
-</div></blockquote>
-</li>
-<li><p class="first">Improved <tt class="docutils literal"><span class="pre">pipeline_printout()</span></tt></p>
-<blockquote>
-<div><ul>
-<li><p class="first"><cite>@split</cite> operations now show the 1->many output in pipeline_printout</p>
-<blockquote>
-<div><p>This make it clearer that <tt class="docutils literal"><span class="pre">@split</span></tt> is creating multiple output parameters (rather than a single output parameter consisting of a list):</p>
-<div class="highlight-python"><pre>Task = split_animals
-     Job = [None
-           -> cows
-           -> horses
-           -> pigs
-            , any_extra_parameters]</pre>
-</div>
-</div></blockquote>
-</li>
-<li><p class="first">File date and time are displayed in human readable form and out of date files are flagged with asterisks.</p>
-</li>
-</ul>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-2">
-<h2>version 2.2<a class="headerlink" href="#version-2-2" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>22nd July, 2010</p>
-<ul>
-<li><p class="first">Simplifying <strong>@transform</strong> syntax with <strong>suffix(...)</strong></p>
-<blockquote>
-<div><p>Regular expressions within ruffus are very powerful, and can allow files to be moved
-from one directory to another and renamed at will.</p>
-<p>However, using consistent file extensions and
-<tt class="docutils literal"><span class="pre">@transform(...,</span> <span class="pre">suffix(...))</span></tt> makes the code much simpler and easier to read.</p>
-<p>Previously, <tt class="docutils literal"><span class="pre">suffix(...)</span></tt> did not cooperate well with <tt class="docutils literal"><span class="pre">inputs(...)</span></tt>.
-For example, finding the corresponding header file (”.h”) for the matching input
-required a complicated <tt class="docutils literal"><span class="pre">regex(...)</span></tt> regular expression and <tt class="docutils literal"><span class="pre">input(...)</span></tt>. This simple case,
-e.g. matching “something.c” with “something.h”, is now much easier in Ruffus.</p>
-<dl class="docutils">
-<dt>For example:</dt>
-<dd><div class="first highlight-python"><div class="highlight"><pre><span class="n">source_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"something.c"</span><span class="p">,</span> <span class="s">"more_code.c"</span><span class="p">]</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".c"</span><span class="p">),</span> <span class="n">add_inputs</span><span class="p">(</span><span class="s">r"\1.h"</span><span class="p">,</span> <span class="s">"common.h"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="p">(</span> <span class="n">source_file</span><span class="p">,</span>
-      <span class="n">header_file</span><span class="p">,</span>
-      <span class="n">common_header</span><span class="p">)</span> <span class="o">=</span> <span class="n">input_files</span>
-    <span class="c"># call compiler to make object file</span>
-</pre></div>
-</div>
-<p>This is equivalent to calling:</p>
-<blockquote class="last">
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nb">compile</span><span class="p">([</span><span class="s">"something.c"</span><span class="p">,</span> <span class="s">"something.h"</span><span class="p">,</span> <span class="s">"common.h"</span><span class="p">],</span> <span class="s">"something.o"</span><span class="p">)</span>
-<span class="nb">compile</span><span class="p">([</span><span class="s">"more_code.c"</span><span class="p">,</span> <span class="s">"more_code.h"</span><span class="p">,</span> <span class="s">"common.h"</span><span class="p">],</span> <span class="s">"more_code.o"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</dd>
-</dl>
-<p>The <tt class="docutils literal"><span class="pre">\1</span></tt> matches everything <em>but</em> the suffix and will be applied to both <tt class="docutils literal"><span class="pre">glob</span></tt>s and file names.</p>
-</div></blockquote>
-</li>
-</ul>
-<p>For simplicity and compatibility with previous versions, there is always an implied r”1” before
-the output parameters. I.e. output parameters strings are <em>always</em> substituted.</p>
-<ul>
-<li><p class="first">Tasks and glob in <strong>inputs(...)</strong> and <strong>add_inputs(...)</strong></p>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">glob</span></tt>s and tasks can be added as the prerequisites / input files using
-<tt class="docutils literal"><span class="pre">inputs(...)</span></tt> and <tt class="docutils literal"><span class="pre">add_inputs(...)</span></tt>. <tt class="docutils literal"><span class="pre">glob</span></tt> expansions will take place when the task
-is run.</p>
-</div></blockquote>
-</li>
-<li><p class="first">Advanced form of <strong>@split</strong> with <strong>regex</strong>:</p>
-<blockquote>
-<div><p>The standard <tt class="docutils literal"><span class="pre">@split</span></tt> divided one set of inputs into multiple outputs (the number of which
-can be determined at runtime).</p>
-<p>This is a <tt class="docutils literal"><span class="pre">one->many</span></tt> operation.</p>
-<p>An advanced form of <tt class="docutils literal"><span class="pre">@split</span></tt> has been added which can split each of several files further.</p>
-<p>In other words, this is a <tt class="docutils literal"><span class="pre">many->"many</span> <span class="pre">more"</span></tt> operation.</p>
-<dl class="docutils">
-<dt>For example, given three starting files:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">original_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"original_0.file"</span><span class="p">,</span>
-                  <span class="s">"original_1.file"</span><span class="p">,</span>
-                  <span class="s">"original_2.file"</span><span class="p">]</span>
-</pre></div>
-</div>
-</dd>
-<dt>We can split each into its own set of sub-sections:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="n">original_files</span><span class="p">,</span>
-   <span class="n">regex</span><span class="p">(</span><span class="s">r"starting_(\d+).fa"</span><span class="p">),</span>                         <span class="c"># match starting files</span>
-         <span class="s">r"files.split.\1.*.fa"</span>                         <span class="c"># glob pattern</span>
-         <span class="s">r"\1"</span><span class="p">)</span>                                         <span class="c"># index of original file</span>
-<span class="k">def</span> <span class="nf">split_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">,</span> <span class="n">original_index</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        Code to split each input_file</span>
-<span class="sd">            "original_0.file" -> "files.split.0.*.fa"</span>
-<span class="sd">            "original_1.file" -> "files.split.1.*.fa"</span>
-<span class="sd">            "original_2.file" -> "files.split.2.*.fa"</span>
-<span class="sd">    """</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>This is, conceptually, the reverse of the @collate(...) decorator</p>
-</div></blockquote>
-</li>
-<li><p class="first">Ruffus will complain about unescaped regular expression special characters:</p>
-<blockquote>
-<div><p>Ruffus uses “\1” and “\2” in regular expression substitutions. Even seasoned python
-users may not remember that these have to be ‘escaped’ in strings. The best option is
-to use ‘raw’ python strings e.g.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="s">r"\1_substitutes\2correctly\3four\4times"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Ruffus will throw an exception if it sees an unescaped “\1” or “\2” in a file name,
-which should catch most of these bugs.</p>
-</div></blockquote>
-</li>
-<li><p class="first">Prettier output from <em>pipeline_printout_graph</em></p>
-<blockquote>
-<div><p>Changed to nicer colours, symbols etc. for a more professional look.
-@split and @merge tasks now look different from @transform.
-Colours, size and resolution are now fully customisable:</p>
-<div class="highlight-python"><pre>pipeline_printout_graph( #...
-                         user_colour_scheme = {
-                                                "colour_scheme_index":1,
-                                                "Task to run"  : {"fillcolor":"blue"},
-                                                 pipeline_name : "My flowchart",
-                                                 size          : (11,8),
-                                                 dpi           : 120)})</pre>
-</div>
-<p>An SVG bug in firefox has been worked around so that font size are displayed correctly.</p>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-1-1">
-<h2>version 2.1.1<a class="headerlink" href="#version-2-1-1" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul>
-<li><dl class="first docutils">
-<dt><strong>@transform(.., add_inputs(...))</strong></dt>
-<dd><p class="first"><tt class="docutils literal"><span class="pre">add_inputs(...)</span></tt> allows the addition of extra input dependencies / parameters for each job.</p>
-<dl class="docutils">
-<dt>Unlike <tt class="docutils literal"><span class="pre">inputs(...)</span></tt>, the original input parameter is retained:</dt>
-<dd><div class="first last highlight-python"><pre>from ruffus import *
- at transform(["a.input", "b.input"], suffix(".input"), add_inputs("just.1.more","just.2.more"), ".output")
-def task(i, o):
-""</pre>
-</div>
-</dd>
-<dt>Produces:</dt>
-<dd><div class="first last highlight-python"><pre>Job = [[a.input, just.1.more, just.2.more] ->a.output]
-Job = [[b.input, just.1.more, just.2.more] ->b.output]</pre>
-</div>
-</dd>
-</dl>
-<p class="last">Like <tt class="docutils literal"><span class="pre">inputs</span></tt>, <tt class="docutils literal"><span class="pre">add_inputs</span></tt> accepts strings, tasks and <tt class="docutils literal"><span class="pre">glob</span></tt> s
-This minor syntactic change promises add much clarity to Ruffus code.
-<tt class="docutils literal"><span class="pre">add_inputs()</span></tt> is available for <tt class="docutils literal"><span class="pre">@transform</span></tt>, <tt class="docutils literal"><span class="pre">@collate</span></tt> and <tt class="docutils literal"><span class="pre">@split</span></tt></p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-1-0">
-<h2>version 2.1.0<a class="headerlink" href="#version-2-1-0" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul>
-<li><p class="first"><strong>@jobs_limit</strong>
-Some tasks are resource intensive and too many jobs should not be run at the
-same time. Examples include disk intensive operations such as unzipping, or
-downloading from FTP sites.</p>
-<p>Adding:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">4</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">new_data_list</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".big_data.gz"</span><span class="p">),</span> <span class="s">".big_data"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">unzip</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
-  <span class="s">"unzip code goes here"</span>
-</pre></div>
-</div>
-<p>would limit the unzip operation to 4 jobs at a time, even if the rest of the
-pipeline runs highly in parallel.</p>
-<p>(Thanks to Rob Young for suggesting this.)</p>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-0-10">
-<h2>version 2.0.10<a class="headerlink" href="#version-2-0-10" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul>
-<li><p class="first"><strong>touch_files_only</strong> option for <strong>pipeline_run</strong></p>
-<p>When the pipeline runs, task functions will not be run. Instead, the output files for
-each job (in each task) will be <tt class="docutils literal"><span class="pre">touch</span></tt>-ed if necessary.
-This can be useful for simulating a pipeline run so that all files look as
-if they are up-to-date.</p>
-<p>Caveats:</p>
-<blockquote>
-<div><ul class="simple">
-<li>This may not work correctly where output files are only determined at runtime, e.g. with <strong>@split</strong></li>
-<li>Only the output from pipelined jobs which are currently out-of-date will be <tt class="docutils literal"><span class="pre">touch</span></tt>-ed.
-In other words, the pipeline runs <em>as normal</em>, the only difference is that the
-output files are <tt class="docutils literal"><span class="pre">touch</span></tt>-ed instead of being created by the python task functions
-which would otherwise have been called.</li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">Parameter substitution for <strong>inputs(...)</strong></p>
-<p>The <strong>inputs(...)</strong> parameter in <strong>@transform</strong>, <strong>@collate</strong> can now take tasks and <tt class="docutils literal"><span class="pre">glob</span></tt> s,
-and these will be expanded appropriately (after regular expression replacement).</p>
-<p>For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="s">"dir/a.input"</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*)\/(.+).input"</span><span class="p">),</span>
-              <span class="n">inputs</span><span class="p">((</span><span class="s">r"\1/\2.other"</span><span class="p">,</span> <span class="s">r"\1/*.more"</span><span class="p">)),</span> <span class="s">r"elsewhere/\2.output"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task1</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
-  <span class="sd">"""</span>
-<span class="sd">  Some pipeline task</span>
-<span class="sd">  """</span>
-</pre></div>
-</div>
-<p>Is equivalent to calling:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">task1</span><span class="p">((</span><span class="s">"dir/a.other"</span><span class="p">,</span> <span class="s">"dir/1.more"</span><span class="p">,</span> <span class="s">"dir/2.more"</span><span class="p">),</span> <span class="s">"elsewhere/a.output"</span><span class="p">)</span>
-</pre></div>
-</div>
-<p></p>
-<blockquote>
-<div><p>Here:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="s">r"\1/*.more"</span>
-</pre></div>
-</div>
-<p>is first converted to:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="s">r"dir/*.more"</span>
-</pre></div>
-</div>
-<p>which matches:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="s">"dir/1.more"</span>
-<span class="s">"dir/2.more"</span>
-</pre></div>
-</div>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-0-9">
-<h2>version 2.0.9<a class="headerlink" href="#version-2-0-9" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul>
-<li><p class="first">Better display of logging output</p>
-</li>
-<li><p class="first">Advanced form of <strong>@split</strong>
-This is an experimental feature.</p>
-<p>Hitherto, <strong>@split</strong> only takes 1 set of input (tasks/files/<tt class="docutils literal"><span class="pre">glob</span></tt> s) and split these
-into an indeterminate number of output.</p>
-<blockquote>
-<div><p>This is a one->many operation.</p>
-</div></blockquote>
-<p>Sometimes it is desirable to take multiple input files, and split each of them further.</p>
-<blockquote>
-<div><p>This is a many->many (more) operation.</p>
-</div></blockquote>
-<p>It is possible to hack something together using <strong>@transform</strong> but downstream tasks would not
-aware that each job in <strong>@transform</strong> produces multiple outputs (rather than one input,
-one output per job).</p>
-<p>The syntax looks like:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="n">get_files</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"(.+).original"</span><span class="p">),</span> <span class="s">r"\1.*.split"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">split_files</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">o</span><span class="p">):</span>
-     <span class="k">pass</span>
-</pre></div>
-</div>
-<p>If <tt class="docutils literal"><span class="pre">get_files()</span></tt> returned <tt class="docutils literal"><span class="pre">A.original</span></tt>, <tt class="docutils literal"><span class="pre">B.original</span></tt> and <tt class="docutils literal"><span class="pre">C.original</span></tt>,
-<tt class="docutils literal"><span class="pre">split_files()</span></tt> might lead to the following operations:</p>
-<div class="highlight-python"><pre>A.original
-        -> A.1.original
-        -> A.2.original
-        -> A.3.original
-B.original
-        -> B.1.original
-        -> B.2.original
-C.original
-        -> C.1.original
-        -> C.2.original
-        -> C.3.original
-        -> C.4.original
-        -> C.5.original</pre>
-</div>
-<p>Note that each input (<tt class="docutils literal"><span class="pre">A/B/C.original</span></tt>) can produce a number of output, the exact
-number of which does not have to be pre-determined.
-This is similar to <strong>@split</strong></p>
-<p>Tasks following <tt class="docutils literal"><span class="pre">split_files</span></tt> will have ten inputs corresponding to each of the
-output from <tt class="docutils literal"><span class="pre">split_files</span></tt>.</p>
-<p>If <strong>@transform</strong> was used instead of <strong>@split</strong>, then tasks following <tt class="docutils literal"><span class="pre">split_files</span></tt>
-would only have 3 inputs.</p>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-0-8">
-<h2>version 2.0.8<a class="headerlink" href="#version-2-0-8" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>File names can be in unicode</li>
-<li>File systems with 1 second timestamp granularity no longer cause problems.</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-0-2">
-<h2>version 2.0.2<a class="headerlink" href="#version-2-0-2" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>Much prettier /useful output from <a class="reference internal" href="pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout</em></a></li>
-<li>New tutorial / manual</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-2-0">
-<h2>version 2.0<a class="headerlink" href="#version-2-0" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul>
-<li><p class="first">Revamped documentation:</p>
-<blockquote>
-<div><ul class="simple">
-<li>Rewritten tutorial</li>
-<li>Comprehensive manual</li>
-<li>New syntax help</li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">Major redesign. New decorators include</p>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="tutorials/new_tutorial/split.html#new-manual-split"><em>@split</em></a></li>
-<li><a class="reference internal" href="tutorials/new_tutorial/transform.html#new-manual-transform"><em>@transform</em></a></li>
-<li><a class="reference internal" href="tutorials/new_tutorial/merge.html#new-manual-merge"><em>@merge</em></a></li>
-<li><a class="reference internal" href="tutorials/new_tutorial/subdivide_collate.html#new-manual-collate"><em>@collate</em></a></li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">Major redesign. Decorator <em>inputs</em> can mix</p>
-<blockquote>
-<div><ul class="simple">
-<li>Output from previous tasks</li>
-<li><a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns e.g. <tt class="docutils literal"><span class="pre">*.txt</span></tt></li>
-<li>Files names</li>
-<li>Any other data type</li>
-</ul>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="version-1-1-4">
-<h2>version 1.1.4<a class="headerlink" href="#version-1-1-4" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>Tasks can get their input by automatically chaining to the output from one or more parent tasks using <a class="reference internal" href="decorators/files_re.html#decorators-files-re"><em>@files_re</em></a></div></blockquote>
-</div>
-<div class="section" id="version-1-0-7">
-<h2>version 1.0.7<a class="headerlink" href="#version-1-0-7" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>Added <cite>proxy_logger</cite> module for accessing a shared log across multiple jobs in different processes.</div></blockquote>
-</div>
-<div class="section" id="version-1-0">
-<h2>version 1.0<a class="headerlink" href="#version-1-0" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>Initial Release in Oxford</div></blockquote>
-</div>
-</div>
-<div class="section" id="fixed-bugs">
-<h1>Fixed Bugs<a class="headerlink" href="#fixed-bugs" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div>Full list at <a class="reference external" href="http://code.google.com/p/ruffus/wiki/LatestChanges">“Latest Changes wiki entry”</a></div></blockquote>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Major Features added to Ruffus</a><ul>
-<li><a class="reference internal" href="#version-2-5rc">version 2.5RC</a><ul>
-<li><a class="reference internal" href="#python3-compatability-but-at-least-python-2-6-is-now-required">1) Python3 compatability (but at least python 2.6 is now required)</a></li>
-<li><a class="reference internal" href="#ctrl-c-interrupts">2) Ctrl-C interrupts</a></li>
-<li><a class="reference internal" href="#customising-flowcharts-in-pipeline-printout-graph-with-graphviz">3) Customising flowcharts in pipeline_printout_graph() with <tt class="docutils literal"><span class="pre">@graphviz</span></tt></a></li>
-<li><a class="reference internal" href="#consistent-verbosity-levels">4. Consistent verbosity levels</a></li>
-<li><a class="reference internal" href="#allow-abbreviated-paths-from-pipeline-run-or-pipeline-printout">5. Allow abbreviated paths from <tt class="docutils literal"><span class="pre">pipeline_run</span></tt> or <tt class="docutils literal"><span class="pre">pipeline_printout</span></tt></a></li>
-<li><a class="reference internal" href="#other-changes">Other changes</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#version-2-4-1">version 2.4.1</a></li>
-<li><a class="reference internal" href="#version-2-4">version 2.4</a><ul>
-<li><a class="reference internal" href="#additions-to-ruffus-namespace">Additions to <tt class="docutils literal"><span class="pre">ruffus</span></tt> namespace</a></li>
-<li><a class="reference internal" href="#installation-use-pip">Installation: use pip</a></li>
-<li><a class="reference internal" href="#command-line-support">1) Command Line support</a></li>
-<li><a class="reference internal" href="#check-pointing">2) Check pointing</a></li>
-<li><a class="reference internal" href="#subdivide-syntax">3) <tt class="docutils literal"><span class="pre">subdivide()</span></tt> (<tt class="docutils literal"><span class="pre">syntax</span></tt>)</a></li>
-<li><a class="reference internal" href="#mkdir-syntax-with-formatter-suffix-and-regex">4) <tt class="docutils literal"><span class="pre">mkdir()</span></tt> (<tt class="docutils literal"><span class="pre">syntax</span></tt>) with <tt class="docutils literal"><span class="pre">formatter()</span></tt>, <tt class="docutils literal"><span class="pre">suffix()</span></tt>  and <tt class="docutils literal"><span class="pre">regex()</span></tt></a></li>
-<li><a class="reference internal" href="#originate-syntax">5) <tt class="docutils literal"><span class="pre">originate()</span></tt> (<tt class="docutils literal"><span class="pre">syntax</span></tt>)</a></li>
-<li><a class="reference internal" href="#new-flexible-formatter-syntax-alternative-to-regex-suffix">6) New flexible <tt class="docutils literal"><span class="pre">formatter()</span></tt> (<tt class="docutils literal"><span class="pre">syntax</span></tt>) alternative to <tt class="docutils literal"><span class="pre">regex()</span></tt>  & <tt class="docutils literal"><span class="pre">suffix()</span></tt></a></li>
-<li><a class="reference internal" href="#combinatorics-all-vs-all-decorators">7) Combinatorics (all vs. all decorators)</a></li>
-<li><a class="reference internal" href="#drmaa-support-and-multithreading">8) drmaa support and multithreading:</a></li>
-<li><a class="reference internal" href="#pipeline-run-and-exceptions">9) <tt class="docutils literal"><span class="pre">pipeline_run(...)</span></tt> and exceptions</a></li>
-<li><a class="reference internal" href="#miscellaneous">10) Miscellaneous</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#version-2-3">version 2.3</a></li>
-<li><a class="reference internal" href="#version-2-2">version 2.2</a></li>
-<li><a class="reference internal" href="#version-2-1-1">version 2.1.1</a></li>
-<li><a class="reference internal" href="#version-2-1-0">version 2.1.0</a></li>
-<li><a class="reference internal" href="#version-2-0-10">version 2.0.10</a></li>
-<li><a class="reference internal" href="#version-2-0-9">version 2.0.9</a></li>
-<li><a class="reference internal" href="#version-2-0-8">version 2.0.8</a></li>
-<li><a class="reference internal" href="#version-2-0-2">version 2.0.2</a></li>
-<li><a class="reference internal" href="#version-2-0">version 2.0</a></li>
-<li><a class="reference internal" href="#version-1-1-4">version 1.1.4</a></li>
-<li><a class="reference internal" href="#version-1-0-7">version 1.0.7</a></li>
-<li><a class="reference internal" href="#version-1-0">version 1.0</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#fixed-bugs">Fixed Bugs</a></li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="design.html"
-                        title="previous chapter">Design & Architecture</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="todo.html"
-                        title="next chapter">Future Changes to Ruffus</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="_sources/history.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-    Enter search terms or a module, class or function name.
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
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-            
-  <div class="section" id="implementation-tips">
-<h1>Implementation Tips<a class="headerlink" href="#implementation-tips" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="release">
-<h2>Release<a class="headerlink" href="#release" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul>
-<li><p class="first">Change <tt class="docutils literal"><span class="pre">ruffus_version.py</span></tt></p>
-</li>
-<li><p class="first">Rebuild pdf and copy it to <tt class="docutils literal"><span class="pre">doc/static_data</span></tt></p>
-<blockquote>
-<div><p>cd doc
-make latexpdf
-cp _build/latex/ruffus.pdf static_data</p>
-</div></blockquote>
-</li>
-<li><p class="first">Rebuild documentation:</p>
-<div class="highlight-python"><pre>make htmlsync</pre>
-</div>
-</li>
-<li><p class="first">tag git with, for example:</p>
-<div class="highlight-python"><pre>git tag -a v2.5RC -m "Version 2.5 Release Candidate"</pre>
-</div>
-</li>
-<li><p class="first">Upload to pypi:</p>
-<div class="highlight-python"><pre>python setup.py sdist --format=gztar upload</pre>
-</div>
-</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="dbdict-py">
-<h2>dbdict.py<a class="headerlink" href="#dbdict-py" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>This is an sqlite backed dictionary originally written by Jacob Sondergaard and
-contributed by Jake Biesinger who added automatic pickling of python objects.</p>
-<p>The pickling code was refactored out by Leo Goodstadt into separate functions as
-part of the preparation to make Ruffus python3 ready.</p>
-<p>Python original saved (pickled) objects as 7 bit ASCII strings. Later formats
-(protocol = -1 is the latest format) uses 8 bit strings and are rather more efficient.</p>
-<p>These then need to be saved as BLOBs to sqlite3 rather than normal strings. We
-can signal this by wrapping the pickled string in a object providing a “buffer interface”.
-This is <tt class="docutils literal"><span class="pre">buffer</span></tt> in python2.6/2.7 and <tt class="docutils literal"><span class="pre">memoryview</span></tt> in python3.</p>
-<p><a class="reference external" href="http://bugs.python.org/issue7723">http://bugs.python.org/issue7723</a> suggests there is no portable python2/3 way to write
-blobs to Sqlite without these two incompatible wrappers.
-This would require conditional compilation:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">hexversion</span> <span class="o">>=</span> <span class="mh">0x03000000</span><span class="p">:</span>
-    <span class="n">value</span> <span class="o">=</span> <span class="n">memoryview</span><span class="p">(</span><span class="n">pickle</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">protocol</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span><span class="p">))</span>
-<span class="k">else</span><span class="p">:</span>
-    <span class="n">value</span> <span class="o">=</span> <span class="nb">buffer</span><span class="p">(</span><span class="n">pickle</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="n">protocol</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span><span class="p">))</span>
-</pre></div>
-</div>
-<p>Despite the discussion on the bug report, sqlite3.Binary seems to work.
-We shall see if this is portable to python3.</p>
-</div></blockquote>
-</div>
-<div class="section" id="how-to-write-new-decorators">
-<h2>how to write new decorators<a class="headerlink" href="#how-to-write-new-decorators" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>New placeholder class. E.g. for <tt class="docutils literal"><span class="pre">@new_deco</span></tt></p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">class</span> <span class="nc">new_deco</span><span class="p">(</span><span class="n">task_decorator</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>Add to list of action names and ids:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">action_names</span> <span class="o">=</span> <span class="p">[</span><span class="s">"unspecified"</span><span class="p">,</span>
-                <span class="o">...</span>
-                <span class="s">"task_new_deco"</span><span class="p">,</span>
-
-<span class="n">action_task_new_deco</span>     <span class="o">=</span>  <span class="mi">15</span>
-</pre></div>
-</div>
-<p>Add function:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">def</span> <span class="nf">task_transform</span> <span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">orig_args</span><span class="p">):</span>
-</pre></div>
-</div>
-<p>Add documentation to:</p>
-<blockquote>
-<div><ul class="simple">
-<li>decorators/NEW_DECORATOR.rst</li>
-<li>decorators/decorators.rst</li>
-<li>_templates/layout.html</li>
-<li>manual</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="implementation-notes">
-<h1>Implementation notes<a class="headerlink" href="#implementation-notes" title="Permalink to this headline">¶</a></h1>
-<p>N.B. Remember to cite Jake Biesinger and see if he is interested to be a co-author if we ever resubmit the drastically changed version...
-He contributed checkpointing, travis and tox etc.</p>
-<div class="section" id="ctrl-c-handling">
-<span id="todo-misfeatures"></span><h2><tt class="docutils literal"><span class="pre">Ctrl-C</span></tt> handling<a class="headerlink" href="#ctrl-c-handling" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Pressing <tt class="docutils literal"><span class="pre">Ctrl-C</span></tt> left dangling process in Ruffus 2.4 because <tt class="docutils literal"><span class="pre">KeyboardInterrupt</span></tt> does not play nice with python <tt class="docutils literal"><span class="pre">multiprocessing.Pool</span></tt>
-See <a class="reference external" href="http://stackoverflow.com/questions/1408356/keyboard-interrupts-with-pythons-multiprocessing-pool/1408476#1408476">http://stackoverflow.com/questions/1408356/keyboard-interrupts-with-pythons-multiprocessing-pool/1408476#1408476</a></p>
-<p><a class="reference external" href="http://bryceboe.com/2012/02/14/python-multiprocessing-pool-and-keyboardinterrupt-revisited/">http://bryceboe.com/2012/02/14/python-multiprocessing-pool-and-keyboardinterrupt-revisited/</a> provides a reimplementation of Pool which
-however only works when you have a fixed number of jobs which should then run in parallel to completion. Ruffus is considerably more
-complicated because we have a variable number of jobs completing and being submitted into the job queue at any one time. Think
-of tasks stalling waiting for the dependent tasks to complete and then all the jobs of the task being released onto the queue</p>
-<p>The solution is</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Use a <tt class="docutils literal"><span class="pre">timeout</span></tt> parameter when using <tt class="docutils literal"><span class="pre">IMapIterator.next(timeout=None)</span></tt> to iterate through <tt class="docutils literal"><span class="pre">pool.imap_unordered</span></tt> because only timed <tt class="docutils literal"><span class="pre">condition</span></tt> s can be interruptible by signals...!!</li>
-<li>This involves rewriting the <tt class="docutils literal"><span class="pre">for</span></tt> loop manually as a <tt class="docutils literal"><span class="pre">while</span></tt> loop</li>
-<li>We use a timeout of <tt class="docutils literal"><span class="pre">99999999</span></tt>, i.e. 3 years, which should be enough for any job to complete...</li>
-<li>Googling after the fact, it looks like the galaxy guys (cool dudes or what) have written similar <a class="reference external" href="https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/objectstore/s3_multipart_upload.html">code</a></li>
-<li><tt class="docutils literal"><span class="pre">next()</span></tt> for normal iterators do not take <tt class="docutils literal"><span class="pre">timeout</span></tt> as an extra parameter so we have to wrap next in a conditional :-(. The galaxy guys do a <a class="reference external" href="http://en.wikipedia.org/wiki/Shim_(computing)">shim</a> around <tt class="docutils literal"><span class="pre">next()</span></tt> but that is as much obsfucation as a simple if...</li>
-<li>After jobs are interrupted by a signal, we rethrow with our own exception because we want something that inherits from <tt class="docutils literal"><span class="pre">Exception</span></tt> unlike <tt class="docutils literal"><span class="pre">KeyboardInterrupt</span></tt></li>
-<li>When a signal happens, we need to immediately stop <tt class="docutils literal"><span class="pre">feed_job_params_to_process_pool()</span></tt> from sending more parameters into the job queue (<tt class="docutils literal"><span class="pre">parameter_q</span></tt>)
-We use a proxy to a <tt class="docutils literal"><span class="pre">multiprocessing.Event</span></tt> (via <tt class="docutils literal"><span class="pre">syncmanager.Event()</span></tt>). When <tt class="docutils literal"><span class="pre">death_event</span></tt> is set, all further processing stops...</li>
-<li>We also signal that all jobs should finish by putting <tt class="docutils literal"><span class="pre">all_tasks_complete()</span></tt> into <tt class="docutils literal"><span class="pre">parameter_q</span></tt> but only <tt class="docutils literal"><span class="pre">death_event</span></tt> prevents jobs already in the queue from going through</li>
-<li>Ater signalling, some of the child processes appear to be dead by the time we start cleaning up. <tt class="docutils literal"><span class="pre">pool.terminate()</span></tt> sometimes tries and fails to
-re-connect to the the <tt class="docutils literal"><span class="pre">death_event</span></tt> proxy via sockets and throws an exception. We should really figure out a better solution but in the meantime
-wrapping it in a <tt class="docutils literal"><span class="pre">try</span> <span class="pre">/</span> <span class="pre">except</span></tt> allows a clean exit.</li>
-<li>If a vanilla exception is raised without multiprocessing running, we still need to first save the exception in <tt class="docutils literal"><span class="pre">job_errors</span></tt> (even if it is just one) before
-cleaning up, because the cleaning up process may lead to further (ignored) exceptions which would overwrite the current exception when we need to rethrow it</li>
-</ol>
-</div></blockquote>
-<p>Exceptions thrown in the middle of a multiprocessing / multithreading job appear to be handled gracefully.</p>
-<p>For drmaa jobs, <tt class="docutils literal"><span class="pre">qdel</span></tt> may still be necessary.</p>
-</div></blockquote>
-</div>
-<div class="section" id="python3-compatability">
-<h2>Python3 compatability<a class="headerlink" href="#python3-compatability" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Required extensive changes especially in unit test code.</p>
-<p>Changes:</p>
-<ol class="arabic">
-<li><p class="first"><tt class="docutils literal"><span class="pre">sort</span></tt> in python3 does not order mixed types, i.e. <tt class="docutils literal"><span class="pre">int()</span></tt>, <tt class="docutils literal"><span class="pre">list()</span></tt> and <tt class="docutils literal"><span class="pre">str()</span></tt> are incommensurate</p>
-<ul>
-<li><p class="first">In <tt class="docutils literal"><span class="pre">task.get_output_files</span> <span class="pre">(...)</span></tt>, sort after conversion to string</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">output_filenames</span><span class="p">,</span> <span class="n">key</span> <span class="o">=</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">x</span><span class="p">))</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">In <tt class="docutils literal"><span class="pre">file_name_parameters.py</span></tt>: <tt class="docutils literal"><span class="pre">collate_param_factory</span> <span class="pre">(...)</span></tt>, <tt class="docutils literal"><span class="pre">sort</span></tt> after conversion to string, then <tt class="docutils literal"><span class="pre">groupby</span></tt> without string conversion. This is
-because we can’t guarantee that two different objects do not have the same string representation. But <tt class="docutils literal"><span class="pre">groupby</span></tt> requires that similar things are adjacent...</p>
-<p>In other words, <tt class="docutils literal"><span class="pre">groupby</span></tt> is a refinement of <tt class="docutils literal"><span class="pre">sorted</span></tt></p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">for</span> <span class="n">output_extra_params</span><span class="p">,</span> <span class="n">grouped_params</span> <span class="ow">in</span> <span class="n">groupby</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">io_params_iter</span><span class="p">,</span> <span class="n">key</span> <span class="o">=</span> <span class="n">get_output_extras_str</span><span cla [...]
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</li>
-</ul>
-</li>
-<li><p class="first"><tt class="docutils literal"><span class="pre">print()</span></tt> is a function</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">print_function</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first"><tt class="docutils literal"><span class="pre">items()</span></tt> only returns a list in python2. Rewrite <tt class="docutils literal"><span class="pre">dict.iteritems()</span></tt> whenever this might cause a performance bottleneck</p>
-</li>
-<li><p class="first"><tt class="docutils literal"><span class="pre">zip</span></tt> and <tt class="docutils literal"><span class="pre">map</span></tt> return iterators. Conditionally import in python2</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">sys</span>
-<span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">hexversion</span> <span class="o"><</span> <span class="mh">0x03000000</span><span class="p">:</span>
-    <span class="kn">from</span> <span class="nn">future_builtins</span> <span class="kn">import</span> <span class="nb">zip</span><span class="p">,</span> <span class="nb">map</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first"><tt class="docutils literal"><span class="pre">cPickle->pickle</span></tt> <tt class="docutils literal"><span class="pre">CStringIO->io</span></tt> need to be conditionally imported</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">try</span><span class="p">:</span>
-    <span class="kn">import</span> <span class="nn">StringIO</span> <span class="kn">as</span> <span class="nn">io</span>
-<span class="k">except</span><span class="p">:</span>
-    <span class="kn">import</span> <span class="nn">io</span> <span class="kn">as</span> <span class="nn">io</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first"><tt class="docutils literal"><span class="pre">map</span></tt> code can be changed to list comprehensions. Use <tt class="docutils literal"><span class="pre">2to3</span></tt> to do heavy lifting</p>
-</li>
-<li><p class="first">All normal strings are unicode in python3. Have to use <tt class="docutils literal"><span class="pre">bytes</span></tt> to support 8-bit char arrays.
-Normally, this means that <tt class="docutils literal"><span class="pre">str</span></tt> “just works”. However, to provide special handling of
-both 8-bit and unicode strings in python2, we often need to check for <tt class="docutils literal"><span class="pre">isinstance(xxx,</span> <span class="pre">basestring)</span></tt>.</p>
-<p>We need to conditionally define:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">if</span> <span class="n">sys</span><span class="o">.</span><span class="n">hexversion</span> <span class="o">>=</span> <span class="mh">0x03000000</span><span class="p">:</span>
-    <span class="c"># everything is unicode in python3</span>
-    <span class="n">path_str_type</span> <span class="o">=</span> <span class="nb">str</span>
-<span class="k">else</span><span class="p">:</span>
-    <span class="n">path_str_type</span> <span class="o">=</span> <span class="nb">basestring</span>
-
-<span class="c"># further down...</span>
-<span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">compiled_regex</span><span class="p">,</span> <span class="n">path_str_type</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</li>
-</ol>
-</div></blockquote>
-</div>
-<div class="section" id="refactoring-parameter-handling">
-<h2>Refactoring: parameter handling<a class="headerlink" href="#refactoring-parameter-handling" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt>Though the code is still split in a not very sensible way between <tt class="docutils literal"><span class="pre">ruffus_utility.py</span></tt>, <tt class="docutils literal"><span class="pre">file_name_parameters.py</span></tt> and <tt class="docutils literal"><span class="pre">task.py</span></tt>,</dt>
-<dd>some rationalisation has taken place, and comments added so further refactoring can be made more easily.</dd>
-</dl>
-<p>Common code for:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">file_name_parameters</span><span class="o">.</span><span class="n">split_ex_param_factory</span><span class="p">()</span>
-<span class="n">file_name_parameters</span><span class="o">.</span><span class="n">transform_param_factory</span><span class="p">()</span>
-<span class="n">file_name_parameters</span><span class="o">.</span><span class="n">collate_param_factory</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>has been moved to <tt class="docutils literal"><span class="pre">file_name_parameters.py.yield_io_params_per_job()</span></tt></p>
-<p>unit tests added to <tt class="docutils literal"><span class="pre">test_file_name_parameters.py</span></tt> and <tt class="docutils literal"><span class="pre">test_ruffus_utility.py</span></tt></p>
-</div></blockquote>
-</div>
-<div class="section" id="formatter">
-<h2><tt class="docutils literal"><span class="pre">formatter</span></tt><a class="headerlink" href="#formatter" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">get_all_paths_components(paths,</span> <span class="pre">regex_str)</span></tt> in <tt class="docutils literal"><span class="pre">ruffus_utility.py</span></tt></p>
-<p>Input files names are first squished into a flat list of files.
-<tt class="docutils literal"><span class="pre">get_all_paths_components()</span></tt> returns both the regular expression matches and the break down of the path.</p>
-<p>In case of name clashes, the classes with higher priority override:</p>
-<blockquote>
-<div><ol class="arabic">
-<li><p class="first">Captures by name</p>
-</li>
-<li><p class="first">Captures by index</p>
-</li>
-<li><dl class="first docutils">
-<dt>Path components:</dt>
-<dd><p class="first last">‘ext’ = extension with dot
-‘basename’ = file name without extension
-‘path’ = path before basename, not ending with slash
-‘subdir’ = list of directories starting with the most nested and ending with the root (if normalised)
-‘subpath’ = list of ‘path’ with successive directories removed starting with the most nested and ending with the root (if normalised)</p>
-</dd>
-</dl>
-</li>
-</ol>
-<p>E.g.  <tt class="docutils literal"><span class="pre">name</span> <span class="pre">=</span> <span class="pre">'/a/b/c/sample1.bam'</span></tt>, <tt class="docutils literal"><span class="pre">formatter=r"(.*)(?P<id>\d+)\.(.+)")</span></tt> returns:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="mi">0</span><span class="p">:</span>          <span class="s">'/a/b/c/sample1.bam'</span><span class="p">,</span>           <span class="o">//</span> <span class="n">Entire</span> <span class="n">match</span> <span class="n">captured</span> <span class="n">by</span> <span class="n">index</span>
-<span class="mi">1</span><span class="p">:</span>          <span class="s">'/a/b/c/sample'</span><span class="p">,</span>                <span class="o">//</span> <span class="n">captured</span> <span class="n">by</span> <span class="n">index</span>
-<span class="mi">2</span><span class="p">:</span>          <span class="s">'bam'</span><span class="p">,</span>                          <span class="o">//</span> <span class="n">captured</span> <span class="n">by</span> <span class="n">index</span>
-<span class="s">'id'</span><span class="p">:</span>       <span class="s">'1'</span>                             <span class="o">//</span> <span class="n">captured</span> <span class="n">by</span> <span class="n">name</span>
-<span class="s">'ext'</span><span class="p">:</span>      <span class="s">'.bam'</span><span class="p">,</span>
-<span class="s">'subdir'</span><span class="p">:</span>   <span class="p">[</span><span class="s">'c'</span><span class="p">,</span> <span class="s">'b'</span><span class="p">,</span> <span class="s">'a'</span><span class="p">,</span> <span class="s">'/'</span><span class="p">],</span>
-<span class="s">'subpath'</span><span class="p">:</span>  <span class="p">[</span><span class="s">'/a/b/c'</span><span class="p">,</span> <span class="s">'/a/b'</span><span class="p">,</span> <span class="s">'/a'</span><span class="p">,</span> <span class="s">'/'</span><span class="p">],</span>
-<span class="s">'path'</span><span class="p">:</span>     <span class="s">'/a/b/c'</span><span class="p">,</span>
-<span class="s">'basename'</span><span class="p">:</span> <span class="s">'sample1'</span><span class="p">,</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The code is in <tt class="docutils literal"><span class="pre">ruffus_utility.py</span></tt>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">results</span> <span class="o">=</span> <span class="n">get_all_paths_components</span><span class="p">(</span><span class="n">paths</span><span class="p">,</span> <span class="n">regex_str</span><span class="p">)</span>
-<span class="n">string</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">results</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>All the magic is hidden inside black boxes <tt class="docutils literal"><span class="pre">filename_transform</span></tt> classes:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">class</span> <span class="nc">t_suffix_filename_transform</span><span class="p">(</span><span class="n">t_filename_transform</span><span class="p">):</span>
-<span class="k">class</span> <span class="nc">t_regex_filename_transform</span><span class="p">(</span><span class="n">t_filename_transform</span><span class="p">):</span>
-<span class="k">class</span> <span class="nc">t_format_filename_transform</span><span class="p">(</span><span class="n">t_filename_transform</span><span class="p">):</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="section" id="formatter-regex-and-suffix">
-<h3><tt class="docutils literal"><span class="pre">formatter()</span></tt>: <tt class="docutils literal"><span class="pre">regex()</span></tt> and <tt class="docutils literal"><span class="pre">suffix()</span></tt><a class="headerlink" href="#formatter-regex-and-suffix" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The previous behaviour with regex() where mismatches fail even if no substitution is made is retained by the use of <tt class="docutils literal"><span class="pre">re.subn()</span></tt>.
-This is a corner case but I didn’t want user code to break</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c"># filter on ".txt"</span>
-<span class="n">input_filenames</span> <span class="o">=</span> <span class="p">[</span><span class="s">"a.wrong"</span><span class="p">,</span> <span class="s">"b.txt"</span><span class="p">]</span>
-<span class="n">regex</span><span class="p">(</span><span class="s">"(.txt)$"</span><span class="p">)</span>
-
-<span class="c"># fails, no substitution possible</span>
-<span class="s">r"\1"</span>
-
-<span class="c"># fails anyway even through regular expression matches not referenced...</span>
-<span class="s">r"output.filename"</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="product">
-<h2>@product()<a class="headerlink" href="#product" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>Use combinatoric generators from itertools and keep that naming scheme</li>
-<li>Put all new generators in an <tt class="docutils literal"><span class="pre">combinatorics</span></tt> submodule namespace to avoid breaking user code. (They can imported if necessary.)</li>
-<li>test code in test/test_combinatorics.py</li>
-<li>The <tt class="docutils literal"><span class="pre">itertools.product(repeat)</span></tt> parameter doesn’t make sense for Ruffus and will not be used</li>
-<li>Flexible number of pairs of <tt class="docutils literal"><span class="pre">task</span></tt> / <tt class="docutils literal"><span class="pre">glob</span></tt> / file names + <tt class="docutils literal"><span class="pre">formatter()</span></tt></li>
-<li>Only <tt class="docutils literal"><span class="pre">formatter([OPTIONAl_REGEX])</span></tt> provides the necessary flexibility to construct the output so we won’t bother with suffix and regex</li>
-<li>Similar to <tt class="docutils literal"><span class="pre">@transform</span></tt> but with extra level of nested-ness</li>
-</ul>
-<dl class="docutils">
-<dt>Retain same code for <tt class="docutils literal"><span class="pre">@product</span></tt> and <tt class="docutils literal"><span class="pre">@transform</span></tt> by adding an additional level of indirection:</dt>
-<dd><ul class="first last">
-<li><p class="first">generator wrap around <tt class="docutils literal"><span class="pre">get_strings_in_nested_sequence</span></tt> to convert nested input parameters either to a single flat list of file names or to nested lists of file names</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">file_name_parameters</span><span class="o">.</span><span class="n">input_param_to_file_name_list</span> <span class="p">(</span><span class="n">input_params</span><span class="p">)</span>
-<span class="n">file_name_parameters</span><span class="o">.</span><span class="n">list_input_param_to_file_name_list</span> <span class="p">(</span><span class="n">input_params</span><span class="p">)</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first"><tt class="docutils literal"><span class="pre">t_file_names_transform</span></tt> class which stores a list of regular expressions, one for each <tt class="docutils literal"><span class="pre">formatter()</span></tt> object corresponding to a single set of input parameters</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">t_formatter_file_names_transform</span>
-<span class="n">t_nested_formatter_file_names_transform</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">string substitution functions which will apply a list of <tt class="docutils literal"><span class="pre">formatter</span></tt> changes</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">ruffus</span><span class="o">.</span><span class="n">utility</span><span class="o">.</span><span class="n">t_formatter_replace</span><span class="p">()</span>
-<span class="n">ruffus</span><span class="o">.</span><span class="n">utility</span><span class="o">.</span><span class="n">t_nested_formatter_replace</span><span class="p">()</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first"><tt class="docutils literal"><span class="pre">ruffus_uilility.swap_doubly_nested_order()</span></tt> makes the syntax / implementation very orthogonal</p>
-</li>
-</ul>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="permutations-combinations-combinations-with-replacement">
-<h2><tt class="docutils literal"><span class="pre">@permutations(...),</span></tt> <tt class="docutils literal"><span class="pre">@combinations(...),</span></tt> <tt class="docutils literal"><span class="pre">@combinations_with_replacement(...)</span></tt><a class="headerlink" href="#permutations-combinations-combinations-with-replacement" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Similar to <tt class="docutils literal"><span class="pre">@product</span></tt> extra level of nested-ness is self versus self</p>
-<dl class="docutils">
-<dt>Retain same code for <tt class="docutils literal"><span class="pre">@product</span></tt></dt>
-<dd><ul class="first last simple">
-<li>forward to a sinble <tt class="docutils literal"><span class="pre">file_name_parameters.combinatorics_param_factory()</span></tt></li>
-<li>use <tt class="docutils literal"><span class="pre">combinatorics_type</span></tt> to dispatch to <tt class="docutils literal"><span class="pre">combinatorics.permutations</span></tt>, <tt class="docutils literal"><span class="pre">combinatorics.combinations</span></tt> and <tt class="docutils literal"><span class="pre">combinatorics.combinations_with_replacement</span></tt></li>
-<li>use <tt class="docutils literal"><span class="pre">list_input_param_to_file_name_list</span></tt> from <tt class="docutils literal"><span class="pre">file_name_parameters.product_param_factory()</span></tt></li>
-</ul>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="drmaa-alternatives">
-<h2>drmaa alternatives<a class="headerlink" href="#drmaa-alternatives" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Alternative, non-drmaa polling code at</p>
-<p><a class="reference external" href="https://github.com/bjpop/rubra/blob/master/rubra/cluster_job.py">https://github.com/bjpop/rubra/blob/master/rubra/cluster_job.py</a></p>
-</div></blockquote>
-</div>
-<div class="section" id="task-completion-monitoring">
-<h2>Task completion monitoring<a class="headerlink" href="#task-completion-monitoring" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="how-easy-is-it-to-abstract-out-the-database">
-<h3>How easy is it to abstract out the database?<a class="headerlink" href="#how-easy-is-it-to-abstract-out-the-database" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul>
-<li><dl class="first docutils">
-<dt>The database is Jacob Sondergaard’s <tt class="docutils literal"><span class="pre">dbdict</span></tt> which is a nosql / key-value store wrapper around sqlite</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">job_history</span> <span class="o">=</span> <span class="n">dbdict</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">RUFFUS_HISTORY_FILE</span><span class="p">,</span> <span class="n">picklevalues</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</li>
-<li><p class="first">The key is the output file name, so it is important not to confuse Ruffus by having different tasks generate the same output file!</p>
-</li>
-<li><p class="first">Is it possible to abstract this so that <strong>jobs</strong> get timestamped as well?</p>
-</li>
-<li><p class="first">If we should ever want to abstract out <tt class="docutils literal"><span class="pre">dbdict</span></tt>, we need to have a similar key-value store class,
-and make sure that a single instance of <tt class="docutils literal"><span class="pre">dbdict</span></tt> is used through <tt class="docutils literal"><span class="pre">pipeline_run</span></tt> which is passed up
-and down the function call chain. <tt class="docutils literal"><span class="pre">dbdict</span></tt> would then be drop-in replaceable by our custom (e.g. flat-file-based) dbdict alternative.</p>
-</li>
-</ul>
-<p>To peek into the database:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>sqlite3 .ruffus_history.sqlite
-sqlite> .tables
-data
-sqlite> .schema data
-CREATE TABLE data <span class="o">(</span>key PRIMARY KEY,value<span class="o">)</span>;
-sqlite> <span class="k">select </span>key from data order by key;
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="can-we-query-the-database-get-job-history-stats">
-<h3>Can we query the database, get Job history / stats?<a class="headerlink" href="#can-we-query-the-database-get-job-history-stats" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div>Yes, if we write a function to read and dump the entire database but this is only useful with timestamps and task names. See below</div></blockquote>
-</div>
-<div class="section" id="what-are-the-run-time-performance-implications">
-<h3>What are the run time performance implications?<a class="headerlink" href="#what-are-the-run-time-performance-implications" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div>Should be fast: a single db connection is created and used inside <tt class="docutils literal"><span class="pre">pipeline_run</span></tt>,  <tt class="docutils literal"><span class="pre">pipeline_printout</span></tt>,  <tt class="docutils literal"><span class="pre">pipeline_printout_graph</span></tt></div></blockquote>
-</div>
-<div class="section" id="avoid-pauses-between-tasks">
-<h3>Avoid pauses between tasks<a class="headerlink" href="#avoid-pauses-between-tasks" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Allows Ruffus to avoid adding an extra 1 second pause between tasks to guard against file systems with low timestamp granularity.</p>
-<blockquote>
-<div><ul class="simple">
-<li>If the local file time looks to be in sync with the underlying file system, saved system time is used instead of file timestamps</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="mkdir">
-<h2><tt class="docutils literal"><span class="pre">@mkdir(...),</span></tt><a class="headerlink" href="#mkdir" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">mkdir</span></tt> continues to work seamlessly inside <tt class="docutils literal"><span class="pre">@follows</span></tt>) but also as its own decorator <tt class="docutils literal"><span class="pre">@mkdir</span></tt> due to the original happy orthogonal design</li>
-<li>fixed bug in checking so that Ruffus does’t blow up if non strings are in the output (number...)</li>
-<li>note: adding the decorator to a previously undecorated function might have unintended consequences. The undecorated function turns into a zombie.</li>
-<li>fixed ugly bug in <tt class="docutils literal"><span class="pre">pipeline_printout</span></tt> for printing single line output</li>
-<li>fixed description and printout indent</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Implementation Tips</a><ul>
-<li><a class="reference internal" href="#release">Release</a></li>
-<li><a class="reference internal" href="#dbdict-py">dbdict.py</a></li>
-<li><a class="reference internal" href="#how-to-write-new-decorators">how to write new decorators</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#implementation-notes">Implementation notes</a><ul>
-<li><a class="reference internal" href="#ctrl-c-handling"><tt class="docutils literal"><span class="pre">Ctrl-C</span></tt> handling</a></li>
-<li><a class="reference internal" href="#python3-compatability">Python3 compatability</a></li>
-<li><a class="reference internal" href="#refactoring-parameter-handling">Refactoring: parameter handling</a></li>
-<li><a class="reference internal" href="#formatter"><tt class="docutils literal"><span class="pre">formatter</span></tt></a><ul>
-<li><a class="reference internal" href="#formatter-regex-and-suffix"><tt class="docutils literal"><span class="pre">formatter()</span></tt>: <tt class="docutils literal"><span class="pre">regex()</span></tt> and <tt class="docutils literal"><span class="pre">suffix()</span></tt></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#product">@product()</a></li>
-<li><a class="reference internal" href="#permutations-combinations-combinations-with-replacement"><tt class="docutils literal"><span class="pre">@permutations(...),</span></tt> <tt class="docutils literal"><span class="pre">@combinations(...),</span></tt> <tt class="docutils literal"><span class="pre">@combinations_with_replacement(...)</span></tt></a></li>
-<li><a class="reference internal" href="#drmaa-alternatives">drmaa alternatives</a></li>
-<li><a class="reference internal" href="#task-completion-monitoring">Task completion monitoring</a><ul>
-<li><a class="reference internal" href="#how-easy-is-it-to-abstract-out-the-database">How easy is it to abstract out the database?</a></li>
-<li><a class="reference internal" href="#can-we-query-the-database-get-job-history-stats">Can we query the database, get Job history / stats?</a></li>
-<li><a class="reference internal" href="#what-are-the-run-time-performance-implications">What are the run time performance implications?</a></li>
-<li><a class="reference internal" href="#avoid-pauses-between-tasks">Avoid pauses between tasks</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#mkdir"><tt class="docutils literal"><span class="pre">@mkdir(...),</span></tt></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="todo.html"
-                        title="previous chapter">Future Changes to Ruffus</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="faq.html"
-                        title="next chapter">FAQ</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="_sources/implementation_notes.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="search.html" method="get">
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-    Enter search terms or a module, class or function name.
-    </p>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="genindex.html" title="General Index"
-             >index</a></li>
-        <li class="right" >
-          <a href="faq.html" title="FAQ"
-             >next</a> |</li>
-        <li class="right" >
-          <a href="todo.html" title="Future Changes to Ruffus"
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-            <li><a href="gallery.html">Gallery</a> |  </li>
-            <li><a href="history.html">Latest Changes</a> » </li>
- 
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-    </div>
-    <div class="footer">
-        © Copyright 2009-2013 Leo Goodstadt.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
-    </div>
-  </body>
-</html>
\ No newline at end of file
diff --git a/doc/_build/html/index.html b/doc/_build/html/index.html
deleted file mode 100644
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--- a/doc/_build/html/index.html
+++ /dev/null
@@ -1,313 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>Ruffus — ruffus 2.5 documentation</title>
-    
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-    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
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-      };
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-    <link rel="top" title="ruffus 2.5 documentation" href="#" /> 
-  </head>
-  <body>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        Ruffus v. 2.5
-            <li><a href="#">Home</a> | </li>
-            <li><a href="contents.html">Contents</a> | </li>
-            <li><a href="installation.html">Install</a>  | </li>
-            <li><a href="tutorials/new_tutorial/introduction.html">Manual</a>  / </li>
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-            <li><a href="history.html">Latest Changes</a> » </li>
- 
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-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-
-<p>
-<a href="why_ruffus.html#why-ruffus"> <img src="_images/logo.jpg" alt="logo"></a>
-</p>
-
-
-Ruffus is a Computation Pipeline library for python. It is open-sourced, 
-powerful and user-friendly, and widely used in science and bioinformatics.
-
-<h1>Welcome</h1>
-
-<table class="Introduction" align="center" style="margin-left: 30px">
-<tr>
-  <td width="50%">
-    <p><I>Ruffus</I> is designed to allow scientific and other analyses to 
-    be automated with the minimum of fuss and the least effort.</p>
-    
-    These are <I>Ruffus</I>'s strengths:
-    <ul>
-      <li><b>Lightweight</b>: Suitable for the simplest of tasks</li>
-
-      <li><b>Scalable</b>: Handles even fiendishly complicated pipelines</a> 
-    which would cause <i>make</i> or <i>scons</i> to go cross-eyed and recursive.</li>
-
-    <li><b>Standard python</b>: No "clever magic", no pre-processing.  </li>
-    <li><b>Unintrusive</b>: Unambitious, lightweight syntax which tries to do this 
-        one small thing well.  </li>
-  </ul>
-    
-    <p>Please join me (email: ruffus_lib at llew.org.uk) in setting the direction of 
-    this project if you are interested.
-    </p>
-    
-  </td>
-  
-  <td width="50%">
-        
-    <img src="_images/front_page_flowchart.png" alt="flowchart">
-    
-  </td>
-                                                                          
-</tr>
-</table>
-
-
-
-                                                            
-
-
-<h1> Documentation</h1>
-
-<table class="contentstable" align="center" style="margin-left: 30px">
-<tr>
-  <td width="50%">
-    
-    <p class="biglink"><a class="biglink" 
-        href="installation.html">Download</a><br/>
-    <span class="linkdescr">to install <I>Ruffus</I></span></p>
-
-    <p class="biglink"><a class="biglink" 
-        href="tutorials/new_tutorial/introduction.html">Simple Tutorial</a><br/>
-    <span class="linkdescr">Start here for a quick introduction to <i>Ruffus</i></span></p>
-
-    <p class="biglink"><a class="biglink" 
-        href="tutorials/new_tutorial/manual_contents.html">Manual</a>
-        <a class="biglink" href="_downloads/ruffus.pdf">(pdf)</a><br/>
-        <span class="linkdescr">for an-depth demonstration of all 
-        <I>Ruffus</I> features</span></p>
-
-  </td>
-  
-  <td width="50%">
-        
-
-    <p class="biglink"><a class="biglink" 
-        href="contents.html">Table of contents</a><br/>
-    <span class="linkdescr">for an complete listing of all the documentation</span></p>
-    
-    <p class="biglink"><a class="biglink" 
-        href="faq.html">Frequently Answered Questions</a><br/>
-    <span class="linkdescr">for any common problems, clever solutions from the community</span></p>
-
-    <p class="biglink"><a class="biglink" 
-        href="design.html">Design</a><br/>
-    <span class="linkdescr">to understand the design of <I>Ruffus</I></span></p>
-
-    <p class="biglink"><a class="biglink" 
-        href="cheatsheet.html">Cheat Sheet</a><br/>
-    <span class="linkdescr">for Ruffus syntax</span></p>
-    </td>
-                                                                          
-</tr>
-</table>
-
-
-
-
-<h2>Get <I>Ruffus</I></h2>
-
-<p>
-    <i>Ruffus</i> is available as an <a 
-    href="http://peak.telecommunity.com/DevCenter/EasyInstall">easy-install</a>able package on the <a href="http://pypi.python.org/pypi/ruffus">Python Package
-    Index</a>.
-  </p>
-Just run:
-
-<div style="margin-left: 30px" class="highlight-python"><pre>sudo pip install ruffus --upgrade</pre> or
-</div>
-
-
-<div style="margin-left: 30px" class="highlight-python"><pre>easy_install -U ruffus</pre>
-</div>
-  
-<br>  
-<p>
-The very latest (in development) code can be obtained via <a href="https://code.google.com/p/ruffus/source/checkout"> git </a>:
-  <div style="color: #ff0000" >
-   <pre>git clone https://bunbun68@code.google.com/p/ruffus/</pre>
-</div>
-</p>
-
-<h1>Feedback and Getting Involved:</h1>
-<ul>
-  <li>
-    The <I>Ruffus</I> project is hosted with <b><a 
-        href="http://code.google.com/p/ruffus">Google 
-      Code here.</a></b><br><br>
-  </li>
-  
-  <li>
-    <img src="https://groups.google.com/forum/my-groups-color.png"
-             height=30 alt="Google Groups"> <b>Subscribe to the <a href="https://groups.google.com/forum/#!forum/ruffus_discuss"><i>ruffus_discuss</i> mailing list </a></b>
-    <br>    
-    <form action="http://groups.google.com/group/ruffus_discuss/boxsubscribe">
-    Email: <input type=text name=email>
-    <input type=submit name="sub" value="Subscribe">
-    </form><br>
-  </li>
-
-
-  <li>
-    <a href="http://groups.google.com/group/ruffus_discuss">Check out the mailing list without subscribing here.</a>
-    <br>
-  </li>
-  
-  <li>
-    <a href="http://code.google.com/p/ruffus/issues/list">Bugs or feature requests can be posted here.</a>
-    <br>
-  </li>
-  
-  
-</ul>
-
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-
-          </div>
-        </div>
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
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-
-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="genindex.html" title="General Index"
-             >index</a></li>
-        Ruffus v. 2.5
-            <li><a href="#">Home</a> | </li>
-            <li><a href="contents.html">Contents</a> | </li>
-            <li><a href="installation.html">Install</a>  | </li>
-            <li><a href="tutorials/new_tutorial/introduction.html">Manual</a>  / </li>
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-            <li><a href="gallery.html">Gallery</a> |  </li>
-            <li><a href="history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>
-    <div class="footer">
-        © Copyright 2009-2013 Leo Goodstadt.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
-    </div>
-  </body>
-</html>
\ No newline at end of file
diff --git a/doc/_build/html/installation.html b/doc/_build/html/installation.html
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--- a/doc/_build/html/installation.html
+++ /dev/null
@@ -1,265 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
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-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>Installation — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    './',
-        VERSION:     '2.5',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true
-      };
-    </script>
-    <script type="text/javascript" src="_static/jquery.js"></script>
-    <script type="text/javascript" src="_static/underscore.js"></script>
-    <script type="text/javascript" src="_static/doctools.js"></script>
-    <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <link rel="top" title="ruffus 2.5 documentation" href="index.html" />
-    <link rel="next" title="Design & Architecture" href="design.html" />
-    <link rel="prev" title="drmaa functions" href="drmaa_wrapper_functions.html" /> 
-  </head>
-  <body>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="design.html" title="Design & Architecture"
-             accesskey="N">next</a> |</li>
-        <li class="right" >
-          <a href="drmaa_wrapper_functions.html" title="drmaa functions"
-             accesskey="P">previous</a> |</li>
-        Ruffus v. 2.5
-            <li><a href="index.html">Home</a> | </li>
-            <li><a href="contents.html">Contents</a> | </li>
-            <li><a href="#">Install</a>  | </li>
-            <li><a href="tutorials/new_tutorial/introduction.html">Manual</a>  / </li>
-            <li><a href="tutorials/new_tutorial/manual_contents.html">(TOC)</a>  | </li>
-            <li><a href="faq.html">FAQ</a>  | </li>
-            <li><a href="cheatsheet.html">Cheat sheet</a> | </li>
-            <li><a href="tutorials/new_tutorial/command_line.html">Command Line</a> | </li>
-            <li><a href="gallery.html">Gallery</a> |  </li>
-            <li><a href="history.html">Latest Changes</a> » </li>
- 
-      </ul>
-    </div>  
-
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body">
-            
-  <div class="section" id="installation">
-<span id="id1"></span><h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
-<p><tt class="xref py py-mod docutils literal"><span class="pre">Ruffus</span></tt> is a lightweight python module for building computational pipelines.</p>
-<div class="section" id="the-easy-way">
-<h2>The easy way<a class="headerlink" href="#the-easy-way" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><em>Ruffus</em> is available as an
-<a class="reference external" href="http://peak.telecommunity.com/DevCenter/EasyInstall">easy-install</a> -able package
-on the <a class="reference external" href="http://pypi.python.org/pypi/Sphinx">Python Package Index</a>.</p>
-<div class="highlight-python"><pre>sudo pip install ruffus --upgrade</pre>
-</div>
-<p>This may also work for older installations</p>
-<ol class="arabic">
-<li><p class="first">Install setuptools:</p>
-<div class="highlight-python"><pre>wget peak.telecommunity.com/dist/ez_setup.py
-sudo python ez_setup.py</pre>
-</div>
-</li>
-<li><p class="first">Install <em>Ruffus</em> automatically:</p>
-<div class="highlight-python"><pre>easy_install -U ruffus</pre>
-</div>
-</li>
-</ol>
-</div></blockquote>
-</div>
-<div class="section" id="the-most-up-to-date-code">
-<h2>The most up-to-date code:<a class="headerlink" href="#the-most-up-to-date-code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul>
-<li><p class="first"><a class="reference external" href="https://pypi.python.org/pypi/ruffus">Download the latest sources</a> or</p>
-</li>
-<li><p class="first">Check out the latest code from Google using git:</p>
-<div class="highlight-python"><pre>git clone https://bunbun68@code.google.com/p/ruffus/ .</pre>
-</div>
-</li>
-<li><p class="first">Bleeding edge Ruffus development takes place on github:</p>
-<div class="highlight-python"><pre>git clone git at github.com:bunbun/ruffus.git .</pre>
-</div>
-</li>
-<li><p class="first">To install after downloading, change to the , type:</p>
-<div class="highlight-python"><pre>python ./setup.py install</pre>
-</div>
-</li>
-</ul>
-</div></blockquote>
-<div class="section" id="graphical-flowcharts">
-<h3>Graphical flowcharts<a class="headerlink" href="#graphical-flowcharts" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><strong>Ruffus</strong> relies on the <tt class="docutils literal"><span class="pre">dot</span></tt> programme from <a class="reference external" href="http://www.graphviz.org/">Graphviz</a>
-(“Graph visualisation”) to make pretty flowchart representations of your pipelines in multiple
-graphical formats (e.g. <tt class="docutils literal"><span class="pre">png</span></tt>, <tt class="docutils literal"><span class="pre">jpg</span></tt>). The crossplatform Graphviz package can be
-<a class="reference external" href="http://www.graphviz.org/Download.php">downloaded here</a> for Windows,
-Linux, Macs and Solaris. Some Linux
-distributions may include prebuilt packages.</p>
-<dl class="docutils">
-<dt>For Fedora, try</dt>
-<dd><div class="first last highlight-python"><pre>yum list 'graphviz*'</pre>
-</div>
-</dd>
-<dt>For ubuntu / Debian, try</dt>
-<dd><div class="first last highlight-python"><pre>sudo apt-get install graphviz</pre>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Installation</a><ul>
-<li><a class="reference internal" href="#the-easy-way">The easy way</a></li>
-<li><a class="reference internal" href="#the-most-up-to-date-code">The most up-to-date code:</a><ul>
-<li><a class="reference internal" href="#graphical-flowcharts">Graphical flowcharts</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
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-            
-  <p id="pipeline-functions">See <a class="reference internal" href="decorators/decorators.html#decorators"><em>Decorators</em></a> for more decorators</p>
-<div class="section" id="id1">
-<h1>Pipeline functions<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><p>There are only four functions for <strong>Ruffus</strong> pipelines:</p>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="#pipeline-functions-pipeline-run"><cite>pipeline_run</cite></a> executes a pipeline</li>
-<li><a class="reference internal" href="#pipeline-functions-pipeline-printout"><cite>pipeline_printout</cite></a> prints a list of tasks and jobs which will be run in a pipeline</li>
-<li><a class="reference internal" href="#pipeline-functions-pipeline-printout-graph"><cite>pipeline_printout_graph</cite></a> prints a schematic flowchart of pipeline tasks in various graphical formats</li>
-<li><a class="reference internal" href="#pipeline-functions-pipeline-get-task-names"><cite>pipeline_get_task_names</cite></a> returns a list of all task names in the pipeline</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-<span class="target" id="pipeline-functions-pipeline-run"></span><div class="section" id="index-0">
-<span id="id2"></span><h2><em>pipeline_run</em><a class="headerlink" href="#index-0" title="Permalink to this headline">¶</a></h2>
-<p><strong>pipeline_run</strong> ( <a class="reference internal" href="#pipeline-functions-pipeline-run-target-tasks"><cite>target_tasks</cite></a> = [],  <a class="reference internal" href="#pipeline-functions-pipeline-run-forcedtorun-tasks"><cite>forcedtorun_tasks</cite></a> = [], <a class="reference internal" href="#pipeline-functions-pipeline-run-multiprocess"><cite>multiprocess</cite></a> = 1, <a class="reference internal" href="#pipeline-functions-pipeline-run-logger"><cite>logger< [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div>Runs all specified pipelined functions if they or any antecedent tasks are
-incomplete or out-of-date.</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   Run task2 whatever its state, and also task1 and antecedents if they are incomplete</span>
-<span class="c">#   Do not log pipeline progress messages to stderr</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">task1</span><span class="p">,</span> <span class="n">task2</span><span class="p">],</span> <span class="n">forcedtorun_tasks</span> <span class="o">=</span> <span class="p">[</span><span class="n">task2</span><span class="p">],</span> <span class="n">logger</span> <span class="o">=</span> <span class="n">blackhole_logger</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-target-tasks">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>target_tasks</em></dt>
-<dd><p class="first last">Pipeline functions and any necessary antecedents (specified implicitly or with <a class="reference internal" href="decorators/follows.html#decorators-follows"><em>@follows</em></a>)
-which should be invoked with the appropriate parameters if they are incomplete or out-of-date.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-forcedtorun-tasks">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>forcedtorun_tasks</em></dt>
-<dd><p class="first last">Optional. These pipeline functions will be invoked regardless of their state.
-Any antecedents tasks will also be executed if they are out-of-date or incomplete.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-multiprocess">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>multiprocess</em></dt>
-<dd><p class="first last">Optional. The number of processes which should be dedicated to running in parallel independent
-tasks and jobs within each task. If <tt class="docutils literal"><span class="pre">multiprocess</span></tt> is set to 1, the pipeline will
-execute in the main process.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-multithread">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>multithread</em></dt>
-<dd><p class="first last">Optional. The number of threads which should be dedicated to running in parallel independent
-tasks and jobs within each task. Should be used only with drmaa. Otherwise the CPython <a class="reference external" href="https://wiki.python.org/moin/GlobalInterpreterLock">global interpreter lock (GIL)</a>
-will slow down your pipeline</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-logger">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>logger</em></dt>
-<dd><p class="first last">For logging messages indicating the progress of the pipeline in terms of tasks and jobs.
-Defaults to outputting to sys.stderr.
-Setting <tt class="docutils literal"><span class="pre">logger=blackhole_logger</span></tt> will prevent any logging output.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-gnu-make">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>gnu_make_maximal_rebuild_mode</em></dt>
-<dd><div class="first admonition warning">
-<p class="first admonition-title">Warning</p>
-<p class="last">This is a dangerous option. Use rarely and with caution</p>
-</div>
-<p>Optional parameter governing how <strong>Ruffus</strong> determines which part of the pipeline is
-out of date and needs to be re-run. If set to <tt class="docutils literal"><span class="pre">False</span></tt>, <strong>ruffus</strong> will work back
-from the <tt class="docutils literal"><span class="pre">target_tasks</span></tt> and only execute the pipeline after the first up-to-date
-tasks that it encounters. For example, if there are four tasks:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   task1 -> task2 -> task3 -> task4 -> task5</span>
-<span class="c">#</span>
-<span class="n">target_tasks</span> <span class="o">=</span> <span class="p">[</span><span class="n">task5</span><span class="p">]</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>If <tt class="docutils literal"><span class="pre">task3()</span></tt> is up-to-date, then only <tt class="docutils literal"><span class="pre">task4()</span></tt> and <tt class="docutils literal"><span class="pre">task5()</span></tt> will be run.
-This will be the case even if <tt class="docutils literal"><span class="pre">task2()</span></tt> and <tt class="docutils literal"><span class="pre">task1()</span></tt> are incomplete.</p>
-<p class="last">This allows you to remove all intermediate results produced by <tt class="docutils literal"><span class="pre">task1</span> <span class="pre">-></span> <span class="pre">task3</span></tt>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-verbose">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>verbose</em></dt>
-<dd><p class="first">Optional parameter indicating the verbosity of the messages sent to <tt class="docutils literal"><span class="pre">logger</span></tt>:
-(Defaults to level 1 if unspecified)</p>
-<ul class="simple">
-<li>level <strong>0</strong> : <em>nothing</em></li>
-<li>level <strong>1</strong> : <em>Out-of-date Task names</em></li>
-<li>level <strong>2</strong> : <em>All Tasks (including any task function docstrings)</em></li>
-<li>level <strong>3</strong> : <em>Out-of-date Jobs in Out-of-date Tasks, no explanation</em></li>
-<li>level <strong>4</strong> : <em>Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings</em></li>
-<li>level <strong>5</strong> : <em>All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)</em></li>
-<li>level <strong>6</strong> : <em>All jobs in All Tasks whether out of date or not</em></li>
-<li>level <strong>10</strong>: <em>logs messages useful only for debugging ruffus pipeline code</em></li>
-</ul>
-<p class="last"><tt class="docutils literal"><span class="pre">verbose</span> <span class="pre">>=</span> <span class="pre">10</span></tt> are intended for debugging <strong>Ruffus</strong> by the developers and the details
-are liable to change from release to release</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-runtime-data">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>runtime_data</em></dt>
-<dd><p class="first last">Experimental feature for passing data to tasks at run time</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-one-second-per-job">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>one_second_per_job</em></dt>
-<dd><p class="first last">To work around poor file timepstamp resolution for some file systems.
-Defaults to True if checksum_level is 0 forcing Tasks to take a minimum of 1 second to complete.
-If your file system has coarse grained time stamps, you can turn on this delay
-by setting <em>one_second_per_job</em> to <tt class="docutils literal"><span class="pre">True</span></tt></p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-touch-files-only">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>touch_files_only</em></dt>
-<dd><p class="first">Create or update output files only to simulate the running of the pipeline.
-Does not invoke real task functions to run jobs. This is most useful to force a
-pipeline to acknowledge that a particular part is now up-to-date.</p>
-<p class="last">This will not work properly if the identities of some files are not known before hand,
-and depend on run time. In other words, not recommended if <tt class="docutils literal"><span class="pre">@split</span></tt> or custom parameter generators are being used.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-exceptions-terminate-immediately">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>exceptions_terminate_immediately</em></dt>
-<dd><p class="first last">Exceptions cause immediate termination of the pipeline.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-log-exceptions">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>log_exceptions</em></dt>
-<dd><p class="first last">Print exceptions to the logger as soon as they occur.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-history-file">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>history_file</em></dt>
-<dd><p class="first last">The database file which stores checksums and file timestamps for input/output files.
-Defaults to <tt class="docutils literal"><span class="pre">.ruffus_history.sqlite</span></tt> if unspecified</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-checksum-level">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>checksum_level</em></dt>
-<dd><p class="first">Several options for checking up-to-dateness are available: Default is level 1.</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>level 0 : Use only file timestamps</li>
-<li>level 1 : above, plus timestamp of successful job completion</li>
-<li>level 2 : above, plus a checksum of the pipeline function body</li>
-<li>level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</li>
-</ul>
-</div></blockquote>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-run-verbose-abbreviated-path">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>verbose_abbreviated_path</em></dt>
-<dd><p class="first">Whether input and output paths are abbreviated. Defaults to 2 if unspecified</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>level 0: The full (expanded, abspath) input or output path</li>
-<li>level > 1: The number of subdirectories to include. Abbreviated paths are prefixed with <tt class="docutils literal"><span class="pre">[,,,]/</span></tt></li>
-<li>level < 0: Input / Output parameters are truncated to <tt class="docutils literal"><span class="pre">MMM</span></tt> letters where <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span> <span class="pre">==-MMM</span></tt>. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by <tt class="docutils literal"><span class="pre"><???></span></tt></li>
-</ul>
-</div></blockquote>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<span class="target" id="pipeline-functions-pipeline-printout"></span></div>
-<div class="section" id="index-1">
-<span id="id3"></span><h2><em>pipeline_printout</em><a class="headerlink" href="#index-1" title="Permalink to this headline">¶</a></h2>
-<p><strong>pipeline_printout</strong> (<a class="reference internal" href="#pipeline-functions-pipeline-printout-output-stream"><cite>output_stream</cite></a> = sys.stdout, <a class="reference internal" href="#pipeline-functions-pipeline-printout-target-tasks"><cite>target_tasks</cite></a> = [], <a class="reference internal" href="#pipeline-functions-pipeline-printout-forcedtorun-tasks"><cite>forcedtorun_tasks</cite></a> = [], <a class="reference internal" href="#pipeline-functions-pipel [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div>Prints out all the pipelined functions which will be invoked given specified <tt class="docutils literal"><span class="pre">target_tasks</span></tt>
-without actually running the pipeline. Because this is a simulation, some of the job
-parameters may be incorrect. For example, the results of a <a class="reference internal" href="tutorials/new_tutorial/split.html#new-manual-split"><em>@split</em></a>
-operation is not predetermined and will only be known after the pipelined function
-splits up the original data. Parameters of all downstream pipelined functions will
-be changed depending on this initial operation.</div></blockquote>
-<dl class="docutils">
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   Simulate running task2 whatever its state, and also task1 and antecedents</span>
-<span class="c">#     if they are incomplete</span>
-<span class="c">#   Print out results to STDOUT</span>
-<span class="c">#</span>
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">task1</span><span class="p">,</span> <span class="n">task2</span><span class="p">],</span> <span class="n">forcedtorun_tasks</span> <span class="o">=</span> <span class="p">[</span><span class="n">task2</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=< [...]
-</pre></div>
-</div>
-</dd>
-</dl>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-output-stream">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_stream</em></dt>
-<dd><p class="first last">Where to printout the results of simulating the running of the pipeline.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-target-tasks">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>target_tasks</em></dt>
-<dd><p class="first last">As in <a class="reference internal" href="#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>: Pipeline functions and any necessary antecedents (specified implicitly or with <a class="reference internal" href="decorators/follows.html#decorators-follows"><em>@follows</em></a>)
-which should be invoked with the appropriate parameters if they are incomplete or out-of-date.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-forcedtorun-tasks">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>forcedtorun_tasks</em></dt>
-<dd><p class="first last">As in <a class="reference internal" href="#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>:These pipeline functions will be invoked regardless of their state.
-Any antecedents tasks will also be executed if they are out-of-date or incomplete.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-verbose">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>verbose</em></dt>
-<dd><p class="first">Optional parameter indicating the verbosity of the messages sent to <tt class="docutils literal"><span class="pre">logger</span></tt>:
-(Defaults to level 4 if unspecified)</p>
-<ul class="simple">
-<li>level <strong>0</strong> : <em>nothing</em></li>
-<li>level <strong>1</strong> : <em>Out-of-date Task names</em></li>
-<li>level <strong>2</strong> : <em>All Tasks (including any task function docstrings)</em></li>
-<li>level <strong>3</strong> : <em>Out-of-date Jobs in Out-of-date Tasks, no explanation</em></li>
-<li>level <strong>4</strong> : <em>Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings</em></li>
-<li>level <strong>5</strong> : <em>All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)</em></li>
-<li>level <strong>6</strong> : <em>All jobs in All Tasks whether out of date or not</em></li>
-<li>level <strong>10</strong>: <em>logs messages useful only for debugging ruffus pipeline code</em></li>
-</ul>
-<p class="last"><tt class="docutils literal"><span class="pre">verbose</span> <span class="pre">>=</span> <span class="pre">10</span></tt> are intended for debugging <strong>Ruffus</strong> by the developers and the details
-are liable to change from release to release</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-indent">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>indent</em></dt>
-<dd><p class="first last">Optional parameter governing the indentation when printing out the component job
-parameters of each task function.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-gnu-make">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>gnu_make_maximal_rebuild_mode</em></dt>
-<dd><div class="first admonition warning">
-<p class="first admonition-title">Warning</p>
-<p class="last">This is a dangerous option. Use rarely and with caution</p>
-</div>
-<p class="last">See explanation in <a class="reference internal" href="#pipeline-functions-pipeline-run-gnu-make"><em>pipeline_run</em></a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-wrap-width">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>wrap_width</em></dt>
-<dd><p class="first last">Optional parameter governing the length of each line before it starts wrapping
-around.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-runtime-data">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>runtime_data</em></dt>
-<dd><p class="first last">Experimental feature for passing data to tasks at run time</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-history-file">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>history_file</em></dt>
-<dd><p class="first last">The database file which stores checksums and file timestamps for input/output files.
-Defaults to <tt class="docutils literal"><span class="pre">.ruffus_history.sqlite</span></tt> if unspecified</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-checksum-level">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>checksum_level</em></dt>
-<dd><p class="first">Several options for checking up-to-dateness are available: Default is level 1.</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>level 0 : Use only file timestamps</li>
-<li>level 1 : above, plus timestamp of successful job completion</li>
-<li>level 2 : above, plus a checksum of the pipeline function body</li>
-<li>level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</li>
-</ul>
-</div></blockquote>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-verbose-abbreviated-path">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>verbose_abbreviated_path</em></dt>
-<dd><p class="first">Whether input and output paths are abbreviated. Defaults to 2 if unspecified</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>level 0: The full (expanded, abspath) input or output path</li>
-<li>level > 1: The number of subdirectories to include. Abbreviated paths are prefixed with <tt class="docutils literal"><span class="pre">[,,,]/</span></tt></li>
-<li>level < 0: Input / Output parameters are truncated to <tt class="docutils literal"><span class="pre">MMM</span></tt> letters where <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span> <span class="pre">==-MMM</span></tt>. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by <tt class="docutils literal"><span class="pre"><???></span></tt></li>
-</ul>
-</div></blockquote>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<span class="target" id="pipeline-functions-pipeline-printout-graph"></span></div>
-<div class="section" id="index-2">
-<span id="id4"></span><h2><em>pipeline_printout_graph</em><a class="headerlink" href="#index-2" title="Permalink to this headline">¶</a></h2>
-<p><strong>pipeline_printout_graph</strong> (<a class="reference internal" href="#pipeline-functions-pipeline-printout-graph-stream"><cite>stream</cite></a>, <a class="reference internal" href="#pipeline-functions-pipeline-printout-graph-output-format"><cite>output_format</cite></a> = None, <a class="reference internal" href="#pipeline-functions-pipeline-printout-graph-target-tasks"><cite>target_tasks</cite></a> = [], <a class="reference internal" href="#pipeline-functions-pipeline-print [...]
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div><p>Prints out flowchart of all the pipelined functions which will be invoked given specified <tt class="docutils literal"><span class="pre">target_tasks</span></tt>
-without actually running the pipeline.</p>
-<p>See <a class="reference internal" href="tutorials/new_tutorial/flowchart_colours.html#new-manual-flowchart-colours"><em>Flowchart colours</em></a></p>
-</div></blockquote>
-<dl class="docutils">
-<dt><strong>Example</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span><span class="p">(</span><span class="s">"flowchart.jpg"</span><span class="p">,</span> <span class="s">"jpg"</span><span class="p">,</span> <span class="p">[</span><span class="n">task1</span><span class="p">,</span> <span class="n">task16</span><span class="p">],</span>
-                            <span class="n">forcedtorun_tasks</span> <span class="o">=</span> <span class="p">[</span><span class="n">task2</span><span class="p">],</span>
-                            <span class="n">no_key_legend</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p><strong>Customising appearance:</strong></p>
-<blockquote>
-<div>The <a class="reference internal" href="#pipeline-functions-pipeline-printout-graph-user-colour-scheme"><em>user_colour_scheme</em></a> parameter can be used to change
-flowchart colours. This allows the default <a class="reference internal" href="tutorials/new_tutorial/flowchart_colours.html#new-manual-flowchart-colours"><em>Colour Schemes</em></a>
-to be set. An example of customising flowchart appearance is available <a class="reference internal" href="tutorials/new_tutorial/flowchart_colours_code.html#new-manual-flowchart-colours-code"><em>(see code)</em></a> .</div></blockquote>
-<p><strong>Parameters:</strong></p>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-stream">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>stream</em></dt>
-<dd><p class="first last">The file or file-like object to which the flowchart should be printed.
-If a string is provided, it is assumed that this is the name of the output file
-which will be opened automatically.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-output-format">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>output_format</em></dt>
-<dd><p class="first">If missing, defaults to the extension of the <em>stream</em> file name (i.e. <tt class="docutils literal"><span class="pre">jpg</span></tt> for <tt class="docutils literal"><span class="pre">a.jpg</span></tt>)</p>
-<div class="last line-block">
-<div class="line">If the programme <tt class="docutils literal"><span class="pre">dot</span></tt> can be found on the executio path, this
-can be any number of <a class="reference external" href="http://www.graphviz.org/doc/info/output.html">formats</a>
-supported by <a class="reference external" href="http://www.graphviz.org/">Graphviz</a>, including, for example,
-<tt class="docutils literal"><span class="pre">jpg</span></tt>, <tt class="docutils literal"><span class="pre">png</span></tt>, <tt class="docutils literal"><span class="pre">pdf</span></tt>, <tt class="docutils literal"><span class="pre">svg</span></tt> etc.</div>
-<div class="line">Otherwise, <strong>ruffus</strong> will only output without error in the <a class="reference external" href="http://en.wikipedia.org/wiki/DOT_language">dot</a> format, which
-is a plain-text graph description language.</div>
-</div>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-target-tasks">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>target_tasks</em></dt>
-<dd><p class="first last">As in <a class="reference internal" href="#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>: Pipeline functions and any necessary antecedents (specified implicitly or with <a class="reference internal" href="decorators/follows.html#decorators-follows"><em>@follows</em></a>)
-which should be invoked with the appropriate parameters if they are incomplete or out-of-date.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-forcedtorun-tasks">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>forcedtorun_tasks</em></dt>
-<dd><p class="first last">As in <a class="reference internal" href="#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>:These pipeline functions will be invoked regardless of their state.
-Any antecedents tasks will also be executed if they are out-of-date or incomplete.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-draw-vertically">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>draw_vertically</em></dt>
-<dd><p class="first last">Draw flowchart in vertical orientation</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-ignore-upstream-of-target">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>ignore_upstream_of_target</em></dt>
-<dd><p class="first last">Start drawing flowchart from specified target tasks. Do not draw tasks which are
-downstream (subsequent) to the targets.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-skip-uptodate-tasks">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>ignore_upstream_of_target</em></dt>
-<dd><p class="first last">Do not draw up-to-date / completed tasks in the flowchart unless they are
-lie on the execution path of the pipeline.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-gnu-make">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>gnu_make_maximal_rebuild_mode</em></dt>
-<dd><div class="first admonition warning">
-<p class="first admonition-title">Warning</p>
-<p class="last">This is a dangerous option. Use rarely and with caution</p>
-</div>
-<p class="last">See explanation in <a class="reference internal" href="#pipeline-functions-pipeline-run-gnu-make"><em>pipeline_run</em></a>.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-test-all-task-for-update">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>test_all_task_for_update</em></dt>
-<dd><div class="first last line-block">
-<div class="line">Indicates whether intermediate tasks are out of date or not. Normally <strong>Ruffus</strong> will
-stop checking dependent tasks for completion or whether they are out-of-date once it has
-discovered the maximal extent of the pipeline which has to be run.</div>
-<div class="line">For displaying the flow of the pipeline, this is hardly very informative.</div>
-</div>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-no-key-legend">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>no_key_legend</em></dt>
-<dd><p class="first last">Do not include key legend explaining the colour scheme of the flowchart.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-minimal-key-legend">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>minimal_key_legend</em></dt>
-<dd><p class="first last">Do not include unused task types in key legend.</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-user-colour-scheme">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>user_colour_scheme</em></dt>
-<dd><p class="first">Dictionary specifying colour scheme for flowchart</p>
-<p>See complete <a class="reference internal" href="tutorials/new_tutorial/flowchart_colours.html#new-manual-flowchart-colours"><em>list of Colour Schemes</em></a>.</p>
-<div class="line-block">
-<div class="line">Colours can be names e.g. <tt class="docutils literal"><span class="pre">"black"</span></tt> or quoted hex e.g. <tt class="docutils literal"><span class="pre">'"#F6F4F4"'</span></tt> (note extra quotes)</div>
-<div class="line">Default values will be used unless specified</div>
-</div>
-<table border="1" class="docutils">
-<colgroup>
-<col width="33%" />
-<col width="33%" />
-<col width="33%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">key</th>
-<th class="head">Subkey</th>
-<th class="head"> </th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'colour_scheme_index'</span></tt></li>
-</ul>
-</td>
-<td><div class="first last line-block">
-<div class="line">index of default colour scheme,</div>
-<div class="line">0-7, defaults to 0 unless specified</div>
-</div>
-</td>
-<td> </td>
-</tr>
-<tr class="row-odd"><td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'Final</span> <span class="pre">target'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Explicitly</span> <span class="pre">specified</span> <span class="pre">task'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Task</span> <span class="pre">to</span> <span class="pre">run'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Down</span> <span class="pre">stream'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Up-to-date</span> <span class="pre">Final</span> <span class="pre">target'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Up-to-date</span> <span class="pre">task</span> <span class="pre">forced</span> <span class="pre">to</span> <span class="pre">rerun'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Up-to-date</span> <span class="pre">task'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Vicious</span> <span class="pre">cycle'</span></tt></li>
-</ul>
-</td>
-<td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'fillcolor'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'fontcolor'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'color'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'dashed'</span></tt>   = <tt class="docutils literal"><span class="pre">0/1</span></tt></li>
-</ul>
-</td>
-<td>Colours / attributes for each task type</td>
-</tr>
-<tr class="row-even"><td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'Vicious</span> <span class="pre">cycle'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Task</span> <span class="pre">to</span> <span class="pre">run'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'Up-to-date'</span></tt></li>
-</ul>
-</td>
-<td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'linecolor'</span></tt></li>
-</ul>
-</td>
-<td>Colours for arrows between tasks</td>
-</tr>
-<tr class="row-odd"><td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'Pipeline'</span></tt></li>
-</ul>
-</td>
-<td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'fontcolor'</span></tt></li>
-</ul>
-</td>
-<td>Flowchart title colour</td>
-</tr>
-<tr class="row-even"><td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'Key'</span></tt></li>
-</ul>
-</td>
-<td><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">'fontcolor'</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">'fillcolor'</span></tt></li>
-</ul>
-</td>
-<td>Legend colours</td>
-</tr>
-</tbody>
-</table>
-<p>Example:</p>
-<blockquote class="last">
-<div><p>Use colour scheme index  = 1</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span> <span class="p">(</span><span class="s">"flowchart.svg"</span><span class="p">,</span> <span class="s">"svg"</span><span class="p">,</span> <span class="p">[</span><span class="n">final_task</span><span class="p">],</span>
-                         <span class="n">user_colour_scheme</span> <span class="o">=</span> <span class="p">{</span>
-                                                <span class="s">"colour_scheme_index"</span> <span class="p">:</span><span class="mi">1</span><span class="p">,</span>
-                                                <span class="s">"Pipeline"</span>      <span class="p">:{</span><span class="s">"fontcolor"</span> <span class="p">:</span> <span class="s">'"#FF3232"'</span> <span class="p">},</span>
-                                                <span class="s">"Key"</span>           <span class="p">:{</span><span class="s">"fontcolor"</span> <span class="p">:</span> <span class="s">"Red"</span><span class="p">,</span>
-                                                                  <span class="s">"fillcolor"</span> <span class="p">:</span> <span class="s">'"#F6F4F4"'</span> <span class="p">},</span>
-                                                <span class="s">"Task to run"</span>   <span class="p">:{</span><span class="s">"linecolor"</span> <span class="p">:</span> <span class="s">'"#0044A0"'</span> <span class="p">},</span>
-                                                <span class="s">"Final target"</span>  <span class="p">:{</span><span class="s">"fillcolor"</span> <span class="p">:</span> <span class="s">'"#EFA03B"'</span><span class="p">,</span>
-                                                                  <span class="s">"fontcolor"</span> <span class="p">:</span> <span class="s">"black"</span><span class="p">,</span>
-                                                                  <span class="s">"dashed"</span>    <span class="p">:</span> <span class="mi">0</span>           <span class="p">}</span>
-                                               <span class="p">})</span>
-</pre></div>
-</div>
-</div></blockquote>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-pipeline-name">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>pipeline_name</em></dt>
-<dd><p class="first last">Specify title for flowchart</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-size">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>size</em></dt>
-<dd><p class="first last">Size in inches for flowchart</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-dpi">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>dpi</em></dt>
-<dd><p class="first last">Resolution in dots per inch. Ignored for svg output</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-runtime-data">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>runtime_data</em></dt>
-<dd><p class="first last">Experimental feature for passing data to tasks at run time</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-history-file">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>history_file</em></dt>
-<dd><p class="first last">The database file which stores checksums and file timestamps for input/output files.
-Defaults to <tt class="docutils literal"><span class="pre">.ruffus_history.sqlite</span></tt> if unspecified</p>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<blockquote id="pipeline-functions-pipeline-printout-graph-checksum-level">
-<div><ul>
-<li><dl class="first docutils">
-<dt><em>checksum_level</em></dt>
-<dd><p class="first">Several options for checking up-to-dateness are available: Default is level 1.</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>level 0 : Use only file timestamps</li>
-<li>level 1 : above, plus timestamp of successful job completion</li>
-<li>level 2 : above, plus a checksum of the pipeline function body</li>
-<li>level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</li>
-</ul>
-</div></blockquote>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<span class="target" id="pipeline-functions-pipeline-get-task-names"></span></div>
-<div class="section" id="index-3">
-<span id="id5"></span><h2><em>pipeline_get_task_names</em><a class="headerlink" href="#index-3" title="Permalink to this headline">¶</a></h2>
-<p><strong>pipeline_get_task_names</strong> ()</p>
-<blockquote>
-<div><p><strong>Purpose:</strong></p>
-<blockquote>
-<div>Returns a list of all task names in the pipeline without running the pipeline or checking to see if the tasks are connected correctly</div></blockquote>
-<p><strong>Example</strong>:</p>
-<blockquote>
-<div><p>Given:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@originate</span><span class="p">([])</span>
-<span class="k">def</span> <span class="nf">create_data</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_data</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".txt"</span><span class="p">),</span> <span class="s">".task1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task1</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".task1"</span><span class="p">),</span> <span class="s">".task2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>Produces a list of three task names:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_get_task_names</span> <span class="p">()</span>
-<span class="go">['create_data', 'task1', 'task2']</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
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-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Pipeline functions</a><ul>
-<li><a class="reference internal" href="#index-0"><em>pipeline_run</em></a></li>
-<li><a class="reference internal" href="#index-1"><em>pipeline_printout</em></a></li>
-<li><a class="reference internal" href="#index-2"><em>pipeline_printout_graph</em></a></li>
-<li><a class="reference internal" href="#index-3"><em>pipeline_get_task_names</em></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="cheatsheet.html"
-                        title="previous chapter">Cheat Sheet</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="drmaa_wrapper_functions.html"
-                        title="next chapter">drmaa functions</a></p>
-  <h3>This Page</h3>
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-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
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-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="##pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="##pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="##pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="##pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
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-            
-  <div class="section" id="ruffus-proxy-logger">
-<h1>ruffus.proxy_logger<a class="headerlink" href="#ruffus-proxy-logger" title="Permalink to this headline">¶</a></h1>
-<span class="target" id="module-ruffus.proxy_logger"><span id="proxy-logger"></span></span><div class="section" id="create-proxy-for-logging-for-use-with-multiprocessing">
-<h2>Create proxy for logging for use with multiprocessing<a class="headerlink" href="#create-proxy-for-logging-for-use-with-multiprocessing" title="Permalink to this headline">¶</a></h2>
-<p>These can be safely sent (marshalled) across process boundaries</p>
-<div class="section" id="example-1">
-<h3>Example 1<a class="headerlink" href="#example-1" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Set up logger from config file:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">proxy_logger</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">args</span><span class="o">=</span><span class="p">{}</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"config_file"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"/my/config/file"</span>
-
-<span class="p">(</span><span class="n">logger_proxy</span><span class="p">,</span>
- <span class="n">logging_mutex</span><span class="p">)</span> <span class="o">=</span> <span class="n">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">setup_std_shared_logger</span><span class="p">,</span>
-                                                <span class="s">"my_logger"</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-2">
-<h3>Example 2<a class="headerlink" href="#example-2" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Log to file <tt class="docutils literal"><span class="pre">"/my/lg.log"</span></tt> in the specified format (Time / Log name / Event type / Message).</p>
-<p>Delay file creation until first log.</p>
-<p>Only log <tt class="docutils literal"><span class="pre">Debug</span></tt> messages</p>
-<blockquote>
-<div><p>Other alternatives for the logging threshold (<tt class="docutils literal"><span class="pre">args["level"]</span></tt>) include</p>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">logging.DEBUG</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">logging.INFO</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">logging.WARNING</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">logging.ERROR</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">logging.CRITICAL</span></tt></li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">proxy_logger</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">args</span><span class="o">=</span><span class="p">{}</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"file_name"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"/my/lg.log"</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"formatter"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"</span><span class="si">%(asctime)s</span><span class="s"> - </span><span class="si">%(name)s</span><span class="s"> - </span><span class="si">%(levelname)6s</span><span class="s"> - </span><span class="si">%(message)s</span><span class="s">"</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"delay"</span><span class="p">]</span>     <span class="o">=</span> <span class="bp">True</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"level"</span><span class="p">]</span>     <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span>
-
-<span class="p">(</span><span class="n">logger_proxy</span><span class="p">,</span>
- <span class="n">logging_mutex</span><span class="p">)</span> <span class="o">=</span> <span class="n">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">setup_std_shared_logger</span><span class="p">,</span>
-                                                <span class="s">"my_logger"</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-3">
-<h3>Example 3<a class="headerlink" href="#example-3" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Rotate log files every 20 Kb, with up to 10 backups.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">proxy_logger</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">args</span><span class="o">=</span><span class="p">{}</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"file_name"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"/my/lg.log"</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"rotating"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"maxBytes"</span><span class="p">]</span><span class="o">=</span><span class="mi">20000</span>
-<span class="n">args</span><span class="p">[</span><span class="s">"backupCount"</span><span class="p">]</span><span class="o">=</span><span class="mi">10</span>
-<span class="p">(</span><span class="n">logger_proxy</span><span class="p">,</span>
- <span class="n">logging_mutex</span><span class="p">)</span> <span class="o">=</span> <span class="n">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">setup_std_shared_logger</span><span class="p">,</span>
-                                                <span class="s">"my_logger"</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="to-use">
-<h3>To use:<a class="headerlink" href="#to-use" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="p">(</span><span class="n">logger_proxy</span><span class="p">,</span>
- <span class="n">logging_mutex</span><span class="p">)</span> <span class="o">=</span> <span class="n">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">setup_std_shared_logger</span><span class="p">,</span>
-                                                <span class="s">"my_logger"</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
-
-<span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-    <span class="n">my_log</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">'This is a debug message'</span><span class="p">)</span>
-    <span class="n">my_log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">'This is an info message'</span><span class="p">)</span>
-    <span class="n">my_log</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s">'This is a warning message'</span><span class="p">)</span>
-    <span class="n">my_log</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s">'This is an error message'</span><span class="p">)</span>
-    <span class="n">my_log</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s">'This is a critical error message'</span><span class="p">)</span>
-    <span class="n">my_log</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">,</span> <span class="s">'This is a debug message'</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>Note that the logging function <tt class="docutils literal"><span class="pre">exception()</span></tt> is not included because python
-stack trace information is not well-marshalled
-(<a class="reference external" href="http://docs.python.org/library/pickle.html">pickle</a>d) across processes.</p>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="proxies-for-a-log">
-<h2>Proxies for a log:<a class="headerlink" href="#proxies-for-a-log" title="Permalink to this headline">¶</a></h2>
-<dl class="function">
-<dt id="ruffus.proxy_logger.make_shared_logger_and_proxy">
-<tt class="descclassname">ruffus.proxy_logger.</tt><tt class="descname">make_shared_logger_and_proxy</tt><big>(</big><em>logger_factory</em>, <em>logger_name</em>, <em>args</em><big>)</big><a class="reference internal" href="_modules/ruffus/proxy_logger.html#make_shared_logger_and_proxy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ruffus.proxy_logger.make_shared_logger_and_proxy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Make a <a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> object
-called “<tt class="docutils literal"><span class="pre">logger_name</span></tt>” by calling <tt class="docutils literal"><span class="pre">logger_factory</span></tt>(<tt class="docutils literal"><span class="pre">args</span></tt>)</p>
-<p>This function will return a proxy to the shared logger which can be copied to jobs
-in other processes, as well as a mutex which can be used to prevent simultaneous logging
-from happening.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>logger_factory</strong> – <p>functions which creates and returns an object with the
-<a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> interface.
-<tt class="docutils literal"><span class="pre">setup_std_shared_logger()</span></tt> is one example of a logger factory.</p>
-</li>
-<li><strong>logger_name</strong> – name of log</li>
-<li><strong>args</strong> – parameters passed (as a single argument) to <tt class="docutils literal"><span class="pre">logger_factory</span></tt></li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">a proxy to the shared logger which can be copied to jobs in other processes</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">a mutex which can be used to prevent simultaneous logging from happening</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</div>
-<div class="section" id="create-a-logging-object">
-<h2>Create a logging object<a class="headerlink" href="#create-a-logging-object" title="Permalink to this headline">¶</a></h2>
-<dl class="function">
-<dt id="ruffus.proxy_logger.setup_std_shared_logger">
-<tt class="descclassname">ruffus.proxy_logger.</tt><tt class="descname">setup_std_shared_logger</tt><big>(</big><em>logger_name</em>, <em>args</em><big>)</big><a class="reference internal" href="_modules/ruffus/proxy_logger.html#setup_std_shared_logger"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ruffus.proxy_logger.setup_std_shared_logger" title="Permalink to this definition">¶</a></dt>
-<dd><p>This function is a simple around wrapper around the python
-<a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> module.</p>
-<p>This <em>logger_factory</em> example creates logging objects which can
-then be managed by proxy via <tt class="docutils literal"><span class="pre">ruffus.proxy_logger.make_shared_logger_and_proxy()</span></tt></p>
-<p>This can be:</p>
-<blockquote>
-<div><ul class="simple">
-<li>a <a class="reference external" href="http://docs.python.org/library/logging.html#filehandler">disk log file</a></li>
-<li>a automatically backed-up <a class="reference external" href="http://docs.python.org/library/logging.html#rotatingfilehandler">(rotating) log</a>.</li>
-<li>any log specified in a <a class="reference external" href="http://docs.python.org/library/logging.html#configuration-file-format">configuration file</a></li>
-</ul>
-</div></blockquote>
-<p>These are specified in the <tt class="docutils literal"><span class="pre">args</span></tt> dictionary forwarded by <tt class="docutils literal"><span class="pre">make_shared_logger_and_proxy()</span></tt></p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>logger_name</strong> – name of log</li>
-<li><strong>args</strong> – <p>a dictionary of parameters forwarded from <tt class="docutils literal"><span class="pre">make_shared_logger_and_proxy()</span></tt></p>
-<p>Valid entries include:</p>
-<blockquote>
-<div><dl class="describe">
-<dt>
-<tt class="descname">"level"</tt></dt>
-<dd><p>Sets the <a class="reference external" href="http://docs.python.org/library/logging.html#logging.Handler.setLevel">threshold</a> for the logger.</p>
-</dd></dl>
-
-<dl class="describe">
-<dt>
-<tt class="descname">"config_file"</tt></dt>
-<dd><p>The logging object is configured from this <a class="reference external" href="http://docs.python.org/library/logging.html#configuration-file-format">configuration file</a>.</p>
-</dd></dl>
-
-<dl class="describe">
-<dt>
-<tt class="descname">"file_name"</tt></dt>
-<dd><p>Sets disk log file name.</p>
-</dd></dl>
-
-<dl class="describe">
-<dt>
-<tt class="descname">"rotating"</tt></dt>
-<dd><p>Chooses a <a class="reference external" href="http://docs.python.org/library/logging.html#rotatingfilehandler">(rotating) log</a>.</p>
-</dd></dl>
-
-<dl class="describe">
-<dt>
-<tt class="descname">"maxBytes"</tt></dt>
-<dd><p>Allows the file to rollover at a predetermined size</p>
-</dd></dl>
-
-<dl class="describe">
-<dt>
-<tt class="descname">"backupCount"</tt></dt>
-<dd><p>If backupCount is non-zero, the system will save old log files by appending the extensions <tt class="docutils literal"><span class="pre">.1</span></tt>, <tt class="docutils literal"><span class="pre">.2</span></tt>, <tt class="docutils literal"><span class="pre">.3</span></tt> etc., to the filename.</p>
-</dd></dl>
-
-<dl class="describe">
-<dt>
-<tt class="descname">"delay"</tt></dt>
-<dd><p>Defer file creation until the log is written to.</p>
-</dd></dl>
-
-<dl class="describe">
-<dt>
-<tt class="descname">"formatter"</tt></dt>
-<dd><p><a class="reference external" href="http://docs.python.org/library/logging.html#formatter-objects">Converts</a> the message to a logged entry string.
-For example,</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="s">"</span><span class="si">%(asctime)s</span><span class="s"> - </span><span class="si">%(name)s</span><span class="s"> - </span><span class="si">%(levelname)6s</span><span class="s"> - </span><span class="si">%(message)s</span><span class="s">"</span>
-</pre></div>
-</div>
-</dd></dl>
-
-</div></blockquote>
-</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">ruffus.proxy_logger</a><ul>
-<li><a class="reference internal" href="#create-proxy-for-logging-for-use-with-multiprocessing">Create proxy for logging for use with multiprocessing</a><ul>
-<li><a class="reference internal" href="#example-1">Example 1</a></li>
-<li><a class="reference internal" href="#example-2">Example 2</a></li>
-<li><a class="reference internal" href="#example-3">Example 3</a></li>
-<li><a class="reference internal" href="#to-use">To use:</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#proxies-for-a-log">Proxies for a log:</a></li>
-<li><a class="reference internal" href="#create-a-logging-object">Create a logging object</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="task.html"
-                        title="previous chapter">ruffus.Task</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="_sources/proxy_logger.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
-
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-      </div>
-      <div class="clearer"></div>
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-            <li><a href="decorators/originate.html">@originate</a>                           </li>
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-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
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-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
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-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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diff --git a/doc/_build/html/refactoring_ruffus_notes.html b/doc/_build/html/refactoring_ruffus_notes.html
deleted file mode 100644
index 2b4fcfd..0000000
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+++ /dev/null
@@ -1,187 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
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-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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\ No newline at end of file
diff --git a/doc/_build/html/search.html b/doc/_build/html/search.html
deleted file mode 100644
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--- a/doc/_build/html/search.html
+++ /dev/null
@@ -1,177 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
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-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    
-    <title>Search — ruffus 2.5 documentation</title>
-    
-    <link rel="stylesheet" href="_static/ruffus.css" type="text/css" />
-    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-    
-    <script type="text/javascript">
-      var DOCUMENTATION_OPTIONS = {
-        URL_ROOT:    './',
-        VERSION:     '2.5',
-        COLLAPSE_INDEX: false,
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-        HAS_SOURCE:  true
-      };
-    </script>
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-    <link rel="top" title="ruffus 2.5 documentation" href="index.html" />
-  <script type="text/javascript">
-    jQuery(function() { Search.loadIndex("searchindex.js"); });
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-            
-  <h1 id="search-documentation">Search</h1>
-  <div id="fallback" class="admonition warning">
-  <script type="text/javascript">$('#fallback').hide();</script>
-  <p>
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-    From here you can search these documents. Enter your search
-    words into the box below and click "search". Note that the search
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-      <div class="sphinxsidebar">
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-    
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
-        </ul>
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-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
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-      </div>
-      <div class="clearer"></div>
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-      <h3>Navigation</h3>
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-  </body>
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\ No newline at end of file
diff --git a/doc/_build/html/searchindex.js b/doc/_build/html/searchindex.js
deleted file mode 100644
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--- a/doc/_build/html/searchindex.js
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/doc/_build/html/task.html b/doc/_build/html/task.html
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+++ /dev/null
@@ -1,516 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
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-<html xmlns="http://www.w3.org/1999/xhtml">
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-  <div class="section" id="ruffus-task">
-<h1>ruffus.Task<a class="headerlink" href="#ruffus-task" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="decorators">
-<h2>Decorators<a class="headerlink" href="#decorators" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Basic Task decorators are:</p>
-<blockquote>
-<div><p><a class="reference internal" href="decorators/follows.html#decorators-follows"><em>@follows()</em></a></p>
-<p>and</p>
-<p><a class="reference internal" href="decorators/files.html#decorators-files"><em>@files()</em></a></p>
-</div></blockquote>
-<p>Task decorators include:</p>
-<blockquote>
-<div><p><a class="reference internal" href="decorators/files.html#decorators-files"><em>@split()</em></a></p>
-<p><a class="reference internal" href="decorators/files.html#decorators-files"><em>@transform()</em></a></p>
-<p><a class="reference internal" href="decorators/files.html#decorators-files"><em>@merge()</em></a></p>
-<p><a class="reference internal" href="decorators/posttask.html#decorators-posttask"><em>@posttask()</em></a></p>
-</div></blockquote>
-<p>More advanced users may require:</p>
-<blockquote>
-<div><p><a class="reference internal" href="decorators/transform_ex.html#decorators-transform-ex"><em>@transform()</em></a></p>
-<p><a class="reference internal" href="decorators/collate.html#decorators-collate"><em>@collate()</em></a></p>
-<p><a class="reference internal" href="decorators/parallel.html#decorators-parallel"><em>@parallel()</em></a></p>
-<p><a class="reference internal" href="decorators/check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate()</em></a></p>
-<p><a class="reference internal" href="decorators/files_re.html#decorators-files-re"><em>@files_re()</em></a></p>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="pipeline-functions">
-<h2>Pipeline functions<a class="headerlink" href="#pipeline-functions" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="pipeline-run">
-<h3>pipeline_run<a class="headerlink" href="#pipeline-run" title="Permalink to this headline">¶</a></h3>
-<dl class="function">
-<dt id="ruffus.task.pipeline_run">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">pipeline_run</tt><big>(</big><em>target_tasks</em>, <em>forcedtorun_tasks=</em><span class="optional">[</span><span class="optional">]</span>, <em>multiprocess=1</em>, <em>logger=stderr_logger</em>, <em>gnu_make_maximal_rebuild_mode=True</em><big>)</big><a class="reference internal" href="_modules/ruffus/task.html#pipeline_run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ruffus.task.pipeline_r [...]
-<dd><p>Run pipelines.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>target_tasks</strong> – targets task functions which will be run if they are out-of-date</li>
-<li><strong>forcedtorun_tasks</strong> – task functions which will be run whether or not they are out-of-date</li>
-<li><strong>multiprocess</strong> – The number of concurrent jobs running on different processes.</li>
-<li><strong>multithread</strong> – The number of concurrent jobs running as different threads. If > 1, ruffus will use multithreading <em>instead of</em> multiprocessing (and ignore the multiprocess parameter). Using multi threading is particularly useful to manage high performance clusters which otherwise are prone to “processor storms” when large number of cores finish jobs at the same time. (Thanks Andreas Heger)</li>
-<li><strong>logger</strong> (<a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> objects) – Where progress will be logged. Defaults to stderr output.</li>
-<li><strong>verbose</strong> – level 0 : nothing
-level 1 : Out-of-date Task names
-level 2 : All Tasks (including any task function docstrings)
-level 3 : Out-of-date Jobs in Out-of-date Tasks, no explanation
-level 4 : Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings
-level 5 : All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)
-level 6 : All jobs in All Tasks whether out of date or not
-level 10: logs messages useful only for debugging ruffus pipeline code</li>
-<li><strong>touch_files_only</strong> – Create or update input/output files only to simulate running the pipeline. Do not run jobs. If set to CHECKSUM_REGENERATE, will regenerate the checksum history file to reflect the existing i/o files on disk.</li>
-<li><strong>exceptions_terminate_immediately</strong> – Exceptions cause immediate termination
-rather than waiting for N jobs to finish where N = multiprocess</li>
-<li><strong>log_exceptions</strong> – Print exceptions to the logger as soon as they occur.</li>
-<li><strong>checksum_level</strong> – Several options for checking up-to-dateness are available: Default is level 1.
-level 0 : Use only file timestamps
-level 1 : above, plus timestamp of successful job completion
-level 2 : above, plus a checksum of the pipeline function body
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</li>
-<li><strong>one_second_per_job</strong> – To work around poor file timepstamp resolution for some file systems. Defaults to True if checksum_level is 0 forcing Tasks to take a minimum of 1 second to complete.</li>
-<li><strong>runtime_data</strong> – Experimental feature for passing data to tasks at run time</li>
-<li><strong>gnu_make_maximal_rebuild_mode</strong> – Defaults to re-running <em>all</em> out-of-date tasks. Runs minimal
-set to build targets if set to <tt class="docutils literal"><span class="pre">True</span></tt>. Use with caution.</li>
-<li><strong>history_file</strong> – The database file which stores checksums and file timestamps for input/output files.</li>
-<li><strong>verbose_abbreviated_path</strong> – whether input and output paths are abbreviated.
-level 0: The full (expanded, abspath) input or output path
-level > 1: The number of subdirectories to include. Abbreviated paths are prefixed with <tt class="docutils literal"><span class="pre">[,,,]/</span></tt>
-level < 0: level < 0: Input / Output parameters are truncated to <tt class="docutils literal"><span class="pre">MMM</span></tt> letters where <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span> <span class="pre">==-MMM</span></tt>. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by <tt class="docutils literal"><span class="pre"><???></span></tt></li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</div>
-<div class="section" id="pipeline-printout">
-<h3>pipeline_printout<a class="headerlink" href="#pipeline-printout" title="Permalink to this headline">¶</a></h3>
-<dl class="function">
-<dt id="ruffus.task.pipeline_printout">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">pipeline_printout</tt><big>(</big><em>output_stream=None</em>, <em>target_tasks=</em><span class="optional">[</span><span class="optional">]</span>, <em>forcedtorun_tasks=</em><span class="optional">[</span><span class="optional">]</span>, <em>verbose=None</em>, <em>indent=4</em>, <em>gnu_make_maximal_rebuild_mode=True</em>, <em>wrap_width=100</em>, <em>runtime_data=None</em>, <em>checksum_level=None</em>, <em>history_file=N [...]
-<dd><p>Printouts the parts of the pipeline which will be run</p>
-<p>Because the parameters of some jobs depend on the results of previous tasks, this function
-produces only the current snap-shot of task jobs. In particular, tasks which generate
-variable number of inputs into following tasks will not produce the full range of jobs.</p>
-<dl class="docutils">
-<dt>::</dt>
-<dd>verbose = 0 : Nothing
-verbose = 1 : Out-of-date Task names
-verbose = 2 : All Tasks (including any task function docstrings)
-verbose = 3 : Out-of-date Jobs in Out-of-date Tasks, no explanation
-verbose = 4 : Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings
-verbose = 5 : All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)
-verbose = 6 : All jobs in All Tasks whether out of date or not</dd>
-</dl>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>output_stream</strong> (file-like object with <tt class="docutils literal"><span class="pre">write()</span></tt> function) – where to print to</li>
-<li><strong>target_tasks</strong> – targets task functions which will be run if they are out-of-date</li>
-<li><strong>forcedtorun_tasks</strong> – task functions which will be run whether or not they are out-of-date</li>
-<li><strong>verbose</strong> – level 0 : nothing
-level 1 : Out-of-date Task names
-level 2 : All Tasks (including any task function docstrings)
-level 3 : Out-of-date Jobs in Out-of-date Tasks, no explanation
-level 4 : Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings
-level 5 : All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)
-level 6 : All jobs in All Tasks whether out of date or not
-level 10: logs messages useful only for debugging ruffus pipeline code</li>
-<li><strong>indent</strong> – How much indentation for pretty format.</li>
-<li><strong>gnu_make_maximal_rebuild_mode</strong> – Defaults to re-running <em>all</em> out-of-date tasks. Runs minimal
-set to build targets if set to <tt class="docutils literal"><span class="pre">True</span></tt>. Use with caution.</li>
-<li><strong>wrap_width</strong> – The maximum length of each line</li>
-<li><strong>runtime_data</strong> – Experimental feature for passing data to tasks at run time</li>
-<li><strong>checksum_level</strong> – Several options for checking up-to-dateness are available: Default is level 1.
-level 0 : Use only file timestamps
-level 1 : As above, plus timestamp of successful job completion
-level 2 : As above, plus a checksum of the pipeline function body
-level 3 : As above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</li>
-<li><strong>history_file</strong> – The database file which stores checksums and file timestamps for input/output files.</li>
-<li><strong>verbose_abbreviated_path</strong> – whether input and output paths are abbreviated.
-level 0: The full (expanded, abspath) input or output path
-level > 1: The number of subdirectories to include. Abbreviated paths are prefixed with <tt class="docutils literal"><span class="pre">[,,,]/</span></tt>
-level < 0: level < 0: Input / Output parameters are truncated to <tt class="docutils literal"><span class="pre">MMM</span></tt> letters where <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span> <span class="pre">==-MMM</span></tt>. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by <tt class="docutils literal"><span class="pre"><???></span></tt></li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</div>
-<div class="section" id="pipeline-printout-graph">
-<h3>pipeline_printout_graph<a class="headerlink" href="#pipeline-printout-graph" title="Permalink to this headline">¶</a></h3>
-<dl class="function">
-<dt id="ruffus.task.pipeline_printout_graph">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">pipeline_printout_graph</tt><big>(</big><em>stream</em>, <em>output_format=None</em>, <em>target_tasks=</em><span class="optional">[</span><span class="optional">]</span>, <em>forcedtorun_tasks=</em><span class="optional">[</span><span class="optional">]</span>, <em>draw_vertically=True</em>, <em>ignore_upstream_of_target=False</em>, <em>skip_uptodate_tasks=False</em>, <em>gnu_make_maximal_rebuild_mode=True</em>, <em>test_al [...]
-<dd><p>print out pipeline dependencies in various formats</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>stream</strong> (file-like object with <tt class="docutils literal"><span class="pre">write()</span></tt> function) – where to print to</li>
-<li><strong>output_format</strong> – [“dot”, “jpg”, “svg”, “ps”, “png”]. All but the first depends on the <a class="reference external" href="http://www.graphviz.org">dot</a> program.</li>
-<li><strong>target_tasks</strong> – targets task functions which will be run if they are out-of-date.</li>
-<li><strong>forcedtorun_tasks</strong> – task functions which will be run whether or not they are out-of-date.</li>
-<li><strong>draw_vertically</strong> – Top to bottom instead of left to right.</li>
-<li><strong>ignore_upstream_of_target</strong> – Don’t draw upstream tasks of targets.</li>
-<li><strong>skip_uptodate_tasks</strong> – Don’t draw up-to-date tasks if possible.</li>
-<li><strong>gnu_make_maximal_rebuild_mode</strong> – Defaults to re-running <em>all</em> out-of-date tasks. Runs minimal
-set to build targets if set to <tt class="docutils literal"><span class="pre">True</span></tt>. Use with caution.</li>
-<li><strong>test_all_task_for_update</strong> – Ask all task functions if they are up-to-date.</li>
-<li><strong>no_key_legend</strong> – Don’t draw key/legend for graph.</li>
-<li><strong>minimal_key_legend</strong> – Only add entries to the legend for task types which appear</li>
-<li><strong>user_colour_scheme</strong> – Dictionary specifying colour scheme for flowchart</li>
-<li><strong>pipeline_name</strong> – Pipeline Title</li>
-<li><strong>size</strong> – tuple of x and y dimensions</li>
-<li><strong>dpi</strong> – print resolution</li>
-<li><strong>runtime_data</strong> – Experimental feature for passing data to tasks at run time</li>
-<li><strong>history_file</strong> – The database file which stores checksums and file timestamps for input/output files.</li>
-<li><strong>checksum_level</strong> – Several options for checking up-to-dateness are available: Default is level 1.
-level 0 : Use only file timestamps
-level 1 : above, plus timestamp of successful job completion
-level 2 : above, plus a checksum of the pipeline function body
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</div>
-</div>
-<div class="section" id="id1">
-<h2>Logging<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
-<dl class="class">
-<dt id="ruffus.task.t_black_hole_logger">
-<em class="property">class </em><tt class="descclassname">ruffus.task.</tt><tt class="descname">t_black_hole_logger</tt><a class="reference internal" href="_modules/ruffus/task.html#t_black_hole_logger"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ruffus.task.t_black_hole_logger" title="Permalink to this definition">¶</a></dt>
-<dd><p>Does nothing!</p>
-</dd></dl>
-
-<dl class="class">
-<dt id="ruffus.task.t_stderr_logger">
-<em class="property">class </em><tt class="descclassname">ruffus.task.</tt><tt class="descname">t_stderr_logger</tt><a class="reference internal" href="_modules/ruffus/task.html#t_stderr_logger"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ruffus.task.t_stderr_logger" title="Permalink to this definition">¶</a></dt>
-<dd><p>Everything to stderr</p>
-</dd></dl>
-
-</div>
-<div class="section" id="implementation">
-<h2>Implementation:<a class="headerlink" href="#implementation" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="parameter-factories">
-<h3>Parameter factories:<a class="headerlink" href="#parameter-factories" title="Permalink to this headline">¶</a></h3>
-<dl class="function">
-<dt id="ruffus.task.merge_param_factory">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">merge_param_factory</tt><big>(</big><em>input_files_task_globs</em>, <em>output_param</em>, <em>*extra_params</em><big>)</big><a class="headerlink" href="#ruffus.task.merge_param_factory" title="Permalink to this definition">¶</a></dt>
-<dd><p>Factory for task_merge</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="ruffus.task.collate_param_factory">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">collate_param_factory</tt><big>(</big><em>input_files_task_globs</em>, <em>flatten_input</em>, <em>file_names_transform</em>, <em>extra_input_files_task_globs</em>, <em>replace_inputs</em>, <em>output_pattern</em>, <em>*extra_specs</em><big>)</big><a class="headerlink" href="#ruffus.task.collate_param_factory" title="Permalink to this definition">¶</a></dt>
-<dd><p>Factory for task_collate</p>
-<p>Looks exactly like @transform except that all [input] which lead to the same [output / extra] are combined together</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="ruffus.task.transform_param_factory">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">transform_param_factory</tt><big>(</big><em>input_files_task_globs</em>, <em>flatten_input</em>, <em>file_names_transform</em>, <em>extra_input_files_task_globs</em>, <em>replace_inputs</em>, <em>output_pattern</em>, <em>*extra_specs</em><big>)</big><a class="headerlink" href="#ruffus.task.transform_param_factory" title="Permalink to this definition">¶</a></dt>
-<dd><p>Factory for task_transform</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="ruffus.task.files_param_factory">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">files_param_factory</tt><big>(</big><em>input_files_task_globs</em>, <em>flatten_input</em>, <em>do_not_expand_single_job_tasks</em>, <em>output_extras</em><big>)</big><a class="headerlink" href="#ruffus.task.files_param_factory" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="docutils">
-<dt>Factory for functions which</dt>
-<dd>yield tuples of inputs, outputs / extras</dd>
-</dl>
-<p>..Note:</p>
-<div class="highlight-python"><pre>1. Each job requires input/output file names
-2. Input/output file names can be a string, an arbitrarily nested sequence
-3. Non-string types are ignored
-3. Either Input or output file name must contain at least one string</pre>
-</div>
-</dd></dl>
-
-<dl class="function">
-<dt id="ruffus.task.args_param_factory">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">args_param_factory</tt><big>(</big><em>orig_args</em><big>)</big><a class="headerlink" href="#ruffus.task.args_param_factory" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="docutils">
-<dt>Factory for functions which</dt>
-<dd>yield tuples of inputs, outputs / extras</dd>
-</dl>
-<p>..Note:</p>
-<div class="highlight-python"><pre>1. Each job requires input/output file names
-2. Input/output file names can be a string, an arbitrarily nested sequence
-3. Non-string types are ignored
-3. Either Input or output file name must contain at least one string</pre>
-</div>
-</dd></dl>
-
-<dl class="function">
-<dt id="ruffus.task.split_param_factory">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">split_param_factory</tt><big>(</big><em>input_files_task_globs</em>, <em>output_files_task_globs</em>, <em>*extra_params</em><big>)</big><a class="headerlink" href="#ruffus.task.split_param_factory" title="Permalink to this definition">¶</a></dt>
-<dd><p>Factory for task_split</p>
-</dd></dl>
-
-</div>
-<div class="section" id="wrappers-around-jobs">
-<h3>Wrappers around jobs:<a class="headerlink" href="#wrappers-around-jobs" title="Permalink to this headline">¶</a></h3>
-<dl class="function">
-<dt id="ruffus.task.job_wrapper_generic">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">job_wrapper_generic</tt><big>(</big><em>param</em>, <em>user_defined_work_func</em>, <em>register_cleanup</em>, <em>touch_files_only</em><big>)</big><a class="reference internal" href="_modules/ruffus/task.html#job_wrapper_generic"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ruffus.task.job_wrapper_generic" title="Permalink to this definition">¶</a></dt>
-<dd><p>run func</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="ruffus.task.job_wrapper_io_files">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">job_wrapper_io_files</tt><big>(</big><em>param</em>, <em>user_defined_work_func</em>, <em>register_cleanup</em>, <em>touch_files_only</em>, <em>output_files_only=False</em><big>)</big><a class="reference internal" href="_modules/ruffus/task.html#job_wrapper_io_files"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ruffus.task.job_wrapper_io_files" title="Permalink to this definition">¶</a></dt>
-<dd><p>run func on any i/o if not up to date</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="ruffus.task.job_wrapper_mkdir">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">job_wrapper_mkdir</tt><big>(</big><em>param</em>, <em>user_defined_work_func</em>, <em>register_cleanup</em>, <em>touch_files_only</em><big>)</big><a class="reference internal" href="_modules/ruffus/task.html#job_wrapper_mkdir"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#ruffus.task.job_wrapper_mkdir" title="Permalink to this definition">¶</a></dt>
-<dd><p>make directories if not exists</p>
-</dd></dl>
-
-</div>
-<div class="section" id="checking-if-job-is-update">
-<h3>Checking if job is update:<a class="headerlink" href="#checking-if-job-is-update" title="Permalink to this headline">¶</a></h3>
-<dl class="function">
-<dt id="ruffus.task.needs_update_check_modify_time">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">needs_update_check_modify_time</tt><big>(</big><em>*params</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#ruffus.task.needs_update_check_modify_time" title="Permalink to this definition">¶</a></dt>
-<dd><p>Given input and output files, see if all exist and whether output files are later than input files
-Each can be</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>string: assumed to be a filename “file1”</li>
-<li>any other type</li>
-<li>arbitrary nested sequence of (1) and (2)</li>
-</ol>
-</div></blockquote>
-</dd></dl>
-
-<dl class="function">
-<dt id="ruffus.task.needs_update_check_directory_missing">
-<tt class="descclassname">ruffus.task.</tt><tt class="descname">needs_update_check_directory_missing</tt><big>(</big><em>*params</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#ruffus.task.needs_update_check_directory_missing" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="docutils">
-<dt>Called per directory:</dt>
-<dd>Does it exist?
-Is it an ordinary file not a directory? (throw exception</dd>
-</dl>
-</dd></dl>
-
-</div>
-</div>
-<div class="section" id="exceptions-and-errors">
-<h2>Exceptions and Errors<a class="headerlink" href="#exceptions-and-errors" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">ruffus.Task</a><ul>
-<li><a class="reference internal" href="#decorators">Decorators</a></li>
-<li><a class="reference internal" href="#pipeline-functions">Pipeline functions</a><ul>
-<li><a class="reference internal" href="#pipeline-run">pipeline_run</a></li>
-<li><a class="reference internal" href="#pipeline-printout">pipeline_printout</a></li>
-<li><a class="reference internal" href="#pipeline-printout-graph">pipeline_printout_graph</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#id1">Logging</a></li>
-<li><a class="reference internal" href="#implementation">Implementation:</a><ul>
-<li><a class="reference internal" href="#parameter-factories">Parameter factories:</a></li>
-<li><a class="reference internal" href="#wrappers-around-jobs">Wrappers around jobs:</a></li>
-<li><a class="reference internal" href="#checking-if-job-is-update">Checking if job is update:</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#exceptions-and-errors">Exceptions and Errors</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="decorators/files_re.html"
-                        title="previous chapter">@files_re</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="proxy_logger.html"
-                        title="next chapter">ruffus.proxy_logger</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="_sources/task.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
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-            
-  <div class="section" id="future-changes-to-ruffus">
-<span id="todo"></span><h1>Future Changes to Ruffus<a class="headerlink" href="#future-changes-to-ruffus" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><p>I would appreciated feedback and help on all these issues and where next to take <em>ruffus</em>.</p>
-<p><strong>Future Changes</strong> are features where we more or less know where we are going and how to get there.</p>
-<p><strong>Planned Improvements</strong> describes features we would like in Ruffus but where the implementation
-or syntax has not yet been (fully) worked out.</p>
-<p>If you have suggestions or contributions, please either write to me ( ruffus_lib at llew.org.uk) or
-send a pull request via the <a class="reference external" href="https://github.com/bunbun/ruffus">git site</a>.</p>
-</div></blockquote>
-<div class="section" id="todo-pipeline-printout-graph-should-print-inactive-tasks">
-<span id="todo-inactive-tasks-in-pipeline-printout-graph"></span><h2>Todo: pipeline_printout_graph should print inactive tasks<a class="headerlink" href="#todo-pipeline-printout-graph-should-print-inactive-tasks" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="todo-mark-input-strings-as-non-file-names-and-add-support-for-dynamically-returned-parameters">
-<span id="todo-dynamic-strings"></span><h2>Todo: Mark input strings as non-file names, and add support for dynamically returned parameters<a class="headerlink" href="#todo-mark-input-strings-as-non-file-names-and-add-support-for-dynamically-returned-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Use indicator object.</li>
-<li>What is a good name? <tt class="docutils literal"><span class="pre">"output_from()"</span></tt>, <tt class="docutils literal"><span class="pre">"NOT_FILE_NAME"</span></tt> :-)</li>
-<li>They will still participate in suffix, formatter and regex replacement</li>
-</ol>
-<p>Bernie Pope suggests that we should generalise this:</p>
-<p>If any object in the input parameters is a (non-list/tuple) class instance, check (getattr) whether it has a <tt class="docutils literal"><span class="pre">ruffus_params()</span></tt> function.
-If it does, call it to obtain a list which is substituted in place.
-If there are string nested within, these will also take part in Ruffus string substitution.
-Objects with <tt class="docutils literal"><span class="pre">ruffus_params()</span></tt> always “decay” to the results of the function call</p>
-<p><tt class="docutils literal"><span class="pre">output_from</span></tt> would be a simple wrapper which returns the internal string via <tt class="docutils literal"><span class="pre">ruffus_params()</span></tt></p>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">class</span> <span class="nc">output_from</span> <span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">str</span> <span class="o">=</span> <span class="nb">str</span>
-    <span class="k">def</span> <span class="nf">ruffus_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">return</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">str</span><span class="p">]</span>
-</pre></div>
-</div>
-<p>Returning a list should be like wildcards and should not introduce an unnecessary level of indirection for output parameters, i.e. suffix(”.txt”) or formatter() / “{basename[0]}” should work.</p>
-<p>Check!</p>
-</div></blockquote>
-</div>
-<div class="section" id="todo-allow-extra-parameters-to-be-used-in-output-substitution">
-<span id="todo-extra-parameters"></span><h2>Todo: Allow “extra” parameters to be used in output substitution<a class="headerlink" href="#todo-allow-extra-parameters-to-be-used-in-output-substitution" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Formatter substitution can refer to the original elements in the input and extra parameters (without converting them to strings either). This refers to the original (nested) data structure.</p>
-<p>This will allow normal python datatypes to be handed down and slipstreamed into a pipeline more easily.</p>
-<p>The syntax would use Ruffus (> version 2.4) formatter:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span> <span class="o">...</span><span class="p">,</span> <span class="n">formatter</span><span class="p">(),</span> <span class="p">[</span>
-<span class="hll">                                <span class="s">"{EXTRAS[0][1][3]}"</span><span class="p">,</span>    <span class="c"># EXTRAS</span>
-</span><span class="hll">                                <span class="s">"[INPUTS[1][2]]"</span><span class="p">],</span><span class="o">...</span><span class="p">)</span>  <span class="c"># INPUTS</span>
-</span><span class="k">def</span> <span class="nf">taskfunc</span><span class="p">():</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p><tt class="docutils literal"><span class="pre">EXTRA</span></tt> and <tt class="docutils literal"><span class="pre">INPUTS</span></tt> indicate that we are referring to the input and extra parameters.</p>
-<p>These are the full (nested) parameters in all their original form. In the case of the input parameters, this obvious depends on the decorator, so</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="s">"a.text"</span><span class="p">,</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="s">"b.text"</span><span class="p">]],</span> <span class="n">formatter</span><span class="p">(),</span> <span class="s">"{INPUTS[0][0]}"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">taskfunc</span><span class="p">():</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>would give</p>
-<div class="highlight-python"><pre>job #1
-   input  == "a.text"
-   output == "a"
-
-job #2
-   input  == [1, "b.text"]
-   output == 1</pre>
-</div>
-<p>The entire string must consist of <tt class="docutils literal"><span class="pre">INPUTS</span></tt> or <tt class="docutils literal"><span class="pre">EXTRAS</span></tt> followed by optionally N levels of square brackets. i.e. They must match <tt class="docutils literal"><span class="pre">"(INPUTS|EXTRAS)(\[\d+\])+"</span></tt></p>
-<p>No string conversion takes place.</p>
-<p>For <tt class="docutils literal"><span class="pre">INPUTS</span></tt> or <tt class="docutils literal"><span class="pre">EXTRAS</span></tt> which have objects with a <tt class="docutils literal"><span class="pre">ruffus_params()</span></tt> function (see Todo item above),
-the original object rather than the result of <tt class="docutils literal"><span class="pre">ruffus_params()</span></tt> is forwarded.</p>
-</div></blockquote>
-</div>
-<div class="section" id="todo-extra-signalling-before-and-after-each-task-and-job">
-<span id="todo-pre-post-job"></span><h2>Todo: Extra signalling before and after each task and job<a class="headerlink" href="#todo-extra-signalling-before-and-after-each-task-and-job" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@prejob</span><span class="p">(</span><span class="n">custom_func</span><span class="p">)</span>
-<span class="nd">@postjob</span><span class="p">(</span><span class="n">custom_func</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task</span><span class="p">():</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p><tt class="docutils literal"><span class="pre">@prejob</span></tt> / <tt class="docutils literal"><span class="pre">@postjob</span></tt> would be run in the child processes.</p>
-</div></blockquote>
-</div>
-<div class="section" id="todo-split-subdivide-returns-the-actual-output-created">
-<span id="todo-new-decorators"></span><h2>Todo: <tt class="docutils literal"><span class="pre">@split</span></tt> / <tt class="docutils literal"><span class="pre">@subdivide</span></tt> returns the actual output created<a class="headerlink" href="#todo-split-subdivide-returns-the-actual-output-created" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul>
-<li><p class="first"><strong>overrides</strong> (not replaces) wild cards.</p>
-</li>
-<li><p class="first">Returns a list, each with output and extra paramters.</p>
-</li>
-<li><p class="first">Won’t include extraneous files which were not created in the pipeline but which just happened to match the wild card</p>
-</li>
-<li><p class="first">We should have <tt class="docutils literal"><span class="pre">ruffus_output_params</span></tt>, <tt class="docutils literal"><span class="pre">ruffus_extra_params</span></tt> wrappers for clarity:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="s">"a.file"</span><span class="p">,</span> <span class="s">"*.txt"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">split_into_txt_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="n">output_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"a.txt"</span><span class="p">,</span> <span class="s">"b.txt"</span><span class="p">,</span> <span class="s">"c.txt"</span><span class="p">]</span>
-    <span class="k">for</span> <span class="n">output_file_name</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span>
-            <span class="k">pass</span>
-    <span class="k">return</span> <span class="p">[</span>
-            <span class="n">ruffus_output</span><span class="p">(</span><span class="s">"a.file"</span><span class="p">),</span>
-            <span class="p">[</span><span class="n">ruffus_output</span><span class="p">([</span><span class="s">"b.file"</span><span class="p">,</span> <span class="s">"c.file"</span><span class="p">]),</span> <span class="n">ruffus_extras</span><span class="p">(</span><span class="mi">13</span><span class="p">,</span> <span class="mi">14</span><span class="p">)],</span>
-            <span class="p">]</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">Consider yielding?</p>
-</li>
-</ul>
-</div></blockquote>
-<div class="section" id="checkpointing">
-<h3>Checkpointing<a class="headerlink" href="#checkpointing" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li>If checkpoint file is used, the actual files are saved and checked the next time</li>
-<li>If no files are generated, no files are checked the next time...</li>
-<li>The output files do not have to match the wildcard though we can output a warning message if that happens...
-This is obviously dangerous because the behavior will change if the pipeline is rerun without using the checkpoint file</li>
-<li>What happens if the task function changes?</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="id1">
-<h2>Todo: New decorators<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="todo-originate">
-<h3>Todo: <tt class="docutils literal"><span class="pre">@originate</span></tt><a class="headerlink" href="#todo-originate" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div>Each (serial) invocation returns lists of output parameters until returns
-None. (Empty list = <tt class="docutils literal"><span class="pre">continue</span></tt>, None = <tt class="docutils literal"><span class="pre">break</span></tt>).</div></blockquote>
-</div>
-<div class="section" id="todo-recombine">
-<h3>Todo: <tt class="docutils literal"><span class="pre">@recombine</span></tt><a class="headerlink" href="#todo-recombine" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Like <tt class="docutils literal"><span class="pre">@collate</span></tt> but automatically regroups jobs which were a result of a previous <tt class="docutils literal"><span class="pre">@subdivide</span></tt> / <tt class="docutils literal"><span class="pre">@split</span></tt> (even after intervening <tt class="docutils literal"><span class="pre">@transform</span></tt> )</p>
-<p>This is the only way job trickling can work without stalling the pipeline: We would know
-how many jobs were pending for each <tt class="docutils literal"><span class="pre">@recombine</span></tt> job and which jobs go together.</p>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="todo-named-parameters-in-decorators-for-clarity">
-<h2>Todo: Named parameters in decorators for clarity<a class="headerlink" href="#todo-named-parameters-in-decorators-for-clarity" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="todo-bioinformatics-example-to-end-all-examples">
-<span id="todo-bioinformatics-example"></span><h2>Todo: Bioinformatics example to end all examples<a class="headerlink" href="#todo-bioinformatics-example-to-end-all-examples" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt>Uses</dt>
-<dd><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">@product</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">@subdivide</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">@transform</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">@collate</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">@merge</span></tt></li>
-</ul>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="todo-allow-the-next-task-to-start-before-all-jobs-in-the-previous-task-have-finished">
-<h2>Todo: Allow the next task to start before all jobs in the previous task have finished<a class="headerlink" href="#todo-allow-the-next-task-to-start-before-all-jobs-in-the-previous-task-have-finished" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Jake (Biesinger) calls this <strong>Job Trickling</strong>!</p>
-<ul class="simple">
-<li>A single long running job no longer will hold up the entire pipeline</li>
-<li>Calculates dependencies dynamically at the job level.</li>
-<li>Goal is to have a long running (months) pipeline to which we can keep adding input...</li>
-<li>We can choose between prioritising completion of the entire pipeline for some jobs
-(depth first) or trying to complete as many tasks as possible (breadth first)</li>
-</ul>
-</div></blockquote>
-<div class="section" id="converting-to-per-job-rather-than-per-task-dependencies">
-<h3>Converting to per-job rather than per task dependencies<a class="headerlink" href="#converting-to-per-job-rather-than-per-task-dependencies" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Some decorators prevent per job (rather than per task) dependency calculations, and
-will call a pipeline stall until the dependent tasks are completed (the current situation):</p>
-<blockquote>
-<div><ul>
-<li><dl class="first docutils">
-<dt>Some types of jobs unavoidably depend on an entire previous task completing:</dt>
-<dd><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">add_inputs()</span></tt>, <tt class="docutils literal"><span class="pre">inputs()</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">@merge</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">@split</span></tt> (implicit <tt class="docutils literal"><span class="pre">@merge</span></tt>)</li>
-</ul>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><tt class="docutils literal"><span class="pre">@split</span></tt>, <tt class="docutils literal"><span class="pre">@originate</span></tt> produce variable amount of output at runtime and must be completed before the next task can be run.</dt>
-<dd><ul class="first last simple">
-<li>Should <tt class="docutils literal"><span class="pre">yield</span></tt> instead of return?</li>
-</ul>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt><tt class="docutils literal"><span class="pre">@collate</span></tt> needs to pattern match all the inputs of a previous task</dt>
-<dd><ul class="first last simple">
-<li>Replace <tt class="docutils literal"><span class="pre">@collate</span></tt> with <tt class="docutils literal"><span class="pre">@recombine</span></tt> which “remembers” and reverses the results of a previous
-<tt class="docutils literal"><span class="pre">@subdivide</span></tt> or <tt class="docutils literal"><span class="pre">@split</span></tt></li>
-<li>Jobs need unique job_id tag</li>
-<li>Jobs are assigned (nested) grouping id which accompany them down the
-pipeline after <tt class="docutils literal"><span class="pre">@subdivide</span></tt> / <tt class="docutils literal"><span class="pre">@split</span></tt> and are removed after <tt class="docutils literal"><span class="pre">@recombine</span></tt></li>
-<li>Should have a count of jobs so we always know <em>when</em> an “input slot” is full</li>
-</ul>
-</dd>
-</dl>
-</li>
-<li><p class="first">Funny “single file” mode for <tt class="docutils literal"><span class="pre">@transform,</span></tt> <tt class="docutils literal"><span class="pre">@files</span></tt> needs to be
-regularised so it is a syntactic (front end) convenience (oddity!)
-and not plague the inards of ruffus</p>
-</li>
-</ul>
-</div></blockquote>
-<p>Breaking change: to force the entirety of the previous task to complete before the next one, use <tt class="docutils literal"><span class="pre">@follows</span></tt></p>
-</div></blockquote>
-</div>
-<div class="section" id="implementation">
-<h3>Implementation<a class="headerlink" href="#implementation" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li>“Push” model. Completing jobs “check in” their outputs to “input slots” for all the sucessor jobs.</li>
-<li>When “input slots” are full for any job, it is put on the dispatch queue to be run.</li>
-<li>The priority (depth first or breadth first) can be set here.</li>
-<li><tt class="docutils literal"><span class="pre">pipeline_run</span></tt> / <tt class="docutils literal"><span class="pre">Pipeline_printout</span></tt> create a task dependency tree structure (from decorator dependencies) (a runtime pipeline object)</li>
-<li>Each task in the pipeline object knows which other tasks wait on it.</li>
-<li>When output is created by a job, it sends messages to (i.e. function calls) all dependent tasks in the pipeline object with the new output</li>
-<li>Sets of output such as from <tt class="docutils literal"><span class="pre">@split</span></tt> and <tt class="docutils literal"><span class="pre">@subdivide</span></tt> and <tt class="docutils literal"><span class="pre">@originate</span></tt> have a
-terminating condition and/or a associated count (# of output)</li>
-<li>Tasks in the pipeline object forward incoming inputs to task input slots (for slots common to all jobs in a
-task: <tt class="docutils literal"><span class="pre">@inputs</span></tt>, <tt class="docutils literal"><span class="pre">@add_inputs</span></tt>) or to slots in new jobs in the pipeline object</li>
-<li>When all slots are full in each job, this triggers putting the job parameters onto the job submission queue</li>
-<li>The pipeline object should allow Ruffus to be reentrant?</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-</div>
-<div class="section" id="planned-improvements-to-ruffus">
-<h1>Planned Improvements to Ruffus<a class="headerlink" href="#planned-improvements-to-ruffus" title="Permalink to this headline">¶</a></h1>
-<blockquote id="todo-run-on-cluster">
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">@split</span></tt> needs to be able to specify at run time the number of
-resulting jobs without using wild cards</li>
-<li>legacy support for wild cards and file names.</li>
-</ul>
-</div></blockquote>
-<div class="section" id="planned-running-python-code-task-functions-transparently-on-remote-cluster-nodes">
-<h2>Planned: Running python code (task functions) transparently on remote cluster nodes<a class="headerlink" href="#planned-running-python-code-task-functions-transparently-on-remote-cluster-nodes" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Wait until next release.</p>
-<p>Will bump Ruffus to v.3.0 if can run python jobs transparently on a cluster!</p>
-<p>abstract out <tt class="docutils literal"><span class="pre">task.run_pooled_job_without_exceptions()</span></tt> as a function which can be supplied to <tt class="docutils literal"><span class="pre">pipeline_run</span></tt></p>
-<p>Common “job” interface:</p>
-<blockquote>
-<div><ul class="simple">
-<li>marshalled arguments</li>
-<li>marshalled function</li>
-<li>submission timestamp</li>
-</ul>
-</div></blockquote>
-<dl class="docutils">
-<dt>Returns</dt>
-<dd><ul class="first last simple">
-<li>completion timestamp</li>
-<li>returned values</li>
-<li>exception</li>
-</ul>
-</dd>
-</dl>
-<ol class="arabic simple">
-<li>Full version use libpythongrid?
-* Christian Widmer <<a class="reference external" href="mailto:ckwidmer%40gmail.com">ckwidmer<span>@</span>gmail<span>.</span>com</a>>
-* Cheng Soon Ong <<a class="reference external" href="mailto:chengsoon.ong%40unimelb.edu.au">chengsoon<span>.</span>ong<span>@</span>unimelb<span>.</span>edu<span>.</span>au</a>>
-* <a class="reference external" href="https://code.google.com/p/pythongrid/source/browse/#git%2Fpythongrid">https://code.google.com/p/pythongrid/source/browse/#git%2Fpythongrid</a>
-* Probably not good to base Ruffus entirely on libpythongrid to minimise dependencies, the use of sophisticated configuration policies etc.</li>
-<li>Start with light-weight file-based protocol
-* specify where the scripts should live
-* use drmaa to start jobs
-* have executable ruffus module which knows how to load deserialise (unmarshall) function / parameters from disk. This would be what drmaa starts up, given the marshalled data as an argument
-* time stamp
-* “heart beat” to check that the job is still running</li>
-<li>Next step: socket-based protocol
-* use specified master port in ruffus script
-* start remote processes using drmaa
-* child receives marshalled data and the address::port in the ruffus script (head node) to initiate hand shake or die
-* process recycling: run successive jobs on the same remote process for reduced overhead, until exceeds max number of jobs on the same process, min/max time on the same process
-* resubmit if die (Don’t do sophisticated stuff like libpythongrid).</li>
-</ol>
-</div></blockquote>
-</div>
-<div class="section" id="planned-custom-parameter-generator">
-<span id="todo-custom-parameters"></span><span id="todo-job-trickling"></span><h2>Planned: Custom parameter generator<a class="headerlink" href="#planned-custom-parameter-generator" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Request on mailing list</p>
-<blockquote>
-<div><blockquote>
-<div>I’ve often wished that I could use an arbitrary function to process the input filepath instead of just a regex.</div></blockquote>
-<div class="highlight-python"><div class="highlight"><pre><span class="k">def</span> <span class="nf">f</span><span class="p">(</span><span class="n">inputs</span><span class="p">,</span> <span class="n">outputs</span><span class="p">,</span> <span class="n">extra_param1</span><span class="p">,</span> <span class="n">extra_param2</span><span class="p">):</span>
-     <span class="c"># do something to generate parameters</span>
-     <span class="k">return</span> <span class="n">new_output_param</span><span class="p">,</span> <span class="n">new_extra_param1</span><span class="p">,</span> <span class="n">new_extra_param2</span>
-</pre></div>
-</div>
-<p>now f() can be used inside a Ruffus decorator to generate the outputs from inputs, instead of being forced to use a regex for the job.</p>
-<p>Cheers,
-Bernie.</p>
-</div></blockquote>
-<p>Leverages built-in Ruffus functionality.
-Don’t have to write entire parameter generation from scratch.</p>
-<ul class="simple">
-<li>Gets passed an iterator where you can do a for loop to get input parameters / a flattened list of files</li>
-<li>Other parameters are forwarded as is</li>
-<li>The duty of the function is to <tt class="docutils literal"><span class="pre">yield</span></tt> input, output, extra parameters</li>
-</ul>
-<p>Simple to do but how do we prevent this from being a job-trickling barrier?</p>
-<p>Postpone until we have an initial design for job-trickling: Ruffus v.4 ;-(</p>
-</div></blockquote>
-</div>
-<div class="section" id="planned-ruffus-gui-interface">
-<span id="todo-gui"></span><h2>Planned: Ruffus GUI interface.<a class="headerlink" href="#planned-ruffus-gui-interface" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>Desktop (PyQT or web-based solution?)  I’d love to see an svg pipeline picture that I could actually interact with</div></blockquote>
-</div>
-<div class="section" id="planned-non-decorator-function-interface-to-ruffus">
-<h2>Planned: Non-decorator / Function interface to Ruffus<a class="headerlink" href="#planned-non-decorator-function-interface-to-ruffus" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="planned-remove-intermediate-files">
-<span id="todo-intermediate-files"></span><h2>Planned: Remove intermediate files<a class="headerlink" href="#planned-remove-intermediate-files" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Often large intermediate files are produced in the middle of a pipeline which could be
-removed. However, their absence would cause the pipeline to appear out of date. What is
-the best way to solve this?</p>
-<p>In gmake, all intermediate files which are not marked <tt class="docutils literal"><span class="pre">.PRECIOUS</span></tt> are deleted.</p>
-<dl class="docutils">
-<dt>We do not want to manually mark intermediate files for several reasons:</dt>
-<dd><ul class="first last simple">
-<li>The syntax would be horrible and clunky</li>
-<li>The gmake distinction between <tt class="docutils literal"><span class="pre">implicit</span></tt> and <tt class="docutils literal"><span class="pre">explicit</span></tt> rules is not one we
-would like to impose on Ruffus</li>
-<li>Gmake uses statically determined (DAG) dependency trees so it is quite natural and
-easy to prune intermediate paths</li>
-</ul>
-</dd>
-</dl>
-<p>Our preferred solution should impose little to no semantic load on Ruffus, i.e. it should
-not make it more complex / difficult to use. There are several alternatives we are
-considering:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Have an <strong>update</strong> mode in which pipeline_run would ignore missing files and only run tasks with existing, out-of-date files.</li>
-<li>Optionally ignore all out-of-date dependencies beyond a specified point in the pipeline</li>
-<li>Add a decorator to flag sections of the pipeline where intermediate files can be removed</li>
-</ol>
-</div></blockquote>
-<p>Option (1) is rather unnerving because it makes inadvertent errors difficult to detect.</p>
-<p>Option (2) involves relying on the user of a script to remember the corect chain of dependencies in
-often complicated pipelines. It would be advised to keep a flowchart to hand. Again,
-the chances of error are much greater.</p>
-<p>Option (3) springs from the observation by Andreas Heger that parts of a pipeline with
-disposable intermediate files can usually be encapsulated as an autonomous section.
-Within this subpipeline, all is well provided that the outputs of the last task are complete
-and up-to-date with reference to the inputs of the first task. Intermediate files
-could be removed with impunity.</p>
-<p>The suggestion is that these autonomous subpipelines could be marked out using the Ruffus
-decorator syntax:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   First task in autonomous subpipeline</span>
-<span class="c">#</span>
-<span class="nd">@files</span><span class="p">(</span><span class="s">"who.isit"</span><span class="p">,</span> <span class="s">"its.me"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="c">#</span>
-<span class="c">#   Several intermediate tasks</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">subpipeline_task1</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".me"</span><span class="p">),</span> <span class="s">".her"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2_etc</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
-   <span class="k">pass</span>
-
-<span class="c">#</span>
-<span class="c">#   Final task</span>
-<span class="c">#</span>
-<span class="nd">@sub_pipeline</span><span class="p">(</span><span class="n">subpipeline_task1</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">subpipeline_task1</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".her"</span><span class="p">),</span> <span class="s">".you"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">final_task</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">):</span>
-   <span class="k">pass</span>
-</pre></div>
-</div>
-<p><strong>@sub_pipeline</strong> marks out all tasks between <tt class="docutils literal"><span class="pre">first_task</span></tt> and <tt class="docutils literal"><span class="pre">final_task</span></tt> and
-intermediate files such as <tt class="docutils literal"><span class="pre">"its.me"</span></tt>, <tt class="docutils literal"><span class="pre">"its.her</span></tt> can be deleted. The pipeline will
-only run if <tt class="docutils literal"><span class="pre">"its.you"</span></tt> is missing or out-of-date compared with <tt class="docutils literal"><span class="pre">"who.isit"</span></tt>.</p>
-<p>Over the next few Ruffus releases we will see if this is a good design, and whether
-better keyword can be found than <strong>@sub_pipeline</strong> (candidates include <strong>@shortcut</strong>
-and <strong>@intermediate</strong>)</p>
-</div></blockquote>
-</div>
-<div class="section" id="planned-retry-on-error-num-of-retries">
-<span id="todo-retry"></span><h2>Planned: @retry_on_error(NUM_OF_RETRIES)<a class="headerlink" href="#planned-retry-on-error-num-of-retries" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="planned-clean-up">
-<span id="todo-cleanup"></span><h2>Planned: Clean up<a class="headerlink" href="#planned-clean-up" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The plan is to store the files and directories created via
-a standard interface.</p>
-<p>The placeholders for this are a function call <tt class="docutils literal"><span class="pre">register_cleanup</span></tt>.</p>
-<p>Jobs can specify the files they created and which need to be
-deleted by returning a list of file names from the job function.</p>
-<p>So:</p>
-<div class="highlight-python"><pre>raise Exception = Error
-
-return False = halt pipeline now
-
-return string / list of strings = cleanup files/directories later
-
-return anything else = ignored</pre>
-</div>
-<p>The cleanup file/directory store interface can be connected to
-a text file or a database.</p>
-<p>The cleanup function would look like this:</p>
-<div class="highlight-python"><pre>pipeline_cleanup(cleanup_log("../cleanup.log"), [instance ="october19th" ])
-pipeline_cleanup(cleanup_msql_db("user", "password", "hash_record_table"))</pre>
-</div>
-<p>The parameters for where and how to store the list of created files could be
-similarly passed to pipeline_run as an extra parameter:</p>
-<div class="highlight-python"><pre>pipeline_run(cleanup_log("../cleanup.log"), [instance ="october19th" ])
-pipeline_run(cleanup_msql_db("user", "password", "hash_record_table"))</pre>
-</div>
-<p>where <cite>cleanup_log</cite> and <cite>cleanup_msql_db</cite> are classes which have functions for</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>storing file</li>
-<li>retrieving file</li>
-<li>clearing entries</li>
-</ol>
-</div></blockquote>
-<ul>
-<li><p class="first">Files would be deleted in reverse order, and directories after files.</p>
-</li>
-<li><p class="first">By default, only empty directories would be removed.</p>
-<p>But this could be changed with a <tt class="docutils literal"><span class="pre">--forced_remove_dir</span></tt> option</p>
-</li>
-<li><p class="first">An <tt class="docutils literal"><span class="pre">--remove_empty_parent_directories</span></tt> option would be
-supported by <a class="reference external" href="http://docs.python.org/library/os.html#os.removedirs">os.removedirs(path)</a>.</p>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Future Changes to Ruffus</a><ul>
-<li><a class="reference internal" href="#todo-pipeline-printout-graph-should-print-inactive-tasks">Todo: pipeline_printout_graph should print inactive tasks</a></li>
-<li><a class="reference internal" href="#todo-mark-input-strings-as-non-file-names-and-add-support-for-dynamically-returned-parameters">Todo: Mark input strings as non-file names, and add support for dynamically returned parameters</a></li>
-<li><a class="reference internal" href="#todo-allow-extra-parameters-to-be-used-in-output-substitution">Todo: Allow “extra” parameters to be used in output substitution</a></li>
-<li><a class="reference internal" href="#todo-extra-signalling-before-and-after-each-task-and-job">Todo: Extra signalling before and after each task and job</a></li>
-<li><a class="reference internal" href="#todo-split-subdivide-returns-the-actual-output-created">Todo: <tt class="docutils literal"><span class="pre">@split</span></tt> / <tt class="docutils literal"><span class="pre">@subdivide</span></tt> returns the actual output created</a><ul>
-<li><a class="reference internal" href="#checkpointing">Checkpointing</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#id1">Todo: New decorators</a><ul>
-<li><a class="reference internal" href="#todo-originate">Todo: <tt class="docutils literal"><span class="pre">@originate</span></tt></a></li>
-<li><a class="reference internal" href="#todo-recombine">Todo: <tt class="docutils literal"><span class="pre">@recombine</span></tt></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#todo-named-parameters-in-decorators-for-clarity">Todo: Named parameters in decorators for clarity</a></li>
-<li><a class="reference internal" href="#todo-bioinformatics-example-to-end-all-examples">Todo: Bioinformatics example to end all examples</a></li>
-<li><a class="reference internal" href="#todo-allow-the-next-task-to-start-before-all-jobs-in-the-previous-task-have-finished">Todo: Allow the next task to start before all jobs in the previous task have finished</a><ul>
-<li><a class="reference internal" href="#converting-to-per-job-rather-than-per-task-dependencies">Converting to per-job rather than per task dependencies</a></li>
-<li><a class="reference internal" href="#implementation">Implementation</a></li>
-</ul>
-</li>
-</ul>
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-<li><a class="reference internal" href="#planned-running-python-code-task-functions-transparently-on-remote-cluster-nodes">Planned: Running python code (task functions) transparently on remote cluster nodes</a></li>
-<li><a class="reference internal" href="#planned-custom-parameter-generator">Planned: Custom parameter generator</a></li>
-<li><a class="reference internal" href="#planned-ruffus-gui-interface">Planned: Ruffus GUI interface.</a></li>
-<li><a class="reference internal" href="#planned-non-decorator-function-interface-to-ruffus">Planned: Non-decorator / Function interface to Ruffus</a></li>
-<li><a class="reference internal" href="#planned-remove-intermediate-files">Planned: Remove intermediate files</a></li>
-<li><a class="reference internal" href="#planned-retry-on-error-num-of-retries">Planned: @retry_on_error(NUM_OF_RETRIES)</a></li>
-<li><a class="reference internal" href="#planned-clean-up">Planned: Clean up</a></li>
-</ul>
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-  <div class="section" id="manual-transform-ex-chapter-num-add-inputs-and-inputs-controlling-both-input-and-output-files-with-transform">
-<span id="manual-advanced-transform"></span><h1><strong>Chapter 15</strong>: <strong>add_inputs()</strong> <cite>and</cite> <strong>inputs()</strong>: <cite>Controlling both input and output files with</cite> <strong>@transform</strong><a class="headerlink" href="#manual-transform-ex-chapter-num-add-inputs-and-inputs-controlling-both-input-and-output-files-with-transform" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> syntax in detail</li>
-</ul>
-</td></tr></table>
-<p id="index-0">The standard <a class="reference internal" href="transform.html#manual-transform"><em>@transform</em></a> allows you to send a list of data files
-to the same pipelined function and for the resulting <em>outputs</em> parameter to be automatically
-inferred from file names in the <em>inputs</em>.</p>
-<dl class="docutils">
-<dt>There are two situations where you might desire additional flexibility:</dt>
-<dd><ol class="first last arabic simple">
-<li>You need to add additional prequisites or filenames to the <em>inputs</em> of every single one
-of your jobs</li>
-<li>(Less often,) the actual <em>inputs</em> file names are some variant of the <em>outputs</em> of another
-task.</li>
-</ol>
-</dd>
-</dl>
-<p>Either way, it is occasionally very useful to be able to generate the actual <em>inputs</em> as
-well as <em>outputs</em> parameters by regular expression substitution. The following examples will show
-you both how and why you would want to do this.</p>
-</div></blockquote>
-<div class="section" id="adding-additional-input-prerequisites-per-job">
-<h2>Adding additional <em>input</em> prerequisites per job<a class="headerlink" href="#adding-additional-input-prerequisites-per-job" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="example-compiling-c-code">
-<h3>1.) Example: compiling c++ code<a class="headerlink" href="#example-compiling-c-code" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><dl class="docutils">
-<dt>Suppose we wished to compile some c++ (<tt class="docutils literal"><span class="pre">"*.cpp"</span></tt>) files:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">source_files</span> <span class="o">=</span> <span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="s">"messy.cpp"</span>
-<span class="k">for</span> <span class="n">source_file</span> <span class="ow">in</span> <span class="n">source_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<dl class="docutils">
-<dt>The ruffus code would look like this:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<dl class="docutils">
-<dt>This results in the following jobs:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="nb">compile</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="go">    Job = [None -> hasty.cpp] completed</span>
-<span class="go">    Job = [None -> tasty.cpp] completed</span>
-<span class="go">    Job = [None -> messy.cpp] completed</span>
-<span class="go">Completed Task = prepare_cpp_source</span>
-
-<span class="go">    Job = [hasty.cpp -> hasty.o] completed</span>
-<span class="go">    Job = [messy.cpp -> messy.o] completed</span>
-<span class="go">    Job = [tasty.cpp -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="example-adding-a-header-file-with-add-inputs">
-<h3>2.) Example: Adding a header file with <strong>add_inputs(..)</strong><a class="headerlink" href="#example-adding-a-header-file-with-add-inputs" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>All this is plain vanilla <strong>@transform</strong> syntax. But suppose that we need to add a
-common header file <tt class="docutils literal"><span class="pre">"universal.h"</span></tt> to our compilation.
-The <strong>add_inputs</strong> provides for this with the minimum of fuss:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># create header file</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c"># compile C++ files with extra header</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">prepare_cpp_source</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="n">add_inputs</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Now the input file is a python list, with <tt class="docutils literal"><span class="pre">"universal.h"</span></tt> added to each <tt class="docutils literal"><span class="pre">"*.cpp"</span></tt></p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="nb">compile</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="go">    Job = [ [hasty.cpp, universal.h] -> hasty.o] completed</span>
-<span class="go">    Job = [ [messy.cpp, universal.h] -> messy.o] completed</span>
-<span class="go">    Job = [ [tasty.cpp, universal.h] -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="additional-input-prerequisites-can-be-globs-tasks-or-pattern-matches">
-<h2>Additional <em>input</em> prerequisites can be globs, tasks or pattern matches<a class="headerlink" href="#additional-input-prerequisites-can-be-globs-tasks-or-pattern-matches" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>A common requirement is to include the corresponding header file in compilations.
-It is easy to use <strong>add_inputs</strong> to look up additional files via pattern matches.</div></blockquote>
-<div class="section" id="example-adding-matching-header-file">
-<h3>3.) Example: Adding matching header file<a class="headerlink" href="#example-adding-matching-header-file" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><dl class="docutils">
-<dt>To make this example more fun, we shall also:</dt>
-<dd><ol class="first last arabic simple">
-<li>Give each source code file its own ordinal</li>
-<li>Use <tt class="docutils literal"><span class="pre">add_inputs</span></tt> to add files produced by another task function</li>
-</ol>
-</dd>
-</dl>
-<div class="highlight-python"><div class="highlight"><pre><span class="c"># each source file has its own index</span>
-<span class="n">source_names</span> <span class="o">=</span> <span class="p">[(</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span>
-                <span class="p">(</span><span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span>
-                <span class="p">(</span><span class="s">"messy.cpp"</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="p">]</span>
-<span class="n">header_names</span> <span class="o">=</span> <span class="p">[</span><span class="n">sn</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">,</span> <span class="s">".h"</span><span class="p">)</span> <span class="k">for</span> <span class="p">(</span><span class="n">sn</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> <span class="ow">in</span> < [...]
-<span class="n">header_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   create header and source files</span>
-<span class="c">#</span>
-<span class="k">for</span> <span class="n">source</span><span class="p">,</span> <span class="n">source_index</span> <span class="ow">in</span> <span class="n">source_names</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="k">for</span> <span class="n">header</span> <span class="ow">in</span> <span class="n">header_names</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">header</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#</span>
-<span class="c">#   lookup embedded strings in each source files</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_names</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="s">".embedded"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">get_embedded_strings</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-
-<span class="c"># compile C++ files with extra header</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_names</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span>
-           <span class="n">add_inputs</span><span class="p">(</span>  <span class="s">"universal.h"</span><span class="p">,</span>
-                        <span class="s">r"\1.h"</span><span class="p">,</span>
-                        <span class="n">get_embedded_strings</span>     <span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_params</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="nb">compile</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This script gives the following output</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="nb">compile</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="go">    Job = [[hasty.cpp,  1] -> hasty.embedded] completed</span>
-<span class="go">    Job = [[messy.cpp,  3] -> messy.embedded] completed</span>
-<span class="go">    Job = [[tasty.cpp,  2] -> tasty.embedded] completed</span>
-<span class="go">Completed Task = get_embedded_strings</span>
-
-<span class="go">    Job = [[[hasty.cpp,  1],                                            # inputs</span>
-<span class="go">            universal.h,                                                # common header</span>
-<span class="go">            hasty.h,                                                    # corresponding header</span>
-<span class="go">            hasty.embedded, messy.embedded, tasty.embedded]             # output of get_embedded_strings()</span>
-<span class="go">           -> hasty.o] completed</span>
-<span class="go">    Job = [[[messy.cpp, 3],                                             # inputs</span>
-<span class="go">            universal.h,                                                # common header</span>
-<span class="go">            messy.h,                                                    # corresponding header</span>
-<span class="go">            hasty.embedded, messy.embedded, tasty.embedded]             # output of get_embedded_strings()</span>
-<span class="go">           -> messy.o] completed</span>
-<span class="go">    Job = [[[tasty.cpp, 2],                                             # inputs</span>
-<span class="go">            universal.h,                                                # common header</span>
-<span class="go">            tasty.h,                                                    # corresponding header</span>
-<span class="go">            hasty.embedded, messy.embedded, tasty.embedded]             # output of get_embedded_strings()</span>
-<span class="go">           -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>We can see that the <tt class="docutils literal"><span class="pre">compile(...)</span></tt> task now has four sets of <em>inputs</em>:</dt>
-<dd><ol class="first last arabic simple">
-<li>The original inputs (e.g. <tt class="docutils literal"><span class="pre">[hasty.cpp,</span>  <span class="pre">1]</span></tt>)</li>
-</ol>
-</dd>
-<dt>And three additional added by <strong>add_inputs(...)</strong></dt>
-<dd><ol class="first last arabic simple" start="2">
-<li>A header file (<tt class="docutils literal"><span class="pre">universal.h</span></tt>) common to all jobs</li>
-<li>The matching header (e.g. <tt class="docutils literal"><span class="pre">hasty.h</span></tt>)</li>
-<li>The output from another task <tt class="docutils literal"><span class="pre">get_embedded_strings()</span></tt> (e.g. <tt class="docutils literal"><span class="pre">hasty.embedded,</span> <span class="pre">messy.embedded,</span> <span class="pre">tasty.embedded</span></tt>)</li>
-</ol>
-</dd>
-</dl>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>For input parameters with nested structures (lists or sets), the pattern matching is
-on the first filename string Ruffus comes across (DFS).</p>
-<p>So for <tt class="docutils literal"><span class="pre">["hasty.c",</span> <span class="pre">0]</span></tt>, the pattern matches <tt class="docutils literal"><span class="pre">"hasty.c"</span></tt>.</p>
-<p class="last">If in doubt, use <a class="reference internal" href="tracing_pipeline_parameters.html#manual-tracing-pipeline-parameters"><em>pipeline_printout</em></a> to
-check what parameters Ruffus is using.</p>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-using-regex-instead-of-suffix">
-<h3>4.) Example: Using <strong>regex(..)</strong> instead of <strong>suffix(..)</strong><a class="headerlink" href="#example-using-regex-instead-of-suffix" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Suffix pattern matching is much simpler and hence is usually preferable to the more
-powerful regular expressions. We can rewrite the above example to use <strong>regex</strong> as well
-to give exactly the same output.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c"># compile C++ files with extra header</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_names</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"(.+)\.cpp"</span><span class="p">),</span>
-           <span class="n">add_inputs</span><span class="p">(</span>  <span class="s">"universal.h"</span><span class="p">,</span>
-                        <span class="s">r"\1.h"</span><span class="p">,</span>
-                        <span class="n">get_embedded_strings</span>     <span class="p">),</span> <span class="s">r"\1.o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_params</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The backreference <tt class="docutils literal"><span class="pre">\g<0></span></tt> usefully substitutes the entire substring matched by
-the regular expression.</p>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="replacing-all-input-parameters-with-inputs">
-<h2>Replacing all input parameters with <strong>inputs(...)</strong><a class="headerlink" href="#replacing-all-input-parameters-with-inputs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>More rarely, it is necessary to replace all the input parameters wholescale.</div></blockquote>
-<div class="section" id="example-running-matching-python-scripts">
-<h3>4.) Example: Running matching python scripts<a class="headerlink" href="#example-running-matching-python-scripts" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>In the following example, we are not compiling C++ source files but invoking
-corresponding python scripts which have the same name.</p>
-<p>Given three c++ files and their corresponding python scripts:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># each source file has its own index</span>
-<span class="n">source_names</span> <span class="o">=</span> <span class="p">[(</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span>
-                <span class="p">(</span><span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span>
-                <span class="p">(</span><span class="s">"messy.cpp"</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="p">]</span>
-
-<span class="c">#</span>
-<span class="c">#   create c++ source files and corresponding python files</span>
-<span class="c">#</span>
-<span class="k">for</span> <span class="n">source</span><span class="p">,</span> <span class="n">source_index</span> <span class="ow">in</span> <span class="n">source_names</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">,</span> <span class="s">".py"</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The Ruffus code will call each python script corresponding to their c++ counterpart:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-
-<span class="c"># run corresponding python files</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_names</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="n">inputs</span><span class="p">(</span>  <span class="s">r"\1.py"</span><span class="p">),</span> <span class="s">".results"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">run_python_file</span><span class="p">(</span><span class="n">input_params</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">run_python_file</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>Resulting in this output:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">run_python_file</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-<span class="go">    Job = [hasty.py -> hasty.results] completed</span>
-<span class="go">    Job = [messy.py -> messy.results] completed</span>
-<span class="go">    Job = [tasty.py -> tasty.results] completed</span>
-<span class="go">Completed Task = run_python_file</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="id1">
-<h3>5.) Example: Using <strong>regex</strong> instead of <strong>suffix</strong><a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Again, the same code can be written (less clearly) using the more powerful
-<strong>regex</strong> and python regular expressions:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>from ruffus import *
-
-
-# run corresponding python files
- at transform(source_names, regex(r"(.+)\.cpp"), inputs(  r"\1.py"), r\"1.results")
-def run_python_file(input_params, output_file_name):
-    open(output_file_name, "w")
-
-
-pipeline_run([run_python_file], verbose = 2, multiprocess = 3)</pre>
-</div>
-</div></blockquote>
-<p>This is about as sophisticated as <strong>@transform</strong> ever gets!</p>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 15</strong>: <strong>add_inputs()</strong> <cite>and</cite> <strong>inputs()</strong>: <cite>Controlling both input and output files with</cite> <strong>@transform</strong></a><ul>
-<li><a class="reference internal" href="#adding-additional-input-prerequisites-per-job">Adding additional <em>input</em> prerequisites per job</a><ul>
-<li><a class="reference internal" href="#example-compiling-c-code">1.) Example: compiling c++ code</a></li>
-<li><a class="reference internal" href="#example-adding-a-header-file-with-add-inputs">2.) Example: Adding a header file with <strong>add_inputs(..)</strong></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#additional-input-prerequisites-can-be-globs-tasks-or-pattern-matches">Additional <em>input</em> prerequisites can be globs, tasks or pattern matches</a><ul>
-<li><a class="reference internal" href="#example-adding-matching-header-file">3.) Example: Adding matching header file</a></li>
-<li><a class="reference internal" href="#example-using-regex-instead-of-suffix">4.) Example: Using <strong>regex(..)</strong> instead of <strong>suffix(..)</strong></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#replacing-all-input-parameters-with-inputs">Replacing all input parameters with <strong>inputs(...)</strong></a><ul>
-<li><a class="reference internal" href="#example-running-matching-python-scripts">4.) Example: Running matching python scripts</a></li>
-<li><a class="reference internal" href="#id1">5.) Example: Using <strong>regex</strong> instead of <strong>suffix</strong></a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="collate.html"
-                        title="previous chapter"><strong>Chapter 14</strong>: <strong>@collate</strong>: <cite>group together disparate input into sets of results</cite></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="parallel.html"
-                        title="next chapter"><strong>Chapter 16</strong>: <cite>Esoteric: Running jobs in parallel without using files with</cite> <strong>@parallel</strong></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/manual/advanced_transform.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" />
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-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../../genindex.html" title="General Index"
-             >index</a></li>
-        <li class="right" >
-          <a href="parallel.html" title="Chapter 16: Esoteric: Running jobs in parallel without using files with @parallel"
-             >next</a> |</li>
-        <li class="right" >
-          <a href="collate.html" title="Chapter 14: @collate: group together disparate input into sets of results"
-             >previous</a> |</li>
-        Ruffus v. 2.5
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-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
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\ No newline at end of file
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+++ /dev/null
@@ -1,269 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
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-  <div class="section" id="manual-check-if-uptodate-chapter-num-writing-custom-functions-to-decide-which-jobs-are-up-to-date">
-<span id="manual-check-if-uptodate"></span><h1><strong>Chapter 17</strong>: <cite>Writing custom functions to decide which jobs are up to date</cite><a class="headerlink" href="#manual-check-if-uptodate-chapter-num-writing-custom-functions-to-decide-which-jobs-are-up-to-date" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate  syntax in detail</em></a></li>
-</ul>
-</td></tr></table>
-</div></blockquote>
-<div class="section" id="check-if-uptodate-manual-dependency-checking">
-<span id="index-0"></span><h2><strong>@check_if_uptodate</strong> : Manual dependency checking<a class="headerlink" href="#check-if-uptodate-manual-dependency-checking" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt>tasks specified with</dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="files.html#manual-files"><em>@files</em></a></li>
-<li><a class="reference internal" href="split.html#manual-split"><em>@split</em></a></li>
-<li><a class="reference internal" href="transform.html#manual-transform"><em>@transform</em></a></li>
-<li><a class="reference internal" href="merge.html#manual-merge"><em>@merge</em></a></li>
-<li><a class="reference internal" href="collate.html#manual-collate"><em>@collate</em></a></li>
-</ul>
-</dd>
-</dl>
-<p>have automatic dependency checking based on file modification times.</p>
-<p>Sometimes, you might want to decide have more control over whether to run jobs, especially
-if a task does not rely on or produce files (i.e. with <a class="reference internal" href="parallel.html#manual-parallel"><em>@parallel</em></a>)</p>
-<p>You can write your own custom function to decide whether to run a job.
-This takes as many parameters as your task function, and needs to return a
-tuple for whether an update is required, and why (i.e. <tt class="docutils literal"><span class="pre">tuple(bool,</span> <span class="pre">str)</span></tt>)</p>
-<p>This simple example which creates the file <tt class="docutils literal"><span class="pre">"a.1"</span></tt> if it does not exist:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>could be rewritten more laboriously as:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">os</span>
-<span class="k">def</span> <span class="nf">check_file_exists</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">False</span><span class="p">,</span> <span class="s">"File already exists"</span>
-    <span class="k">return</span> <span class="bp">True</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> is missing"</span> <span class="o">%</span> <span class="n">output_file</span>
-
-<span class="nd">@parallel</span><span class="p">([[</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">]])</span>
-<span class="nd">@check_if_uptodate</span><span class="p">(</span><span class="n">check_file_exists</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>Both produce the same output:</dt>
-<dd><div class="first last highlight-python"><pre>Task = create_if_necessary
-    Job = [null, "a.1"] completed</pre>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>The function specified by <a class="reference internal" href="#manual-check-if-uptodate"><em>@check_if_uptodate</em></a> can be called
-more than once for each job.</p>
-<p class="last">See the <a class="reference internal" href="dependencies.html#manual-dependencies"><em>description here</em></a> of how <strong>Ruffus</strong> decides which tasks to run.</p>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
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-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 17</strong>: <cite>Writing custom functions to decide which jobs are up to date</cite></a><ul>
-<li><a class="reference internal" href="#check-if-uptodate-manual-dependency-checking"><strong>@check_if_uptodate</strong> : Manual dependency checking</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="parallel.html"
-                        title="previous chapter"><strong>Chapter 16</strong>: <cite>Esoteric: Running jobs in parallel without using files with</cite> <strong>@parallel</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="exceptions.html"
-                        title="next chapter"><strong>Chapter 18</strong>: <cite>Exceptions thrown inside a pipeline</cite></a></p>
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-            
-  <div class="section" id="manual-collate-chapter-num-collate-group-together-disparate-input-into-sets-of-results">
-<span id="manual-collate"></span><h1><strong>Chapter 14</strong>: <strong>@collate</strong>: <cite>group together disparate input into sets of results</cite><a class="headerlink" href="#manual-collate-chapter-num-collate-group-together-disparate-input-into-sets-of-results" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate syntax in detail</em></a></li>
-</ul>
-</td></tr></table>
-<p>It is often very useful to group together disparate <em>inputs</em> into several categories, each of which
-lead to a separate <em>output</em>. In the example shown below, we produce separate summaries of results
-depending on which species the file belongs to.</p>
-<p><strong>Ruffus</strong> uses the term <tt class="docutils literal"><span class="pre">collate</span></tt> in a rough analogy to the way printers group together
-copies of documents appropriately.</p>
-</div></blockquote>
-<div class="section" id="collating-many-inputs-each-into-a-single-output">
-<span id="index-0"></span><h2>Collating many <em>inputs</em> each into a single <em>output</em><a class="headerlink" href="#collating-many-inputs-each-into-a-single-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Our example starts with some files which presumably have been created by some
-earlier stages of our pipeline. We simulate this here with this code:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">files_names</span> <span class="o">=</span> <span class="p">[</span>     <span class="s">"mammals.tiger.wild.animals"</span>
-                    <span class="s">"mammals.lion.wild.animals"</span>
-                    <span class="s">"mammals.lion.handreared.animals"</span>
-                    <span class="s">"mammals.dog.tame.animals"</span>
-                    <span class="s">"mammals.dog.wild.animals"</span>
-                    <span class="s">"mammals.dog.feral.animals"</span>
-                    <span class="s">"reptiles.crocodile.wild.animals"</span> <span class="p">]</span>
-<span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">files_names</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>However, we are only interested in mammals, and we would like the files of each species to
-end up in its own directory, i.e. <tt class="docutils literal"><span class="pre">tiger</span></tt>, <tt class="docutils literal"><span class="pre">lion</span></tt> and <tt class="docutils literal"><span class="pre">dog</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">os</span>
-<span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="s">"tiger"</span><span class="p">)</span>
-<span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="s">"lion"</span><span class="p">)</span>
-<span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="s">"dog"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Now we would like to place each file in a different destination, depending on its
-species. The following regular expression marks out the species name <tt class="docutils literal"><span class="pre">r'mammals.([^.]+)'</span></tt>.
-For <tt class="docutils literal"><span class="pre">mammals.tiger.wild.animals</span></tt>, the first matching group (<tt class="docutils literal"><span class="pre">\1</span></tt>) == <tt class="docutils literal"><span class="pre">"tiger"</span></tt></p>
-<p>Then, the following:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@collate</span><span class="p">(</span><span class="s">'*.animals'</span><span class="p">,</span>                     <span class="c"># inputs = all *.animal files</span>
-            <span class="n">regex</span><span class="p">(</span><span class="s">r'mammals.([^.]+)'</span><span class="p">),</span>    <span class="c"># regular expression</span>
-            <span class="s">r'\1/animals.in_my_zoo'</span><span class="p">,</span>      <span class="c"># single output file per species</span>
-            <span class="s">r'\1'</span> <span class="p">)</span>                       <span class="c"># species name</span>
-<span class="k">def</span> <span class="nf">capture_mammals</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>
-    <span class="c"># summarise all animals of this species</span>
-    <span class="k">print</span> <span class="s">"Collating </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">species</span>
-
-    <span class="n">o</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">infiles</span><span class="p">:</span>
-        <span class="n">o</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">captured</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">capture_mammals</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>puts each captured mammal in its own directory:</p>
-<div class="highlight-python"><pre>Task = capture_mammals
-    Job = [(mammals.lion.handreared.animals, mammals.lion.wild.animals) -> lion/animals.in_my_zoo] completed
-    Job = [(mammals.tiger.wild.animals, ) -> tiger/animals.in_my_zoo] completed
-    Job = [(mammals.dog.tame.animals, mammals.dog.wild.animals, mammals.dog.feral.animals) -> dog/animals.in_my_zoo] completed</pre>
-</div>
-<p>The crocodile has been discarded because it isn’t a mammal and the file name
-doesn’t match the <tt class="docutils literal"><span class="pre">mammal</span></tt> part of the regular expression.</p>
-</div></blockquote>
-</div>
-</div>
-
-
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 14</strong>: <strong>@collate</strong>: <cite>group together disparate input into sets of results</cite></a><ul>
-<li><a class="reference internal" href="#collating-many-inputs-each-into-a-single-output">Collating many <em>inputs</em> each into a single <em>output</em></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="onthefly.html"
-                        title="previous chapter"><strong>Chapter 13</strong>: <cite>Generating parameters on the fly with</cite> <strong>@files</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="advanced_transform.html"
-                        title="next chapter"><strong>Chapter 15</strong>: <strong>add_inputs()</strong> <cite>and</cite> <strong>inputs()</strong>: <cite>Controlling both input and output files with</cite> <strong>@transform</strong></a></p>
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-  <div class="section" id="manual-dependencies-chapter-num-checking-dependencies-to-run-tasks-in-order">
-<span id="manual-dependencies"></span><h1><strong>Chapter 12</strong>: <cite>Checking dependencies to run tasks in order</cite><a class="headerlink" href="#manual-dependencies-chapter-num-checking-dependencies-to-run-tasks-in-order" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-</ul>
-</td></tr></table>
-<p id="index-0">How does <strong>Ruffus</strong> decide how to run your pipeline?</p>
-<blockquote>
-<div><ul class="simple">
-<li>In which order should pipelined functions be called?</li>
-<li>Which parts of the pipeline are up-to-date and do not need to be rerun?</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="running-all-out-of-date-tasks-and-dependents">
-<h2>Running all out-of-date tasks and dependents<a class="headerlink" href="#running-all-out-of-date-tasks-and-dependents" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><img alt="../../_images/manual_dependencies_flowchart_intro.png" src="../../_images/manual_dependencies_flowchart_intro.png" />
-<p>By default, <em>ruffus</em> will</p>
-<blockquote>
-<div><ul class="simple">
-<li>build a flow chart (dependency tree) of pipelined tasks (functions)</li>
-<li>start from the most ancestral tasks with the fewest dependencies (<tt class="docutils literal"><span class="pre">task1</span></tt> and <tt class="docutils literal"><span class="pre">task4</span></tt> in the flowchart above).</li>
-<li>walk up the tree to find the first incomplete / out-of-date tasks (i.e. <tt class="docutils literal"><span class="pre">task3</span></tt> and <tt class="docutils literal"><span class="pre">task5</span></tt>.</li>
-<li>start running from there</li>
-</ul>
-</div></blockquote>
-<dl class="docutils">
-<dt>All down-stream (dependent) tasks will be re-run anyway, so we don’t have to test</dt>
-<dd>whether they are up-to-date or not.</dd>
-</dl>
-<div class="admonition note" id="manual-dependencies-checking-multiple-times">
-<p class="first admonition-title">Note</p>
-<p>This means that <strong>ruffus</strong> <em>may</em> ask any task if their jobs are out of date more than once:</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>once when deciding which parts of the pipeline have to be run</li>
-<li>once just before executing the task.</li>
-</ul>
-</div></blockquote>
-</div>
-<p><em>Ruffus</em> tries to be clever / efficient, and does the minimal amount of querying.</p>
-</div></blockquote>
-</div>
-<div class="section" id="a-simple-example">
-<span id="manual-dependencies-example"></span><h2>A simple example<a class="headerlink" href="#a-simple-example" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="four-successive-tasks-to-run">
-<h3>Four successive tasks to run:<a class="headerlink" href="#four-successive-tasks-to-run" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The full code is available <a class="reference internal" href="dependencies_code.html#manual-dependencies-code"><em>here</em></a>.</p>
-</div>
-<p>Suppose we have four successive tasks to run, whose flowchart we can print out
-by running:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span> <span class="p">(</span><span class="s">"flowchart.png"</span><span class="p">,</span> <span class="s">"png"</span><span class="p">,</span> <span class="p">[</span><span class="n">task4</span><span class="p">],</span>
-                            <span class="n">draw_vertically</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<img alt="../../_images/manual_dependencies_flowchart1.png" src="../../_images/manual_dependencies_flowchart1.png" />
-<p>We can see that all four tasks need to run reach the target task4.</p>
-</div></blockquote>
-</div>
-<div class="section" id="pipeline-tasks-are-up-to-date">
-<h3>Pipeline tasks are up-to-date:<a class="headerlink" href="#pipeline-tasks-are-up-to-date" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>After the pipeline runs (<tt class="docutils literal"><span class="pre">python</span> <span class="pre">simpler.py</span> <span class="pre">-d</span> <span class="pre">""</span></tt>), all tasks are up to date and the flowchart shows:</p>
-<img alt="../../_images/manual_dependencies_flowchart2.png" src="../../_images/manual_dependencies_flowchart2.png" />
-</div></blockquote>
-</div>
-<div class="section" id="some-tasks-out-of-date">
-<h3>Some tasks out of date:<a class="headerlink" href="#some-tasks-out-of-date" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><dl class="docutils">
-<dt>If we then made task2 and task4 out of date by modifying their <em>inputs</em> files:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">open</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"a.3"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>the flowchart would show:</p>
-<ol class="arabic simple">
-<li>the pipeline only has to rerun from <tt class="docutils literal"><span class="pre">task2</span></tt>.</li>
-<li><tt class="docutils literal"><span class="pre">task1</span></tt> is complete / up-to-date</li>
-<li><tt class="docutils literal"><span class="pre">task3</span></tt> will have to be re-run because it follows (depends on) <tt class="docutils literal"><span class="pre">task2</span></tt>.</li>
-</ol>
-<img alt="../../_images/manual_dependencies_flowchart3.png" src="../../_images/manual_dependencies_flowchart3.png" />
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="forced-reruns">
-<h2>Forced Reruns<a class="headerlink" href="#forced-reruns" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Even if a pipeline stage appears to be up to date,
-you can always force the pipeline to include from one or more task functions.</p>
-<p>This is particularly useful, for example, if the pipeline data hasn’t changed but
-the analysis or computional code has.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">task4</span><span class="p">],</span> <span class="p">[</span><span class="n">task1</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>will run all tasks from <tt class="docutils literal"><span class="pre">task1</span></tt> to <tt class="docutils literal"><span class="pre">task4</span></tt></p>
-</div></blockquote>
-<p>Both the “target” and the “forced” lists can include as many tasks as you wish. All dependencies
-are still carried out and out-of-date jobs rerun.</p>
-</div></blockquote>
-</div>
-<div class="section" id="esoteric-option-minimal-reruns">
-<h2>Esoteric option: Minimal Reruns<a class="headerlink" href="#esoteric-option-minimal-reruns" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>In the above example, you could point out that <tt class="docutils literal"><span class="pre">task3</span></tt> is not out of date. And if we were only interested
-in the immediate dependencies or prerequisites leading up to <tt class="docutils literal"><span class="pre">task4</span></tt>, we might not
-need task2 to rerun at all, only <tt class="docutils literal"><span class="pre">task4</span></tt>.</p>
-<p>This rather dangerous option is useful if you don’t want to keep all the intermediate
-files/results from upstream tasks. The pipeline will only not involve any incomplete
-tasks which precede an up-to-date result.</p>
-<p>This is seldom what you intend, and you should always check that the appropriate stages
-of the pipeline are executed in the flowchart output.</p>
-<p>In such cases, we can rerun the pipeline with the following option:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">task4</span><span class="p">],</span> <span class="n">gnu_make_maximal_rebuild_mode</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>and only <tt class="docutils literal"><span class="pre">task4</span></tt> will rerun.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 12</strong>: <cite>Checking dependencies to run tasks in order</cite></a><ul>
-<li><a class="reference internal" href="#running-all-out-of-date-tasks-and-dependents">Running all out-of-date tasks and dependents</a></li>
-<li><a class="reference internal" href="#a-simple-example">A simple example</a><ul>
-<li><a class="reference internal" href="#four-successive-tasks-to-run">Four successive tasks to run:</a></li>
-<li><a class="reference internal" href="#pipeline-tasks-are-up-to-date">Pipeline tasks are up-to-date:</a></li>
-<li><a class="reference internal" href="#some-tasks-out-of-date">Some tasks out of date:</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#forced-reruns">Forced Reruns</a></li>
-<li><a class="reference internal" href="#esoteric-option-minimal-reruns">Esoteric option: Minimal Reruns</a></li>
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-                        title="previous chapter"><strong>Chapter 11</strong>: <cite>Manage concurrency for a specific task with</cite> <strong>@jobs_limit</strong></a></p>
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-  <div class="section" id="code-for-chapter-9-checking-dependencies-to-run-tasks-in-order">
-<span id="manual-dependencies-code"></span><h1>Code for Chapter 9: Checking dependencies to run tasks in order<a class="headerlink" href="#code-for-chapter-9-checking-dependencies-to-run-tasks-in-order" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-<li><a class="reference internal" href="dependencies.html#manual-dependencies-example"><em>Back</em></a></li>
-</ul>
-<p>This example shows how dependencies work</p>
-</div></blockquote>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">json</span>
-
-<span class="kn">import</span> <span class="nn">time</span>
-<span class="k">def</span> <span class="nf">task_helper</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    cat input file content to output file</span>
-<span class="sd">        after writing out job parameters</span>
-<span class="sd">    """</span>
-    <span class="k">if</span> <span class="n">infile</span><span class="p">:</span>
-        <span class="n">output_text</span> <span class="o">=</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">()))</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">output_text</span> <span class="o">=</span> <span class="s">"None"</span>
-    <span class="n">output_text</span> <span class="o">+=</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span> <span class="o">+</span> <span class="s">" -> "</span> <span class="o">+</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">outfile</span><span class="p">)</span> <span class="o">+</ [...]
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">output_text</span><span class="p">)</span>
-
-
-
-<span class="c">#</span>
-<span class="c">#    task1</span>
-<span class="c">#</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">'a.1'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task1</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    First task</span>
-<span class="sd">    """</span>
-    <span class="n">task_helper</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">)</span>
-
-
-
-<span class="c">#</span>
-<span class="c">#    task2</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r'.1'</span><span class="p">),</span> <span class="s">'.2'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Second task</span>
-<span class="sd">    """</span>
-    <span class="n">task_helper</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">)</span>
-
-
-
-<span class="c">#</span>
-<span class="c">#    task3</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task2</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r'.2'</span><span class="p">),</span> <span class="s">'.3'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task3</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Third task</span>
-<span class="sd">    """</span>
-    <span class="n">task_helper</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">)</span>
-
-
-
-<span class="c">#</span>
-<span class="c">#    task4</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task3</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r'.3'</span><span class="p">),</span> <span class="s">'.4'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task4</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Fourth task</span>
-<span class="sd">    """</span>
-    <span class="n">task_helper</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">)</span>
-
-<span class="n">pipeline_printout_graph</span> <span class="p">(</span><span class="s">"flowchart.png"</span><span class="p">,</span> <span class="s">"png"</span><span class="p">,</span> <span class="p">[</span><span class="n">task4</span><span class="p">],</span> <span class="n">draw_vertically</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">no_key_legend</span> <span class="o">=</span> <span class="bp">True</span> [...]
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">task4</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">task4</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">logger</span> <span class="o">=</span> <span class="n">logger_proxy</span><span class="p">)</span>
-<span class="go">    job = [null, "a.1"]</span>
-<span class="go">    job = ["a.1", "a.2"]</span>
-<span class="go">    job = ["a.2", "a.3"]</span>
-<span class="go">    job = ["a.3", "a.4"]</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Chapter 9: Checking dependencies to run tasks in order</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="../simple_tutorial/step8_posttask.html"
-                        title="previous chapter">Step 8: Signal the completion of each stage of our pipeline</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="logging_code.html"
-                        title="next chapter">Code for Chapter 16: Logging progress through a pipeline</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/manual/dependencies_code.txt"
-           rel="nofollow">Show Source</a></li>
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-      <input type="hidden" name="area" value="default" />
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
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-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
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-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
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-  <div class="section" id="manual-exceptions-chapter-num-exceptions-thrown-inside-a-pipeline">
-<span id="manual-exceptions"></span><h1><strong>Chapter 18</strong>: <cite>Exceptions thrown inside a pipeline</cite><a class="headerlink" href="#manual-exceptions-chapter-num-exceptions-thrown-inside-a-pipeline" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-</ul>
-</td></tr></table>
-<p id="index-0">The goal for <strong>Ruffus</strong> is that exceptions should just work <em>out-of-the-box</em> without any fuss.
-This is especially important for exceptions that come from your code which may be raised
-in a different process. Often multiple parallel operations (jobs or tasks) fail at the
-same time. <strong>Ruffus</strong> will forward each of these exceptions with the tracebacks so you
-can jump straight to the offending line.</p>
-<p>This example shows separate exceptions from two jobs running in parallel:</p>
-<blockquote>
-<div><img alt="../../_images/manual_exceptions.png" src="../../_images/manual_exceptions.png" />
-</div></blockquote>
-</div></blockquote>
-<span class="target" id="manual-exceptions-multiple-errors"></span><div class="section" id="multiple-errors">
-<span id="index-1"></span><h2>Multiple Errors<a class="headerlink" href="#multiple-errors" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>For any task where exceptions are thrown, <em>Ruffus</em> will continue executing all the jobs
-currently in progress (up to the maximum number of concurrent jobs
-(<tt class="docutils literal"><span class="pre">multiprocess</span></tt>) set in <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>).
-Each of these may raise separate exceptions.
-This seems a fair tradeoff between being able to gather detailed error information for
-running jobs, and not wasting too much time for a task that is going to fail anyway.</div></blockquote>
-</div>
-<div class="section" id="interrupting-the-pipeline">
-<span id="manual-exceptions-interrupting"></span><span id="index-2"></span><h2>Interrupting the pipeline<a class="headerlink" href="#interrupting-the-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If your task function raises a <tt class="docutils literal"><span class="pre">Ruffus.JobSignalledBreak</span></tt> Exception, this will immediately
-halt the pipeline at that point, without waiting for other jobs in the queue to complete:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="nd">@parallel</span><span class="p">([[</span><span class="s">'A'</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="s">'B'</span><span class="p">,</span><span class="mi">3</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">parallel_task</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">param1</span><span class="p">):</span>
-    <span class="k">if</span> <span class="n">name</span> <span class="o">==</span> <span class="s">'A'</span><span class="p">:</span> <span class="k">return</span> <span class="bp">False</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>produces the following (abbreviated):</p>
-<blockquote>
-<div><div class="highlight-python"><pre>task.RethrownJobError:
-
-    Exceptions running jobs for
-    'def parallel_task(...):'
-
-    Original exception:
-
-    Exception #1
-    task.JobSignalledBreak: Job = ["A", 1] returned False
-    for Job = ["A", 1]</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 18</strong>: <cite>Exceptions thrown inside a pipeline</cite></a><ul>
-<li><a class="reference internal" href="#multiple-errors">Multiple Errors</a></li>
-<li><a class="reference internal" href="#interrupting-the-pipeline">Interrupting the pipeline</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="check_if_uptodate.html"
-                        title="previous chapter"><strong>Chapter 17</strong>: <cite>Writing custom functions to decide which jobs are up to date</cite></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="logging.html"
-                        title="next chapter"><strong>Chapter 19</strong>: <cite>Logging progress through a pipeline</cite></a></p>
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-            
-  <div class="section" id="manual-files-chapter-num-passing-parameters-to-the-pipeline-with-files">
-<span id="manual-files"></span><h1><strong>Chapter  3</strong>: <cite>Passing parameters to the pipeline with</cite> <strong>@files</strong><a class="headerlink" href="#manual-files-chapter-num-passing-parameters-to-the-pipeline-with-files" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/files.html#decorators-files"><em>@files syntax in detail</em></a></li>
-</ul>
-</td></tr></table>
-<div class="line-block">
-<div class="line">The python functions which do the actual work of each stage  or
-<a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> of a <strong>Ruffus</strong> pipeline are written by you.</div>
-<div class="line">The role of <strong>Ruffus</strong> is to make sure these functions are called in the right order,
-with the right parameters, running in parallel using multiprocessing if desired.</div>
-</div>
-<p>The easiest way to specify parameters to <em>Ruffus</em> <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> functions is to use
-the <a class="reference internal" href="../../decorators/files.html#decorators-files"><em>@files</em></a> decorator.</p>
-</div></blockquote>
-<div class="section" id="files">
-<span id="index-0"></span><h2><strong>@files</strong><a class="headerlink" href="#files" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Running this code:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="p">[</span><span class="s">'a.2'</span><span class="p">,</span> <span class="s">'b.2'</span><span class="p">],</span> <span class="s">'A file'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">single_job_io_task</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="n">text</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">outfiles</span><span class="p">:</span> <span class="nb">open</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c"># prepare input file</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<dl class="docutils">
-<dt>Is equivalent to calling:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">single_job_io_task</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="p">[</span><span class="s">'a.2'</span><span class="p">,</span> <span class="s">'b.2'</span><span class="p">],</span> <span class="s">'A file'</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-<dt>And produces:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job = [a.1 -> [a.2, b.2], A file] completed</span>
-<span class="go">Completed Task = single_job_io_task</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-<p><strong>Ruffus</strong> will automatically check if your task is up to date. The second time <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a>
-is called, nothing will happen. But if you update <tt class="docutils literal"><span class="pre">a.1</span></tt>, the task will rerun:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="nb">open</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job = [a.1 -> [a.2, b.2], A file] completed</span>
-<span class="go">Completed Task = single_job_io_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>See <a class="reference internal" href="tasks_as_recipes.html#manual-skip-up-to-date"><em>chapter 2</em></a> for a more in-depth discussion of how <strong>Ruffus</strong>
-decides which parts of the pipeline are complete and up-to-date.</p>
-</div></blockquote>
-</div>
-<div class="section" id="running-the-same-code-on-different-parameters-in-parallel">
-<span id="manual-files-parallel"></span><span id="index-1"></span><h2>Running the same code on different parameters in parallel<a class="headerlink" href="#running-the-same-code-on-different-parameters-in-parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Your pipeline may require the same function to be called multiple times on independent parameters.
-In which case, you can supply all the parameters to @files, each will be sent to separate jobs that
-may run in parallel if necessary. <strong>Ruffus</strong> will check if each separate <a class="reference internal" href="../../glossary.html#term-job"><em class="xref std std-term">job</em></a> is up-to-date using
-the <em>inputs</em> and <em>outputs</em> (first two) parameters (See the <a class="reference internal" href="tasks_as_recipes.html#manual-io-parameters"><em>chapter 2</em></a> ).</p>
-<p>For example, if a sequence
-(e.g. a list or tuple) of 5 parameters are passed to <strong>@files</strong>, that indicates
-there will also be 5 separate jobs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="s">'job1.file'</span>           <span class="p">],</span>             <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="s">'job2.file'</span><span class="p">,</span> <span class="mi">4</span>        <span class="p">],</span>             <span class="c"># 2st job</span>
-                    <span class="p">[</span> <span class="s">'job3.file'</span><span class="p">,</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>   <span class="p">],</span>             <span class="c"># 3st job</span>
-                    <span class="p">[</span> <span class="mi">67</span><span class="p">,</span> <span class="p">[</span><span class="mi">13</span><span class="p">,</span> <span class="s">'job4.file'</span><span class="p">]</span> <span class="p">],</span>             <span class="c"># 4st job</span>
-                    <span class="p">[</span> <span class="s">'job5.file'</span>           <span class="p">],</span>             <span class="c"># 5st job</span>
-              <span class="p">]</span>
-<span class="nd">@files</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task_file</span><span class="p">(</span><span class="o">*</span><span class="n">params</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="line-block">
-<div class="line"><strong>Ruffus</strong> creates as many jobs as there are elements in <tt class="docutils literal"><span class="pre">parameters</span></tt>.</div>
-<div class="line">In turn, each of these elements consist of series of parameters which will be
-passed to each separate job.</div>
-</div>
-<p>Thus the above code is equivalent to calling:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">task_file</span><span class="p">(</span><span class="s">'job1.file'</span><span class="p">)</span>
-<span class="n">task_file</span><span class="p">(</span><span class="s">'job2.file'</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
-<span class="n">task_file</span><span class="p">(</span><span class="s">'job3.file'</span><span class="p">,</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">2</span><span class="p">])</span>
-<span class="n">task_file</span><span class="p">(</span><span class="mi">67</span><span class="p">,</span> <span class="p">[</span><span class="mi">13</span><span class="p">,</span> <span class="s">'job4.file'</span><span class="p">])</span>
-<span class="n">task_file</span><span class="p">(</span><span class="s">'job5.file'</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>What <tt class="docutils literal"><span class="pre">task_file()</span></tt> does with these parameters is up to you!</p>
-<p>The only constraint on the parameters is that <strong>Ruffus</strong> will treat any first
-parameter of each job as the <em>inputs</em> and any second as the <em>output</em>. Any
-strings in the <em>inputs</em> or <em>output</em> parameters (including those nested in sequences)
-will be treated as file names.</p>
-<p>Thus, to pick the parameters out of one of the above jobs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">task_file</span><span class="p">(</span><span class="mi">67</span><span class="p">,</span> <span class="p">[</span><span class="mi">13</span><span class="p">,</span> <span class="s">'job4.file'</span><span class="p">])</span>
-</pre></div>
-</div>
-<div class="line-block">
-<div class="line"><em>inputs</em>  == <tt class="docutils literal"><span class="pre">67</span></tt></div>
-<div class="line"><em>outputs</em> == <tt class="docutils literal"><span class="pre">[13,</span> <span class="pre">'job4.file']</span></tt></div>
-<div class="line"><br /></div>
-<div class="line-block">
-<div class="line">The solitary output filename is <tt class="docutils literal"><span class="pre">job4.file</span></tt></div>
-</div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="checking-if-jobs-are-up-to-date">
-<span id="manual-files-example"></span><span id="manual-files-is-uptodate"></span><span id="index-2"></span><h3>Checking if jobs are up to date<a class="headerlink" href="#checking-if-jobs-are-up-to-date" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="line-block">
-<div class="line">Usually we do not want to run all the stages in a pipeline but only where
-the input data has changed or is no longer up to date.</div>
-<div class="line">One easy way to do this is to check the modification times for files produced
-at each stage of the pipeline.</div>
-</div>
-<div class="line-block">
-<div class="line">Let us first create our starting files <tt class="docutils literal"><span class="pre">a.1</span></tt> and <tt class="docutils literal"><span class="pre">b.1</span></tt></div>
-<div class="line">We can then run the following pipeline function to create</div>
-</div>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">a.2</span></tt> from <tt class="docutils literal"><span class="pre">a.1</span></tt> and</li>
-<li><tt class="docutils literal"><span class="pre">b.2</span></tt> from <tt class="docutils literal"><span class="pre">b.1</span></tt></li>
-</ul>
-<div class="highlight-python"><div class="highlight"><pre><span class="c"># create starting files</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"b.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="s">'a.1'</span><span class="p">,</span> <span class="s">'a.2'</span><span class="p">,</span> <span class="s">'A file'</span><span class="p">],</span> <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="s">'b.1'</span><span class="p">,</span> <span class="s">'b.2'</span><span class="p">,</span> <span class="s">'B file'</span><span class="p">],</span> <span class="c"># 2nd job</span>
-              <span class="p">]</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">parallel_io_task</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">text</span><span class="p">):</span>
-    <span class="c"># copy infile contents to outfile</span>
-    <span class="n">infile_text</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">infile_text</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span> <span class="o">+</span> <span class="n">text</spa [...]
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>This produces the following output:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job = [a.1 -> a.2, A file] completed</span>
-<span class="go">    Job = [b.1 -> b.2, B file] completed</span>
-<span class="go">Completed Task = parallel_io_task</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<div class="line-block">
-<div class="line">If you called <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> again, nothing would happen because the files are up to date:</div>
-<div class="line"><tt class="docutils literal"><span class="pre">a.2</span></tt> is more recent than <tt class="docutils literal"><span class="pre">a.1</span></tt> and</div>
-<div class="line"><tt class="docutils literal"><span class="pre">b.2</span></tt> is more recent than <tt class="docutils literal"><span class="pre">b.1</span></tt></div>
-</div>
-<dl class="docutils">
-<dt>However, if you subsequently modified <tt class="docutils literal"><span class="pre">a.1</span></tt> again:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">open</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>you would see the following:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_io_task</span><span class="p">])</span>
-<span class="go">Task = parallel_io_task</span>
-<span class="go">    Job = ["a.1" -> "a.2", "A file"] completed</span>
-<span class="go">    Job = ["b.1" -> "b.2", "B file"] unnecessary: already up to date</span>
-<span class="go">Completed Task = parallel_io_task</span>
-</pre></div>
-</div>
-<p>The 2nd job is up to date and will be skipped.</p>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  3</strong>: <cite>Passing parameters to the pipeline with</cite> <strong>@files</strong></a><ul>
-<li><a class="reference internal" href="#files"><strong>@files</strong></a></li>
-<li><a class="reference internal" href="#running-the-same-code-on-different-parameters-in-parallel">Running the same code on different parameters in parallel</a><ul>
-<li><a class="reference internal" href="#checking-if-jobs-are-up-to-date">Checking if jobs are up to date</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="tasks_as_recipes.html"
-                        title="previous chapter"><strong>Chapter  2</strong>: <cite>Tasks and Recipes</cite></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="tasks_and_globs_in_inputs.html"
-                        title="next chapter"><strong>Chapter  4</strong>: Chaining pipeline <cite>Tasks</cite> together automatically</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/manual/files.txt"
-           rel="nofollow">Show Source</a></li>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
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-            
-  <div class="section" id="manual-files-re-chapter-num-files-re-deprecated-syntax-using-regular-expressions">
-<span id="manual-files-re"></span><h1><strong>Chapter 20</strong>: <strong>@files_re</strong>: Deprecated <cite>syntax using regular expressions</cite><a class="headerlink" href="#manual-files-re-chapter-num-files-re-deprecated-syntax-using-regular-expressions" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/files_re.html#decorators-files-re"><em>@files_re</em></a> syntax in detail</li>
-</ul>
-</td></tr></table>
-</div></blockquote>
-<div class="section" id="files-re">
-<span id="index-0"></span><h2><strong>@files_re</strong><a class="headerlink" href="#files-re" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>This is older, now deprecated syntax.</p>
-<p><strong>@files_re</strong> combines the functionality of @transform, @collate and @merge in
-one overloaded decorator.</p>
-<p>This is the reason why its use is discouraged. <strong>@files_re</strong> syntax is far too overloaded
-and context-dependent to support its myriad of different functions.</p>
-<p>The following documentation is provided to help maintain historical <strong>ruffus</strong> usage.</p>
-</div></blockquote>
-<div class="section" id="transforming-input-and-output-filenames">
-<h3>Transforming input and output filenames<a class="headerlink" href="#transforming-input-and-output-filenames" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>For example, the following code from <strong>Chapter  8</strong> takes files from
-the previous pipeline task, and makes new output parameters with the <tt class="docutils literal"><span class="pre">.sums</span></tt> suffix
-in place of the <tt class="docutils literal"><span class="pre">.chunks</span></tt> suffix:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">step_4_split_numbers_into_chunks</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".chunks"</span><span class="p">),</span> <span class="s">".sums"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_5_calculate_sum_of_squares</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="c">#</span>
-    <span class="c">#   calculate sums and sums of squares for all values in the input_file_name</span>
-    <span class="c">#       writing to output_file_name</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This can be written using @files_re equivalently:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>@files_re(step_4_split_numbers_into_chunks, r".chunks", r".sums")
-def step_5_calculate_sum_of_squares (input_file_name, output_file_name):
-""</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-<span class="target" id="manual-files-re-combine"></span></div>
-<div class="section" id="collating-many-inputs-into-a-single-output">
-<span id="index-1"></span><h3>Collating many <em>inputs</em> into a single <em>output</em><a class="headerlink" href="#collating-many-inputs-into-a-single-output" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Similarly, the following code from <a class="reference internal" href="collate.html#manual-collate"><em>|manual.collate.chapter_num|</em></a> collects <strong>inputs</strong>
-from the same species in the same directory:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@collate</span><span class="p">(</span><span class="s">'*.animals'</span><span class="p">,</span>                     <span class="c"># inputs = all *.animal files</span>
-            <span class="n">regex</span><span class="p">(</span><span class="s">r'mammals.([^.]+)'</span><span class="p">),</span>    <span class="c"># regular expression</span>
-            <span class="s">r'\1/animals.in_my_zoo'</span><span class="p">,</span>      <span class="c"># single output file per species</span>
-            <span class="s">r'\1'</span> <span class="p">)</span>                       <span class="c"># species name</span>
-<span class="k">def</span> <span class="nf">capture_mammals</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>
-    <span class="c"># summarise all animals of this species</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This can be written using @files_re equivalently using the <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-combine"><em>combine</em></a> indicator:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@files_re</span><span class="p">(</span><span class="s">'*.animals'</span><span class="p">,</span>                           <span class="c"># inputs = all *.animal files</span>
-            <span class="s">r'mammals.([^.]+)'</span><span class="p">,</span>                  <span class="c"># regular expression</span>
-            <span class="n">combine</span><span class="p">(</span><span class="s">r'\1/animals.in_my_zoo'</span><span class="p">),</span>    <span class="c"># single output file per species</span>
-            <span class="s">r'\1'</span> <span class="p">)</span>                              <span class="c"># species name</span>
-<span class="k">def</span> <span class="nf">capture_mammals</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>
-    <span class="c"># summarise all animals of this species</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="generating-input-and-output-parameter-using-regular-expresssions">
-<h3>Generating <em>input</em> and <em>output</em> parameter using regular expresssions<a class="headerlink" href="#generating-input-and-output-parameter-using-regular-expresssions" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The following code generates additional <em>Input</em> prerequisite file names which match the original <em>Input</em> files names.</p>
-<p>We want each job of our <tt class="docutils literal"><span class="pre">analyse()</span></tt> function to get corresponding pairs
-of <tt class="docutils literal"><span class="pre">xx.chunks</span></tt> and <tt class="docutils literal"><span class="pre">xx.red_indian</span></tt> files when</p>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">*.chunks</span></tt> are generated by the task function <tt class="docutils literal"><span class="pre">split_up_problem()</span></tt> and
-<tt class="docutils literal"><span class="pre">*.red_indian</span></tt> are generated by the task function <tt class="docutils literal"><span class="pre">make_red_indians()</span></tt>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="n">make_red_indians</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">split_up_problem</span><span class="p">,</span>                <span class="c"># starting set of *inputs*</span>
-            <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*).chunks"</span><span class="p">),</span>          <span class="c"># regular expression</span>
-            <span class="n">inputs</span><span class="p">([</span><span class="s">r"\g<0>"</span><span class="p">,</span>               <span class="c"># xx.chunks</span>
-                    <span class="s">r"\1.red_indian"</span><span class="p">]),</span>     <span class="c"># important.file</span>
-             <span class="s">r"\1.results"</span>                  <span class="c"># xx.results</span>
-              <span class="p">)</span>
-<span class="k">def</span> <span class="nf">analyse</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="s">"Do analysis here"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The equivalent code using @files_re looks very similar:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>@follows(make_red_indians)
- at files_re( split_up_problem,        # starting set of *inputs*
-           r"(.*).chunks",          # regular expression
-           [r"\g<0>",               # xx.chunks
-            r"\1.red_indian"]),     # important.file
-             r"\1.results")         # xx.results
-def analyse(input_filenames, output_file_name):
-    "Do analysis here"</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-</div>
-
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-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 20</strong>: <strong>@files_re</strong>: Deprecated <cite>syntax using regular expressions</cite></a><ul>
-<li><a class="reference internal" href="#files-re"><strong>@files_re</strong></a><ul>
-<li><a class="reference internal" href="#transforming-input-and-output-filenames">Transforming input and output filenames</a></li>
-<li><a class="reference internal" href="#collating-many-inputs-into-a-single-output">Collating many <em>inputs</em> into a single <em>output</em></a></li>
-<li><a class="reference internal" href="#generating-input-and-output-parameter-using-regular-expresssions">Generating <em>input</em> and <em>output</em> parameter using regular expresssions</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="logging.html"
-                        title="previous chapter"><strong>Chapter 19</strong>: <cite>Logging progress through a pipeline</cite></a></p>
-  <h4>Next topic</h4>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
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-  <div class="section" id="manual-follows-chapter-num-arranging-tasks-into-a-pipeline-with-follows">
-<span id="manual-follows"></span><h1><strong>Chapter  1</strong> : <cite>Arranging tasks into a pipeline with</cite> <strong>@follows</strong><a class="headerlink" href="#manual-follows-chapter-num-arranging-tasks-into-a-pipeline-with-follows" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows syntax in detail</em></a></li>
-</ul>
-</div></blockquote>
-<div class="section" id="follows">
-<span id="index-0"></span><h2><strong>@follows</strong><a class="headerlink" href="#follows" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The order in which stages or <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>s of a pipeline are arranged are set
-explicitly by the <a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows(...)</em></a> python decorator:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"First task"</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">first_task</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"Second task"</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">second_task</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">final_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"Final task"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>the <tt class="docutils literal"><span class="pre">@follows</span></tt> decorator indicate that the <tt class="docutils literal"><span class="pre">first_task</span></tt> function precedes <tt class="docutils literal"><span class="pre">second_task</span></tt> in
-the pipeline.</p>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>We shall see in <a class="reference internal" href="tasks_and_globs_in_inputs.html#manual-tasks-as-input"><em>Chapter 2</em></a> that the order of pipeline <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>s can also be inferred implicitly
-for the following decorators</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><a class="reference internal" href="split.html#manual-split"><em>@split(...)</em></a></li>
-<li><a class="reference internal" href="transform.html#manual-transform"><em>@transform(...)</em></a></li>
-<li><a class="reference internal" href="merge.html#manual-merge"><em>@merge(...)</em></a></li>
-<li><a class="reference internal" href="collate.html#manual-collate"><em>@collate(...)</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="running">
-<span id="index-1"></span><h3>Running<a class="headerlink" href="#running" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><dl class="docutils">
-<dt>Now we can run the pipeline by:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">final_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>Because <tt class="docutils literal"><span class="pre">final_task</span></tt> depends on <tt class="docutils literal"><span class="pre">second_task</span></tt> which depends on <tt class="docutils literal"><span class="pre">first_task</span></tt> , all
-three functions will be executed in order.</p>
-</div></blockquote>
-</div>
-<div class="section" id="displaying">
-<span id="index-2"></span><h3>Displaying<a class="headerlink" href="#displaying" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><dl class="docutils">
-<dt>We can see a flowchart of our fledgling pipeline by executing:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span> <span class="p">(</span> <span class="s">"manual_follows1.png"</span><span class="p">,</span>
-                         <span class="s">"png"</span><span class="p">,</span>
-                         <span class="p">[</span><span class="n">final_task</span><span class="p">],</span>
-                         <span class="n">no_key_legend</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>producing the following flowchart</p>
-<blockquote>
-<div><img alt="../../_images/manual_follows1.png" src="../../_images/manual_follows1.png" />
-</div></blockquote>
-<dl class="docutils">
-<dt>or in text format with:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">final_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</dd>
-<dt>which produces the following:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">Task</span> <span class="o">=</span> <span class="n">first_task</span>
-<span class="n">Task</span> <span class="o">=</span> <span class="n">second_task</span>
-<span class="n">Task</span> <span class="o">=</span> <span class="n">final_task</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="defining-pipeline-tasks-out-of-order">
-<span id="manual-follows-out-of-order"></span><span id="index-3"></span><h2>Defining pipeline tasks out of order<a class="headerlink" href="#defining-pipeline-tasks-out-of-order" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>All this assumes that all your pipelined tasks are defined in order.
-(<tt class="docutils literal"><span class="pre">first_task</span></tt> before <tt class="docutils literal"><span class="pre">second_task</span></tt> before <tt class="docutils literal"><span class="pre">final_task</span></tt>)</p>
-<div class="line-block">
-<div class="line">This is usually the most sensible way to arrange your code.</div>
-</div>
-<p>If you wish to refer to tasks which are not yet defined, you can do so by quoting the function name as a string:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="s">"second_task"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">final_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"Final task"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>You can refer to tasks (functions) in other modules, in which case the full
-qualified name must be used:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="s">"other_module.second_task"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">final_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"Final task"</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="multiple-dependencies">
-<span id="manual-follows-multiple-dependencies"></span><span id="index-4"></span><h2>Multiple dependencies<a class="headerlink" href="#multiple-dependencies" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Each task can depend on more than one antecedent task.</p>
-<dl class="docutils">
-<dt>This can be indicated either by stacking <tt class="docutils literal"><span class="pre">@follows</span></tt>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="n">first_task</span><span class="p">)</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="s">"second_task"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">final_task</span><span class="p">():</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</dd>
-<dt>or in a more concise way:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="s">"second_task"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">final_task</span><span class="p">():</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-<span class="target" id="manual-follows-mkdir"></span></div>
-<div class="section" id="making-directories-automatically-with-mkdir">
-<span id="index-5"></span><h2>Making directories automatically with <a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>mkdir</em></a><a class="headerlink" href="#making-directories-automatically-with-mkdir" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>A common prerequisite for any computational task, is making sure that the destination
-directories exist.</p>
-<p><strong>Ruffus</strong> provides special syntax to support this, using the special
-<a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>mkdir</em></a> dependency. For example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">mkdir</span><span class="p">(</span><span class="s">"output/results/here"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"Second task"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>will make sure that <tt class="docutils literal"><span class="pre">output/results/here</span></tt> exists before <cite>second_task</cite> is run.</p>
-<p>In other words, it will make the <tt class="docutils literal"><span class="pre">output/results/here</span></tt> directory if it does not exist.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
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-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  1</strong> : <cite>Arranging tasks into a pipeline with</cite> <strong>@follows</strong></a><ul>
-<li><a class="reference internal" href="#follows"><strong>@follows</strong></a><ul>
-<li><a class="reference internal" href="#running">Running</a></li>
-<li><a class="reference internal" href="#displaying">Displaying</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#defining-pipeline-tasks-out-of-order">Defining pipeline tasks out of order</a></li>
-<li><a class="reference internal" href="#multiple-dependencies">Multiple dependencies</a></li>
-<li><a class="reference internal" href="#making-directories-automatically-with-mkdir">Making directories automatically with <tt class="docutils literal"><span class="pre">mkdir</span></tt></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="manual_introduction.html"
-                        title="previous chapter"><strong>Ruffus</strong> Manual</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="tasks_as_recipes.html"
-                        title="next chapter"><strong>Chapter  2</strong>: <cite>Tasks and Recipes</cite></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
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-            
-  <div class="section" id="manual-jobs-limit-chapter-num-manage-concurrency-for-a-specific-task-with-jobs-limit">
-<span id="manual-jobs-limit"></span><h1><strong>Chapter 11</strong>: <cite>Manage concurrency for a specific task with</cite> <strong>@jobs_limit</strong><a class="headerlink" href="#manual-jobs-limit-chapter-num-manage-concurrency-for-a-specific-task-with-jobs-limit" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit</em></a> syntax in detail</li>
-</ul>
-</td></tr></table>
-</div></blockquote>
-<div class="section" id="jobs-limit">
-<span id="index-0"></span><h2><strong>@jobs_limit</strong><a class="headerlink" href="#jobs-limit" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Calling <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(multiprocess = NNN)</em></a> allows
-multiple jobs (from multiple independent tasks) to be run in parallel. However, there
-are some operations which consume so many resources that we might want them to run
-with less or no concurrency.</p>
-<p>For example, we might want to download some files via FTP but the server restricts
-requests from each IP address. Even if the rest of the pipeline is running 100 jobs in
-parallel, the FTP downloading must be restricted to 2 files at a time. We would really
-like to keep the pipeline running as is, but let this one operation run either serially,
-or with little concurrency.</p>
-<p>If setting <tt class="docutils literal"><span class="pre">multiprocess</span> <span class="pre">=</span> <span class="pre">NNN</span></tt> sets the pipeline-wide concurrency to <tt class="docutils literal"><span class="pre">NNN</span></tt>, then
-<tt class="docutils literal"><span class="pre">@jobs_limit(MMM)</span></tt> sets concurrency at a much finer level, at <tt class="docutils literal"><span class="pre">MMM</span></tt> just for jobs
-in the indicated task.</p>
-<p>The optional name (e.g. <tt class="docutils literal"><span class="pre">@jobs_limit(3,</span> <span class="pre">"ftp_download_limit")</span></tt>) allows the same limit to
-be shared across multiple tasks. To be pedantic: a limit of <tt class="docutils literal"><span class="pre">3</span></tt> jobs at a time would be applied
-across all tasks which have a <tt class="docutils literal"><span class="pre">@jobs_limit</span></tt> named <tt class="docutils literal"><span class="pre">"ftp_download_limit"</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c"># make list of 10 files</span>
-<span class="nd">@split</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"*stage1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">make_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">):</span>
-        <span class="k">if</span> <span class="n">i</span> <span class="o"><</span> <span class="mi">5</span><span class="p">:</span>
-            <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.small_stage1"</span> <span class="o">%</span> <span class="n">i</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.big_stage1"</span> <span class="o">%</span> <span class="n">i</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s">"ftp_download_limit"</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">make_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".small_stage1"</span><span class="p">),</span> <span class="s">".stage2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage1_small</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s">"ftp_download_limit"</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">make_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".big_stage1"</span><span class="p">),</span> <span class="s">".stage2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage1_big</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">([</span><span class="n">stage1_small</span><span class="p">,</span> <span class="n">stage1_big</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".stage2"</span><span class="p">),</span> <span class="s">".stage3"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage2</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">stage2</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">10</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>will run the 10 jobs of <tt class="docutils literal"><span class="pre">stage1_big</span></tt> and <tt class="docutils literal"><span class="pre">stage1_small</span></tt> 3 at a time (highlighted in blue),
-a limit shared across the two tasks. <tt class="docutils literal"><span class="pre">stage2</span></tt> jobs run 5 at a time (in red).
-These limits override the numbers set in <tt class="docutils literal"><span class="pre">pipeline_run</span></tt> (<tt class="docutils literal"><span class="pre">multiprocess</span> <span class="pre">=</span> <span class="pre">10</span></tt>):</p>
-<blockquote>
-<div><img alt="../../_images/jobs_limit2.png" src="../../_images/jobs_limit2.png" />
-</div></blockquote>
-</div></blockquote>
-</div></blockquote>
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-<li><a class="reference internal" href="#"><strong>Chapter 11</strong>: <cite>Manage concurrency for a specific task with</cite> <strong>@jobs_limit</strong></a><ul>
-<li><a class="reference internal" href="#jobs-limit"><strong>@jobs_limit</strong></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="posttask.html"
-                        title="previous chapter"><strong>Chapter 10</strong>: <cite>Signal the completion of each stage of our pipeline with</cite> <strong>@posttask</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="dependencies.html"
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-            
-  <div class="section" id="manual-logging-chapter-num-logging-progress-through-a-pipeline">
-<span id="manual-logging"></span><h1><strong>Chapter 19</strong>: <cite>Logging progress through a pipeline</cite><a class="headerlink" href="#manual-logging-chapter-num-logging-progress-through-a-pipeline" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-</ul>
-</td></tr></table>
-<p id="index-0">There are two parts to logging with <strong>Ruffus</strong>:</p>
-<ul>
-<li><p class="first">Logging progress through the pipeline</p>
-<blockquote>
-<div><p>This produces the sort of output displayed in this manual:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_io_task</span><span class="p">])</span>
-<span class="go">Task = parallel_io_task</span>
-<span class="go">    Job = ["a.1" -> "a.2", "A file"] completed</span>
-<span class="go">    Job = ["b.1" -> "b.2", "B file"] unnecessary: already up to date</span>
-<span class="go">Completed Task = parallel_io_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</li>
-<li><p class="first">Logging your own messages from within your pipelined functions.</p>
-<blockquote>
-<div><p>Because <strong>Ruffus</strong> may run these in separate process (multiprocessing), some
-attention has to be paid to how to send and synchronise your log messages
-across process boundaries.</p>
-</div></blockquote>
-</li>
-</ul>
-<p>We shall deal with these in turn.</p>
-</div></blockquote>
-<div class="section" id="logging-task-job-completion">
-<span id="manual-logging-pipeline"></span><h2>Logging task/job completion<a class="headerlink" href="#logging-task-job-completion" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>By default, <em>Ruffus</em> logs each task and each job as it is completed to
-<tt class="docutils literal"><span class="pre">sys.stderr</span></tt>.</p>
-<p><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a>  includes an optional <tt class="docutils literal"><span class="pre">logger</span></tt> parameter which defaults to
-<tt class="docutils literal"><span class="pre">stderr_logger</span></tt>. Set this to <tt class="docutils literal"><span class="pre">black_hole_logger</span></tt> to turn off all tracking messages as
-the pipeline runs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">pipelined_task</span><span class="p">],</span> <span class="n">logger</span> <span class="o">=</span> <span class="n">black_hole_logger</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="controlling-logging-verbosity">
-<h3>Controlling logging verbosity<a class="headerlink" href="#controlling-logging-verbosity" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> currently has five levels of verbosity, set by the optional <tt class="docutils literal"><span class="pre">verbose</span></tt>
-parameter which defaults to 1:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>verbose = 0: nothing
-verbose = 1: logs completed jobs/tasks;
-verbose = 2: logs up to date jobs in incomplete tasks
-verbose = 3: logs reason for running job
-verbose = 4: logs messages useful only for debugging ruffus pipeline code</pre>
-</div>
-<p><tt class="docutils literal"><span class="pre">Verbose</span></tt> > 2 are intended for debugging <strong>Ruffus</strong> by the developers and the details
-are liable to change from release to release</p>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="using-your-own-logging">
-<h3>Using your own logging<a class="headerlink" href="#using-your-own-logging" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>You can specify your own logging by providing a log object  to <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> .
-This log object should have <tt class="docutils literal"><span class="pre">debug()</span></tt> and <tt class="docutils literal"><span class="pre">info()</span></tt> methods.</p>
-<p>Instead of writing your own, it is usually more convenient to use the python
-<a class="reference external" href="http://docs.python.org/library/logging.html">logging</a>
-module which provides logging classes with rich functionality. The following sets up
-a logger to a rotating set of files:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">logging</span>
-<span class="kn">import</span> <span class="nn">logging.handlers</span>
-
-<span class="n">LOG_FILENAME</span> <span class="o">=</span> <span class="s">'/tmp/ruffus.log'</span>
-
-<span class="c"># Set up a specific logger with our desired output level</span>
-<span class="n">my_ruffus_logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s">'My_Ruffus_logger'</span><span class="p">)</span>
-<span class="n">my_ruffus_logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
-
-<span class="c"># Add the log message handler to the logger</span>
-<span class="n">handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">handlers</span><span class="o">.</span><span class="n">RotatingFileHandler</span><span class="p">(</span>
-              <span class="n">LOG_FILENAME</span><span class="p">,</span> <span class="n">maxBytes</span><span class="o">=</span><span class="mi">2000</span><span class="p">,</span> <span class="n">backupCount</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
-
-<span class="n">my_ruffus_logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">handler</span><span class="p">)</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="sd">"""Description: Create the file if it does not exists"""</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">],</span> <span class="p">[</span><span class="n">create_if_necessary</span><span class="p">],</span> <span class="n">logger</span><span class="o">=</span><span class="n">my_ruffus_logger</span><span class="p">)</span>
-<span class="k">print</span> <span class="nb">open</span><span class="p">(</span><span class="s">"/tmp/ruffus.log"</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>The contents of <tt class="docutils literal"><span class="pre">/tmp/ruffus.log</span></tt> are as specified:</dt>
-<dd><div class="first last highlight-python"><pre>Task = create_if_necessary
-    Description: Create the file if it does not exists
-    Job = [null -> "a.1"] completed</pre>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="your-own-logging-within-each-job">
-<span id="manual-logging-per-job"></span><h2>Your own logging <em>within</em> each job<a class="headerlink" href="#your-own-logging-within-each-job" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>It is often useful to log the messages from within each of your pipelined functions.</p>
-<p>However, each job runs in a separate process, and it is <em>not</em> a good
-idea to pass the logging object itself between jobs:</p>
-<ol class="arabic simple">
-<li>logging is not synchronised between processes</li>
-<li><a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> objects can not be
-<a class="reference external" href="http://docs.python.org/library/pickle.html">pickle</a>d and sent across processes</li>
-</ol>
-<p>The best thing to do is to have a centralised log and to have each job invoke the
-logging methods (e.g. <cite>debug</cite>, <cite>warning</cite>, <cite>info</cite> etc.) across the process boundaries in
-the centralised log.</p>
-<p>The <strong>Ruffus</strong> <a class="reference internal" href="../../proxy_logger.html#proxy-logger"><em>proxy_logger</em></a> module provides an easy way to share
-<a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> objects among
-jobs. This requires just two simple steps:</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last"><a class="reference internal" href="logging_code.html#manual-logging-code"><em>The full code</em></a> shows how this can be coded.</p>
-</div>
-</div></blockquote>
-<div class="section" id="set-up-log-from-config-file">
-<h3>1. Set up log from config file<a class="headerlink" href="#set-up-log-from-config-file" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus.proxy_logger</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="p">(</span><span class="n">logger_proxy</span><span class="p">,</span>
- <span class="n">logging_mutex</span><span class="p">)</span> <span class="o">=</span> <span class="n">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">setup_std_shared_logger</span><span class="p">,</span>
-                                                <span class="s">"my_logger"</span><span class="p">,</span>
-                                                <span class="p">{</span><span class="s">"file_name"</span> <span class="p">:</span><span class="s">"/my/lg.log"</span><span class="p">})</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="give-each-job-proxy-to-logger">
-<h3>2. Give each job proxy to logger<a class="headerlink" href="#give-each-job-proxy-to-logger" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Now, pass:</p>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">logger_proxy</span></tt> (which forwards logging calls across jobs) and</li>
-<li><tt class="docutils literal"><span class="pre">logging_mutex</span></tt> (which prevents different jobs which are logging simultaneously
-from being jumbled up)</li>
-</ul>
-</div></blockquote>
-<p>to each job:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">'a.1'</span><span class="p">,</span> <span class="n">logger_proxy</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task1</span><span class="p">(</span><span class="n">ignore_infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">logger_proxy</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Log within task</span>
-<span class="sd">    """</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Here we go"</span><span class="p">)</span>
-    <span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-        <span class="n">logger_proxy</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"Here we go logging"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 19</strong>: <cite>Logging progress through a pipeline</cite></a><ul>
-<li><a class="reference internal" href="#logging-task-job-completion">Logging task/job completion</a><ul>
-<li><a class="reference internal" href="#controlling-logging-verbosity">Controlling logging verbosity</a></li>
-<li><a class="reference internal" href="#using-your-own-logging">Using your own logging</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#your-own-logging-within-each-job">Your own logging <em>within</em> each job</a><ul>
-<li><a class="reference internal" href="#set-up-log-from-config-file">1. Set up log from config file</a></li>
-<li><a class="reference internal" href="#give-each-job-proxy-to-logger">2. Give each job proxy to logger</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="exceptions.html"
-                        title="previous chapter"><strong>Chapter 18</strong>: <cite>Exceptions thrown inside a pipeline</cite></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="files_re.html"
-                        title="next chapter"><strong>Chapter 20</strong>: <strong>@files_re</strong>: Deprecated <cite>syntax using regular expressions</cite></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/manual/logging.txt"
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-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
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-            
-  <div class="section" id="code-for-chapter-16-logging-progress-through-a-pipeline">
-<span id="manual-logging-code"></span><h1>Code for Chapter 16: Logging progress through a pipeline<a class="headerlink" href="#code-for-chapter-16-logging-progress-through-a-pipeline" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-<li><a class="reference internal" href="logging.html#manual-logging-per-job"><em>Back</em></a></li>
-</ul>
-<p>This example shows how to log messages from within each of your pipelined functions.</p>
-</div></blockquote>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.proxy_logger</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">logging</span>
-
-<span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span><span class="nn">os</span>
-<span class="c"># use simplejson in place of json for python < 2.6</span>
-<span class="k">try</span><span class="p">:</span>
-    <span class="kn">import</span> <span class="nn">json</span>
-<span class="k">except</span> <span class="ne">ImportError</span><span class="p">:</span>
-    <span class="kn">import</span> <span class="nn">simplejson</span>
-    <span class="n">json</span> <span class="o">=</span> <span class="n">simplejson</span>
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Shared logging</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="n">logger_args</span><span class="o">=</span><span class="p">{}</span>
-<span class="n">logger_args</span><span class="p">[</span><span class="s">"file_name"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"pipeline.log"</span>
-<span class="n">logger_args</span><span class="p">[</span><span class="s">"level"</span><span class="p">]</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span>
-<span class="n">logger_args</span><span class="p">[</span><span class="s">"rotating"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="n">logger_args</span><span class="p">[</span><span class="s">"maxBytes"</span><span class="p">]</span><span class="o">=</span><span class="mi">20000</span>
-<span class="n">logger_args</span><span class="p">[</span><span class="s">"backupCount"</span><span class="p">]</span><span class="o">=</span><span class="mi">10</span>
-<span class="n">logger_args</span><span class="p">[</span><span class="s">"formatter"</span><span class="p">]</span><span class="o">=</span><span class="s">"</span><span class="si">%(asctime)s</span><span class="s"> - </span><span class="si">%(name)s</span><span class="s"> - </span><span class="si">%(levelname)6s</span><span class="s"> - </span><span class="si">%(message)s</span><span class="s">"</span>
-
-<span class="p">(</span><span class="n">logger_proxy</span><span class="p">,</span>
- <span class="n">logging_mutex</span><span class="p">)</span> <span class="o">=</span> <span class="n">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">setup_std_shared_logger</span><span class="p">,</span>
-                                                <span class="s">"my_logger"</span><span class="p">,</span> <span class="n">logger_args</span><span class="p">)</span>
-
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Helper Function which writes to a shared log</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="kn">import</span> <span class="nn">time</span>
-<span class="k">def</span> <span class="nf">test_job_io</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    cat input files content to output files</span>
-<span class="sd">        after writing out job parameters</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c"># dump parameters</span>
-    <span class="n">params</span> <span class="o">=</span> <span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">)</span><span class="c"># + extra_params[0:-3]</span>
-    <span class="c">#</span>
-    <span class="n">logger_proxy</span><span class="p">,</span> <span class="n">logging_mutex</span> <span class="o">=</span> <span class="n">extra_params</span>
-    <span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-        <span class="n">logger_proxy</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">"job = </span><span class="si">%s</span><span class="s">, process name = </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span>
-                            <span class="p">(</span><span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">params</span><span class="p">),</span>
-                                <span class="n">multiprocessing</span><span class="o">.</span><span class="n">current_process</span><span class="p">()</span><span class="o">.</span><span class="n">name</span><span class="p">))</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'    job = </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">params</span><span class="p">))</span>
-    <span class="c">#</span>
-    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
-        <span class="n">infiles</span> <span class="o">=</span> <span class="p">[</span><span class="n">infiles</span><span class="p">]</span>
-    <span class="k">elif</span> <span class="n">infiles</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-        <span class="n">infiles</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">outfiles</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
-        <span class="n">outfiles</span> <span class="o">=</span> <span class="p">[</span><span class="n">outfiles</span><span class="p">]</span>
-    <span class="n">output_text</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">infiles</span><span class="p">:</span>
-        <span class="n">output_text</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">f</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
-    <span class="n">output_text</span> <span class="o">=</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">output_text</span><span class="p">))</span>
-    <span class="n">output_text</span> <span class="o">+=</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">infiles</span><span class="p">)</span> <span class="o">+</span> <span class="s">" -> "</span> <span class="o">+</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">outfiles</span><span class="p">)</span> <span class="o">+ [...]
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">outfiles</span><span class="p">:</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">output_text</span><span class="p">)</span>
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Tasks</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#</span>
-<span class="c">#    task1</span>
-<span class="c">#</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">'a.1'</span><span class="p">,</span> <span class="n">logger_proxy</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task1</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="o">*</span><span class="n">extra_params</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    First task</span>
-<span class="sd">    """</span>
-    <span class="n">test_job_io</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">)</span>
-
-
-
-<span class="c">#</span>
-<span class="c">#    task2</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">'.1'</span><span class="p">),</span> <span class="s">'.2'</span><span class="p">,</span> <span class="n">logger_proxy</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="o">*</span><span class="n">extra_params</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Second task</span>
-<span class="sd">    """</span>
-    <span class="n">test_job_io</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">)</span>
-
-
-
-<span class="c">#</span>
-<span class="c">#    task3</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task2</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">'.2'</span><span class="p">),</span> <span class="s">'.3'</span><span class="p">,</span> <span class="n">logger_proxy</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task3</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="o">*</span><span class="n">extra_params</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Third task</span>
-<span class="sd">    """</span>
-    <span class="n">test_job_io</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">)</span>
-
-
-
-<span class="c">#</span>
-<span class="c">#    task4</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">task3</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">'.3'</span><span class="p">),</span> <span class="s">'.4'</span><span class="p">,</span> <span class="n">logger_proxy</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task4</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="o">*</span><span class="n">extra_params</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Fourth task</span>
-<span class="sd">    """</span>
-    <span class="n">test_job_io</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Necessary to protect the "entry point" of the program under windows.</span>
-<span class="c">#       see: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">task4</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">logger</span> <span class="o">=</span> <span class="n">logger_proxy</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">task4</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">logger</span> <span class="o">=</span> <span class="n">logger_proxy</span><span class="p">)</span>
-<span class="go">    job = [null, "a.1"]</span>
-<span class="go">    job = ["a.1", "a.2"]</span>
-<span class="go">    job = ["a.2", "a.3"]</span>
-<span class="go">    job = ["a.3", "a.4"]</span>
-</pre></div>
-</div>
-<p>Pipeline.log will contain our unimaginative log messages:</p>
-<div class="highlight-python"><pre>2009-11-15 03:04:55,884 - my_logger -  DEBUG - job = [null, "a.1"], process name = PoolWorker-2
-2009-11-15 03:04:56,941 - my_logger -   INFO -     Job = [None -> a.1, <LoggingProxy>, <thread.lock>] completed
-2009-11-15 03:04:56,942 - my_logger -   INFO - Completed Task = task1
-2009-11-15 03:04:56,945 - my_logger -  DEBUG - job = ["a.1", "a.2"], process name = PoolWorker-4
-2009-11-15 03:04:57,962 - my_logger -   INFO -     Job = [a.1 -> a.2, <LoggingProxy>, <thread.lock>] completed
-2009-11-15 03:04:57,962 - my_logger -   INFO - Completed Task = task2
-2009-11-15 03:04:57,965 - my_logger -  DEBUG - job = ["a.2", "a.3"], process name = PoolWorker-3
-2009-11-15 03:04:59,009 - my_logger -   INFO -     Job = [a.2 -> a.3, <LoggingProxy>, <thread.lock>] completed
-2009-11-15 03:04:59,010 - my_logger -   INFO - Completed Task = task3
-2009-11-15 03:04:59,013 - my_logger -  DEBUG - job = ["a.3", "a.4"], process name = PoolWorker-5
-2009-11-15 03:05:00,024 - my_logger -   INFO -     Job = [a.3 -> a.4, <LoggingProxy>, <thread.lock>] completed
-2009-11-15 03:05:00,025 - my_logger -   INFO - Completed Task = task4</pre>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Chapter 16: Logging progress through a pipeline</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="dependencies_code.html"
-                        title="previous chapter">Code for Chapter 9: Checking dependencies to run tasks in order</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="onthefly_code.html"
-                        title="next chapter">Code for Chapter 10: Generating parameters on the fly</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-    Enter search terms or a module, class or function name.
-    </p>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
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-        </ul>
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
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-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-<span id="manual"></span><h1><strong>Ruffus</strong> Manual: Table of Contents:<a class="headerlink" href="#ruffus-manual-table-of-contents" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><p><a class="reference internal" href="manual_introduction.html#manual-introduction"><em>manual_introduction</em></a></p>
-<ol class="arabic simple">
-<li><a class="reference internal" href="follows.html#manual-follows"><em>follows</em></a></li>
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-<li><a class="reference internal" href="files.html#manual-files"><em>files</em></a></li>
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-<li><a class="reference internal" href="tracing_pipeline_parameters.html#manual-tracing-pipeline-parameters"><em>tracing_pipeline_parameters</em></a></li>
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-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
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-  <span class="target" id="manual-introduction"></span><div class="section" id="ruffus-manual">
-<span id="index-0"></span><h1><strong>Ruffus</strong> Manual<a class="headerlink" href="#ruffus-manual" title="Permalink to this headline">¶</a></h1>
-<div class="line-block">
-<div class="line">The chapters of this manual go through each of the features of <strong>Ruffus</strong> in turn.</div>
-<div class="line">Some of these (especially those labelled <strong>esoteric</strong> or <strong>deprecated</strong>) may not
-be of interest to all users of <strong>Ruffus</strong>.</div>
-</div>
-<p>If you are looking for a quick introduction to <strong>Ruffus</strong>, you may want to look at the
-<a class="reference internal" href="../simple_tutorial/simple_tutorial.html#simple-tutorial"><em>Simple Tutorial</em></a> first, some of which content is shared with,
-or elaborated on, by this manual.</p>
-<div class="section" id="introduction">
-<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <strong>Ruffus</strong> module is a lightweight way to run computational pipelines.</p>
-<p>Computational pipelines often become quite simple
-if we breakdown the process into simple stages.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Ruffus refers to each stage of your pipeline as a <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>.</p>
-</div>
-<div class="line-block">
-<div class="line">Let us start with the usual “Hello World”.</div>
-<div class="line">We have the following two python functions which
-we would like to turn into an automatic pipeline:</div>
-</div>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_hello_world.png" src="../../_images/simple_tutorial_hello_world.png" />
-</div></blockquote>
-<p>The simplest <strong>Ruffus</strong> pipeline would look like this:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_intro_follows.png" src="../../_images/simple_tutorial_intro_follows.png" />
-</div></blockquote>
-<p>The functions which do the actual work of each stage of the pipeline remain unchanged.
-The role of <strong>Ruffus</strong> is to make sure these functions are called in the right order,
-with the right parameters, running in parallel using multiprocessing if desired.</p>
-<p>There are three simple parts to building a <strong>ruffus</strong> pipeline</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>importing ruffus</li>
-<li>“Decorating” functions which are part of the pipeline</li>
-<li>Running the pipeline!</li>
-</ol>
-</div></blockquote>
-</div></blockquote>
-<span class="target" id="manual-introduction-import"></span></div>
-<div class="section" id="importing-ruffus">
-<span id="index-1"></span><h2>Importing ruffus<a class="headerlink" href="#importing-ruffus" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The most convenient way to use ruffus is to import the various names directly:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This will allow <strong>ruffus</strong> terms to be used directly in your code. This is also
-the style we have adopted for this manual.</p>
-<table border="1" class="docutils">
-<colgroup>
-<col width="50%" />
-<col width="50%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head stub">Category</th>
-<th class="head">Terms</th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><th class="stub"><em>Pipeline functions</em></th>
-<td><div class="first last highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout</span>
-<span class="n">pipeline_printout_graph</span>
-<span class="n">pipeline_run</span>
-<span class="n">register_cleanup</span>
-</pre></div>
-</div>
-</td>
-</tr>
-<tr class="row-odd"><th class="stub"><em>Decorators</em></th>
-<td><div class="first last highlight-python"><pre>@follows
- at files
- at split
- at transform
- at merge
- at collate
- at posttask
- at jobs_limit
- at parallel
- at check_if_uptodate
- at files_re</pre>
-</div>
-</td>
-</tr>
-<tr class="row-even"><th class="stub"><em>Loggers</em></th>
-<td><div class="first last highlight-python"><div class="highlight"><pre><span class="n">stderr_logger</span>
-<span class="n">black_hole_logger</span>
-</pre></div>
-</div>
-</td>
-</tr>
-<tr class="row-odd"><th class="stub"><em>Parameter disambiguating Indicators</em></th>
-<td><div class="first last highlight-python"><div class="highlight"><pre><span class="n">suffix</span>
-<span class="n">regex</span>
-<span class="n">inputs</span>
-<span class="n">touch_file</span>
-<span class="n">combine</span>
-<span class="n">mkdir</span>
-<span class="n">output_from</span>
-</pre></div>
-</div>
-</td>
-</tr>
-</tbody>
-</table>
-</div></blockquote>
-<dl class="docutils">
-<dt>If any of these clash with names in your code, you can use qualified names instead:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ruffus</span>
-
-<span class="n">ruffus</span><span class="o">.</span><span class="n">pipeline_printout</span><span class="p">(</span><span class="s">"..."</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div>
-<div class="section" id="decorating-functions">
-<span id="manual-introduction-decorators"></span><span id="index-2"></span><h2>“Decorating” functions<a class="headerlink" href="#decorating-functions" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>You need to tag or <a class="reference internal" href="../../glossary.html#term-decorator"><em class="xref std std-term">decorator</em></a> existing code to tell <strong>Ruffus</strong> that they are part
-of the pipeline.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><a class="reference internal" href="../../glossary.html#term-decorator"><em class="xref std std-term">decorator</em></a>s are ways to tag or mark out functions.</p>
-<p>They start with an <tt class="docutils literal"><span class="pre">@</span></tt> prefix and take a number of parameters in parenthesis.</p>
-<img alt="../../_images/simple_tutorial_decorator_syntax.png" class="last" src="../../_images/simple_tutorial_decorator_syntax.png" />
-</div>
-<p>The <strong>ruffus</strong> decorator <a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows</em></a> makes sure that
-<tt class="docutils literal"><span class="pre">second_task</span></tt> follows <tt class="docutils literal"><span class="pre">first_task</span></tt>.</p>
-<div class="line-block">
-<div class="line">Multiple <a class="reference internal" href="../../glossary.html#term-decorator"><em class="xref std std-term">decorator</em></a>s can be used for each <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function to add functionality
-to <em>Ruffus</em> pipeline functions.</div>
-<div class="line">However, the decorated python functions can still be
-called normally, outside of <em>Ruffus</em>.</div>
-<div class="line"><em>Ruffus</em> <a class="reference internal" href="../../glossary.html#term-decorator"><em class="xref std std-term">decorator</em></a>s can be added to (stacked on top of) any function in any order.</div>
-</div>
-<ul class="simple">
-<li><a class="reference internal" href="follows.html#manual-follows"><em>More on @follows in |manual.follows.chapter_num|</em></a></li>
-<li><a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows syntax in detail</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="running-the-pipeline">
-<span id="manual-introduction-running-pipeline"></span><span id="index-3"></span><h2>Running the pipeline<a class="headerlink" href="#running-the-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>We run the pipeline by specifying the <strong>last</strong> stage (<a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function) of your pipeline.
-Ruffus will know what other functions this depends on, following the appropriate chain of
-dependencies automatically, making sure that the entire pipeline is up-to-date.</p>
-<p>In our example above, because <tt class="docutils literal"><span class="pre">second_task</span></tt> depends on <tt class="docutils literal"><span class="pre">first_task</span></tt>, both functions are executed in order.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><strong>Ruffus</strong> by default prints out the <tt class="docutils literal"><span class="pre">verbose</span></tt> progress through your pipeline,
-interleaved with our <tt class="docutils literal"><span class="pre">Hello</span></tt> and <tt class="docutils literal"><span class="pre">World</span></tt>.</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_hello_world_output.png" src="../../_images/simple_tutorial_hello_world_output.png" />
-</div></blockquote>
-</div></blockquote>
-</div>
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-  <ul>
-<li><a class="reference internal" href="#"><strong>Ruffus</strong> Manual</a><ul>
-<li><a class="reference internal" href="#introduction">Introduction</a></li>
-<li><a class="reference internal" href="#importing-ruffus">Importing ruffus</a></li>
-<li><a class="reference internal" href="#decorating-functions">“Decorating” functions</a></li>
-<li><a class="reference internal" href="#running-the-pipeline">Running the pipeline</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="manual_contents.html"
-                        title="previous chapter"><strong>Ruffus</strong> Manual: Table of Contents:</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="follows.html"
-                        title="next chapter"><strong>Chapter  1</strong> : <cite>Arranging tasks into a pipeline with</cite> <strong>@follows</strong></a></p>
-  <h3>This Page</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
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-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
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-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-            
-  <div class="section" id="manual-merge-chapter-num-merge-multiple-input-into-a-single-result">
-<span id="manual-merge"></span><h1><strong>Chapter  9</strong>: <strong>Merge</strong> <cite>multiple input into a single result</cite><a class="headerlink" href="#manual-merge-chapter-num-merge-multiple-input-into-a-single-result" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> syntax in detail</li>
-</ul>
-</td></tr></table>
-<p>At the conclusion of our pipeline, or at key selected points, we might need a
-summary of our progress, gathering data from a multitude of files or disparate <em>inputs</em>,
-and summarised in the <em>output</em>  of a single <a class="reference internal" href="../../glossary.html#term-job"><em class="xref std std-term">job</em></a>.</p>
-<p><em>Ruffus</em> uses the <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> decorator for this purpose.</p>
-<p>Although, <strong>@merge</strong> tasks multiple <em>inputs</em> and produces a single <em>output</em>, <strong>Ruffus</strong>
-is again agnostic as to the sort of data contained within <em>output</em>. It can be a single
-(string) file name, or an arbitrary complicated nested structure with numbers, objects etc.
-As always, strings contained (even with nested sequences) within <em>output</em> will be treated
-as file names for the purpose of checking if the <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> is up-to-date.</p>
-</div></blockquote>
-<div class="section" id="merge">
-<span id="index-0"></span><h2><strong>@merge</strong><a class="headerlink" href="#merge" title="Permalink to this headline">¶</a></h2>
-<p>This example is borrowed from <a class="reference internal" href="../simple_tutorial/step6_transform.html#simple-tutorial-6th-step"><em>step 6</em></a> of the simple tutorial.</p>
-<blockquote>
-<div><div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last"><a class="reference internal" href="../simple_tutorial/step6_transform_code.html#simple-tutorial-6th-step-code"><em>Accompanying Python Code</em></a></p>
-</div>
-</div></blockquote>
-<div class="section" id="combining-partial-solutions-calculating-variances">
-<h3>Combining partial solutions: Calculating variances<a class="headerlink" href="#combining-partial-solutions-calculating-variances" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><table border="1" class="borderless docutils">
-<colgroup>
-<col width="1%" />
-<col width="99%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><p class="first centered">
-<strong>Step 6 from:</strong></p><img alt="../../_images/simple_tutorial_step5_sans_key.png" class="last" src="../../_images/simple_tutorial_step5_sans_key.png" />
-</td>
-<td><blockquote class="first last">
-<div><p>We wanted to calculate the sample variance of a large list of random numbers. We
-have seen previously how we can split up this large problem into small pieces
-(using <a class="reference internal" href="split.html#manual-split"><em>@split</em></a> in <strong>Chapter  7</strong>), and work out the
-partial solutions for each sub-problem (calculating sums with <a class="reference internal" href="transform.html#manual-transform"><em>@transform</em></a>
-in <strong>Chapter  8</strong> ).</p>
-<p>All that remains is to join up the partial solutions from the different <tt class="docutils literal"><span class="pre">.sums</span></tt> files
-and turn these into the variance as follows:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">variance</span> <span class="o">=</span> <span class="p">(</span><span class="n">sum_squared</span> <span class="o">-</span> <span class="nb">sum</span> <span class="o">*</span> <span class="nb">sum</span> <span class="o">/</span> <span class="n">N</span><span class="p">)</span><span class="o">/</span><span class="n">N</span>
-</pre></div>
-</div>
-<p>where <tt class="docutils literal"><span class="pre">N</span></tt> is the number of values</p>
-<p>See the <a class="reference external" href="http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance">wikipedia</a> entry for a discussion of
-why this is a very naive approach!</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-<p>To do this, all we have to do is go through all the values in <tt class="docutils literal"><span class="pre">*.sums</span></tt>, i.e.
-add up the <tt class="docutils literal"><span class="pre">sums</span></tt> and <tt class="docutils literal"><span class="pre">sum_squared</span></tt> for each chunk. We can then apply the above (naive) formula.</p>
-<dl class="docutils">
-<dt>Merging files is straightforward in <strong>Ruffus</strong>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nd">@merge</span><span class="p">(</span><span class="n">step_5_calculate_sum_of_squares</span><span class="p">,</span> <span class="s">"variance.result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_6_calculate_variance</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="c">#</span>
-    <span class="c">#   add together sums and sums of squares from each input_file_name</span>
-    <span class="c">#       calculate variance and write to output_file_name</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>The <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> decorator tells <em>Ruffus</em> to take all the files from the step 5 task (i.e. <tt class="docutils literal"><span class="pre">*.sums</span></tt>),
-and produced a merge file in the form of <tt class="docutils literal"><span class="pre">variance.result</span></tt>.</p>
-<dl class="docutils">
-<dt>Thus if <tt class="docutils literal"><span class="pre">step_5_calculate_sum_of_squares</span></tt> created</dt>
-<dd><div class="first last line-block">
-<div class="line"><tt class="docutils literal"><span class="pre">1.sums</span></tt> and</div>
-<div class="line"><tt class="docutils literal"><span class="pre">2.sums</span></tt> etc.</div>
-</div>
-</dd>
-</dl>
-<p>This would result in the following function call:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">step_6_calculate_variance</span> <span class="p">([</span><span class="s">"1.sums"</span><span class="p">,</span> <span class="s">"2.sums"</span><span class="p">],</span> <span class="s">"variance.result"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The final result is, of course, in <tt class="docutils literal"><span class="pre">variance.result</span></tt>.</p>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  9</strong>: <strong>Merge</strong> <cite>multiple input into a single result</cite></a><ul>
-<li><a class="reference internal" href="#merge"><strong>@merge</strong></a><ul>
-<li><a class="reference internal" href="#combining-partial-solutions-calculating-variances">Combining partial solutions: Calculating variances</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
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-  <div class="section" id="manual-on-the-fly-chapter-num-generating-parameters-on-the-fly-with-files">
-<span id="manual-on-the-fly"></span><h1><strong>Chapter 13</strong>: <cite>Generating parameters on the fly with</cite> <strong>@files</strong><a class="headerlink" href="#manual-on-the-fly-chapter-num-generating-parameters-on-the-fly-with-files" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files on-the-fly syntax in detail</em></a></li>
-</ul>
-</td></tr></table>
-<div class="line-block">
-<div class="line">Sometimes, it is necessary, or perhaps more convenient, to generate parameters on the fly or
-at runtime.</div>
-<div class="line">This  powerful ability to generate the exact parameters you need is
-sometimes worth the slight increase in complexity.</div>
-</div>
-</div></blockquote>
-<div class="section" id="files">
-<span id="index-0"></span><h2><strong>@files</strong><a class="headerlink" href="#files" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>To generate parameters on the fly, pass the decorator <strong>files</strong> with a <a class="reference internal" href="../../glossary.html#term-generator"><em class="xref std std-term">generator</em></a> function which
-yields one list / tuple of parameters per job. For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="k">def</span> <span class="nf">generate_parameters_on_the_fly</span><span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    returns one list of parameters per job</span>
-<span class="sd">    """</span>
-    <span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                        <span class="p">[</span><span class="s">'A.input'</span><span class="p">,</span> <span class="s">'A.output'</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)],</span> <span class="c"># 1st job</span>
-                        <span class="p">[</span><span class="s">'B.input'</span><span class="p">,</span> <span class="s">'B.output'</span><span class="p">,</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">)],</span> <span class="c"># 2nd job</span>
-                        <span class="p">[</span><span class="s">'C.input'</span><span class="p">,</span> <span class="s">'C.output'</span><span class="p">,</span> <span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">)],</span> <span class="c"># 3rd job</span>
-                    <span class="p">]</span>
-    <span class="k">for</span> <span class="n">job_parameters</span> <span class="ow">in</span> <span class="n">parameters</span><span class="p">:</span>
-        <span class="k">yield</span> <span class="n">job_parameters</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">generate_parameters_on_the_fly</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">pipeline_task</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">,</span> <span class="n">extra</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s"> + </span><span class="si">%d</span><span class="s"> => </span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">extra</span><span class="p">[</span><span class=" [...]
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">pipeline_task</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>Produces:</p>
-<div class="highlight-python"><pre>Task = parallel_task
-    1 + 2 = 3
-    Job = ["A", 1, 2] completed
-    3 + 4 = 7
-    Job = ["B", 3, 4] completed
-    5 + 6 = 11
-    Job = ["C", 5, 6] completed</pre>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Be aware that the parameter generating function may be invoked
-<a class="reference internal" href="dependencies.html#manual-dependencies-checking-multiple-times"><em>more than once</em></a>:</p>
-<blockquote class="last">
-<div><div class="line-block">
-<div class="line">The first time to check if this part of the pipeline is up-to-date.</div>
-<div class="line">The second time when the pipeline task function is run.</div>
-</div>
-</div></blockquote>
-</div>
-<p>The resulting <em>inputs</em>, <em>outputs</em> and any additional extra parameters per job are
-treated normally for the purposes of checking to see if jobs are up-to-date and
-need to be re-run.</p>
-</div></blockquote>
-</div>
-<div class="section" id="permutations-and-combinations">
-<h2>Permutations and Combinations<a class="headerlink" href="#permutations-and-combinations" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <a class="reference internal" href="onthefly_code.html#manual-on-the-fly-code"><em>accompanying example</em></a> provides a more realistic reason why
-you would want to generate parameters on the fly. It is a fun piece of code, which generates
-N x M combinations from two sets of files as the <em>inputs</em> of a pipeline stage.</p>
-<p>The <em>inputs</em> / <em>outputs</em> filenames are generated as a pair of nested for-loops to produce
-the N (outside loop) x M (inside loop) combinations, with the appropriate parameters
-for each job <tt class="docutils literal"><span class="pre">yield</span></tt>ed per iteration of the inner loop. The gist of this is:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   Step 1:</span>
-<span class="c">#</span>
-<span class="c">#        N x M jobs</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">generate_simulation_params</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    Custom function to generate</span>
-<span class="sd">    file names for gene/gwas simulation study</span>
-<span class="sd">    """</span>
-    <span class="k">for</span> <span class="n">sim_file</span> <span class="ow">in</span> <span class="n">get_simulation_files</span><span class="p">():</span>
-        <span class="k">for</span> <span class="p">(</span><span class="n">gene</span><span class="p">,</span> <span class="n">gwas</span><span class="p">)</span> <span class="ow">in</span> <span class="n">get_gene_gwas_file_pairs</span><span class="p">():</span>
-            <span class="n">result_file</span> <span class="o">=</span> <span class="s">"</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">.results"</span> <span class="o">%</span> <span class="p">(</span><span class="n">gene</span><span class="p">,</span> <span class="n">sim_file</span><span class="p">)</span>
-            <span class="k">yield</span> <span class="p">(</span><span class="n">gene</span><span class="p">,</span> <span class="n">gwas</span><span class="p">,</span> <span class="n">sim_file</span><span class="p">),</span> <span class="n">result_file</span>
-
-
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">generate_simulation_params</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">gwas_simulation</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="s">"..."</span>
-</pre></div>
-</div>
-<dl class="docutils">
-<dt>If <tt class="docutils literal"><span class="pre">get_gene_gwas_file_pairs()</span></tt> produces:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="p">[</span><span class="s">'a.sim'</span><span class="p">,</span> <span class="s">'b.sim'</span><span class="p">,</span> <span class="s">'c.sim'</span><span class="p">]</span>
-</pre></div>
-</div>
-</dd>
-<dt>and <tt class="docutils literal"><span class="pre">get_gene_gwas_file_pairs()</span></tt> produces:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="p">[(</span><span class="s">'1.gene'</span><span class="p">,</span> <span class="s">'1.gwas'</span><span class="p">),</span> <span class="p">(</span><span class="s">'2.gene'</span><span class="p">,</span> <span class="s">'2.gwas'</span><span class="p">)]</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>then we would end up with <tt class="docutils literal"><span class="pre">3</span></tt> x <tt class="docutils literal"><span class="pre">2</span></tt> = <tt class="docutils literal"><span class="pre">6</span></tt> jobs and the following equivalent function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'1.gene'</span><span class="p">,</span> <span class="s">'1.gwas'</span><span class="p">,</span> <span class="s">'a.sim'</span><span class="p">),</span> <span class="s">"1.gene.a.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'2.gene'</span><span class="p">,</span> <span class="s">'2.gwas'</span><span class="p">,</span> <span class="s">'a.sim'</span><span class="p">),</span> <span class="s">"2.gene.a.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'1.gene'</span><span class="p">,</span> <span class="s">'1.gwas'</span><span class="p">,</span> <span class="s">'b.sim'</span><span class="p">),</span> <span class="s">"1.gene.b.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'2.gene'</span><span class="p">,</span> <span class="s">'2.gwas'</span><span class="p">,</span> <span class="s">'b.sim'</span><span class="p">),</span> <span class="s">"2.gene.b.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'1.gene'</span><span class="p">,</span> <span class="s">'1.gwas'</span><span class="p">,</span> <span class="s">'c.sim'</span><span class="p">),</span> <span class="s">"1.gene.c.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'2.gene'</span><span class="p">,</span> <span class="s">'2.gwas'</span><span class="p">,</span> <span class="s">'c.sim'</span><span class="p">),</span> <span class="s">"2.gene.c.sim.results"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<p>The <a class="reference internal" href="onthefly_code.html#manual-on-the-fly-code"><em>accompanying code</em></a> looks slightly more complicated because
-of some extra bookkeeping.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 13</strong>: <cite>Generating parameters on the fly with</cite> <strong>@files</strong></a><ul>
-<li><a class="reference internal" href="#files"><strong>@files</strong></a></li>
-<li><a class="reference internal" href="#permutations-and-combinations">Permutations and Combinations</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="dependencies.html"
-                        title="previous chapter"><strong>Chapter 12</strong>: <cite>Checking dependencies to run tasks in order</cite></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="collate.html"
-                        title="next chapter"><strong>Chapter 14</strong>: <strong>@collate</strong>: <cite>group together disparate input into sets of results</cite></a></p>
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-  <div class="section" id="code-for-chapter-10-generating-parameters-on-the-fly">
-<span id="manual-on-the-fly-code"></span><h1>Code for Chapter 10: Generating parameters on the fly<a class="headerlink" href="#code-for-chapter-10-generating-parameters-on-the-fly" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files on-the-fly syntax in detail</em></a></li>
-<li><a class="reference internal" href="onthefly.html#manual-on-the-fly"><em>Back</em></a></li>
-</ul>
-<div class="line-block">
-<div class="line">This script takes N pairs of input file pairs (with the suffices .gene and .gwas)</div>
-<div class="line">and runs them against M sets of simulation data (with the suffix .simulation)</div>
-<div class="line">A summary per input file pair is then produced</div>
-</div>
-<p>In pseudo-code:</p>
-<blockquote>
-<div><p>STEP_1:</p>
-<div class="highlight-python"><pre>for n_file in NNN_pairs_of_input_files:
-    for m_file in MMM_simulation_data:
-
-        [n_file.gene,
-         n_file.gwas,
-         m_file.simulation] -> n_file.m_file.simulation_res</pre>
-</div>
-<p>STEP_2:</p>
-<div class="highlight-python"><pre>for n_file in NNN_pairs_of_input_files:
-
-    n_file.*.simulation_res -> n_file.mean</pre>
-</div>
-<div class="line-block">
-<div class="line">n = CNT_GENE_GWAS_FILES</div>
-<div class="line">m = CNT_SIMULATION_FILES</div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">os</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   constants</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="n">working_dir</span>             <span class="o">=</span> <span class="s">"temp_NxM"</span>
-<span class="n">simulation_data_dir</span>     <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation"</span><span class="p">)</span>
-<span class="n">gene_data_dir</span>           <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"gene"</span><span class="p">)</span>
-<span class="n">CNT_GENE_GWAS_FILES</span>     <span class="o">=</span> <span class="mi">2</span>
-<span class="n">CNT_SIMULATION_FILES</span>    <span class="o">=</span> <span class="mi">3</span>
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   imports</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
-<span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">izip</span>
-<span class="kn">import</span> <span class="nn">glob</span>
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Functions</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   get gene gwas file pairs</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">get_gene_gwas_file_pairs</span><span class="p">(</span>  <span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Helper function to get all *.gene, *.gwas from the direction specified</span>
-<span class="sd">        in --gene_data_dir</span>
-
-<span class="sd">    Returns</span>
-<span class="sd">        file pairs with both .gene and .gwas extensions,</span>
-<span class="sd">        corresponding roots (no extension) of each file</span>
-<span class="sd">    """</span>
-    <span class="n">gene_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gene"</span><span class="p">))</span>
-    <span class="n">gwas_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gwas"</span><span class="p">))</span>
-    <span class="c">#</span>
-    <span class="n">common_roots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o" [...]
-    <span class="n">common_roots</span> <span class="o">&=</span><span class="nb">set</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class [...]
-    <span class="n">common_roots</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">common_roots</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="n">p</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="p">;</span> <span class="n">g_dir</span> <span class="o">=</span> <span class="n">gene_data_dir</span>
-    <span class="n">file_pairs</span> <span class="o">=</span> <span class="p">[[</span><span class="n">p</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">g_dir</span><span class="p">,</span> <span class="n">x</span> <span class="o">+</span> <span class="s">".gene"</span><span class="p">),</span> <span class="n">p</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">g_dir</span><span cla [...]
-    <span class="k">return</span> <span class="n">file_pairs</span><span class="p">,</span> <span class="n">common_roots</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   get simulation files</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">get_simulation_files</span><span class="p">(</span>  <span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Helper function to get all *.simulation from the direction specified</span>
-<span class="sd">        in --simulation_data_dir</span>
-<span class="sd">        Returns</span>
-<span class="sd">            file with .simulation extensions,</span>
-<span class="sd">            corresponding roots (no extension) of each file</span>
-<span class="sd">    """</span>
-    <span class="n">simulation_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">,</span> <span class="s">"*.simulation"</span><span class="p">))</span>
-    <span class="n">simulation_roots</span> <span class="o">=</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class [...]
-    <span class="k">return</span> <span class="n">simulation_files</span><span class="p">,</span> <span class="n">simulation_roots</span>
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Main logic</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-
-
-
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   setup_simulation_data</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#</span>
-<span class="c"># mkdir: makes sure output directories exist before task</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">mkdir</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="n">simulation_data_dir</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">setup_simulation_data</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    create simulation files</span>
-<span class="sd">    """</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">CNT_GENE_GWAS_FILES</span><span class="p">):</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"</span><span class="si">%03d</span><span class="s">.gene"</span> <span class="o">%</span> <span class="n">i</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"</span><span class="si">%03d</span><span class="s">.gwas"</span> <span class="o">%</span> <span class="n">i</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c"># gene files without corresponding gwas and vice versa</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"orphan1.gene"</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"orphan2.gwas"</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"orphan3.gwas"</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">CNT_SIMULATION_FILES</span><span class="p">):</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">,</span> <span class="s">"</span><span class="si">%03d</span><span class="s">.simulation"</span> <span class="o">%</span> <span class="n">i</span><span class="p">),</span> <span class="s">"w"</span><span [...]
-
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   cleanup_simulation_data</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">try_rmdir</span> <span class="p">(</span><span class="n">d</span><span class="p">):</span>
-    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">d</span><span class="p">):</span>
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">os</span><span class="o">.</span><span class="n">rmdir</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
-        <span class="k">except</span> <span class="ne">OSError</span><span class="p">:</span>
-            <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Warning:</span><span class="se">\t</span><span class="si">%s</span><span class="s"> is not empty and will not be removed.</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="n">d</span><span class="p">)</span>
-
-
-
-<span class="k">def</span> <span class="nf">cleanup_simulation_data</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    cleanup files</span>
-<span class="sd">    """</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Cleanup working directory and simulation files.</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   cleanup gene and gwas files</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gene"</span><span class="p">)):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gwas"</span><span class="p">)):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="n">try_rmdir</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   cleanup simulation</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">,</span> <span class="s">"*.simulation"</span><span class="p">)):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="n">try_rmdir</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   cleanup working_dir</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation_results"</span><span class="p">,</span> <span class="s">&qu [...]
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="n">try_rmdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation_results"</span><span class="p">))</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"*.mean"</span><span class="p">)):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="n">try_rmdir</span><span class="p">(</span><span class="n">working_dir</span><span class="p">)</span>
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   Step 1:</span>
-<span class="c">#</span>
-<span class="c">#        for n_file in NNN_pairs_of_input_files:</span>
-<span class="c">#            for m_file in MMM_simulation_data:</span>
-<span class="c">#</span>
-<span class="c">#                [n_file.gene,</span>
-<span class="c">#                 n_file.gwas,</span>
-<span class="c">#                 m_file.simulation] -> working_dir/n_file.m_file.simulation_res</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">generate_simulation_params</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    Custom function to generate</span>
-<span class="sd">    file names for gene/gwas simulation study</span>
-<span class="sd">    """</span>
-    <span class="n">simulation_files</span><span class="p">,</span> <span class="n">simulation_file_roots</span>    <span class="o">=</span> <span class="n">get_simulation_files</span><span class="p">()</span>
-    <span class="n">gene_gwas_file_pairs</span><span class="p">,</span> <span class="n">gene_gwas_file_roots</span> <span class="o">=</span>  <span class="n">get_gene_gwas_file_pairs</span><span class="p">()</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">sim_file</span><span class="p">,</span> <span class="n">sim_file_root</span> <span class="ow">in</span> <span class="n">izip</span><span class="p">(</span><span class="n">simulation_files</span><span class="p">,</span> <span class="n">simulation_file_roots</span><span class="p">):</span>
-        <span class="k">for</span> <span class="p">(</span><span class="n">gene</span><span class="p">,</span> <span class="n">gwas</span><span class="p">),</span> <span class="n">gene_file_root</span> <span class="ow">in</span> <span class="n">izip</span><span class="p">(</span><span class="n">gene_gwas_file_pairs</span><span class="p">,</span> <span class="n">gene_gwas_file_roots</span><span class="p">):</span>
-            <span class="c">#</span>
-            <span class="n">result_file</span> <span class="o">=</span> <span class="s">"</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">.simulation_res"</span> <span class="o">%</span> <span class="p">(</span><span class="n">gene_file_root</span><span class="p">,</span> <span class="n">sim_file_root</span><span class="p">)</span>
-            <span class="n">result_file_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation_results"</span><span class="p">,</span> <span class="n">result_file</span><span class="p">)</span>
-            <span class="c">#</span>
-            <span class="k">yield</span> <span class="p">[</span><span class="n">gene</span><span class="p">,</span> <span class="n">gwas</span><span class="p">,</span> <span class="n">sim_file</span><span class="p">],</span> <span class="n">result_file_path</span><span class="p">,</span> <span class="n">gene_file_root</span><span class="p">,</span> <span class="n">sim_file_root</span><span class="p">,</span> <span class="n">result_file</span>
-
-
-
-<span class="c">#</span>
-<span class="c"># mkdir: makes sure output directories exist before task</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">mkdir</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation_results"</span><span class="p">)))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="n">generate_simulation_params</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">gwas_simulation</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">result_file_path</span><span class="p">,</span> <span class="n">gene_file_root</span><span class="p">,</span> <span class="n">sim_file_root</span><span class="p">,</span> <span class="n">result_file</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Dummy calculation of gene gwas vs simulation data</span>
-<span class="sd">    Normally runs in parallel on a computational cluster</span>
-<span class="sd">    """</span>
-    <span class="p">(</span><span class="n">gene_file</span><span class="p">,</span>
-    <span class="n">gwas_file</span><span class="p">,</span>
-    <span class="n">simulation_data_file</span><span class="p">)</span> <span class="o">=</span> <span class="n">input_files</span>
-    <span class="c">#</span>
-    <span class="n">simulation_res_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">result_file_path</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="n">simulation_res_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> + </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">gene_file_root</span><span class="p">,</span> <span class="n">sim_file_root</span><spa [...]
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   Step 2:</span>
-<span class="c">#</span>
-<span class="c">#       Statistical summary per gene/gwas file pair</span>
-<span class="c">#</span>
-<span class="c">#        for n_file in NNN_pairs_of_input_files:</span>
-<span class="c">#            working_dir/simulation_results/n.*.simulation_res</span>
-<span class="c">#               -> working_dir/n.mean</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-
-
-<span class="nd">@collate</span><span class="p">(</span><span class="n">gwas_simulation</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"simulation_results/(\d+).\d+.simulation_res"</span><span class="p">),</span> <span class="s">r"\1.mean"</span><span class="p">)</span>
-<span class="nd">@posttask</span><span class="p">(</span><span class="k">lambda</span> <span class="p">:</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">OK</span><span class="se">\n</span><span class="s">"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">statistical_summary</span> <span class="p">(</span><span class="n">result_files</span><span class="p">,</span> <span class="n">summary_file</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Simulate statistical summary</span>
-<span class="sd">    """</span>
-    <span class="n">summary_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">summary_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">result_files</span><span class="p">:</span>
-        <span class="n">summary_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">f</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
-
-
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">setup_simulation_data</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">statistical_summary</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-
-<span class="c"># uncomment to printout flowchar</span>
-<span class="c">#</span>
-<span class="c"># pipeline_printout(sys.stdout, [statistical_summary], verbose=2)</span>
-<span class="c"># graph_printout ("flowchart.jpg", "jpg", [statistical_summary])</span>
-<span class="c">#</span>
-
-<span class="n">cleanup_simulation_data</span> <span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">setup_simulation_data</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-<span class="go">    Make directories [temp_NxM/gene, temp_NxM/simulation] completed</span>
-<span class="go">Completed Task = setup_simulation_data_mkdir_1</span>
-<span class="go">    Job completed</span>
-<span class="go">Completed Task = setup_simulation_data</span>
-
-
-<span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">statistical_summary</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-<span class="go">    Make directories [temp_NxM, temp_NxM/simulation_results] completed</span>
-<span class="go">Completed Task = gwas_simulation_mkdir_1</span>
-<span class="go">    Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/000.simulation] -> temp_NxM/simulation_results/001.000.simulation_res, 001, 000, 001.000.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/000.simulation] -> temp_NxM/simulation_results/000.000.simulation_res, 000, 000, 000.000.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/001.simulation] -> temp_NxM/simulation_results/001.001.simulation_res, 001, 001, 001.001.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/001.simulation] -> temp_NxM/simulation_results/000.001.simulation_res, 000, 001, 000.001.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/002.simulation] -> temp_NxM/simulation_results/000.002.simulation_res, 000, 002, 000.002.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/002.simulation] -> temp_NxM/simulation_results/001.002.simulation_res, 001, 002, 001.002.simulation_res] completed</span>
-<span class="go">Completed Task = gwas_simulation</span>
-<span class="go">    Job = [[temp_NxM/simulation_results/000.000.simulation_res, temp_NxM/simulation_results/000.001.simulation_res, temp_NxM/simulation_results/000.002.simulation_res] -> temp_NxM/000.mean] completed</span>
-<span class="go">    Job = [[temp_NxM/simulation_results/001.000.simulation_res, temp_NxM/simulation_results/001.001.simulation_res, temp_NxM/simulation_results/001.002.simulation_res] -> temp_NxM/001.mean] completed</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Chapter 10: Generating parameters on the fly</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="logging_code.html"
-                        title="previous chapter">Code for Chapter 16: Logging progress through a pipeline</a></p>
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-  <div class="section" id="manual-parallel-chapter-num-esoteric-running-jobs-in-parallel-without-using-files-with-parallel">
-<span id="manual-parallel"></span><h1><strong>Chapter 16</strong>: <cite>Esoteric: Running jobs in parallel without using files with</cite> <strong>@parallel</strong><a class="headerlink" href="#manual-parallel-chapter-num-esoteric-running-jobs-in-parallel-without-using-files-with-parallel" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/parallel.html#decorators-parallel"><em>@parallel</em></a> syntax in detail</li>
-</ul>
-</td></tr></table>
-</div></blockquote>
-<div class="section" id="parallel">
-<span id="index-0"></span><h2><strong>@parallel</strong><a class="headerlink" href="#parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>@parallel</strong> supplies parameters for multiple <strong>jobs</strong> exactly like <a class="reference internal" href="files.html#manual-files"><em>@files</em></a> except that:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>The first two parameters are not treated like <em>inputs</em> and <em>ouputs</em> parameters,
-and strings are not assumed to be file names</li>
-<li>Thus no checking of whether each job is up-to-date is made using <em>inputs</em> and <em>outputs</em> files</li>
-<li>No expansions of <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns or <em>output</em> from previous tasks is carried out.</li>
-</ol>
-</div></blockquote>
-<p>This syntax is most useful when a pipeline stage does not involve creating or consuming any files, and
-you wish to forego the conveniences of <a class="reference internal" href="files.html#manual-files"><em>@files</em></a>, <a class="reference internal" href="transform.html#manual-transform"><em>@transform</em></a> etc.</p>
-<p>The following code performs some arithmetic in parallel:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">sys</span>
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                 <span class="p">[</span><span class="s">'A'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="c"># 1st job</span>
-                 <span class="p">[</span><span class="s">'B'</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="c"># 2nd job</span>
-                 <span class="p">[</span><span class="s">'C'</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span> <span class="c"># 3rd job</span>
-             <span class="p">]</span>
-<span class="nd">@parallel</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">parallel_task</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">param1</span><span class="p">,</span> <span class="n">param2</span><span class="p">):</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"    Parallel task </span><span class="si">%s</span><span class="s">: "</span> <span class="o">%</span> <span class="n">name</span><span class="p">)</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s"> + </span><span class="si">%d</span><span class="s"> = </span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">param1</span><span class="p">,</span> <span class="n" [...]
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_task</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>produces the following:</p>
-<div class="highlight-python"><pre>Task = parallel_task
-    Parallel task A: 1 + 2 = 3
-    Job = ["A", 1, 2] completed
-    Parallel task B: 3 + 4 = 7
-    Job = ["B", 3, 4] completed
-    Parallel task C: 5 + 6 = 11
-    Job = ["C", 5, 6] completed</pre>
-</div>
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-<li><a class="reference internal" href="#"><strong>Chapter 16</strong>: <cite>Esoteric: Running jobs in parallel without using files with</cite> <strong>@parallel</strong></a><ul>
-<li><a class="reference internal" href="#parallel"><strong>@parallel</strong></a></li>
-</ul>
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-  <p class="topless"><a href="advanced_transform.html"
-                        title="previous chapter"><strong>Chapter 15</strong>: <strong>add_inputs()</strong> <cite>and</cite> <strong>inputs()</strong>: <cite>Controlling both input and output files with</cite> <strong>@transform</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="check_if_uptodate.html"
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-  <div class="section" id="manual-multiprocessing-chapter-num-running-tasks-and-jobs-in-parallel">
-<span id="manual-multiprocessing"></span><h1><strong>Chapter  6</strong>: <cite>Running Tasks and Jobs in parallel</cite><a class="headerlink" href="#manual-multiprocessing-chapter-num-running-tasks-and-jobs-in-parallel" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-</ul>
-</td></tr></table>
-</div></blockquote>
-<div class="section" id="multi-processing">
-<h2>Multi Processing<a class="headerlink" href="#multi-processing" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><em>Ruffus</em> uses python <a class="reference external" href="http://docs.python.org/library/multiprocessing.html">multiprocessing</a> to run
-each job in a separate process.</p>
-<p>This means that jobs do <em>not</em> necessarily complete in the order of the defined parameters.
-Task hierachies are, of course, inviolate: upstream tasks run before downstream, dependent tasks.</p>
-<p>Tasks that are independent (i.e. do not precede each other) may be run in parallel as well.</p>
-<p>The number of concurrent jobs can be set in <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>If <tt class="docutils literal"><span class="pre">multiprocess</span></tt> is set to 1, then jobs will be run on a single process.</p>
-</div></blockquote>
-</div>
-<div class="section" id="data-sharing">
-<h2>Data sharing<a class="headerlink" href="#data-sharing" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Running jobs in separate processes allows <em>Ruffus</em> to make full use of the multiple
-processors in modern computers. However, some of the
-<a class="reference external" href="http://docs.python.org/library/multiprocessing.html#multiprocessing-programming">multiprocessing guidelines</a>
-should be borne in mind when writing <em>Ruffus</em> pipelines. In particular:</p>
-<ul class="simple">
-<li>Try not to pass large amounts of data between jobs, or at least be aware that this has to be marshalled
-across process boundaries.</li>
-<li>Only data which can be <a class="reference external" href="http://docs.python.org/library/pickle.html">pickled</a> can be passed as
-parameters to <em>Ruffus</em> task functions. Happily, that applies to almost any Python data type.
-The use of the rare, unpicklable object will cause python to complain (fail) loudly when <em>Ruffus</em> pipelines
-are run.</li>
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-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  6</strong>: <cite>Running Tasks and Jobs in parallel</cite></a><ul>
-<li><a class="reference internal" href="#multi-processing">Multi Processing</a></li>
-<li><a class="reference internal" href="#data-sharing">Data sharing</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="tracing_pipeline_parameters.html"
-                        title="previous chapter"><strong>Chapter  5</strong>: Tracing pipeline parameters</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="split.html"
-                        title="next chapter"><strong>Chapter  7</strong>: <cite>Splitting up large tasks / files with</cite> <strong>@split</strong></a></p>
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-            
-  <div class="section" id="manual-posttask-chapter-num-signal-the-completion-of-each-stage-of-our-pipeline-with-posttask">
-<span id="manual-posttask"></span><h1><strong>Chapter 10</strong>: <cite>Signal the completion of each stage of our pipeline with</cite> <strong>@posttask</strong><a class="headerlink" href="#manual-posttask-chapter-num-signal-the-completion-of-each-stage-of-our-pipeline-with-posttask" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> syntax in detail</li>
-</ul>
-</td></tr></table>
-<p>It is often useful to signal the completion of each task by specifying a specific
-action to be taken or function to be called. This can range from
-printing out some message, or <tt class="docutils literal"><span class="pre">touching</span></tt> some sentinel file,
-to emailing the author.This is particular useful if the <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> is a recipe apply to an unspecified number
-of parameters in parallel in different <a class="reference internal" href="../../glossary.html#term-job"><em class="xref std std-term">job</em></a>s. If the task is never run, or if it
-fails, needless-to-say no task completion action will happen.</p>
-<p><em>Ruffus</em> uses the <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> decorator for this purpose.</p>
-</div></blockquote>
-<div class="section" id="posttask">
-<span id="index-0"></span><h2><strong>@posttask</strong><a class="headerlink" href="#posttask" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>We can signal the completion of each task by specifying
-one or more function(s) using <tt class="docutils literal"><span class="pre">@posttask</span></tt></p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="k">def</span> <span class="nf">task_finished</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"hooray"</span>
-
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">task_finished</span><span class="p">)</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>This is such a short function, we might as well write it in-line:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@posttask</span><span class="p">(</span><span class="k">lambda</span><span class="p">:</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"hooray</span><span class="se">\n</span><span class="s">"</span><span class="p">))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The function(s) provided to <tt class="docutils literal"><span class="pre">@posttask</span></tt> will be called if the pipeline passes
-through a task, even if none of its jobs are run because they are up-to-date.
-This happens when a upstream task is out-of-date, and the execution passes through
-this point in the pipeline. See the example in <a class="reference internal" href="dependencies.html#manual-dependencies"><em>Chapter 9</em></a>
-of this manual.</p>
-</div>
-</div>
-<div class="section" id="touch-file">
-<span id="manual-posttask-touch-file"></span><span id="index-1"></span><h2><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-touch-file"><em>touch_file</em></a><a class="headerlink" href="#touch-file" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The most common way to note the completion of a task is to create some sort of
-“flag” file. Each stage in a traditional <tt class="docutils literal"><span class="pre">make</span></tt> pipeline would contain a
-<tt class="docutils literal"><span class="pre">touch</span> <span class="pre">completed.flag</span></tt>.</p>
-<p>This is so common that <strong>Ruffus</strong> provides a special shorthand called
-<a class="reference internal" href="../../decorators/indicator_objects.html#decorators-touch-file"><em>touch_file</em></a>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">touch_file</span><span class="p">(</span><span class="s">"task_completed.flag"</span><span class="p">))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="adding-several-post-task-actions">
-<h2>Adding several post task actions<a class="headerlink" href="#adding-several-post-task-actions" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>You can, of course, add more than one different action to be taken on completion of the
-task, either by stacking up as many <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> decorators
-as necessary, or by including several functions in the same <strong>@posttask</strong>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@posttask</span><span class="p">(</span><span class="n">print_hooray</span><span class="p">,</span> <span class="n">print_whoppee</span><span class="p">)</span>
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">print_hip_hip</span><span class="p">,</span> <span class="n">touch_file</span><span class="p">(</span><span class="s">"sentinel_flag"</span><span class="p">))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">your_pipeline_function</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 10</strong>: <cite>Signal the completion of each stage of our pipeline with</cite> <strong>@posttask</strong></a><ul>
-<li><a class="reference internal" href="#posttask"><strong>@posttask</strong></a></li>
-<li><a class="reference internal" href="#touch-file"><tt class="docutils literal"><span class="pre">touch_file</span></tt></a></li>
-<li><a class="reference internal" href="#adding-several-post-task-actions">Adding several post task actions</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="merge.html"
-                        title="previous chapter"><strong>Chapter  9</strong>: <strong>Merge</strong> <cite>multiple input into a single result</cite></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="jobs_limit.html"
-                        title="next chapter"><strong>Chapter 11</strong>: <cite>Manage concurrency for a specific task with</cite> <strong>@jobs_limit</strong></a></p>
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-            
-  <div class="section" id="manual-split-chapter-num-splitting-up-large-tasks-files-with-split">
-<span id="manual-split"></span><h1><strong>Chapter  7</strong>: <cite>Splitting up large tasks / files with</cite> <strong>@split</strong><a class="headerlink" href="#manual-split-chapter-num-splitting-up-large-tasks-files-with-split" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> syntax in detail</li>
-</ul>
-</td></tr></table>
-<p>A common requirement in computational pipelines is to split up a large task into
-small jobs which can be run on different processors, (or sent to a computational
-cluster). Very often, the number of jobs depends dynamically on the size of the
-task, and cannot be known for sure beforehand.</p>
-<p><em>Ruffus</em> uses the <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> decorator to indicate that
-the <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function will produce an indeterminate number of output files.</p>
-</div></blockquote>
-<div class="section" id="split">
-<span id="index-0"></span><h2><strong>@split</strong><a class="headerlink" href="#split" title="Permalink to this headline">¶</a></h2>
-<p>This example is borrowed from <a class="reference internal" href="../simple_tutorial/step5_split.html#simple-tutorial-5th-step"><em>step 4</em></a> of the simple tutorial.</p>
-<blockquote>
-<div><div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">See <a class="reference internal" href="../simple_tutorial/step5_split_code.html#simple-tutorial-5th-step-code"><em>accompanying Python Code</em></a></p>
-</div>
-</div></blockquote>
-<div class="section" id="splitting-up-a-long-list-of-random-numbers-to-calculate-their-variance">
-<h3>Splitting up a long list of random numbers to calculate their variance<a class="headerlink" href="#splitting-up-a-long-list-of-random-numbers-to-calculate-their-variance" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><table border="1" class="borderless docutils">
-<colgroup>
-<col width="1%" />
-<col width="99%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><p class="first centered">
-<strong>Step 5 from the tutorial:</strong></p><img alt="../../_images/simple_tutorial_step5_sans_key.png" class="last" src="../../_images/simple_tutorial_step5_sans_key.png" />
-</td>
-<td><blockquote class="first last">
-<div><p>Suppose we had a list of 100,000 random numbers in the file <tt class="docutils literal"><span class="pre">random_numbers.list</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">random</span>
-<span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'random_numbers.list'</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
-<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">NUMBER_OF_RANDOMS</span><span class="p">):</span>
-    <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="si">%g</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mf">100.0</span><span class="p">))</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>We might want to calculate the sample variance more quickly by splitting them
-into <tt class="docutils literal"><span class="pre">NNN</span></tt> parcels of 1000 numbers each and working on them in parallel.
-In this case we known that <tt class="docutils literal"><span class="pre">NNN</span> <span class="pre">==</span> <span class="pre">100</span></tt> but usually the number of resulting files
-is only apparent after we have finished processing our starting file.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-<p>Our pipeline function needs to take the random numbers file <tt class="docutils literal"><span class="pre">random_numbers.list</span></tt>,
-read the random numbers from it, and write to a new file every 100 lines.</p>
-<p>The <em>Ruffus</em> decorator <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> is designed specifically for
-splitting up <em>inputs</em> into an indeterminate <tt class="docutils literal"><span class="pre">NNN</span></tt> number of <em>outputs</em>:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_split.png" src="../../_images/simple_tutorial_split.png" />
-</div></blockquote>
-<p>Ruffus will set</p>
-<blockquote>
-<div><div class="line-block">
-<div class="line"><tt class="docutils literal"><span class="pre">input_file_name</span></tt> to <tt class="docutils literal"><span class="pre">"random_numbers.list"</span></tt></div>
-<div class="line"><tt class="docutils literal"><span class="pre">output_files</span></tt> to all files which match <tt class="docutils literal"><span class="pre">*.chunks</span></tt> (i.e. <tt class="docutils literal"><span class="pre">"1.chunks"</span></tt>, <tt class="docutils literal"><span class="pre">"2.chunks"</span></tt> etc.).</div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="output-files">
-<span id="manual-split-output-files"></span><h2>Output files<a class="headerlink" href="#output-files" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <em>output</em> (second) parameter of <strong>@split</strong> usually contains a
-<a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> pattern like the <tt class="docutils literal"><span class="pre">*.chunks</span></tt> above.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last"><strong>Ruffus</strong> is quite relaxed about the contents of the <tt class="docutils literal"><span class="pre">output</span></tt> parameter.
-Strings are treated as file names. Strings containing <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> pattern are expanded.
-Other types are passed verbatim to the decorated task function.</p>
-</div>
-<p>The files which match the <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> will be passed as the actual parameters to the job
-function. Thus, the first time you run the example code <tt class="docutils literal"><span class="pre">*.chunks</span></tt> will return an empty list because
-no <tt class="docutils literal"><span class="pre">.chunks</span></tt> files have been created, resulting in the following:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">step_4_split_numbers_into_chunks</span> <span class="p">(</span><span class="s">"random_numbers.list"</span><span class="p">,</span> <span class="p">[])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>After that <tt class="docutils literal"><span class="pre">*.chunks</span></tt> will match the list of current <tt class="docutils literal"><span class="pre">.chunks</span></tt> files created by
-the previous pipeline run.</p>
-<p>File names in <em>output</em> are generally out of date or superfluous. They are useful
-mainly for cleaning-up detritus from previous runs
-(have a look at <a class="reference internal" href="../simple_tutorial/step5_split_code.html#simple-tutorial-5th-step-code"><em>step_4_split_numbers_into_chunks(...)</em></a>).</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>It is important, nevertheless, to specify correctly the list of <em>output</em> files.
-Otherwise, dependent tasks will not know what files you have created, and it will
-not be possible automatically to chain together the <em>ouput</em> of this pipeline task into the
-<em>inputs</em> of the next step.</p>
-<p>You can specify multiple <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns to match <em>all</em> the files which are the
-result of the splitting task function. These can even cover different directories,
-or groups of file names. This is a more extreme example:</p>
-<blockquote class="last">
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="s">"input.file"</span><span class="p">,</span> <span class="p">[</span><span class="s">'a*.bits'</span><span class="p">,</span> <span class="s">'b*.pieces'</span><span class="p">,</span> <span class="s">'somewhere_else/c*.stuff'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">split_function</span> <span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="s">"Code to split up 'input.file'"</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<p>The actual resulting files of this task function are not constrained by the file names
-in the <em>output</em> parameter of the function. The whole point of <strong>@split</strong> is that number
-of resulting output files cannot be known beforehand, after all.</p>
-</div></blockquote>
-<div class="section" id="example">
-<h3>Example<a class="headerlink" href="#example" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><dl class="docutils">
-<dt>Suppose random_numbers.list can be split into four pieces, this function will create</dt>
-<dd><tt class="docutils literal"><span class="pre">1.chunks</span></tt>, <tt class="docutils literal"><span class="pre">2.chunks</span></tt>, <tt class="docutils literal"><span class="pre">3.chunks</span></tt>, <tt class="docutils literal"><span class="pre">4.chunks</span></tt></dd>
-</dl>
-<p>Subsequently, we receive a larger <tt class="docutils literal"><span class="pre">random_numbers.list</span></tt> which should be split into 10
-pieces. If the pipeline is called again, the task function receives the following parameters:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">step_4_split_numbers_into_chunks</span><span class="p">(</span><span class="s">"random_numbers.list"</span><span class="p">,</span>
-                                 <span class="p">[</span><span class="s">"1.chunks"</span><span class="p">,</span>               <span class="c">#   previously created files</span>
-                                  <span class="s">"2.chunks"</span><span class="p">,</span>               <span class="c">#</span>
-                                  <span class="s">"3.chunks"</span><span class="p">,</span>               <span class="c">#</span>
-                                  <span class="s">"4.chunks"</span> <span class="p">])</span>             <span class="c">#</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This doesn’t stop the function from creating the extra <tt class="docutils literal"><span class="pre">5.chunks</span></tt>, <tt class="docutils literal"><span class="pre">6.chunks</span></tt> etc.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Any tasks <strong>@follow</strong>ing and specifying
-<tt class="docutils literal"><span class="pre">step_4_split_numbers_into_chunks(...)</span></tt> as its <em>inputs</em> parameter is going to receive
-<tt class="docutils literal"><span class="pre">1.chunks</span></tt>, <tt class="docutils literal"><span class="pre">...</span></tt>, <tt class="docutils literal"><span class="pre">10.chunks</span></tt> and not merely the first four files.</p>
-<p class="last">In other words, dependent / down-stream tasks which obtain output files automatically
-from the task decorated by <strong>@split</strong> receive the most current file list.
-The <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns will be matched again to see exactly what files the task function
-has created in reality <em>after</em> the task completes.</p>
-</div>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  7</strong>: <cite>Splitting up large tasks / files with</cite> <strong>@split</strong></a><ul>
-<li><a class="reference internal" href="#split"><strong>@split</strong></a><ul>
-<li><a class="reference internal" href="#splitting-up-a-long-list-of-random-numbers-to-calculate-their-variance">Splitting up a long list of random numbers to calculate their variance</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#output-files">Output files</a><ul>
-<li><a class="reference internal" href="#example">Example</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="parallel_processing.html"
-                        title="previous chapter"><strong>Chapter  6</strong>: <cite>Running Tasks and Jobs in parallel</cite></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="transform.html"
-                        title="next chapter"><strong>Chapter  8</strong>: <cite>Applying the same recipe to create many different files with</cite> <strong>@transform</strong></a></p>
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-  <div class="section" id="manual-tasks-and-globs-in-inputs-chapter-num-chaining-pipeline-tasks-together-automatically">
-<span id="manual-tasks-and-globs-in-inputs"></span><h1><strong>Chapter  4</strong>: Chaining pipeline <cite>Tasks</cite> together automatically<a class="headerlink" href="#manual-tasks-and-globs-in-inputs-chapter-num-chaining-pipeline-tasks-together-automatically" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-<p id="index-0">In the previous chapter, we explained that <strong>ruffus</strong> determines the data flow through
-your pipeline by calling your <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> functions (normal python functions written
-by you) with the right parameters at the right time, making sure that</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>only out-of-date parts of the pipeline will be re-run</li>
-<li>multiple jobs can be run in parallel (on different processors if possible)</li>
-<li>pipeline stages can be chained together automatically</li>
-</ol>
-</div></blockquote>
-<p>This chapter is devoted to the last item: how the output of one stage of the pipeline
-is piped into as the input of the next stage.</p>
-</div></blockquote>
-<span class="target" id="manual-tasks-as-input"></span><div class="section" id="tasks-in-the-inputs-parameters-implicit-dependencies">
-<span id="index-1"></span><h2>Tasks in the <em>inputs</em> parameters: Implicit dependencies<a class="headerlink" href="#tasks-in-the-inputs-parameters-implicit-dependencies" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>Ruffus</strong> treats the first two parameters of each job in each task as the <em>inputs</em> and
-<em>outputs</em> parameters respectively. If the <em>inputs</em> parameter contains strings, these
-will be treated as the names of files required by that job.</p>
-<p>If the <em>inputs</em> parameter contains any <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>s, <strong>Ruffus</strong> will take the output
-from these specified tasks as part of the current <em>inputs</em> parameter. In addition,
-such tasks will be listed as prequisites, much as if you had included them in a
-separate <tt class="docutils literal"><span class="pre">@follows</span></tt> decorator.</p>
-<p>For example, supposed we wanted to take the output files from <tt class="docutils literal"><span class="pre">task1</span></tt> and feed
-them automatically to <tt class="docutils literal"><span class="pre">task2</span></tt>, we might write the following code</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">task1_ouput_files</span> <span class="o">=</span> <span class="p">(</span><span class="s">"task1.output_a"</span><span class="p">,</span> <span class="s">"task1.output_b"</span><span class="p">,</span> <span class="s">"task1.output_c"</span><span class="p">)</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">task1</span><span class="p">)</span>
-<span class="nd">@files</span><span class="p">(</span><span class="n">task1_ouput_files</span><span class="p">,</span> <span class="s">"task2.output"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This can be replaced by the much more concise syntax:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@files</span><span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="s">"task2.output"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>This means:</dt>
-<dd><ul class="first last simple">
-<li>Take the output from <tt class="docutils literal"><span class="pre">task1</span></tt>, and feed it automatically into <tt class="docutils literal"><span class="pre">task2</span></tt>.</li>
-<li>Also make sure that <tt class="docutils literal"><span class="pre">task2</span></tt> becomes a dependency of <tt class="docutils literal"><span class="pre">task1</span></tt>.</li>
-</ul>
-</dd>
-</dl>
-<p>In other words, <tt class="docutils literal"><span class="pre">task1</span></tt> and <tt class="docutils literal"><span class="pre">task2</span></tt> have been chained together automatically.
-This is both a great convenience and makes the flow of data through a pipeline much clearer.</p>
-</div></blockquote>
-</div>
-<div class="section" id="refering-to-tasks-by-name-in-the-inputs-parameters">
-<span id="manual-output-from"></span><span id="index-2"></span><h2>Refering to tasks by name in the <em>inputs</em> parameters<a class="headerlink" href="#refering-to-tasks-by-name-in-the-inputs-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="follows.html#manual-follows-out-of-order"><em>Chapter 1</em></a> explains that task functions can be
-defined in any order so long as undefined tasks are referred to by their (fully qualified if
-necessary) function name string.</p>
-<p>You can similarly refer to tasks in the <em>inputs</em> parameter by name, as a text string.
-Normally <strong>Ruffus</strong> assumes that strings are file names. To indicate that that
-you are referring to task function names instead, you need to
-wrap the relevant parameter or (nested) parts of the parameter with the indicator object
-<a class="reference internal" href="../../decorators/indicator_objects.html#decorators-output-from"><em>output_from(“task_name”)</em></a>. Thus,</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">([</span><span class="s">"a.file"</span><span class="p">,</span> <span class="p">(</span><span class="s">"b.file"</span><span class="p">,</span> <span class="n">output_from</span><span class="p">(</span><span class="s">"task1"</span><span class="p">,</span> <span class="mi">76</span><span class="p">,</span> <span class="s">"task2"</span><spa [...]
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>is equivalent to:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">([</span><span class="s">"a.file"</span><span class="p">,</span> <span class="p">(</span><span class="s">"b.file"</span><span class="p">,</span> <span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="mi">76</span><span class="p">,</span> <span class="n">task2</span><span class="p">))],</span> <span class="s">"*.split&quot [...]
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="globs-in-the-inputs-parameters">
-<span id="manual-globs-as-input"></span><span id="index-3"></span><h2>Globs in the <em>inputs</em> parameters<a class="headerlink" href="#globs-in-the-inputs-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>As a syntactic convenience, <strong>Ruffus</strong> also allows you to specify a
-<a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> pattern (e.g. <tt class="docutils literal"><span class="pre">*.txt</span></tt>) in the
-<em>input</em> parameter, it will be expanded automatically to the actually matching
-file names. This applies to any strings within <em>inputs</em> which contain the letters: <tt class="docutils literal"><span class="pre">*?[]</span></tt>.</div></blockquote>
-</div>
-<div class="section" id="mixing-globs-tasks-and-files-as-inputs">
-<span id="manual-mixing-tasks-globs-files"></span><span id="index-4"></span><h2>Mixing globs, tasks and files as <strong>inputs</strong><a class="headerlink" href="#mixing-globs-tasks-and-files-as-inputs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>Ruffus</strong> is very flexible in allowing you to mix
-<a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns, references to tasks and file names
-in the data structures you pass as the <strong>inputs</strong> parameters.</p>
-<p>Suppose, in the previous example,</p>
-<blockquote>
-<div><ul>
-<li><dl class="first docutils">
-<dt>that <tt class="docutils literal"><span class="pre">task1</span></tt> produces the files</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="s">"task1.output_a"</span>
-<span class="s">"task1.output_b"</span>
-<span class="s">"task1.output_c"</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</li>
-<li><dl class="first docutils">
-<dt>that the following additional files are also present</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="s">"extra.a"</span>
-<span class="s">"extra.c"</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</li>
-</ul>
-</div></blockquote>
-<p>Then,</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@files</span><span class="p">([</span><span class="s">"1_more.file"</span><span class="p">,</span> <span class="s">"2_more.file"</span><span class="p">,</span> <span class="n">task1</span><span class="p">,</span> <span class="s">"extra.*"</span><span class="p">],</span> <span class="s">"task2.output"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>would result in the combination of the specified file name, the expansion of the <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>,
-and the results from the previous task:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nb">input</span> <span class="o">==</span> <span class="p">[</span>
-            <span class="s">"1_more.file"</span>   <span class="p">,</span>           <span class="c"># specified file</span>
-            <span class="s">"2_more.file"</span>   <span class="p">,</span>           <span class="c"># specified file</span>
-            <span class="s">"task1.output_a"</span><span class="p">,</span>           <span class="c"># from previous task</span>
-            <span class="s">"task1.output_b"</span><span class="p">,</span>           <span class="c"># from previous task</span>
-            <span class="s">"task1.output_c"</span><span class="p">,</span>           <span class="c"># from previous task</span>
-            <span class="s">"extra.a"</span>       <span class="p">,</span>           <span class="c"># from glob expansion</span>
-            <span class="s">"extra.c"</span>       <span class="p">,</span>           <span class="c"># from glob expansion</span>
-         <span class="p">]</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>In other words, <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns and tasks are expanded “in place” when they are part of
-python lists, sets, or tuples.</p>
-</div></blockquote>
-</div>
-<div class="section" id="appending-globs-or-tasks-to-pre-existing-lists-sets-or-tuples">
-<span id="manual-appending-tasks-globs-to-lists-sets-tuples"></span><h2>Appending globs or tasks to pre-existing lists, sets or tuples<a class="headerlink" href="#appending-globs-or-tasks-to-pre-existing-lists-sets-or-tuples" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Sometimes we want to the <em>inputs</em> parameter to contain be a combination of <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>s and tasks,
-and an existing list of file names.</p>
-<p>To elaborate on the above example, suppose we have a list of files:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">file_list</span> <span class="o">=</span> <span class="p">[</span>   <span class="s">"1_more.file"</span><span class="p">,</span>
-                <span class="s">"2_more.file"</span><span class="p">]</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Now we want the input to <tt class="docutils literal"><span class="pre">task2</span></tt> to be:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">file_list</span> <span class="o">+</span> <span class="n">task1</span> <span class="o">+</span> <span class="s">"extra.*"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The closest that we can express this in python syntax is by turning task1 and the <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>
-to a list first then adding them together:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@files</span><span class="p">(</span><span class="n">file_list</span> <span class="o">+</span> <span class="p">[</span><span class="n">task1</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="s">"extra.*"</span><span class="p">],</span> <span class="s">"task2.output"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The same also works with tuples:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">file_list</span> <span class="o">=</span> <span class="p">(</span>   <span class="s">"1_more.file"</span><span class="p">,</span>
-                <span class="s">"2_more.file"</span><span class="p">)</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">file_list</span> <span class="o">+</span> <span class="p">(</span><span class="n">task1</span><span class="p">,</span> <span class="s">"extra.*"</span><span class="p">),</span> <span class="s">"task2.output"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>and sets (using the set concatenation operator):</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">file_list</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span>   <span class="s">"1_more.file"</span><span class="p">,</span>
-                    <span class="s">"2_more.file"</span><span class="p">])</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">file_list</span> <span class="o">|</span> <span class="nb">set</span><span class="p">([</span><span class="n">task1</span> <span class="o">+</span> <span class="s">"extra.*"</span><span class="p">]),</span> <span class="s">"task2.output"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task2</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="understanding-complex-inputs-and-outputs-parameters">
-<span id="manual-understanding-complex-inputs"></span><h2>Understanding complex <em>inputs</em> and <em>outputs</em> parameters<a class="headerlink" href="#understanding-complex-inputs-and-outputs-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>In all cases, <strong>Ruffus</strong> tries to do the right thing, and to make the simple or
-obvious case require the simplest, least onerous syntax.</p>
-<p>If sometimes <strong>Ruffus</strong> does not behave the way you expect, please write to the authors:
-it may be a bug!</p>
-<p>In all other cases, the best thing to do, is write your <strong>Ruffus</strong> specifications, and
-check the results of <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout</em></a>
-to make sure that your wishes are properly
-reflected in the parameters sent to your pipelined tasks.</p>
-<p>In other words, read the <a class="reference internal" href="tracing_pipeline_parameters.html#manual-tracing-pipeline-parameters"><em>next chapter</em></a>!</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  4</strong>: Chaining pipeline <cite>Tasks</cite> together automatically</a><ul>
-<li><a class="reference internal" href="#tasks-in-the-inputs-parameters-implicit-dependencies">Tasks in the <em>inputs</em> parameters: Implicit dependencies</a></li>
-<li><a class="reference internal" href="#refering-to-tasks-by-name-in-the-inputs-parameters">Refering to tasks by name in the <em>inputs</em> parameters</a></li>
-<li><a class="reference internal" href="#globs-in-the-inputs-parameters">Globs in the <em>inputs</em> parameters</a></li>
-<li><a class="reference internal" href="#mixing-globs-tasks-and-files-as-inputs">Mixing globs, tasks and files as <strong>inputs</strong></a></li>
-<li><a class="reference internal" href="#appending-globs-or-tasks-to-pre-existing-lists-sets-or-tuples">Appending globs or tasks to pre-existing lists, sets or tuples</a></li>
-<li><a class="reference internal" href="#understanding-complex-inputs-and-outputs-parameters">Understanding complex <em>inputs</em> and <em>outputs</em> parameters</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="files.html"
-                        title="previous chapter"><strong>Chapter  3</strong>: <cite>Passing parameters to the pipeline with</cite> <strong>@files</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="tracing_pipeline_parameters.html"
-                        title="next chapter"><strong>Chapter  5</strong>: Tracing pipeline parameters</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-            
-  <div class="section" id="manual-tasks-as-recipes-chapter-num-tasks-and-recipes">
-<span id="manual-tasks-as-recipes"></span><h1><strong>Chapter  2</strong>: <cite>Tasks and Recipes</cite><a class="headerlink" href="#manual-tasks-as-recipes-chapter-num-tasks-and-recipes" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-<div class="line-block" id="index-0">
-<div class="line">The python functions which do the actual work of each stage  or
-<a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> of a <strong>Ruffus</strong> pipeline are written by you.</div>
-<div class="line">The role of <strong>Ruffus</strong> is to make sure these functions are called in the right order,
-with the right parameters, running in parallel using multiprocessing if desired.</div>
-</div>
-<p><strong>Ruffus</strong> manages the data flowing through your pipeline by supplying the correct
-parameters to your pipeline functions. In this way, you will get the following features
-for free:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>only out-of-date parts of the pipeline will be re-run</li>
-<li>multiple jobs can be run in parallel (on different processors if possible)</li>
-<li>pipeline stages can be chained together automatically</li>
-</ol>
-</div></blockquote>
-<p>Much of the functionality of <strong>ruffus</strong> involves determining the data flow through
-your pipeline, by governing how the output of one stage of the pipeline is supplied
-as parameters to the functions of the next.</p>
-</div></blockquote>
-<div class="section" id="skip-jobs-which-are-up-to-date">
-<span id="manual-skip-up-to-date"></span><span id="index-1"></span><h2>Skip jobs which are up to date<a class="headerlink" href="#skip-jobs-which-are-up-to-date" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Very often it will necessary to re-run a computational pipeline, because part of the
-data has changed. <strong>Ruffus</strong> will run only those stages of the pipeline
-which are absolutely necessary.</p>
-<p>By default, <strong>Ruffus</strong> uses file modification times to see which parts of the pipeline
-are out of date, and which <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>s need to be run again. This is so convenient that
-even if a pipeline is not file-based (if it, for example, uses database tables instead),
-it may be worth while to use dummy, “sentinel” files to manage the stages of a pipeline.</p>
-<p>(It is also possible, as we shall
-see later, to add custom functions to determine which parts of the pipeline are out
-of date. see <a class="reference internal" href="../../decorators/parallel.html#decorators-parallel"><em>@parallel</em></a> and
-<a class="reference internal" href="../../decorators/check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate</em></a>.)</p>
-</div></blockquote>
-<span class="target" id="manual-io-parameters"><span id="index-2"></span></span></div>
-<div class="section" id="inputs-and-outputs-parameters">
-<span id="index-3"></span><h2><em>Inputs</em> and <em>Outputs</em> parameters<a class="headerlink" href="#inputs-and-outputs-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>Ruffus</strong> treats the first two parameters of each job in each task as the <em>inputs</em> and
-<em>outputs</em> parameters respectively. If these parameters are strings, or are sequences
-which contain strings, these will be treated as the names of files required by and
-produced by that job. The presence and modification times of the <em>inputs</em> and <em>outputs</em> files
-will be used to check if it is necessry to rerun the job.</p>
-<p>Apart from this, <strong>Ruffus</strong> imposes no other restrictions on the parameters for jobs, which
-are passed verbatim to task functions.</p>
-<p>Most of the time, it is sensible to stick with file names (strings) in the <em>inputs</em> and
-<em>outputs</em> parameters but <strong>Ruffus</strong> does not try to second-guess what sort of data you
-will be passing through your pipelines (except that strings represent file names).</p>
-<p>Thus, given the following over-elaborate parameters (parameter passing will be discussed in
-more detail from <a class="reference internal" href="files.html#manual-files"><em>|manual.files.chapter_num|</em></a>):</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="p">[</span>   <span class="p">[[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">],</span> <span class="s">"afile.name"</span><span class="p">,</span> <span class="p">(</span><span class="s">"bfile.name"</span><span class="p">,</span> <span class="mi">72</span><span class="p">)],</span>
-    <span class="p">[[</span><span class="mi">56</span><span class="p">,</span> <span class="mf">3.3</span><span class="p">],</span> <span class="nb">set</span><span class="p">(</span><span class="n">custom_object</span><span class="p">(),</span> <span class="s">"output.file"</span><span class="p">)],</span>
-    <span class="mf">33.3</span><span class="p">,</span>
-    <span class="s">"oops"</span><span class="p">]</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This will be passed <cite>“as is”</cite> to your task function:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">do_something</span><span class="p">([[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">],</span> <span class="s">"afile.name"</span><span class="p">,</span> <span class="p">(</span><span class="s">"bfile.name"</span><span class="p">,</span> <span class="mi">72</span><span class="p">)],</span>        <span class="c"># input</span>
-            <span class="p">[[</span><span class="mi">56</span><span class="p">,</span> <span class="mf">3.3</span><span class="p">],</span> <span class="nb">set</span><span class="p">(</span><span class="n">custom_object</span><span class="p">(),</span> <span class="s">"output.file"</span><span class="p">)],</span>   <span class="c"># output</span>
-            <span class="mf">33.3</span><span class="p">,</span>                                               <span class="c"># extra parameter</span>
-            <span class="s">"oops"</span><span class="p">)</span>                                             <span class="c"># extra parameter</span>
-</pre></div>
-</div>
-<p><strong>Ruffus</strong> will interprete this as:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">Input_parameter</span>   <span class="o">=</span> <span class="p">[[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">],</span> <span class="s">"afile.name"</span><span class="p">,</span> <span class="p">(</span><span class="s">"bfile.name"</span><span class="p">,</span> <span class="mi">72</span><span class="p">)]</span>
-<span class="n">Output_parameter</span>  <span class="o">=</span> <span class="p">[[</span><span class="mi">56</span><span class="p">,</span> <span class="mf">3.3</span><span class="p">],</span> <span class="nb">set</span><span class="p">(</span><span class="n">custom_object</span><span class="p">(),</span> <span class="s">"output.file"</span><span class="p">)]</span>
-<span class="n">Other_parameter_1</span> <span class="o">=</span> <span class="mf">33.3</span>
-<span class="n">Other_parameter_2</span> <span class="o">=</span> <span class="s">"oops"</span>
-</pre></div>
-</div>
-<p><strong>Ruffus</strong> disregards the <em>structure</em> of your data, only identifying the (nested) strings.
-Thus there are 2 input files:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="s">"afile.name"</span>
-<span class="s">"bfile.name"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>and 1 output file:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="s">"output.file"</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="checking-if-files-are-up-to-date">
-<span id="manual-skip-up-to-date-rules"></span><span id="index-4"></span><h2>Checking if files are up to date<a class="headerlink" href="#checking-if-files-are-up-to-date" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The following simple rules are used by <strong>Ruffus</strong>.</p>
-<ol class="arabic">
-<li><p class="first">The pipeline stage will be rerun if:</p>
-<blockquote>
-<div><ul class="simple">
-<li>If any of the <em>inputs</em> files are new (newer than the <em>output</em> files)</li>
-<li>If any of the <em>output</em> files are missing</li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">In addition, it is possible to run jobs which create files from scratch.</p>
-<blockquote>
-<div><ul class="simple">
-<li>If no <em>inputs</em> file names are supplied, the job will only run if any <em>output</em> file is missing.</li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">Finally, if no <em>outputs</em> file names are supplied, the job will always run.</p>
-</li>
-</ol>
-<p>The <a class="reference internal" href="files.html#manual-files-example"><em>example</em></a> in the next chapter shows how this works in practice.</p>
-</div></blockquote>
-</div>
-<div class="section" id="missing-files">
-<span id="index-5"></span><h2>Missing files<a class="headerlink" href="#missing-files" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If the <em>inputs</em> files for a job are missing, the task function will have no way
-to produce its <em>output</em>. In this case, a <tt class="docutils literal"><span class="pre">MissingInputFileError</span></tt> exception will be raised
-automatically. For example,</p>
-<blockquote>
-<div><div class="highlight-python"><pre>task.MissingInputFileError: No way to run job: Input file ['a.1'] does not exist
-for Job = ["a.1" -> "a.2", "A file"]</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="caveats-timestamp-resolution">
-<span id="index-6"></span><h2>Caveats: Timestamp resolution<a class="headerlink" href="#caveats-timestamp-resolution" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="line-block">
-<div class="line">Note that modification times have precision to the nearest second under some older file systems
-(ext2/ext3?). This may be also be true for networked file systems.</div>
-<div class="line"><strong>Ruffus</strong> is very conservative, and assumes that files with <em>exactly</em> the same date stamp might have been
-created in the wrong order, and will treat the job as out-of-date. This would result in some
-jobs re-running unnecessarily, simple because an underlying coarse-grained file system does not
-distinguish between successively created files with sufficiently accuracy.</div>
-</div>
-<p>To get around this, <strong>Ruffus</strong> makes sure that each task is punctuated by a 1 second pause
-(via <tt class="docutils literal"><span class="pre">time.sleep()</span></tt>). If this is gets in the way, and you are using a modern file system with
-nanosecond timestamp resolution, you can turn off the delay by setting
-<tt class="docutils literal"><span class="pre">one_second_per_job</span></tt> to <tt class="docutils literal"><span class="pre">False</span></tt> in <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a></p>
-<p>Later versions of <strong>Ruffus</strong> will allow file modification times to be saved at higher precision
-in a log file or database to get around this.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  2</strong>: <cite>Tasks and Recipes</cite></a><ul>
-<li><a class="reference internal" href="#skip-jobs-which-are-up-to-date">Skip jobs which are up to date</a></li>
-<li><a class="reference internal" href="#inputs-and-outputs-parameters"><em>Inputs</em> and <em>Outputs</em> parameters</a></li>
-<li><a class="reference internal" href="#checking-if-files-are-up-to-date">Checking if files are up to date</a></li>
-<li><a class="reference internal" href="#missing-files">Missing files</a></li>
-<li><a class="reference internal" href="#caveats-timestamp-resolution">Caveats: Timestamp resolution</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="follows.html"
-                        title="previous chapter"><strong>Chapter  1</strong> : <cite>Arranging tasks into a pipeline with</cite> <strong>@follows</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="files.html"
-                        title="next chapter"><strong>Chapter  3</strong>: <cite>Passing parameters to the pipeline with</cite> <strong>@files</strong></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/manual/tasks_as_recipes.txt"
-           rel="nofollow">Show Source</a></li>
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-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
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-            
-  <div class="section" id="manual-tracing-pipeline-parameters-chapter-num-tracing-pipeline-parameters">
-<span id="manual-tracing-pipeline-parameters"></span><h1><strong>Chapter  5</strong>: Tracing pipeline parameters<a class="headerlink" href="#manual-tracing-pipeline-parameters-chapter-num-tracing-pipeline-parameters" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-<p id="index-0">The trickiest part of developing pipelines is understanding how your
-data flows through the pipeline.</p>
-<p>In <strong>Ruffus</strong>, your data is passed from one task function to another down
-the pipeline by the chain of linked parameters. Sometimes, it may be difficult to
-choose the right <strong>Ruffus</strong> syntax at first, or to understand which parameters in
-what format are being passed to your function.</p>
-<p>Whether you are learning how to use <strong>ruffus</strong>, or trying out a new
-feature in <strong>ruffus</strong>, or just have a horrendously complicated pipeline
-to debug (we have colleagues with >100 criss-crossing pipelined stages),
-your best friend is <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a>.</p>
-<p><strong>pipeline_printout</strong> displays the parameters which would be passed to each task function
-for each job in your pipeline. In other words, it traces how each of the functions in
-the pipeline are called in detail.</p>
-<p>It makes good sense to alternate between calls to <strong>pipeline_printout</strong> and <strong>pipeline_run</strong>
-in the development of <strong>Ruffus</strong> pipelines (perhaps with the use of a command-line option),
-so that you always know exactly how the pipeline is being invoked.</p>
-</div></blockquote>
-<div class="section" id="printing-out-which-jobs-will-be-run">
-<h2>Printing out which jobs will be run<a class="headerlink" href="#printing-out-which-jobs-will-be-run" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>pipeline_printout</strong> is called in exactly the same way as <strong>pipeline_run</strong> but
-instead of running the pipeline, just prints the tasks which are and are not up-to-date.</p>
-<p>The <tt class="docutils literal"><span class="pre">verbose</span></tt> parameter controls how much detail is displayed.</p>
-<blockquote>
-<div><div class="highlight-python"><pre>verbose = 0 : prints nothing
-verbose = 1 : logs warnings and tasks which are not up-to-date and which will be run
-verbose = 2 : logs doc strings for task functions as well
-verbose = 3 : logs job parameters for jobs which are out-of-date
-verbose = 4 : logs list of up-to-date tasks but parameters for out-of-date jobs
-verbose = 5 : logs parameters for all jobs whether up-to-date or not
-verbose = 10: logs messages useful only for debugging ruffus pipeline code</pre>
-</div>
-</div></blockquote>
-<p>Let us take the two step <a class="reference internal" href="../simple_tutorial/step3_run_pipeline_code.html#simple-tutorial-3nd-step-code"><em>pipeline</em></a> from
-the tutorial. <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>Pipeline_printout(...)</em></a>
-by default merely lists the two tasks which will be run in the pipeline:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_pipeline_printout1.png" src="../../_images/simple_tutorial_pipeline_printout1.png" />
-</div></blockquote>
-<p>To see the input and output parameters of out-of-date jobs in the pipeline, we can increase the verbosity from the default (<tt class="docutils literal"><span class="pre">1</span></tt>) to <tt class="docutils literal"><span class="pre">3</span></tt>:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_pipeline_printout2.png" src="../../_images/simple_tutorial_pipeline_printout2.png" />
-</div></blockquote>
-<dl class="docutils">
-<dt>This is very useful for checking that the input and output parameters have been specified</dt>
-<dd>correctly.</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="determining-which-jobs-are-out-of-date-or-not">
-<h2>Determining which jobs are out-of-date or not<a class="headerlink" href="#determining-which-jobs-are-out-of-date-or-not" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>It is often useful to see which tasks are or are not up-to-date. For example, if we
-were to run the pipeline in full, and then modify one of the intermediate files, the
-pipeline would be partially out of date.</p>
-<p>Let us start by run the pipeline in full but then modify <tt class="docutils literal"><span class="pre">job1.stage</span></tt> so that the second task is no longer up-to-date:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-
-<span class="c"># modify job1.stage1</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"job1.stage1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>At a verbosity of <tt class="docutils literal"><span class="pre">5</span></tt>, even jobs which are up-to-date will be displayed.
-We can now see that the there is only one job in <tt class="docutils literal"><span class="pre">second_task(...)</span></tt> which needs to be re-run
-because <tt class="docutils literal"><span class="pre">job1.stage1</span></tt> has been modified after <tt class="docutils literal"><span class="pre">job1.stage2</span></tt> (highlighted in blue):</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_pipeline_printout3.png" src="../../_images/simple_tutorial_pipeline_printout3.png" />
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  5</strong>: Tracing pipeline parameters</a><ul>
-<li><a class="reference internal" href="#printing-out-which-jobs-will-be-run">Printing out which jobs will be run</a></li>
-<li><a class="reference internal" href="#determining-which-jobs-are-out-of-date-or-not">Determining which jobs are out-of-date or not</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="tasks_and_globs_in_inputs.html"
-                        title="previous chapter"><strong>Chapter  4</strong>: Chaining pipeline <cite>Tasks</cite> together automatically</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="parallel_processing.html"
-                        title="next chapter"><strong>Chapter  6</strong>: <cite>Running Tasks and Jobs in parallel</cite></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/manual/tracing_pipeline_parameters.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
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-    Enter search terms or a module, class or function name.
-    </p>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
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-  <div class="section" id="manual-transform-chapter-num-applying-the-same-recipe-to-create-many-different-files-with-transform">
-<span id="manual-transform"></span><h1><strong>Chapter  8</strong>: <cite>Applying the same recipe to create many different files with</cite> <strong>@transform</strong><a class="headerlink" href="#manual-transform-chapter-num-applying-the-same-recipe-to-create-many-different-files-with-transform" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><table class="hlist"><tr><td><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-</ul>
-</td><td><ul class="simple">
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> syntax in detail</li>
-</ul>
-</td></tr></table>
-<p>Sometimes you might have a list of data files which you might want to send to the
-same pipelined function, to apply
-the same operation. The best way to manage this would be to produce a corresponding
-list of results files:</p>
-<blockquote>
-<div><div class="line-block">
-<div class="line">Compiling c source files might <em>@transform</em> an <tt class="docutils literal"><span class="pre">a.c</span></tt> file to an <tt class="docutils literal"><span class="pre">a.o</span></tt> file.</div>
-<div class="line">A <tt class="docutils literal"><span class="pre">grep</span></tt> operation might <em>@transform</em> a <tt class="docutils literal"><span class="pre">plays.king_lear.txt</span></tt> file to an <tt class="docutils literal"><span class="pre">plays.king_lear.counts</span></tt> file.</div>
-</div>
-</div></blockquote>
-<p><em>Ruffus</em> uses the <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> decorator for this purpose.</p>
-<p>When you <strong>@transform</strong> your data from one file type to another, you are not restricted just
-to changing the file suffix. We shall see how, with the full power of regular
-expressions behind you, you can sort the resulting
-data into different directories, add indices and so on.</p>
-</div></blockquote>
-<div class="section" id="transform">
-<span id="index-0"></span><h2><strong>@transform</strong><a class="headerlink" href="#transform" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="worked-example-calculating-sums-and-sum-of-squares-in-parallel">
-<h3>Worked example: calculating sums and sum of squares in parallel<a class="headerlink" href="#worked-example-calculating-sums-and-sum-of-squares-in-parallel" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>This example is borrowed from <a class="reference internal" href="../simple_tutorial/step5_split.html#simple-tutorial-5th-step"><em>step 5</em></a> of the simple tutorial.</p>
-<blockquote>
-<div><div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">See <a class="reference internal" href="../simple_tutorial/step5_split_code.html#simple-tutorial-5th-step-code"><em>example code here</em></a></p>
-</div>
-</div></blockquote>
-<p>Given a set of files, each with a set of random numbers, we want to calculate thier
-sums and sum of squares. The easiest way to do this is by providing a recipe for
-transforming a <tt class="docutils literal"><span class="pre">*.chunk</span></tt> file containing a list of numbers into a <tt class="docutils literal"><span class="pre">*.sums</span></tt> file
-with our sums and sum of squares.</p>
-<p><em>Ruffus</em> magically takes care of applying the same recipe (task function) to all the different
-data files in parallel.</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_transform.png" src="../../_images/simple_tutorial_transform.png" />
-</div></blockquote>
-<p>The <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> decorator tells <em>Ruffus</em> to take files from the step 4 task (i.e. <tt class="docutils literal"><span class="pre">*.chunks</span></tt>),
-and produce files having the <tt class="docutils literal"><span class="pre">.sums</span></tt> suffix instead.
-ending.</p>
-<dl class="docutils">
-<dt>Thus if <tt class="docutils literal"><span class="pre">step_4_split_numbers_into_chunks</span></tt> created</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="s">"1.chunks"</span>
-<span class="s">"2.chunks"</span>
-<span class="s">"3.chunks"</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>This would result in the following function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">step_5_calculate_sum_of_squares</span> <span class="p">(</span><span class="s">"1.chunk"</span><span class="p">,</span> <span class="s">"1.sums"</span><span class="p">)</span>
-<span class="n">step_5_calculate_sum_of_squares</span> <span class="p">(</span><span class="s">"2.chunk"</span><span class="p">,</span> <span class="s">"2.sums"</span><span class="p">)</span>
-<span class="n">step_5_calculate_sum_of_squares</span> <span class="p">(</span><span class="s">"3.chunk"</span><span class="p">,</span> <span class="s">"3.sums"</span><span class="p">)</span>
-
-<span class="c"># etc...</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="using-suffix-to-change-give-each-output-file-a-new-suffix">
-<h2>Using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix(...)</em></a> to change give each output file a new suffix<a class="headerlink" href="#using-suffix-to-change-give-each-output-file-a-new-suffix" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix</em></a> specification indicates that</p>
-<blockquote>
-<div><ul class="simple">
-<li>only filenames with ending with the suffix term (e.g. <tt class="docutils literal"><span class="pre">.chunk</span></tt>) should be considered</li>
-<li>The text matching the suffix term should be replaced with the string in the output pattern.</li>
-</ul>
-</div></blockquote>
-<p>This example assumes that both the <em>inputs</em> and the <em>outputs</em> consist each of a single string but
-<strong>Ruffus</strong> places no such constraints on the data flowing through your pipeline.</p>
-<blockquote>
-<div><ul class="simple">
-<li>If there are multiple file names (strings) contained within each <em>inputs</em> parameter,
-then only the first will be used to generate the <em>output</em></li>
-<li>Each string that is encountered in each <em>output</em> parameter will be used for suffix replacement.</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="an-example-with-more-complex-data-structures">
-<h3>An example with more complex data structures<a class="headerlink" href="#an-example-with-more-complex-data-structures" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>This will become much clearer with this example:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>    inputs = [
-                    ["file1.ext", 10   ],               #job 1
-                    [37.0, "file2.wrong_extension",
-                           "file2_ignored.ext"],        #job 2
-                    "file3.ext"                         #job 3
-                    ]
-
- at transform(inputs, suffix(".ext"), [(".ext1", ), ".ext2"])
-def pipelinetask (input_file_name, output_file_name):
-    ""</pre>
-</div>
-</div></blockquote>
-<div class="line-block">
-<div class="line">Granted, it may seem rather odd that the <em>inputs</em> parameter including numbers as well
-as file names, but <strong>Ruffus</strong> does not second guess how you wish to arrange your pipelines.</div>
-<div class="line"><tt class="docutils literal"><span class="pre">inputs</span></tt> contains the parameters for three jobs.</div>
-<div class="line">In each case, the first file name string encountered will be used to generate the <em>output</em> parameter:</div>
-</div>
-<blockquote>
-<div><img alt="../../_images/manual_transform_complex_outputs.png" src="../../_images/manual_transform_complex_outputs.png" />
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The first filename in the prospective job #2 does not have the <tt class="docutils literal"><span class="pre">.ext</span></tt> suffix so this job will be eliminated.</p>
-</div>
-</div></blockquote>
-<p>Thus, the original code:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">inputs</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".ext"</span><span class="p">),</span> <span class="p">[(</span><span class="mi">15</span><span class="p">,</span> <span class="s">".ext1"</span><span class="p">),</span> <span class="s">".ext2"</span><span class="p">] [...]
-<span class="k">def</span> <span class="nf">pipelinetask</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>is equivalent to calling:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipelinetask</span><span class="p">([</span><span class="s">"file1.ext"</span><span class="p">,</span> <span class="mi">10</span><span class="p">],</span> <span class="p">[(</span><span class="mi">15</span><span class="p">,</span> <span class="s">'file1.ext1'</span><span class="p">),</span> <span class="s">'file1.ext2'</span><span class="p">])</span>  <span class="c"># job 1</span>
-<span class="n">pipelinetask</span><span class="p">(</span><span class="s">"file3.ext"</span><span class="p">,</span>       <span class="p">[(</span><span class="mi">15</span><span class="p">,</span> <span class="s">'file3.ext1'</span><span class="p">),</span> <span class="s">'file3.ext2'</span><span class="p">])</span>  <span class="c"># job 3</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Hopefully, your code will simpler than this rather pathological case!</p>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="regular-expressions-regex-provide-maximum-flexibility">
-<h2>Regular expressions <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex(...)</em></a> provide maximum flexibility<a class="headerlink" href="#regular-expressions-regex-provide-maximum-flexibility" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Exactly the same function could be written using regular expressions:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">inputs</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">".ext"</span><span class="p">),</span> <span class="p">[(</span><span class="mi">15</span><span class="p">,</span> <span class="s">".ext1"</span><span class="p">),</span> <span class="s">".ext2"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">pipelinetask</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="line-block">
-<div class="line">However, regular expressions are not limited to suffix matches.</div>
-<div class="line">We can sort our <em>ouputs</em> to different subdirectories, depending on category.</div>
-<div class="line"><br /></div>
-<div class="line">Our example starts off with data file for different zoo animals.</div>
-<div class="line">We are only interested in mammals, and we would like the files of each species to</div>
-<div class="line">end up in its own directory after processing.</div>
-<div class="line">Starting with these species files:</div>
-</div>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="s">"mammals.tiger.wild.animals"</span>
-<span class="s">"mammals.lion.wild.animals"</span>
-<span class="s">"mammals.lion.handreared.animals"</span>
-<span class="s">"mammals.dog.tame.animals"</span>
-<span class="s">"mammals.dog.wild.animals"</span>
-<span class="s">"reptiles.crocodile.wild.animals"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>Then, the following:</dt>
-<dd><img alt="../../_images/manual_transform.png" class="first last" src="../../_images/manual_transform.png" />
-</dd>
-<dt>will put each captured mammal in its own directory:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">capture_mammals</span><span class="p">])</span>
-<span class="go">    Job = [mammals.dog.tame.animals        -> dog/dog.tame.in_my_zoo, dog] completed</span>
-<span class="go">    Job = [mammals.dog.wild.animals        -> dog/dog.wild.in_my_zoo, dog] completed</span>
-<span class="go">    Job = [mammals.lion.handreared.animals -> lion/lion.handreared.in_my_zoo, lion] completed</span>
-<span class="go">    Job = [mammals.lion.wild.animals       -> lion/lion.wild.in_my_zoo, lion] completed</span>
-<span class="go">    Job = [mammals.tiger.wild.animals      -> tiger/tiger.wild.in_my_zoo, tiger] completed</span>
-<span class="go">Completed Task = capture_mammals</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The code can be found <a class="reference internal" href="transform_code.html#manual-transform-code"><em>here</em></a></p>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter  8</strong>: <cite>Applying the same recipe to create many different files with</cite> <strong>@transform</strong></a><ul>
-<li><a class="reference internal" href="#transform"><strong>@transform</strong></a><ul>
-<li><a class="reference internal" href="#worked-example-calculating-sums-and-sum-of-squares-in-parallel">Worked example: calculating sums and sum of squares in parallel</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#using-suffix-to-change-give-each-output-file-a-new-suffix">Using <tt class="docutils literal"><span class="pre">suffix(...)</span></tt> to change give each output file a new suffix</a><ul>
-<li><a class="reference internal" href="#an-example-with-more-complex-data-structures">An example with more complex data structures</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#regular-expressions-regex-provide-maximum-flexibility">Regular expressions <tt class="docutils literal"><span class="pre">regex(...)</span></tt> provide maximum flexibility</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="split.html"
-                        title="previous chapter"><strong>Chapter  7</strong>: <cite>Splitting up large tasks / files with</cite> <strong>@split</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="merge.html"
-                        title="next chapter"><strong>Chapter  9</strong>: <strong>Merge</strong> <cite>multiple input into a single result</cite></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/manual/transform.txt"
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-  <div class="section" id="code-for-chapter-6-applying-the-same-recipe-to-create-many-different-files">
-<span id="manual-transform-code"></span><h1>Code for Chapter 6: Applying the same recipe to create many different files<a class="headerlink" href="#code-for-chapter-6-applying-the-same-recipe-to-create-many-different-files" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#manual"><em>Manual overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform syntax in detail</em></a></li>
-<li><a class="reference internal" href="transform.html#manual-transform"><em>Back</em></a></li>
-</ul>
-<div class="line-block">
-<div class="line">Our example starts off with data file for different zoo animals.</div>
-<div class="line">We are only interested in mammals, and we would like the files of each species to</div>
-<div class="line">end up in its own directory after processing.</div>
-</div>
-</div></blockquote>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   Start with species files</span>
-<span class="c">#</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"mammals.tiger.wild.animals"</span>     <span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"mammals.lion.wild.animals"</span>      <span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"mammals.lion.handreared.animals"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"mammals.dog.tame.animals"</span>       <span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"mammals.dog.wild.animals"</span>       <span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"reptiles.crocodile.wild.animals"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   create destinations for each species</span>
-<span class="c">#</span>
-<span class="kn">import</span> <span class="nn">os</span>
-<span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="p">(</span><span class="s">"tiger"</span><span class="p">,</span> <span class="s">"lion"</span><span class="p">,</span> <span class="s">"dog"</span><span class="p">):</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">s</span><span class="p">):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Now summarise files in directories organised by species</span>
-<span class="c">#</span>
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="s">'*.animals'</span><span class="p">,</span>
-            <span class="n">regex</span><span class="p">(</span><span class="s">r'mammals\.(.+)\.(.+)\.animals'</span><span class="p">),</span> <span class="c"># save species and wild/tame</span>
-            <span class="s">r'\1/\1.\2.in_my_zoo'</span><span class="p">,</span>                  <span class="c"># same species go together</span>
-            <span class="s">r'\1'</span><span class="p">)</span>                                  <span class="c"># extra species name</span>
-<span class="k">def</span> <span class="nf">capture_mammals</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span> <span class="o">+</span> <span class="s">"</span><span cla [...]
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">capture_mammals</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">capture_mammals</span><span class="p">])</span>
-<span class="go">    Job = [mammals.dog.tame.animals        -> dog/dog.tame.in_my_zoo, dog] completed</span>
-<span class="go">    Job = [mammals.dog.wild.animals        -> dog/dog.wild.in_my_zoo, dog] completed</span>
-<span class="go">    Job = [mammals.lion.handreared.animals -> lion/lion.handreared.in_my_zoo, lion] completed</span>
-<span class="go">    Job = [mammals.lion.wild.animals       -> lion/lion.wild.in_my_zoo, lion] completed</span>
-<span class="go">    Job = [mammals.tiger.wild.animals      -> tiger/tiger.wild.in_my_zoo, tiger] completed</span>
-<span class="go">Completed Task = capture_mammals</span>
-</pre></div>
-</div>
-</div></blockquote>
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-            
-  <div class="section" id="new-manual-active-if-chapter-num-turning-parts-of-the-pipeline-on-and-off-at-runtime-with-active-if">
-<span id="new-manual-active-if"></span><span id="index-0"></span><h1><strong>Chapter 18</strong>: Turning parts of the pipeline on and off at runtime with <a class="reference internal" href="../../decorators/active_if.html#decorators-active-if"><em>@active_if</em></a><a class="headerlink" href="#new-manual-active-if-chapter-num-turning-parts-of-the-pipeline-on-and-off-at-runtime-with-active-if" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/active_if.html#decorators-active-if"><em>@active_if syntax in detail</em></a></li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>It is sometimes useful to be able to switch on and off parts of a pipeline. For example, a pipeline
-might have two difference code paths depending on the type of data it is being asked to analyse.</p>
-<p>One surprisingly easy way to do this is to use a python <tt class="docutils literal"><span class="pre">if</span></tt> statement around particular task functions:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre> <span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="hll"> <span class="n">run_task1</span> <span class="o">=</span> <span class="bp">True</span>
-</span>
-<span class="hll"> <span class="nd">@originate</span><span class="p">([</span><span class="s">'a.foo'</span><span class="p">,</span> <span class="s">'b.foo'</span><span class="p">])</span>
-</span> <span class="k">def</span> <span class="nf">create_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-     <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
- <span class="k">if</span> <span class="n">run_task1</span><span class="p">:</span>
-     <span class="c"># might not run</span>
-     <span class="nd">@transform</span><span class="p">(</span><span class="n">create_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".foo"</span><span class="p">),</span> <span class="s">".bar"</span><span class="p">)</span>
-     <span class="k">def</span> <span class="nf">foobar</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-         <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
- <span class="nd">@transform</span><span class="p">(</span><span class="n">foobar</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".bar"</span><span class="p">),</span> <span class="s">".result"</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">wrap_up</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-         <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
- <span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>This simple solution has a number of drawbacks:</dt>
-<dd><ol class="first last arabic simple">
-<li>The on/off decision is a one off event that happens when the script is loaded. Ideally, we
-would like some flexibility, and postpone the decision until <tt class="docutils literal"><span class="pre">pipeline_run()</span></tt> is invoked.</li>
-<li>When <tt class="docutils literal"><span class="pre">if</span></tt> is false, the entire task function becomes invisible, and if there are any
-downstream tasks, as in the above example, <em>Ruffus</em> will complain loudly about
-missing dependencies.</li>
-</ol>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="active-if-controls-the-state-of-tasks">
-<h2><a class="reference internal" href="../../decorators/active_if.html#decorators-active-if"><em>@active_if</em></a>  controls the state of tasks<a class="headerlink" href="#active-if-controls-the-state-of-tasks" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>Switches tasks on and off at run time depending on its parameters</li>
-<li>Evaluated each time <tt class="docutils literal"><span class="pre">pipeline_run</span></tt>, <tt class="docutils literal"><span class="pre">pipeline_printout</span></tt> or <tt class="docutils literal"><span class="pre">pipeline_printout_graph</span></tt> is called.</li>
-<li>Dormant tasks behave as if they are up to date and have no output.</li>
-</ul>
-<p>The Design and initial implementation were contributed by Jacob Biesinger</p>
-<p>The following example shows its flexibility and syntax:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">run_if_true_1</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="n">run_if_true_2</span> <span class="o">=</span> <span class="bp">False</span>
-<span class="n">run_if_true_3</span> <span class="o">=</span> <span class="bp">True</span>
-
-
-<span class="c">#</span>
-<span class="c">#    task1</span>
-<span class="c">#</span>
-<span class="nd">@originate</span><span class="p">([</span><span class="s">'a.foo'</span><span class="p">,</span> <span class="s">'b.foo'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_files</span><span class="p">(</span><span class="n">outfile</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    create_files</span>
-<span class="sd">    """</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">outfile</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   Only runs if all three run_if_true conditions are met</span>
-<span class="c">#</span>
-<span class="hll"><span class="c">#   @active_if determines if task is active</span>
-</span><span class="nd">@active_if</span><span class="p">(</span><span class="n">run_if_true_1</span><span class="p">,</span> <span class="k">lambda</span><span class="p">:</span> <span class="n">run_if_true_2</span><span class="p">)</span>
-<span class="nd">@active_if</span><span class="p">(</span><span class="n">run_if_true_3</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".foo"</span><span class="p">),</span> <span class="s">".bar"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">this_task_might_be_inactive</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">infile</span> [...]
-
-
-<span class="c"># @active_if switches off task because run_if_true_2 == False</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="c"># @active_if switches on task because all run_if_true conditions are met</span>
-<span class="n">run_if_true_2</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The task starts off inactive:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="hll"><span class="gp">>>> </span><span class="c"># @active_if switches off task "this_task_might_be_inactive" because run_if_true_2 == False</span>
-</span><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="go">Task enters queue = create_files</span>
-<span class="go">create_files</span>
-<span class="go">    Job  = [None -> a.foo] Missing file [a.foo]</span>
-<span class="go">    Job  = [None -> b.foo] Missing file [b.foo]</span>
-<span class="go">    Job  = [None -> a.foo] completed</span>
-<span class="go">    Job  = [None -> b.foo] completed</span>
-<span class="go">Completed Task = create_files</span>
-<span class="go">Inactive Task = this_task_might_be_inactive</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Now turn on the task:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="hll"><span class="gp">>>> </span><span class="c"># @active_if switches on task "this_task_might_be_inactive" because all run_if_true conditions are met</span>
-</span><span class="gp">>>> </span><span class="n">run_if_true_2</span> <span class="o">=</span> <span class="bp">True</span>
-<span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-
-<span class="go">Task enters queue = this_task_might_be_inactive</span>
-
-<span class="go">    Job  = [a.foo -> a.bar] Missing file [a.bar]</span>
-<span class="go">    Job  = [b.foo -> b.bar] Missing file [b.bar]</span>
-<span class="go">    Job  = [a.foo -> a.bar] completed</span>
-<span class="go">    Job  = [b.foo -> b.bar] completed</span>
-<span class="go">Completed Task = this_task_might_be_inactive</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
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-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 18</strong>: Turning parts of the pipeline on and off at runtime with <tt class="docutils literal"><span class="pre">@active_if</span></tt></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#active-if-controls-the-state-of-tasks"><tt class="docutils literal"><span class="pre">@active_if</span></tt>  controls the state of tasks</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="combinatorics.html"
-                        title="previous chapter"><strong>Chapter 17</strong>: <tt class="docutils literal"><span class="pre">@combinations</span></tt>, <tt class="docutils literal"><span class="pre">@permutations</span></tt> and all versus all <tt class="docutils literal"><span class="pre">@product</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="posttask.html"
-                        title="next chapter"><strong>Chapter 19</strong>: Signal the completion of each stage of our pipeline with <tt class="docutils literal"><span class="pre">@posttask</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/active_if.txt"
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-    Enter search terms or a module, class or function name.
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            
-  <div class="section" id="new-manual-check-if-uptodate-chapter-num-esoteric-writing-custom-functions-to-decide-which-jobs-are-up-to-date-with-check-if-uptodate">
-<span id="new-manual-check-if-uptodate"></span><span id="index-0"></span><h1><strong>Chapter 23</strong>: Esoteric: Writing custom functions to decide which jobs are up to date with <a class="reference internal" href="../../decorators/check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate</em></a><a class="headerlink" href="#new-manual-check-if-uptodate-chapter-num-esoteric-writing-custom-functions-to-decide-which-jobs-are-up-to-date-with-check-if-uptodate" title [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate  syntax in detail</em></a></li>
-</ul>
-</div>
-<div class="section" id="check-if-uptodate-manual-dependency-checking">
-<h2><strong>@check_if_uptodate</strong> : Manual dependency checking<a class="headerlink" href="#check-if-uptodate-manual-dependency-checking" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt>tasks specified with most decorators such as</dt>
-<dd><ul class="first last simple">
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a></li>
-<li><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a></li>
-<li><a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a></li>
-<li><a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@collate</em></a></li>
-</ul>
-</dd>
-</dl>
-<p>have automatic dependency checking based on file modification times.</p>
-<p>Sometimes, you might want to decide have more control over whether to run jobs, especially
-if a task does not rely on or produce files (i.e. with <a class="reference internal" href="../../decorators/parallel.html#decorators-parallel"><em>@parallel</em></a>)</p>
-<p>You can write your own custom function to decide whether to run a job.
-This takes as many parameters as your task function, and needs to return a
-tuple for whether an update is required, and why (i.e. <tt class="docutils literal"><span class="pre">tuple(bool,</span> <span class="pre">str)</span></tt>)</p>
-<p>This simple example which creates the file <tt class="docutils literal"><span class="pre">"a.1"</span></tt> if it does not exist:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="nd">@originate</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>could be rewritten more laboriously as:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">os</span>
-<span class="k">def</span> <span class="nf">check_file_exists</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-        <span class="k">return</span> <span class="bp">False</span><span class="p">,</span> <span class="s">"File already exists"</span>
-    <span class="k">return</span> <span class="bp">True</span><span class="p">,</span> <span class="s">"</span><span class="si">%s</span><span class="s"> is missing"</span> <span class="o">%</span> <span class="n">output_file</span>
-
-<span class="nd">@parallel</span><span class="p">([[</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">]])</span>
-<span class="nd">@check_if_uptodate</span><span class="p">(</span><span class="n">check_file_exists</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>Both produce the same output:</dt>
-<dd><div class="first last highlight-python"><pre>Task = create_if_necessary
-    Job = [null, "a.1"] completed</pre>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>The function specified by <a class="reference internal" href="../../decorators/check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate</em></a> can be called
-more than once for each job.</p>
-<p class="last">See the <a class="reference internal" href="dependencies.html#new-manual-dependencies"><em>description here</em></a> of how <em>Ruffus</em> decides which tasks to run.</p>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
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-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 23</strong>: Esoteric: Writing custom functions to decide which jobs are up to date with <tt class="docutils literal"><span class="pre">@check_if_uptodate</span></tt></a><ul>
-<li><a class="reference internal" href="#check-if-uptodate-manual-dependency-checking"><strong>@check_if_uptodate</strong> : Manual dependency checking</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="parallel.html"
-                        title="previous chapter"><strong>Chapter 22</strong>: Esoteric: Running jobs in parallel without files using <tt class="docutils literal"><span class="pre">@parallel</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="flowchart_colours.html"
-                        title="next chapter"><strong>Appendix 1</strong>: Flow Chart Colours with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/check_if_uptodate.txt"
-           rel="nofollow">Show Source</a></li>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
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-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-         <a href="../../todo.html">Future plans</a>
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-            
-  <div class="section" id="new-manual-checkpointing-chapter-num-checkpointing-interrupted-pipelines-and-exceptions">
-<span id="new-manual-checkpointing"></span><span id="index-0"></span><h1><strong>Chapter 10</strong>: Checkpointing: Interrupted Pipelines and Exceptions<a class="headerlink" href="#new-manual-checkpointing-chapter-num-checkpointing-interrupted-pipelines-and-exceptions" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="checkpointing_code.html#new-manual-checkpointing-code"><em>Chapter 10: Python Code for Checkpointing: Interrupted Pipelines and Exceptions</em></a></li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/theoretical_pipeline_schematic.png"><img alt="../../_images/theoretical_pipeline_schematic.png" src="../../_images/theoretical_pipeline_schematic.png" style="width: 610.0px; height: 71.0px;" /></a>
-<p>Computational pipelines transform your data in stages until the final result is produced.</p>
-<p>By default, <em>Ruffus</em> uses file modification times for the <strong>input</strong> and <strong>output</strong> to determine
-whether each stage of a pipeline is up-to-date or not. But what happens when the task
-function is interrupted, whether from the command line or by error, half way through writing the output?</p>
-<p>In this case, the half-formed, truncated and corrupt <strong>Output</strong> file will look newer than its <strong>Input</strong> and hence up-to-date.</p>
-</div></blockquote>
-</div>
-<div class="section" id="interrupting-tasks">
-<span id="new-manual-interrupting-tasks"></span><span id="index-1"></span><h2>Interrupting tasks<a class="headerlink" href="#interrupting-tasks" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Let us try with an example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">time</span>
-
-<span class="c">#   create initial files</span>
-<span class="nd">@originate</span><span class="p">([</span><span class="s">'job1.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   long task to interrupt</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span> <span class="s">".output"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">long_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">ff</span><span class="p">:</span>
-        <span class="n">ff</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Unfinished..."</span><span class="p">)</span>
-        <span class="c"># sleep for 2 seconds here so you can interrupt me</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Job started. Press ^C to interrupt me now...</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-<span class="hll">        <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
-</span>        <span class="n">ff</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">Finished"</span><span class="p">)</span>
-        <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Job completed.</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-
-
-<span class="c">#       Run</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">long_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>When this script runs, it pauses in the middle with this message:</p>
-<div class="highlight-python"><pre>Job started. Press ^C to interrupt me now...</pre>
-</div>
-<p>If you interrupted the script by pressing Control-C at this point, you will see that <tt class="docutils literal"><span class="pre">job1.output</span></tt> contains only <tt class="docutils literal"><span class="pre">Unfinished...</span></tt>.
-However, if you should rerun the interrupted pipeline again, Ruffus ignores the corrupt, incomplete file:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">long_task</span><span class="p">])</span>
-<span class="go">Job started. Press ^C to interrupt me now...</span>
-<span class="go">Job completed</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>And if you had run <tt class="docutils literal"><span class="pre">pipeline_printout</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">long_task</span><span class="p">],</span> <span class="n">verbose</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
-<span class="go">________________________________________</span>
-<span class="go">Tasks which will be run:</span>
-
-<span class="go">Task = long_task</span>
-<span class="go">       Job  = [job1.start</span>
-<span class="go">             -> job1.output]</span>
-<span class="hll"><span class="go">         # Job needs update: Previous incomplete run leftover: [job1.output]</span>
-</span></pre></div>
-</div>
-</div></blockquote>
-<p>We can see that <em>Ruffus</em> magically knows that the previous run was incomplete, and that <tt class="docutils literal"><span class="pre">job1.output</span></tt> is detritus that needs to be discarded.</p>
-</div></blockquote>
-</div>
-<div class="section" id="checkpointing-only-log-completed-jobs">
-<span id="new-manual-logging-completed-jobs"></span><h2>Checkpointing: only log completed jobs<a class="headerlink" href="#checkpointing-only-log-completed-jobs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>All is revealed if you were to look in the working directory. <em>Ruffus</em> has created a file called <tt class="docutils literal"><span class="pre">.ruffus_history.sqlite</span></tt>.
-In this <a class="reference external" href="https://sqlite.org/">SQLite</a> database, <em>Ruffus</em> logs only those files which are the result of a completed job,
-all other files are suspect.
-This file checkpoint database is a fail-safe, not a substitute for checking file modification times. If the <strong>Input</strong> or <strong>Output</strong> files are
-modified, the pipeline will rerun.</p>
-<p>By default, <em>Ruffus</em> saves only file timestamps to the SQLite database but you can also add a checksum of the pipeline task function body or parameters.
-This behaviour can be controlled by setting the <tt class="docutils literal"><span class="pre">checksum_level</span></tt> parameter
-in <tt class="docutils literal"><span class="pre">pipeline_run()</span></tt>. For example, if you do not want to save any timestamps or checksums:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="n">checksum_level</span> <span class="o">=</span> <span class="mi">0</span><span class="p">)</span>
-
-<span class="n">CHECKSUM_FILE_TIMESTAMPS</span>      <span class="o">=</span> <span class="mi">0</span>     <span class="c"># only rerun when the file timestamps are out of date (classic mode)</span>
-<span class="n">CHECKSUM_HISTORY_TIMESTAMPS</span>   <span class="o">=</span> <span class="mi">1</span>     <span class="c"># Default: also rerun when the history shows a job as being out of date</span>
-<span class="n">CHECKSUM_FUNCTIONS</span>            <span class="o">=</span> <span class="mi">2</span>     <span class="c"># also rerun when function body has changed</span>
-<span class="n">CHECKSUM_FUNCTIONS_AND_PARAMS</span> <span class="o">=</span> <span class="mi">3</span>     <span class="c"># also rerun when function parameters or function body change</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Checksums are calculated from the <a class="reference external" href="http://docs.python.org/2/library/pickle.html">pickled</a> string for the function code and parameters.
-If pickling fails, Ruffus will degrade gracefully to saving just the timestamp in the SQLite database.</p>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="do-not-share-the-same-checkpoint-file-across-for-multiple-pipelines">
-<span id="new-manual-history-files-cannot-be-shared"></span><h2>Do not share the same checkpoint file across for multiple pipelines!<a class="headerlink" href="#do-not-share-the-same-checkpoint-file-across-for-multiple-pipelines" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The name of the Ruffus python script is not saved in the checkpoint file along side timestamps and checksums.
-That means that you can rename your pipeline source code file without having to rerun the pipeline!
-The tradeoff is that if multiple pipelines are run from the same directory, and save their histories to the
-same SQlite database file, and if their file names overlap (all of these are bad ideas anyway!), this is
-bound to be a source of confusion.</p>
-<p>Luckily, the name and path of the checkpoint file can be also changed for each pipeline</p>
-</div></blockquote>
-</div>
-<div class="section" id="setting-checkpoint-file-names">
-<span id="new-manual-changing-history-file-name"></span><h2>Setting checkpoint file names<a class="headerlink" href="#setting-checkpoint-file-names" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<p>Some file systems do not appear to support SQLite at all:</p>
-<p>There are reports that SQLite databases have <a class="reference external" href="http://beets.radbox.org/blog/sqlite-nightmare.html">file locking problems</a> on Lustre.</p>
-<p class="last">The best solution would be to keep the SQLite database on an alternate compatible file system away from the working directory if possible.</p>
-</div>
-</div></blockquote>
-<div class="section" id="environment-variable-default-ruffus-history-file">
-<h3>environment variable <tt class="docutils literal"><span class="pre">DEFAULT_RUFFUS_HISTORY_FILE</span></tt><a class="headerlink" href="#environment-variable-default-ruffus-history-file" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The name of the checkpoint file is the value of the environment variable <tt class="docutils literal"><span class="pre">DEFAULT_RUFFUS_HISTORY_FILE</span></tt>.</p>
-<blockquote>
-<div>export DEFAULT_RUFFUS_HISTORY_FILE=/some/where/.ruffus_history.sqlite</div></blockquote>
-<p>This gives considerable flexibility, and allows a system-wide policy to be set so that all Ruffus checkpoint files are set logically to particular paths.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">It is your responsibility to make sure that the requisite destination directories for the checkpoint files exist beforehand!</p>
-</div>
-<p>Where this is missing, the checkpoint file defaults to <tt class="docutils literal"><span class="pre">.ruffus_history.sqlite</span></tt> in your working directory</p>
-</div></blockquote>
-</div>
-<div class="section" id="setting-the-checkpoint-file-name-manually">
-<h3>Setting the checkpoint file name manually<a class="headerlink" href="#setting-the-checkpoint-file-name-manually" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>This checkpoint file name can always be overridden as a parameter to Ruffus functions:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="n">history_file</span> <span class="o">=</span> <span class="s">"XXX"</span><span class="p">)</span>
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">history_file</span> <span class="o">=</span> <span class="s">"XXX"</span><span class="p">)</span>
-<span class="n">pipeline_printout_graph</span><span class="p">(</span><span class="n">history_file</span> <span class="o">=</span> <span class="s">"XXX"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>There is also built in support in <tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt>. So if you use this module, you can simply add to your command line:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="c"># use a custom checkpoint file</span>
-myscript --checksum_file_name .myscript.ruffus_history.sqlite
-</pre></div>
-</div>
-</div></blockquote>
-<p>This takes precedence over everything else.</p>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="useful-checkpoint-file-name-policies-default-ruffus-history-file">
-<h2>Useful checkpoint file name policies <tt class="docutils literal"><span class="pre">DEFAULT_RUFFUS_HISTORY_FILE</span></tt><a class="headerlink" href="#useful-checkpoint-file-name-policies-default-ruffus-history-file" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>If the pipeline script is called <tt class="docutils literal"><span class="pre">test/bin/scripts/run.me.py</span></tt>, then these are the resulting checkpoint files locations:</div></blockquote>
-<div class="section" id="example-1-same-directory-different-name">
-<h3>Example 1: same directory, different name<a class="headerlink" href="#example-1-same-directory-different-name" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>If the environment variable is:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span class="nb">export </span><span class="nv">DEFAULT_RUFFUS_HISTORY_FILE</span><span class="o">=</span>.<span class="o">{</span>basename<span class="o">}</span>.ruffus_history.sqlite
-</pre></div>
-</div>
-<p>Then the job checkpoint database for <tt class="docutils literal"><span class="pre">run.me.py</span></tt> will be <tt class="docutils literal"><span class="pre">.run.me.ruffus_history.sqlite</span></tt></p>
-<div class="highlight-bash"><div class="highlight"><pre>/test/bin/scripts/run.me.py
-/common/path/for/job_history/scripts/.run.me.ruffus_history.sqlite
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-2-different-directory-same-name">
-<h3>Example 2: Different directory, same name<a class="headerlink" href="#example-2-different-directory-same-name" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="nb">export </span><span class="nv">DEFAULT_RUFFUS_HISTORY_FILE</span><span class="o">=</span>/common/path/for/job_history/.<span class="o">{</span>basename<span class="o">}</span>.ruffus_history.sqlite
-</pre></div>
-</div>
-<div class="highlight-bash"><div class="highlight"><pre>/common/path/for/job_history/.run.me.ruffus_history.sqlite
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-2-different-directory-same-name-but-keep-one-level-of-subdirectory-to-disambiguate">
-<h3>Example 2: Different directory, same name but keep one level of subdirectory to disambiguate<a class="headerlink" href="#example-2-different-directory-same-name-but-keep-one-level-of-subdirectory-to-disambiguate" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="nb">export </span><span class="nv">DEFAULT_RUFFUS_HISTORY_FILE</span><span class="o">=</span>/common/path/for/job_history/<span class="o">{</span>subdir<span class="o">[</span>0<span class="o">]}</span>/.<span class="o">{</span>basename<span class="o">}</span>.ruffus_history.sqlite
-</pre></div>
-</div>
-<div class="highlight-bash"><div class="highlight"><pre>/common/path/for/job_history/scripts/.run.me.ruffus_history.sqlite
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-2-nested-in-common-directory">
-<h3>Example 2: nested in common directory<a class="headerlink" href="#example-2-nested-in-common-directory" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="nb">export </span><span class="nv">DEFAULT_RUFFUS_HISTORY_FILE</span><span class="o">=</span>/common/path/for/job_history/<span class="o">{</span>path<span class="o">}</span>/.<span class="o">{</span>basename<span class="o">}</span>.ruffus_history.sqlite
-</pre></div>
-</div>
-<div class="highlight-bash"><div class="highlight"><pre>/common/path/for/job_history/test/bin/scripts/.run.me.ruffus_history.sqlite
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="regenerating-the-checkpoint-file">
-<span id="new-manual-regenerating-history-file"></span><span id="index-2"></span><h2>Regenerating the checkpoint file<a class="headerlink" href="#regenerating-the-checkpoint-file" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Occasionally you may need to re-generate the checkpoint file.</p>
-<p>This could be necessary:</p>
-<blockquote>
-<div><ul class="simple">
-<li>because you are upgrading from a previous version of Ruffus without checkpoint file support</li>
-<li>on the rare occasions when the SQLite file becomes corrupted and has to deleted</li>
-<li>if you wish to circumvent the file checking of Ruffus after making some manual changes!</li>
-</ul>
-</div></blockquote>
-<p>To do this, it is only necessary to call <tt class="docutils literal"><span class="pre">pipeline_run</span></tt> appropriately:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">CHECKSUM_REGENERATE</span> <span class="o">=</span> <span class="mi">2</span>
-<span class="n">pipeline</span><span class="p">(</span><span class="n">touch_files_only</span> <span class="o">=</span> <span class="n">CHECKSUM_REGENERATE</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Similarly, if you are using <tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt>, you can call:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>myscript --recreate_database
-</pre></div>
-</div>
-</div></blockquote>
-<p>Note that this regenerates the checkpoint file to reflect the existing <em>Input</em>, <em>Output</em> files on disk.
-In other words, the onus is on you to make sure there are no half-formed, corrupt files. On the other hand,
-the pipeline does not need to have been previously run successfully for this to work. Essentially, Ruffus,
-pretends to run the pipeline, while logging all the files with consistent file modication times, stopping
-at the first tasks which appear out of date or incomplete.</p>
-</div></blockquote>
-</div>
-<div class="section" id="rules-for-determining-if-files-are-up-to-date">
-<span id="new-manual-skip-up-to-date-rules"></span><span id="index-3"></span><h2>Rules for determining if files are up to date<a class="headerlink" href="#rules-for-determining-if-files-are-up-to-date" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The following simple rules are used by <em>Ruffus</em>.</p>
-<ol class="arabic">
-<li><p class="first">The pipeline stage will be rerun if:</p>
-<blockquote>
-<div><ul class="simple">
-<li>If any of the <strong>Input</strong> files are new (newer than the <strong>Output</strong> files)</li>
-<li>If any of the <strong>Output</strong> files are missing</li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">In addition, it is possible to run jobs which create files from scratch.</p>
-<blockquote>
-<div><ul class="simple">
-<li>If no <strong>Input</strong> file names are supplied, the job will only run if any <em>output</em> file is missing.</li>
-</ul>
-</div></blockquote>
-</li>
-<li><p class="first">Finally, if no <strong>Output</strong> file names are supplied, the job will always run.</p>
-</li>
-</ol>
-</div></blockquote>
-</div>
-<div class="section" id="missing-files-generate-exceptions">
-<span id="index-4"></span><h2>Missing files generate exceptions<a class="headerlink" href="#missing-files-generate-exceptions" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If the <em>inputs</em> files for a job are missing, the task function will have no way
-to produce its <em>output</em>. In this case, a <tt class="docutils literal"><span class="pre">MissingInputFileError</span></tt> exception will be raised
-automatically. For example,</p>
-<blockquote>
-<div><div class="highlight-python"><pre>task.MissingInputFileError: No way to run job: Input file ['a.1'] does not exist
-for Job = ["a.1" -> "a.2", "A file"]</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="caveats-coarse-timestamp-resolution">
-<span id="index-5"></span><h2>Caveats: Coarse Timestamp resolution<a class="headerlink" href="#caveats-coarse-timestamp-resolution" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Note that modification times have precision to the nearest second under some older file systems
-(ext2/ext3?). This may be also be true for networked file systems.</p>
-<p><em>Ruffus</em> supplements the file system time resolution by independently recording the timestamp at
-full OS resolution (usually to at least the millisecond) at job completion, when presumably the <strong>Output</strong>
-files will have been created.</p>
-<p>However, <em>Ruffus</em> only does this if the discrepancy between file time and system time is less than a second
-(due to poor file system timestamp resolution). If there are large mismatches between the two, due for example
-to network time slippage, misconfiguration etc, <em>Ruffus</em> reverts to using the file system time and adds a one second
-delay between jobs (via <tt class="docutils literal"><span class="pre">time.sleep()</span></tt>) to make sure input and output file stamps are different.</p>
-<p>If you know that your filesystem has coarse-grained timestamp resolution, you can always revert to this very conservative behaviour,
-at the prices of some annoying 1s pauses, by setting <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(one_second_per_job = True)</em></a></p>
-</div></blockquote>
-</div>
-<div class="section" id="flag-files-checkpointing-for-the-paranoid">
-<span id="index-6"></span><h2>Flag files: Checkpointing for the paranoid<a class="headerlink" href="#flag-files-checkpointing-for-the-paranoid" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>One other way of checkpointing your pipelines is to create an extra “flag” file as an additional
-<strong>Output</strong> file name. The flag file is only created or updated when everything else in the
-job has completed successifully and written to disk. A missing or out of date flag file then
-would be a sign for Ruffus that the task never completed properly in the first place.</p>
-<p>This used to be much the best way of performing checkpointing in Ruffus and is still
-the most bulletproof way of proceeding. For example, even the loss or corruption
-of the checkpoint file, would not affect things greatly.</p>
-<p>Nevertheless flag files are largely superfluous in modern <em>Ruffus</em>.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 10</strong>: Checkpointing: Interrupted Pipelines and Exceptions</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#interrupting-tasks">Interrupting tasks</a></li>
-<li><a class="reference internal" href="#checkpointing-only-log-completed-jobs">Checkpointing: only log completed jobs</a></li>
-<li><a class="reference internal" href="#do-not-share-the-same-checkpoint-file-across-for-multiple-pipelines">Do not share the same checkpoint file across for multiple pipelines!</a></li>
-<li><a class="reference internal" href="#setting-checkpoint-file-names">Setting checkpoint file names</a><ul>
-<li><a class="reference internal" href="#environment-variable-default-ruffus-history-file">environment variable <tt class="docutils literal"><span class="pre">DEFAULT_RUFFUS_HISTORY_FILE</span></tt></a></li>
-<li><a class="reference internal" href="#setting-the-checkpoint-file-name-manually">Setting the checkpoint file name manually</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#useful-checkpoint-file-name-policies-default-ruffus-history-file">Useful checkpoint file name policies <tt class="docutils literal"><span class="pre">DEFAULT_RUFFUS_HISTORY_FILE</span></tt></a><ul>
-<li><a class="reference internal" href="#example-1-same-directory-different-name">Example 1: same directory, different name</a></li>
-<li><a class="reference internal" href="#example-2-different-directory-same-name">Example 2: Different directory, same name</a></li>
-<li><a class="reference internal" href="#example-2-different-directory-same-name-but-keep-one-level-of-subdirectory-to-disambiguate">Example 2: Different directory, same name but keep one level of subdirectory to disambiguate</a></li>
-<li><a class="reference internal" href="#example-2-nested-in-common-directory">Example 2: nested in common directory</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#regenerating-the-checkpoint-file">Regenerating the checkpoint file</a></li>
-<li><a class="reference internal" href="#rules-for-determining-if-files-are-up-to-date">Rules for determining if files are up to date</a></li>
-<li><a class="reference internal" href="#missing-files-generate-exceptions">Missing files generate exceptions</a></li>
-<li><a class="reference internal" href="#caveats-coarse-timestamp-resolution">Caveats: Coarse Timestamp resolution</a></li>
-<li><a class="reference internal" href="#flag-files-checkpointing-for-the-paranoid">Flag files: Checkpointing for the paranoid</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="mkdir.html"
-                        title="previous chapter"><strong>Chapter 9</strong>: Preparing directories for output with <tt class="docutils literal"><span class="pre">@mkdir()</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="decorators_compendium.html"
-                        title="next chapter"><strong>Chapter 11</strong>: Pipeline topologies and a compendium of <em>Ruffus</em> decorators</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/checkpointing.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-<span id="new-manual-checkpointing-code"></span><h1><strong>Chapter 10</strong>: Python Code for Checkpointing: Interrupted Pipelines and Exceptions<a class="headerlink" href="#new-manual-checkpointing-chapter-num-python-code-for-checkpointing-interrupted-pipelines-and-exceptions" title="Permalink to this headline">¶</a></h1>
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-<span id="new-manual-combinatorics"></span><span id="index-0"></span><h1><strong>Chapter 17</strong>: <a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a>, <a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a> and all versus all <a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a><a cl [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a></li>
-<li><a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a></li>
-<li><a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a></li>
-<li><a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a></li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a></li>
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-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><a class="reference internal" href="combinatorics_code.html#new-manual-combinatorics-code"><em>Chapter 17: Python Code for @combinations, @permutations and all versus all @product</em></a></li>
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-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>A surprising number of computational problems involve some sort of all versus all calculations.
-Previously, this would have required all the parameters to be supplied using a custom function
-on the fly with <a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files</em></a>.</p>
-<p>From version 2.4, <em>Ruffus</em> supports  <a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a>,
-<a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a>, <a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a>,
-<a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a>.</p>
-<p>These provide as far as possible all the functionality of the four combinatorics iterators
-from the standard python <a class="reference external" href="http://docs.python.org/2/library/itertools.html">itertools</a>
-functions of the same name.</p>
-</div></blockquote>
-</div>
-<div class="section" id="generating-output-with-formatter">
-<h2>Generating output with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a><a class="headerlink" href="#generating-output-with-formatter" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>String replacement always takes place via <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a>. Unfortunately,
-the other <em>Ruffus</em> workhorses of  <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> and  <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a>
-do not have sufficient syntactic flexibility.</p>
-<p>Each combinatorics decorator deals with multiple sets of inputs whether this might be:</p>
-<blockquote>
-<div><ul class="simple">
-<li>a self-self comparison (such as <a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a>,
-<a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a>, <a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a>) or,</li>
-<li>a self-other comparison (<a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a>)</li>
-</ul>
-</div></blockquote>
-<p>The replacement strings thus require an extra level of indirection to refer to
-parsed components.</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>The first level refers to which <em>set</em> of inputs.</li>
-<li>The second level refers to which input file in any particular <em>set</em> of inputs.</li>
-</ol>
-</div></blockquote>
-<p>For example, if the <em>inputs</em> are  <strong>[A1,A2],[B1,B2],[C1,C2] vs [P1,P2],[Q1,Q2],[R1,R2] vs [X1,X2],[Y1,Y2],[Z1,Z2]</strong>,
-then <tt class="docutils literal"><span class="pre">'{basename[2][0]}'</span></tt> is the <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.basename">basename</a> for</p>
-<blockquote>
-<div><ul class="simple">
-<li>the third set of inputs (<strong>X,Y,Z</strong>) and</li>
-<li>the first file name string in each <strong>Input</strong> of that set (<strong>X1, Y1, Z1</strong>)</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="all-vs-all-comparisons-with-product">
-<span id="new-manual-product"></span><h2>All vs all comparisons with <a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a><a class="headerlink" href="#all-vs-all-comparisons-with-product" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a> generates the Cartesian <strong>product</strong> between sets of input files,
-i.e. all vs all comparisons.</p>
-<p>The effect is analogous to a nested for loop.</p>
-<p><a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a> can be useful, for example, in bioinformatics for finding
-the corresponding genes (orthologues) for a set of proteins in multiple species.</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">product</span>
-<span class="hll"><span class="gp">>>> </span><span class="c"># product('ABC', 'XYZ') --> AX AY AZ BX BY BZ CX CY CZ</span>
-</span><span class="gp">>>> </span><span class="p">[</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">product</span><span class="p">(</span><span class="s">'ABC'</span><span class="p">,</span> <span class="s">'XYZ'</span><span class="p">)]</span>
-<span class="go">['AX', 'AY', 'AZ', 'BX', 'BY', 'BZ', 'CX', 'CY', 'CZ']</span>
-</pre></div>
-</div>
-<p>This example Calculates the <strong>@product</strong> of <strong>A,B</strong> and <strong>P,Q</strong> and <strong>X,Y</strong> files</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="hll"><span class="c">#   Three sets of initial files</span>
-</span><span class="nd">@originate</span><span class="p">([</span> <span class="s">'a.start'</span><span class="p">,</span> <span class="s">'b.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ab</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="nd">@originate</span><span class="p">([</span> <span class="s">'p.start'</span><span class="p">,</span> <span class="s">'q.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_pq</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'x.1_start'</span><span class="p">,</span> <span class="s">'x.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'y.1_start'</span><span class="p">,</span> <span class="s">'y.2_start'</span><span class="p">]</span> <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_xy</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-<span class="hll">
-</span><span class="c">#   @product</span>
-<span class="hll"><span class="nd">@product</span><span class="p">(</span>   <span class="n">create_initial_files_ab</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 1</span>
-
-<span class="hll">            <span class="n">create_initial_files_pq</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 2</span>
-
-<span class="hll">            <span class="n">create_initial_files_xy</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 3</span>
-<span class="hll">
-</span><span class="hll">            <span class="s">"{path[0][0]}/"</span>                 <span class="c"># Output Replacement string</span>
-</span><span class="hll">            <span class="s">"{basename[0][0]}_vs_"</span>          <span class="c">#</span>
-</span><span class="hll">            <span class="s">"{basename[1][0]}_vs_"</span>          <span class="c">#</span>
-</span>            <span class="s">"{basename[2][0]}.product"</span><span class="p">,</span>     <span class="c">#</span>
-<span class="hll">
-</span>            <span class="s">"{path[0][0]}"</span><span class="p">,</span>                 <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-<span class="hll">
-</span><span class="hll">            <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>            <span class="c"># Extra parameter: basename for 1st set of files, 1st file name</span>
-</span><span class="hll">             <span class="s">"{basename[1][0]}"</span><span class="p">,</span>            <span class="c">#                               2nd</span>
-</span>             <span class="s">"{basename[2][0]}"</span><span class="p">,</span>            <span class="c">#                               3rd</span>
-             <span class="p">])</span>
-<span class="k">def</span> <span class="nf">product_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"# basenames      = "</span><span class="p">,</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-    <span class="k">print</span> <span class="s">"input_parameter  = "</span><span class="p">,</span> <span class="n">input_file</span>
-    <span class="k">print</span> <span class="s">"output_parameter = "</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This results in:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a p x</span>
-<span class="go">input_parameter  =  ('a.start', 'p.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_p_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a p y</span>
-<span class="go">input_parameter  =  ('a.start', 'p.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_p_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a q x</span>
-<span class="go">input_parameter  =  ('a.start', 'q.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_q_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a q y</span>
-<span class="go">input_parameter  =  ('a.start', 'q.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_q_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b p x</span>
-<span class="go">input_parameter  =  ('b.start', 'p.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_p_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b p y</span>
-<span class="go">input_parameter  =  ('b.start', 'p.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_p_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b q x</span>
-<span class="go">input_parameter  =  ('b.start', 'q.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_q_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b q y</span>
-<span class="go">input_parameter  =  ('b.start', 'q.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_q_vs_y.product</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="permute-all-k-tuple-orderings-of-inputs-without-repeats-using-permutations">
-<span id="new-manual-permutations"></span><h2>Permute all k-tuple orderings of inputs without repeats using <a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a><a class="headerlink" href="#permute-all-k-tuple-orderings-of-inputs-without-repeats-using-permutations" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt>Generates the <strong>permutations</strong> for all the elements of a set of <strong>Input</strong> (e.g. <strong>A B C D</strong>),</dt>
-<dd><ul class="first last simple">
-<li>r-length tuples of <em>input</em> elements</li>
-<li>excluding repeated elements (<strong>A A</strong>)</li>
-<li>and order of the tuples is significant (both <strong>A B</strong> and  <strong>B A</strong>).</li>
-</ul>
-</dd>
-</dl>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">permutations</span>
-<span class="hll"><span class="gp">>>> </span><span class="c"># permutations('ABCD', 2) --> AB AC AD BA BC BD CA CB CD DA DB DC</span>
-</span><span class="gp">>>> </span><span class="p">[</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">permutations</span><span class="p">(</span><span class="s">"ABCD"</span><span class="p">,</span> <span class="mi">2</span><span class="p">)]</span>
-<span class="go">['AB', 'AC', 'AD', 'BA', 'BC', 'BD', 'CA', 'CB', 'CD', 'DA', 'DB', 'DC']</span>
-</pre></div>
-</div>
-<p>This following example calculates the <strong>@permutations</strong> of <strong>A,B,C,D</strong> files</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @permutations</span>
-</span><span class="nd">@permutations</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>      <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                    <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 2 at a time</span>
-</span>              <span class="mi">2</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}.permutations"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-</span>              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span><span class="hll">               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#                                2nd</span>
-</span>               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">permutations_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This results in:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-
-<span class="go">A - B</span>
-<span class="go">A - C</span>
-<span class="go">A - D</span>
-<span class="go">B - A</span>
-<span class="go">B - C</span>
-<span class="go">B - D</span>
-<span class="go">C - A</span>
-<span class="go">C - B</span>
-<span class="go">C - D</span>
-<span class="go">D - A</span>
-<span class="go">D - B</span>
-<span class="go">D - C</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="select-unordered-k-tuples-within-inputs-excluding-repeated-elements-using-combinations">
-<span id="new-manual-combinations"></span><h2>Select unordered k-tuples within inputs excluding repeated elements using <a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a><a class="headerlink" href="#select-unordered-k-tuples-within-inputs-excluding-repeated-elements-using-combinations" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><dl class="docutils">
-<dt>Generates the <strong>combinations</strong> for all the elements of a set of <strong>Input</strong> (e.g. <strong>A B C D</strong>),</dt>
-<dd><ul class="first last simple">
-<li>r-length tuples of <em>input</em> elements</li>
-<li>without repeated elements (<strong>A A</strong>)</li>
-<li>where order of the tuples is irrelevant (either <strong>A B</strong> or  <strong>B A</strong>, not both).</li>
-</ul>
-</dd>
-</dl>
-<p><a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a> can be useful, for example, in calculating a transition probability matrix
-for a set of states. The diagonals are meaningless “self-self” transitions which are excluded.</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">combinations</span>
-<span class="hll"><span class="gp">>>> </span><span class="c"># combinations('ABCD', 3) --> ABC ABD ACD BCD</span>
-</span><span class="gp">>>> </span><span class="p">[</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">combinations</span><span class="p">(</span><span class="s">"ABCD"</span><span class="p">,</span> <span class="mi">3</span><span class="p">)]</span>
-<span class="go">['ABC', 'ABD', 'ACD', 'BCD']</span>
-</pre></div>
-</div>
-<p>This example calculates the <strong>@combinations</strong> of <strong>A,B,C,D</strong> files</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @combinations</span>
-</span><span class="nd">@combinations</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>      <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                    <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 3 at a time</span>
-</span>              <span class="mi">3</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}_vs_"</span>
-              <span class="s">"{basename[2][1]}.combinations"</span><span class="p">,</span>
-<span class="hll">
-</span>              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-<span class="hll">
-</span><span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span>               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#              2nd</span>
-               <span class="s">"{basename[2][0]}"</span><span class="p">,</span>  <span class="c">#              3rd</span>
-               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">combinations_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This results in:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">A - B - C</span>
-<span class="go">A - B - D</span>
-<span class="go">A - C - D</span>
-<span class="go">B - C - D</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="select-unordered-k-tuples-within-inputs-including-repeated-elements-with-combinations-with-replacement">
-<span id="new-manual-combinations-with-replacement"></span><h2>Select unordered k-tuples within inputs <em>including</em> repeated elements with <a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a><a class="headerlink" href="#select-unordered-k-tuples-within-inputs-including-repeated-elements-with-combinations-with-replacement" title="Permalink to this headline">¶< [...]
-<blockquote>
-<div><dl class="docutils">
-<dt>Generates the <strong>combinations_with_replacement</strong> for all the elements of a set of <strong>Input</strong> (e.g. <strong>A B C D</strong>),</dt>
-<dd><ul class="first last simple">
-<li>r-length tuples of <em>input</em> elements</li>
-<li>including repeated elements (<strong>A A</strong>)</li>
-<li>where order of the tuples is irrelevant (either <strong>A B</strong> or  <strong>B A</strong>, not both).</li>
-</ul>
-</dd>
-</dl>
-<p><a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a> can be useful,
-for example, in bioinformatics for finding evolutionary relationships between genetic elements such as proteins
-and genes. Self-self comparisons can be used a baseline for scaling similarity scores.</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">combinations_with_replacement</span>
-<span class="hll"><span class="gp">>>> </span><span class="c"># combinations_with_replacement('ABCD', 2) --> AA AB AC AD BB BC BD CC CD DD</span>
-</span><span class="gp">>>> </span><span class="p">[</span> <span class="s">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">a</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">combinations_with_replacement</span><span class="p">(</span><span class="s">'ABCD'</span><span class="p">,</span> <span class="mi">2</span><span class="p">)]</span>
-<span class="go">['AA', 'AB', 'AC', 'AD', 'BB', 'BC', 'BD', 'CC', 'CD', 'DD']</span>
-</pre></div>
-</div>
-<p>This example calculates the <strong>@combinations_with_replacement</strong> of <strong>A,B,C,D</strong> files</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @combinations_with_replacement</span>
-</span><span class="nd">@combinations_with_replacement</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>   <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                                  <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 2 at a time</span>
-</span>              <span class="mi">2</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}.combinations_with_replacement"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-</span>              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span><span class="hll">               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#              2rd</span>
-</span>               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">combinations_with_replacement_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This results in:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">A - A</span>
-<span class="go">A - B</span>
-<span class="go">A - C</span>
-<span class="go">A - D</span>
-<span class="go">B - B</span>
-<span class="go">B - C</span>
-<span class="go">B - D</span>
-<span class="go">C - C</span>
-<span class="go">C - D</span>
-<span class="go">D - D</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 17</strong>: <tt class="docutils literal"><span class="pre">@combinations</span></tt>, <tt class="docutils literal"><span class="pre">@permutations</span></tt> and all versus all <tt class="docutils literal"><span class="pre">@product</span></tt></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#generating-output-with-formatter">Generating output with <tt class="docutils literal"><span class="pre">formatter()</span></tt></a></li>
-<li><a class="reference internal" href="#all-vs-all-comparisons-with-product">All vs all comparisons with <tt class="docutils literal"><span class="pre">@product</span></tt></a></li>
-<li><a class="reference internal" href="#permute-all-k-tuple-orderings-of-inputs-without-repeats-using-permutations">Permute all k-tuple orderings of inputs without repeats using <tt class="docutils literal"><span class="pre">@permutations</span></tt></a></li>
-<li><a class="reference internal" href="#select-unordered-k-tuples-within-inputs-excluding-repeated-elements-using-combinations">Select unordered k-tuples within inputs excluding repeated elements using <tt class="docutils literal"><span class="pre">@combinations</span></tt></a></li>
-<li><a class="reference internal" href="#select-unordered-k-tuples-within-inputs-including-repeated-elements-with-combinations-with-replacement">Select unordered k-tuples within inputs <em>including</em> repeated elements with <tt class="docutils literal"><span class="pre">@combinations_with_replacement</span></tt></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="subdivide_collate.html"
-                        title="previous chapter"><strong>Chapter 16</strong>: <tt class="docutils literal"><span class="pre">@subdivide</span></tt> tasks to run efficiently and regroup with <tt class="docutils literal"><span class="pre">@collate</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="active_if.html"
-                        title="next chapter"><strong>Chapter 18</strong>: Turning parts of the pipeline on and off at runtime with <tt class="docutils literal"><span class="pre">@active_if</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/combinatorics.txt"
-           rel="nofollow">Show Source</a></li>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
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-            
-  <div class="section" id="new-manual-combinatorics-chapter-num-python-code-for-combinations-permutations-and-all-versus-all-product">
-<span id="new-manual-combinatorics-code"></span><h1><strong>Chapter 17</strong>: Python Code for <a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a>, <a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a> and all versus all <a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a><a class=" [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a></li>
-<li><a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a></li>
-<li><a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a></li>
-<li><a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a></li>
-<li>Back to <strong>Chapter 17</strong>: <a class="reference internal" href="combinatorics.html#new-manual-combinatorics"><em>Preparing directories for output with @combinatorics()</em></a></li>
-</ul>
-</div>
-<div class="section" id="example-code-for-product">
-<h2>Example code for <a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a><a class="headerlink" href="#example-code-for-product" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="hll"><span class="c">#   Three sets of initial files</span>
-</span><span class="nd">@originate</span><span class="p">([</span> <span class="s">'a.start'</span><span class="p">,</span> <span class="s">'b.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ab</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="nd">@originate</span><span class="p">([</span> <span class="s">'p.start'</span><span class="p">,</span> <span class="s">'q.start'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_pq</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'x.1_start'</span><span class="p">,</span> <span class="s">'x.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'y.1_start'</span><span class="p">,</span> <span class="s">'y.2_start'</span><span class="p">]</span> <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_xy</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-<span class="hll">
-</span><span class="c">#   @product</span>
-<span class="hll"><span class="nd">@product</span><span class="p">(</span>   <span class="n">create_initial_files_ab</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 1</span>
-
-<span class="hll">            <span class="n">create_initial_files_pq</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 2</span>
-
-<span class="hll">            <span class="n">create_initial_files_xy</span><span class="p">,</span>        <span class="c"># Input</span>
-</span>            <span class="n">formatter</span><span class="p">(</span><span class="s">"(.start)$"</span><span class="p">),</span>         <span class="c"># match input file set # 3</span>
-<span class="hll">
-</span><span class="hll">            <span class="s">"{path[0][0]}/"</span>                 <span class="c"># Output Replacement string</span>
-</span><span class="hll">            <span class="s">"{basename[0][0]}_vs_"</span>          <span class="c">#</span>
-</span><span class="hll">            <span class="s">"{basename[1][0]}_vs_"</span>          <span class="c">#</span>
-</span>            <span class="s">"{basename[2][0]}.product"</span><span class="p">,</span>     <span class="c">#</span>
-<span class="hll">
-</span>            <span class="s">"{path[0][0]}"</span><span class="p">,</span>                 <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-<span class="hll">
-</span><span class="hll">            <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>            <span class="c"># Extra parameter: basename for 1st set of files, 1st file name</span>
-</span><span class="hll">             <span class="s">"{basename[1][0]}"</span><span class="p">,</span>            <span class="c">#                               2nd</span>
-</span>             <span class="s">"{basename[2][0]}"</span><span class="p">,</span>            <span class="c">#                               3rd</span>
-             <span class="p">])</span>
-<span class="k">def</span> <span class="nf">product_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"# basenames      = "</span><span class="p">,</span> <span class="s">" "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-    <span class="k">print</span> <span class="s">"input_parameter  = "</span><span class="p">,</span> <span class="n">input_file</span>
-    <span class="k">print</span> <span class="s">"output_parameter = "</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a p x</span>
-<span class="go">input_parameter  =  ('a.start', 'p.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_p_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a p y</span>
-<span class="go">input_parameter  =  ('a.start', 'p.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_p_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a q x</span>
-<span class="go">input_parameter  =  ('a.start', 'q.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_q_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  a q y</span>
-<span class="go">input_parameter  =  ('a.start', 'q.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/a_vs_q_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b p x</span>
-<span class="go">input_parameter  =  ('b.start', 'p.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_p_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b p y</span>
-<span class="go">input_parameter  =  ('b.start', 'p.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_p_vs_y.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b q x</span>
-<span class="go">input_parameter  =  ('b.start', 'q.start', 'x.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_q_vs_x.product</span>
-<span class="hll">
-</span><span class="go"># basenames      =  b q y</span>
-<span class="go">input_parameter  =  ('b.start', 'q.start', 'y.start')</span>
-<span class="go">output_parameter =  /home/lg/temp/b_vs_q_vs_y.product</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="example-code-for-permutations">
-<h2>Example code for <a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a><a class="headerlink" href="#example-code-for-permutations" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @permutations</span>
-</span><span class="nd">@permutations</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>      <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                    <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 2 at a time</span>
-</span>              <span class="mi">2</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}.permutations"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-</span>              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span><span class="hll">               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#                                2nd</span>
-</span>               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">permutations_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-
-<span class="go">A - B</span>
-<span class="go">A - C</span>
-<span class="go">A - D</span>
-<span class="go">B - A</span>
-<span class="go">B - C</span>
-<span class="go">B - D</span>
-<span class="go">C - A</span>
-<span class="go">C - B</span>
-<span class="go">C - D</span>
-<span class="go">D - A</span>
-<span class="go">D - B</span>
-<span class="go">D - C</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="example-code-for-combinations">
-<h2>Example code for <a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a><a class="headerlink" href="#example-code-for-combinations" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @combinations</span>
-</span><span class="nd">@combinations</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>      <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                    <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 3 at a time</span>
-</span>              <span class="mi">3</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}_vs_"</span>
-              <span class="s">"{basename[2][1]}.combinations"</span><span class="p">,</span>
-<span class="hll">
-</span>              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-<span class="hll">
-</span><span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span>               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#              2nd</span>
-               <span class="s">"{basename[2][0]}"</span><span class="p">,</span>  <span class="c">#              3rd</span>
-               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">combinations_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">A - B - C</span>
-<span class="go">A - B - D</span>
-<span class="go">A - C - D</span>
-<span class="go">B - C - D</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="example-code-for-combinations-with-replacement">
-<h2>Example code for <a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a><a class="headerlink" href="#example-code-for-combinations-with-replacement" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   initial file pairs</span>
-<span class="nd">@originate</span><span class="p">([</span> <span class="p">[</span><span class="s">'A.1_start'</span><span class="p">,</span> <span class="s">'A.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'B.1_start'</span><span class="p">,</span> <span class="s">'B.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'C.1_start'</span><span class="p">,</span> <span class="s">'C.2_start'</span><span class="p">],</span>
-             <span class="p">[</span><span class="s">'D.1_start'</span><span class="p">,</span> <span class="s">'D.2_start'</span><span class="p">]])</span>
-<span class="k">def</span> <span class="nf">create_initial_files_ABCD</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   @combinations_with_replacement</span>
-</span><span class="nd">@combinations_with_replacement</span><span class="p">(</span><span class="n">create_initial_files_ABCD</span><span class="p">,</span>   <span class="c"># Input</span>
-              <span class="n">formatter</span><span class="p">(),</span>                                  <span class="c"># match input files</span>
-
-<span class="hll">              <span class="c"># tuple of 2 at a time</span>
-</span>              <span class="mi">2</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Output Replacement string</span>
-</span>              <span class="s">"{path[0][0]}/"</span>
-              <span class="s">"{basename[0][1]}_vs_"</span>
-              <span class="s">"{basename[1][1]}.combinations_with_replacement"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter: path for 1st set of files, 1st file name</span>
-</span>              <span class="s">"{path[0][0]}"</span><span class="p">,</span>
-
-<span class="hll">              <span class="c"># Extra parameter</span>
-</span><span class="hll">              <span class="p">[</span><span class="s">"{basename[0][0]}"</span><span class="p">,</span>  <span class="c"># basename for 1st set of files, 1st file name</span>
-</span><span class="hll">               <span class="s">"{basename[1][0]}"</span><span class="p">,</span>  <span class="c">#              2rd</span>
-</span>               <span class="p">])</span>
-<span class="k">def</span> <span class="nf">combinations_with_replacement_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_parameter</span><span class="p">,</span> <span class="n">shared_path</span><span class="p">,</span> <span class="n">basenames</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">basenames</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">A - A</span>
-<span class="go">A - B</span>
-<span class="go">A - C</span>
-<span class="go">A - D</span>
-<span class="go">B - B</span>
-<span class="go">B - C</span>
-<span class="go">B - D</span>
-<span class="go">C - C</span>
-<span class="go">C - D</span>
-<span class="go">D - D</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 17</strong>: Python Code for <tt class="docutils literal"><span class="pre">@combinations</span></tt>, <tt class="docutils literal"><span class="pre">@permutations</span></tt> and all versus all <tt class="docutils literal"><span class="pre">@product</span></tt></a><ul>
-<li><a class="reference internal" href="#example-code-for-product">Example code for <tt class="docutils literal"><span class="pre">@product</span></tt></a></li>
-<li><a class="reference internal" href="#example-code-for-permutations">Example code for <tt class="docutils literal"><span class="pre">@permutations</span></tt></a></li>
-<li><a class="reference internal" href="#example-code-for-combinations">Example code for <tt class="docutils literal"><span class="pre">@combinations</span></tt></a></li>
-<li><a class="reference internal" href="#example-code-for-combinations-with-replacement">Example code for <tt class="docutils literal"><span class="pre">@combinations_with_replacement</span></tt></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="subdivide_collate_code.html"
-                        title="previous chapter"><strong>Chapter 16</strong>: Python Code for <tt class="docutils literal"><span class="pre">@subdivide</span></tt> tasks to run efficiently and regroup with <tt class="docutils literal"><span class="pre">@collate</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="inputs_code.html"
-                        title="next chapter"><strong>Chapter 20</strong>: Python Code for Manipulating task inputs via string substitution using <tt class="docutils literal"><span class="pre">inputs()</span></tt>  and  <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-           rel="nofollow">Show Source</a></li>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
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-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-  <div class="section" id="new-manual-cmdline-chapter-num-running-ruffus-from-the-command-line-with-ruffus-cmdline">
-<span id="new-manual-cmdline"></span><span id="index-0"></span><h1><strong>Chapter 6</strong>: Running <em>Ruffus</em> from the command line with ruffus.cmdline<a class="headerlink" href="#new-manual-cmdline-chapter-num-running-ruffus-from-the-command-line-with-ruffus-cmdline" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual table of Contents</em></a></li>
-</ul>
-</div>
-<p>We find that much of our <em>Ruffus</em> pipeline code is built on the same template and this is generally
-a good place to start developing a new pipeline.</p>
-<p>From version 2.4, <em>Ruffus</em> includes an optional <tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt> module that provides
-support for a set of common command line arguments. This makes writing <em>Ruffus</em> pipelines much more pleasant.</p>
-<div class="section" id="template-for-argparse">
-<span id="new-manual-cmdline-setup-logging"></span><span id="new-manual-cmdline-run"></span><span id="new-manual-cmdline-get-argparse"></span><h2>Template for <a class="reference external" href="http://docs.python.org/2.7/library/argparse.html">argparse</a><a class="headerlink" href="#template-for-argparse" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>All you need to do is copy these 6 lines</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ruffus.cmdline</span> <span class="kn">as</span> <span class="nn">cmdline</span>
-
-<span class="n">parser</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">get_argparse</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s">'WHAT DOES THIS PIPELINE DO?'</span><span class="p">)</span>
-
-<span class="hll"><span class="c">#   <<<---- add your own command line options like --input_file here</span>
-</span><span class="c"># parser.add_argument("--input_file")</span>
-
-<span class="n">options</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
-
-<span class="c">#  standard python logger which can be synchronised across concurrent Ruffus tasks</span>
-<span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">setup_logging</span> <span class="p">(</span><span class="n">__name__</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">log_file</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">verbose</span><span class= [...]
-
-<span class="hll"><span class="c">#   <<<----  pipelined functions go here</span>
-</span>
-<span class="n">cmdline</span><span class="o">.</span><span class="n">run</span> <span class="p">(</span><span class="n">options</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>You are recommended to use the standard <a class="reference external" href="http://docs.python.org/2.7/library/argparse.html">argparse</a> module
-but the deprecated <a class="reference external" href="http://docs.python.org/2.7/library/optparse.html">optparse</a> module works as well. (See <a class="reference internal" href="#code-template-optparse"><em>below</em></a> for the template)</p>
-</div></blockquote>
-</div>
-<div class="section" id="command-line-arguments">
-<h2>Command Line Arguments<a class="headerlink" href="#command-line-arguments" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt> by default provides these predefined options:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>-v, --verbose
-    --version
--L, --log_file
-
-<span class="hll">    <span class="c"># tasks</span>
-</span>-T, --target_tasks
-    --forced_tasks
--j, --jobs
-    --use_threads
-
-
-<span class="hll">    <span class="c"># printout</span>
-</span>-n, --just_print
-
-<span class="hll">    <span class="c"># flow chart</span>
-</span>    --flowchart
-    --key_legend_in_graph
-    --draw_graph_horizontally
-    --flowchart_format
-
-
-<span class="hll">    <span class="c"># check sum</span>
-</span>    --touch_files_only
-    --checksum_file_name
-    --recreate_database
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="logging">
-<h2>1) Logging<a class="headerlink" href="#logging" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The script provides for logging both to the command line:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>myscript -v
-myscript --verbose
-</pre></div>
-</div>
-</div></blockquote>
-<p>and an optional log file:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="c"># keep tabs on yourself</span>
-myscript --log_file /var/log/secret.logbook
-</pre></div>
-</div>
-</div></blockquote>
-<p>Logging is ignored if neither <tt class="docutils literal"><span class="pre">--verbose</span></tt> or <tt class="docutils literal"><span class="pre">--log_file</span></tt> are specified on the command line</p>
-<p><tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt> automatically allows you to write to a shared log file via a proxy from multiple processes.
-However, you do need to use <tt class="docutils literal"><span class="pre">logging_mutex</span></tt> for the log files to be synchronised properly across different jobs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-
-    <span class="n">logger_proxy</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"Look Ma. No hands"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Logging is set up so that you can write</p>
-</div></blockquote>
-<div class="section" id="a-only-to-the-log-file">
-<h3>A) Only to the log file:<a class="headerlink" href="#a-only-to-the-log-file" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"A message"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="b-only-to-the-display">
-<h3>B) Only to the display:<a class="headerlink" href="#b-only-to-the-display" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s">"A message"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="c-to-both-simultaneously">
-<span id="new-manual-cmdline-message"></span><h3>C) To both simultaneously:<a class="headerlink" href="#c-to-both-simultaneously" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus.cmdline</span> <span class="kn">import</span> <span class="n">MESSAGE</span>
-
-<span class="n">logger</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">MESSAGE</span><span class="p">,</span> <span class="s">"A message"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="tracing-pipeline-progress">
-<h2>2) Tracing pipeline progress<a class="headerlink" href="#tracing-pipeline-progress" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>This is extremely useful for understanding what is happening with your pipeline, what tasks and which
-jobs are up-to-date etc.</p>
-<p>See <a class="reference internal" href="pipeline_printout.html#new-manual-pipeline-printout"><em>Chapter 5: Understanding how your pipeline works with pipeline_printout(...)</em></a></p>
-<p>To trace the pipeline, call script with the following options</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="c"># well-mannered, reserved</span>
-myscript --just_print
-myscript -n
-
-or
-
-<span class="c"># extremely loquacious</span>
-myscript --just_print --verbose 5
-myscript -n -v5
-</pre></div>
-</div>
-</div></blockquote>
-<p>Increasing levels of verbosity (<tt class="docutils literal"><span class="pre">--verbose</span></tt> to <tt class="docutils literal"><span class="pre">--verbose</span> <span class="pre">5</span></tt>) provide more detailed output</p>
-</div></blockquote>
-</div>
-<div class="section" id="printing-a-flowchart">
-<h2>3) Printing a flowchart<a class="headerlink" href="#printing-a-flowchart" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>This is the subject of <a class="reference internal" href="pipeline_printout_graph.html#new-manual-pipeline-printout-graph"><em>Chapter 7: Displaying the pipeline visually with pipeline_printout_graph(...)</em></a>.</p>
-<p>Flowcharts can be specified using the following option:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>myscript --flowchart xxxchart.svg
-</pre></div>
-</div>
-</div></blockquote>
-<p>The extension of the flowchart file indicates what format the flowchart should take,
-for example, <tt class="docutils literal"><span class="pre">svg</span></tt>, <tt class="docutils literal"><span class="pre">jpg</span></tt> etc.</p>
-<p>Override with <tt class="docutils literal"><span class="pre">--flowchart_format</span></tt></p>
-</div></blockquote>
-</div>
-<div class="section" id="running-in-parallel-on-multiple-processors">
-<h2>4) Running in parallel on multiple processors<a class="headerlink" href="#running-in-parallel-on-multiple-processors" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Optionally specify the number of parallel strands of execution and which is the last <em>target</em> task to run.
-The pipeline will run starting from any out-of-date tasks which precede the <em>target</em> and proceed no further
-beyond the <em>target</em>.</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>myscript --jobs 15 --target_tasks <span class="s2">"final_task"</span>
-myscript -j 15
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="setup-checkpointing-so-that-ruffus-knows-which-files-are-out-of-date">
-<h2>5) Setup checkpointing so that <em>Ruffus</em> knows which files are out of date<a class="headerlink" href="#setup-checkpointing-so-that-ruffus-knows-which-files-are-out-of-date" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <a class="reference internal" href="checkpointing.html#new-manual-checkpointing"><em>checkpoint file</em></a> uses to the value set in the
-environment (<tt class="docutils literal"><span class="pre">DEFAULT_RUFFUS_HISTORY_FILE</span></tt>).</p>
-<p>If this is not set, it will default to <tt class="docutils literal"><span class="pre">.ruffus_history.sqlite</span></tt> in the current working directory.</p>
-<p>Either can be changed on the command line:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>myscript --checksum_file_name mychecksum.sqlite
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="recreating-checkpoints">
-<h3>Recreating checkpoints<a class="headerlink" href="#recreating-checkpoints" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Create or update the checkpoint file so that all existing files in completed jobs appear up to date</p>
-<p>Will stop sensibly if current state is incomplete or inconsistent</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">myscript</span> <span class="o">--</span><span class="n">recreate_database</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="touch-files">
-<h3>Touch files<a class="headerlink" href="#touch-files" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>As far as possible, create empty files with the correct timestamp to make the pipeline appear up to date.</p>
-<div class="highlight-bash"><div class="highlight"><pre>myscript --touch_files_only
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="skipping-specified-options">
-<h2>6) Skipping specified options<a class="headerlink" href="#skipping-specified-options" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Note that particular options can be skipped (not added to the command line), if they conflict with your own options, for example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># see below for how to use get_argparse</span>
-<span class="n">parser</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">get_argparse</span><span class="p">(</span>  <span class="n">description</span><span class="o">=</span><span class="s">'WHAT DOES THIS PIPELINE DO?'</span><span class="p">,</span>
-<span class="hll">                                <span class="c"># Exclude the following options: --log_file --key_legend_in_graph</span>
-</span>                                <span class="n">ignored_args</span> <span class="o">=</span> <span class="p">[</span><span class="s">"log_file"</span><span class="p">,</span> <span class="s">"key_legend_in_graph"</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="specifying-verbosity-and-abbreviating-long-paths">
-<h2>7) Specifying verbosity and abbreviating long paths<a class="headerlink" href="#specifying-verbosity-and-abbreviating-long-paths" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The verbosity can be specified on the command line</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>myscript --verbose 5
-
-<span class="c"># verbosity of 5 + 1 = 6</span>
-myscript --verbose 5 --verbose
-
-<span class="c"># verbosity reset to 2</span>
-myscript --verbose 5 --verbose --verbose 2
-</pre></div>
-</div>
-</div></blockquote>
-<p>If the printed paths are too long, and need to be abbreviated, or alternatively, if you want see the full absolute paths of your input and output parameters,
-you can specify an extension to the verbosity. See the manual discussion of <a class="reference internal" href="pipeline_printout.html#new-manual-pipeline-printout-verbose-abbreviated-path"><em>verbose_abbreviated_path</em></a> for
-more details. This is specified as <tt class="docutils literal"><span class="pre">--verbose</span> <span class="pre">VERBOSITY:VERBOSE_ABBREVIATED_PATH</span></tt>. (No spaces!)</p>
-<p>For example:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre> <span class="c"># verbosity of 4</span>
- myscript.py --verbose 4
-
-<span class="hll"> <span class="c"># display three levels of nested directories</span>
-</span> myscript.py --verbose 4:3
-
-<span class="hll"> <span class="c"># restrict input and output parameters to 60 letters</span>
-</span> myscript.py --verbose 4:-60
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="displaying-the-version">
-<h2>8) Displaying the version<a class="headerlink" href="#displaying-the-version" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Note that the version for your script will default to <tt class="docutils literal"><span class="pre">"%(prog)s</span> <span class="pre">1.0"</span></tt> unless specified:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">parser</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">get_argparse</span><span class="p">(</span>  <span class="n">description</span><span class="o">=</span><span class="s">'WHAT DOES THIS PIPELINE DO?'</span><span class="p">,</span>
-                                <span class="n">version</span> <span class="o">=</span> <span class="s">"my_programme.py v. 2.23"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="template-for-optparse">
-<span id="code-template-optparse"></span><h2>Template for <a class="reference external" href="http://docs.python.org/2.7/library/optparse.html">optparse</a><a class="headerlink" href="#template-for-optparse" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>deprecated since python 2.7</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   Using optparse (new in python v 2.6)</span>
-<span class="c">#</span>
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="n">parser</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">get_optgparse</span><span class="p">(</span><span class="n">version</span><span class="o">=</span><span class="s">"%prog 1.0"</span><span class="p">,</span> <span class="n">usage</span> <span class="o">=</span> <span class="s">"</span><span class="se">\n\n</span><span class="s">    %prog [options]"</span><span class="p">)</span>
-
-<span class="hll"><span class="c">#   <<<---- add your own command line options like --input_file here</span>
-</span><span class="c"># parser.add_option("-i", "--input_file", dest="input_file", help="Input file")</span>
-
-<span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">remaining_args</span><span class="p">)</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
-
-<span class="c">#  logger which can be passed to ruffus tasks</span>
-<span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">setup_logging</span> <span class="p">(</span><span class="s">"this_program"</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">log_file</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">verbose</s [...]
-
-<span class="hll"><span class="c">#   <<<----  pipelined functions go here</span>
-</span>
-<span class="n">cmdline</span><span class="o">.</span><span class="n">run</span> <span class="p">(</span><span class="n">options</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 6</strong>: Running <em>Ruffus</em> from the command line with ruffus.cmdline</a><ul>
-<li><a class="reference internal" href="#template-for-argparse">Template for argparse</a></li>
-<li><a class="reference internal" href="#command-line-arguments">Command Line Arguments</a></li>
-<li><a class="reference internal" href="#logging">1) Logging</a><ul>
-<li><a class="reference internal" href="#a-only-to-the-log-file">A) Only to the log file:</a></li>
-<li><a class="reference internal" href="#b-only-to-the-display">B) Only to the display:</a></li>
-<li><a class="reference internal" href="#c-to-both-simultaneously">C) To both simultaneously:</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#tracing-pipeline-progress">2) Tracing pipeline progress</a></li>
-<li><a class="reference internal" href="#printing-a-flowchart">3) Printing a flowchart</a></li>
-<li><a class="reference internal" href="#running-in-parallel-on-multiple-processors">4) Running in parallel on multiple processors</a></li>
-<li><a class="reference internal" href="#setup-checkpointing-so-that-ruffus-knows-which-files-are-out-of-date">5) Setup checkpointing so that <em>Ruffus</em> knows which files are out of date</a><ul>
-<li><a class="reference internal" href="#recreating-checkpoints">Recreating checkpoints</a></li>
-<li><a class="reference internal" href="#touch-files">Touch files</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#skipping-specified-options">6) Skipping specified options</a></li>
-<li><a class="reference internal" href="#specifying-verbosity-and-abbreviating-long-paths">7) Specifying verbosity and abbreviating long paths</a></li>
-<li><a class="reference internal" href="#displaying-the-version">8) Displaying the version</a></li>
-<li><a class="reference internal" href="#template-for-optparse">Template for optparse</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="pipeline_printout.html"
-                        title="previous chapter"><strong>Chapter 5</strong>: Understanding how your pipeline works with <tt class="docutils literal"><span class="pre">pipeline_printout(...)</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="pipeline_printout_graph.html"
-                        title="next chapter"><strong>Chapter 7</strong>: Displaying the pipeline visually with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></p>
-  <h3>This Page</h3>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
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-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-         <a href="../../todo.html">Future plans</a>
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-  <div class="section" id="new-manual-decorators-compendium-chapter-num-pipeline-topologies-and-a-compendium-of-ruffus-decorators">
-<span id="new-manual-decorators-compendium"></span><span id="index-0"></span><h1><strong>Chapter 11</strong>: Pipeline topologies and a compendium of <em>Ruffus</em> decorators<a class="headerlink" href="#new-manual-decorators-compendium-chapter-num-pipeline-topologies-and-a-compendium-of-ruffus-decorators" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/decorators.html#decorators"><em>decorators</em></a></li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Computational pipelines transform your data in stages until the final result is produced.</p>
-<p>You can visualise your pipeline data flowing like water down a system of pipes.
-<em>Ruffus</em> has many ways of joining up your pipes to create different topologies.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><strong>The best way to design a pipeline is to:</strong></p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><strong>Write down the file names of the data as it flows across your pipeline.</strong></li>
-<li><strong>Draw lines between the file names to show how they should be connected together.</strong></li>
-</ul>
-</div></blockquote>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="transform">
-<h2><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a><a class="headerlink" href="#transform" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>So far, our data files have been flowing through our pipelines independently in lockstep.</p>
-<a class="reference internal image-reference" href="../../_images/bestiary_transform.png"><img alt="../../_images/bestiary_transform.png" src="../../_images/bestiary_transform.png" style="width: 733.5px; height: 262.0px;" /></a>
-<p>If we drew a graph of the data files moving through the pipeline, all of our flowcharts would look like something like this.</p>
-<p>The <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> decorator connects up your data files in 1 to 1 operations, ensuring that for every <strong>Input</strong>, a corresponding <strong>Output</strong> is
-generated, ready to got into the next pipeline stage. If we start with three sets of starting data, we would end up with three final sets of results.</p>
-</div></blockquote>
-</div>
-<div class="section" id="a-bestiary-of-ruffus-decorators">
-<h2>A bestiary of <em>Ruffus</em> decorators<a class="headerlink" href="#a-bestiary-of-ruffus-decorators" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Very often, we would like to transform our data in more complex ways, this is where other <em>Ruffus</em> decorators come in.</p>
-<a class="reference internal image-reference" href="../../_images/bestiary_decorators.png"><img alt="../../_images/bestiary_decorators.png" src="../../_images/bestiary_decorators.png" style="width: 1359.5px; height: 294.5px;" /></a>
-</div></blockquote>
-</div>
-<div class="section" id="originate">
-<h2><a class="reference internal" href="../../decorators/originate.html#decorators-originate"><em>@originate</em></a><a class="headerlink" href="#originate" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>Introduced in <strong>Chapter 3</strong> <a class="reference internal" href="transform_in_parallel.html#new-manual-transform-in-parallel"><em>More on @transform-ing data and @originate</em></a>,
-<a class="reference internal" href="../../decorators/originate.html#decorators-originate"><em>@originate</em></a> generates <strong>Output</strong> files from scratch without the benefits of any <strong>Input</strong> files.</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="merge">
-<h2><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a><a class="headerlink" href="#merge" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>A <strong>many to one</strong> operator.</li>
-<li>The last decorator at the far right to the figure, <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> merges multiple <strong>Input</strong> into one <strong>Output</strong>.</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="split">
-<h2><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a><a class="headerlink" href="#split" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>A  <strong>one to many</strong> operator,</li>
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> is the evil twin of <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a>. It takes a single set of <strong>Input</strong> and splits them into multiple smaller pieces.</li>
-<li>The best part of <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> is that we don’t necessarily have to decide ahead of time <em>how many</em> smaller pieces it should produce. If we have encounter a larger file,
-we might need to split it up into more fragments for greater parallelism.</li>
-<li>Since <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> is a  <strong>one to many</strong> operator, if you pass it <strong>many</strong> inputs (e.g. via <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a>, it performs an implicit <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> step to make one
-set of <strong>Input</strong> that you can redistribute into a different number of pieces. If you are looking to split <em>each</em> <strong>Input</strong> into further smaller fragments, then you
-need <a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="subdivide">
-<h2><a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a><a class="headerlink" href="#subdivide" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>A <strong>many to even more</strong> operator.</li>
-<li>It takes each of multiple <strong>Input</strong>, and further subdivides them.</li>
-<li>Uses <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a>, <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> or <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> to generate <strong>Output</strong> names from its <strong>Input</strong> files but like <a class="reference internal" href= [...]
-<em>how many</em> smaller pieces each <strong>Input</strong> should be further divided into. For example, a large <strong>Input</strong> files might be subdivided into 7 pieces while the next job might,
-however, split its <strong>Input</strong> into just 4 pieces.</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="collate">
-<h2><a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a><a class="headerlink" href="#collate" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>A <strong>many to fewer</strong> operator.</li>
-<li><a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a> is the opposite twin of <tt class="docutils literal"><span class="pre">subdivide</span></tt>: it takes multiple <strong>Output</strong> and groups or collates them into bundles of <strong>Output</strong>.</li>
-<li><a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a> uses <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> or <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> to generate <strong>Output</strong> names.</li>
-<li>All <strong>Input</strong> files which map to the same <strong>Output</strong> are grouped together into one job (one task function call) which
-produces one <strong>Output</strong>.</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="combinatorics">
-<h2>Combinatorics<a class="headerlink" href="#combinatorics" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>More rarely, we need to generate a set of <strong>Output</strong> based on a combination or permutation or product of the <strong>Input</strong>.</p>
-<p>For example, in bioinformatics, we might need to look for all instances of a set of genes in the genomes of a different number of species.
-In other words, we need to find the <a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a> of XXX genes x YYY species.</p>
-<p><em>Ruffus</em> provides decorators modelled on the “Combinatoric generators” in the Standard Python <a class="reference external" href="http://docs.python.org/2/library/itertools.html">itertools</a> library.</p>
-<p>To use combinatoric decorators, you need to explicitly include them from <em>Ruffus</em>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ruffus</span>
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.combinatorics</span> <span class="kn">import</span> <span class="o">*</span>
-</pre></div>
-</div>
-<a class="reference internal image-reference" href="../../_images/bestiary_combinatorics.png"><img alt="../../_images/bestiary_combinatorics.png" src="../../_images/bestiary_combinatorics.png" style="width: 1360.5px; height: 271.5px;" /></a>
-</div></blockquote>
-</div>
-<div class="section" id="product">
-<h2><a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a><a class="headerlink" href="#product" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>Given several sets of <strong>Input</strong>, it generates all versus all <strong>Output</strong>. For example, if there are four sets of <strong>Input</strong> files, <a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a> will generate <tt class="docutils literal"><span class="pre">WWW</span> <span class="pre">x</span> <span class="pre">XXX</span> <span class="pre">x</span> <span class="pre">YYY</span> <span class="pre">x</spa [...]
-<li>Uses <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>formatter</em></a> to generate unique <strong>Output</strong> names from components parsed from <em>any</em> parts of <em>any</em> specified files in
-all <strong>Input</strong> sets. In the above example, this allows the generation of  <tt class="docutils literal"><span class="pre">WWW</span> <span class="pre">x</span> <span class="pre">XXX</span> <span class="pre">x</span> <span class="pre">YYY</span> <span class="pre">x</span> <span class="pre">ZZZ</span></tt> unique names.</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="combinations">
-<h2><a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a><a class="headerlink" href="#combinations" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>Given one set of <strong>Input</strong>, it generates the combinations of r-length tuples among them.</li>
-<li>Uses <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>formatter</em></a> to generate unique <strong>Output</strong> names from components parsed from <em>any</em> parts of <em>any</em> specified files in all <strong>Input</strong> sets.</li>
-<li>For example, given <strong>Input</strong> called <tt class="docutils literal"><span class="pre">A</span></tt>, <tt class="docutils literal"><span class="pre">B</span></tt> and <tt class="docutils literal"><span class="pre">C</span></tt>, it will generate: <tt class="docutils literal"><span class="pre">A-B</span></tt>,  <tt class="docutils literal"><span class="pre">A-C</span></tt>,  <tt class="docutils literal"><span class="pre">B-C</span></tt></li>
-<li>The order of <strong>Input</strong> items is ignored so either <tt class="docutils literal"><span class="pre">A-B</span></tt> or <tt class="docutils literal"><span class="pre">B-A</span></tt> will be included, not both</li>
-<li>Self-vs-self combinations (<tt class="docutils literal"><span class="pre">A-A</span></tt>) are excluded.</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="combinations-with-replacement">
-<h2><a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a><a class="headerlink" href="#combinations-with-replacement" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>Given one set of <strong>Input</strong>, it generates the combinations of r-length tuples among them but includes self-vs-self conbinations.</li>
-<li>Uses <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>formatter</em></a> to generate unique <strong>Output</strong> names from components parsed from <em>any</em> parts of <em>any</em> specified files in all <strong>Input</strong> sets.</li>
-<li>For example, given <strong>Input</strong> called <tt class="docutils literal"><span class="pre">A</span></tt>, <tt class="docutils literal"><span class="pre">B</span></tt> and <tt class="docutils literal"><span class="pre">C</span></tt>, it will generate: <tt class="docutils literal"><span class="pre">A-A</span></tt>, <tt class="docutils literal"><span class="pre">A-B</span></tt>,  <tt class="docutils literal"><span class="pre">A-C</span></tt>, <tt class="docutils literal"><span clas [...]
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="permutations">
-<h2><a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a><a class="headerlink" href="#permutations" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>Given one set of <strong>Input</strong>, it generates the permutations of r-length tuples among them. This excludes self-vs-self combinations but includes all orderings (<tt class="docutils literal"><span class="pre">A-B</span></tt> and <tt class="docutils literal"><span class="pre">B-A</span></tt>).</li>
-<li>Uses <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>formatter</em></a> to generate unique <strong>Output</strong> names from components parsed from <em>any</em> parts of <em>any</em> specified files in all <strong>Input</strong> sets.</li>
-<li>For example, given <strong>Input</strong> called <tt class="docutils literal"><span class="pre">A</span></tt>, <tt class="docutils literal"><span class="pre">B</span></tt> and <tt class="docutils literal"><span class="pre">C</span></tt>, it will generate: <tt class="docutils literal"><span class="pre">A-A</span></tt>, <tt class="docutils literal"><span class="pre">A-B</span></tt>,  <tt class="docutils literal"><span class="pre">A-C</span></tt>, <tt class="docutils literal"><span clas [...]
-</ul>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 11</strong>: Pipeline topologies and a compendium of <em>Ruffus</em> decorators</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#transform"><tt class="docutils literal"><span class="pre">@transform</span></tt></a></li>
-<li><a class="reference internal" href="#a-bestiary-of-ruffus-decorators">A bestiary of <em>Ruffus</em> decorators</a></li>
-<li><a class="reference internal" href="#originate"><tt class="docutils literal"><span class="pre">@originate</span></tt></a></li>
-<li><a class="reference internal" href="#merge"><tt class="docutils literal"><span class="pre">@merge</span></tt></a></li>
-<li><a class="reference internal" href="#split"><tt class="docutils literal"><span class="pre">@split</span></tt></a></li>
-<li><a class="reference internal" href="#subdivide"><tt class="docutils literal"><span class="pre">@subdivide</span></tt></a></li>
-<li><a class="reference internal" href="#collate"><tt class="docutils literal"><span class="pre">@collate</span></tt></a></li>
-<li><a class="reference internal" href="#combinatorics">Combinatorics</a></li>
-<li><a class="reference internal" href="#product"><tt class="docutils literal"><span class="pre">@product</span></tt></a></li>
-<li><a class="reference internal" href="#combinations"><tt class="docutils literal"><span class="pre">@combinations</span></tt></a></li>
-<li><a class="reference internal" href="#combinations-with-replacement"><tt class="docutils literal"><span class="pre">@combinations_with_replacement</span></tt></a></li>
-<li><a class="reference internal" href="#permutations"><tt class="docutils literal"><span class="pre">@permutations</span></tt></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="checkpointing.html"
-                        title="previous chapter"><strong>Chapter 10</strong>: Checkpointing: Interrupted Pipelines and Exceptions</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="split.html"
-                        title="next chapter"><strong>Chapter 12</strong>: Splitting up large tasks / files with <strong>@split</strong></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/decorators_compendium.txt"
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-  <div class="section" id="new-manual-dependencies-chapter-num-how-dependency-is-checked">
-<span id="new-manual-dependencies"></span><span id="index-0"></span><h1><strong>Appendix 2</strong>: How dependency is checked<a class="headerlink" href="#new-manual-dependencies-chapter-num-how-dependency-is-checked" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>How does <em>Ruffus</em> decide how to run your pipeline?</p>
-<blockquote>
-<div><ul class="simple">
-<li>In which order should pipelined functions be called?</li>
-<li>Which parts of the pipeline are up-to-date and do not need to be rerun?</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="running-all-out-of-date-tasks-and-dependents">
-<h3>Running all out-of-date tasks and dependents<a class="headerlink" href="#running-all-out-of-date-tasks-and-dependents" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/manual_dependencies_flowchart_intro.png"><img alt="../../_images/manual_dependencies_flowchart_intro.png" src="../../_images/manual_dependencies_flowchart_intro.png" style="width: 275.0px; height: 222.0px;" /></a>
-<p>By default, <em>Ruffus</em> will</p>
-<blockquote>
-<div><ul class="simple">
-<li>build a flow chart (dependency tree) of pipelined tasks (functions)</li>
-<li>start from the most ancestral tasks with the fewest dependencies (<tt class="docutils literal"><span class="pre">task1</span></tt> and <tt class="docutils literal"><span class="pre">task4</span></tt> in the flowchart above).</li>
-<li>walk up the tree to find the first incomplete / out-of-date tasks (i.e. <tt class="docutils literal"><span class="pre">task3</span></tt> and <tt class="docutils literal"><span class="pre">task5</span></tt>.</li>
-<li>start running from there</li>
-</ul>
-</div></blockquote>
-<dl class="docutils">
-<dt>All down-stream (dependent) tasks will be re-run anyway, so we don’t have to test</dt>
-<dd>whether they are up-to-date or not.</dd>
-</dl>
-<div class="admonition note" id="new-manual-dependencies-checking-multiple-times">
-<p class="first admonition-title">Note</p>
-<p>This means that <em>Ruffus</em> <em>may</em> ask any task if their jobs are out of date more than once:</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li>once when deciding which parts of the pipeline have to be run</li>
-<li>once just before executing the task.</li>
-</ul>
-</div></blockquote>
-</div>
-<p><em>Ruffus</em> tries to be clever / efficient, and does the minimal amount of querying.</p>
-</div></blockquote>
-</div>
-<div class="section" id="forced-reruns">
-<span id="new-manual-dependencies-forced-reruns"></span><h3>Forced Reruns<a class="headerlink" href="#forced-reruns" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Even if a pipeline stage appears to be up to date,
-you can always force the pipeline to include from one or more task functions.</p>
-<p>This is particularly useful, for example, if the pipeline data hasn’t changed but
-the analysis or computional code has.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="n">forcedtorun_tasks</span> <span class="o">=</span> <span class="p">[</span><span class="n">up_to_date_task1</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>will run all tasks from <tt class="docutils literal"><span class="pre">up_to_date_task1</span></tt> to <tt class="docutils literal"><span class="pre">final_task</span></tt></p>
-</div></blockquote>
-<p>Both the “target” and the “forced” lists can include as many tasks as you wish. All dependencies
-are still carried out and out-of-date jobs rerun.</p>
-</div></blockquote>
-</div>
-<div class="section" id="esoteric-option-minimal-reruns">
-<span id="new-manual-dependencies-minimal-reruns"></span><h3>Esoteric option: Minimal Reruns<a class="headerlink" href="#esoteric-option-minimal-reruns" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>In the above example, if we were to delete the results of <tt class="docutils literal"><span class="pre">up_to_date_task1</span></tt>, <em>Ruffus</em>
-would rerun <tt class="docutils literal"><span class="pre">up_to_date_task1</span></tt>, <tt class="docutils literal"><span class="pre">up_to_date_task2</span></tt> and <tt class="docutils literal"><span class="pre">task3</span></tt>.</p>
-<p>However, you might argue that so long as <tt class="docutils literal"><span class="pre">up_to_date_task2</span></tt> is up-to-date, and it
-is the only necessary prerequisite for <tt class="docutils literal"><span class="pre">task3</span></tt>, we should not be concerned about
-<tt class="docutils literal"><span class="pre">up_to_date_task1</span></tt>.</p>
-<p>This is enabled with:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">task6</span><span class="p">],</span> <span class="n">gnu_make_maximal_rebuild_mode</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This option walks down the dependency tree and proceeds no further when it encounters
-an up-to-date task (<tt class="docutils literal"><span class="pre">up_to_date_task2</span></tt>) whatever the state of what lies beyond it.</p>
-<p>This rather dangerous option is useful if you don’t want to keep all the intermediate
-files/results from upstream tasks. The pipeline will only not involve any incomplete
-tasks which precede an up-to-date result.</p>
-<p>This is seldom what you intend, and you should always check that the appropriate stages
-of the pipeline are executed in the flowchart output.</p>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
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-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Appendix 2</strong>: How dependency is checked</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a><ul>
-<li><a class="reference internal" href="#running-all-out-of-date-tasks-and-dependents">Running all out-of-date tasks and dependents</a></li>
-<li><a class="reference internal" href="#forced-reruns">Forced Reruns</a></li>
-<li><a class="reference internal" href="#esoteric-option-minimal-reruns">Esoteric option: Minimal Reruns</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="flowchart_colours.html"
-                        title="previous chapter"><strong>Appendix 1</strong>: Flow Chart Colours with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="exceptions.html"
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diff --git a/doc/_build/html/tutorials/new_tutorial/deprecated_files.html b/doc/_build/html/tutorials/new_tutorial/deprecated_files.html
deleted file mode 100644
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--- a/doc/_build/html/tutorials/new_tutorial/deprecated_files.html
+++ /dev/null
@@ -1,411 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-  <div class="section" id="new-manual-deprecated-files-chapter-num-files-deprecated-syntax">
-<span id="new-manual-deprecated-files"></span><span id="index-0"></span><h1><strong>Appendix 5</strong>: <strong>@files</strong>: Deprecated syntax<a class="headerlink" href="#new-manual-deprecated-files-chapter-num-files-deprecated-syntax" title="Permalink to this headline">¶</a></h1>
-<div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<ul class="last">
-<li><p class="first"><strong>This is deprecated syntax</strong></p>
-<p><strong>which is no longer supported and</strong></p>
-<p><strong>should NOT be used in new code.</strong></p>
-</li>
-</ul>
-</div>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/decorators.html#decorators"><em>decorators</em></a></li>
-<li><a class="reference internal" href="../../decorators/files.html#decorators-files"><em>@files</em></a> syntax in detail</li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="line-block">
-<div class="line">The python functions which do the actual work of each stage  or
-<a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> of a <em>Ruffus</em> pipeline are written by you.</div>
-<div class="line">The role of <em>Ruffus</em> is to make sure these functions are called in the right order,
-with the right parameters, running in parallel using multiprocessing if desired.</div>
-</div>
-<p>The easiest way to specify parameters to <em>Ruffus</em> <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> functions is to use
-the <a class="reference internal" href="../../decorators/files.html#decorators-files"><em>@files</em></a> decorator.</p>
-</div></blockquote>
-</div>
-<div class="section" id="files">
-<span id="index-1"></span><h2><strong>@files</strong><a class="headerlink" href="#files" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Running this code:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="p">[</span><span class="s">'a.2'</span><span class="p">,</span> <span class="s">'b.2'</span><span class="p">],</span> <span class="s">'A file'</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">single_job_io_task</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfiles</span><span class="p">,</span> <span class="n">text</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">o</span> <span class="ow">in</span> <span class="n">outfiles</span><span class="p">:</span> <span class="nb">open</span><span class="p">(</span><span class="n">o</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c"># prepare input file</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<dl class="docutils">
-<dt>Is equivalent to calling:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">single_job_io_task</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="p">[</span><span class="s">'a.2'</span><span class="p">,</span> <span class="s">'b.2'</span><span class="p">],</span> <span class="s">'A file'</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-<dt>And produces:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job = [a.1 -> [a.2, b.2], A file] completed</span>
-<span class="go">Completed Task = single_job_io_task</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-</div></blockquote>
-<p><em>Ruffus</em> will automatically check if your task is up to date. The second time <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a>
-is called, nothing will happen. But if you update <tt class="docutils literal"><span class="pre">a.1</span></tt>, the task will rerun:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="nb">open</span><span class="p">(</span><span class="s">'a.1'</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job = [a.1 -> [a.2, b.2], A file] completed</span>
-<span class="go">Completed Task = single_job_io_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>See <a class="reference internal" href="checkpointing.html#new-manual-skip-up-to-date-rules"><em>chapter 2</em></a> for a more in-depth discussion of how <em>Ruffus</em>
-decides which parts of the pipeline are complete and up-to-date.</p>
-</div></blockquote>
-</div>
-<div class="section" id="running-the-same-code-on-different-parameters-in-parallel">
-<span id="new-manual-files-parallel"></span><span id="index-2"></span><h2>Running the same code on different parameters in parallel<a class="headerlink" href="#running-the-same-code-on-different-parameters-in-parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Your pipeline may require the same function to be called multiple times on independent parameters.
-In which case, you can supply all the parameters to @files, each will be sent to separate jobs that
-may run in parallel if necessary. <em>Ruffus</em> will check if each separate <a class="reference internal" href="../../glossary.html#term-job"><em class="xref std std-term">job</em></a> is up-to-date using
-the <em>inputs</em> and <em>outputs</em> (first two) parameters (See the <a class="reference internal" href="transform_in_parallel.html#new-manual-only-rerun-out-of-date"><em>Up-to-date jobs are not re-run unnecessarily</em></a> ).</p>
-<p>For example, if a sequence
-(e.g. a list or tuple) of 5 parameters are passed to <strong>@files</strong>, that indicates
-there will also be 5 separate jobs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="s">'job1.file'</span>           <span class="p">],</span>             <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="s">'job2.file'</span><span class="p">,</span> <span class="mi">4</span>        <span class="p">],</span>             <span class="c"># 2st job</span>
-                    <span class="p">[</span> <span class="s">'job3.file'</span><span class="p">,</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>   <span class="p">],</span>             <span class="c"># 3st job</span>
-                    <span class="p">[</span> <span class="mi">67</span><span class="p">,</span> <span class="p">[</span><span class="mi">13</span><span class="p">,</span> <span class="s">'job4.file'</span><span class="p">]</span> <span class="p">],</span>             <span class="c"># 4st job</span>
-                    <span class="p">[</span> <span class="s">'job5.file'</span>           <span class="p">],</span>             <span class="c"># 5st job</span>
-              <span class="p">]</span>
-<span class="nd">@files</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">task_file</span><span class="p">(</span><span class="o">*</span><span class="n">params</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="line-block">
-<div class="line"><em>Ruffus</em> creates as many jobs as there are elements in <tt class="docutils literal"><span class="pre">parameters</span></tt>.</div>
-<div class="line">In turn, each of these elements consist of series of parameters which will be
-passed to each separate job.</div>
-</div>
-<p>Thus the above code is equivalent to calling:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">task_file</span><span class="p">(</span><span class="s">'job1.file'</span><span class="p">)</span>
-<span class="n">task_file</span><span class="p">(</span><span class="s">'job2.file'</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
-<span class="n">task_file</span><span class="p">(</span><span class="s">'job3.file'</span><span class="p">,</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">2</span><span class="p">])</span>
-<span class="n">task_file</span><span class="p">(</span><span class="mi">67</span><span class="p">,</span> <span class="p">[</span><span class="mi">13</span><span class="p">,</span> <span class="s">'job4.file'</span><span class="p">])</span>
-<span class="n">task_file</span><span class="p">(</span><span class="s">'job5.file'</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>What <tt class="docutils literal"><span class="pre">task_file()</span></tt> does with these parameters is up to you!</p>
-<p>The only constraint on the parameters is that <em>Ruffus</em> will treat any first
-parameter of each job as the <em>inputs</em> and any second as the <em>output</em>. Any
-strings in the <em>inputs</em> or <em>output</em> parameters (including those nested in sequences)
-will be treated as file names.</p>
-<p>Thus, to pick the parameters out of one of the above jobs:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">task_file</span><span class="p">(</span><span class="mi">67</span><span class="p">,</span> <span class="p">[</span><span class="mi">13</span><span class="p">,</span> <span class="s">'job4.file'</span><span class="p">])</span>
-</pre></div>
-</div>
-<div class="line-block">
-<div class="line"><em>inputs</em>  == <tt class="docutils literal"><span class="pre">67</span></tt></div>
-<div class="line"><em>outputs</em> == <tt class="docutils literal"><span class="pre">[13,</span> <span class="pre">'job4.file']</span></tt></div>
-<div class="line"><br /></div>
-<div class="line-block">
-<div class="line">The solitary output filename is <tt class="docutils literal"><span class="pre">job4.file</span></tt></div>
-</div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="checking-if-jobs-are-up-to-date">
-<span id="new-manual-files-example"></span><span id="new-manual-files-is-uptodate"></span><span id="index-3"></span><h3>Checking if jobs are up to date<a class="headerlink" href="#checking-if-jobs-are-up-to-date" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="line-block">
-<div class="line">Usually we do not want to run all the stages in a pipeline but only where
-the input data has changed or is no longer up to date.</div>
-<div class="line">One easy way to do this is to check the modification times for files produced
-at each stage of the pipeline.</div>
-</div>
-<div class="line-block">
-<div class="line">Let us first create our starting files <tt class="docutils literal"><span class="pre">a.1</span></tt> and <tt class="docutils literal"><span class="pre">b.1</span></tt></div>
-<div class="line">We can then run the following pipeline function to create</div>
-</div>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">a.2</span></tt> from <tt class="docutils literal"><span class="pre">a.1</span></tt> and</li>
-<li><tt class="docutils literal"><span class="pre">b.2</span></tt> from <tt class="docutils literal"><span class="pre">b.1</span></tt></li>
-</ul>
-<div class="highlight-python"><div class="highlight"><pre><span class="c"># create starting files</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"b.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="s">'a.1'</span><span class="p">,</span> <span class="s">'a.2'</span><span class="p">,</span> <span class="s">'A file'</span><span class="p">],</span> <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="s">'b.1'</span><span class="p">,</span> <span class="s">'b.2'</span><span class="p">,</span> <span class="s">'B file'</span><span class="p">],</span> <span class="c"># 2nd job</span>
-              <span class="p">]</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">parallel_io_task</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">text</span><span class="p">):</span>
-    <span class="c"># copy infile contents to outfile</span>
-    <span class="n">infile_text</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">infile_text</span> <span class="o">+</span> <span class="s">"</span><span class="se">\n</span><span class="s">"</span> <span class="o">+</span> <span class="n">text</spa [...]
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>This produces the following output:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job = [a.1 -> a.2, A file] completed</span>
-<span class="go">    Job = [b.1 -> b.2, B file] completed</span>
-<span class="go">Completed Task = parallel_io_task</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<div class="line-block">
-<div class="line">If you called <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> again, nothing would happen because the files are up to date:</div>
-<div class="line"><tt class="docutils literal"><span class="pre">a.2</span></tt> is more recent than <tt class="docutils literal"><span class="pre">a.1</span></tt> and</div>
-<div class="line"><tt class="docutils literal"><span class="pre">b.2</span></tt> is more recent than <tt class="docutils literal"><span class="pre">b.1</span></tt></div>
-</div>
-<dl class="docutils">
-<dt>However, if you subsequently modified <tt class="docutils literal"><span class="pre">a.1</span></tt> again:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">open</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>you would see the following:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_io_task</span><span class="p">])</span>
-<span class="go">Task = parallel_io_task</span>
-<span class="go">    Job = ["a.1" -> "a.2", "A file"] completed</span>
-<span class="go">    Job = ["b.1" -> "b.2", "B file"] unnecessary: already up to date</span>
-<span class="go">Completed Task = parallel_io_task</span>
-</pre></div>
-</div>
-<p>The 2nd job is up to date and will be skipped.</p>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Appendix 5</strong>: <strong>@files</strong>: Deprecated syntax</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#files"><strong>@files</strong></a></li>
-<li><a class="reference internal" href="#running-the-same-code-on-different-parameters-in-parallel">Running the same code on different parameters in parallel</a><ul>
-<li><a class="reference internal" href="#checking-if-jobs-are-up-to-date">Checking if jobs are up to date</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="list_of_ruffus_names.html"
-                        title="previous chapter"><strong>Appendix 4</strong>: Names exported from Ruffus</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="deprecated_files_re.html"
-                        title="next chapter"><strong>Appendix 6</strong>: <strong>@files_re</strong>: Deprecated <cite>syntax using regular expressions</cite></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/deprecated_files.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
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-          <a href="../../genindex.html" title="General Index"
-             >index</a></li>
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-          <a href="deprecated_files_re.html" title="Appendix 6: @files_re: Deprecated syntax using regular expressions"
-             >next</a> |</li>
-        <li class="right" >
-          <a href="list_of_ruffus_names.html" title="Appendix 4: Names exported from Ruffus"
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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
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-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
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-  <div class="section" id="new-manual-deprecated-files-re-chapter-num-files-re-deprecated-syntax-using-regular-expressions">
-<span id="new-manual-deprecated-files-re"></span><span id="index-0"></span><h1><strong>Appendix 6</strong>: <strong>@files_re</strong>: Deprecated <cite>syntax using regular expressions</cite><a class="headerlink" href="#new-manual-deprecated-files-re-chapter-num-files-re-deprecated-syntax-using-regular-expressions" title="Permalink to this headline">¶</a></h1>
-<div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<ul class="last">
-<li><p class="first"><strong>This is deprecated syntax</strong></p>
-<p><strong>which is no longer supported and</strong></p>
-<p><strong>should NOT be used in new code.</strong></p>
-</li>
-</ul>
-</div>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/decorators.html#decorators"><em>decorators</em></a></li>
-<li><a class="reference internal" href="../../decorators/files_re.html#decorators-files-re"><em>@files_re</em></a> syntax in detail</li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>@files_re</strong> combines the functionality of @transform, @collate and @merge in
-one overloaded decorator.</p>
-<p>This is the reason why its use is discouraged. <strong>@files_re</strong> syntax is far too overloaded
-and context-dependent to support its myriad of different functions.</p>
-<p>The following documentation is provided to help maintain historical <em>Ruffus</em> usage.</p>
-</div></blockquote>
-<div class="section" id="transforming-input-and-output-filenames">
-<h3>Transforming input and output filenames<a class="headerlink" href="#transforming-input-and-output-filenames" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>For example, the following code takes files from
-the previous pipeline task, and makes new output parameters with the <tt class="docutils literal"><span class="pre">.sums</span></tt> suffix
-in place of the <tt class="docutils literal"><span class="pre">.chunks</span></tt> suffix:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">step_4_split_numbers_into_chunks</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".chunks"</span><span class="p">),</span> <span class="s">".sums"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_5_calculate_sum_of_squares</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="c">#</span>
-    <span class="c">#   calculate sums and sums of squares for all values in the input_file_name</span>
-    <span class="c">#       writing to output_file_name</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This can be written using @files_re equivalently:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>@files_re(step_4_split_numbers_into_chunks, r".chunks", r".sums")
-def step_5_calculate_sum_of_squares (input_file_name, output_file_name):
-""</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-<span class="target" id="new-manual-files-re-combine"></span></div>
-<div class="section" id="collating-many-inputs-into-a-single-output">
-<span id="index-1"></span><h3>Collating many <em>inputs</em> into a single <em>output</em><a class="headerlink" href="#collating-many-inputs-into-a-single-output" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Similarly, the following code collects <strong>inputs</strong>
-from the same species in the same directory:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@collate</span><span class="p">(</span><span class="s">'*.animals'</span><span class="p">,</span>                     <span class="c"># inputs = all *.animal files</span>
-            <span class="n">regex</span><span class="p">(</span><span class="s">r'mammals.([^.]+)'</span><span class="p">),</span>    <span class="c"># regular expression</span>
-            <span class="s">r'\1/animals.in_my_zoo'</span><span class="p">,</span>      <span class="c"># single output file per species</span>
-            <span class="s">r'\1'</span> <span class="p">)</span>                       <span class="c"># species name</span>
-<span class="k">def</span> <span class="nf">capture_mammals</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>
-    <span class="c"># summarise all animals of this species</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This can be written using @files_re equivalently using the <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-combine"><em>combine</em></a> indicator:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@files_re</span><span class="p">(</span><span class="s">'*.animals'</span><span class="p">,</span>                           <span class="c"># inputs = all *.animal files</span>
-            <span class="s">r'mammals.([^.]+)'</span><span class="p">,</span>                  <span class="c"># regular expression</span>
-            <span class="n">combine</span><span class="p">(</span><span class="s">r'\1/animals.in_my_zoo'</span><span class="p">),</span>    <span class="c"># single output file per species</span>
-            <span class="s">r'\1'</span> <span class="p">)</span>                              <span class="c"># species name</span>
-<span class="k">def</span> <span class="nf">capture_mammals</span><span class="p">(</span><span class="n">infiles</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>
-    <span class="c"># summarise all animals of this species</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="generating-input-and-output-parameter-using-regular-expresssions">
-<h3>Generating <em>input</em> and <em>output</em> parameter using regular expresssions<a class="headerlink" href="#generating-input-and-output-parameter-using-regular-expresssions" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The following code generates additional
-<em>input</em> prerequisite file names which match the original <em>input</em> files.</p>
-<p>We want each job of our <tt class="docutils literal"><span class="pre">analyse()</span></tt> function to get corresponding pairs
-of <tt class="docutils literal"><span class="pre">xx.chunks</span></tt> and <tt class="docutils literal"><span class="pre">xx.red_indian</span></tt> files when</p>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">*.chunks</span></tt> are generated by the task function <tt class="docutils literal"><span class="pre">split_up_problem()</span></tt> and
-<tt class="docutils literal"><span class="pre">*.red_indian</span></tt> are generated by the task function <tt class="docutils literal"><span class="pre">make_red_indians()</span></tt>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="n">make_red_indians</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">split_up_problem</span><span class="p">,</span>                <span class="c"># starting set of *inputs*</span>
-            <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*).chunks"</span><span class="p">),</span>          <span class="c"># regular expression</span>
-            <span class="n">inputs</span><span class="p">([</span><span class="s">r"\g<0>"</span><span class="p">,</span>               <span class="c"># xx.chunks</span>
-                    <span class="s">r"\1.red_indian"</span><span class="p">]),</span>     <span class="c"># important.file</span>
-             <span class="s">r"\1.results"</span>                  <span class="c"># xx.results</span>
-              <span class="p">)</span>
-<span class="k">def</span> <span class="nf">analyse</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="s">"Do analysis here"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The equivalent code using @files_re looks very similar:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>@follows(make_red_indians)
- at files_re( split_up_problem,        # starting set of *inputs*
-           r"(.*).chunks",          # regular expression
-           [r"\g<0>",               # xx.chunks
-            r"\1.red_indian"]),     # important.file
-             r"\1.results")         # xx.results
-def analyse(input_filenames, output_file_name):
-    "Do analysis here"</pre>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-</div>
-
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Appendix 6</strong>: <strong>@files_re</strong>: Deprecated <cite>syntax using regular expressions</cite></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a><ul>
-<li><a class="reference internal" href="#transforming-input-and-output-filenames">Transforming input and output filenames</a></li>
-<li><a class="reference internal" href="#collating-many-inputs-into-a-single-output">Collating many <em>inputs</em> into a single <em>output</em></a></li>
-<li><a class="reference internal" href="#generating-input-and-output-parameter-using-regular-expresssions">Generating <em>input</em> and <em>output</em> parameter using regular expresssions</a></li>
-</ul>
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-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="deprecated_files.html"
-                        title="previous chapter"><strong>Appendix 5</strong>: <strong>@files</strong>: Deprecated syntax</a></p>
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-        <ul>
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-  <div class="section" id="new-manual-exceptions-chapter-num-exceptions-thrown-inside-pipelines">
-<span id="new-manual-exceptions"></span><span id="index-0"></span><h1><strong>Appendix 3</strong>: Exceptions thrown inside pipelines<a class="headerlink" href="#new-manual-exceptions-chapter-num-exceptions-thrown-inside-pipelines" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The goal for <em>Ruffus</em> is that exceptions should just work <em>out-of-the-box</em> without any fuss.
-This is especially important for exceptions that come from your code which may be raised
-in a different process. Often multiple parallel operations (jobs or tasks) fail at the
-same time. <em>Ruffus</em> will forward each of these exceptions with the tracebacks so you
-can jump straight to the offending line.</p>
-<p>This example shows separate exceptions from two jobs running in parallel:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@originate</span><span class="p">([</span><span class="s">"a.start"</span><span class="p">,</span> <span class="s">"b.start"</span><span class="p">,</span> <span class="s">"c.start"</span><span class="p">,</span> <span class="s">"d.start"</span><span class="p">,</span> <span class="s">"e.start"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">throw_exceptions_here</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"OOPS"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-</pre></div>
-</div>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="go">    >>> pipeline_run(multiprocess = 2)</span>
-
-<span class="go">    ruffus.ruffus_exceptions.RethrownJobError:</span>
-
-<span class="hll"><span class="go">    Original exceptions:</span>
-</span>
-<span class="go">        Exception #1</span>
-<span class="go">          'exceptions.Exception(OOPS)' raised in ...</span>
-<span class="go">           Task = def throw_exceptions_here(...):</span>
-<span class="go">           Job  = [None -> b.start]</span>
-
-<span class="go">        Traceback (most recent call last):</span>
-<span class="go">          File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 685, in run_pooled_job_without_exceptions</span>
-<span class="go">            return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)</span>
-<span class="go">          File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 549, in job_wrapper_output_files</span>
-<span class="go">            job_wrapper_io_files(param, user_defined_work_func, register_cleanup, touch_files_only, output_files_only = True)</span>
-<span class="go">          File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 504, in job_wrapper_io_files</span>
-<span class="go">            ret_val = user_defined_work_func(*(param[1:]))</span>
-<span class="go">          File "<stdin>", line 3, in throw_exceptions_here</span>
-<span class="go">        Exception: OOPS</span>
-<span class="hll">
-</span>
-<span class="go">        Exception #2</span>
-<span class="go">          'exceptions.Exception(OOPS)' raised in ...</span>
-<span class="go">           Task = def throw_exceptions_here(...):</span>
-<span class="go">           Job  = [None -> a.start]</span>
-
-<span class="go">        Traceback (most recent call last):</span>
-<span class="go">          File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 685, in run_pooled_job_without_exceptions</span>
-<span class="go">            return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)</span>
-<span class="go">          File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 549, in job_wrapper_output_files</span>
-<span class="go">            job_wrapper_io_files(param, user_defined_work_func, register_cleanup, touch_files_only, output_files_only = True)</span>
-<span class="go">          File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 504, in job_wrapper_io_files</span>
-<span class="go">            ret_val = user_defined_work_func(*(param[1:]))</span>
-<span class="go">          File "<stdin>", line 3, in throw_exceptions_here</span>
-<span class="go">        Exception: OOPS</span>
-
-
-<span class="go">.. image:: ../../images/manual_exceptions.png</span>
-</pre></div>
-</div>
-</div></blockquote>
-<span class="target" id="new-manual-exceptions-multiple-errors"></span></div>
-<div class="section" id="pipelines-running-in-parallel-accumulate-exceptions">
-<span id="index-1"></span><h2>Pipelines running in parallel accumulate Exceptions<a class="headerlink" href="#pipelines-running-in-parallel-accumulate-exceptions" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>As show above, by default <em>Ruffus</em> accumulates <tt class="docutils literal"><span class="pre">NN</span></tt> exceptions before interrupting the pipeline prematurely where
-<tt class="docutils literal"><span class="pre">NN</span></tt> is the specified parallelism for <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(multiprocess = NN)</em></a></p>
-<p>This seems a fair tradeoff between being able to gather detailed error information for
-running jobs, and not wasting too much time for a task that is going to fail anyway.</p>
-</div></blockquote>
-</div>
-<div class="section" id="terminate-pipeline-immediately-upon-exceptions">
-<h2>Terminate pipeline immediately upon Exceptions<a class="headerlink" href="#terminate-pipeline-immediately-upon-exceptions" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="set-pipeline-run-exceptions-terminate-immediately-true">
-<h3>Set <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(exceptions_terminate_immediately = True)</em></a><a class="headerlink" href="#set-pipeline-run-exceptions-terminate-immediately-true" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>To have all exceptions interrupt the pipeline immediately, invoke:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="n">exceptions_terminate_immediately</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>For example, with this change, only a single exception will be thrown before the pipeline is interrupted:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@originate</span><span class="p">([</span><span class="s">"a.start"</span><span class="p">,</span> <span class="s">"b.start"</span><span class="p">,</span> <span class="s">"c.start"</span><span class="p">,</span> <span class="s">"d.start"</span><span class="p">,</span> <span class="s">"e.start"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">throw_exceptions_here</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"OOPS"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">2</span><span class="p">,</span> <span class="n">exceptions_terminate_immediately</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="go">    >>> pipeline_run(multiprocess = 2)</span>
-
-<span class="go">    ruffus.ruffus_exceptions.RethrownJobError:</span>
-
-<span class="hll"><span class="go">    Original exception:</span>
-</span>
-<span class="go">        Exception #1</span>
-<span class="go">          'exceptions.Exception(OOPS)' raised in ...</span>
-<span class="go">           Task = def throw_exceptions_here(...):</span>
-<span class="go">           Job  = [None -> a.start]</span>
-
-<span class="go">        Traceback (most recent call last):</span>
-<span class="go">          [Tedious traceback snipped out!!!....]</span>
-<span class="go">        Exception: OOPS</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="raise-ruffus-jobsignalledbreak">
-<h3>raise <tt class="docutils literal"><span class="pre">Ruffus.JobSignalledBreak</span></tt><a class="headerlink" href="#raise-ruffus-jobsignalledbreak" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The same can be accomplished on a finer scale by throwing the <tt class="docutils literal"><span class="pre">Ruffus.JobSignalledBreak</span></tt> Exception. Unlike
-other exceptions, this causes an immediate halt in pipeline execution. If there are other exceptions in play at that
-point, they will be rethrown in the main process but no new exceptions will be added.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@originate</span><span class="p">([</span><span class="s">"a.start"</span><span class="p">,</span> <span class="s">"b.start"</span><span class="p">,</span> <span class="s">"c.start"</span><span class="p">,</span> <span class="s">"d.start"</span><span class="p">,</span> <span class="s">"e.start"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">throw_exceptions_here</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">raise</span> <span class="n">JobSignalledBreak</span><span class="p">(</span><span class="s">"OOPS"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="display-exceptions-as-they-occur">
-<h2>Display exceptions as they occur<a class="headerlink" href="#display-exceptions-as-they-occur" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>In the following example, the jobs throw exceptions
-at two second staggered intervals into the job. With <tt class="docutils literal"><span class="pre">log_exceptions</span> <span class="pre">=</span> <span class="pre">True</span></tt>, the
-exceptions are displayed as they occur even though the pipeline continues running.</p>
-<p>logger.error(...) will be invoked with the string representation of the each exception, and associated stack trace.</p>
-<p>The default logger prints to sys.stderr, but as usual can be changed to any class from the logging module or compatible object via
-<a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(logger = XXX)</em></a></p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">time</span><span class="o">,</span> <span class="nn">os</span>
-
-<span class="nd">@originate</span><span class="p">([</span><span class="s">"1.start"</span><span class="p">,</span> <span class="s">"2.start"</span><span class="p">,</span> <span class="s">"3.start"</span><span class="p">,</span> <span class="s">"4.start"</span><span class="p">,</span> <span class="s">"5.start"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">throw_exceptions_here</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="n">delay</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">output_file</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
-    <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="n">delay</span> <span class="o">*</span> <span class="mi">2</span><span class="p">)</span>
-    <span class="k">raise</span> <span class="n">JobSignalledBreak</span><span class="p">(</span><span class="s">"OOPS"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">log_exceptions</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Appendix 3</strong>: Exceptions thrown inside pipelines</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#pipelines-running-in-parallel-accumulate-exceptions">Pipelines running in parallel accumulate Exceptions</a></li>
-<li><a class="reference internal" href="#terminate-pipeline-immediately-upon-exceptions">Terminate pipeline immediately upon Exceptions</a><ul>
-<li><a class="reference internal" href="#set-pipeline-run-exceptions-terminate-immediately-true">Set <tt class="docutils literal"><span class="pre">pipeline_run(exceptions_terminate_immediately</span> <span class="pre">=</span> <span class="pre">True)</span></tt></a></li>
-<li><a class="reference internal" href="#raise-ruffus-jobsignalledbreak">raise <tt class="docutils literal"><span class="pre">Ruffus.JobSignalledBreak</span></tt></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#display-exceptions-as-they-occur">Display exceptions as they occur</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="dependencies.html"
-                        title="previous chapter"><strong>Appendix 2</strong>: How dependency is checked</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="list_of_ruffus_names.html"
-                        title="next chapter"><strong>Appendix 4</strong>: Names exported from Ruffus</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/exceptions.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-    Enter search terms or a module, class or function name.
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
-
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-  <div class="section" id="new-manual-flowchart-colours-chapter-num-flow-chart-colours-with-pipeline-printout-graph">
-<span id="new-manual-flowchart-colours"></span><span id="index-0"></span><h1><strong>Appendix 1</strong>: Flow Chart Colours with <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a><a class="headerlink" href="#new-manual-flowchart-colours-chapter-num-flow-chart-colours-with-pipeline-printout-graph" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a></li>
-<li><a class="reference download internal" href="../../_downloads/play_with_colours.py"><tt class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">code</span></tt></a></li>
-<li><a class="reference internal" href="flowchart_colours_code.html#new-manual-flowchart-colours-code"><em>Code</em></a> for experimenting with colours</li>
-</ul>
-</div>
-<div class="section" id="flowchart-colours">
-<h2>Flowchart colours<a class="headerlink" href="#flowchart-colours" title="Permalink to this headline">¶</a></h2>
-<p>The appearance of <em>Ruffus</em> flowcharts produced by <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph</em></a>
-can be extensively customised.</p>
-<p>This is mainly controlled by the <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph-user-colour-scheme"><em>user_colour_scheme</em></a>  (note UK spelling of “colour”) parameter</p>
-<p>Example:</p>
-<blockquote>
-<div><p>Use colour scheme index  = 1</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span> <span class="p">(</span><span class="s">"flowchart.svg"</span><span class="p">,</span> <span class="s">"svg"</span><span class="p">,</span> <span class="p">[</span><span class="n">final_task</span><span class="p">],</span>
-                         <span class="n">user_colour_scheme</span> <span class="o">=</span> <span class="p">{</span>
-                                                <span class="s">"colour_scheme_index"</span> <span class="p">:</span><span class="mi">1</span><span class="p">,</span>
-                                                <span class="s">"Pipeline"</span>      <span class="p">:{</span><span class="s">"fontcolor"</span> <span class="p">:</span> <span class="s">'"#FF3232"'</span> <span class="p">},</span>
-                                                <span class="s">"Key"</span>           <span class="p">:{</span><span class="s">"fontcolor"</span> <span class="p">:</span> <span class="s">"Red"</span><span class="p">,</span>
-                                                                  <span class="s">"fillcolor"</span> <span class="p">:</span> <span class="s">'"#F6F4F4"'</span> <span class="p">},</span>
-                                                <span class="s">"Task to run"</span>   <span class="p">:{</span><span class="s">"linecolor"</span> <span class="p">:</span> <span class="s">'"#0044A0"'</span> <span class="p">},</span>
-                                                <span class="s">"Final target"</span>  <span class="p">:{</span><span class="s">"fillcolor"</span> <span class="p">:</span> <span class="s">'"#EFA03B"'</span><span class="p">,</span>
-                                                                  <span class="s">"fontcolor"</span> <span class="p">:</span> <span class="s">"black"</span><span class="p">,</span>
-                                                                  <span class="s">"dashed"</span>    <span class="p">:</span> <span class="mi">0</span>           <span class="p">}</span>
-                                               <span class="p">})</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>There are 8 colour schemes by setting <tt class="docutils literal"><span class="pre">"colour_scheme_index"</span></tt>:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span> <span class="p">(</span><span class="s">"flowchart.svg"</span><span class="p">,</span> <span class="s">"svg"</span><span class="p">,</span> <span class="p">[</span><span class="n">final_task</span><span class="p">],</span>
-                          <span class="n">user_colour_scheme</span> <span class="o">=</span> <span class="p">{</span><span class="s">"colour_scheme_index"</span> <span class="p">:</span><span class="mi">6</span><span class="p">})</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>These colours were chosen after much fierce arguments between the authors and friends, and much
-inspiration from  <a class="reference external" href="http://kuler.adobe.com/#create/fromacolor">http://kuler.adobe.com/#create/fromacolor</a>. Please
-feel free to submit any additional sets of colours for our consideration.</p>
-<p>(Click here for image in <a class="reference download internal" href="../../_downloads/flowchart_colour_schemes.svg"><tt class="xref download docutils literal"><span class="pre">svg</span></tt></a>.)</p>
-<img alt="../../_images/flowchart_colour_schemes.png" src="../../_images/flowchart_colour_schemes.png" />
-</div>
-</div>
-
-
-          </div>
-        </div>
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-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Appendix 1</strong>: Flow Chart Colours with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a><ul>
-<li><a class="reference internal" href="#flowchart-colours">Flowchart colours</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="check_if_uptodate.html"
-                        title="previous chapter"><strong>Chapter 23</strong>: Esoteric: Writing custom functions to decide which jobs are up to date with <tt class="docutils literal"><span class="pre">@check_if_uptodate</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="dependencies.html"
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-  <div class="section" id="new-manual-flowchart-colours-chapter-num-python-code-for-flow-chart-colours-with-pipeline-printout-graph">
-<span id="new-manual-flowchart-colours-code"></span><span id="index-0"></span><h1><strong>Appendix 1</strong>: Python code for Flow Chart Colours with <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a><a class="headerlink" href="#new-manual-flowchart-colours-chapter-num-python-code-for-flow-chart-colours-with-pipeline-printout-graph" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a></li>
-<li><a class="reference download internal" href="../../_downloads/play_with_colours.py"><tt class="xref download docutils literal"><span class="pre">Download</span> <span class="pre">code</span></tt></a></li>
-<li>Back to <a class="reference internal" href="flowchart_colours.html#new-manual-flowchart-colours"><em>Flowchart colours</em></a></li>
-</ul>
-<p class="last">This example shows how flowchart colours can be customised.</p>
-</div>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#!/usr/bin/env python</span>
-<span class="sd">"""</span>
-
-<span class="sd">    play_with_colours.py</span>
-<span class="sd">    [--log_file PATH]</span>
-<span class="sd">    [--verbose]</span>
-
-<span class="sd">"""</span>
-
-<span class="c">################################################################################</span>
-<span class="c">#</span>
-<span class="c">#   play_with_colours.py</span>
-<span class="c">#</span>
-<span class="c">#</span>
-<span class="c">#   Copyright (c) 7/13/2010 Leo Goodstadt</span>
-<span class="c">#</span>
-<span class="c">#   Permission is hereby granted, free of charge, to any person obtaining a copy</span>
-<span class="c">#   of this software and associated documentation files (the "Software"), to deal</span>
-<span class="c">#   in the Software without restriction, including without limitation the rights</span>
-<span class="c">#   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
-<span class="c">#   copies of the Software, and to permit persons to whom the Software is</span>
-<span class="c">#   furnished to do so, subject to the following conditions:</span>
-<span class="c">#</span>
-<span class="c">#   The above copyright notice and this permission notice shall be included in</span>
-<span class="c">#   all copies or substantial portions of the Software.</span>
-<span class="c">#</span>
-<span class="c">#   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
-<span class="c">#   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
-<span class="c">#   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</span>
-<span class="c">#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
-<span class="c">#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</span>
-<span class="c">#   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN</span>
-<span class="c">#   THE SOFTWARE.</span>
-<span class="c">#################################################################################</span>
-
-<span class="kn">import</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">os</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   options</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-
-<span class="kn">from</span> <span class="nn">optparse</span> <span class="kn">import</span> <span class="n">OptionParser</span>
-<span class="kn">import</span> <span class="nn">StringIO</span>
-
-<span class="n">parser</span> <span class="o">=</span> <span class="n">OptionParser</span><span class="p">(</span><span class="n">version</span><span class="o">=</span><span class="s">"%play_with_colours 1.0"</span><span class="p">,</span>
-                      <span class="n">usage</span> <span class="o">=</span> <span class="s">"</span><span class="se">\n\n</span><span class="s">    play_with_colours "</span>
-                                <span class="s">"--flowchart FILE [options] "</span>
-                                <span class="s">"[--colour_scheme_index INT ] "</span>
-                                <span class="s">"[--key_legend_in_graph]"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   pipeline</span>
-<span class="c">#</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"--flowchart"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"flowchart"</span><span class="p">,</span>
-                    <span class="n">metavar</span><span class="o">=</span><span class="s">"FILE"</span><span class="p">,</span>
-                    <span class="nb">type</span><span class="o">=</span><span class="s">"string"</span><span class="p">,</span>
-                    <span class="n">help</span><span class="o">=</span><span class="s">"Don't actually run any commands; just print the pipeline "</span>
-                         <span class="s">"as a flowchart."</span><span class="p">)</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"--colour_scheme_index"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"colour_scheme_index"</span><span class="p">,</span>
-                    <span class="n">metavar</span><span class="o">=</span><span class="s">"INTEGER"</span><span class="p">,</span>
-                    <span class="nb">type</span><span class="o">=</span><span class="s">"int"</span><span class="p">,</span>
-                    <span class="n">help</span><span class="o">=</span><span class="s">"Index of colour scheme for flow chart."</span><span class="p">)</span>
-<span class="n">parser</span><span class="o">.</span><span class="n">add_option</span><span class="p">(</span><span class="s">"--key_legend_in_graph"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s">"key_legend_in_graph"</span><span class="p">,</span>
-                    <span class="n">action</span><span class="o">=</span><span class="s">"store_true"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
-                    <span class="n">help</span><span class="o">=</span><span class="s">"Print out legend and key for dependency graph."</span><span class="p">)</span>
-
-<span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">remaining_args</span><span class="p">)</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
-<span class="k">if</span> <span class="ow">not</span> <span class="n">options</span><span class="o">.</span><span class="n">flowchart</span><span class="p">:</span>
-    <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"Missing mandatory parameter: --flowchart.</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   imports</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.ruffus_exceptions</span> <span class="kn">import</span> <span class="n">JobSignalledBreak</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Pipeline</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-
-<span class="c">#</span>
-<span class="c"># up to date tasks</span>
-<span class="c">#</span>
-<span class="nd">@check_if_uptodate</span> <span class="p">(</span><span class="k">lambda</span> <span class="p">:</span> <span class="p">(</span><span class="bp">False</span><span class="p">,</span> <span class="s">""</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">Up_to_date_task1</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@check_if_uptodate</span> <span class="p">(</span><span class="k">lambda</span> <span class="p">:</span> <span class="p">(</span><span class="bp">False</span><span class="p">,</span> <span class="s">""</span><span class="p">))</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Up_to_date_task1</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Up_to_date_task2</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@check_if_uptodate</span> <span class="p">(</span><span class="k">lambda</span> <span class="p">:</span> <span class="p">(</span><span class="bp">False</span><span class="p">,</span> <span class="s">""</span><span class="p">))</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Up_to_date_task2</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Up_to_date_task3</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-<span class="nd">@check_if_uptodate</span> <span class="p">(</span><span class="k">lambda</span> <span class="p">:</span> <span class="p">(</span><span class="bp">False</span><span class="p">,</span> <span class="s">""</span><span class="p">))</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Up_to_date_task3</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Up_to_date_final_target</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-<span class="c">#</span>
-<span class="c"># Explicitly specified</span>
-<span class="c">#</span>
-<span class="nd">@check_if_uptodate</span> <span class="p">(</span><span class="k">lambda</span> <span class="p">:</span> <span class="p">(</span><span class="bp">False</span><span class="p">,</span> <span class="s">""</span><span class="p">))</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Up_to_date_task1</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Explicitly_specified_task</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-
-<span class="c">#</span>
-<span class="c"># Tasks to run</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Explicitly_specified_task</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Task_to_run1</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Task_to_run1</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Task_to_run2</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Task_to_run2</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Task_to_run3</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@check_if_uptodate</span> <span class="p">(</span><span class="k">lambda</span> <span class="p">:</span> <span class="p">(</span><span class="bp">False</span><span class="p">,</span> <span class="s">""</span><span class="p">))</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Task_to_run2</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Up_to_date_task_forced_to_rerun</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-<span class="c">#</span>
-<span class="c"># Final target</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Up_to_date_task_forced_to_rerun</span><span class="p">,</span> <span class="n">Task_to_run3</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Final_target</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="c">#</span>
-<span class="c"># Ignored downstream</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Final_target</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Downstream_task1_ignored</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">Final_target</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Downstream_task2_ignored</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-
-
-
-
-
-
-
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Main logic</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">defaultdict</span>
-<span class="n">custom_flow_chart_colour_scheme</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">dict</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   Base chart on this overall colour scheme index</span>
-<span class="c">#</span>
-<span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"colour_scheme_index"</span><span class="p">]</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">colour_scheme_index</span>
-
-<span class="c">#</span>
-<span class="c">#   Overriding colours</span>
-<span class="c">#</span>
-<span class="k">if</span> <span class="n">options</span><span class="o">.</span><span class="n">colour_scheme_index</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Vicious cycle"</span><span class="p">][</span><span class="s">"linecolor"</span><span class="p">]</span>                        <span class="o">=</span> <span class="s">'"#FF3232"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Pipeline"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>                             <span class="o">=</span> <span class="s">'"#FF3232"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Key"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>                                  <span class="o">=</span> <span class="s">"black"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Key"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>                                  <span class="o">=</span> <span class="s">'"#F6F4F4"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Task to run"</span><span class="p">][</span><span class="s">"linecolor"</span><span class="p">]</span>                          <span class="o">=</span> <span class="s">'"#0044A0"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date"</span><span class="p">][</span><span class="s">"linecolor"</span><span class="p">]</span>                           <span class="o">=</span> <span class="s">"gray"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Final target"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>                         <span class="o">=</span> <span class="s">'"#EFA03B"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Final target"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>                         <span class="o">=</span> <span class="s">"black"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Final target"</span><span class="p">][</span><span class="s">"color"</span><span class="p">]</span>                             <span class="o">=</span> <span class="s">"black"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Final target"</span><span class="p">][</span><span class="s">"dashed"</span><span class="p">]</span>                            <span class="o">=</span> <span class="mi">0</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Vicious cycle"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>                        <span class="o">=</span> <span class="s">'"#FF3232"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Vicious cycle"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>                        <span class="o">=</span> <span class="s">'white'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Vicious cycle"</span><span class="p">][</span><span class="s">"color"</span><span class="p">]</span>                            <span class="o">=</span> <span class="s">"white"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Vicious cycle"</span><span class="p">][</span><span class="s">"dashed"</span><span class="p">]</span>                           <span class="o">=</span> <span class="mi">0</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date task"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>                      <span class="o">=</span> <span class="s">'"#B8CC6E"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date task"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>                      <span class="o">=</span> <span class="s">'"#006000"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date task"</span><span class="p">][</span><span class="s">"color"</span><span class="p">]</span>                          <span class="o">=</span> <span class="s">'"#006000"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date task"</span><span class="p">][</span><span class="s">"dashed"</span><span class="p">]</span>                         <span class="o">=</span> <span class="mi">0</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Down stream"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>                          <span class="o">=</span> <span class="s">"white"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Down stream"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>                          <span class="o">=</span> <span class="s">"gray"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Down stream"</span><span class="p">][</span><span class="s">"color"</span><span class="p">]</span>                              <span class="o">=</span> <span class="s">"gray"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Down stream"</span><span class="p">][</span><span class="s">"dashed"</span><span class="p">]</span>                             <span class="o">=</span> <span class="mi">0</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Explicitly specified task"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>            <span class="o">=</span> <span class="s">"transparent"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Explicitly specified task"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>            <span class="o">=</span> <span class="s">"black"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Explicitly specified task"</span><span class="p">][</span><span class="s">"color"</span><span class="p">]</span>                <span class="o">=</span> <span class="s">"black"</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Explicitly specified task"</span><span class="p">][</span><span class="s">"dashed"</span><span class="p">]</span>               <span class="o">=</span> <span class="mi">0</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Task to run"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>                          <span class="o">=</span> <span class="s">'"#EBF3FF"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Task to run"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>                          <span class="o">=</span> <span class="s">'"#0044A0"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Task to run"</span><span class="p">][</span><span class="s">"color"</span><span class="p">]</span>                              <span class="o">=</span> <span class="s">'"#0044A0"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Task to run"</span><span class="p">][</span><span class="s">"dashed"</span><span class="p">]</span>                             <span class="o">=</span> <span class="mi">0</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date task forced to rerun"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>      <span class="o">=</span> <span class="s">'transparent'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date task forced to rerun"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>      <span class="o">=</span> <span class="s">'"#0044A0"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date task forced to rerun"</span><span class="p">][</span><span class="s">"color"</span><span class="p">]</span>          <span class="o">=</span> <span class="s">'"#0044A0"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date task forced to rerun"</span><span class="p">][</span><span class="s">"dashed"</span><span class="p">]</span>         <span class="o">=</span> <span class="mi">1</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date Final target"</span><span class="p">][</span><span class="s">"fillcolor"</span><span class="p">]</span>              <span class="o">=</span> <span class="s">'"#EFA03B"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date Final target"</span><span class="p">][</span><span class="s">"fontcolor"</span><span class="p">]</span>              <span class="o">=</span> <span class="s">'"#006000"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date Final target"</span><span class="p">][</span><span class="s">"color"</span><span class="p">]</span>                  <span class="o">=</span> <span class="s">'"#006000"'</span>
-    <span class="n">custom_flow_chart_colour_scheme</span><span class="p">[</span><span class="s">"Up-to-date Final target"</span><span class="p">][</span><span class="s">"dashed"</span><span class="p">]</span>                 <span class="o">=</span> <span class="mi">0</span>
-
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
-    <span class="n">pipeline_printout_graph</span> <span class="p">(</span>
-
-                                    <span class="nb">open</span><span class="p">(</span><span class="n">options</span><span class="o">.</span><span class="n">flowchart</span><span class="p">,</span> <span class="s">"w"</span><span class="p">),</span>
-                                    <span class="c"># use flowchart file name extension to decide flowchart format</span>
-                                    <span class="c">#   e.g. svg, jpg etc.</span>
-                                    <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">options</span><span class="o">.</span><span class="n">flowchart</span><span class="p">)[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">:],</span>
-
-                                    <span class="c"># final targets</span>
-                                    <span class="p">[</span><span class="n">Final_target</span><span class="p">,</span> <span class="n">Up_to_date_final_target</span><span class="p">],</span>
-
-                                    <span class="c"># Explicitly specified tasks</span>
-                                    <span class="p">[</span><span class="n">Explicitly_specified_task</span><span class="p">],</span>
-
-                                    <span class="c"># Do we want key legend</span>
-                                    <span class="n">no_key_legend</span>   <span class="o">=</span> <span class="ow">not</span> <span class="n">options</span><span class="o">.</span><span class="n">key_legend_in_graph</span><span class="p">,</span>
-
-                                    <span class="c"># Print all the task types whether used or not</span>
-                                    <span class="n">minimal_key_legend</span>             <span class="o">=</span> <span class="bp">False</span><span class="p">,</span>
-
-                                    <span class="n">user_colour_scheme</span> <span class="o">=</span> <span class="n">custom_flow_chart_colour_scheme</span><span class="p">,</span>
-                                    <span class="n">pipeline_name</span> <span class="o">=</span> <span class="s">"Colour schemes"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
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-        <div class="sphinxsidebarwrapper">
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-  <div class="section" id="new-manual-inputs-chapter-num-manipulating-task-inputs-via-string-substitution-using-inputs-and-add-inputs">
-<span id="new-manual-inputs"></span><span id="index-0"></span><h1><strong>Chapter 20</strong>: Manipulating task inputs via string substitution using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs()</em></a> and  <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a><a class="headerlink" href="#new-manual-inputs-chapter-num-manipulating-task-inputs-via-string-s [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs()</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a> syntax</li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><a class="reference internal" href="inputs_code.html#new-manual-inputs-code"><em>Chapter 20: Python Code for Manipulating task inputs via string substitution using inputs()  and  add_inputs()</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The previous chapters have been described how <em>Ruffus</em> allows the <strong>Output</strong> names for each job
-to be generated from the <em>Input</em> names via string substitution. This is how <em>Ruffus</em> can
-automatically chain multiple tasks in a pipeline together seamlessly.</p>
-<p>Sometimes it is useful to be able to modify the <strong>Input</strong>  by string substitution
-as well. There are two situations where this additional flexibility is needed:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>You need to add additional prequisites or filenames to the <strong>Input</strong> of every single job</li>
-<li>You need to add additional <strong>Input</strong> file names which are some variant of the existing ones.</li>
-</ol>
-</div></blockquote>
-<p>Both will be much more obvious with some examples</p>
-</div></blockquote>
-</div>
-<div class="section" id="adding-additional-input-prerequisites-per-job-with-add-inputs">
-<h2>Adding additional <em>input</em> prerequisites per job with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a><a class="headerlink" href="#adding-additional-input-prerequisites-per-job-with-add-inputs" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="example-compiling-c-code">
-<h3>1. Example: compiling c++ code<a class="headerlink" href="#example-compiling-c-code" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Let us first compile some c++ (<tt class="docutils literal"><span class="pre">"*.cpp"</span></tt>) files using plain <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> syntax:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c"># source files exist before our pipeline</span>
-<span class="n">source_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="s">"messy.cpp"</span><span class="p">]</span>
-<span class="k">for</span> <span class="n">source_file</span> <span class="ow">in</span> <span class="n">source_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-adding-a-common-header-file-with-add-inputs">
-<h3>2. Example: Adding a common header file with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a><a class="headerlink" href="#example-adding-a-common-header-file-with-add-inputs" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># source files exist before our pipeline</span>
-<span class="n">source_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="s">"messy.cpp"</span><span class="p">]</span>
-<span class="k">for</span> <span class="n">source_file</span> <span class="ow">in</span> <span class="n">source_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c"># common (universal) header exists before our pipeline</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="hll"><span class="c"># make header files</span>
-</span><span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="s">".h"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_matching_headers</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span>
-<span class="hll">                        <span class="c"># add header to the input of every job</span>
-</span>            <span class="n">add_inputs</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span>
-<span class="hll">                        <span class="c"># add result of task create_matching_headers to the input of every job</span>
-</span>                       <span class="n">create_matching_headers</span><span class="p">),</span>
-            <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-
-    <span class="o">>>></span> <span class="n">pipeline_run</span><span class="p">()</span>
-        <span class="n">Job</span>  <span class="o">=</span> <span class="p">[</span><span class="n">hasty</span><span class="o">.</span><span class="n">cpp</span> <span class="o">-></span> <span class="n">hasty</span><span class="o">.</span><span class="n">h</span><span class="p">]</span> <span class="n">completed</span>
-        <span class="n">Job</span>  <span class="o">=</span> <span class="p">[</span><span class="n">messy</span><span class="o">.</span><span class="n">cpp</span> <span class="o">-></span> <span class="n">messy</span><span class="o">.</span><span class="n">h</span><span class="p">]</span> <span class="n">completed</span>
-        <span class="n">Job</span>  <span class="o">=</span> <span class="p">[</span><span class="n">tasty</span><span class="o">.</span><span class="n">cpp</span> <span class="o">-></span> <span class="n">tasty</span><span class="o">.</span><span class="n">h</span><span class="p">]</span> <span class="n">completed</span>
-    <span class="n">Completed</span> <span class="n">Task</span> <span class="o">=</span> <span class="n">create_matching_headers</span>
-        <span class="n">Job</span>  <span class="o">=</span> <span class="p">[[</span><span class="n">hasty</span><span class="o">.</span><span class="n">cpp</span><span class="p">,</span> <span class="n">universal</span><span class="o">.</span><span class="n">h</span><span class="p">,</span> <span class="n">hasty</span><span class="o">.</span><span class="n">h</span><span class="p">,</span> <span class="n">messy</span><span class="o">.</span><span class="n">h</span><span class="p">,</sp [...]
-        <span class="n">Job</span>  <span class="o">=</span> <span class="p">[[</span><span class="n">messy</span><span class="o">.</span><span class="n">cpp</span><span class="p">,</span> <span class="n">universal</span><span class="o">.</span><span class="n">h</span><span class="p">,</span> <span class="n">hasty</span><span class="o">.</span><span class="n">h</span><span class="p">,</span> <span class="n">messy</span><span class="o">.</span><span class="n">h</span><span class="p">,</sp [...]
-        <span class="n">Job</span>  <span class="o">=</span> <span class="p">[[</span><span class="n">tasty</span><span class="o">.</span><span class="n">cpp</span><span class="p">,</span> <span class="n">universal</span><span class="o">.</span><span class="n">h</span><span class="p">,</span> <span class="n">hasty</span><span class="o">.</span><span class="n">h</span><span class="p">,</span> <span class="n">messy</span><span class="o">.</span><span class="n">h</span><span class="p">,</sp [...]
-    <span class="n">Completed</span> <span class="n">Task</span> <span class="o">=</span> <span class="nb">compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-additional-input-can-be-tasks">
-<h3>3. Example: Additional <em>Input</em> can be tasks<a class="headerlink" href="#example-additional-input-can-be-tasks" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>We can also add a task name to <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a>.
-This chains the <strong>Output</strong>, i.e. run time results, of any previous task as
-an additional <strong>Input</strong> to every single job in the task.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="hll"><span class="c"># make header files</span>
-</span><span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="s">".h"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_matching_headers</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span>
-<span class="hll">                        <span class="c"># add header to the input of every job</span>
-</span>            <span class="n">add_inputs</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span>
-<span class="hll">                        <span class="c"># add result of task create_matching_headers to the input of every job</span>
-</span>                       <span class="n">create_matching_headers</span><span class="p">),</span>
-            <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [[hasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> hasty.o] completed</span>
-<span class="go">    Job  = [[messy.cpp, universal.h, hasty.h, messy.h, tasty.h] -> messy.o] completed</span>
-<span class="go">    Job  = [[tasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="example-add-corresponding-files-using-add-inputs-with-formatter-or-regex">
-<h3>4. Example: Add corresponding files using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a> with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter</em></a> or <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex</em></a><a class="headerlink" href="#example-add-corresponding-files-using-add-inputs-wi [...]
-<blockquote>
-<div><p>The previous example created headers corresponding to our source files and added them
-as the <strong>Input</strong> to the compilation. That is generally not what you want. Instead,
-what is generally need is a way to</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Look up the exact corresponding header for the <em>specific</em> job, and not add all
-possible files to all jobs in a task. When compiling <tt class="docutils literal"><span class="pre">hasty.cpp</span></tt>, we just need
-to add <tt class="docutils literal"><span class="pre">hasty.h</span></tt> (and <tt class="docutils literal"><span class="pre">universal.h</span></tt>).</li>
-<li>Add a pre-existing file name (<tt class="docutils literal"><span class="pre">hasty.h</span></tt> already exists. Don’t create it via
-another task.)</li>
-</ol>
-</div></blockquote>
-<p>This is a surprisingly common requirement: In bioinformatics sometimes DNA or RNA
-sequence files come singly in  <a class="reference external" href="http://en.wikipedia.org/wiki/FASTQ_format">*.fastq</a>
-and sometimes in <a class="reference external" href="http://en.wikipedia.org/wiki/DNA_sequencing_theory#Pairwise_end-sequencing">matching pairs</a>:
-<tt class="docutils literal"><span class="pre">*1.fastq,</span> <span class="pre">*2.fastq</span></tt> etc. In the latter case, we often need to make sure that both
-sequence files are being processed in tandem. One way is to take one file name (<tt class="docutils literal"><span class="pre">*1.fastq</span></tt>)
-and look up the other.</p>
-<blockquote>
-<div><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a> uses standard <em>Ruffus</em> string substitution
-via <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter</em></a> and <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex</em></a> to lookup (generate) <strong>Input</strong> file names.
-(As a rule <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix</em></a> only substitutes <strong>Output</strong> file names.)</div></blockquote>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span> <span class="n">source_files</span><span class="p">,</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">".cpp$"</span><span class="p">),</span>
-<span class="hll">                        <span class="c"># corresponding header for each source file</span>
-</span>            <span class="n">add_inputs</span><span class="p">(</span><span class="s">"{basename[0]}.h"</span><span class="p">,</span>
-<span class="hll">                       <span class="c"># add header to the input of every job</span>
-</span>                       <span class="s">"universal.h"</span><span class="p">),</span>
-            <span class="s">"{basename[0]}.o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This script gives the following output</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [[hasty.cpp, hasty.h, universal.h] -> hasty.o] completed</span>
-<span class="go">    Job  = [[messy.cpp, messy.h, universal.h] -> messy.o] completed</span>
-<span class="go">    Job  = [[tasty.cpp, tasty.h, universal.h] -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="replacing-all-input-parameters-with-inputs">
-<h2>Replacing all input parameters with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs()</em></a><a class="headerlink" href="#replacing-all-input-parameters-with-inputs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div>The previous examples all <em>added</em> to the set of <strong>Input</strong> file names.
-Sometimes it is necessary to replace all the <strong>Input</strong> parameters altogether.</div></blockquote>
-<div class="section" id="example-running-matching-python-scripts-using-inputs">
-<h3>5. Example: Running matching python scripts using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs()</em></a><a class="headerlink" href="#example-running-matching-python-scripts-using-inputs" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Here is a contrived example: we wish to find all cython/python files which have been
-compiled into corresponding c++ source files.
-Instead of compiling the c++, we shall invoke the corresponding python scripts.</p>
-<p>Given three c++ files and their corresponding python scripts:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span> <span class="n">source_files</span><span class="p">,</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">".cpp$"</span><span class="p">),</span>
-
-<span class="hll">            <span class="c"># corresponding python file for each source file</span>
-</span>            <span class="n">inputs</span><span class="p">(</span><span class="s">"{basename[0]}.py"</span><span class="p">),</span>
-
-            <span class="s">"{basename[0]}.results"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">run_corresponding_python</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The <em>Ruffus</em> code will call each python script corresponding to their c++ counterpart:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [hasty.py -> hasty.results] completed</span>
-<span class="go">    Job  = [messy.py -> messy.results] completed</span>
-<span class="go">    Job  = [tasty.py -> tasty.results] completed</span>
-<span class="go">Completed Task = run_corresponding_python</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 20</strong>: Manipulating task inputs via string substitution using <tt class="docutils literal"><span class="pre">inputs()</span></tt> and  <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#adding-additional-input-prerequisites-per-job-with-add-inputs">Adding additional <em>input</em> prerequisites per job with <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a><ul>
-<li><a class="reference internal" href="#example-compiling-c-code">1. Example: compiling c++ code</a></li>
-<li><a class="reference internal" href="#example-adding-a-common-header-file-with-add-inputs">2. Example: Adding a common header file with <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a></li>
-<li><a class="reference internal" href="#example-additional-input-can-be-tasks">3. Example: Additional <em>Input</em> can be tasks</a></li>
-<li><a class="reference internal" href="#example-add-corresponding-files-using-add-inputs-with-formatter-or-regex">4. Example: Add corresponding files using <tt class="docutils literal"><span class="pre">add_inputs()</span></tt> with <tt class="docutils literal"><span class="pre">formatter</span></tt> or <tt class="docutils literal"><span class="pre">regex</span></tt></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#replacing-all-input-parameters-with-inputs">Replacing all input parameters with <tt class="docutils literal"><span class="pre">inputs()</span></tt></a><ul>
-<li><a class="reference internal" href="#example-running-matching-python-scripts-using-inputs">5. Example: Running matching python scripts using <tt class="docutils literal"><span class="pre">inputs()</span></tt></a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="posttask.html"
-                        title="previous chapter"><strong>Chapter 19</strong>: Signal the completion of each stage of our pipeline with <tt class="docutils literal"><span class="pre">@posttask</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="onthefly.html"
-                        title="next chapter"><strong>Chapter 21</strong>: Esoteric: Generating parameters on the fly with <tt class="docutils literal"><span class="pre">@files</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/inputs.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
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-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-         <a href="../../todo.html">Future plans</a>
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-  <div class="section" id="new-manual-inputs-chapter-num-python-code-for-manipulating-task-inputs-via-string-substitution-using-inputs-and-add-inputs">
-<span id="new-manual-inputs-code"></span><h1><strong>Chapter 20</strong>: Python Code for Manipulating task inputs via string substitution using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs()</em></a>  and  <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a><a class="headerlink" href="#new-manual-inputs-chapter-num-python-code-for-manipulating-task-inputs- [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs()</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a> syntax</li>
-<li>Back to <strong>Chapter 20</strong>: <a class="reference internal" href="inputs.html#new-manual-inputs"><em>Manipulating task inputs via string substitution</em></a></li>
-</ul>
-</div>
-<div class="section" id="example-code-for-adding-additional-input-prerequisites-per-job-with-add-inputs">
-<h2>Example code for adding additional <em>input</em> prerequisites per job with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a><a class="headerlink" href="#example-code-for-adding-additional-input-prerequisites-per-job-with-add-inputs" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="example-compiling-c-code">
-<span id="new-manual-inputs-example1"></span><h3>1. Example: compiling c++ code<a class="headerlink" href="#example-compiling-c-code" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># source files exist before our pipeline</span>
-<span class="n">source_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="s">"messy.cpp"</span><span class="p">]</span>
-<span class="k">for</span> <span class="n">source_file</span> <span class="ow">in</span> <span class="n">source_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>Giving:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [hasty.cpp -> hasty.o] completed</span>
-<span class="go">    Job  = [messy.cpp -> messy.o] completed</span>
-<span class="go">    Job  = [tasty.cpp -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="example-adding-a-common-header-file-with-add-inputs">
-<span id="new-manual-inputs-example2"></span><h3>2. Example: Adding a common header file with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a><a class="headerlink" href="#example-adding-a-common-header-file-with-add-inputs" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># source files exist before our pipeline</span>
-<span class="n">source_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="s">"messy.cpp"</span><span class="p">]</span>
-<span class="k">for</span> <span class="n">source_file</span> <span class="ow">in</span> <span class="n">source_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c"># common (universal) header exists before our pipeline</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@transform</span><span class="p">(</span> <span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span>
-<span class="hll">            <span class="c"># add header to the input of every job</span>
-</span>            <span class="n">add_inputs</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">),</span>
-            <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>Giving:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [[hasty.cpp, universal.h] -> hasty.o] completed</span>
-<span class="go">    Job  = [[messy.cpp, universal.h] -> messy.o] completed</span>
-<span class="go">    Job  = [[tasty.cpp, universal.h] -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="example-additional-input-can-be-tasks">
-<span id="new-manual-inputs-example3"></span><h3>3. Example: Additional <em>Input</em> can be tasks<a class="headerlink" href="#example-additional-input-can-be-tasks" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># source files exist before our pipeline</span>
-<span class="n">source_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="s">"messy.cpp"</span><span class="p">]</span>
-<span class="k">for</span> <span class="n">source_file</span> <span class="ow">in</span> <span class="n">source_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c"># common (universal) header exists before our pipeline</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="hll"><span class="c"># make header files</span>
-</span><span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span> <span class="s">".h"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_matching_headers</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">source_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".cpp"</span><span class="p">),</span>
-<span class="hll">                        <span class="c"># add header to the input of every job</span>
-</span>            <span class="n">add_inputs</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span>
-<span class="hll">                        <span class="c"># add result of task create_matching_headers to the input of every job</span>
-</span>                       <span class="n">create_matching_headers</span><span class="p">),</span>
-            <span class="s">".o"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>Giving:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [hasty.cpp -> hasty.h] completed</span>
-<span class="go">    Job  = [messy.cpp -> messy.h] completed</span>
-<span class="go">    Job  = [tasty.cpp -> tasty.h] completed</span>
-<span class="go">Completed Task = create_matching_headers</span>
-<span class="go">    Job  = [[hasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> hasty.o] completed</span>
-<span class="go">    Job  = [[messy.cpp, universal.h, hasty.h, messy.h, tasty.h] -> messy.o] completed</span>
-<span class="go">    Job  = [[tasty.cpp, universal.h, hasty.h, messy.h, tasty.h] -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="example-add-corresponding-files-using-add-inputs-with-formatter-or-regex">
-<span id="new-manual-inputs-example4"></span><h3>4. Example: Add corresponding files using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>add_inputs()</em></a> with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter</em></a> or <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex</em></a><a class="headerlink" href="#exampl [...]
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># source files exist before our pipeline</span>
-<span class="n">source_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="s">"messy.cpp"</span><span class="p">]</span>
-<span class="n">header_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.h"</span><span class="p">,</span> <span class="s">"tasty.h"</span><span class="p">,</span> <span class="s">"messy.h"</span><span class="p">]</span>
-<span class="k">for</span> <span class="n">source_file</span> <span class="ow">in</span> <span class="n">source_files</span> <span class="o">+</span> <span class="n">header_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c"># common (universal) header exists before our pipeline</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="hll">
-</span><span class="nd">@transform</span><span class="p">(</span> <span class="n">source_files</span><span class="p">,</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">".cpp$"</span><span class="p">),</span>
-                        <span class="c"># corresponding header for each source file</span>
-            <span class="n">add_inputs</span><span class="p">(</span><span class="s">"{basename[0]}.h"</span><span class="p">,</span>
-                       <span class="c"># add header to the input of every job</span>
-<span class="hll">                       <span class="s">"universal.h"</span><span class="p">),</span>
-</span>            <span class="s">"{basename[0]}.o"</span><span class="p">)</span>
-<span class="hll"><span class="k">def</span> <span class="nf">compile</span><span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-</span>    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>Giving:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [[hasty.cpp, hasty.h, universal.h] -> hasty.o] completed</span>
-<span class="go">    Job  = [[messy.cpp, messy.h, universal.h] -> messy.o] completed</span>
-<span class="go">    Job  = [[tasty.cpp, tasty.h, universal.h] -> tasty.o] completed</span>
-<span class="go">Completed Task = compile</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="example-code-for-replacing-all-input-parameters-with-inputs">
-<h2>Example code for replacing all input parameters with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs()</em></a><a class="headerlink" href="#example-code-for-replacing-all-input-parameters-with-inputs" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="example-running-matching-python-scripts-using-inputs">
-<span id="new-manual-inputs-example5"></span><h3>5. Example: Running matching python scripts using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs()</em></a><a class="headerlink" href="#example-running-matching-python-scripts-using-inputs" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># source files exist before our pipeline</span>
-<span class="n">source_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.cpp"</span><span class="p">,</span> <span class="s">"tasty.cpp"</span><span class="p">,</span> <span class="s">"messy.cpp"</span><span class="p">]</span>
-<span class="n">python_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"hasty.py"</span><span class="p">,</span> <span class="s">"tasty.py"</span><span class="p">,</span> <span class="s">"messy.py"</span><span class="p">]</span>
-<span class="k">for</span> <span class="n">source_file</span> <span class="ow">in</span> <span class="n">source_files</span> <span class="o">+</span> <span class="n">python_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">source_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c"># common (universal) header exists before our pipeline</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"universal.h"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="hll">
-</span><span class="nd">@transform</span><span class="p">(</span> <span class="n">source_files</span><span class="p">,</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">".cpp$"</span><span class="p">),</span>
-            <span class="c"># corresponding python file for each source file</span>
-            <span class="n">inputs</span><span class="p">(</span><span class="s">"{basename[0]}.py"</span><span class="p">),</span>
-
-<span class="hll">            <span class="s">"{basename[0]}.results"</span><span class="p">)</span>
-</span><span class="k">def</span> <span class="nf">run_corresponding_python</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-<span class="hll">    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>Giving:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [hasty.py -> hasty.results] completed</span>
-<span class="go">    Job  = [messy.py -> messy.results] completed</span>
-<span class="go">    Job  = [tasty.py -> tasty.results] completed</span>
-<span class="go">Completed Task = run_corresponding_python</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 20</strong>: Python Code for Manipulating task inputs via string substitution using <tt class="docutils literal"><span class="pre">inputs()</span></tt>  and  <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a><ul>
-<li><a class="reference internal" href="#example-code-for-adding-additional-input-prerequisites-per-job-with-add-inputs">Example code for adding additional <em>input</em> prerequisites per job with <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a><ul>
-<li><a class="reference internal" href="#example-compiling-c-code">1. Example: compiling c++ code</a></li>
-<li><a class="reference internal" href="#example-adding-a-common-header-file-with-add-inputs">2. Example: Adding a common header file with <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a></li>
-<li><a class="reference internal" href="#example-additional-input-can-be-tasks">3. Example: Additional <em>Input</em> can be tasks</a></li>
-<li><a class="reference internal" href="#example-add-corresponding-files-using-add-inputs-with-formatter-or-regex">4. Example: Add corresponding files using <tt class="docutils literal"><span class="pre">add_inputs()</span></tt> with <tt class="docutils literal"><span class="pre">formatter</span></tt> or <tt class="docutils literal"><span class="pre">regex</span></tt></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#example-code-for-replacing-all-input-parameters-with-inputs">Example code for replacing all input parameters with <tt class="docutils literal"><span class="pre">inputs()</span></tt></a><ul>
-<li><a class="reference internal" href="#example-running-matching-python-scripts-using-inputs">5. Example: Running matching python scripts using <tt class="docutils literal"><span class="pre">inputs()</span></tt></a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="combinatorics_code.html"
-                        title="previous chapter"><strong>Chapter 17</strong>: Python Code for <tt class="docutils literal"><span class="pre">@combinations</span></tt>, <tt class="docutils literal"><span class="pre">@permutations</span></tt> and all versus all <tt class="docutils literal"><span class="pre">@product</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="onthefly_code.html"
-                        title="next chapter"><strong>Chapter 21</strong>: Esoteric: Python Code for Generating parameters on the fly with <tt class="docutils literal"><span class="pre">@files</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/inputs_code.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../../search.html" method="get">
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-      <input type="hidden" name="area" value="default" />
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-<div class="section" id="new-manual-introduction-chapter-num-an-introduction-to-basic-ruffus-syntax">
-<span id="new-manual-introduction"></span><span id="index-0"></span><h1><strong>Chapter 1</strong>: An introduction to basic <em>Ruffus</em> syntax<a class="headerlink" href="#new-manual-introduction-chapter-num-an-introduction-to-basic-ruffus-syntax" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/theoretical_pipeline_schematic.png"><img alt="../../_images/theoretical_pipeline_schematic.png" src="../../_images/theoretical_pipeline_schematic.png" style="width: 610.0px; height: 71.0px;" /></a>
-<p>Computational pipelines transform your data in stages until the final result is produced.
-One easy way to understand pipelines is by imagining your data flowing across a series of
-pipes until it reaches its final destination. Even quite complicated processes can be
-broken into simple stages. Of course, it helps to visualise the whole process.</p>
-<p><em>Ruffus</em> is a way of automating the plumbing in your pipeline: You supply the python functions
-which perform the data transformation, and tell <em>Ruffus</em> how these pipeline <tt class="docutils literal"><span class="pre">task</span></tt> functions
-are connected up. <em>Ruffus</em> will make sure that the right data flows down your pipeline in the
-right way at the right time.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last"><em>Ruffus</em> refers to each stage of your pipeline as a <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>.</p>
-</div>
-</div></blockquote>
-<span class="target" id="new-manual-introduction-import"></span></div>
-<div class="section" id="importing-ruffus">
-<span id="index-1"></span><h2>Importing <em>Ruffus</em><a class="headerlink" href="#importing-ruffus" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The most convenient way to use <em>Ruffus</em> is to import the various names directly:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This will allow <em>Ruffus</em> terms to be used directly in your code. This is also
-the style we have adopted for this manual.</p>
-<dl class="docutils">
-<dt>If any of these clash with names in your code, you can use qualified names instead:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">ruffus</span>
-
-<span class="n">ruffus</span><span class="o">.</span><span class="n">pipeline_printout</span><span class="p">(</span><span class="s">"..."</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p><em>Ruffus</em> uses only standard python syntax.</p>
-<p>There is no need to install anything extra or to have your script “preprocessed” to run
-your pipeline.</p>
-</div></blockquote>
-</div>
-<div class="section" id="ruffus-decorators">
-<h2><em>Ruffus</em> <a class="reference external" href="https://docs.python.org/2/glossary.html#term-decorator">decorators</a><a class="headerlink" href="#ruffus-decorators" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>To let <em>Ruffus</em> know that which python functions are part of your pipeline,
-they need to be tagged or annotated using
-<em>Ruffus</em> <a class="reference external" href="https://docs.python.org/2/glossary.html#term-decorator">decorators</a> .</p>
-<p><a class="reference external" href="https://docs.python.org/2/glossary.html#term-decorator">Decorators</a> have been part of the Python language since version 2.4.
-Common examples from the standard library include <a class="reference external" href="https://docs.python.org/2/library/functions.html#staticmethod">@staticmethod</a> and
-<a class="reference external" href="https://docs.python.org/2/library/functions.html#classmethod">classmethod</a>.</p>
-<p><a class="reference external" href="https://docs.python.org/2/glossary.html#term-decorator">decorators</a>  start with a <tt class="docutils literal"><span class="pre">@</span></tt>
-prefix, and take a number of parameters in parenthesis, much like in a function call.</p>
-<p><a class="reference external" href="https://docs.python.org/2/glossary.html#term-decorator">decorators</a>   are placed before a normal python function.</p>
-<blockquote>
-<div><img alt="../../_images/tutorial_step1_decorator_syntax.png" src="../../_images/tutorial_step1_decorator_syntax.png" />
-</div></blockquote>
-<p>Multiple decorators can be stacked as necessary in whichever order:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@follows</span><span class="p">(</span><span class="n">first_task</span><span class="p">)</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">another_task</span><span class="p">)</span>
-<span class="nd">@originate</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="mi">5</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">():</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><em>Ruffus</em> <a class="reference external" href="https://docs.python.org/2/glossary.html#term-decorator">decorators</a> do not
-otherwise alter the underlying function. These can still be called normally.</p>
-</div></blockquote>
-</div>
-<div class="section" id="your-first-ruffus-pipeline">
-<h2>Your first <em>Ruffus</em> pipeline<a class="headerlink" href="#your-first-ruffus-pipeline" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="write-down-the-file-names">
-<h3>1. Write down the file names<a class="headerlink" href="#write-down-the-file-names" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><em>Ruffus</em> is designed for data moving through a computational pipeline as a series of files.</p>
-<p>It is also possible to use <em>Ruffus</em> pipelines without using intermediate data files but for your
-first efforts, it is probably best not to subvert its canonical design.</p>
-<p>The first thing when designing a new <em>Ruffus</em> pipeline is to sketch out the set of file names for
-the pipeline on paper:</p>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/tutorial_ruffus_files.jpg"><img alt="../../_images/tutorial_ruffus_files.jpg" src="../../_images/tutorial_ruffus_files.jpg" style="width: 600.0px; height: 212.5px;" /></a>
-</div></blockquote>
-<dl class="docutils">
-<dt>Here we have a number of DNA sequence files (<tt class="docutils literal"><span class="pre">*.fasta</span></tt>)</dt>
-<dd><ol class="first last arabic simple">
-<li>mapped to a genome (<tt class="docutils literal"><span class="pre">*.sam</span></tt>), and</li>
-<li>compressed (<tt class="docutils literal"><span class="pre">*.bam</span></tt>) before being</li>
-<li>summarised statistically (<tt class="docutils literal"><span class="pre">*.statistics</span></tt>)</li>
-</ol>
-</dd>
-</dl>
-<p>The first striking thing is that all of the files following the same <strong>consistent naming scheme</strong>.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><span class="highlight-red">The most important part of a Ruffus pipeline is to have a consistent naming scheme for your files.</span></p>
-<p class="last">This allows you to build sane pipelines.</p>
-</div>
-<p>In this case, each of the files at the same stage share the same file extension, e.g. (<tt class="docutils literal"><span class="pre">.sam</span></tt>).
-This is usually the simplest and most sensible choice. (We shall see in later chapters
-that <em>Ruffus</em> supports more complicated naming patterns so long as they are consistent.)</p>
-</div></blockquote>
-</div>
-<div class="section" id="write-the-python-functions-for-each-stage">
-<h3>2. Write the python functions for each stage<a class="headerlink" href="#write-the-python-functions-for-each-stage" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Next, we can sketch out the python functions which do the actual work for the pipeline.</p>
-<blockquote>
-<div><div class="admonition note">
-<p class="first admonition-title">Note</p>
-<ol class="last arabic">
-<li><p class="first"><span class="highlight-red">These are normal python functions with the important proviso that</span></p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>The first parameter contains the <strong>Input</strong> (file names)</li>
-<li>The second parameter contains the <strong>Output</strong> (file names)</li>
-</ol>
-<p>You can otherwise supply as many parameters as is required.</p>
-</div></blockquote>
-</li>
-<li><p class="first"><span class="highlight-red">Each python function should only take a</span> <em>Single</em> <strong>Input</strong> at a time</p>
-<blockquote>
-<div><p>All the parallelism in your pipeline should be handled by <em>Ruffus</em>. Make sure
-each function analyses one thing at a time.</p>
-</div></blockquote>
-</li>
-</ol>
-</div>
-</div></blockquote>
-<p><em>Ruffus</em> refers to a pipelined function as a <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>.</p>
-<p>The code for our three task functions look something like:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="hll"><span class="c">#   STAGE 1 fasta->sam</span>
-</span><span class="c">#</span>
-<span class="hll"><span class="k">def</span> <span class="nf">map_dna_sequence</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>               <span class="c"># 1st parameter is Input</span>
-</span><span class="hll">                    <span class="n">output_file</span><span class="p">):</span>              <span class="c"># 2nd parameter is Output</span>
-</span>    <span class="sd">"""</span>
-<span class="sd">    Sketch of real mapping function</span>
-<span class="sd">    We can do the mapping ourselves</span>
-<span class="sd">        or call some other programme:</span>
-<span class="sd">            os.system("stampy %s %s..." % (input_file, output_file))</span>
-<span class="sd">    """</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="hll"><span class="c">#   STAGE 2 sam->bam</span>
-</span><span class="c">#</span>
-<span class="k">def</span> <span class="nf">compress_sam_file</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>              <span class="c"># Input  parameter</span>
-                      <span class="n">output_file</span><span class="p">):</span>            <span class="c"># Output parameter</span>
-    <span class="sd">"""</span>
-<span class="sd">    Sketch of real compression function</span>
-<span class="sd">    """</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="hll"><span class="c">#   STAGE 3 bam->statistics</span>
-</span><span class="c">#</span>
-<span class="k">def</span> <span class="nf">summarise_bam_file</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>             <span class="c"># Input  parameter</span>
-                       <span class="n">output_file</span><span class="p">,</span>            <span class="c"># Output parameter</span>
-                       <span class="n">extra_stats_parameter</span><span class="p">):</span> <span class="c"># Any number of extra parameters as required</span>
-    <span class="sd">"""</span>
-<span class="sd">    Sketch of real analysis function</span>
-<span class="sd">    """</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>If we were calling our functions manually, without the benefit of <em>Ruffus</em>, we would need
-the following sequence of calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># STAGE 1</span>
-<span class="n">map_dna_sequence</span><span class="p">(</span><span class="s">"a.fasta"</span><span class="p">,</span> <span class="s">"a.sam"</span><span class="p">)</span>
-<span class="n">map_dna_sequence</span><span class="p">(</span><span class="s">"b.fasta"</span><span class="p">,</span> <span class="s">"b.sam"</span><span class="p">)</span>
-<span class="n">map_dna_sequence</span><span class="p">(</span><span class="s">"c.fasta"</span><span class="p">,</span> <span class="s">"c.sam"</span><span class="p">)</span>
-
-<span class="c"># STAGE 2</span>
-<span class="n">compress_sam_file</span><span class="p">(</span><span class="s">"a.sam"</span><span class="p">,</span> <span class="s">"a.bam"</span><span class="p">)</span>
-<span class="n">compress_sam_file</span><span class="p">(</span><span class="s">"b.sam"</span><span class="p">,</span> <span class="s">"b.bam"</span><span class="p">)</span>
-<span class="n">compress_sam_file</span><span class="p">(</span><span class="s">"c.sam"</span><span class="p">,</span> <span class="s">"c.bam"</span><span class="p">)</span>
-
-<span class="c"># STAGE 3</span>
-<span class="n">summarise_bam_file</span><span class="p">(</span><span class="s">"a.bam"</span><span class="p">,</span> <span class="s">"a.statistics"</span><span class="p">)</span>
-<span class="n">summarise_bam_file</span><span class="p">(</span><span class="s">"b.bam"</span><span class="p">,</span> <span class="s">"b.statistics"</span><span class="p">)</span>
-<span class="n">summarise_bam_file</span><span class="p">(</span><span class="s">"c.bam"</span><span class="p">,</span> <span class="s">"c.statistics"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="link-the-python-functions-into-a-pipeline">
-<h3>3. Link the python functions into a pipeline<a class="headerlink" href="#link-the-python-functions-into-a-pipeline" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><em>Ruffus</em> makes exactly the same function calls on your behalf. However, first, we need to
-tell <em>Ruffus</em> what the arguments should be for each of the function calls.</p>
-<ul class="simple">
-<li>The <strong>Input</strong> is easy: This is either the starting file set (<tt class="docutils literal"><span class="pre">*.fasta</span></tt>) or whatever is produced
-by the previous stage.</li>
-<li>The <strong>Output</strong> file name is the same as the <strong>Input</strong> but with the appropriate extension.</li>
-</ul>
-<p>These are specified using the <em>Ruffus</em> <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> decorator as follows:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="n">starting_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"a.fasta"</span><span class="p">,</span> <span class="s">"b.fasta"</span><span class="p">,</span> <span class="s">"c.fasta"</span><span class="p">]</span>
-
-<span class="c">#</span>
-<span class="hll"><span class="c">#   STAGE 1 fasta->sam</span>
-</span><span class="hll"><span class="c">#</span>
-</span><span class="hll"><span class="nd">@transform</span><span class="p">(</span><span class="n">starting_files</span><span class="p">,</span>                     <span class="c"># Input = starting files</span>
-</span>            <span class="n">suffix</span><span class="p">(</span><span class="s">".fasta"</span><span class="p">),</span>                  <span class="c">#         suffix = .fasta</span>
-            <span class="s">".sam"</span><span class="p">)</span>                            <span class="c"># Output  suffix = .sam</span>
-<span class="k">def</span> <span class="nf">map_dna_sequence</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                    <span class="n">output_file</span><span class="p">):</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="hll"><span class="c">#   STAGE 2 sam->bam</span>
-</span><span class="hll"><span class="c">#</span>
-</span><span class="hll"><span class="nd">@transform</span><span class="p">(</span><span class="n">map_dna_sequence</span><span class="p">,</span>                   <span class="c"># Input = previous stage</span>
-</span>            <span class="n">suffix</span><span class="p">(</span><span class="s">".sam"</span><span class="p">),</span>                    <span class="c">#         suffix = .sam</span>
-            <span class="s">".bam"</span><span class="p">)</span>                            <span class="c"># Output  suffix = .bam</span>
-<span class="k">def</span> <span class="nf">compress_sam_file</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                      <span class="n">output_file</span><span class="p">):</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   STAGE 3 bam->statistics</span>
-<span class="hll"><span class="c">#</span>
-</span><span class="hll"><span class="nd">@transform</span><span class="p">(</span><span class="n">compress_sam_file</span><span class="p">,</span>                  <span class="c"># Input = previous stage</span>
-</span><span class="hll">            <span class="n">suffix</span><span class="p">(</span><span class="s">".bam"</span><span class="p">),</span>                    <span class="c">#         suffix = .bam</span>
-</span>            <span class="s">".statistics"</span><span class="p">,</span>                     <span class="c"># Output  suffix = .statistics</span>
-            <span class="s">"use_linear_model"</span><span class="p">)</span>                <span class="c"># Extra statistics parameter</span>
-<span class="k">def</span> <span class="nf">summarise_bam_file</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                       <span class="n">output_file</span><span class="p">,</span>
-                       <span class="n">extra_stats_parameter</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Sketch of real analysis function</span>
-<span class="sd">    """</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="transform-syntax">
-<h3>4. @transform syntax<a class="headerlink" href="#transform-syntax" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ol class="arabic">
-<li><div class="first line-block">
-<div class="line">The 1st parameter for <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> is the <strong>Input</strong>.</div>
-<div class="line">This is either the set of starting data or the name of the previous pipeline function.</div>
-<div class="line"><em>Ruffus</em> <em>chains</em> together the stages of a pipeline by linking the <strong>Output</strong> of the previous stage into the <strong>Input</strong> of the next.</div>
-</div>
-</li>
-<li><div class="first line-block">
-<div class="line">The 2nd parameter is the current <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix</em></a></div>
-<div class="line">(i.e. our <strong>Input</strong> file extensions of <tt class="docutils literal"><span class="pre">".fasta"</span></tt> or  <tt class="docutils literal"><span class="pre">".sam"</span></tt> or  <tt class="docutils literal"><span class="pre">".bam"</span></tt>)</div>
-</div>
-</li>
-<li><div class="first line-block">
-<div class="line">The 3rd parameter is what we want our <strong>Output</strong> file name to be after <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix</em></a> string substitution (e.g. <tt class="docutils literal"><span class="pre">.fasta</span> <span class="pre">-</span> <span class="pre">></span> <span class="pre">.sam</span></tt>).</div>
-<div class="line">This works because we are using a sane naming scheme for our data files.</div>
-</div>
-</li>
-<li><p class="first">Other parameters can be passed to <tt class="docutils literal"><span class="pre">@transform</span></tt> and they will be forwarded to our python
-pipeline function.</p>
-</li>
-</ol>
-<p>The functions that do the actual work of each stage of the pipeline remain unchanged.
-The role of <em>Ruffus</em> is to make sure each is called in the right order,
-with the right parameters, running in parallel (using multiprocessing if desired).</p>
-</div></blockquote>
-</div>
-<div class="section" id="run-the-pipeline">
-<span id="new-manual-pipeline-run"></span><span id="index-2"></span><h3>5. Run the pipeline!<a class="headerlink" href="#run-the-pipeline" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><strong>Key Ruffus Terminology</strong>:</p>
-<p>A  <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> is an annotated python function which represents a recipe or stage of your pipeline.</p>
-<p>A  <a class="reference internal" href="../../glossary.html#term-job"><em class="xref std std-term">job</em></a> is each time your recipe is applied to a piece of data, i.e. each time <em>Ruffus</em> calls your function.</p>
-<p class="last">Each <strong>task</strong> or pipeline recipe can thus have many <strong>jobs</strong> each of which can work in parallel on different data.</p>
-</div>
-<p>Now we can run the pipeline with the <em>Ruffus</em> function <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>This produces three sets of results in parallel, as you might expect:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [a.fasta -> a.sam] completed</span>
-<span class="go">    Job  = [b.fasta -> b.sam] completed</span>
-<span class="go">    Job  = [c.fasta -> c.sam] completed</span>
-<span class="go">Completed Task = map_dna_sequence</span>
-<span class="go">    Job  = [a.sam -> a.bam] completed</span>
-<span class="go">    Job  = [b.sam -> b.bam] completed</span>
-<span class="go">    Job  = [c.sam -> c.bam] completed</span>
-<span class="go">Completed Task = compress_sam_file</span>
-<span class="go">    Job  = [a.bam -> a.statistics, use_linear_model] completed</span>
-<span class="go">    Job  = [b.bam -> b.statistics, use_linear_model] completed</span>
-<span class="go">    Job  = [c.bam -> c.statistics, use_linear_model] completed</span>
-<span class="go">Completed Task = summarise_bam_file</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>To work out which functions to call, <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>
-finds the <strong>last</strong> <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function of your pipeline, then
-works out all the other functions this depends on, working backwards up the chain of
-dependencies automatically.</p>
-<p>We can specify this end point of your pipeline explicitly:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">target_tasks</span> <span class="o">=</span> <span class="p">[</span><span class="n">summarise_bam_file</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>This allows us to only run part of the pipeline, for example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">target_tasks</span> <span class="o">=</span> <span class="p">[</span><span class="n">compress_sam_file</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The <a class="reference internal" href="introduction_code.html#new-manual-introduction-code"><em>example code</em></a> can be copied and pasted into a python
-command shell.</p>
-</div>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 1</strong>: An introduction to basic <em>Ruffus</em> syntax</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#importing-ruffus">Importing <em>Ruffus</em></a></li>
-<li><a class="reference internal" href="#ruffus-decorators"><em>Ruffus</em> decorators</a></li>
-<li><a class="reference internal" href="#your-first-ruffus-pipeline">Your first <em>Ruffus</em> pipeline</a><ul>
-<li><a class="reference internal" href="#write-down-the-file-names">1. Write down the file names</a></li>
-<li><a class="reference internal" href="#write-the-python-functions-for-each-stage">2. Write the python functions for each stage</a></li>
-<li><a class="reference internal" href="#link-the-python-functions-into-a-pipeline">3. Link the python functions into a pipeline</a></li>
-<li><a class="reference internal" href="#transform-syntax">4. @transform syntax</a></li>
-<li><a class="reference internal" href="#run-the-pipeline">5. Run the pipeline!</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="manual_contents.html"
-                        title="previous chapter"><strong>Ruffus</strong> Manual: List of Chapters and Example code</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="transform.html"
-                        title="next chapter"><strong>Chapter 2</strong>: Transforming data in a pipeline with <tt class="docutils literal"><span class="pre">@transform</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-  <div class="section" id="new-manual-introduction-chapter-num-python-code-for-an-introduction-to-basic-ruffus-syntax">
-<span id="new-manual-introduction-code"></span><h1><strong>Chapter 1</strong>: Python Code for An introduction to basic Ruffus syntax<a class="headerlink" href="#new-manual-introduction-chapter-num-python-code-for-an-introduction-to-basic-ruffus-syntax" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform syntax in detail</em></a></li>
-<li>Back to <strong>Chapter 1</strong>: <a class="reference internal" href="introduction.html#new-manual-introduction"><em>An introduction to basic Ruffus syntax</em></a></li>
-</ul>
-</div>
-<div class="section" id="your-first-ruffus-script">
-<h2>Your first Ruffus script<a class="headerlink" href="#your-first-ruffus-script" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="p">::</span>
-
-<span class="c">#</span>
-<span class="c">#   The starting data files would normally exist beforehand!</span>
-<span class="c">#       We create some empty files for this example</span>
-<span class="c">#</span>
-<span class="n">starting_files</span> <span class="o">=</span> <span class="p">[</span><span class="s">"a.fasta"</span><span class="p">,</span> <span class="s">"b.fasta"</span><span class="p">,</span> <span class="s">"c.fasta"</span><span class="p">]</span>
-
-<span class="k">for</span> <span class="n">ff</span> <span class="ow">in</span> <span class="n">starting_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">ff</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#</span>
-<span class="c">#   STAGE 1 fasta->sam</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">starting_files</span><span class="p">,</span>                     <span class="c"># Input = starting files</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".fasta"</span><span class="p">),</span>                  <span class="c">#         suffix = .fasta</span>
-            <span class="s">".sam"</span><span class="p">)</span>                            <span class="c"># Output  suffix = .sam</span>
-<span class="k">def</span> <span class="nf">map_dna_sequence</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                    <span class="n">output_file</span><span class="p">):</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   STAGE 2 sam->bam</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">map_dna_sequence</span><span class="p">,</span>                   <span class="c"># Input = previous stage</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".sam"</span><span class="p">),</span>                    <span class="c">#         suffix = .sam</span>
-            <span class="s">".bam"</span><span class="p">)</span>                            <span class="c"># Output  suffix = .bam</span>
-<span class="k">def</span> <span class="nf">compress_sam_file</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                      <span class="n">output_file</span><span class="p">):</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   STAGE 3 bam->statistics</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">compress_sam_file</span><span class="p">,</span>                  <span class="c"># Input = previous stage</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".bam"</span><span class="p">),</span>                    <span class="c">#         suffix = .bam</span>
-            <span class="s">".statistics"</span><span class="p">,</span>                     <span class="c"># Output  suffix = .statistics</span>
-            <span class="s">"use_linear_model"</span><span class="p">)</span>                <span class="c"># Extra statistics parameter</span>
-<span class="k">def</span> <span class="nf">summarise_bam_file</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                       <span class="n">output_file</span><span class="p">,</span>
-                       <span class="n">extra_stats_parameter</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Sketch of real analysis function</span>
-<span class="sd">    """</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [a.fasta -> a.sam] completed</span>
-<span class="go">    Job  = [b.fasta -> b.sam] completed</span>
-<span class="go">    Job  = [c.fasta -> c.sam] completed</span>
-<span class="go">Completed Task = map_dna_sequence</span>
-<span class="go">    Job  = [a.sam -> a.bam] completed</span>
-<span class="go">    Job  = [b.sam -> b.bam] completed</span>
-<span class="go">    Job  = [c.sam -> c.bam] completed</span>
-<span class="go">Completed Task = compress_sam_file</span>
-<span class="go">    Job  = [a.bam -> a.statistics, use_linear_model] completed</span>
-<span class="go">    Job  = [b.bam -> b.statistics, use_linear_model] completed</span>
-<span class="go">    Job  = [c.bam -> c.statistics, use_linear_model] completed</span>
-<span class="go">Completed Task = summarise_bam_file</span>
-</pre></div>
-</div>
-</div></blockquote>
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-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
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-  <h4>Previous topic</h4>
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-                        title="previous chapter"><strong>Appendix 6</strong>: <strong>@files_re</strong>: Deprecated <cite>syntax using regular expressions</cite></a></p>
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-  <div class="section" id="new-manual-ruffus-names-chapter-num-names-exported-from-ruffus">
-<span id="new-manual-ruffus-names"></span><span id="index-0"></span><h1><strong>Appendix 4</strong>: Names exported from Ruffus<a class="headerlink" href="#new-manual-ruffus-names-chapter-num-names-exported-from-ruffus" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-</ul>
-</div>
-<div class="section" id="ruffus-names">
-<h2>Ruffus Names<a class="headerlink" href="#ruffus-names" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>This is a list of all the names <em>Ruffus</em> makes available:</p>
-<table border="1" class="docutils">
-<colgroup>
-<col width="28%" />
-<col width="72%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head">Category</th>
-<th class="head">Manual</th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td><strong>Pipeline functions</strong></td>
-<td><div class="first last line-block">
-<div class="line"><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout()</em></a> (<a class="reference internal" href="pipeline_printout.html#new-manual-pipeline-printout"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout()</em></a> (<a class="reference internal" href="pipeline_printout_graph.html#new-manual-pipeline-printout-graph"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_printout()</em></a> (<a class="reference internal" href="introduction.html#new-manual-pipeline-run"><em>Manual</em></a>)</div>
-</div>
-</td>
-</tr>
-<tr class="row-odd"><td><strong>Decorators</strong></td>
-<td><div class="first last line-block">
-<div class="line"><a class="reference internal" href="../../decorators/active_if.html#decorators-active-if"><em>@active_if</em></a> (<a class="reference internal" href="active_if.html#new-manual-active-if"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/check_if_uptodate.html#decorators-check-if-uptodate"><em>@check_if_uptodate</em></a> (<a class="reference internal" href="check_if_uptodate.html#new-manual-check-if-uptodate"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a> (<a class="reference internal" href="subdivide_collate.html#new-manual-collate"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/files.html#decorators-files"><em>@files</em></a> (<a class="reference internal" href="deprecated_files.html#new-manual-deprecated-files"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows</em></a> (<a class="reference internal" href="transform_in_parallel.html#new-manual-follows"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit</em></a> (<a class="reference internal" href="multiprocessing.html#new-manual-jobs-limit"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> (<a class="reference internal" href="merge.html#new-manual-merge"><em>Manual</em></a>)</div>
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-<div class="line"><a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> (<a class="reference internal" href="posttask.html#new-manual-posttask"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> (<a class="reference internal" href="split.html#new-manual-split"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> (<a class="reference internal" href="subdivide_collate.html#new-manual-subdivide"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> (<a class="reference internal" href="transform.html#new-manual-transform"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/files_re.html#decorators-files-re"><em>@files_re</em></a> (<a class="reference internal" href="deprecated_files_re.html#new-manual-deprecated-files-re"><em>Manual</em></a>)</div>
-</div>
-</td>
-</tr>
-<tr class="row-even"><td><strong>Loggers</strong></td>
-<td><div class="first last line-block">
-<div class="line">stderr_logger</div>
-<div class="line">black_hole_logger</div>
-</div>
-</td>
-</tr>
-<tr class="row-odd"><td><strong>Parameter disambiguating Indicators</strong></td>
-<td><div class="first last line-block">
-<div class="line"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix</em></a> (<a class="reference internal" href="output_file_names.html#new-manual-suffix"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex</em></a> (<a class="reference internal" href="output_file_names.html#new-manual-regex"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter</em></a> (<a class="reference internal" href="output_file_names.html#new-manual-formatter"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-inputs"><em>inputs</em></a> (<a class="reference internal" href="inputs.html#new-manual-inputs"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-add-inputs"><em>inputs</em></a> (<a class="reference internal" href="inputs.html#new-manual-inputs"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-touch-file"><em>touch_file</em></a> (<a class="reference internal" href="posttask.html#new-manual-posttask-touch-file"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-combine"><em>combine</em></a></div>
-<div class="line"><a class="reference internal" href="../../decorators/follows.html#decorators-follows-mkdir"><em>mkdir</em></a> (<a class="reference internal" href="transform_in_parallel.html#new-manual-follows-mkdir"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-output-from"><em>output_from</em></a> (<a class="reference internal" href="transform_in_parallel.html#new-manual-output-from"><em>Manual</em></a>)</div>
-</div>
-</td>
-</tr>
-<tr class="row-even"><td><strong>Decorators in ruffus.combinatorics</strong></td>
-<td><div class="first last line-block">
-<div class="line"><a class="reference internal" href="../../decorators/combinations.html#decorators-combinations"><em>@combinations</em></a> (<a class="reference internal" href="combinatorics.html#new-manual-combinations"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/combinations_with_replacement.html#decorators-combinations-with-replacement"><em>@combinations_with_replacement</em></a> (<a class="reference internal" href="combinatorics.html#new-manual-combinations-with-replacement"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/permutations.html#decorators-permutations"><em>@permutations</em></a> (<a class="reference internal" href="combinatorics.html#new-manual-permutations"><em>Manual</em></a>)</div>
-<div class="line"><a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a> (<a class="reference internal" href="combinatorics.html#new-manual-product"><em>Manual</em></a>)</div>
-</div>
-</td>
-</tr>
-<tr class="row-odd"><td><strong>Decorators in ruffus.cmdline</strong></td>
-<td><div class="first last line-block">
-<div class="line"><a class="reference internal" href="command_line.html#new-manual-cmdline-get-argparse"><em>get_argparse</em></a></div>
-<div class="line"><a class="reference internal" href="command_line.html#new-manual-cmdline-setup-logging"><em>setup_logging</em></a></div>
-<div class="line"><a class="reference internal" href="command_line.html#new-manual-cmdline-run"><em>run</em></a></div>
-<div class="line"><a class="reference internal" href="command_line.html#new-manual-cmdline-message"><em>MESSAGE</em></a></div>
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-  <div class="section" id="new-manual-logging-chapter-num-logging-progress-through-a-pipeline">
-<span id="new-manual-logging"></span><span id="index-0"></span><h1><strong>Chapter 15</strong>: Logging progress through a pipeline<a class="headerlink" href="#new-manual-logging-chapter-num-logging-progress-through-a-pipeline" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Remember to look at the <a class="reference internal" href="logging_code.html#new-manual-logging-code"><em>example code</em></a></p>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>There are two parts to logging with <strong>Ruffus</strong>:</p>
-<ul>
-<li><p class="first">Logging progress through the pipeline</p>
-<blockquote>
-<div><p>This produces the sort of output displayed in this manual:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_io_task</span><span class="p">])</span>
-<span class="go">Task = parallel_io_task</span>
-<span class="go">    Job = ["a.1" -> "a.2", "A file"] completed</span>
-<span class="go">    Job = ["b.1" -> "b.2", "B file"] unnecessary: already up to date</span>
-<span class="go">Completed Task = parallel_io_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</li>
-<li><p class="first">Logging your own messages from within your pipelined functions.</p>
-<blockquote>
-<div><p>Because <strong>Ruffus</strong> may run each task function in separate process on a separate
-CPU (multiprocessing), some attention has to be paid to how to send and
-synchronise your log messages across process boundaries.</p>
-</div></blockquote>
-</li>
-</ul>
-<p>We shall deal with these in turn.</p>
-</div></blockquote>
-</div>
-<div class="section" id="logging-task-job-completion">
-<span id="new-manual-logging-pipeline"></span><h2>Logging task/job completion<a class="headerlink" href="#logging-task-job-completion" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>By default, <em>Ruffus</em> logs each task and each job as it is completed to
-<a class="reference external" href="http://docs.python.org/2/library/sys.html#sys.stderr">sys.stderr</a>.</p>
-<p>By default, Ruffus logs to <tt class="docutils literal"><span class="pre">STDERR</span></tt>: <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(logger = stderr_logger)</em></a>.</p>
-<p>If you want to turn off all tracking messages as the pipeline runs, apart from setting <tt class="docutils literal"><span class="pre">verbose</span> <span class="pre">=</span> <span class="pre">0</span></tt>, you
-can also use the aptly named Ruffus <tt class="docutils literal"><span class="pre">black_hole_logger</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span><span class="n">logger</span> <span class="o">=</span> <span class="n">black_hole_logger</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="controlling-logging-verbosity">
-<span id="index-1"></span><h3>Controlling logging verbosity<a class="headerlink" href="#controlling-logging-verbosity" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> currently has five levels of verbosity, set by the optional <tt class="docutils literal"><span class="pre">verbose</span></tt>
-parameter which defaults to 1:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>verbose = 0: nothing
-verbose = 1: logs completed jobs/tasks;
-verbose = 2: logs up to date jobs in incomplete tasks
-verbose = 3: logs reason for running job
-verbose = 4: logs messages useful only for debugging ruffus pipeline code</pre>
-</div>
-<p><tt class="docutils literal"><span class="pre">verbose</span></tt> > <tt class="docutils literal"><span class="pre">5</span></tt> are intended for debugging <strong>Ruffus</strong> by the developers and the details
-are liable to change from release to release</p>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="use-ruffus-cmdline">
-<span id="index-2"></span><h2>Use <a class="reference internal" href="command_line.html#new-manual-cmdline"><em>ruffus.cmdline</em></a><a class="headerlink" href="#use-ruffus-cmdline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>As always, it is easiest to use <a class="reference internal" href="command_line.html#new-manual-cmdline"><em>ruffus.cmdline</em></a>.</p>
-<p>Set your script to</p>
-<blockquote>
-<div><ul class="simple">
-<li>write messages to <tt class="docutils literal"><span class="pre">STDERR</span></tt> with the <tt class="docutils literal"><span class="pre">--verbose</span></tt> option and</li>
-<li>to a log file with the <tt class="docutils literal"><span class="pre">--log_file</span></tt> option.</li>
-</ul>
-<div class="highlight-python"><div class="highlight"><pre> <span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="hll"> <span class="c">#  Python logger which can be synchronised across concurrent Ruffus tasks</span>
-</span> <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">setup_logging</span> <span class="p">(</span><span class="n">__name__</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">log_file</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">verbose</span><spa [...]
-
- <span class="nd">@transform</span><span class="p">(</span> <span class="p">[</span><span class="s">"job1.input"</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".input"</span><span class="p">),</span> <span class="s">".output1"</span><span class="p">),</span>
- <span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-     <span class="k">pass</span>
-
- <span class="n">pipeline_run</span><span class="p">(</span><span class="n">logger</span><span class="o">=</span><span class="n">logger</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="customising-logging">
-<span id="index-3"></span><h2>Customising logging<a class="headerlink" href="#customising-logging" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>You can also specify exactly how logging works by providing a <a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> object
-to <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> .
-This log object should have <tt class="docutils literal"><span class="pre">debug()</span></tt> and <tt class="docutils literal"><span class="pre">info()</span></tt> methods.</p>
-<p>Instead of writing your own, it is usually more convenient to use the python
-<a class="reference external" href="http://docs.python.org/library/logging.html">logging</a>
-module which provides logging classes with rich functionality.</p>
-<p>The <a class="reference internal" href="logging_code.html#new-manual-logging-code"><em>example code</em></a> sets up a logger to a rotating set of files</p>
-</div></blockquote>
-</div>
-<div class="section" id="log-your-own-messages">
-<span id="new-manual-logging-per-job"></span><span id="index-4"></span><h2>Log your own messages<a class="headerlink" href="#log-your-own-messages" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>You need to take a little care when logging your custom messages <em>within</em> your pipeline.</p>
-<ul class="simple">
-<li>If your Ruffus pipeline may run in parallel, make sure that logging is synchronised.</li>
-<li>If your Ruffus pipeline may run across separate processes, send your logging object across process boundaries.</li>
-</ul>
-<p><a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> objects can not be
-<a class="reference external" href="http://docs.python.org/library/pickle.html">pickled</a> and shared naively across
-processes. Instead, we need to create proxies which forward the logging to a single
-shared log.</p>
-<p>The <a class="reference internal" href="../../proxy_logger.html#proxy-logger"><em>ruffus.proxy_logger</em></a> module provides an easy way to share
-<a class="reference external" href="http://docs.python.org/library/logging.html">logging</a> objects among
-jobs. This requires just two simple steps:</p>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<ul class="last simple">
-<li>This is a good template for sharing <a class="reference external" href="http://docs.python.org/2/library/pickle.html#what-can-be-pickled-and-unpickled">non-picklable objects</a>
-across processes.</li>
-</ul>
-</div>
-<div class="section" id="set-up-logging">
-<span id="new-manual-sharing-proxy-object"></span><h3>1. Set up logging<a class="headerlink" href="#set-up-logging" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Things are easiest if you are using <tt class="docutils literal"><span class="pre">ruffus.cmdline</span></tt>:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#  standard python logger which can be synchronised across concurrent Ruffus tasks</span>
-<span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">setup_logging</span> <span class="p">(</span><span class="n">__name__</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">log_file</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">verbose</span><span class= [...]
-</pre></div>
-</div>
-<p>Otherwise, manually:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus.proxy_logger</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="p">(</span><span class="n">logger</span><span class="p">,</span>
- <span class="n">logging_mutex</span><span class="p">)</span> <span class="o">=</span> <span class="n">make_shared_logger_and_proxy</span> <span class="p">(</span><span class="n">setup_std_shared_logger</span><span class="p">,</span>
-                                                <span class="s">"my_logger"</span><span class="p">,</span>
-                                                <span class="p">{</span><span class="s">"file_name"</span> <span class="p">:</span><span class="s">"/my/lg.log"</span><span class="p">})</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="share-the-proxy">
-<h3>2. Share the proxy<a class="headerlink" href="#share-the-proxy" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Now, pass:</p>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">logger</span></tt> (which forwards logging calls across jobs) and</li>
-<li><tt class="docutils literal"><span class="pre">logging_mutex</span></tt> (which prevents different jobs which are logging simultaneously
-from being jumbled up)</li>
-</ul>
-</div></blockquote>
-<p>to each job:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span> <span class="n">initial_file</span><span class="p">,</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".input"</span><span class="p">),</span>
-            <span class="s">".output1"</span><span class="p">,</span>
-<span class="hll">            <span class="n">logger</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">),</span>         <span class="c"># pass log and synchronisation as parameters</span>
-</span><span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span>
-<span class="hll">            <span class="n">logger</span><span class="p">,</span> <span class="n">logging_mutex</span><span class="p">):</span>         <span class="c"># pass log and synchronisation as parameters</span>
-</span>    <span class="k">pass</span>
-
-<span class="hll">    <span class="c"># synchronise logging</span>
-</span>    <span class="k">with</span> <span class="n">logging_mutex</span><span class="p">:</span>
-        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s">"Here we go logging..."</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 15</strong>: Logging progress through a pipeline</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#logging-task-job-completion">Logging task/job completion</a><ul>
-<li><a class="reference internal" href="#controlling-logging-verbosity">Controlling logging verbosity</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#use-ruffus-cmdline">Use <tt class="docutils literal"><span class="pre">ruffus.cmdline</span></tt></a></li>
-<li><a class="reference internal" href="#customising-logging">Customising logging</a></li>
-<li><a class="reference internal" href="#log-your-own-messages">Log your own messages</a><ul>
-<li><a class="reference internal" href="#set-up-logging">1. Set up logging</a></li>
-<li><a class="reference internal" href="#share-the-proxy">2. Share the proxy</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="multiprocessing.html"
-                        title="previous chapter"><strong>Chapter 14</strong>: Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="subdivide_collate.html"
-                        title="next chapter"><strong>Chapter 16</strong>: <tt class="docutils literal"><span class="pre">@subdivide</span></tt> tasks to run efficiently and regroup with <tt class="docutils literal"><span class="pre">@collate</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/logging.txt"
-           rel="nofollow">Show Source</a></li>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-            
-  <div class="section" id="new-manual-logging-chapter-num-python-code-for-logging-progress-through-a-pipeline">
-<span id="new-manual-logging-code"></span><h1><strong>Chapter 15</strong>: Python Code for Logging progress through a pipeline<a class="headerlink" href="#new-manual-logging-chapter-num-python-code-for-logging-progress-through-a-pipeline" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li>Back to <strong>Chapter 15</strong>: <a class="reference internal" href="logging.html#new-manual-logging"><em>Logging progress through a pipeline</em></a></li>
-</ul>
-</div>
-<div class="section" id="rotating-set-of-file-logs">
-<h2>Rotating set of file logs<a class="headerlink" href="#rotating-set-of-file-logs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">logging</span>
-<span class="kn">import</span> <span class="nn">logging.handlers</span>
-
-<span class="n">LOG_FILENAME</span> <span class="o">=</span> <span class="s">'/tmp/ruffus.log'</span>
-
-<span class="c"># Set up a specific logger with our desired output level</span>
-<span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s">'My_Ruffus_logger'</span><span class="p">)</span>
-<span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
-
-<span class="hll"><span class="c"># Rotate a set of 5 log files every 2kb</span>
-</span><span class="n">handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">handlers</span><span class="o">.</span><span class="n">RotatingFileHandler</span><span class="p">(</span>
-              <span class="n">LOG_FILENAME</span><span class="p">,</span> <span class="n">maxBytes</span><span class="o">=</span><span class="mi">2000</span><span class="p">,</span> <span class="n">backupCount</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
-
-<span class="hll"><span class="c"># Add the log message handler to the logger</span>
-</span><span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">handler</span><span class="p">)</span>
-
-<span class="hll"><span class="c"># Ruffus pipeline</span>
-</span><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c"># Start with some initial data file of yours...</span>
-<span class="n">initial_file</span> <span class="o">=</span> <span class="s">"job1.input"</span>
-<span class="nb">open</span><span class="p">(</span><span class="n">initial_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@transform</span><span class="p">(</span> <span class="n">initial_file</span><span class="p">,</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".input"</span><span class="p">),</span>
-            <span class="s">".output1"</span><span class="p">),</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="s">"Some detailed description"</span>
-    <span class="k">pass</span>
-
-<span class="hll"><span class="c">#   use our custom logging object</span>
-</span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">logger</span><span class="o">=</span><span class="n">logger</span><span class="p">)</span>
-<span class="k">print</span> <span class="nb">open</span><span class="p">(</span><span class="s">"/tmp/ruffus.log"</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
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-
-
-          </div>
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 15</strong>: Python Code for Logging progress through a pipeline</a><ul>
-<li><a class="reference internal" href="#rotating-set-of-file-logs">Rotating set of file logs</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="multiprocessing_code.html"
-                        title="previous chapter"><strong>Chapter 14</strong>: Python Code for Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="subdivide_collate_code.html"
-                        title="next chapter"><strong>Chapter 16</strong>: Python Code for <tt class="docutils literal"><span class="pre">@subdivide</span></tt> tasks to run efficiently and regroup with <tt class="docutils literal"><span class="pre">@collate</span></tt></a></p>
-  <h3>This Page</h3>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-<span id="new-manual-table-of-contents"></span><h1><strong>Ruffus</strong> Manual: List of Chapters and Example code<a class="headerlink" href="#ruffus-manual-list-of-chapters-and-example-code" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><p>Download as <a class="reference download internal" href="../../_downloads/ruffus.pdf"><tt class="xref download docutils literal"><span class="pre">pdf</span></tt></a>.</p>
-<ul class="simple">
-<li><strong>Chapter 1</strong>: <a class="reference internal" href="introduction.html#new-manual-introduction"><em>An introduction to basic Ruffus syntax</em></a></li>
-<li><strong>Chapter 2</strong>: <a class="reference internal" href="transform.html#new-manual-transform"><em>Transforming data in a pipeline with @transform</em></a></li>
-<li><strong>Chapter 3</strong>: <a class="reference internal" href="transform_in_parallel.html#new-manual-transform-in-parallel"><em>More on @transform-ing data</em></a></li>
-<li><strong>Chapter 4</strong>: <a class="reference internal" href="originate.html#new-manual-originate"><em>Creating files with @originate</em></a></li>
-<li><strong>Chapter 5</strong>: <a class="reference internal" href="pipeline_printout.html#new-manual-pipeline-printout"><em>Understanding how your pipeline works with pipeline_printout()</em></a></li>
-<li><strong>Chapter 6</strong>: <a class="reference internal" href="command_line.html#new-manual-cmdline"><em>Running Ruffus from the command line with ruffus.cmdline</em></a></li>
-<li><strong>Chapter 7</strong>: <a class="reference internal" href="pipeline_printout_graph.html#new-manual-pipeline-printout-graph"><em>Displaying the pipeline visually with pipeline_printout_graph()</em></a></li>
-<li><strong>Chapter 8</strong>: <a class="reference internal" href="output_file_names.html#new-manual-output-file-names"><em>Specifying output file names with formatter() and regex()</em></a></li>
-<li><strong>Chapter 9</strong>: <a class="reference internal" href="mkdir.html#new-manual-mkdir"><em>Preparing directories for output with @mkdir</em></a></li>
-<li><strong>Chapter 10</strong>: <a class="reference internal" href="checkpointing.html#new-manual-checkpointing"><em>Checkpointing: Interrupted Pipelines and Exceptions</em></a></li>
-<li><strong>Chapter 11</strong>: <a class="reference internal" href="decorators_compendium.html#new-manual-decorators-compendium"><em>Pipeline topologies and a compendium of Ruffus decorators</em></a></li>
-<li><strong>Chapter 12</strong>: <a class="reference internal" href="split.html#new-manual-split"><em>Splitting up large tasks / files with @split</em></a></li>
-<li><strong>Chapter 13</strong>: <a class="reference internal" href="merge.html#new-manual-merge"><em>@merge multiple input into a single result</em></a></li>
-<li><strong>Chapter 15</strong>: <a class="reference internal" href="logging.html#new-manual-logging"><em>Logging progress through a pipeline</em></a></li>
-<li><strong>Chapter 14</strong>: <a class="reference internal" href="multiprocessing.html#new-manual-multiprocessing"><em>Multiprocessing, drmaa and Computation Clusters</em></a></li>
-<li><strong>Chapter 16</strong>: <a class="reference internal" href="subdivide_collate.html#new-manual-subdivide-collate"><em>@subdivide tasks to run efficiently and regroup with @collate</em></a></li>
-<li><strong>Chapter 17</strong>: <a class="reference internal" href="combinatorics.html#new-manual-combinatorics"><em>@combinations, @permutations and all versus all @product</em></a></li>
-<li><strong>Chapter 18</strong>: <a class="reference internal" href="active_if.html#new-manual-active-if"><em>Turning parts of the pipeline on and off at runtime with @active_if</em></a></li>
-<li><strong>Chapter 20</strong>: <a class="reference internal" href="inputs.html#new-manual-inputs"><em>Manipulating task inputs via string substitution with inputs() and add_inputs()</em></a></li>
-<li><strong>Chapter 19</strong>: <a class="reference internal" href="posttask.html#new-manual-posttask"><em>Signal the completion of each stage of our pipeline with @posttask</em></a></li>
-<li><strong>Chapter 21</strong>: <a class="reference internal" href="onthefly.html#new-manual-on-the-fly"><em>Esoteric: Generating parameters on the fly with @files</em></a></li>
-<li><strong>Chapter 22</strong>: <a class="reference internal" href="parallel.html#new-manual-deprecated-parallel"><em>Esoteric: Running jobs in parallel without files using @parallel</em></a></li>
-<li><strong>Chapter 23</strong>: <a class="reference internal" href="check_if_uptodate.html#new-manual-check-if-uptodate"><em>Esoteric: Writing custom functions to decide which jobs are up to date with @check_if_uptodate</em></a></li>
-<li><strong>Appendix 1</strong> <a class="reference internal" href="flowchart_colours.html#new-manual-flowchart-colours"><em>Flow Chart Colours with pipeline_printout_graph</em></a></li>
-<li><strong>Appendix 2</strong> <a class="reference internal" href="dependencies.html#new-manual-dependencies"><em>Under the hood: How dependency works</em></a></li>
-<li><strong>Appendix 3</strong> <a class="reference internal" href="exceptions.html#new-manual-exceptions"><em>Exceptions thrown inside pipelines</em></a></li>
-<li><strong>Appendix 4</strong> <a class="reference internal" href="list_of_ruffus_names.html#new-manual-ruffus-names"><em>Names (keywords) exported from Ruffus</em></a></li>
-<li><strong>Appendix 5</strong>: <a class="reference internal" href="deprecated_files.html#new-manual-deprecated-files"><em>Legacy and deprecated syntax @files</em></a></li>
-<li><strong>Appendix 6</strong>: <a class="reference internal" href="deprecated_files_re.html#new-manual-deprecated-files-re"><em>Legacy and deprecated syntax @files_re</em></a></li>
-</ul>
-</div></blockquote>
-<p><strong>Ruffus</strong> Manual: List of Example Code for Each Chapter:</p>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="introduction_code.html#new-manual-introduction-code"><em>Chapter 1: Python Code for An introduction to basic Ruffus syntax</em></a></li>
-<li><a class="reference internal" href="transform_code.html#new-manual-transform-code"><em>Chapter 1: Python Code for Transforming data in a pipeline with @transform</em></a></li>
-<li><a class="reference internal" href="transform_in_parallel_code.html#new-manual-transform-in-parallel-code"><em>Chapter 3: Python Code for More on @transform-ing data</em></a></li>
-<li><a class="reference internal" href="originate_code.html#new-manual-originate-code"><em>Chapter 4: Python Code for Creating files with @originate</em></a></li>
-<li><a class="reference internal" href="pipeline_printout_code.html#new-manual-pipeline-printout-code"><em>Chapter 5: Python Code for Understanding how your pipeline works with pipeline_printout(...)</em></a></li>
-<li><a class="reference internal" href="pipeline_printout_graph_code.html#new-manual-pipeline-printout-graph-code"><em>Chapter 7: Python Code for Displaying the pipeline visually with pipeline_printout_graph(...)</em></a></li>
-<li><a class="reference internal" href="output_file_names_code.html#new-manual-output-file-names-code"><em>Chapter 8: Python Code for Specifying output file names with formatter() and regex()</em></a></li>
-<li><a class="reference internal" href="mkdir_code.html#new-manual-mkdir-code"><em>Chapter 9: Python Code for Preparing directories for output with @mkdir()</em></a></li>
-<li><a class="reference internal" href="checkpointing_code.html#new-manual-checkpointing-code"><em>Chapter 10: Python Code for Checkpointing: Interrupted Pipelines and Exceptions</em></a></li>
-<li><a class="reference internal" href="split_code.html#new-manual-split-code"><em>Chapter 12: Python Code for Splitting up large tasks / files with @split</em></a></li>
-<li><a class="reference internal" href="merge_code.html#new-manual-merge-code"><em>Chapter 13: Python Code for  @merge multiple input into a single result</em></a></li>
-<li><a class="reference internal" href="multiprocessing_code.html#new-manual-multiprocessing-code"><em>Chapter 14: Python Code for Multiprocessing, drmaa and Computation Clusters</em></a></li>
-<li><a class="reference internal" href="logging_code.html#new-manual-logging-code"><em>Chapter 15: Python Code for Logging progress through a pipeline</em></a></li>
-<li><a class="reference internal" href="subdivide_collate_code.html#new-manual-subdivide-collate-code"><em>Chapter 16: Python Code for @subdivide tasks to run efficiently and regroup with @collate</em></a></li>
-<li><a class="reference internal" href="combinatorics_code.html#new-manual-combinatorics-code"><em>Chapter 17: Python Code for @combinations, @permutations and all versus all @product</em></a></li>
-<li><a class="reference internal" href="inputs_code.html#new-manual-inputs-code"><em>Chapter 20: Python Code for Manipulating task inputs via string substitution using inputs()  and  add_inputs()</em></a></li>
-<li><a class="reference internal" href="onthefly_code.html#new-manual-on-the-fly-code"><em>Chapter 21: Esoteric: Python Code for Generating parameters on the fly with @files</em></a></li>
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-            
-  <div class="section" id="new-manual-merge-chapter-num-merge-multiple-input-into-a-single-result">
-<span id="new-manual-merge"></span><span id="index-0"></span><h1><strong>Chapter 13</strong>: <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result<a class="headerlink" href="#new-manual-merge-chapter-num-merge-multiple-input-into-a-single-result" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> syntax</li>
-<li><a class="reference internal" href="merge_code.html#new-manual-merge-code"><em>Example code for this chapter</em></a></li>
-</ul>
-</div>
-<div class="section" id="overview-of-merge">
-<h2>Overview of <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a><a class="headerlink" href="#overview-of-merge" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <a class="reference internal" href="split.html#new-manual-split"><em>previous chapter</em></a> explained how <strong>Ruffus</strong> allows large
-jobs to be split into small pieces with <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> and analysed
-in parallel using for example, our old friend <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a>.</p>
-<p>Having done this, our next task is to recombine the fragments into a seamless whole.</p>
-<p>This is the role of the <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> decorator.</p>
-</div></blockquote>
-</div>
-<div class="section" id="merge-is-a-many-to-one-operator">
-<h2><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a>  is a many to one operator<a class="headerlink" href="#merge-is-a-many-to-one-operator" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> tasks multiple <em>inputs</em> and produces a single <em>output</em>, <strong>Ruffus</strong>
-is again agnostic as to the sort of data contained within this single <em>output</em>. It can be a single
-(string) file name, an arbitrary complicated nested structure with numbers, objects etc.
-Or even a list.</p>
-<p>The main thing is that downstream tasks will interpret this output as a single entity leading to a single
-job.</p>
-<p><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> and <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> are, in other words, about network topology.</p>
-<p>Because of this <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> is also very useful for summarising the progress
-in our pipeline. At key selected points, we can gather data from the multitude of data or disparate <em>inputs</em>
-and <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> them to a single set of summaries.</p>
-</div></blockquote>
-</div>
-<div class="section" id="example-combining-partial-solutions-calculating-variances">
-<h2>Example: Combining partial solutions: Calculating variances<a class="headerlink" href="#example-combining-partial-solutions-calculating-variances" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <a class="reference internal" href="split.html#new-manual-split"><em>previous chapter</em></a> we had almost completed all the pieces of our flowchart:</p>
-<a class="reference internal image-reference" href="../../_images/manual_split_merge_example.jpg"><img alt="../../_images/manual_split_merge_example.jpg" src="../../_images/manual_split_merge_example.jpg" style="width: 251.1px; height: 197.4px;" /></a>
-<p>What remains is to take the partial solutions from the different <tt class="docutils literal"><span class="pre">.sums</span></tt> files
-and turn these into the variance as follows:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">variance</span> <span class="o">=</span> <span class="p">(</span><span class="n">sum_squared</span> <span class="o">-</span> <span class="nb">sum</span> <span class="o">*</span> <span class="nb">sum</span> <span class="o">/</span> <span class="n">N</span><span class="p">)</span><span class="o">/</span><span class="n">N</span>
-</pre></div>
-</div>
-<p>where <tt class="docutils literal"><span class="pre">N</span></tt> is the number of values</p>
-<p>See the <a class="reference external" href="http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance">wikipedia</a> entry for a discussion of
-why this is a very naive approach.</p>
-</div></blockquote>
-<p>To do this, all we have to do is iterate through all the values in <tt class="docutils literal"><span class="pre">*.sums</span></tt>,
-add up the <tt class="docutils literal"><span class="pre">sums</span></tt> and <tt class="docutils literal"><span class="pre">sum_squared</span></tt>, and apply the above (naive) formula.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="hll"><span class="c">#   @merge files together</span>
-</span><span class="c">#</span>
-<span class="nd">@merge</span><span class="p">(</span><span class="n">sum_of_squares</span><span class="p">,</span> <span class="s">"variance.result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">calculate_variance</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Calculate variance naively</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   initialise variables</span>
-    <span class="c">#</span>
-    <span class="n">all_sum_squared</span> <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="n">all_sum</span>         <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="n">all_cnt_values</span>  <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="c">#</span>
-    <span class="c"># added up all the sum_squared, and sum and cnt_values from all the chunks</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">input_file_name</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span><span class="p">,</span> <span class="n">cnt_values</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">())</span>
-        <span class="n">all_sum_squared</span> <span class="o">+=</span> <span class="n">sum_squared</span>
-        <span class="n">all_sum</span>         <span class="o">+=</span> <span class="nb">sum</span>
-        <span class="n">all_cnt_values</span>  <span class="o">+=</span> <span class="n">cnt_values</span>
-    <span class="n">all_mean</span> <span class="o">=</span> <span class="n">all_sum</span> <span class="o">/</span> <span class="n">all_cnt_values</span>
-    <span class="n">variance</span> <span class="o">=</span> <span class="p">(</span><span class="n">all_sum_squared</span> <span class="o">-</span> <span class="n">all_sum</span> <span class="o">*</span> <span class="n">all_mean</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">all_cnt_values</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   print output</span>
-    <span class="c">#</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="n">variance</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This results in the following equivalent function call:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">calculate_variance</span> <span class="p">([</span><span class="s">"1.sums"</span><span class="p">,</span> <span class="s">"2.sums"</span><span class="p">,</span> <span class="s">"3.sums"</span><span class="p">,</span>
-<span class="hll">                     <span class="s">"4.sums"</span><span class="p">,</span> <span class="s">"5.sums"</span><span class="p">,</span> <span class="s">"6.sums"</span><span class="p">,</span>
-</span>                     <span class="s">"7.sums"</span><span class="p">,</span> <span class="s">"8.sums"</span><span class="p">,</span> <span class="s">"9.sums, "</span><span class="mf">10.</span><span class="n">sums</span><span class="s">"], "</span><span class="n">variance</span><span class="o">.</span><span class="n">result</span><span class="s">")</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>and the following display:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [[1.sums, 10.sums, 2.sums, 3.sums, 4.sums, 5.sums, 6.sums, 7.sums, 8.sums, 9.sums] -> variance.result] completed</span>
-<span class="go">Completed Task = calculate_variance</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The final result is in <tt class="docutils literal"><span class="pre">variance.result</span></tt></p>
-<p>Have a look at the <a class="reference internal" href="merge_code.html#new-manual-merge-code"><em>complete example code for this chapter</em></a>.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 13</strong>: <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result</a><ul>
-<li><a class="reference internal" href="#overview-of-merge">Overview of <tt class="docutils literal"><span class="pre">@merge</span></tt></a></li>
-<li><a class="reference internal" href="#merge-is-a-many-to-one-operator"><tt class="docutils literal"><span class="pre">@merge</span></tt>  is a many to one operator</a></li>
-<li><a class="reference internal" href="#example-combining-partial-solutions-calculating-variances">Example: Combining partial solutions: Calculating variances</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="split.html"
-                        title="previous chapter"><strong>Chapter 12</strong>: Splitting up large tasks / files with <strong>@split</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="multiprocessing.html"
-                        title="next chapter"><strong>Chapter 14</strong>: Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
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-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-  <div class="section" id="new-manual-merge-chapter-num-python-code-for-merge-multiple-input-into-a-single-result">
-<span id="new-manual-merge-code"></span><h1><strong>Chapter 13</strong>: Python Code for  <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result<a class="headerlink" href="#new-manual-merge-chapter-num-python-code-for-merge-multiple-input-into-a-single-result" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge syntax in detail</em></a></li>
-<li>Back to <strong>Chapter 13</strong>: <a class="reference internal" href="merge.html#new-manual-merge"><em>Splitting up large tasks / files with @merge</em></a></li>
-</ul>
-</div>
-<div class="section" id="splitting-large-jobs">
-<h2>Splitting large jobs<a class="headerlink" href="#splitting-large-jobs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="n">NUMBER_OF_RANDOMS</span> <span class="o">=</span> <span class="mi">10000</span>
-<span class="n">CHUNK_SIZE</span> <span class="o">=</span> <span class="mi">1000</span>
-
-
-<span class="kn">import</span> <span class="nn">random</span><span class="o">,</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">glob</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Create random numbers</span>
-<span class="c">#</span>
-<span class="nd">@originate</span><span class="p">(</span><span class="s">"random_numbers.list"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_random_numbers</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">NUMBER_OF_RANDOMS</span><span class="p">):</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%g</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mf">100.0</span><span class="p">))</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   split initial file</span>
-<span class="c">#</span>
-<span class="nd">@split</span><span class="p">(</span><span class="n">create_random_numbers</span><span class="p">,</span> <span class="s">"*.chunks"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">split_problem</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        splits random numbers file into xxx files of chunk_size each</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   clean up any files from previous runs</span>
-    <span class="c">#</span>
-    <span class="c">#for ff in glob.glob("*.chunks"):</span>
-    <span class="k">for</span> <span class="n">ff</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">ff</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#   create new file every chunk_size lines and</span>
-    <span class="c">#       copy each line into current file</span>
-    <span class="c">#</span>
-    <span class="n">output_file</span> <span class="o">=</span> <span class="bp">None</span>
-    <span class="n">cnt_files</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">input_file_name</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)):</span>
-            <span class="k">if</span> <span class="n">i</span> <span class="o">%</span> <span class="n">CHUNK_SIZE</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-                <span class="n">cnt_files</span> <span class="o">+=</span> <span class="mi">1</span>
-                <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.chunks"</span> <span class="o">%</span> <span class="n">cnt_files</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-            <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate sum and sum of squares for each chunk file</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">split_problem</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".chunks"</span><span class="p">),</span> <span class="s">".sums"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">sum_of_squares</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">output</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">]</span>
-    <span class="n">cnt_values</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">):</span>
-        <span class="n">cnt_values</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="n">val</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">rstrip</span><span class="p">())</span>
-        <span class="n">sum_squared</span> <span class="o">+=</span> <span class="n">val</span> <span class="o">*</span> <span class="n">val</span>
-        <span class="nb">sum</span> <span class="o">+=</span> <span class="n">val</span>
-    <span class="n">output</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="n">sum_squared</span><span class="p">),</span> <span c [...]
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate variance from sums</span>
-<span class="c">#</span>
-<span class="nd">@merge</span><span class="p">(</span><span class="n">sum_of_squares</span><span class="p">,</span> <span class="s">"variance.result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">calculate_variance</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Calculate variance naively</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   initialise variables</span>
-    <span class="c">#</span>
-    <span class="n">all_sum_squared</span> <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="n">all_sum</span>         <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="n">all_cnt_values</span>  <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="c">#</span>
-    <span class="c"># added up all the sum_squared, and sum and cnt_values from all the chunks</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">input_file_name</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span><span class="p">,</span> <span class="n">cnt_values</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">())</span>
-        <span class="n">all_sum_squared</span> <span class="o">+=</span> <span class="n">sum_squared</span>
-        <span class="n">all_sum</span>         <span class="o">+=</span> <span class="nb">sum</span>
-        <span class="n">all_cnt_values</span>  <span class="o">+=</span> <span class="n">cnt_values</span>
-    <span class="n">all_mean</span> <span class="o">=</span> <span class="n">all_sum</span> <span class="o">/</span> <span class="n">all_cnt_values</span>
-    <span class="n">variance</span> <span class="o">=</span> <span class="p">(</span><span class="n">all_sum_squared</span> <span class="o">-</span> <span class="n">all_sum</span> <span class="o">*</span> <span class="n">all_mean</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">all_cnt_values</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   print output</span>
-    <span class="c">#</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="n">variance</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [None -> random_numbers.list] completed</span>
-<span class="go">Completed Task = create_random_numbers</span>
-<span class="go">    Job  = [[random_numbers.list] -> *.chunks] completed</span>
-<span class="go">Completed Task = split_problem</span>
-<span class="go">    Job  = [1.chunks -> 1.sums] completed</span>
-<span class="go">    Job  = [10.chunks -> 10.sums] completed</span>
-<span class="go">    Job  = [2.chunks -> 2.sums] completed</span>
-<span class="go">    Job  = [3.chunks -> 3.sums] completed</span>
-<span class="go">    Job  = [4.chunks -> 4.sums] completed</span>
-<span class="go">    Job  = [5.chunks -> 5.sums] completed</span>
-<span class="go">    Job  = [6.chunks -> 6.sums] completed</span>
-<span class="go">    Job  = [7.chunks -> 7.sums] completed</span>
-<span class="go">    Job  = [8.chunks -> 8.sums] completed</span>
-<span class="go">    Job  = [9.chunks -> 9.sums] completed</span>
-<span class="go">Completed Task = sum_of_squares</span>
-<span class="go">    Job  = [[1.sums, 10.sums, 2.sums, 3.sums, 4.sums, 5.sums, 6.sums, 7.sums, 8.sums, 9.sums] -> variance.result] completed</span>
-<span class="go">Completed Task = calculate_variance</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 13</strong>: Python Code for  <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result</a><ul>
-<li><a class="reference internal" href="#splitting-large-jobs">Splitting large jobs</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="split_code.html"
-                        title="previous chapter"><strong>Chapter 12</strong>: Python Code for Splitting up large tasks / files with <strong>@split</strong></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="multiprocessing_code.html"
-                        title="next chapter"><strong>Chapter 14</strong>: Python Code for Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters</a></p>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
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-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
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-<span id="new-manual-mkdir"></span><span id="index-0"></span><h1><strong>Chapter 9</strong>: Preparing directories for output with <a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>@mkdir()</em></a><a class="headerlink" href="#new-manual-mkdir-chapter-num-preparing-directories-for-output-with-mkdir" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows(mkdir()) syntax in detail</em></a></li>
-<li><a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>@mkdir syntax in detail</em></a></li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><a class="reference internal" href="mkdir_code.html#new-manual-mkdir-code"><em>Chapter 9: Python Code for Preparing directories for output with @mkdir()</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>In <strong>Chapter 3</strong>, we saw that we could use <a class="reference internal" href="transform_in_parallel.html#new-manual-follows-mkdir"><em>@follows(mkdir())</em></a> to
-ensure that output directories exist:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   create_new_files() @follows mkdir</span>
-<span class="c">#</span>
-<span class="hll"><span class="nd">@follows</span><span class="p">(</span><span class="n">mkdir</span><span class="p">(</span><span class="s">"output/results/here"</span><span class="p">))</span>
-</span><span class="nd">@originate</span><span class="p">([</span><span class="s">"output/results/here/a.start_file"</span><span class="p">,</span>
-            <span class="s">"output/results/here/b.start_file"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_new_files</span><span class="p">(</span><span class="n">output_file_pair</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>This ensures that the decorated task follows (<a class="reference internal" href="transform_in_parallel.html#new-manual-follows-mkdir"><em>@follows</em></a>) the
-making of the specified directory (<tt class="docutils literal"><span class="pre">mkdir()</span></tt>).</p>
-<p>Sometimes, however, the <strong>Output</strong> is intended not for any single directory but a group
-of destinations depending on the parsed contents of <strong>Input</strong> paths.</p>
-</div></blockquote>
-</div>
-<div class="section" id="creating-directories-after-string-substitution-in-a-zoo">
-<h2>Creating directories after string substitution in a zoo...<a class="headerlink" href="#creating-directories-after-string-substitution-in-a-zoo" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>You may remember <a class="reference internal" href="output_file_names.html#new-manual-output-file-names-formatter-zoo"><em>this example</em></a> from <strong>Chapter 8</strong>:</p>
-<p>We want to feed the denizens of a zoo. The original file names are spread over several directories and we
-group their food supply by the <em>clade</em> of the animal in the following manner:</p>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/simple_tutorial_zoo_animals_formatter_example.jpg"><img alt="../../_images/simple_tutorial_zoo_animals_formatter_example.jpg" src="../../_images/simple_tutorial_zoo_animals_formatter_example.jpg" style="width: 915.5px; height: 208.5px;" /></a>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#   Put different animals in different directories depending on their clade</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food"</span><span class="p">,</span> <span class="c"># Replacement</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}"</span><span class="p">,</span>                               <span class="c"># new_directory</span>
-           <span class="s">"{subdir[0][0]}"</span><span class="p">,</span>                                           <span class="c"># animal_name</span>
-           <span class="s">"{tame[0]}"</span><span class="p">)</span>                                                <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"</span><span class="si">%40s</span><span class="s"> -> </span><span class="si">%90s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-<span class="hll">    <span class="c"># this blows up</span>
-</span><span class="hll">    <span class="c"># open(output_file, "w")</span>
-</span></pre></div>
-</div>
-</div></blockquote>
-<p>The example code from <strong>Chapter 8</strong> is, however, incomplete. If we were to actually create the specified
-files we would realise that we had forgotten to create the destination directories <tt class="docutils literal"><span class="pre">reptiles</span></tt>, <tt class="docutils literal"><span class="pre">mammals</span></tt> first!</p>
-</div></blockquote>
-<div class="section" id="using-formatter">
-<h3>using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a><a class="headerlink" href="#using-formatter" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>We could of course create directories manually.
-However, apart from being tedious and error prone, we have already gone to some lengths
-to parse out the diretories for <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a>.
-Why don’t we use the same logic to make the directories?</p>
-<p>Can you see the parallels between the syntax for <a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>@mkdir</em></a> and <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a>?</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># create directories for each clade</span>
-<span class="nd">@mkdir</span><span class="p">(</span>    <span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-           <span class="s">"{subpath[0][1]}/{clade[0]})                                # new_directory</span>
-
-<span class="c">#   Put animals of each clade in the same directory</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food"</span><span class="p">,</span> <span class="c"># Replacement</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}"</span><span class="p">,</span>                               <span class="c"># new_directory</span>
-           <span class="s">"{subdir[0][0]}"</span><span class="p">,</span>                                           <span class="c"># animal_name</span>
-           <span class="s">"{tame[0]}"</span><span class="p">)</span>                                                <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"</span><span class="si">%40s</span><span class="s"> -> </span><span class="si">%90s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-    <span class="c"># this works now</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>See the <a class="reference internal" href="mkdir_code.html#new-manual-mkdir-code"><em>example code</em></a></p>
-</div></blockquote>
-</div>
-<div class="section" id="using-regex">
-<h3>using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a><a class="headerlink" href="#using-regex" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>If you are particularly fond of using regular expression to parse file paths,
-you could also use <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># create directories for each clade</span>
-<span class="nd">@mkdir</span><span class="p">(</span>    <span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*?)/?(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span> <span class="c"># Only animals: ignore plants!</span>
-           <span class="s">r"\1/\g<clade>"</span><span class="p">)</span>                                             <span class="c"># new_directory</span>
-
-<span class="c">#   Put animals of each clade in the same directory</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food"</span><span class="p">,</span> <span class="c"># Replacement</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}"</span><span class="p">,</span>                               <span class="c"># new_directory</span>
-           <span class="s">"{subdir[0][0]}"</span><span class="p">,</span>                                           <span class="c"># animal_name</span>
-           <span class="s">"{tame[0]}"</span><span class="p">)</span>                                                <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"</span><span class="si">%40s</span><span class="s"> -> </span><span class="si">%90s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-    <span class="c"># this works now</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 9</strong>: Preparing directories for output with <tt class="docutils literal"><span class="pre">@mkdir()</span></tt></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#creating-directories-after-string-substitution-in-a-zoo">Creating directories after string substitution in a zoo...</a><ul>
-<li><a class="reference internal" href="#using-formatter">using <tt class="docutils literal"><span class="pre">formatter()</span></tt></a></li>
-<li><a class="reference internal" href="#using-regex">using <tt class="docutils literal"><span class="pre">regex()</span></tt></a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="output_file_names.html"
-                        title="previous chapter"><strong>Chapter 8</strong>: Specifying output file names with <tt class="docutils literal"><span class="pre">formatter()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="checkpointing.html"
-                        title="next chapter"><strong>Chapter 10</strong>: Checkpointing: Interrupted Pipelines and Exceptions</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/mkdir.txt"
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
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-<span id="new-manual-mkdir-code"></span><h1><strong>Chapter 9</strong>: Python Code for Preparing directories for output with <a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>@mkdir()</em></a><a class="headerlink" href="#new-manual-mkdir-chapter-num-python-code-for-preparing-directories-for-output-with-mkdir" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>mkdir()</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> syntax</li>
-<li>Back to <strong>Chapter 9</strong>: <a class="reference internal" href="mkdir.html#new-manual-mkdir"><em>Preparing directories for output with @mkdir()</em></a></li>
-</ul>
-</div>
-<div class="section" id="code-for-formatter-zoo-example">
-<h2>Code for <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> Zoo example<a class="headerlink" href="#code-for-formatter-zoo-example" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   Make directories</span>
-<span class="nd">@mkdir</span><span class="p">([</span><span class="s">"tiger"</span><span class="p">,</span> <span class="s">"lion"</span><span class="p">,</span> <span class="s">"dog"</span><span class="p">,</span> <span class="s">"crocodile"</span><span class="p">,</span> <span class="s">"rose"</span><span class="p">])</span>
-<span class="nd">@originate</span><span class="p">(</span>
-            <span class="c">#   List of animals and plants</span>
-            <span class="p">[</span>    <span class="s">"tiger/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.handreared.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.tame.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"crocodile/reptiles.wild.animals"</span><span class="p">,</span>
-                <span class="s">"rose/flowering.handreared.plants"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c"># create directories for each clade</span>
-<span class="nd">@mkdir</span><span class="p">(</span>    <span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}"</span><span class="p">)</span>                               <span class="c"># new_directory</span>
-<span class="c">#   Put different animals in different directories depending on their clade</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food"</span><span class="p">,</span> <span class="c"># Replacement</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}"</span><span class="p">,</span>                               <span class="c"># new_directory</span>
-           <span class="s">"{subdir[0][0]}"</span><span class="p">,</span>                                           <span class="c"># animal_name</span>
-           <span class="s">"{tame[0]}"</span><span class="p">)</span>                                                <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-        <span class="k">print</span> <span class="s">"</span><span class="si">%40s</span><span class="s"> -> </span><span class="si">%90s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-        <span class="c"># this works now</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="code-for-regex-zoo-example">
-<h2>Code for <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> Zoo example<a class="headerlink" href="#code-for-regex-zoo-example" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   Make directories</span>
-<span class="nd">@mkdir</span><span class="p">([</span><span class="s">"tiger"</span><span class="p">,</span> <span class="s">"lion"</span><span class="p">,</span> <span class="s">"dog"</span><span class="p">,</span> <span class="s">"crocodile"</span><span class="p">,</span> <span class="s">"rose"</span><span class="p">])</span>
-<span class="nd">@originate</span><span class="p">(</span>
-            <span class="c">#   List of animals and plants</span>
-            <span class="p">[</span>    <span class="s">"tiger/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.handreared.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.tame.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"crocodile/reptiles.wild.animals"</span><span class="p">,</span>
-                <span class="s">"rose/flowering.handreared.plants"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c"># create directories for each clade</span>
-<span class="nd">@mkdir</span><span class="p">(</span>    <span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span> <span class="c"># Only animals: ignore plants!</span>
-           <span class="s">r"\g<clade>"</span><span class="p">)</span>                                             <span class="c"># new_directory</span>
-<span class="c">#   Put different animals in different directories depending on their clade</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                        <span class="c"># Input</span>
-
-           <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span> <span class="c"># Only animals: ignore plants!</span>
-
-           <span class="s">r"\1\g<clade>/\g<tame>.\2.food"</span><span class="p">,</span>                            <span class="c"># Replacement</span>
-
-           <span class="s">r"\1\g<clade>"</span><span class="p">,</span>                                             <span class="c"># new_directory</span>
-           <span class="s">r"\2"</span><span class="p">,</span>                                                       <span class="c"># animal_name</span>
-           <span class="s">"\g<tame>"</span><span class="p">)</span>                                                  <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"</span><span class="si">%40s</span><span class="s"> -> </span><span class="si">%90s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-    <span class="c"># this works now</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
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-<li><a class="reference internal" href="#code-for-formatter-zoo-example">Code for <tt class="docutils literal"><span class="pre">formatter()</span></tt> Zoo example</a></li>
-<li><a class="reference internal" href="#code-for-regex-zoo-example">Code for <tt class="docutils literal"><span class="pre">regex()</span></tt> Zoo example</a></li>
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-  <h4>Previous topic</h4>
-  <p class="topless"><a href="output_file_names_code.html"
-                        title="previous chapter"><strong>Chapter 8</strong>: Python Code for Specifying output file names with <tt class="docutils literal"><span class="pre">formatter()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt></a></p>
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
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-<span id="new-manual-multiprocessing"></span><span id="index-0"></span><h1><strong>Chapter 14</strong>: Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters<a class="headerlink" href="#new-manual-multiprocessing-chapter-num-multiprocessing-drmaa-and-computation-clusters" title="Permalink to this headline">¶</a></h1>
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-<li><a class="reference internal" href="../../decorators/jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit</em></a> syntax</li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> syntax</li>
-<li><a class="reference internal" href="../../drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>drmaa_wrapper.run_job()</em></a> syntax</li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><a class="reference internal" href="multiprocessing_code.html#new-manual-multiprocessing-code"><em>Chapter 14: Python Code for Multiprocessing, drmaa and Computation Clusters</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="multi-processing">
-<span id="index-1"></span><h3>Multi Processing<a class="headerlink" href="#multi-processing" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><em>Ruffus</em> uses python <a class="reference external" href="http://docs.python.org/library/multiprocessing.html">multiprocessing</a> to run
-each job in a separate process.</p>
-<p>This means that jobs do <em>not</em> necessarily complete in the order of the defined parameters.
-Task hierachies are, of course, inviolate: upstream tasks run before downstream, dependent tasks.</p>
-<p>Tasks that are independent (i.e. do not precede each other) may be run in parallel as well.</p>
-<p>The number of concurrent jobs can be set in <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>If <tt class="docutils literal"><span class="pre">multiprocess</span></tt> is set to 1, then jobs will be run on a single process.</p>
-</div></blockquote>
-</div>
-<div class="section" id="data-sharing">
-<span id="index-2"></span><h3>Data sharing<a class="headerlink" href="#data-sharing" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Running jobs in separate processes allows <em>Ruffus</em> to make full use of the multiple
-processors in modern computers. However, some <a class="reference external" href="http://docs.python.org/library/multiprocessing.html#multiprocessing-programming">multiprocessing guidelines</a>
-should be borne in mind when writing <em>Ruffus</em> pipelines. In particular:</p>
-<ul class="simple">
-<li>Try not to pass large amounts of data between jobs, or at least be aware that this has to be marshalled
-across process boundaries.</li>
-<li>Only data which can be <a class="reference external" href="http://docs.python.org/library/pickle.html">pickled</a> can be passed as
-parameters to <em>Ruffus</em> task functions. Happily, that applies to almost any native Python data type.
-The use of the rare, unpicklable object will cause python to complain (fail) loudly when <em>Ruffus</em> pipelines
-are run.</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="restricting-parallelism-with-jobs-limit">
-<span id="new-manual-jobs-limit"></span><span id="index-3"></span><h2>Restricting parallelism with <a class="reference internal" href="../../decorators/jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit</em></a><a class="headerlink" href="#restricting-parallelism-with-jobs-limit" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Calling <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(multiprocess = NNN)</em></a> allows
-multiple jobs (from multiple independent tasks) to be run in parallel. However, there
-are some operations that consume so many resources that we might want them to run
-with less or no concurrency.</p>
-<p>For example, we might want to download some files via FTP but the server restricts
-requests from each IP address. Even if the rest of the pipeline is running 100 jobs in
-parallel, the FTP downloading must be restricted to 2 files at a time. We would really
-like to keep the pipeline running as is, but let this one operation run either serially,
-or with little concurrency.</p>
-<ul class="simple">
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(multiprocess = NNN)</em></a> sets the pipeline-wide concurrency but</li>
-<li><a class="reference internal" href="../../decorators/jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit(MMM)</em></a> sets concurrency at <tt class="docutils literal"><span class="pre">MMM</span></tt> only for jobs in the decorated task.</li>
-</ul>
-<p>The optional name (e.g. <tt class="docutils literal"><span class="pre">@jobs_limit(3,</span> <span class="pre">"ftp_download_limit")</span></tt>) allows the same limit to
-be shared across multiple tasks. To be pedantic: a limit of <tt class="docutils literal"><span class="pre">3</span></tt> jobs at a time would be applied
-across all tasks which have a <tt class="docutils literal"><span class="pre">@jobs_limit</span></tt> named <tt class="docutils literal"><span class="pre">"ftp_download_limit"</span></tt>.</p>
-<p>The <a class="reference internal" href="multiprocessing_code.html#new-manual-multiprocessing-code"><em>example code</em></a> uses up to 10 processes across the
-pipeline, but runs the <tt class="docutils literal"><span class="pre">stage1_big</span></tt> and <tt class="docutils literal"><span class="pre">stage1_small</span></tt> tasks 3 at a time (shared across
-both tasks). <tt class="docutils literal"><span class="pre">stage2</span></tt> jobs run 5 at a time.</p>
-</div></blockquote>
-</div>
-<div class="section" id="using-drmaa-to-dispatch-work-to-computational-clusters-or-grid-engines-from-ruffus-jobs">
-<span id="new-manual-ruffus-drmaa-wrapper-run-job"></span><h2>Using <tt class="docutils literal"><span class="pre">drmaa</span></tt> to dispatch work to Computational Clusters or Grid engines from Ruffus jobs<a class="headerlink" href="#using-drmaa-to-dispatch-work-to-computational-clusters-or-grid-engines-from-ruffus-jobs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Ruffus has been widely used to manage work on computational clusters or grid engines. Though Ruffus
-task functions cannot (yet!) run natively and transparently on remote cluster nodes, it is trivial
-to dispatch work across the cluster.</p>
-<p>From version 2.4 onwards, Ruffus includes an optional helper module which interacts with
-<a class="reference external" href="https://github.com/drmaa-python/drmaa-python">python bindings</a> for the widely used <a class="reference external" href="http://en.wikipedia.org/wiki/DRMAA">drmaa</a>
-Open Grid Forum API specification. This allows jobs to dispatch work to a computational cluster and wait until it completes.</p>
-<p>Here are the necessary steps</p>
-</div></blockquote>
-<div class="section" id="use-a-shared-drmaa-session">
-<h3>1) Use a shared drmaa session:<a class="headerlink" href="#use-a-shared-drmaa-session" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Before your pipeline runs:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   start shared drmaa session for all jobs / tasks in pipeline</span>
-<span class="c">#</span>
-<span class="kn">import</span> <span class="nn">drmaa</span>
-<span class="n">drmaa_session</span> <span class="o">=</span> <span class="n">drmaa</span><span class="o">.</span><span class="n">Session</span><span class="p">()</span>
-<span class="n">drmaa_session</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>Cleanup after your pipeline completes:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   pipeline functions go here</span>
-<span class="c">#</span>
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
-    <span class="n">drmaa_session</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="import-ruffus-drmaa-wrapper">
-<h3>2) import <tt class="docutils literal"><span class="pre">ruffus.drmaa_wrapper</span></tt><a class="headerlink" href="#import-ruffus-drmaa-wrapper" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><ul class="simple">
-<li>The optional <tt class="docutils literal"><span class="pre">ruffus.drmaa_wrapper</span></tt> module needs to be imported explicitly:</li>
-</ul>
-<div class="highlight-python"><div class="highlight"><pre><span class="hll"><span class="c"># imported ruffus.drmaa_wrapper explicitly</span>
-</span><span class="kn">from</span> <span class="nn">ruffus.drmaa_wrapper</span> <span class="kn">import</span> <span class="n">run_job</span><span class="p">,</span> <span class="n">error_drmaa_job</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="call-drmaa-wrapper-run-job">
-<h3>3) call <a class="reference internal" href="../../drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>drmaa_wrapper.run_job()</em></a><a class="headerlink" href="#call-drmaa-wrapper-run-job" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><a class="reference internal" href="../../drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>drmaa_wrapper.run_job()</em></a> dispatches the work to a cluster node within a normal Ruffus job and waits for completion</p>
-<p>This is the equivalent of <a class="reference external" href="http://docs.python.org/2/library/os.html#os.system">os.system</a>  or
-<a class="reference external" href="http://docs.python.org/2/library/subprocess.html#subprocess.check_call">subprocess.check_output</a> but the code will run remotely as specified:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="hll">    <span class="c"># ruffus.drmaa_wrapper.run_job</span>
-</span>    <span class="n">stdout_res</span><span class="p">,</span> <span class="n">stderr_res</span>  <span class="o">=</span> <span class="n">run_job</span><span class="p">(</span><span class="n">cmd_str</span>           <span class="o">=</span> <span class="s">"touch "</span> <span class="o">+</span> <span class="n">output_file</span><span class="p">,</span>
-                                      <span class="n">job_name</span>          <span class="o">=</span> <span class="n">job_name</span><span class="p">,</span>
-                                      <span class="n">logger</span>            <span class="o">=</span> <span class="n">logger</span><span class="p">,</span>
-                                      <span class="n">drmaa_session</span>     <span class="o">=</span> <span class="n">drmaa_session</span><span class="p">,</span>
-                                      <span class="n">run_locally</span>       <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">local_run</span><span class="p">,</span>
-                                      <span class="n">job_other_options</span> <span class="o">=</span> <span class="n">job_other_options</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>The complete code is available <a class="reference internal" href="multiprocessing_code.html#using-ruffus-drmaa-wrapper"><em>here</em></a></p>
-</div></blockquote>
-<ul class="simple">
-<li><a class="reference internal" href="../../drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>drmaa_wrapper.run_job()</em></a> is a convenience wrapper around the <a class="reference external" href="https://github.com/drmaa-python/drmaa-python">python drmaa bindings</a>
-<a class="reference external" href="http://drmaa-python.readthedocs.org/en/latest/tutorials.html#waiting-for-a-job">RunJob</a> function.
-It takes care of writing drmaa <em>job templates</em> for you.</li>
-<li>Each call creates a separate drmaa <em>job template</em>.</li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="use-multithread-pipeline-run-multithread-nnn">
-<h3>4) Use multithread: <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(multithread = NNN)</em></a><a class="headerlink" href="#use-multithread-pipeline-run-multithread-nnn" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<p><a class="reference internal" href="../../drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>drmaa_wrapper.run_job()</em></a></p>
-<blockquote class="last">
-<div><p><strong>requires</strong> <tt class="docutils literal"><span class="pre">pipeline_run</span></tt> <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>(multithread = NNN)</em></a></p>
-<p><strong>and will not work with</strong>  <tt class="docutils literal"><span class="pre">pipeline_run</span></tt> <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>(multiprocess = NNN)</em></a></p>
-</div></blockquote>
-</div>
-<dl class="docutils">
-<dt>Using multithreading rather than multiprocessing</dt>
-<dd><ul class="first simple">
-<li>allows the drmaa session to be shared</li>
-<li>prevents “processing storms” which lock up the queue submission node when hundreds or thousands of grid engine / cluster commands complete at the same time.</li>
-</ul>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span> <span class="p">(</span><span class="o">...</span><span class="p">,</span> <span class="n">multithread</span> <span class="o">=</span> <span class="n">NNN</span><span class="p">,</span> <span class="o">...</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>or if you are using ruffus.cmdline:</p>
-<div class="last highlight-python"><div class="highlight"><pre><span class="n">cmdline</span><span class="o">.</span><span class="n">run</span> <span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">multithread</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">jobs</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>Normally multithreading reduces the amount of parallelism in python due to the python <a class="reference external" href="http://en.wikipedia.org/wiki/Global_Interpreter_Lock">Global interpreter Lock (GIL)</a>.
-However, as the work load is almost entirely on another computer (i.e. a cluster / grid engine node) with a separate python interpreter, any cost benefit calculations of this sort are moot.</p>
-</div></blockquote>
-</div>
-<div class="section" id="develop-locally">
-<h3>5) Develop locally<a class="headerlink" href="#develop-locally" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><a class="reference internal" href="../../drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>drmaa_wrapper.run_job()</em></a> provides two convenience parameters for developing grid engine pipelines:</p>
-<ul>
-<li><p class="first">commands can run locally, i.e. on the local machine rather than on cluster nodes:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">run_job</span><span class="p">(</span><span class="n">cmd_str</span><span class="p">,</span> <span class="n">run_locally</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</li>
-<li><p class="first">Output files can be <a class="reference external" href="http://en.wikipedia.org/wiki/Touch_(Unix)">touch</a>ed, i.e. given the appearance of the work having being done without actually running the commands</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">run_job</span><span class="p">(</span><span class="n">cmd_str</span><span class="p">,</span> <span class="n">touch_only</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</li>
-</ul>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="forcing-a-pipeline-to-appear-up-to-date">
-<span id="new-manual-pipeline-run-touch"></span><span id="index-4"></span><h2>Forcing a pipeline to appear up to date<a class="headerlink" href="#forcing-a-pipeline-to-appear-up-to-date" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Sometimes, we <em>know</em> that a pipeline has run to completion, that everything is up-to-date. However, Ruffus still insists on the basis
-of file modification times that you need to rerun.</p>
-<p>For example, sometimes a trivial accounting modification needs to be made to a data file.
-Even though you know that this changes nothing in practice, Ruffus will detect the modification and
-ask to rerun everything from that point forwards.</p>
-<p>One way to convince Ruffus that everything is fine is to manually <a class="reference external" href="http://en.wikipedia.org/wiki/Touch_(Unix)">touch</a>
-all subsequent data files one by one in sequence so that the file timestamps follow the appropriate progression.</p>
-<p>You can also ask <em>Ruffus</em> to do this automatically for you by running the pipeline in <a class="reference external" href="http://en.wikipedia.org/wiki/Touch_(Unix)">touch</a>
-mode:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">(</span> <span class="n">touch_files_only</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run</em></a> will run your pipeline script normally working backwards from any specified final target, or else the
-last task in the pipeline. It works out where it should begin running, i.e. with the first out-of-date data files.
-After that point, instead of calling your pipeline task functions, each missing or out-of-date file is
-<a class="reference external" href="http://en.wikipedia.org/wiki/Touch_(Unix)">touch-ed</a> in turn so that the file modification dates
-follow on successively.</p>
-<p>This turns out to be useful way to check that your pipeline runs correctly by creating a series of dummy (empty files).
-However, <em>Ruffus</em> does not know how to read your mind to know which files to create from <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> or
-<a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> tasks.</p>
-<p>Using <a class="reference internal" href="command_line.html#new-manual-cmdline"><em>ruffus.cmdline</em></a> from version 2.4, you can just specify:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>your script --touch_files_only <span class="o">[</span>--other_options_of_your_own_etc<span class="o">]</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 14</strong>: Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a><ul>
-<li><a class="reference internal" href="#multi-processing">Multi Processing</a></li>
-<li><a class="reference internal" href="#data-sharing">Data sharing</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#restricting-parallelism-with-jobs-limit">Restricting parallelism with <tt class="docutils literal"><span class="pre">@jobs_limit</span></tt></a></li>
-<li><a class="reference internal" href="#using-drmaa-to-dispatch-work-to-computational-clusters-or-grid-engines-from-ruffus-jobs">Using <tt class="docutils literal"><span class="pre">drmaa</span></tt> to dispatch work to Computational Clusters or Grid engines from Ruffus jobs</a><ul>
-<li><a class="reference internal" href="#use-a-shared-drmaa-session">1) Use a shared drmaa session:</a></li>
-<li><a class="reference internal" href="#import-ruffus-drmaa-wrapper">2) import <tt class="docutils literal"><span class="pre">ruffus.drmaa_wrapper</span></tt></a></li>
-<li><a class="reference internal" href="#call-drmaa-wrapper-run-job">3) call <tt class="docutils literal"><span class="pre">drmaa_wrapper.run_job()</span></tt></a></li>
-<li><a class="reference internal" href="#use-multithread-pipeline-run-multithread-nnn">4) Use multithread: <tt class="docutils literal"><span class="pre">pipeline_run(multithread</span> <span class="pre">=</span> <span class="pre">NNN)</span></tt></a></li>
-<li><a class="reference internal" href="#develop-locally">5) Develop locally</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#forcing-a-pipeline-to-appear-up-to-date">Forcing a pipeline to appear up to date</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="merge.html"
-                        title="previous chapter"><strong>Chapter 13</strong>: <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="logging.html"
-                        title="next chapter"><strong>Chapter 15</strong>: Logging progress through a pipeline</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/multiprocessing.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
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-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-  <div class="section" id="new-manual-multiprocessing-chapter-num-python-code-for-multiprocessing-drmaa-and-computation-clusters">
-<span id="new-manual-multiprocessing-code"></span><h1><strong>Chapter 14</strong>: Python Code for Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters<a class="headerlink" href="#new-manual-multiprocessing-chapter-num-python-code-for-multiprocessing-drmaa-and-computation-clusters" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit</em></a> syntax</li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> syntax</li>
-<li><a class="reference internal" href="../../drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>drmaa_wrapper.run_job()</em></a> syntax</li>
-<li>Back to <strong>Chapter 14</strong>: <a class="reference internal" href="multiprocessing.html#new-manual-multiprocessing"><em>Multiprocessing, drmaa and Computation Clusters</em></a></li>
-</ul>
-</div>
-<div class="section" id="jobs-limit">
-<h2><a class="reference internal" href="../../decorators/jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit</em></a><a class="headerlink" href="#jobs-limit" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>First 2 tasks are constrained to a parallelism of 3 shared jobs at a time</li>
-<li>Final task is constrained to a parallelism of 5 jobs at a time</li>
-<li>The entire pipeline is constrained to a (theoretical) parallelism of 10 jobs at a time</li>
-</ul>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">time</span>
-
-<span class="c"># make list of 10 files</span>
-<span class="nd">@split</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"*stage1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">make_files</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">10</span><span class="p">):</span>
-        <span class="k">if</span> <span class="n">i</span> <span class="o"><</span> <span class="mi">5</span><span class="p">:</span>
-            <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.small_stage1"</span> <span class="o">%</span> <span class="n">i</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.big_stage1"</span> <span class="o">%</span> <span class="n">i</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="hll">
-</span><span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s">"ftp_download_limit"</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">make_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".small_stage1"</span><span class="p">),</span> <span class="s">".stage2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage1_small</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"FTP downloading </span><span class="si">%s</span><span class="s"> ->Start"</span> <span class="o">%</span> <span class="n">input_file</span>
-<span class="hll">    <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
-</span>    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">print</span> <span class="s">"FTP downloading </span><span class="si">%s</span><span class="s"> ->Finished"</span> <span class="o">%</span> <span class="n">input_file</span>
-
-<span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="s">"ftp_download_limit"</span><span class="p">)</span>
-<span class="hll"><span class="nd">@transform</span><span class="p">(</span><span class="n">make_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".big_stage1"</span><span class="p">),</span> <span class="s">".stage2"</span><span class="p">)</span>
-</span><span class="k">def</span> <span class="nf">stage1_big</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"FTP downloading </span><span class="si">%s</span><span class="s"> ->Start"</span> <span class="o">%</span> <span class="n">input_file</span>
-    <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">print</span> <span class="s">"FTP downloading </span><span class="si">%s</span><span class="s"> ->Finished"</span> <span class="o">%</span> <span class="n">input_file</span>
-
-<span class="nd">@jobs_limit</span><span class="p">(</span><span class="mi">5</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">([</span><span class="n">stage1_small</span><span class="p">,</span> <span class="n">stage1_big</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".stage2"</span><span class="p">),</span> <span class="s">".stage3"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">stage2</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"Processing stage2 </span><span class="si">%s</span><span class="s"> ->Start"</span> <span class="o">%</span> <span class="n">input_file</span>
-    <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">print</span> <span class="s">"Processing stage2 </span><span class="si">%s</span><span class="s"> ->Finished"</span> <span class="o">%</span> <span class="n">input_file</span>
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>Giving:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">0</span><span class="p">)</span>
-
-<span class="hll"><span class="gp">>>> </span><span class="c"># 3 jobs at a time, interleaved</span>
-</span><span class="go">FTP downloading 5.big_stage1 ->Start</span>
-<span class="go">FTP downloading 6.big_stage1 ->Start</span>
-<span class="go">FTP downloading 7.big_stage1 ->Start</span>
-<span class="go">FTP downloading 5.big_stage1 ->Finished</span>
-<span class="go">FTP downloading 8.big_stage1 ->Start</span>
-<span class="go">FTP downloading 6.big_stage1 ->Finished</span>
-<span class="go">FTP downloading 9.big_stage1 ->Start</span>
-<span class="go">FTP downloading 7.big_stage1 ->Finished</span>
-<span class="go">FTP downloading 0.small_stage1 ->Start</span>
-<span class="go">FTP downloading 8.big_stage1 ->Finished</span>
-<span class="go">FTP downloading 1.small_stage1 ->Start</span>
-<span class="go">FTP downloading 9.big_stage1 ->Finished</span>
-<span class="go">FTP downloading 2.small_stage1 ->Start</span>
-<span class="go">FTP downloading 0.small_stage1 ->Finished</span>
-<span class="go">FTP downloading 3.small_stage1 ->Start</span>
-<span class="go">FTP downloading 1.small_stage1 ->Finished</span>
-<span class="go">FTP downloading 4.small_stage1 ->Start</span>
-<span class="go">FTP downloading 2.small_stage1 ->Finished</span>
-<span class="go">FTP downloading 3.small_stage1 ->Finished</span>
-<span class="go">FTP downloading 4.small_stage1 ->Finished</span>
-
-<span class="hll"><span class="gp">>>> </span><span class="c"># 5 jobs at a time, interleaved</span>
-</span><span class="go">Processing stage2 0.stage2 ->Start</span>
-<span class="go">Processing stage2 1.stage2 ->Start</span>
-<span class="go">Processing stage2 2.stage2 ->Start</span>
-<span class="go">Processing stage2 3.stage2 ->Start</span>
-<span class="go">Processing stage2 4.stage2 ->Start</span>
-<span class="go">Processing stage2 0.stage2 ->Finished</span>
-<span class="go">Processing stage2 5.stage2 ->Start</span>
-<span class="go">Processing stage2 1.stage2 ->Finished</span>
-<span class="go">Processing stage2 6.stage2 ->Start</span>
-<span class="go">Processing stage2 2.stage2 ->Finished</span>
-<span class="go">Processing stage2 4.stage2 ->Finished</span>
-<span class="go">Processing stage2 7.stage2 ->Start</span>
-<span class="go">Processing stage2 8.stage2 ->Start</span>
-<span class="go">Processing stage2 3.stage2 ->Finished</span>
-<span class="go">Processing stage2 9.stage2 ->Start</span>
-<span class="go">Processing stage2 5.stage2 ->Finished</span>
-<span class="go">Processing stage2 7.stage2 ->Finished</span>
-<span class="go">Processing stage2 6.stage2 ->Finished</span>
-<span class="go">Processing stage2 8.stage2 ->Finished</span>
-<span class="go">Processing stage2 9.stage2 ->Finished</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="using-ruffus-drmaa-wrapper">
-<span id="id1"></span><h2>Using  <tt class="docutils literal"><span class="pre">ruffus.drmaa_wrapper</span></tt><a class="headerlink" href="#using-ruffus-drmaa-wrapper" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#!/usr/bin/python</span>
-<span class="n">job_queue_name</span>    <span class="o">=</span> <span class="s">"YOUR_QUEUE_NAME_GOES_HERE"</span>
-<span class="n">job_other_options</span> <span class="o">=</span> <span class="s">"-P YOUR_PROJECT_NAME_GOES_HERE"</span>
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">ruffus.drmaa_wrapper</span> <span class="kn">import</span> <span class="n">run_job</span><span class="p">,</span> <span class="n">error_drmaa_job</span>
-
-<span class="n">parser</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">get_argparse</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s">'WHAT DOES THIS PIPELINE DO?'</span><span class="p">)</span>
-
-<span class="n">options</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
-
-<span class="c">#  logger which can be passed to multiprocessing ruffus tasks</span>
-<span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span> <span class="o">=</span> <span class="n">cmdline</span><span class="o">.</span><span class="n">setup_logging</span> <span class="p">(</span><span class="n">__name__</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">log_file</span><span class="p">,</span> <span class="n">options</span><span class="o">.</span><span class="n">verbose</span><span class= [...]
-
-
-<span class="c">#</span>
-<span class="hll"><span class="c">#   start shared drmaa session for all jobs / tasks in pipeline</span>
-</span><span class="c">#</span>
-<span class="kn">import</span> <span class="nn">drmaa</span>
-<span class="n">drmaa_session</span> <span class="o">=</span> <span class="n">drmaa</span><span class="o">.</span><span class="n">Session</span><span class="p">()</span>
-<span class="n">drmaa_session</span><span class="o">.</span><span class="n">initialize</span><span class="p">()</span>
-
-<span class="nd">@originate</span><span class="p">([</span><span class="s">"1.chromosome"</span><span class="p">,</span> <span class="s">"X.chromosome"</span><span class="p">],</span>
-           <span class="n">logger</span><span class="p">,</span> <span class="n">logger_mutex</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_test_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">try</span><span class="p">:</span>
-        <span class="n">stdout_res</span><span class="p">,</span> <span class="n">stderr_res</span> <span class="o">=</span> <span class="s">""</span><span class="p">,</span><span class="s">""</span>
-        <span class="n">job_queue_name</span><span class="p">,</span> <span class="n">job_other_options</span> <span class="o">=</span> <span class="n">get_queue_options</span><span class="p">()</span>
-
-        <span class="c">#</span>
-<span class="hll">        <span class="c">#   ruffus.drmaa_wrapper.run_job</span>
-</span>        <span class="c">#</span>
-        <span class="n">stdout_res</span><span class="p">,</span> <span class="n">stderr_res</span>  <span class="o">=</span> <span class="n">run_job</span><span class="p">(</span><span class="n">cmd_str</span>           <span class="o">=</span> <span class="s">"touch "</span> <span class="o">+</span> <span class="n">output_file</span><span class="p">,</span>
-                                          <span class="n">job_name</span>          <span class="o">=</span> <span class="n">job_name</span><span class="p">,</span>
-                                          <span class="n">logger</span>            <span class="o">=</span> <span class="n">logger</span><span class="p">,</span>
-                                          <span class="n">drmaa_session</span>     <span class="o">=</span> <span class="n">drmaa_session</span><span class="p">,</span>
-                                          <span class="n">run_locally</span>       <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">local_run</span><span class="p">,</span>
-                                          <span class="n">job_queue_name</span>    <span class="o">=</span> <span class="n">job_queue_name</span><span class="p">,</span>
-                                          <span class="n">job_other_options</span> <span class="o">=</span> <span class="n">job_other_options</span><span class="p">)</span>
-
-    <span class="c"># relay all the stdout, stderr, drmaa output to diagnose failures</span>
-    <span class="k">except</span> <span class="n">error_drmaa_job</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span>
-                            <span class="s">"Failed to run:"</span>
-                            <span class="n">cmd</span><span class="p">,</span>
-                            <span class="n">err</span><span class="p">,</span>
-                            <span class="n">stdout_res</span><span class="p">,</span>
-                            <span class="n">stderr_res</span><span class="p">)))</span>
-
-
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
-    <span class="n">cmdline</span><span class="o">.</span><span class="n">run</span> <span class="p">(</span><span class="n">options</span><span class="p">,</span> <span class="n">multithread</span> <span class="o">=</span> <span class="n">options</span><span class="o">.</span><span class="n">jobs</span><span class="p">)</span>
-<span class="hll">    <span class="c"># cleanup drmaa</span>
-</span>    <span class="n">drmaa_session</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 14</strong>: Python Code for Multiprocessing, <tt class="docutils literal"><span class="pre">drmaa</span></tt> and Computation Clusters</a><ul>
-<li><a class="reference internal" href="#jobs-limit"><tt class="docutils literal"><span class="pre">@jobs_limit</span></tt></a></li>
-<li><a class="reference internal" href="#using-ruffus-drmaa-wrapper">Using  <tt class="docutils literal"><span class="pre">ruffus.drmaa_wrapper</span></tt></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="merge_code.html"
-                        title="previous chapter"><strong>Chapter 13</strong>: Python Code for  <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="logging_code.html"
-                        title="next chapter"><strong>Chapter 15</strong>: Python Code for Logging progress through a pipeline</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-            
-  <div class="section" id="new-manual-on-the-fly-chapter-num-esoteric-generating-parameters-on-the-fly-with-files">
-<span id="new-manual-on-the-fly"></span><span id="index-0"></span><h1><strong>Chapter 21</strong>: Esoteric: Generating parameters on the fly with <a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files</em></a><a class="headerlink" href="#new-manual-on-the-fly-chapter-num-esoteric-generating-parameters-on-the-fly-with-files" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files on-the-fly syntax in detail</em></a></li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="onthefly_code.html#new-manual-on-the-fly-code"><em>Chapter 21: Esoteric: Python Code for Generating parameters on the fly with @files</em></a></li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The different <em>Ruffus</em> <a class="reference internal" href="../../decorators/decorators.html#decorators"><em>decorators</em></a> connect up different tasks and
-generate <em>Output</em> (file names) from your <em>Input</em> in all sorts of different ways.</p>
-<p>However, sometimes, none of them <em>quite</em> do exactly what you need. And it becomes
-necessary to generate your own <em>Input</em> and <em>Output</em> parameters on the fly.</p>
-<p>Although this additional flexibility comes at the cost of a lot of extra inconvenient
-code, you can continue to leverage the rest of <em>Ruffus</em> functionality such as
-checking whether files are up to date or not.</p>
-</div></blockquote>
-</div>
-<div class="section" id="files-syntax">
-<span id="index-1"></span><h2><a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files</em></a> syntax<a class="headerlink" href="#files-syntax" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>To generate parameters on the fly, use the <a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files</em></a>
-with a <a class="reference internal" href="../../glossary.html#term-generator"><em class="xref std std-term">generator</em></a> function which yields one list / tuple of parameters per job.</p>
-<p>For example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="hll"><span class="c"># generator function</span>
-</span><span class="k">def</span> <span class="nf">generate_parameters_on_the_fly</span><span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    returns one list of parameters per job</span>
-<span class="sd">    """</span>
-    <span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                        <span class="p">[</span><span class="s">'A.input'</span><span class="p">,</span> <span class="s">'A.output'</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)],</span> <span class="c"># 1st job</span>
-                        <span class="p">[</span><span class="s">'B.input'</span><span class="p">,</span> <span class="s">'B.output'</span><span class="p">,</span> <span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">)],</span> <span class="c"># 2nd job</span>
-                        <span class="p">[</span><span class="s">'C.input'</span><span class="p">,</span> <span class="s">'C.output'</span><span class="p">,</span> <span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">)],</span> <span class="c"># 3rd job</span>
-                    <span class="p">]</span>
-    <span class="k">for</span> <span class="n">job_parameters</span> <span class="ow">in</span> <span class="n">parameters</span><span class="p">:</span>
-        <span class="k">yield</span> <span class="n">job_parameters</span>
-
-<span class="hll"><span class="c"># tell ruffus that parameters should be generated on the fly</span>
-</span><span class="nd">@files</span><span class="p">(</span><span class="n">generate_parameters_on_the_fly</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">pipeline_task</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span> <span class="n">output</span><span class="p">,</span> <span class="n">extra</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="nb">input</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s"> + </span><span class="si">%d</span><span class="s"> => </span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">extra</span><span class="p">[</span><span class=" [...]
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>Produces:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre>
-</pre></div>
-</div>
-<dl class="docutils">
-<dt>Task = parallel_task</dt>
-<dd>1 + 2 = 3
-Job = [“A”, 1, 2] completed
-3 + 4 = 7
-Job = [“B”, 3, 4] completed
-5 + 6 = 11
-Job = [“C”, 5, 6] completed</dd>
-</dl>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Be aware that the parameter generating function may be invoked
-<a class="reference internal" href="dependencies.html#new-manual-dependencies-checking-multiple-times"><em>more than once</em></a>:
-* The first time to check if this part of the pipeline is up-to-date.
-* The second time when the pipeline task function is run.</p>
-</div>
-<p>The resulting custom <em>inputs</em>, <em>outputs</em> parameters per job are
-treated normally for the purposes of checking to see if jobs are up-to-date and
-need to be re-run.</p>
-</div></blockquote>
-</div>
-<div class="section" id="a-cartesian-product-all-vs-all-example">
-<h2>A Cartesian Product, all vs all example<a class="headerlink" href="#a-cartesian-product-all-vs-all-example" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <a class="reference internal" href="onthefly_code.html#new-manual-on-the-fly-code"><em>accompanying example</em></a> provides a more realistic reason why
-you would want to generate parameters on the fly. It is a fun piece of code, which generates
-N x M combinations from two sets of files as the <em>inputs</em> of a pipeline stage.</p>
-<p>The <em>inputs</em> / <em>outputs</em> filenames are generated as a pair of nested for-loops to produce
-the N (outside loop) x M (inside loop) combinations, with the appropriate parameters
-for each job <tt class="docutils literal"><span class="pre">yield</span></tt>ed per iteration of the inner loop. The gist of this is:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="hll"><span class="c">#   Generator function</span>
-</span><span class="c">#</span>
-<span class="c">#        N x M jobs</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">generate_simulation_params</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    Custom function to generate</span>
-<span class="sd">    file names for gene/gwas simulation study</span>
-<span class="sd">    """</span>
-    <span class="k">for</span> <span class="n">sim_file</span> <span class="ow">in</span> <span class="n">get_simulation_files</span><span class="p">():</span>
-        <span class="k">for</span> <span class="p">(</span><span class="n">gene</span><span class="p">,</span> <span class="n">gwas</span><span class="p">)</span> <span class="ow">in</span> <span class="n">get_gene_gwas_file_pairs</span><span class="p">():</span>
-            <span class="n">result_file</span> <span class="o">=</span> <span class="s">"</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">.results"</span> <span class="o">%</span> <span class="p">(</span><span class="n">gene</span><span class="p">,</span> <span class="n">sim_file</span><span class="p">)</span>
-            <span class="k">yield</span> <span class="p">(</span><span class="n">gene</span><span class="p">,</span> <span class="n">gwas</span><span class="p">,</span> <span class="n">sim_file</span><span class="p">),</span> <span class="n">result_file</span>
-
-
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">generate_simulation_params</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">gwas_simulation</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="s">"..."</span>
-</pre></div>
-</div>
-<dl class="docutils">
-<dt>If <tt class="docutils literal"><span class="pre">get_gene_gwas_file_pairs()</span></tt> produces:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="p">[</span><span class="s">'a.sim'</span><span class="p">,</span> <span class="s">'b.sim'</span><span class="p">,</span> <span class="s">'c.sim'</span><span class="p">]</span>
-</pre></div>
-</div>
-</dd>
-<dt>and <tt class="docutils literal"><span class="pre">get_gene_gwas_file_pairs()</span></tt> produces:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="p">[(</span><span class="s">'1.gene'</span><span class="p">,</span> <span class="s">'1.gwas'</span><span class="p">),</span> <span class="p">(</span><span class="s">'2.gene'</span><span class="p">,</span> <span class="s">'2.gwas'</span><span class="p">)]</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>then we would end up with <tt class="docutils literal"><span class="pre">3</span></tt> x <tt class="docutils literal"><span class="pre">2</span></tt> = <tt class="docutils literal"><span class="pre">6</span></tt> jobs and the following equivalent function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'1.gene'</span><span class="p">,</span> <span class="s">'1.gwas'</span><span class="p">,</span> <span class="s">'a.sim'</span><span class="p">),</span> <span class="s">"1.gene.a.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'2.gene'</span><span class="p">,</span> <span class="s">'2.gwas'</span><span class="p">,</span> <span class="s">'a.sim'</span><span class="p">),</span> <span class="s">"2.gene.a.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'1.gene'</span><span class="p">,</span> <span class="s">'1.gwas'</span><span class="p">,</span> <span class="s">'b.sim'</span><span class="p">),</span> <span class="s">"1.gene.b.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'2.gene'</span><span class="p">,</span> <span class="s">'2.gwas'</span><span class="p">,</span> <span class="s">'b.sim'</span><span class="p">),</span> <span class="s">"2.gene.b.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'1.gene'</span><span class="p">,</span> <span class="s">'1.gwas'</span><span class="p">,</span> <span class="s">'c.sim'</span><span class="p">),</span> <span class="s">"1.gene.c.sim.results"</span><span class="p">)</span>
-<span class="n">gwas_simulation</span><span class="p">((</span><span class="s">'2.gene'</span><span class="p">,</span> <span class="s">'2.gwas'</span><span class="p">,</span> <span class="s">'c.sim'</span><span class="p">),</span> <span class="s">"2.gene.c.sim.results"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<p>The <a class="reference internal" href="onthefly_code.html#new-manual-on-the-fly-code"><em>accompanying code</em></a> looks slightly more complicated because
-of some extra bookkeeping.</p>
-<p>You can compare this approach with the alternative of using <a class="reference internal" href="../../decorators/product.html#decorators-product"><em>@product</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="hll"><span class="c">#        N x M jobs</span>
-</span><span class="c">#_________________________________________________________________________________________</span>
-<span class="nd">@product</span><span class="p">(</span>   <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">,</span> <span class="s">"*.simulation"</span><span class="p">),</span>
-            <span class="n">formatter</span><span class="p">(),</span>
-
-            <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gene"</span><span class="p">),</span>
-            <span class="n">formatter</span><span class="p">(),</span>
-
-            <span class="c"># add gwas as an input: looks like *.gene but with a differnt extension</span>
-            <span class="n">add_inputs</span><span class="p">(</span><span class="s">"{path[1][0]/{basename[1][0]}.gwas"</span><span class="p">)</span>
-
-            <span class="s">"{basename[0][0]}.{basename[1][0]}.results"</span><span class="p">)</span>    <span class="c"># output file</span>
-<span class="k">def</span> <span class="nf">gwas_simulation</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="s">"..."</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 21</strong>: Esoteric: Generating parameters on the fly with <tt class="docutils literal"><span class="pre">@files</span></tt></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#files-syntax"><tt class="docutils literal"><span class="pre">@files</span></tt> syntax</a></li>
-<li><a class="reference internal" href="#a-cartesian-product-all-vs-all-example">A Cartesian Product, all vs all example</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="inputs.html"
-                        title="previous chapter"><strong>Chapter 20</strong>: Manipulating task inputs via string substitution using <tt class="docutils literal"><span class="pre">inputs()</span></tt> and  <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="parallel.html"
-                        title="next chapter"><strong>Chapter 22</strong>: Esoteric: Running jobs in parallel without files using <tt class="docutils literal"><span class="pre">@parallel</span></tt></a></p>
-  <h3>This Page</h3>
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-        <h4 >Pipeline functions</h4>
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-            
-  <div class="section" id="new-manual-on-the-fly-chapter-num-esoteric-python-code-for-generating-parameters-on-the-fly-with-files">
-<span id="new-manual-on-the-fly-code"></span><h1><strong>Chapter 21</strong>: Esoteric: Python Code for Generating parameters on the fly with <a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files</em></a><a class="headerlink" href="#new-manual-on-the-fly-chapter-num-esoteric-python-code-for-generating-parameters-on-the-fly-with-files" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/files_ex.html#decorators-files-on-the-fly"><em>@files on-the-fly syntax in detail</em></a></li>
-<li>Back to <strong>Chapter 21</strong>: <a class="reference internal" href="onthefly.html#new-manual-on-the-fly"><em>Generating parameters on the fly</em></a></li>
-</ul>
-</div>
-<div class="section" id="introduction">
-<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="line-block">
-<div class="line">This script takes N pairs of input file pairs (with the suffices .gene and .gwas)</div>
-<div class="line">and runs them against M sets of simulation data (with the suffix .simulation)</div>
-<div class="line">A summary per input file pair is then produced</div>
-</div>
-<p>In pseudo-code:</p>
-<blockquote>
-<div><p>STEP_1:</p>
-<div class="highlight-python"><pre>for n_file in NNN_pairs_of_input_files:
-    for m_file in MMM_simulation_data:
-
-        [n_file.gene,
-         n_file.gwas,
-         m_file.simulation] -> n_file.m_file.simulation_res</pre>
-</div>
-<p>STEP_2:</p>
-<div class="highlight-python"><pre>for n_file in NNN_pairs_of_input_files:
-
-    n_file.*.simulation_res -> n_file.mean</pre>
-</div>
-<div class="line-block">
-<div class="line">n = CNT_GENE_GWAS_FILES</div>
-<div class="line">m = CNT_SIMULATION_FILES</div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">os</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   constants</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="n">working_dir</span>             <span class="o">=</span> <span class="s">"temp_NxM"</span>
-<span class="n">simulation_data_dir</span>     <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation"</span><span class="p">)</span>
-<span class="n">gene_data_dir</span>           <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"gene"</span><span class="p">)</span>
-<span class="n">CNT_GENE_GWAS_FILES</span>     <span class="o">=</span> <span class="mi">2</span>
-<span class="n">CNT_SIMULATION_FILES</span>    <span class="o">=</span> <span class="mi">3</span>
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   imports</span>
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
-<span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">izip</span>
-<span class="kn">import</span> <span class="nn">glob</span>
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Functions</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   get gene gwas file pairs</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">get_gene_gwas_file_pairs</span><span class="p">(</span>  <span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Helper function to get all *.gene, *.gwas from the direction specified</span>
-<span class="sd">        in --gene_data_dir</span>
-
-<span class="sd">    Returns</span>
-<span class="sd">        file pairs with both .gene and .gwas extensions,</span>
-<span class="sd">        corresponding roots (no extension) of each file</span>
-<span class="sd">    """</span>
-    <span class="n">gene_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gene"</span><span class="p">))</span>
-    <span class="n">gwas_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gwas"</span><span class="p">))</span>
-    <span class="c">#</span>
-    <span class="n">common_roots</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o" [...]
-    <span class="n">common_roots</span> <span class="o">&=</span><span class="nb">set</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class [...]
-    <span class="n">common_roots</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">common_roots</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="n">p</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="p">;</span> <span class="n">g_dir</span> <span class="o">=</span> <span class="n">gene_data_dir</span>
-    <span class="n">file_pairs</span> <span class="o">=</span> <span class="p">[[</span><span class="n">p</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">g_dir</span><span class="p">,</span> <span class="n">x</span> <span class="o">+</span> <span class="s">".gene"</span><span class="p">),</span> <span class="n">p</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">g_dir</span><span cla [...]
-    <span class="k">return</span> <span class="n">file_pairs</span><span class="p">,</span> <span class="n">common_roots</span>
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   get simulation files</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">get_simulation_files</span><span class="p">(</span>  <span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Helper function to get all *.simulation from the direction specified</span>
-<span class="sd">        in --simulation_data_dir</span>
-<span class="sd">        Returns</span>
-<span class="sd">            file with .simulation extensions,</span>
-<span class="sd">            corresponding roots (no extension) of each file</span>
-<span class="sd">    """</span>
-    <span class="n">simulation_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">,</span> <span class="s">"*.simulation"</span><span class="p">))</span>
-    <span class="n">simulation_roots</span> <span class="o">=</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class [...]
-    <span class="k">return</span> <span class="n">simulation_files</span><span class="p">,</span> <span class="n">simulation_roots</span>
-
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-<span class="c">#   Main logic</span>
-
-
-<span class="c">#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888</span>
-
-
-
-
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   setup_simulation_data</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-
-<span class="c">#</span>
-<span class="c"># mkdir: makes sure output directories exist before task</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">mkdir</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="n">simulation_data_dir</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">setup_simulation_data</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    create simulation files</span>
-<span class="sd">    """</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">CNT_GENE_GWAS_FILES</span><span class="p">):</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"</span><span class="si">%03d</span><span class="s">.gene"</span> <span class="o">%</span> <span class="n">i</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"</span><span class="si">%03d</span><span class="s">.gwas"</span> <span class="o">%</span> <span class="n">i</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c"># gene files without corresponding gwas and vice versa</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"orphan1.gene"</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"orphan2.gwas"</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"orphan3.gwas"</span><span class="p">),</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">CNT_SIMULATION_FILES</span><span class="p">):</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">,</span> <span class="s">"</span><span class="si">%03d</span><span class="s">.simulation"</span> <span class="o">%</span> <span class="n">i</span><span class="p">),</span> <span class="s">"w"</span><span [...]
-
-
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   cleanup_simulation_data</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">try_rmdir</span> <span class="p">(</span><span class="n">d</span><span class="p">):</span>
-    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">d</span><span class="p">):</span>
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">os</span><span class="o">.</span><span class="n">rmdir</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
-        <span class="k">except</span> <span class="ne">OSError</span><span class="p">:</span>
-            <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Warning:</span><span class="se">\t</span><span class="si">%s</span><span class="s"> is not empty and will not be removed.</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="n">d</span><span class="p">)</span>
-
-
-
-<span class="k">def</span> <span class="nf">cleanup_simulation_data</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    cleanup files</span>
-<span class="sd">    """</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"Cleanup working directory and simulation files.</span><span class="se">\n</span><span class="s">"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   cleanup gene and gwas files</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gene"</span><span class="p">)):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">,</span> <span class="s">"*.gwas"</span><span class="p">)):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="n">try_rmdir</span><span class="p">(</span><span class="n">gene_data_dir</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   cleanup simulation</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">,</span> <span class="s">"*.simulation"</span><span class="p">)):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="n">try_rmdir</span><span class="p">(</span><span class="n">simulation_data_dir</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   cleanup working_dir</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation_results"</span><span class="p">,</span> <span class="s">&qu [...]
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="n">try_rmdir</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation_results"</span><span class="p">))</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"*.mean"</span><span class="p">)):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="n">try_rmdir</span><span class="p">(</span><span class="n">working_dir</span><span class="p">)</span>
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   Step 1:</span>
-<span class="c">#</span>
-<span class="c">#        for n_file in NNN_pairs_of_input_files:</span>
-<span class="c">#            for m_file in MMM_simulation_data:</span>
-<span class="c">#</span>
-<span class="c">#                [n_file.gene,</span>
-<span class="c">#                 n_file.gwas,</span>
-<span class="c">#                 m_file.simulation] -> working_dir/n_file.m_file.simulation_res</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="k">def</span> <span class="nf">generate_simulation_params</span> <span class="p">():</span>
-    <span class="sd">"""</span>
-<span class="sd">    Custom function to generate</span>
-<span class="sd">    file names for gene/gwas simulation study</span>
-<span class="sd">    """</span>
-    <span class="n">simulation_files</span><span class="p">,</span> <span class="n">simulation_file_roots</span>    <span class="o">=</span> <span class="n">get_simulation_files</span><span class="p">()</span>
-    <span class="n">gene_gwas_file_pairs</span><span class="p">,</span> <span class="n">gene_gwas_file_roots</span> <span class="o">=</span>  <span class="n">get_gene_gwas_file_pairs</span><span class="p">()</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">sim_file</span><span class="p">,</span> <span class="n">sim_file_root</span> <span class="ow">in</span> <span class="n">izip</span><span class="p">(</span><span class="n">simulation_files</span><span class="p">,</span> <span class="n">simulation_file_roots</span><span class="p">):</span>
-        <span class="k">for</span> <span class="p">(</span><span class="n">gene</span><span class="p">,</span> <span class="n">gwas</span><span class="p">),</span> <span class="n">gene_file_root</span> <span class="ow">in</span> <span class="n">izip</span><span class="p">(</span><span class="n">gene_gwas_file_pairs</span><span class="p">,</span> <span class="n">gene_gwas_file_roots</span><span class="p">):</span>
-            <span class="c">#</span>
-            <span class="n">result_file</span> <span class="o">=</span> <span class="s">"</span><span class="si">%s</span><span class="s">.</span><span class="si">%s</span><span class="s">.simulation_res"</span> <span class="o">%</span> <span class="p">(</span><span class="n">gene_file_root</span><span class="p">,</span> <span class="n">sim_file_root</span><span class="p">)</span>
-            <span class="n">result_file_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation_results"</span><span class="p">,</span> <span class="n">result_file</span><span class="p">)</span>
-            <span class="c">#</span>
-            <span class="k">yield</span> <span class="p">[</span><span class="n">gene</span><span class="p">,</span> <span class="n">gwas</span><span class="p">,</span> <span class="n">sim_file</span><span class="p">],</span> <span class="n">result_file_path</span><span class="p">,</span> <span class="n">gene_file_root</span><span class="p">,</span> <span class="n">sim_file_root</span><span class="p">,</span> <span class="n">result_file</span>
-
-
-
-<span class="c">#</span>
-<span class="c"># mkdir: makes sure output directories exist before task</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">mkdir</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">working_dir</span><span class="p">,</span> <span class="s">"simulation_results"</span><span class="p">)))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="n">generate_simulation_params</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">gwas_simulation</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">result_file_path</span><span class="p">,</span> <span class="n">gene_file_root</span><span class="p">,</span> <span class="n">sim_file_root</span><span class="p">,</span> <span class="n">result_file</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Dummy calculation of gene gwas vs simulation data</span>
-<span class="sd">    Normally runs in parallel on a computational cluster</span>
-<span class="sd">    """</span>
-    <span class="p">(</span><span class="n">gene_file</span><span class="p">,</span>
-    <span class="n">gwas_file</span><span class="p">,</span>
-    <span class="n">simulation_data_file</span><span class="p">)</span> <span class="o">=</span> <span class="n">input_files</span>
-    <span class="c">#</span>
-    <span class="n">simulation_res_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">result_file_path</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="n">simulation_res_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s"> + </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">gene_file_root</span><span class="p">,</span> <span class="n">sim_file_root</span><spa [...]
-
-
-<span class="c">#_________________________________________________________________________________________</span>
-<span class="c">#</span>
-<span class="c">#   Step 2:</span>
-<span class="c">#</span>
-<span class="c">#       Statistical summary per gene/gwas file pair</span>
-<span class="c">#</span>
-<span class="c">#        for n_file in NNN_pairs_of_input_files:</span>
-<span class="c">#            working_dir/simulation_results/n.*.simulation_res</span>
-<span class="c">#               -> working_dir/n.mean</span>
-<span class="c">#</span>
-<span class="c">#_________________________________________________________________________________________</span>
-
-
-<span class="nd">@collate</span><span class="p">(</span><span class="n">gwas_simulation</span><span class="p">,</span> <span class="n">regex</span><span class="p">(</span><span class="s">r"simulation_results/(\d+).\d+.simulation_res"</span><span class="p">),</span> <span class="s">r"\1.mean"</span><span class="p">)</span>
-<span class="nd">@posttask</span><span class="p">(</span><span class="k">lambda</span> <span class="p">:</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="se">\n</span><span class="s">OK</span><span class="se">\n</span><span class="s">"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">statistical_summary</span> <span class="p">(</span><span class="n">result_files</span><span class="p">,</span> <span class="n">summary_file</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Simulate statistical summary</span>
-<span class="sd">    """</span>
-    <span class="n">summary_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">summary_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">result_files</span><span class="p">:</span>
-        <span class="n">summary_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">f</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">())</span>
-
-
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">setup_simulation_data</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">statistical_summary</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-
-<span class="c"># uncomment to printout flowchar</span>
-<span class="c">#</span>
-<span class="c"># pipeline_printout(sys.stdout, [statistical_summary], verbose=2)</span>
-<span class="c"># graph_printout ("flowchart.jpg", "jpg", [statistical_summary])</span>
-<span class="c">#</span>
-
-<span class="n">cleanup_simulation_data</span> <span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">setup_simulation_data</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-<span class="go">    Make directories [temp_NxM/gene, temp_NxM/simulation] completed</span>
-<span class="go">Completed Task = setup_simulation_data_mkdir_1</span>
-<span class="go">    Job completed</span>
-<span class="go">Completed Task = setup_simulation_data</span>
-
-
-<span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">statistical_summary</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-<span class="go">    Make directories [temp_NxM, temp_NxM/simulation_results] completed</span>
-<span class="go">Completed Task = gwas_simulation_mkdir_1</span>
-<span class="go">    Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/000.simulation] -> temp_NxM/simulation_results/001.000.simulation_res, 001, 000, 001.000.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/000.simulation] -> temp_NxM/simulation_results/000.000.simulation_res, 000, 000, 000.000.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/001.simulation] -> temp_NxM/simulation_results/001.001.simulation_res, 001, 001, 001.001.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/001.simulation] -> temp_NxM/simulation_results/000.001.simulation_res, 000, 001, 000.001.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/000.gene, temp_NxM/gene/000.gwas, temp_NxM/simulation/002.simulation] -> temp_NxM/simulation_results/000.002.simulation_res, 000, 002, 000.002.simulation_res] completed</span>
-<span class="go">    Job = [[temp_NxM/gene/001.gene, temp_NxM/gene/001.gwas, temp_NxM/simulation/002.simulation] -> temp_NxM/simulation_results/001.002.simulation_res, 001, 002, 001.002.simulation_res] completed</span>
-<span class="go">Completed Task = gwas_simulation</span>
-<span class="go">    Job = [[temp_NxM/simulation_results/000.000.simulation_res, temp_NxM/simulation_results/000.001.simulation_res, temp_NxM/simulation_results/000.002.simulation_res] -> temp_NxM/000.mean] completed</span>
-<span class="go">    Job = [[temp_NxM/simulation_results/001.000.simulation_res, temp_NxM/simulation_results/001.001.simulation_res, temp_NxM/simulation_results/001.002.simulation_res] -> temp_NxM/001.mean] completed</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 21</strong>: Esoteric: Python Code for Generating parameters on the fly with <tt class="docutils literal"><span class="pre">@files</span></tt></a><ul>
-<li><a class="reference internal" href="#introduction">Introduction</a></li>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
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-  <h4>Previous topic</h4>
-  <p class="topless"><a href="inputs_code.html"
-                        title="previous chapter"><strong>Chapter 20</strong>: Python Code for Manipulating task inputs via string substitution using <tt class="docutils literal"><span class="pre">inputs()</span></tt>  and  <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="flowchart_colours_code.html"
-                        title="next chapter"><strong>Appendix 1</strong>: Python code for Flow Chart Colours with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></p>
-  <h3>This Page</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
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-  <div class="section" id="new-manual-originate-chapter-num-creating-files-with-originate">
-<span id="new-manual-originate"></span><span id="index-0"></span><h1><strong>Chapter 4</strong>: Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt><a class="headerlink" href="#new-manual-originate-chapter-num-creating-files-with-originate" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/originate.html#decorators-originate"><em>@originate syntax in detail</em></a></li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="originate_code.html#new-manual-originate-code"><em>Chapter 4: Python Code for Creating files with @originate</em></a></li>
-</ul>
-</div>
-<div class="section" id="simplifying-our-example-with-originate">
-<h2>Simplifying our example with <a class="reference internal" href="../../decorators/originate.html#decorators-originate"><em>@originate</em></a><a class="headerlink" href="#simplifying-our-example-with-originate" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Our previous pipeline example started off with a set of files which we had to create first.</p>
-<p>This is a common task: pipelines have to start <em>somewhere</em>.</p>
-<p>Ideally, though, we would only want to create these starting files if they didn’t already exist. In other words, we want a sort of <tt class="docutils literal"><span class="pre">@transform</span></tt> which makes files from nothing (<tt class="docutils literal"><span class="pre">None</span></tt>?).</p>
-<p>This is exactly what <a class="reference internal" href="../../decorators/originate.html#decorators-originate"><em>@originate</em></a> helps you to do.</p>
-<p>Rewriting our pipeline with <a class="reference internal" href="../../decorators/originate.html#decorators-originate"><em>@originate</em></a> gives the following three steps:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   create initial files</span>
-<span class="c">#</span>
-<span class="hll"><span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-</span>               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="c"># create both files as necessary</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   first task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span> <span class="s">".output.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   second task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output.2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-</pre></div>
-</div>
-<div class="highlight-python"><pre>    Job  = [None -> [job1.a.start, job1.b.start]] completed
-    Job  = [None -> [job2.a.start, job2.b.start]] completed
-    Job  = [None -> [job3.a.start, job3.b.start]] completed
-Completed Task = create_initial_file_pairs
-    Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1] completed
-    Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1] completed
-    Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1] completed
-Completed Task = first_task
-    Job  = [job1.a.output.1 -> job1.a.output.2] completed
-    Job  = [job2.a.output.1 -> job2.a.output.2] completed
-    Job  = [job3.a.output.1 -> job3.a.output.2] completed
-Completed Task = second_task</pre>
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-<li><a class="reference internal" href="#simplifying-our-example-with-originate">Simplifying our example with <tt class="docutils literal"><span class="pre">@originate</span></tt></a></li>
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-<span id="new-manual-originate-code"></span><h1><strong>Chapter 4</strong>: Python Code for Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt><a class="headerlink" href="#new-manual-originate-chapter-num-python-code-for-creating-files-with-originate" title="Permalink to this headline">¶</a></h1>
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-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform syntax in detail</em></a></li>
-<li>Back to <strong>Chapter 4</strong>: <a class="reference internal" href="originate.html#new-manual-originate"><em>@originate</em></a></li>
-</ul>
-</div>
-<div class="section" id="using-originate">
-<h2>Using <tt class="docutils literal"><span class="pre">@originate</span></tt><a class="headerlink" href="#using-originate" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   create initial files</span>
-<span class="c">#</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="c"># create both files as necessary</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   first task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span> <span class="s">".output.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   second task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output.2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><pre>    Job  = [None -> [job1.a.start, job1.b.start]] completed
-    Job  = [None -> [job2.a.start, job2.b.start]] completed
-    Job  = [None -> [job3.a.start, job3.b.start]] completed
-Completed Task = create_initial_file_pairs
-    Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1] completed
-    Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1] completed
-    Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1] completed
-Completed Task = first_task
-    Job  = [job1.a.output.1 -> job1.a.output.2] completed
-    Job  = [job2.a.output.1 -> job2.a.output.2] completed
-    Job  = [job3.a.output.1 -> job3.a.output.2] completed
-Completed Task = second_task</pre>
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-<li><a class="reference internal" href="#"><strong>Chapter 4</strong>: Python Code for Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt></a><ul>
-<li><a class="reference internal" href="#using-originate">Using <tt class="docutils literal"><span class="pre">@originate</span></tt></a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
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-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="transform_in_parallel_code.html"
-                        title="previous chapter"><strong>Chapter 3</strong>: Python Code for More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data</a></p>
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-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
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-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
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-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
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-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-            
-  <div class="section" id="new-manual-output-file-names-chapter-num-specifying-output-file-names-with-formatter-and-regex">
-<span id="new-manual-output-file-names"></span><span id="index-0"></span><h1><strong>Chapter 8</strong>: Specifying output file names with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> and <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a><a class="headerlink" href="#new-manual-output-file-names-chapter-num-specifying-output-file-names-with-formatte [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> syntax</li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="output_file_names_code.html#new-manual-output-file-names-code"><em>Chapter 8: Python Code for Specifying output file names with formatter() and regex()</em></a></li>
-</ul>
-</div>
-<div class="section" id="review">
-<h2>Review<a class="headerlink" href="#review" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/theoretical_pipeline_schematic.png"><img alt="../../_images/theoretical_pipeline_schematic.png" src="../../_images/theoretical_pipeline_schematic.png" style="width: 610.0px; height: 71.0px;" /></a>
-<p>Computational pipelines transform your data in stages until the final result is produced.
-The most straightforward way to use Ruffus is to hold the intermediate results after each stage
-in a series of files with related file names.</p>
-<p>Part of telling Ruffus how these pipeline stages or <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> functions are connected
-together is to write simple rules for how to the file names for each stage follow on from each other.
-Ruffus helps you to specify these file naming rules.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><strong>The best way to design a pipeline is to:</strong></p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><strong>Write down the file names of the data as it flows across your pipeline.</strong>
-Do these file names follow a <em>pattern</em> ?</li>
-<li><strong>Write down the names of functions which transforms the data at each stage of the pipeline.</strong></li>
-</ul>
-</div></blockquote>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="a-different-file-name-suffix-for-each-pipeline-stage">
-<span id="new-manual-suffix"></span><h2>A different file name <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a> for each pipeline stage<a class="headerlink" href="#a-different-file-name-suffix-for-each-pipeline-stage" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The easiest and cleanest way to write Ruffus pipelines is to use a different suffix
-for each stage of your pipeline.</p>
-<p>We used this approach in <a class="reference internal" href="introduction.html#new-manual-introduction"><em>Chapter 1: An introduction to basic Ruffus syntax</em></a>  and in <a class="reference internal" href="transform_in_parallel_code.html#new-manual-transform-in-parallel-code"><em>code</em></a> from <a class="reference internal" href="transform_in_parallel.html#new-manual-transform-in-parallel"><em>Chapter 3: More on @transform-ing data</em></a>:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span class="hll">    <span class="c">#Task Name:                  File suffices</span>
-</span>    _________________________      ______________________
-    create_initial_file_pairs            *.start
-    first_task                           *.output.1
-    second_task                          *.output.2
-</pre></div>
-</div>
-<p>There is a long standing convention of using file suffices to denote file type: For example, a <strong>“compile”</strong> task might convert <strong>source</strong> files of type <tt class="docutils literal"><span class="pre">*.c</span></tt> to <strong>object</strong> files of type <tt class="docutils literal"><span class="pre">*.o</span></tt>.</p>
-<dl class="docutils">
-<dt>We can think of Ruffus tasks comprising :</dt>
-<dd><ul class="first last simple">
-<li>recipes in <tt class="docutils literal"><span class="pre">@transform(...)</span></tt> for transforming file names: changing  <tt class="docutils literal"><span class="pre">.c</span></tt> to a <tt class="docutils literal"><span class="pre">.o</span></tt> (e.g. <tt class="docutils literal"><span class="pre">AA.c</span> <span class="pre">-></span> <span class="pre">AA.o</span></tt> <tt class="docutils literal"><span class="pre">BB.c</span> <span class="pre">-></span> <span cla [...]
-<li>recipes in a task function <tt class="docutils literal"><span class="pre">def</span> <span class="pre">foo_bar()</span></tt> for transforming your data: from <strong>source</strong> <tt class="docutils literal"><span class="pre">.c</span></tt> to <strong>object</strong> <tt class="docutils literal"><span class="pre">.o</span></tt></li>
-</ul>
-</dd>
-</dl>
-<p>Let us review the Ruffus syntax for doing this:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="hll">@transform<span class="o">(</span> create_initial_file_pairs,  <span class="c"># Input:   Name of previous task(s)</span>
-</span><span class="hll">            suffix<span class="o">(</span><span class="s2">".start"</span><span class="o">)</span>,           <span class="c"># Matching suffix</span>
-</span><span class="hll">            <span class="s2">".output.1"</span><span class="o">)</span>                <span class="c"># Replacement string</span>
-</span>def first_task<span class="o">(</span>input_files, output_file<span class="o">)</span>:
-    with open<span class="o">(</span>output_file, <span class="s2">"w"</span><span class="o">)</span>: pass
-</pre></div>
-</div>
-</div></blockquote>
-<ol class="arabic">
-<li><p class="first"><strong>Input</strong>:</p>
-<blockquote>
-<div><dl class="docutils">
-<dt>The first parameter for <tt class="docutils literal"><span class="pre">@transform</span></tt> can be a mixture of one or more:</dt>
-<dd><ul class="first last simple">
-<li>previous tasks (e.g. <tt class="docutils literal"><span class="pre">create_initial_file_pairs</span></tt>)</li>
-<li>file names (all python strings are treated as paths)</li>
-<li>glob specifications (e.g <tt class="docutils literal"><span class="pre">*.c</span></tt>, <tt class="docutils literal"><span class="pre">/my/path/*.foo</span></tt>)</li>
-</ul>
-</dd>
-</dl>
-<p>Each element provides an input for the task. So if the previous task <tt class="docutils literal"><span class="pre">create_initial_file_pairs</span></tt> has five outputs, the next <tt class="docutils literal"><span class="pre">@transform</span></tt> task will accept
-these as five separate inputs leading to five independent jobs.</p>
-</div></blockquote>
-</li>
-<li><p class="first"><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a>:</p>
-<blockquote>
-<div><p>The second parameter <tt class="docutils literal"><span class="pre">suffix(".start")</span></tt> must match the end of the first string in each input.
-For example, <tt class="docutils literal"><span class="pre">create_initial_file_pairs</span></tt> produces the list <tt class="docutils literal"><span class="pre">['job1.a.start',</span> <span class="pre">'job1.b.start']</span></tt>, then <tt class="docutils literal"><span class="pre">suffix(".start")</span></tt>  must matches the first string, i.e. <tt class="docutils literal"><span class="pre">'job1.a.start'</span></tt>.
-If the input is nested structure, this would be iterated through recursively to find the first string.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Inputs which do not match the suffix are discarded altogether.</p>
-</div>
-</div></blockquote>
-</li>
-<li><p class="first"><strong>Replacement</strong>:</p>
-<blockquote>
-<div><p>The third parameter is the replacement for the suffix.
-The pair of input strings in the step3 example produces the following output parameter</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">input_parameters</span>   <span class="o">=</span> <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">]</span>
-<span class="n">matching_input</span>     <span class="o">=</span> <span class="s">'job1.a.start'</span>
-<span class="n">output_parameter</span>   <span class="o">=</span> <span class="s">'job1.a.output.1'</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>When the pipeline is run, this results in the following equivalent call to <tt class="docutils literal"><span class="pre">first_task(...)</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">first_task</span><span class="p">([</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span> <span class="s">'job1.a.output.1'</span><span class="p">):</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The replacement parameter can itself be a list or any arbitrary complicated structure:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="hll">@transform<span class="o">(</span>create_initial_file_pairs,            <span class="c"># Input</span>
-</span><span class="hll">            suffix<span class="o">(</span><span class="s2">".a.start"</span><span class="o">)</span>,                  <span class="c"># Matching suffix</span>
-</span><span class="hll">            <span class="o">[</span><span class="s2">".output.a.1"</span>, <span class="s2">".output.b.1"</span>, 45<span class="o">])</span>  <span class="c"># Replacement list</span>
-</span>def first_task<span class="o">(</span>input_files, output_parameters<span class="o">)</span>:
-    print <span class="s2">"input_parameters = "</span>, input_files
-    print <span class="s2">"output_parameters = "</span>, output_parameters
-</pre></div>
-</div>
-</div></blockquote>
-<p>In which case, all the strings are used as replacements, other values are left untouched, and we obtain the following:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="hll"><span class="c"># job #1</span>
-</span><span class="nv">input</span>  <span class="o">=</span>  <span class="o">[</span><span class="s1">'job1.a.start'</span>,    <span class="s1">'job1.b.start'</span><span class="o">]</span>
-<span class="nv">output</span> <span class="o">=</span>  <span class="o">[</span><span class="s1">'job1.output.a.1'</span>, <span class="s1">'job1.output.b.1'</span>, 45<span class="o">]</span>
-
-<span class="hll"><span class="c"># job #2</span>
-</span><span class="nv">input</span>  <span class="o">=</span>  <span class="o">[</span><span class="s1">'job2.a.start'</span>,    <span class="s1">'job2.b.start'</span><span class="o">]</span>
-<span class="nv">output</span> <span class="o">=</span>  <span class="o">[</span><span class="s1">'job2.output.a.1'</span>, <span class="s1">'job2.output.b.1'</span>, 45<span class="o">]</span>
-
-<span class="hll"><span class="c"># job #3</span>
-</span><span class="nv">input</span>  <span class="o">=</span>  <span class="o">[</span><span class="s1">'job3.a.start'</span>,    <span class="s1">'job3.b.start'</span><span class="o">]</span>
-<span class="nv">output</span> <span class="o">=</span>  <span class="o">[</span><span class="s1">'job3.output.a.1'</span>, <span class="s1">'job3.output.b.1'</span>, 45<span class="o">]</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Note how task function is called with the value <tt class="docutils literal"><span class="pre">45</span></tt> <em>verbatim</em> because it is not a string.</p>
-</div></blockquote>
-</li>
-</ol>
-</div></blockquote>
-</div>
-<div class="section" id="formatter-manipulates-pathnames-and-regular-expression">
-<span id="new-manual-formatter"></span><h2><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> manipulates pathnames and regular expression<a class="headerlink" href="#formatter-manipulates-pathnames-and-regular-expression" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a> replacement is the cleanest and easiest way to generate suitable output file names for each stage in a pipeline.
-Often, however, we require more complicated manipulations to specify our file names.
-For example,</p>
-<blockquote>
-<div><ul class="simple">
-<li>It is common to have to change directories from a <em>data</em> directory to a <em>working</em> directory as the first step of a pipeline.</li>
-<li>Data management can be simplified by separate files from each pipeline stage into their own directory.</li>
-<li>Information may have to be decoded from data file names, e.g. <tt class="docutils literal"><span class="pre">"experiment373.IBM.03March2002.txt"</span></tt></li>
-</ul>
-</div></blockquote>
-<p>Though <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> is much more powerful, the principle and syntax are the same:
-we take string elements from the <strong>Input</strong> and perform some replacements to generate the <strong>Output</strong> parameters.</p>
-<p><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a></p>
-<blockquote>
-<div><ul class="simple">
-<li>Allows easy manipulation of path subcomponents in the style of <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.split">os.path.split()</a>, and <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.basename">os.path.basename</a></li>
-<li>Uses familiar python <a class="reference external" href="http://docs.python.org/2/library/string.html#string-formatting">string.format</a> syntax (See <a class="reference external" href="http://docs.python.org/2/library/string.html#format-examples">string.format examples</a>. )</li>
-<li>Supports optional regular expression (<a class="reference external" href="http://docs.python.org/2/library/re.html#re.MatchObject.group">re</a>) matches including named captures.</li>
-<li>Can refer to any file path (i.e. python string) in each input and is not limited like <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a> to the first string.</li>
-<li>Can even refer to individual letters within a match</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="path-name-components">
-<h3>Path name components<a class="headerlink" href="#path-name-components" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> breaks down each input pathname into path name components which can then be recombined in whichever way by the replacement string.</p>
-<p>Given an example string of :</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">input_string</span> <span class="o">=</span> <span class="s">"/directory/to/a/file.name.ext"</span>
-<span class="n">formatter</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>the path components are:</p>
-<ul class="simple">
-<li><tt class="docutils literal"><span class="pre">basename</span></tt>: The <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.basename">base name</a> <em>excluding</em> <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.splitext">extension</a>, <tt class="docutils literal"><span class="pre">"file.name"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">ext</span></tt>     : The <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.splitext">extension</a>, <tt class="docutils literal"><span class="pre">".ext"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">path</span></tt>    : The <a class="reference external" href="http://docs.python.org/2/library/os.path.html#os.path.dirname">dirname</a>, <tt class="docutils literal"><span class="pre">"/directory/to/a"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">subdir</span></tt>  : A list of sub-directories in the <tt class="docutils literal"><span class="pre">path</span></tt> in reverse order, <tt class="docutils literal"><span class="pre">["a",</span> <span class="pre">"to",</span> <span class="pre">"directory",</span> <span class="pre">"/"]</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">subpath</span></tt> : A list of descending sub-paths in reverse order, <tt class="docutils literal"><span class="pre">["/directory/to/a",</span> <span class="pre">"/directory/to",</span> <span class="pre">"/directory",</span> <span class="pre">"/"]</span></tt></li>
-</ul>
-</div></blockquote>
-<p>The replacement string refers to these components by using python <a class="reference external" href="http://docs.python.org/2/library/string.html#string-formatting">string.format</a> style curly braces. <tt class="docutils literal"><span class="pre">"{NAME}"</span></tt></p>
-<p>We refer to an element from the Nth input string by index, for example:</p>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">"{ext[0]}"</span></tt>     is the extension of the first file name string in <strong>Input</strong>.</li>
-<li><tt class="docutils literal"><span class="pre">"{basename[1]}"</span></tt> is the basename of the second file name in <strong>Input</strong>.</li>
-<li><tt class="docutils literal"><span class="pre">"{basename[1][0:3]}"</span></tt> are the first three letters from the basename of the second file name in <strong>Input</strong>.</li>
-</ul>
-</div></blockquote>
-<p><tt class="docutils literal"><span class="pre">subdir</span></tt>, <tt class="docutils literal"><span class="pre">subpath</span></tt> were designed to help you navigate directory hierachies with the minimum of fuss.
-For example, you might want to graft a hierachical path to another location:
-<tt class="docutils literal"><span class="pre">"{subpath[0][2]}/from/{subdir[0][0]}/{basename[0]}"</span></tt> neatly replaces just one directory (<tt class="docutils literal"><span class="pre">"to"</span></tt>) in the path with another  (<tt class="docutils literal"><span class="pre">"from"</span></tt>):</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">replacement_string</span> <span class="o">=</span> <span class="s">"{subpath[0][2]}/from/{subdir[0][0]}/{basename[0]}"</span>
-
-<span class="n">input_string</span>    <span class="o">=</span> <span class="s">"/directory/to/a/file.name.ext"</span>
-<span class="n">result_string</span>   <span class="o">=</span> <span class="s">"/directory/from/a/file.name.ext"</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="filter-and-parse-using-regular-expressions">
-<span id="new-manual-formatter-regex"></span><h3>Filter and parse using regular expressions<a class="headerlink" href="#filter-and-parse-using-regular-expressions" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p><a class="reference external" href="http://docs.python.org/2/library/re.html#re.MatchObject.group">Regular expression</a> matches can be used with the similar syntax.
-Our example string can be parsed using the following regular expression:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">input_string</span> <span class="o">=</span> <span class="s">"/directory/to/a/file.name.ext"</span>
-<span class="n">formatter</span><span class="p">(</span><span class="s">r"/directory/(.+)/(?P<MYFILENAME>)\.ext"</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>We capture part of the path using <tt class="docutils literal"><span class="pre">(.+)</span></tt>, and the base name using <tt class="docutils literal"><span class="pre">(?P<MYFILENAME>)</span></tt>.
-These <a class="reference external" href="http://docs.python.org/2/library/re.html#re.MatchObject.group">matching subgroups</a> can be referred to by index
-but for greater clarity the second named capture can also be referred to by name, i.e. <tt class="docutils literal"><span class="pre">{MYFILENAME}</span></tt>.</p>
-</div></blockquote>
-<p>The regular expression components for the first string can thus be referred to as follows:</p>
-<blockquote>
-<div><ul class="simple">
-<li><tt class="docutils literal"><span class="pre">{0[0]}</span></tt>          : The entire match captured by index, <tt class="docutils literal"><span class="pre">"/directory/to/a/file.name.ext"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">{1[0]}</span></tt>          : The first match captured by index, <tt class="docutils literal"><span class="pre">"to/a"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">{2[0]}</span></tt>          : The second match captured by index, <tt class="docutils literal"><span class="pre">"file.name"</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">{MYFILENAME[0]}</span></tt> : The match captured by name, <tt class="docutils literal"><span class="pre">"file.name"</span></tt></li>
-</ul>
-</div></blockquote>
-<p>If each input consists of a list of paths such as <tt class="docutils literal"><span class="pre">['job1.a.start',</span> <span class="pre">'job1.b.start',</span> <span class="pre">'job1.c.start']</span></tt>, we can match each of them separately
-by using as many regular expressions as necessary. For example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">input_string</span> <span class="o">=</span> <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">,</span> <span class="s">'job1.c.start'</span><span class="p">]</span>
-<span class="c"># Regular expression matches for 1st, 2nd but not 3rd element</span>
-<span class="n">formatter</span><span class="p">(</span><span class="s">".+a.start"</span><span class="p">,</span> <span class="s">"b.start$"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Or if you only wanted regular expression matches for the second file name (string), pad with <tt class="docutils literal"><span class="pre">None</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">input_string</span> <span class="o">=</span> <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">,</span> <span class="s">'job1.c.start'</span><span class="p">]</span>
-<span class="c"># Regular expression matches for 2nd but not 1st or 3rd elements</span>
-<span class="n">formatter</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"b.start$"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="using-transform-with-formatter">
-<h3>Using <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform()</em></a> with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a><a class="headerlink" href="#using-transform-with-formatter" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>We can put these together in the following example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   create initial files</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.c.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="c"># create both files as necessary</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   formatter</span>
-<span class="c">#</span>
-
-<span class="c">#   first task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span>                               <span class="c"># Input</span>
-
-<span class="hll">            <span class="n">formatter</span><span class="p">(</span><span class="s">".+/job(?P<JOBNUMBER>\d+).a.start"</span><span class="p">,</span>           <span class="c"># Extract job number</span>
-</span><span class="hll">                      <span class="s">".+/job[123].b.start"</span><span class="p">),</span>                       <span class="c"># Match only "b" files</span>
-</span>
-            <span class="p">[</span><span class="s">"{path[0]}/jobs{JOBNUMBER[0]}.output.a.1"</span><span class="p">,</span>             <span class="c"># Replacement list</span>
-             <span class="s">"{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"</span><span class="p">,</span> <span class="mi">45</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_parameters</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"input_parameters = "</span><span class="p">,</span> <span class="n">input_files</span>
-    <span class="k">print</span> <span class="s">"output_parameters = "</span><span class="p">,</span> <span class="n">output_parameters</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This produces:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="go">input_parameters  =  ['job1.a.start',</span>
-<span class="go">                      'job1.b.start']</span>
-<span class="go">output_parameters =  ['/home/lg/src/temp/jobs1.output.a.1',</span>
-<span class="go">                      '/home/lg/src/temp/jobs1.output.b.1', 45]</span>
-
-<span class="go">input_parameters  =  ['job2.a.start',</span>
-<span class="go">                      'job2.b.start']</span>
-<span class="go">output_parameters =  ['/home/lg/src/temp/jobs2.output.a.1',</span>
-<span class="go">                      '/home/lg/src/temp/jobs2.output.b.1', 45]</span>
-</pre></div>
-</div>
-<p>Notice that <tt class="docutils literal"><span class="pre">job3</span></tt> has <tt class="docutils literal"><span class="pre">'job3.c.start'</span></tt> as the second file.
-This fails to match the regular expression and is discarded.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Failed regular expression mismatches are ignored.</p>
-<p><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> regular expressions are thus very useful in filtering out all
-files which do not match your specified criteria.</p>
-<p class="last">If your some of your task inputs have a mixture of different file types, a simple <tt class="docutils literal"><span class="pre">Formatter(".txt$")</span></tt>, for example, will make
-your code a lot simpler...</p>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="string-substitution-for-extra-arguments">
-<h3>string substitution for “extra” arguments<a class="headerlink" href="#string-substitution-for-extra-arguments" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The first two arguments for Ruffus task functions are special because they are the <strong>Input</strong> and <strong>Output</strong>
-parameters which link different stages of a pipeline.</p>
-<p>Python strings in these arguments are names of data files whose modification times indicate whether the pipeline is up to date or not.</p>
-<p>Other arguments to task functions are not passed down the pipeline but consumed.
-Any python strings they contain do not need to be file names. These extra arguments are very useful
-for passing data to pipelined tasks, such as shared values, loggers, programme options etc.</p>
-<p>One helpful feature is that strings in these extra arguments are also subject to <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> string substitution.
-This means you can leverage the parsing capabilities of Ruffus to decode any information about the pipeline data files,
-These might include the directories you are running in and parts of the file name.</p>
-<p>For example, if we would want to know which files go with which “job number” in the previous example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   create initial files</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.c.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   print job number as an extra argument</span>
-<span class="c">#</span>
-
-<span class="c">#   first task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span>                               <span class="c"># Input</span>
-
-            <span class="n">formatter</span><span class="p">(</span><span class="s">".+/job(?P<JOBNUMBER>\d+).a.start"</span><span class="p">,</span>           <span class="c"># Extract job number</span>
-<span class="hll">                      <span class="s">".+/job[123].b.start"</span><span class="p">),</span>                       <span class="c"># Match only "b" files</span>
-</span><span class="hll">
-</span>            <span class="p">[</span><span class="s">"{path[0]}/jobs{JOBNUMBER[0]}.output.a.1"</span><span class="p">,</span>             <span class="c"># Replacement list</span>
-             <span class="s">"{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"</span><span class="p">],</span>
-
-             <span class="s">"{JOBNUMBER[0]}"</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_parameters</span><span class="p">,</span> <span class="n">job_number</span><span class="p">):</span>
-    <span class="k">print</span> <span class="n">job_number</span><span class="p">,</span> <span class="s">":"</span><span class="p">,</span> <span class="n">input_files</span>
-
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">1 : ['job1.a.start', 'job1.b.start']</span>
-<span class="go">2 : ['job2.a.start', 'job2.b.start']</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="changing-directories-using-formatter-in-a-zoo">
-<span id="new-manual-output-file-names-formatter-zoo"></span><h3>Changing directories using <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> in a zoo...<a class="headerlink" href="#changing-directories-using-formatter-in-a-zoo" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Here is a more fun example. We would like to feed the denizens of a zoo. Unfortunately, the file names for
-these are spread over several directories. Ideally, we would like their food supply to be grouped more
-sensibly. And, of course, we only want to feed the animals, not the plants.</p>
-<p>I have colour coded the input and output files for this task to show how we would like to rearrange them:</p>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/simple_tutorial_zoo_animals_formatter_example.jpg"><img alt="../../_images/simple_tutorial_zoo_animals_formatter_example.jpg" src="../../_images/simple_tutorial_zoo_animals_formatter_example.jpg" style="width: 915.5px; height: 208.5px;" /></a>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   Make directories</span>
-<span class="nd">@mkdir</span><span class="p">([</span><span class="s">"tiger"</span><span class="p">,</span> <span class="s">"lion"</span><span class="p">,</span> <span class="s">"dog"</span><span class="p">,</span> <span class="s">"crocodile"</span><span class="p">,</span> <span class="s">"rose"</span><span class="p">])</span>
-
-<span class="nd">@originate</span><span class="p">(</span>
-<span class="hll">            <span class="c">#   List of animals and plants</span>
-</span>            <span class="p">[</span>    <span class="s">"tiger/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.handreared.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.tame.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"crocodile/reptiles.wild.animals"</span><span class="p">,</span>
-                <span class="s">"rose/flowering.handreared.plants"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#   Put different animals in different directories depending on their clade</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-<span class="hll">           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-</span>
-           <span class="s">"{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food"</span><span class="p">,</span> <span class="c"># Replacement</span>
-
-<span class="hll">           <span class="s">"{subpath[0][1]}/{clade[0]}"</span><span class="p">,</span>                               <span class="c"># new_directory</span>
-</span><span class="hll">           <span class="s">"{subdir[0][0]}"</span><span class="p">,</span>                                           <span class="c"># animal_name</span>
-</span><span class="hll">           <span class="s">"{tame[0]}"</span><span class="p">)</span>                                                <span class="c"># tameness</span>
-</span><span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span>
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>We can see that the food for each animal are now grouped by clade in the same directory, which makes a lot more sense...</p>
-<p>Note how we used <tt class="docutils literal"><span class="pre">subpath[0][1]</span></tt> to move down one level of the file path to build a new file name.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-<span class="go">Food for the wild        crocodile = ./reptiles/wild.crocodile.food will be placed in ./reptiles</span>
-<span class="go">Food for the tame        dog       = ./mammals/tame.dog.food        will be placed in ./mammals</span>
-<span class="go">Food for the wild        dog       = ./mammals/wild.dog.food        will be placed in ./mammals</span>
-<span class="go">Food for the handreared  lion      = ./mammals/handreared.lion.food will be placed in ./mammals</span>
-<span class="go">Food for the wild        lion      = ./mammals/wild.lion.food       will be placed in ./mammals</span>
-<span class="go">Food for the wild        tiger     = ./mammals/wild.tiger.food      will be placed in ./mammals</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="regex-manipulates-via-regular-expressions">
-<span id="new-manual-regex"></span><h2><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> manipulates via regular expressions<a class="headerlink" href="#regex-manipulates-via-regular-expressions" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If you are a hard core regular expressions fan, you may want to use <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> instead of <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a> or <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a>.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> uses regular expressions like <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> but</p>
-<blockquote>
-<div><ul class="simple">
-<li>It only matches the first file name in the input. As described above, <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> can match any one or more of the input filename strings.</li>
-<li>It does not understand file paths so you may have to perform your own directory / file name parsing.</li>
-<li>String replacement uses syntax borrowed from <a class="reference external" href="http://docs.python.org/2/library/re.html#re.sub">re.sub()</a>, rather than building a result from parsed regular expression (and file path) components</li>
-</ul>
-</div></blockquote>
-<p class="last">In general <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> is more powerful and was introduced from version 2.4 is intended to be a more user friendly replacement for <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a>.</p>
-</div>
-<p>Let us see how the previous zoo example looks with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a>:</p>
-<blockquote>
-<div><p><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> code:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#   Put different animals in different directories depending on their clade</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-<span class="hll">           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-</span>
-<span class="hll">           <span class="s">"{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food"</span><span class="p">,</span> <span class="c"># Replacement</span>
-</span>
-           <span class="s">"{subpath[0][1]}/{clade[0]}"</span><span class="p">,</span>                               <span class="c"># new_directory</span>
-           <span class="s">"{subdir[0][0]}"</span><span class="p">,</span>                                           <span class="c"># animal_name</span>
-           <span class="s">"{tame[0]}"</span><span class="p">)</span>                                                <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span>
-</pre></div>
-</div>
-<p><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> code:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#   Put different animals in different directories depending on their clade</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                        <span class="c"># Input</span>
-
-<span class="hll">           <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span> <span class="c"># Only animals: ignore plants!</span>
-</span>
-<span class="hll">           <span class="s">r"\1/\g<clade>/\g<tame>.\2.food"</span><span class="p">,</span>                            <span class="c"># Replacement</span>
-</span>
-           <span class="s">r"\1/\g<clade>"</span><span class="p">,</span>                                             <span class="c"># new_directory</span>
-           <span class="s">r"\2"</span><span class="p">,</span>                                                       <span class="c"># animal_name</span>
-           <span class="s">"\g<tame>"</span><span class="p">)</span>                                                  <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The regular expression to parse the input file path safely was a bit hairy to write, and it is not
-clear that it handles all edge conditions (e.g. files in the root directory). Apart from that, if the
-limitations of <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> do not preclude its use, then the two approaches
-are not so different in practice.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 8</strong>: Specifying output file names with <tt class="docutils literal"><span class="pre">formatter()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt></a><ul>
-<li><a class="reference internal" href="#review">Review</a></li>
-<li><a class="reference internal" href="#a-different-file-name-suffix-for-each-pipeline-stage">A different file name <tt class="docutils literal"><span class="pre">suffix()</span></tt> for each pipeline stage</a></li>
-<li><a class="reference internal" href="#formatter-manipulates-pathnames-and-regular-expression"><tt class="docutils literal"><span class="pre">formatter()</span></tt> manipulates pathnames and regular expression</a><ul>
-<li><a class="reference internal" href="#path-name-components">Path name components</a></li>
-<li><a class="reference internal" href="#filter-and-parse-using-regular-expressions">Filter and parse using regular expressions</a></li>
-<li><a class="reference internal" href="#using-transform-with-formatter">Using <tt class="docutils literal"><span class="pre">@transform()</span></tt> with <tt class="docutils literal"><span class="pre">formatter()</span></tt></a></li>
-<li><a class="reference internal" href="#string-substitution-for-extra-arguments">string substitution for “extra” arguments</a></li>
-<li><a class="reference internal" href="#changing-directories-using-formatter-in-a-zoo">Changing directories using <tt class="docutils literal"><span class="pre">formatter()</span></tt> in a zoo...</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#regex-manipulates-via-regular-expressions"><tt class="docutils literal"><span class="pre">regex()</span></tt> manipulates via regular expressions</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="pipeline_printout_graph.html"
-                        title="previous chapter"><strong>Chapter 7</strong>: Displaying the pipeline visually with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="mkdir.html"
-                        title="next chapter"><strong>Chapter 9</strong>: Preparing directories for output with <tt class="docutils literal"><span class="pre">@mkdir()</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/output_file_names.txt"
-           rel="nofollow">Show Source</a></li>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
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-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
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-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
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-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-  <div class="section" id="new-manual-output-file-names-chapter-num-python-code-for-specifying-output-file-names-with-formatter-and-regex">
-<span id="new-manual-output-file-names-code"></span><h1><strong>Chapter 8</strong>: Python Code for Specifying output file names with <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> and <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a><a class="headerlink" href="#new-manual-output-file-names-chapter-num-python-code-for-specifying-output-file-names-wi [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> syntax</li>
-<li>Back to <strong>Chapter 8</strong>: <a class="reference internal" href="output_file_names.html#new-manual-output-file-names"><em>Specifying output file names</em></a></li>
-</ul>
-</div>
-<div class="section" id="example-code-for-suffix">
-<h2>Example Code for <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix()</em></a><a class="headerlink" href="#example-code-for-suffix" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   create initial files</span>
-<span class="c">#</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="c"># create both files as necessary</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   suffix</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span>             <span class="c"># name of previous task(s) (or list of files, or a glob)</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>                     <span class="c"># matching suffix of the "input file"</span>
-            <span class="p">[</span><span class="s">".output.a.1"</span><span class="p">,</span> <span class="mi">45</span><span class="p">,</span> <span class="s">".output.b.1"</span><span class="p">])</span>   <span class="c"># resulting suffix</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_parameters</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"  input_parameters  = "</span><span class="p">,</span> <span class="n">input_files</span>
-    <span class="k">print</span> <span class="s">"  output_parameters = "</span><span class="p">,</span> <span class="n">output_parameters</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">first_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-code-for-formatter">
-<h2>Example Code for <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a><a class="headerlink" href="#example-code-for-formatter" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   create initial files</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.c.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="c"># create both files as necessary</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   formatter</span>
-<span class="c">#</span>
-
-<span class="c">#   first task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span>                               <span class="c"># Input</span>
-
-            <span class="n">formatter</span><span class="p">(</span><span class="s">".+/job(?P<JOBNUMBER>\d+).a.start"</span><span class="p">,</span>           <span class="c"># Extract job number</span>
-                      <span class="s">".+/job[123].b.start"</span><span class="p">),</span>                       <span class="c"># Match only "b" files</span>
-
-            <span class="p">[</span><span class="s">"{path[0]}/jobs{JOBNUMBER[0]}.output.a.1"</span><span class="p">,</span>             <span class="c"># Replacement list</span>
-             <span class="s">"{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"</span><span class="p">,</span> <span class="mi">45</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_parameters</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"input_parameters = "</span><span class="p">,</span> <span class="n">input_files</span>
-    <span class="k">print</span> <span class="s">"output_parameters = "</span><span class="p">,</span> <span class="n">output_parameters</span>
-
-
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-code-for-formatter-with-replacements-in-extra-arguments">
-<h2>Example Code for <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> with replacements in <em>extra</em> arguments<a class="headerlink" href="#example-code-for-formatter-with-replacements-in-extra-arguments" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   create initial files</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.c.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   print job number as an extra argument</span>
-<span class="c">#</span>
-
-<span class="c">#   first task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span>                               <span class="c"># Input</span>
-
-            <span class="n">formatter</span><span class="p">(</span><span class="s">".+/job(?P<JOBNUMBER>\d+).a.start"</span><span class="p">,</span>           <span class="c"># Extract job number</span>
-                      <span class="s">".+/job[123].b.start"</span><span class="p">),</span>                       <span class="c"># Match only "b" files</span>
-
-            <span class="p">[</span><span class="s">"{path[0]}/jobs{JOBNUMBER[0]}.output.a.1"</span><span class="p">,</span>             <span class="c"># Replacement list</span>
-             <span class="s">"{path[1]}/jobs{JOBNUMBER[0]}.output.b.1"</span><span class="p">],</span>
-
-             <span class="s">"{JOBNUMBER[0]}"</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_parameters</span><span class="p">,</span> <span class="n">job_number</span><span class="p">):</span>
-    <span class="k">print</span> <span class="n">job_number</span><span class="p">,</span> <span class="s">":"</span><span class="p">,</span> <span class="n">input_files</span>
-
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-code-for-formatter-in-zoos">
-<h2>Example Code for <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-formatter"><em>formatter()</em></a> in Zoos<a class="headerlink" href="#example-code-for-formatter-in-zoos" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   Make directories</span>
-<span class="nd">@mkdir</span><span class="p">([</span><span class="s">"tiger"</span><span class="p">,</span> <span class="s">"lion"</span><span class="p">,</span> <span class="s">"dog"</span><span class="p">,</span> <span class="s">"crocodile"</span><span class="p">,</span> <span class="s">"rose"</span><span class="p">])</span>
-
-<span class="nd">@originate</span><span class="p">(</span>
-            <span class="c">#   List of animals and plants</span>
-            <span class="p">[</span>    <span class="s">"tiger/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.handreared.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.tame.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"crocodile/reptiles.wild.animals"</span><span class="p">,</span>
-                <span class="s">"rose/flowering.handreared.plants"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-<span class="c">#   Put different animals in different directories depending on their clade</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                       <span class="c"># Input</span>
-
-           <span class="n">formatter</span><span class="p">(</span><span class="s">".+/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span>       <span class="c"># Only animals: ignore plants!</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}/{tame[0]}.{subdir[0][0]}.food"</span><span class="p">,</span> <span class="c"># Replacement</span>
-
-           <span class="s">"{subpath[0][1]}/{clade[0]}"</span><span class="p">,</span>                               <span class="c"># new_directory</span>
-           <span class="s">"{subdir[0][0]}"</span><span class="p">,</span>                                           <span class="c"># animal_name</span>
-           <span class="s">"{tame[0]}"</span><span class="p">)</span>                                                <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span>
-
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-
-
-<span class="n">Results</span> <span class="ow">in</span><span class="p">:</span>
-
-<span class="p">::</span>
-
-    <span class="o">>>></span> <span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">wild</span>        <span class="n">crocodile</span> <span class="o">=</span> <span class="o">./</span><span class="n">reptiles</span><span class="o">/</span><span class="n">wild</span><span class="o">.</span><span class="n">crocodile</span><span class="o">.</span><span class="n">food</span> <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="o [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">tame</span>        <span class="n">dog</span>       <span class="o">=</span> <span class="o">./</span><span class="n">mammals</span><span class="o">/</span><span class="n">tame</span><span class="o">.</span><span class="n">dog</span><span class="o">.</span><span class="n">food</span>        <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="o [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">wild</span>        <span class="n">dog</span>       <span class="o">=</span> <span class="o">./</span><span class="n">mammals</span><span class="o">/</span><span class="n">wild</span><span class="o">.</span><span class="n">dog</span><span class="o">.</span><span class="n">food</span>        <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="o [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">handreared</span>  <span class="n">lion</span>      <span class="o">=</span> <span class="o">./</span><span class="n">mammals</span><span class="o">/</span><span class="n">handreared</span><span class="o">.</span><span class="n">lion</span><span class="o">.</span><span class="n">food</span> <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="o [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">wild</span>        <span class="n">lion</span>      <span class="o">=</span> <span class="o">./</span><span class="n">mammals</span><span class="o">/</span><span class="n">wild</span><span class="o">.</span><span class="n">lion</span><span class="o">.</span><span class="n">food</span>       <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="o [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">wild</span>        <span class="n">tiger</span>     <span class="o">=</span> <span class="o">./</span><span class="n">mammals</span><span class="o">/</span><span class="n">wild</span><span class="o">.</span><span class="n">tiger</span><span class="o">.</span><span class="n">food</span>      <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="o [...]
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="example-code-for-regex-in-zoos">
-<h2>Example Code for <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-regex"><em>regex()</em></a> in zoos<a class="headerlink" href="#example-code-for-regex-in-zoos" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#   Make directories</span>
-<span class="nd">@mkdir</span><span class="p">([</span><span class="s">"tiger"</span><span class="p">,</span> <span class="s">"lion"</span><span class="p">,</span> <span class="s">"dog"</span><span class="p">,</span> <span class="s">"crocodile"</span><span class="p">,</span> <span class="s">"rose"</span><span class="p">])</span>
-
-<span class="nd">@originate</span><span class="p">(</span>
-            <span class="c">#   List of animals and plants</span>
-            <span class="p">[</span>    <span class="s">"tiger/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"lion/mammals.handreared.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.tame.animals"</span><span class="p">,</span>
-                <span class="s">"dog/mammals.wild.animals"</span><span class="p">,</span>
-                <span class="s">"crocodile/reptiles.wild.animals"</span><span class="p">,</span>
-                <span class="s">"rose/flowering.handreared.plants"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-
-
-<span class="c">#   Put different animals in different directories depending on their clade</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span>                                        <span class="c"># Input</span>
-
-           <span class="n">regex</span><span class="p">(</span><span class="s">r"(.*?/?)(\w+)/(?P<clade>\w+).(?P<tame>\w+).animals"</span><span class="p">),</span> <span class="c"># Only animals: ignore plants!</span>
-
-           <span class="s">r"\1/\g<clade>/\g<tame>.\2.food"</span><span class="p">,</span>                            <span class="c"># Replacement</span>
-
-           <span class="s">r"\1/\g<clade>"</span><span class="p">,</span>                                             <span class="c"># new_directory</span>
-           <span class="s">r"\2"</span><span class="p">,</span>                                                       <span class="c"># animal_name</span>
-           <span class="s">"\g<tame>"</span><span class="p">)</span>                                                  <span class="c"># tameness</span>
-<span class="k">def</span> <span class="nf">feed</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">new_directory</span><span class="p">,</span> <span class="n">animal_name</span><span class="p">,</span> <span class="n">tameness</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"Food for the {tameness:11s} {animal_name:9s} = {output_file:90s} will be placed in {new_directory}"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="nb">locals</span><span class="p">())</span>
-
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-
-
-<span class="n">Results</span> <span class="ow">in</span><span class="p">:</span>
-
-<span class="p">::</span>
-
-    <span class="o">>>></span> <span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">wild</span>        <span class="n">crocodile</span> <span class="o">=</span> <span class="n">reptiles</span><span class="o">/</span><span class="n">wild</span><span class="o">.</span><span class="n">crocodile</span><span class="o">.</span><span class="n">food</span> <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="ow">in</span> <span class= [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">tame</span>        <span class="n">dog</span>       <span class="o">=</span> <span class="n">mammals</span><span class="o">/</span><span class="n">tame</span><span class="o">.</span><span class="n">dog</span><span class="o">.</span><span class="n">food</span>        <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="ow">in</span> <span class= [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">wild</span>        <span class="n">dog</span>       <span class="o">=</span> <span class="n">mammals</span><span class="o">/</span><span class="n">wild</span><span class="o">.</span><span class="n">dog</span><span class="o">.</span><span class="n">food</span>        <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="ow">in</span> <span class= [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">handreared</span>  <span class="n">lion</span>      <span class="o">=</span> <span class="n">mammals</span><span class="o">/</span><span class="n">handreared</span><span class="o">.</span><span class="n">lion</span><span class="o">.</span><span class="n">food</span> <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="ow">in</span> <span class= [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">wild</span>        <span class="n">lion</span>      <span class="o">=</span> <span class="n">mammals</span><span class="o">/</span><span class="n">wild</span><span class="o">.</span><span class="n">lion</span><span class="o">.</span><span class="n">food</span>       <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="ow">in</span> <span class= [...]
-    <span class="n">Food</span> <span class="k">for</span> <span class="n">the</span> <span class="n">wild</span>        <span class="n">tiger</span>     <span class="o">=</span> <span class="n">mammals</span><span class="o">/</span><span class="n">wild</span><span class="o">.</span><span class="n">tiger</span><span class="o">.</span><span class="n">food</span>      <span class="n">will</span> <span class="n">be</span> <span class="n">placed</span> <span class="ow">in</span> <span class= [...]
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 8</strong>: Python Code for Specifying output file names with <tt class="docutils literal"><span class="pre">formatter()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt></a><ul>
-<li><a class="reference internal" href="#example-code-for-suffix">Example Code for <tt class="docutils literal"><span class="pre">suffix()</span></tt></a></li>
-<li><a class="reference internal" href="#example-code-for-formatter">Example Code for <tt class="docutils literal"><span class="pre">formatter()</span></tt></a></li>
-<li><a class="reference internal" href="#example-code-for-formatter-with-replacements-in-extra-arguments">Example Code for <tt class="docutils literal"><span class="pre">formatter()</span></tt> with replacements in <em>extra</em> arguments</a></li>
-<li><a class="reference internal" href="#example-code-for-formatter-in-zoos">Example Code for <tt class="docutils literal"><span class="pre">formatter()</span></tt> in Zoos</a></li>
-<li><a class="reference internal" href="#example-code-for-regex-in-zoos">Example Code for <tt class="docutils literal"><span class="pre">regex()</span></tt> in zoos</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="pipeline_printout_graph_code.html"
-                        title="previous chapter"><strong>Chapter 7</strong>: Python Code for Displaying the pipeline visually with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="mkdir_code.html"
-                        title="next chapter"><strong>Chapter 9</strong>: Python Code for Preparing directories for output with <tt class="docutils literal"><span class="pre">@mkdir()</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/output_file_names_code.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../../search.html" method="get">
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-<span id="new-manual-deprecated-parallel"></span><span id="index-0"></span><h1><strong>Chapter 22</strong>: Esoteric: Running jobs in parallel without files using <a class="reference internal" href="../../decorators/parallel.html#decorators-parallel"><em>@parallel</em></a><a class="headerlink" href="#new-manual-parallel-chapter-num-esoteric-running-jobs-in-parallel-without-files-using-parallel" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/parallel.html#decorators-parallel"><em>@parallel</em></a> syntax in detail</li>
-</ul>
-</div>
-<div class="section" id="parallel">
-<h2><strong>@parallel</strong><a class="headerlink" href="#parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>@parallel</strong> supplies parameters for multiple <strong>jobs</strong> exactly like <a class="reference internal" href="deprecated_files.html#new-manual-deprecated-files"><em>@files</em></a> except that:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>The first two parameters are not treated like <em>inputs</em> and <em>ouputs</em> parameters,
-and strings are not assumed to be file names</li>
-<li>Thus no checking of whether each job is up-to-date is made using <em>inputs</em> and <em>outputs</em> files</li>
-<li>No expansions of <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns or <em>output</em> from previous tasks is carried out.</li>
-</ol>
-</div></blockquote>
-<p>This syntax is most useful when a pipeline stage does not involve creating or consuming any files, and
-you wish to forego the conveniences of <a class="reference internal" href="deprecated_files.html#new-manual-deprecated-files"><em>@files</em></a>, <a class="reference internal" href="transform.html#new-manual-transform"><em>@transform</em></a> etc.</p>
-<p>The following code performs some arithmetic in parallel:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">sys</span>
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="p">[</span>
-                 <span class="p">[</span><span class="s">'A'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="c"># 1st job</span>
-                 <span class="p">[</span><span class="s">'B'</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="c"># 2nd job</span>
-                 <span class="p">[</span><span class="s">'C'</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span> <span class="c"># 3rd job</span>
-             <span class="p">]</span>
-<span class="nd">@parallel</span><span class="p">(</span><span class="n">parameters</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">parallel_task</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="n">param1</span><span class="p">,</span> <span class="n">param2</span><span class="p">):</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"    Parallel task </span><span class="si">%s</span><span class="s">: "</span> <span class="o">%</span> <span class="n">name</span><span class="p">)</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s"> + </span><span class="si">%d</span><span class="s"> = </span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">param1</span><span class="p">,</span> <span class="n" [...]
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">parallel_task</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>produces the following:</p>
-<div class="highlight-python"><pre>Task = parallel_task
-    Parallel task A: 1 + 2 = 3
-    Job = ["A", 1, 2] completed
-    Parallel task B: 3 + 4 = 7
-    Job = ["B", 3, 4] completed
-    Parallel task C: 5 + 6 = 11
-    Job = ["C", 5, 6] completed</pre>
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-<li><a class="reference internal" href="#parallel"><strong>@parallel</strong></a></li>
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-  <div class="section" id="new-manual-pipeline-printout-chapter-num-understanding-how-your-pipeline-works-with-pipeline-printout">
-<span id="new-manual-pipeline-printout"></span><span id="index-0"></span><h1><strong>Chapter 5</strong>: Understanding how your pipeline works with <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a><a class="headerlink" href="#new-manual-pipeline-printout-chapter-num-understanding-how-your-pipeline-works-with-pipeline-printout" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> syntax</li>
-<li><a class="reference internal" href="pipeline_printout_code.html#new-manual-pipeline-printout-code"><em>Python Code for this chapter</em></a></li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<ul class="last simple">
-<li><strong>Whether you are learning or developing ruffus pipelines, your best friend is</strong> <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a>
-<strong>This shows the exact parameters and files as they are passed through the pipeline.</strong></li>
-<li><strong>We also</strong> <em>strongly</em> <strong>recommend you use the</strong> <tt class="docutils literal"><span class="pre">Ruffus.cmdline</span></tt> <strong>convenience module which</strong>
-<strong>will take care of all the command line arguments for you. See</strong> <a class="reference internal" href="command_line.html#new-manual-cmdline"><em>Chapter 6: Running Ruffus from the command line with ruffus.cmdline</em></a>.</li>
-</ul>
-</div>
-<div class="section" id="printing-out-which-jobs-will-be-run">
-<h2>Printing out which jobs will be run<a class="headerlink" href="#printing-out-which-jobs-will-be-run" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> takes the same parameters as pipeline_run but just prints
-the tasks which are and are not up-to-date.</p>
-<p>The <tt class="docutils literal"><span class="pre">verbose</span></tt> parameter controls how much detail is displayed.</p>
-<p>Let us take the pipelined code we previously wrote in
-<strong>Chapter 3</strong> <a class="reference internal" href="transform_in_parallel_code.html#new-manual-transform-in-parallel-code"><em>More on @transform-ing data and @originate</em></a>
-but call <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> instead of
-<a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(...)</em></a>.
-This lists the tasks which will be run in the pipeline:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">import</span> <span class="nn">sys</span>
-<span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">])</span>
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which will be run:</span>
-
-<span class="go">Task = create_initial_file_pairs</span>
-<span class="go">Task = first_task</span>
-<span class="go">Task = second_task</span>
-<span class="go">________________________________________</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>To see the input and output parameters of each job in the pipeline, try increasing the verbosity from the default (<tt class="docutils literal"><span class="pre">1</span></tt>) to <tt class="docutils literal"><span class="pre">3</span></tt>
-(See <a class="reference internal" href="pipeline_printout_code.html#new-manual-pipeline-printout-code"><em>code</em></a>)</p>
-<p>This is very useful for checking that the input and output parameters have been specified correctly.</p>
-</div></blockquote>
-</div>
-<div class="section" id="determining-which-jobs-are-out-of-date-or-not">
-<h2>Determining which jobs are out-of-date or not<a class="headerlink" href="#determining-which-jobs-are-out-of-date-or-not" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>It is often useful to see which tasks are or are not up-to-date. For example, if we
-were to run the pipeline in full, and then modify one of the intermediate files, the
-pipeline would be partially out of date.</p>
-<p>Let us start by run the pipeline in full but then modify <tt class="docutils literal"><span class="pre">job1.a.output.1</span></tt> so that the second task appears out-of-date:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-
-<span class="hll"><span class="c"># "touch" job1.stage1</span>
-</span><span class="nb">open</span><span class="p">(</span><span class="s">"job1.a.output.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Run <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> with a verbosity of <tt class="docutils literal"><span class="pre">5</span></tt>.</p>
-<p>This will tell you exactly why <tt class="docutils literal"><span class="pre">second_task(...)</span></tt> needs to be re-run:
-because <tt class="docutils literal"><span class="pre">job1.a.output.1</span></tt> has a file modification time <em>after</em> <tt class="docutils literal"><span class="pre">job1.a.output.2</span></tt> (highlighted):</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which are up-to-date:</span>
-
-<span class="go">Task = create_initial_file_pairs</span>
-<span class="go">Task = first_task</span>
-
-<span class="hll"><span class="go">________________________________________</span>
-</span>
-<span class="go">________________________________________</span>
-<span class="go">Tasks which will be run:</span>
-
-<span class="go">Task = second_task</span>
-<span class="go">       Job  = [job1.a.output.1</span>
-<span class="go">             -> job1.a.output.2]</span>
-<span class="gp">>>> </span><span class="c"># File modification times shown for out of date files</span>
-<span class="go">         Job needs update:</span>
-<span class="go">         Input files:</span>
-<span class="go">          * 22 Jul 2014 15:29:19.33: job1.a.output.1</span>
-<span class="go">         Output files:</span>
-<span class="go">          * 22 Jul 2014 15:29:07.53: job1.a.output.2</span>
-
-<span class="go">       Job  = [job2.a.output.1</span>
-<span class="go">             -> job2.a.output.2]</span>
-<span class="go">       Job  = [job3.a.output.1</span>
-<span class="go">             -> job3.a.output.2]</span>
-
-<span class="go">________________________________________</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>N.B. At a verbosity of 5, even jobs which are up-to-date in <tt class="docutils literal"><span class="pre">second_task</span></tt> are displayed.</p>
-</div></blockquote>
-</div>
-<div class="section" id="verbosity-levels">
-<h2>Verbosity levels<a class="headerlink" href="#verbosity-levels" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The verbosity levels for <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> and <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(...)</em></a>
-can be specified from <tt class="docutils literal"><span class="pre">verbose</span> <span class="pre">=</span> <span class="pre">0</span></tt> (print out nothing) to the extreme verbosity of <tt class="docutils literal"><span class="pre">verbose=6</span></tt>.  A verbosity of above 10 is reserved for the internal
-debugging of Ruffus</p>
-<blockquote>
-<div><ul class="simple">
-<li>level <strong>0</strong> : <em>nothing</em></li>
-<li>level <strong>1</strong> : <em>Out-of-date Task names</em></li>
-<li>level <strong>2</strong> : <em>All Tasks (including any task function docstrings)</em></li>
-<li>level <strong>3</strong> : <em>Out-of-date Jobs in Out-of-date Tasks, no explanation</em></li>
-<li>level <strong>4</strong> : <em>Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings</em></li>
-<li>level <strong>5</strong> : <em>All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)</em></li>
-<li>level <strong>6</strong> : <em>All jobs in All Tasks whether out of date or not</em></li>
-<li>level <strong>10</strong>: <em>logs messages useful only for debugging ruffus pipeline code</em></li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="abbreviating-long-file-paths-with-verbose-abbreviated-path">
-<span id="new-manual-pipeline-printout-verbose-abbreviated-path"></span><h2>Abbreviating long file paths with <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span></tt><a class="headerlink" href="#abbreviating-long-file-paths-with-verbose-abbreviated-path" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Pipelines often produce interminable lists of deeply nested filenames. It would be nice to be able to abbreviate this
-to just enough information to follow the progress.</p>
-<p>The <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span></tt> parameter specifies that   <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> and <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(...)</em></a> only display</p>
-<blockquote>
-<div><ol class="arabic">
-<li><p class="first">the <tt class="docutils literal"><span class="pre">NNN</span></tt> th top level sub-directories to be included, or that</p>
-</li>
-<li><p class="first">the message to be truncated to a specified <tt class="docutils literal"><span class="pre">`MMM</span></tt> characters (to fit onto a line, for example). <tt class="docutils literal"><span class="pre">MMM</span></tt> is specified by setting <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span> <span class="pre">=</span> <span class="pre">-MMM</span></tt>, i.e. negative values.</p>
-<p>Note that the number of characters specified is just the separate lengths of the input and output parameters,
-not the entire indented line. You many need to specify a smaller limit that you expect (e.g. <tt class="docutils literal"><span class="pre">60</span></tt> rather than <cite>80</cite>)</p>
-</li>
-</ol>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="n">NNN</span><span class="p">)</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="o">-</span><span class="n">MMM</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span></tt> defaults to <tt class="docutils literal"><span class="pre">2</span></tt></p>
-<p>For example:</p>
-<blockquote>
-<div><p>Given <tt class="docutils literal"><span class="pre">["aa/bb/cc/dddd.txt",</span> <span class="pre">"aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt"]</span></tt></p>
-<div class="highlight-python"><div class="highlight"><pre><span class="hll"> <span class="c"># Original relative paths</span>
-</span> <span class="s">"[aa/bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"</span>
-
-<span class="hll"> <span class="c"># Full abspath</span>
-</span> <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="s">"[/test/ruffus/src/aa/bb/cc/dddd.txt, /test/ruffus/src/aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"</span>
-
-<span class="hll"> <span class="c"># Specifed level of nested directories</span>
-</span> <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="mi">1</span>
- <span class="s">"[.../dddd.txt, .../gggg.txt]"</span>
-
- <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="mi">2</span>
- <span class="s">"[.../cc/dddd.txt, .../ffff/gggg.txt]"</span>
-
- <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="mi">3</span>
- <span class="s">"[.../bb/cc/dddd.txt, .../eeee/ffff/gggg.txt]"</span>
-
-
-<span class="hll"> <span class="c"># Truncated to MMM characters</span>
-</span> <span class="n">verbose_abbreviated_path</span> <span class="o">=</span> <span class="o">-</span><span class="mi">60</span>
- <span class="s">"<???> /bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]"</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="getting-a-list-of-all-tasks-in-a-pipeline">
-<h2>Getting a list of all tasks in a pipeline<a class="headerlink" href="#getting-a-list-of-all-tasks-in-a-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If you just wanted a list of all tasks (Ruffus decorated function names), then you can
-just run Run <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names"><em>pipeline_get_task_names(...)</em></a>.</p>
-<p>This doesn’t touch any pipeline code or even check to see if the pipeline is connected up properly.</p>
-<p>However, it is sometimes useful to allow users at the command line to choose from a list of
-possible tasks as a target.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 5</strong>: Understanding how your pipeline works with <tt class="docutils literal"><span class="pre">pipeline_printout(...)</span></tt></a><ul>
-<li><a class="reference internal" href="#printing-out-which-jobs-will-be-run">Printing out which jobs will be run</a></li>
-<li><a class="reference internal" href="#determining-which-jobs-are-out-of-date-or-not">Determining which jobs are out-of-date or not</a></li>
-<li><a class="reference internal" href="#verbosity-levels">Verbosity levels</a></li>
-<li><a class="reference internal" href="#abbreviating-long-file-paths-with-verbose-abbreviated-path">Abbreviating long file paths with <tt class="docutils literal"><span class="pre">verbose_abbreviated_path</span></tt></a></li>
-<li><a class="reference internal" href="#getting-a-list-of-all-tasks-in-a-pipeline">Getting a list of all tasks in a pipeline</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="originate.html"
-                        title="previous chapter"><strong>Chapter 4</strong>: Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="command_line.html"
-                        title="next chapter"><strong>Chapter 6</strong>: Running <em>Ruffus</em> from the command line with ruffus.cmdline</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/pipeline_printout.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
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-  <div class="section" id="new-manual-pipeline-printout-chapter-num-python-code-for-understanding-how-your-pipeline-works-with-pipeline-printout">
-<span id="new-manual-pipeline-printout-code"></span><h1><strong>Chapter 5</strong>: Python Code for Understanding how your pipeline works with <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a><a class="headerlink" href="#new-manual-pipeline-printout-chapter-num-python-code-for-understanding-how-your-pipeline-works-with-pipeline-printout" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> syntax</li>
-<li>Back to <strong>Chapter 5</strong>: <a class="reference internal" href="pipeline_printout.html#new-manual-pipeline-printout"><em>Understanding how your pipeline works</em></a></li>
-</ul>
-</div>
-<div class="section" id="display-the-initial-state-of-the-pipeline">
-<h2>Display the initial state of the pipeline<a class="headerlink" href="#display-the-initial-state-of-the-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   create initial files</span>
-<span class="c">#</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="c"># create both files as necessary</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   first task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span> <span class="s">".output.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   second task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output.2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="normal-output">
-<h2>Normal Output<a class="headerlink" href="#normal-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which will be run:</span>
-
-<span class="go">Task = create_initial_file_pairs</span>
-<span class="go">Task = first_task</span>
-<span class="go">Task = second_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="high-verbosity-output">
-<h2>High Verbosity Output<a class="headerlink" href="#high-verbosity-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which will be run:</span>
-
-<span class="go">Task = create_initial_file_pairs</span>
-<span class="go">       Job  = [None</span>
-<span class="go">             -> job1.a.start</span>
-<span class="go">             -> job1.b.start]</span>
-<span class="go">         Job needs update: Missing files [job1.a.start, job1.b.start]</span>
-<span class="go">       Job  = [None</span>
-<span class="go">             -> job2.a.start</span>
-<span class="go">             -> job2.b.start]</span>
-<span class="go">         Job needs update: Missing files [job2.a.start, job2.b.start]</span>
-<span class="go">       Job  = [None</span>
-<span class="go">             -> job3.a.start</span>
-<span class="go">             -> job3.b.start]</span>
-<span class="go">         Job needs update: Missing files [job3.a.start, job3.b.start]</span>
-
-<span class="go">Task = first_task</span>
-<span class="go">       Job  = [[job1.a.start, job1.b.start]</span>
-<span class="go">             -> job1.a.output.1]</span>
-<span class="go">         Job needs update: Missing files [job1.a.start, job1.b.start, job1.a.output.1]</span>
-<span class="go">       Job  = [[job2.a.start, job2.b.start]</span>
-<span class="go">             -> job2.a.output.1]</span>
-<span class="go">         Job needs update: Missing files [job2.a.start, job2.b.start, job2.a.output.1]</span>
-<span class="go">       Job  = [[job3.a.start, job3.b.start]</span>
-<span class="go">             -> job3.a.output.1]</span>
-<span class="go">         Job needs update: Missing files [job3.a.start, job3.b.start, job3.a.output.1]</span>
-
-<span class="go">Task = second_task</span>
-<span class="go">       Job  = [job1.a.output.1</span>
-<span class="go">             -> job1.a.output.2]</span>
-<span class="go">         Job needs update: Missing files [job1.a.output.1, job1.a.output.2]</span>
-<span class="go">       Job  = [job2.a.output.1</span>
-<span class="go">             -> job2.a.output.2]</span>
-<span class="go">         Job needs update: Missing files [job2.a.output.1, job2.a.output.2]</span>
-<span class="go">       Job  = [job3.a.output.1</span>
-<span class="go">             -> job3.a.output.2]</span>
-<span class="go">         Job needs update: Missing files [job3.a.output.1, job3.a.output.2]</span>
-
-<span class="go">________________________________________</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="display-the-partially-up-to-date-pipeline">
-<h2>Display the partially up-to-date pipeline<a class="headerlink" href="#display-the-partially-up-to-date-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Run the pipeline, modify <tt class="docutils literal"><span class="pre">job1.stage</span></tt> so that the second task is no longer up-to-date
-and printout the pipeline stage again:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
-<span class="go">Task enters queue = create_initial_file_pairs</span>
-<span class="go">    Job  = [None -> [job1.a.start, job1.b.start]]</span>
-<span class="go">    Job  = [None -> [job2.a.start, job2.b.start]]</span>
-<span class="go">    Job  = [None -> [job3.a.start, job3.b.start]]</span>
-<span class="go">    Job  = [None -> [job1.a.start, job1.b.start]] completed</span>
-<span class="go">    Job  = [None -> [job2.a.start, job2.b.start]] completed</span>
-<span class="go">    Job  = [None -> [job3.a.start, job3.b.start]] completed</span>
-<span class="go">Completed Task = create_initial_file_pairs</span>
-<span class="go">Task enters queue = first_task</span>
-<span class="go">    Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1]</span>
-<span class="go">    Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1]</span>
-<span class="go">    Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1]</span>
-<span class="go">    Job  = [[job1.a.start, job1.b.start] -> job1.a.output.1] completed</span>
-<span class="go">    Job  = [[job2.a.start, job2.b.start] -> job2.a.output.1] completed</span>
-<span class="go">    Job  = [[job3.a.start, job3.b.start] -> job3.a.output.1] completed</span>
-<span class="go">Completed Task = first_task</span>
-<span class="go">Task enters queue = second_task</span>
-<span class="go">    Job  = [job1.a.output.1 -> job1.a.output.2]</span>
-<span class="go">    Job  = [job2.a.output.1 -> job2.a.output.2]</span>
-<span class="go">    Job  = [job3.a.output.1 -> job3.a.output.2]</span>
-<span class="go">    Job  = [job1.a.output.1 -> job1.a.output.2] completed</span>
-<span class="go">    Job  = [job2.a.output.1 -> job2.a.output.2] completed</span>
-<span class="go">    Job  = [job3.a.output.1 -> job3.a.output.2] completed</span>
-<span class="go">Completed Task = second_task</span>
-
-
-<span class="go"># modify job1.stage1</span>
-<span class="gp">>>> </span><span class="nb">open</span><span class="p">(</span><span class="s">"job1.a.output.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>At a verbosity of 6, even jobs which are up-to-date will be displayed:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">6</span><span class="p">)</span>
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which are up-to-date:</span>
-
-<span class="go">Task = create_initial_file_pairs</span>
-<span class="go">       Job  = [None</span>
-<span class="go">             -> job1.a.start</span>
-<span class="go">             -> job1.b.start]</span>
-<span class="go">       Job  = [None</span>
-<span class="go">             -> job2.a.start</span>
-<span class="go">             -> job2.b.start]</span>
-<span class="go">       Job  = [None</span>
-<span class="go">             -> job3.a.start</span>
-<span class="go">             -> job3.b.start]</span>
-
-<span class="go">Task = first_task</span>
-<span class="go">       Job  = [[job1.a.start, job1.b.start]</span>
-<span class="go">             -> job1.a.output.1]</span>
-<span class="go">       Job  = [[job2.a.start, job2.b.start]</span>
-<span class="go">             -> job2.a.output.1]</span>
-<span class="go">       Job  = [[job3.a.start, job3.b.start]</span>
-<span class="go">             -> job3.a.output.1]</span>
-
-<span class="go">________________________________________</span>
-
-
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which will be run:</span>
-
-<span class="go">Task = second_task</span>
-<span class="go">       Job  = [job1.a.output.1</span>
-<span class="go">             -> job1.a.output.2]</span>
-<span class="go">         Job needs update:</span>
-<span class="go">         Input files:</span>
-<span class="go">          * 22 Jul 2014 15:29:19.33: job1.a.output.1</span>
-<span class="go">         Output files:</span>
-<span class="go">          * 22 Jul 2014 15:29:07.53: job1.a.output.2</span>
-
-<span class="go">       Job  = [job2.a.output.1</span>
-<span class="go">             -> job2.a.output.2]</span>
-<span class="go">       Job  = [job3.a.output.1</span>
-<span class="go">             -> job3.a.output.2]</span>
-
-<span class="go">________________________________________</span>
-</pre></div>
-</div>
-<p>We can now see that the there is only one job in “second_task” which needs to be re-run
-because ‘job1.stage1’ has been modified after ‘job1.stage2’</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 5</strong>: Python Code for Understanding how your pipeline works with <tt class="docutils literal"><span class="pre">pipeline_printout(...)</span></tt></a><ul>
-<li><a class="reference internal" href="#display-the-initial-state-of-the-pipeline">Display the initial state of the pipeline</a></li>
-<li><a class="reference internal" href="#normal-output">Normal Output</a></li>
-<li><a class="reference internal" href="#high-verbosity-output">High Verbosity Output</a></li>
-<li><a class="reference internal" href="#display-the-partially-up-to-date-pipeline">Display the partially up-to-date pipeline</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="originate_code.html"
-                        title="previous chapter"><strong>Chapter 4</strong>: Python Code for Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="pipeline_printout_graph_code.html"
-                        title="next chapter"><strong>Chapter 7</strong>: Python Code for Displaying the pipeline visually with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/pipeline_printout_code.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    <p class="searchtip" style="font-size: 90%">
-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-  <div class="section" id="new-manual-pipeline-printout-graph-chapter-num-displaying-the-pipeline-visually-with-pipeline-printout-graph">
-<span id="new-manual-pipeline-printout-graph"></span><span id="index-0"></span><h1><strong>Chapter 7</strong>: Displaying the pipeline visually with <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a><a class="headerlink" href="#new-manual-pipeline-printout-graph-chapter-num-displaying-the-pipeline-visually-with-pipeline-printout-graph" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/graphviz.html#decorators-graphviz"><em>@graphviz(...)</em></a> syntax</li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="pipeline_printout_graph_code.html#new-manual-pipeline-printout-graph-code"><em>Chapter 7: Python Code for Displaying the pipeline visually with pipeline_printout_graph(...)</em></a></li>
-</ul>
-</div>
-<div class="section" id="printing-out-a-flowchart-of-our-pipeline">
-<h2>Printing out a flowchart of our pipeline<a class="headerlink" href="#printing-out-a-flowchart-of-our-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>It is all very well being able to trace the data flow through the pipeline as text.
-Sometimes, however, we need a bit of eye-candy!</p>
-<p>We can see a flowchart for our fledgling pipeline by executing:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span> <span class="p">(</span>   <span class="s">'flowchart.svg'</span><span class="p">,</span>
-                            <span class="s">'svg'</span><span class="p">,</span>
-                            <span class="p">[</span><span class="n">second_task</span><span class="p">],</span>
-                            <span class="n">no_key_legend</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
-</pre></div>
-</div>
-<a class="reference internal image-reference" href="../../_images/simple_tutorial_stage5_flowchart.png"><img alt="../../_images/simple_tutorial_stage5_flowchart.png" src="../../_images/simple_tutorial_stage5_flowchart.png" style="width: 588.0px; height: 318.5px;" /></a>
-</div></blockquote>
-<p>Flowcharts can be printed in a large number of formats including <tt class="docutils literal"><span class="pre">jpg</span></tt>, <tt class="docutils literal"><span class="pre">svg</span></tt>, <tt class="docutils literal"><span class="pre">png</span></tt> and <tt class="docutils literal"><span class="pre">pdf</span></tt>.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Flowcharts rely on the <tt class="docutils literal"><span class="pre">dot</span></tt> programme from <a class="reference external" href="http://www.graphviz.org/">Graphviz</a>.</p>
-<p class="last">Please make sure this is installed.</p>
-</div>
-<p>There are 8 standard colour schemes, but you can further customise all the colours to your satisfaction:</p>
-<blockquote>
-<div><img alt="../../_images/flowchart_colour_schemes.png" src="../../_images/flowchart_colour_schemes.png" />
-</div></blockquote>
-<p>See <a class="reference internal" href="flowchart_colours.html#new-manual-flowchart-colours"><em>here</em></a> for example code.</p>
-</div></blockquote>
-</div>
-<div class="section" id="command-line-options-made-easier-with-ruffus-cmdline">
-<h2>Command line options made easier with <tt class="docutils literal"><span class="pre">ruffus.cmdline</span></tt><a class="headerlink" href="#command-line-options-made-easier-with-ruffus-cmdline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If you are using <tt class="docutils literal"><span class="pre">ruffus.cmdline</span></tt>, then you can easily ask for a flowchart from the command line:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre>your_script.py --flowchart pipeline_flow_chart.png
-</pre></div>
-</div>
-</div></blockquote>
-<p>The output format is deduced from the extension but can be specified manually:</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="c"># specify format. Otherwise, deduced from the extension</span>
-your_script.py --flowchart pipeline_flow_chart.png --flowchart_format png
-</pre></div>
-</div>
-</div></blockquote>
-<p>Print the flow chart horizontally or vertically...</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="c"># flowchart proceeds from left to right , rather than from  top to bottom</span>
-your_script.py --flowchart pipeline_flow_chart.png --draw_graph_horizontally
-</pre></div>
-</div>
-</div></blockquote>
-<p>...with or without a key legend</p>
-<blockquote>
-<div><div class="highlight-bash"><div class="highlight"><pre><span class="c"># Draw key legend</span>
-your_script.py --flowchart pipeline_flow_chart.png --key_legend_in_graph
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="horribly-complicated-pipelines">
-<h2>Horribly complicated pipelines!<a class="headerlink" href="#horribly-complicated-pipelines" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Flowcharts are especially useful if you have really complicated pipelines, such as</p>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/simple_tutorial_complex_flowchart.png"><img alt="../../_images/simple_tutorial_complex_flowchart.png" src="../../_images/simple_tutorial_complex_flowchart.png" style="width: 389.2px; height: 656.6px;" /></a>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="circular-dependency-errors-in-pipelines">
-<h2>Circular dependency errors in pipelines!<a class="headerlink" href="#circular-dependency-errors-in-pipelines" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Especially, if the pipeline is not set up properly, and vicious circular dependencies
-are present:</p>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/simple_tutorial_complex_flowchart_error.png"><img alt="../../_images/simple_tutorial_complex_flowchart_error.png" src="../../_images/simple_tutorial_complex_flowchart_error.png" style="width: 389.2px; height: 656.6px;" /></a>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="graphviz-customising-the-appearance-of-each-task">
-<h2><tt class="docutils literal"><span class="pre">@graphviz</span></tt>: Customising the appearance of each task<a class="headerlink" href="#graphviz-customising-the-appearance-of-each-task" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The graphic for each task can be further customised as you please by adding
-<a class="reference external" href="http://www.graphviz.org/doc/info/attrs.html">graphviz attributes</a> such as the URL, shape, colour
-directly to that node using the decorator <tt class="docutils literal"><span class="pre">`@graphviz</span></tt>.</p>
-<p>For example, we can customise the graphic for <tt class="docutils literal"><span class="pre">myTask()</span></tt> to look like:</p>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/history_html_flowchart2.png"><img alt="../../_images/history_html_flowchart2.png" src="../../_images/history_html_flowchart2.png" style="width: 336.6px; height: 316.5px;" /></a>
-</div></blockquote>
-<p>by adding the requisite attributes as follows:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@graphviz</span><span class="p">(</span><span class="n">URL</span><span class="o">=</span><span class="s">'"http://cnn.com"'</span><span class="p">,</span> <span class="n">fillcolor</span> <span class="o">=</span> <span class="s">'"#FFCCCC"'</span><span class="p">,</span>
-                <span class="n">color</span> <span class="o">=</span> <span class="s">'"#FF0000"'</span><span class="p">,</span> <span class="n">pencolor</span><span class="o">=</span><span class="s">'"#FF0000"'</span><span class="p">,</span> <span class="n">fontcolor</span><span class="o">=</span><span class="s">'"#4B6000"'</span><span class="p">,</span>
-                <span class="n">label_suffix</span> <span class="o">=</span> <span class="s">"???"</span><span class="p">,</span> <span class="n">label_prefix</span> <span class="o">=</span> <span class="s">"What is this?<BR/> "</span><span class="p">,</span>
-                <span class="n">label</span> <span class="o">=</span> <span class="s">"<What <FONT COLOR=</span><span class="se">\"</span><span class="s">red</span><span class="se">\"</span><span class="s">>is</FONT>this>"</span><span class="p">,</span>
-                <span class="n">shape</span><span class="o">=</span> <span class="s">"component"</span><span class="p">,</span> <span class="n">height</span> <span class="o">=</span> <span class="mf">1.5</span><span class="p">,</span> <span class="n">peripheries</span> <span class="o">=</span> <span class="mi">5</span><span class="p">,</span>
-                <span class="n">style</span><span class="o">=</span><span class="s">"dashed"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">Up_to_date_task2</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
-    <span class="k">pass</span>
-
-<span class="c">#   Can use dictionary if you wish...</span>
-<span class="n">graphviz_params</span> <span class="o">=</span> <span class="p">{</span><span class="s">"URL"</span><span class="p">:</span><span class="s">"http://cnn.com"</span><span class="p">,</span> <span class="s">"fontcolor"</span><span class="p">:</span> <span class="s">'"#FF00FF"'</span><span class="p">}</span>
-<span class="nd">@graphviz</span><span class="p">(</span><span class="o">**</span><span class="n">graphviz_params</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">myTask</span><span class="p">(</span><span class="nb">input</span><span class="p">,</span><span class="n">output</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>You can even using HTML formatting in task names, including specifying line wraps (as in the above example),
-using the <tt class="docutils literal"><span class="pre">label</span></tt> parameter. However, HTML labels <strong>must</strong> be enclosed in <tt class="docutils literal"><span class="pre"><</span></tt> and <tt class="docutils literal"><span class="pre">></span></tt>.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">label</span> <span class="o">=</span> <span class="s">"<Line <BR/> wrapped task_name()>"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Otherwise, you can also opt to keep the task name and wrap it with a prefix and suffix:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">label_suffix</span> <span class="o">=</span> <span class="s">"??? "</span><span class="p">,</span> <span class="n">label_prefix</span> <span class="o">=</span> <span class="s">": What is this?"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>The <tt class="docutils literal"><span class="pre">URL</span></tt> attribute allows the generation of clickable svg, and also client / server</dt>
-<dd>side image maps usable in web pages.
-See <a class="reference external" href="http://www.graphviz.org/content/output-formats#dimap">Graphviz documentation</a></dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 7</strong>: Displaying the pipeline visually with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a><ul>
-<li><a class="reference internal" href="#printing-out-a-flowchart-of-our-pipeline">Printing out a flowchart of our pipeline</a></li>
-<li><a class="reference internal" href="#command-line-options-made-easier-with-ruffus-cmdline">Command line options made easier with <tt class="docutils literal"><span class="pre">ruffus.cmdline</span></tt></a></li>
-<li><a class="reference internal" href="#horribly-complicated-pipelines">Horribly complicated pipelines!</a></li>
-<li><a class="reference internal" href="#circular-dependency-errors-in-pipelines">Circular dependency errors in pipelines!</a></li>
-<li><a class="reference internal" href="#graphviz-customising-the-appearance-of-each-task"><tt class="docutils literal"><span class="pre">@graphviz</span></tt>: Customising the appearance of each task</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="command_line.html"
-                        title="previous chapter"><strong>Chapter 6</strong>: Running <em>Ruffus</em> from the command line with ruffus.cmdline</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="output_file_names.html"
-                        title="next chapter"><strong>Chapter 8</strong>: Specifying output file names with <tt class="docutils literal"><span class="pre">formatter()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/pipeline_printout_graph.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
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-  <h3>Quick search</h3>
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-    Enter search terms or a module, class or function name.
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
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-<span id="new-manual-pipeline-printout-graph-code"></span><h1><strong>Chapter 7</strong>: Python Code for Displaying the pipeline visually with <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a><a class="headerlink" href="#new-manual-pipeline-printout-graph-chapter-num-python-code-for-displaying-the-pipeline-visually-with-pipeline-printout-graph" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph"><em>pipeline_printout_graph(...)</em></a> syntax</li>
-<li>Back to <strong>Chapter 7</strong>: <a class="reference internal" href="pipeline_printout_graph.html#new-manual-pipeline-printout-graph"><em>Displaying the pipeline visually</em></a></li>
-</ul>
-</div>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
- 2
- 3
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-61</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   create initial files</span>
-<span class="c">#</span>
-<span class="nd">@originate</span><span class="p">([</span>   <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-               <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">]</span>    <span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_initial_file_pairs</span><span class="p">(</span><span class="n">output_files</span><span class="p">):</span>
-    <span class="c"># create both files as necessary</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span> <span class="k">pass</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   first task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_file_pairs</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span> <span class="s">".output.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   second task</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output.2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-<span class="hll"><span class="c">#  Print graph before running pipeline</span>
-</span>
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Show flow chart and tasks before running the pipeline</span>
-<span class="c">#</span>
-<span class="k">print</span> <span class="s">"Show flow chart and tasks before running the pipeline"</span>
-<span class="n">pipeline_printout_graph</span> <span class="p">(</span> <span class="nb">open</span><span class="p">(</span><span class="s">"simple_tutorial_stage5_before.png"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">),</span>
-                         <span class="s">"png"</span><span class="p">,</span>
-                         <span class="p">[</span><span class="n">second_task</span><span class="p">],</span>
-                         <span class="n">minimal_key_legend</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-
-
-<span class="c"># modify job1.stage1</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"job1.a.output.1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-
-
-<span class="hll"><span class="c">#  Print graph after everything apart from ``job1.a.output.1`` is update</span>
-</span>
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Show flow chart and tasks after running the pipeline</span>
-<span class="c">#</span>
-<span class="k">print</span> <span class="s">"Show flow chart and tasks after running the pipeline"</span>
-<span class="n">pipeline_printout_graph</span> <span class="p">(</span> <span class="nb">open</span><span class="p">(</span><span class="s">"simple_tutorial_stage5_after.png"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">),</span>
-                         <span class="s">"png"</span><span class="p">,</span>
-                         <span class="p">[</span><span class="n">second_task</span><span class="p">],</span>
-                         <span class="n">no_key_legend</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</td></tr></table></div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-flowcharts">
-<h2>Resulting Flowcharts<a class="headerlink" href="#resulting-flowcharts" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><table border="1" class="docutils">
-<colgroup>
-<col width="46%" />
-<col width="54%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><a class="first reference internal image-reference" href="../../_images/simple_tutorial_stage5_before.png"><img alt="Before running the pipeline" class="align-center" src="../../_images/simple_tutorial_stage5_before.png" style="width: 462.65px; height: 375.25px;" /></a>
-<p class="last centered">
-<strong>Before</strong></p></td>
-<td><a class="first reference internal image-reference" href="../../_images/simple_tutorial_stage5_after.png"><img alt="After running the pipeline" class="align-center" src="../../_images/simple_tutorial_stage5_after.png" style="width: 462.65px; height: 375.25px;" /></a>
-<p class="last centered">
-<strong>After</strong></p></td>
-</tr>
-</tbody>
-</table>
-<table border="1" class="docutils">
-<colgroup>
-<col width="100%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><a class="first reference internal image-reference" href="../../_images/tutorial_key.png"><img alt="Legend key" class="align-center" src="../../_images/tutorial_key.png" style="width: 1358.0px; height: 117.0px;" /></a>
-<p class="last centered">
-<strong>Legend</strong></p></td>
-</tr>
-</tbody>
-</table>
-</div></blockquote>
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-</div>
-
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-<li><a class="reference internal" href="#"><strong>Chapter 7</strong>: Python Code for Displaying the pipeline visually with <tt class="docutils literal"><span class="pre">pipeline_printout_graph(...)</span></tt></a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-flowcharts">Resulting Flowcharts</a></li>
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-  <h4>Previous topic</h4>
-  <p class="topless"><a href="pipeline_printout_code.html"
-                        title="previous chapter"><strong>Chapter 5</strong>: Python Code for Understanding how your pipeline works with <tt class="docutils literal"><span class="pre">pipeline_printout(...)</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="output_file_names_code.html"
-                        title="next chapter"><strong>Chapter 8</strong>: Python Code for Specifying output file names with <tt class="docutils literal"><span class="pre">formatter()</span></tt> and <tt class="docutils literal"><span class="pre">regex()</span></tt></a></p>
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-        <h4 >Pipeline functions</h4>
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-  <div class="section" id="new-manual-posttask-chapter-num-signal-the-completion-of-each-stage-of-our-pipeline-with-posttask">
-<span id="new-manual-posttask"></span><span id="index-0"></span><h1><strong>Chapter 19</strong>: Signal the completion of each stage of our pipeline with <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a><a class="headerlink" href="#new-manual-posttask-chapter-num-signal-the-completion-of-each-stage-of-our-pipeline-with-posttask" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> syntax</li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>It is often useful to signal the completion of each task by specifying a specific
-action to be taken or function to be called. This can range from
-printing out some message, or  <a class="reference external" href="http://en.wikipedia.org/wiki/Touch_(Unix)">touching</a> some sentinel file,
-to emailing the author. This is particular useful if the <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> is a recipe apply to an unspecified number
-of parameters in parallel in different <a class="reference internal" href="../../glossary.html#term-job"><em class="xref std std-term">job</em></a>s. If the task is never run, or if it
-fails, needless-to-say no task completion action will happen.</p>
-<p><em>Ruffus</em> uses the <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> decorator for this purpose.</p>
-</div></blockquote>
-<div class="section" id="posttask">
-<h3><strong>@posttask</strong><a class="headerlink" href="#posttask" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>We can signal the completion of each task by specifying
-one or more function(s) using <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a></p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="k">def</span> <span class="nf">task_finished</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"hooray"</span>
-
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">task_finished</span><span class="p">)</span>
-<span class="nd">@originate</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">create_if_necessary</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>This is such a short function, we might as well write it in-line:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@posttask</span><span class="p">(</span><span class="k">lambda</span><span class="p">:</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"hooray</span><span class="se">\n</span><span class="s">"</span><span class="p">))</span>
-<span class="nd">@originate</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">The function(s) provided to <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> will be called if the pipeline passes
-through a task, even if none of its jobs are run because they are up-to-date.
-This happens when a upstream task is out-of-date, and the execution passes through
-this point in the pipeline. See the example in <a class="reference internal" href="dependencies.html#new-manual-dependencies"><em>Appendix 2: How dependency is checked</em></a>
-of this manual.</p>
-</div>
-</div>
-<div class="section" id="touch-file">
-<span id="new-manual-posttask-touch-file"></span><span id="index-1"></span><h3><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-touch-file"><em>touch_file</em></a><a class="headerlink" href="#touch-file" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>One way to note the completion of a task is to create some sort of
-“flag” file. Each stage in a traditional <tt class="docutils literal"><span class="pre">make</span></tt> pipeline would contain a
-<tt class="docutils literal"><span class="pre">touch</span> <span class="pre">completed.flag</span></tt>.</p>
-<p>This is such a useful idiom that <em>Ruffus</em> provides the shorthand <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-touch-file"><em>touch_file</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">touch_file</span><span class="p">(</span><span class="s">"task_completed.flag"</span><span class="p">))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="adding-several-post-task-actions">
-<h3>Adding several post task actions<a class="headerlink" href="#adding-several-post-task-actions" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>You can, of course, add more than one different action to be taken on completion of the
-task, either by stacking up as many <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> decorators
-as necessary, or by including several functions in the same <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">print_hooray</span><span class="p">,</span> <span class="n">print_whoppee</span><span class="p">)</span>
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">print_hip_hip</span><span class="p">,</span> <span class="n">touch_file</span><span class="p">(</span><span class="s">"sentinel_flag"</span><span class="p">))</span>
-<span class="nd">@originate</span><span class="p">(</span><span class="s">"a.1"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_if_necessary</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-</div>
-
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-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 19</strong>: Signal the completion of each stage of our pipeline with <tt class="docutils literal"><span class="pre">@posttask</span></tt></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a><ul>
-<li><a class="reference internal" href="#posttask"><strong>@posttask</strong></a></li>
-<li><a class="reference internal" href="#touch-file"><tt class="docutils literal"><span class="pre">touch_file</span></tt></a></li>
-<li><a class="reference internal" href="#adding-several-post-task-actions">Adding several post task actions</a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="active_if.html"
-                        title="previous chapter"><strong>Chapter 18</strong>: Turning parts of the pipeline on and off at runtime with <tt class="docutils literal"><span class="pre">@active_if</span></tt></a></p>
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-                        title="next chapter"><strong>Chapter 20</strong>: Manipulating task inputs via string substitution using <tt class="docutils literal"><span class="pre">inputs()</span></tt> and  <tt class="docutils literal"><span class="pre">add_inputs()</span></tt></a></p>
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-            
-  <div class="section" id="new-manual-split-chapter-num-splitting-up-large-tasks-files-with-split">
-<span id="new-manual-split"></span><span id="index-0"></span><h1><strong>Chapter 12</strong>: Splitting up large tasks / files with <strong>@split</strong><a class="headerlink" href="#new-manual-split-chapter-num-splitting-up-large-tasks-files-with-split" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> syntax</li>
-<li><a class="reference internal" href="split_code.html#new-manual-split-code"><em>Example code for this chapter</em></a></li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>A common requirement in computational pipelines is to split up a large task into
-small jobs which can be run on different processors, (or sent to a computational
-cluster). Very often, the number of jobs depends dynamically on the size of the
-task, and cannot be known beforehand.</p>
-<p><em>Ruffus</em> uses the <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> decorator to indicate that
-the <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function will produce an indeterminate number of independent <em>Outputs</em> from a single <em>Input</em>.</p>
-</div></blockquote>
-</div>
-<div class="section" id="example-calculate-variance-for-a-large-list-of-numbers-in-parallel">
-<h2>Example: Calculate variance for a large list of numbers in parallel<a class="headerlink" href="#example-calculate-variance-for-a-large-list-of-numbers-in-parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Suppose we wanted to calculate the <a class="reference external" href="http://en.wikipedia.org/wiki/Variance">variance</a> for
-100,000 numbers, how can we parallelise the calculation so that we can get an answer as
-speedily as possible?</p>
-<p>We need to</p>
-<blockquote>
-<div><ul class="simple">
-<li>break down the problem into manageable chunks</li>
-<li>solve these in parallel, possibly on a computational cluster and then</li>
-<li>merge the partial solutions back together for a final result.</li>
-</ul>
-</div></blockquote>
-<p>To complicate things, we usually do not want to hard-code the number of parallel chunks beforehand.
-The degree of parallelism is often only apparent as we process our data.</p>
-<p><strong>Ruffus</strong> was designed to solve such problems which are common, for example, in bioinformatics and genomics.</p>
-<p>A flowchart for our variance problem might look like this:</p>
-<a class="reference internal image-reference" href="../../_images/manual_split_merge_example.jpg"><img alt="../../_images/manual_split_merge_example.jpg" src="../../_images/manual_split_merge_example.jpg" style="width: 251.1px; height: 197.4px;" /></a>
-<p>(In this toy example, we create our own starting data in <tt class="docutils literal"><span class="pre">create_random_numbers()</span></tt>.)</p>
-</div></blockquote>
-</div>
-<div class="section" id="output-files-for-split">
-<h2>Output files for <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a><a class="headerlink" href="#output-files-for-split" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The <em>Ruffus</em> decorator <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> is designed specifically with this run-time flexibility in mind:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="n">create_random_numbers</span><span class="p">,</span> <span class="s">"*.chunks"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">split_problem</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-<p>This will split the incoming <tt class="docutils literal"><span class="pre">input_file_names</span></tt> into <tt class="docutils literal"><span class="pre">NNN</span></tt> number of <em>outputs</em> where <tt class="docutils literal"><span class="pre">NNN</span></tt> is not predetermined:</p>
-<p>The <em>output</em> (second) parameter of <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> often contains a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> pattern like the <tt class="docutils literal"><span class="pre">*.chunks</span></tt> above.</p>
-<p>Only <strong>after</strong> the task function has completed, will Ruffus match the <strong>Output</strong> parameter (<tt class="docutils literal"><span class="pre">*.chunks</span></tt>)
-against the files which have been created by <tt class="docutils literal"><span class="pre">split_problem()</span></tt> (e.g. <tt class="docutils literal"><span class="pre">1.chunks</span></tt>, <tt class="docutils literal"><span class="pre">2.chunks</span></tt>, <tt class="docutils literal"><span class="pre">3.chunks</span></tt>)</p>
-</div></blockquote>
-</div>
-<div class="section" id="be-careful-in-specifying-output-globs">
-<h2>Be careful in specifying  <strong>Output</strong> globs<a class="headerlink" href="#be-careful-in-specifying-output-globs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Note that it is your responsibility to keep the <strong>Output</strong> specification tight enough so that Ruffus does not
-pick up extraneous files.</p>
-<p>You can specify multiple <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns to match <em>all</em> the files which are the
-result of the splitting task function. These can even cover different directories,
-or groups of file names. This is a more extreme example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="s">"input.file"</span><span class="p">,</span> <span class="p">[</span><span class="s">'a*.bits'</span><span class="p">,</span> <span class="s">'b*.pieces'</span><span class="p">,</span> <span class="s">'somewhere_else/c*.stuff'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">split_function</span> <span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="s">"Code to split up 'input.file'"</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="clean-up-previous-pipeline-runs">
-<h2>Clean up previous pipeline runs<a class="headerlink" href="#clean-up-previous-pipeline-runs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Problem arise when the current directory contains results of previous pipeline runs.</p>
-<ul class="simple">
-<li>For example, if the previous analysis involved a large data set, there might be 3 chunks: <tt class="docutils literal"><span class="pre">1.chunks</span></tt>, <tt class="docutils literal"><span class="pre">2.chunks</span></tt>, <tt class="docutils literal"><span class="pre">3.chunks</span></tt>.</li>
-<li>In the current analysis, there might be a smaller data set which divides into only 2 chunks, <tt class="docutils literal"><span class="pre">1.chunks</span></tt> and <tt class="docutils literal"><span class="pre">2.chunks</span></tt>.</li>
-<li>Unfortunately, <tt class="docutils literal"><span class="pre">3.chunks</span></tt> from the previous run is still hanging around and will be included erroneously by the glob <tt class="docutils literal"><span class="pre">*.chunks</span></tt>.</li>
-</ul>
-<div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<p class="last"><strong>Your first duty in</strong> <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> <strong>tasks functions should be to clean up</strong></p>
-</div>
-<p>To help you clean up thoroughly, Ruffus initialises the <strong>output</strong> parameter to all files which match specification.</p>
-<p>The first order of business is thus invariably to cleanup ( delete with <tt class="docutils literal"><span class="pre">os.unlink</span></tt>) all files in <strong>Output</strong>.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   split initial file</span>
-<span class="c">#</span>
-<span class="nd">@split</span><span class="p">(</span><span class="n">create_random_numbers</span><span class="p">,</span> <span class="s">"*.chunks"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">split_problem</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        splits random numbers file into xxx files of chunk_size each</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-<span class="hll">    <span class="c">#   clean up any files from previous runs</span>
-</span>    <span class="c">#</span>
-    <span class="c">#for ff in glob.glob("*.chunks"):</span>
-    <span class="k">for</span> <span class="n">ff</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">ff</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>(The first time you run the example code, <tt class="docutils literal"><span class="pre">*.chunks</span></tt> will initialise <tt class="docutils literal"><span class="pre">output_files</span></tt> to an empty list. )</p>
-</div></blockquote>
-</div>
-<div class="section" id="to-many">
-<span id="new-manual-split-one-to-many"></span><h2>1 to many<a class="headerlink" href="#to-many" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> is a one to many operator because its
-outputs are a list of <em>independent</em> items.</p>
-<p>If <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> generates 5 files, then this will lead to 5 jobs downstream.</p>
-<p>This means we can just connect our old friend <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> to our pipeline
-and the results of <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> will be analysed in parallel. This code should look
-familiar:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate sum and sum of squares for each chunk file</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">split_problem</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".chunks"</span><span class="p">),</span> <span class="s">".sums"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">sum_of_squares</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Which results in output like this:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [[random_numbers.list] -> *.chunks] completed</span>
-<span class="go">Completed Task = split_problem</span>
-<span class="go">    Job  = [1.chunks -> 1.sums] completed</span>
-<span class="go">    Job  = [10.chunks -> 10.sums] completed</span>
-<span class="go">    Job  = [2.chunks -> 2.sums] completed</span>
-<span class="go">    Job  = [3.chunks -> 3.sums] completed</span>
-<span class="go">    Job  = [4.chunks -> 4.sums] completed</span>
-<span class="go">    Job  = [5.chunks -> 5.sums] completed</span>
-<span class="go">    Job  = [6.chunks -> 6.sums] completed</span>
-<span class="go">    Job  = [7.chunks -> 7.sums] completed</span>
-<span class="go">    Job  = [8.chunks -> 8.sums] completed</span>
-<span class="go">    Job  = [9.chunks -> 9.sums] completed</span>
-<span class="go">Completed Task = sum_of_squares</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Have a look at the <a class="reference internal" href="split_code.html#new-manual-split-code"><em>Example code for this chapter</em></a></p>
-</div></blockquote>
-</div>
-<div class="section" id="nothing-to-many">
-<span id="new-manual-split-nothing-to-many"></span><h2>Nothing to many<a class="headerlink" href="#nothing-to-many" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Normally we would use <a class="reference internal" href="originate.html#new-manual-originate"><em>@originate</em></a> to create files from
-scratch, for example at the beginning of the pipeline.</p>
-<p>However, sometimes, it is not possible to determine ahead of time how many files you
-will be creating from scratch. <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> can also be useful even in such cases:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">random</span> <span class="kn">import</span> <span class="n">randint</span>
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">os</span>
-
-<span class="c"># Create between 2 and 5 files</span>
-<span class="hll"><span class="nd">@split</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"*.start"</span><span class="p">)</span>
-</span><span class="k">def</span> <span class="nf">create_initial_files</span><span class="p">(</span><span class="n">no_input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="c"># cleanup first</span>
-    <span class="k">for</span> <span class="n">oo</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">oo</span><span class="p">)</span>
-    <span class="c"># make new files</span>
-    <span class="k">for</span> <span class="n">ii</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">randint</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span><span class="mi">5</span><span class="p">)):</span>
-        <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.start"</span> <span class="o">%</span> <span class="n">ii</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="nd">@transform</span><span class="p">(</span><span class="n">create_initial_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span> <span class="s">".processed"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">process_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>Giving:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [None -> *.start] completed</span>
-<span class="go">Completed Task = create_initial_files</span>
-<span class="go">    Job  = [0.start -> 0.processed] completed</span>
-<span class="go">    Job  = [1.start -> 1.processed] completed</span>
-<span class="go">Completed Task = process_files</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 12</strong>: Splitting up large tasks / files with <strong>@split</strong></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#example-calculate-variance-for-a-large-list-of-numbers-in-parallel">Example: Calculate variance for a large list of numbers in parallel</a></li>
-<li><a class="reference internal" href="#output-files-for-split">Output files for <tt class="docutils literal"><span class="pre">@split</span></tt></a></li>
-<li><a class="reference internal" href="#be-careful-in-specifying-output-globs">Be careful in specifying  <strong>Output</strong> globs</a></li>
-<li><a class="reference internal" href="#clean-up-previous-pipeline-runs">Clean up previous pipeline runs</a></li>
-<li><a class="reference internal" href="#to-many">1 to many</a></li>
-<li><a class="reference internal" href="#nothing-to-many">Nothing to many</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="decorators_compendium.html"
-                        title="previous chapter"><strong>Chapter 11</strong>: Pipeline topologies and a compendium of <em>Ruffus</em> decorators</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="merge.html"
-                        title="next chapter"><strong>Chapter 13</strong>: <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/new_tutorial/split.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
-<div id="searchbox" style="display: none">
-  <h3>Quick search</h3>
-    <form class="search" action="../../search.html" method="get">
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-      <input type="hidden" name="area" value="default" />
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
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-  <div class="section" id="new-manual-split-chapter-num-python-code-for-splitting-up-large-tasks-files-with-split">
-<span id="new-manual-split-code"></span><h1><strong>Chapter 12</strong>: Python Code for Splitting up large tasks / files with <strong>@split</strong><a class="headerlink" href="#new-manual-split-chapter-num-python-code-for-splitting-up-large-tasks-files-with-split" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split syntax in detail</em></a></li>
-<li>Back to <strong>Chapter 12</strong>: <a class="reference internal" href="split.html#new-manual-split"><em>Splitting up large tasks / files with @split</em></a></li>
-</ul>
-</div>
-<div class="section" id="splitting-large-jobs">
-<h2>Splitting large jobs<a class="headerlink" href="#splitting-large-jobs" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="n">NUMBER_OF_RANDOMS</span> <span class="o">=</span> <span class="mi">10000</span>
-<span class="n">CHUNK_SIZE</span> <span class="o">=</span> <span class="mi">1000</span>
-
-
-<span class="kn">import</span> <span class="nn">random</span><span class="o">,</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">glob</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Create random numbers</span>
-<span class="c">#</span>
-<span class="nd">@originate</span><span class="p">(</span><span class="s">"random_numbers.list"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_random_numbers</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">NUMBER_OF_RANDOMS</span><span class="p">):</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%g</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mf">100.0</span><span class="p">))</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   split initial file</span>
-<span class="c">#</span>
-<span class="nd">@split</span><span class="p">(</span><span class="n">create_random_numbers</span><span class="p">,</span> <span class="s">"*.chunks"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">split_problem</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        splits random numbers file into xxx files of chunk_size each</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   clean up any files from previous runs</span>
-    <span class="c">#</span>
-    <span class="c">#for ff in glob.glob("*.chunks"):</span>
-    <span class="k">for</span> <span class="n">ff</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">ff</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#   create new file every chunk_size lines and</span>
-    <span class="c">#       copy each line into current file</span>
-    <span class="c">#</span>
-    <span class="n">output_file</span> <span class="o">=</span> <span class="bp">None</span>
-    <span class="n">cnt_files</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">input_file_name</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)):</span>
-            <span class="k">if</span> <span class="n">i</span> <span class="o">%</span> <span class="n">CHUNK_SIZE</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-                <span class="n">cnt_files</span> <span class="o">+=</span> <span class="mi">1</span>
-                <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.chunks"</span> <span class="o">%</span> <span class="n">cnt_files</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-            <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate sum and sum of squares for each chunk file</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">split_problem</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".chunks"</span><span class="p">),</span> <span class="s">".sums"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">sum_of_squares</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">output</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">]</span>
-    <span class="n">cnt_values</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">):</span>
-        <span class="n">cnt_values</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="n">val</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">rstrip</span><span class="p">())</span>
-        <span class="n">sum_squared</span> <span class="o">+=</span> <span class="n">val</span> <span class="o">*</span> <span class="n">val</span>
-        <span class="nb">sum</span> <span class="o">+=</span> <span class="n">val</span>
-    <span class="n">output</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="n">sum_squared</span><span class="p">),</span> <span c [...]
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [None -> random_numbers.list] completed</span>
-<span class="go">Completed Task = create_random_numbers</span>
-<span class="go">    Job  = [[random_numbers.list] -> *.chunks] completed</span>
-<span class="go">Completed Task = split_problem</span>
-<span class="go">    Job  = [1.chunks -> 1.sums] completed</span>
-<span class="go">    Job  = [10.chunks -> 10.sums] completed</span>
-<span class="go">    Job  = [2.chunks -> 2.sums] completed</span>
-<span class="go">    Job  = [3.chunks -> 3.sums] completed</span>
-<span class="go">    Job  = [4.chunks -> 4.sums] completed</span>
-<span class="go">    Job  = [5.chunks -> 5.sums] completed</span>
-<span class="go">    Job  = [6.chunks -> 6.sums] completed</span>
-<span class="go">    Job  = [7.chunks -> 7.sums] completed</span>
-<span class="go">    Job  = [8.chunks -> 8.sums] completed</span>
-<span class="go">    Job  = [9.chunks -> 9.sums] completed</span>
-<span class="go">Completed Task = sum_of_squares</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 12</strong>: Python Code for Splitting up large tasks / files with <strong>@split</strong></a><ul>
-<li><a class="reference internal" href="#splitting-large-jobs">Splitting large jobs</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="checkpointing_code.html"
-                        title="previous chapter"><strong>Chapter 10</strong>: Python Code for Checkpointing: Interrupted Pipelines and Exceptions</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="merge_code.html"
-                        title="next chapter"><strong>Chapter 13</strong>: Python Code for  <tt class="docutils literal"><span class="pre">@merge</span></tt> multiple input into a single result</a></p>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
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-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
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-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-            
-  <div class="section" id="new-manual-subdivide-collate-chapter-num-subdivide-tasks-to-run-efficiently-and-regroup-with-collate">
-<span id="new-manual-subdivide-collate"></span><span id="index-0"></span><h1><strong>Chapter 16</strong>: <a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> tasks to run efficiently and regroup with <a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a><a class="headerlink" href="#new-manual-subdivide-collate-chapter-num-subdivide-tasks-to-run-efficiently-and-regrou [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> syntax</li>
-<li><a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a> syntax</li>
-</ul>
-</div>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>In <strong>Chapter 12</strong> and <strong>Chapter 13</strong>, we saw how a large
-task can be <a class="reference internal" href="split.html#new-manual-split"><em>@split</em></a> into small jobs to be analysed efficiently
-in parallel. Ruffus can then <a class="reference internal" href="split.html#new-manual-split"><em>@merge</em></a> these back together
-to give a single, unified result.</p>
-<p>This assumes that your pipeline is processing one item at a time. Usually, however, we
-will have, for example, 10 large pieces of data in play, each of which has to be
-subdivided into smaller pieces for analysis before being put back together.</p>
-<p>This is the role of <a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> and  <a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@subdivide</em></a>.</p>
-<p>Like <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a>,  the number of output files
-<a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> produces for <em>each</em> <strong>Input</strong> is not predetermined.</p>
-<p>On the other hand, these output files should be named in such a way that they can
-later be grouped back together later using <a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@subdivide</em></a>.</p>
-<p>This will be clearer with some worked examples.</p>
-</div></blockquote>
-</div>
-<div class="section" id="subdivide-in-parallel">
-<span id="new-manual-subdivide"></span><h2><a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> in parallel<a class="headerlink" href="#subdivide-in-parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Let us start from 3 files with varying number of lines. We wish to process these two
-lines at a time but we do not know ahead of time how long each file is:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">random</span><span class="o">,</span> <span class="nn">sys</span>
-<span class="hll">
-</span><span class="c"># Create files a random number of lines</span>
-<span class="hll"><span class="nd">@originate</span><span class="p">([</span><span class="s">"a.start"</span><span class="p">,</span>
-</span>            <span class="s">"b.start"</span><span class="p">,</span>
-            <span class="s">"c.start"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_test_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="n">cnt_lines</span> <span class="o">=</span> <span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="mi">2</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">ii</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">cnt_lines</span><span class="p">):</span>
-            <span class="n">oo</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"data item = </span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="n">ii</span><span class="p">)</span>
-        <span class="k">print</span> <span class="s">"        </span><span class="si">%s</span><span class="s"> has </span><span class="si">%d</span><span class="s"> lines"</span> <span class="o">%</span> <span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="n">cnt_lines</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   subdivide the input files into NNN fragment files of 2 lines each</span>
-<span class="c">#</span>
-<span class="nd">@subdivide</span><span class="p">(</span> <span class="n">create_test_files</span><span class="p">,</span>
-            <span class="n">formatter</span><span class="p">(),</span>
-            <span class="s">"{path[0]}/{basename[0]}.*.fragment"</span><span class="p">,</span>
-            <span class="s">"{path[0]}/{basename[0]}"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">subdivide_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">,</span> <span class="n">output_file_name_stem</span><span class="p">):</span>
-    <span class="c">#</span>
-    <span class="c">#   cleanup any previous results</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">oo</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">oo</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   Output files contain two lines each</span>
-    <span class="c">#       (new output files every even line)</span>
-    <span class="c">#</span>
-    <span class="n">cnt_output_files</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">ii</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)):</span>
-        <span class="k">if</span> <span class="n">ii</span> <span class="o">%</span> <span class="mi">2</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="n">cnt_output_files</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">output_file_name</span> <span class="o">=</span> <span class="s">"</span><span class="si">%s</span><span class="s">.</span><span class="si">%d</span><span class="s">.fragment"</span> <span class="o">%</span> <span class="p">(</span><span class="n">output_file_name_stem</span><span class="p">,</span> <span class="n">cnt_output_files</span><span class="p">)</span>
-            <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-            <span class="k">print</span> <span class="s">"        Subdivide </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">)</span>
-        <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Analyse each fragment independently</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">subdivide_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".fragment"</span><span class="p">),</span> <span class="s">".analysed"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">analyse_fragments</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"        Analysing </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">):</span>
-            <span class="n">oo</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"analysed "</span> <span class="o">+</span> <span class="n">line</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This produces the following output:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-<span class="go">        a.start has 2 lines</span>
-<span class="go">    Job  = [None -> a.start] completed</span>
-<span class="go">        b.start has 6 lines</span>
-<span class="go">    Job  = [None -> b.start] completed</span>
-<span class="go">        c.start has 6 lines</span>
-<span class="go">    Job  = [None -> c.start] completed</span>
-<span class="hll"><span class="go">Completed Task = create_test_files</span>
-</span>
-<span class="go">        Subdivide a.start -> /home/lg/temp/a.1.fragment</span>
-<span class="go">    Job  = [a.start -> a.*.fragment, a] completed</span>
-
-<span class="go">        Subdivide b.start -> /home/lg/temp/b.1.fragment</span>
-<span class="go">        Subdivide b.start -> /home/lg/temp/b.2.fragment</span>
-<span class="go">        Subdivide b.start -> /home/lg/temp/b.3.fragment</span>
-<span class="go">    Job  = [b.start -> b.*.fragment, b] completed</span>
-
-<span class="go">        Subdivide c.start -> /home/lg/temp/c.1.fragment</span>
-<span class="go">        Subdivide c.start -> /home/lg/temp/c.2.fragment</span>
-<span class="hll"><span class="go">        Subdivide c.start -> /home/lg/temp/c.3.fragment</span>
-</span><span class="go">    Job  = [c.start -> c.*.fragment, c] completed</span>
-
-<span class="go">Completed Task = subdivide_files</span>
-
-<span class="go">        Analysing /home/lg/temp/a.1.fragment -> /home/lg/temp/a.1.analysed</span>
-<span class="go">    Job  = [a.1.fragment -> a.1.analysed] completed</span>
-<span class="go">        Analysing /home/lg/temp/b.1.fragment -> /home/lg/temp/b.1.analysed</span>
-<span class="go">    Job  = [b.1.fragment -> b.1.analysed] completed</span>
-
-<span class="go">    [ ...SEE EXAMPLE CODE FOR MORE LINES ...]</span>
-
-<span class="go">Completed Task = analyse_fragments</span>
-</pre></div>
-</div>
-<p><tt class="docutils literal"><span class="pre">a.start</span></tt> has two lines and results in a single <tt class="docutils literal"><span class="pre">.fragment</span></tt> file,
-while there are 3 <tt class="docutils literal"><span class="pre">b.*.fragment</span></tt> files because it has 6 lines.
-Whatever their origin, all of the different fragment files are treated equally
-in <tt class="docutils literal"><span class="pre">analyse_fragments()</span></tt> and processed (in parallel) in the same way.</p>
-</div></blockquote>
-</div>
-<div class="section" id="grouping-using-collate">
-<span id="new-manual-collate"></span><h2>Grouping using <a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a><a class="headerlink" href="#grouping-using-collate" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>All that is left in our example is to reassemble the analysed fragments back together into
-3 sets of results corresponding to the original 3 pieces of starting data.</p>
-<p>This is straightforward by eye: the file names all have the same pattern: <tt class="docutils literal"><span class="pre">[abc].*.analysed</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><pre>a.1.analysed    ->   a.final_result
-b.1.analysed    ->   b.final_result
-b.2.analysed    ->   ..
-b.3.analysed    ->   ..
-c.1.analysed    ->   c.final_result
-c.2.analysed    ->   ..</pre>
-</div>
-</div></blockquote>
-<p><a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a> does something similar:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Specify a string substitution e.g. <tt class="docutils literal"><span class="pre">c.??.analysed</span>  <span class="pre">-></span> <span class="pre">c.final_result</span></tt> and</li>
-<li>Ask <em>ruffus</em> to group together any <strong>Input</strong> (e.g. <tt class="docutils literal"><span class="pre">c.1.analysed</span></tt>, <tt class="docutils literal"><span class="pre">c.2.analysed</span></tt>)
-that will result in the same <strong>Output</strong> (e.g. <tt class="docutils literal"><span class="pre">c.final_result</span></tt>)</li>
-</ol>
-<div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   ``XXX.??.analysed  -> XXX.final_result``</span>
-<span class="hll"><span class="c">#   Group results using original names</span>
-</span><span class="c">#</span>
-<span class="hll"><span class="nd">@collate</span><span class="p">(</span>   <span class="n">analyse_fragments</span><span class="p">,</span>
-</span>
-            <span class="c"># split file name into [abc].NUMBER.analysed</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">"/(?P<NAME>[abc]+)\.\d+\.analysed$"</span><span class="p">),</span>
-
-            <span class="s">"{path[0]}/{NAME[0]}.final_result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">recombine_analyses</span><span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">input_file</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-            <span class="k">print</span> <span class="s">"        Recombine </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-            <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">):</span>
-                <span class="n">oo</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>This produces the following output:</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="go">        Recombine /home/lg/temp/a.1.analysed -> /home/lg/temp/a.final_result</span>
-<span class="go">    Job  = [[a.1.analysed] -> a.final_result] completed</span>
-<span class="go">        Recombine /home/lg/temp/b.1.analysed -> /home/lg/temp/b.final_result</span>
-<span class="go">        Recombine /home/lg/temp/b.2.analysed -> /home/lg/temp/b.final_result</span>
-<span class="go">        Recombine /home/lg/temp/b.3.analysed -> /home/lg/temp/b.final_result</span>
-<span class="go">    Job  = [[b.1.analysed, b.2.analysed, b.3.analysed] -> b.final_result] completed</span>
-<span class="go">        Recombine /home/lg/temp/c.1.analysed -> /home/lg/temp/c.final_result</span>
-<span class="go">        Recombine /home/lg/temp/c.2.analysed -> /home/lg/temp/c.final_result</span>
-<span class="go">        Recombine /home/lg/temp/c.3.analysed -> /home/lg/temp/c.final_result</span>
-<span class="go">    Job  = [[c.1.analysed, c.2.analysed, c.3.analysed] -> c.final_result] completed</span>
-<span class="hll"><span class="go">Completed Task = recombine_analyses</span>
-</span></pre></div>
-</div>
-</div></blockquote>
-<div class="admonition warning">
-<p class="first admonition-title">Warning</p>
-<ul class="last">
-<li><p class="first"><strong>Input</strong> file names are grouped together not in a guaranteed order.</p>
-<blockquote>
-<div><p>For example, the fragment files may not be sent to <tt class="docutils literal"><span class="pre">recombine_analyses(input_file_names,</span> <span class="pre">...)</span></tt>
-in alphabetically or any other useful order.</p>
-<p>You may want to sort <strong>Input</strong> before concatenation.</p>
-</div></blockquote>
-</li>
-<li><p class="first">All <strong>Input</strong> are grouped together if they have both the same <strong>Output</strong> <em>and</em> <strong>Extra</strong>
-parameters. If any string substitution is specified in any of the other <strong>Extra</strong> parameters
-to <a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a>, they must give the same answers for <strong>Input</strong>
-in the same group.</p>
-</li>
-</ul>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 16</strong>: <tt class="docutils literal"><span class="pre">@subdivide</span></tt> tasks to run efficiently and regroup with <tt class="docutils literal"><span class="pre">@collate</span></tt></a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#subdivide-in-parallel"><tt class="docutils literal"><span class="pre">@subdivide</span></tt> in parallel</a></li>
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-  <div class="section" id="new-manual-subdivide-collate-chapter-num-python-code-for-subdivide-tasks-to-run-efficiently-and-regroup-with-collate">
-<span id="new-manual-subdivide-collate-code"></span><h1><strong>Chapter 16</strong>: Python Code for <a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> tasks to run efficiently and regroup with <a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a><a class="headerlink" href="#new-manual-subdivide-collate-chapter-num-python-code-for-subdivide-tasks-to-run-efficiently [...]
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/jobs_limit.html#decorators-jobs-limit"><em>@jobs_limit</em></a> syntax</li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run()</em></a> syntax</li>
-<li><a class="reference internal" href="../../drmaa_wrapper_functions.html#drmaa-wrapper-run-job"><em>drmaa_wrapper.run_job()</em></a> syntax</li>
-<li>Back to <strong>Chapter 16</strong>: <a class="reference internal" href="subdivide_collate.html#new-manual-subdivide-collate"><em>:ref:`@subdivide tasks to run efficiently and regroup with @collate</em></a></li>
-</ul>
-</div>
-<div class="section" id="subdivide-and-regroup-with-collate-example">
-<h2><a class="reference internal" href="../../decorators/subdivide.html#decorators-subdivide"><em>@subdivide</em></a> and regroup with <a class="reference internal" href="../../decorators/collate.html#decorators-collate"><em>@collate</em></a> example<a class="headerlink" href="#subdivide-and-regroup-with-collate-example" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">random</span><span class="o">,</span> <span class="nn">sys</span>
-
-<span class="c"># Create files a random number of lines</span>
-<span class="nd">@originate</span><span class="p">([</span><span class="s">"a.start"</span><span class="p">,</span>
-            <span class="s">"b.start"</span><span class="p">,</span>
-            <span class="s">"c.start"</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">create_test_files</span><span class="p">(</span><span class="n">output_file</span><span class="p">):</span>
-    <span class="n">cnt_lines</span> <span class="o">=</span> <span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="mi">2</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">ii</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">cnt_lines</span><span class="p">):</span>
-            <span class="n">oo</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"data item = </span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="n">ii</span><span class="p">)</span>
-        <span class="k">print</span> <span class="s">"        </span><span class="si">%s</span><span class="s"> has </span><span class="si">%d</span><span class="s"> lines"</span> <span class="o">%</span> <span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="n">cnt_lines</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="hll"><span class="c">#   subdivide the input files into NNN fragment files of 2 lines each</span>
-</span><span class="c">#</span>
-<span class="nd">@subdivide</span><span class="p">(</span> <span class="n">create_test_files</span><span class="p">,</span>
-            <span class="n">formatter</span><span class="p">(),</span>
-            <span class="s">"{path[0]}/{basename[0]}.*.fragment"</span><span class="p">,</span>
-            <span class="s">"{path[0]}/{basename[0]}"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">subdivide_files</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_files</span><span class="p">,</span> <span class="n">output_file_name_stem</span><span class="p">):</span>
-    <span class="c">#</span>
-    <span class="c">#   cleanup any previous results</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">oo</span> <span class="ow">in</span> <span class="n">output_files</span><span class="p">:</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">oo</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   Output files contain two lines each</span>
-    <span class="c">#       (new output files every even line)</span>
-    <span class="c">#</span>
-    <span class="n">cnt_output_files</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">ii</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)):</span>
-        <span class="k">if</span> <span class="n">ii</span> <span class="o">%</span> <span class="mi">2</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="n">cnt_output_files</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">output_file_name</span> <span class="o">=</span> <span class="s">"</span><span class="si">%s</span><span class="s">.</span><span class="si">%d</span><span class="s">.fragment"</span> <span class="o">%</span> <span class="p">(</span><span class="n">output_file_name_stem</span><span class="p">,</span> <span class="n">cnt_output_files</span><span class="p">)</span>
-            <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-            <span class="k">print</span> <span class="s">"        Subdivide </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">)</span>
-        <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Analyse each fragment independently</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">subdivide_files</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".fragment"</span><span class="p">),</span> <span class="s">".analysed"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">analyse_fragments</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">print</span> <span class="s">"        Analysing </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">):</span>
-            <span class="n">oo</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"analysed "</span> <span class="o">+</span> <span class="n">line</span><span class="p">)</span>
-
-
-<span class="c">#</span>
-<span class="c">#   Group results using original names</span>
-<span class="c">#</span>
-<span class="nd">@collate</span><span class="p">(</span>   <span class="n">analyse_fragments</span><span class="p">,</span>
-
-            <span class="c"># split file name into [abc].NUMBER.analysed</span>
-            <span class="n">formatter</span><span class="p">(</span><span class="s">"/(?P<NAME>[abc]+)\.\d+\.analysed$"</span><span class="p">),</span>
-
-            <span class="s">"{path[0]}/{NAME[0]}.final_result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">recombine_analyses</span><span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">oo</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">input_file</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-            <span class="k">print</span> <span class="s">"        Recombine </span><span class="si">%s</span><span class="s"> -> </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">)</span>
-            <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">):</span>
-                <span class="n">oo</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-
-
-
-<span class="c">#pipeline_printout(sys.stdout, verbose = 3)</span>
-
-
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>Results in</p>
-<div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-
-<span class="go">        a.start has 2 lines</span>
-<span class="go">    Job  = [None -> a.start] completed</span>
-<span class="go">        b.start has 6 lines</span>
-<span class="go">    Job  = [None -> b.start] completed</span>
-<span class="go">        c.start has 6 lines</span>
-<span class="go">    Job  = [None -> c.start] completed</span>
-<span class="go">Completed Task = create_test_files</span>
-
-<span class="go">        Subdivide a.start -> /home/lg/temp/a.1.fragment</span>
-<span class="go">    Job  = [a.start -> a.*.fragment, a] completed</span>
-<span class="go">        Subdivide b.start -> /home/lg/temp/b.1.fragment</span>
-<span class="go">        Subdivide b.start -> /home/lg/temp/b.2.fragment</span>
-<span class="go">        Subdivide b.start -> /home/lg/temp/b.3.fragment</span>
-<span class="go">    Job  = [b.start -> b.*.fragment, b] completed</span>
-<span class="go">        Subdivide c.start -> /home/lg/temp/c.1.fragment</span>
-<span class="go">        Subdivide c.start -> /home/lg/temp/c.2.fragment</span>
-<span class="go">        Subdivide c.start -> /home/lg/temp/c.3.fragment</span>
-<span class="go">    Job  = [c.start -> c.*.fragment, c] completed</span>
-<span class="go">Completed Task = subdivide_files</span>
-
-<span class="go">        Analysing /home/lg/temp/a.1.fragment -> /home/lg/temp/a.1.analysed</span>
-<span class="go">    Job  = [a.1.fragment -> a.1.analysed] completed</span>
-<span class="go">        Analysing /home/lg/temp/b.1.fragment -> /home/lg/temp/b.1.analysed</span>
-<span class="go">    Job  = [b.1.fragment -> b.1.analysed] completed</span>
-<span class="go">        Analysing /home/lg/temp/b.2.fragment -> /home/lg/temp/b.2.analysed</span>
-<span class="go">    Job  = [b.2.fragment -> b.2.analysed] completed</span>
-<span class="go">        Analysing /home/lg/temp/b.3.fragment -> /home/lg/temp/b.3.analysed</span>
-<span class="go">    Job  = [b.3.fragment -> b.3.analysed] completed</span>
-<span class="go">        Analysing /home/lg/temp/c.1.fragment -> /home/lg/temp/c.1.analysed</span>
-<span class="go">    Job  = [c.1.fragment -> c.1.analysed] completed</span>
-<span class="go">        Analysing /home/lg/temp/c.2.fragment -> /home/lg/temp/c.2.analysed</span>
-<span class="go">    Job  = [c.2.fragment -> c.2.analysed] completed</span>
-<span class="go">        Analysing /home/lg/temp/c.3.fragment -> /home/lg/temp/c.3.analysed</span>
-<span class="go">    Job  = [c.3.fragment -> c.3.analysed] completed</span>
-<span class="go">Completed Task = analyse_fragments</span>
-
-<span class="go">        Recombine /home/lg/temp/a.1.analysed -> /home/lg/temp/a.final_result</span>
-<span class="go">    Job  = [[a.1.analysed] -> a.final_result] completed</span>
-<span class="go">        Recombine /home/lg/temp/b.1.analysed -> /home/lg/temp/b.final_result</span>
-<span class="go">        Recombine /home/lg/temp/b.2.analysed -> /home/lg/temp/b.final_result</span>
-<span class="go">        Recombine /home/lg/temp/b.3.analysed -> /home/lg/temp/b.final_result</span>
-<span class="go">    Job  = [[b.1.analysed, b.2.analysed, b.3.analysed] -> b.final_result] completed</span>
-<span class="go">        Recombine /home/lg/temp/c.1.analysed -> /home/lg/temp/c.final_result</span>
-<span class="go">        Recombine /home/lg/temp/c.2.analysed -> /home/lg/temp/c.final_result</span>
-<span class="go">        Recombine /home/lg/temp/c.3.analysed -> /home/lg/temp/c.final_result</span>
-<span class="go">    Job  = [[c.1.analysed, c.2.analysed, c.3.analysed] -> c.final_result] completed</span>
-<span class="go">Completed Task = recombine_analyses</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
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-<li><a class="reference internal" href="#subdivide-and-regroup-with-collate-example"><tt class="docutils literal"><span class="pre">@subdivide</span></tt> and regroup with <tt class="docutils literal"><span class="pre">@collate</span></tt> example</a></li>
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-  <div class="section" id="new-manual-transform-chapter-num-transforming-data-in-a-pipeline-with-transform">
-<span id="new-manual-transform"></span><span id="index-0"></span><h1><strong>Chapter 2</strong>: Transforming data in a pipeline with <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a><a class="headerlink" href="#new-manual-transform-chapter-num-transforming-data-in-a-pipeline-with-transform" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> syntax</li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="transform_code.html#new-manual-transform-code"><em>Chapter 1: Python Code for Transforming data in a pipeline with @transform</em></a></li>
-</ul>
-</div>
-<div class="section" id="review">
-<h2>Review<a class="headerlink" href="#review" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/theoretical_pipeline_schematic.png"><img alt="../../_images/theoretical_pipeline_schematic.png" src="../../_images/theoretical_pipeline_schematic.png" style="width: 610.0px; height: 71.0px;" /></a>
-<p>Computational pipelines transform your data in stages until the final result is produced.
-Ruffus automates the plumbing in your pipeline. You supply the python functions which perform the data transformation,
-and tell Ruffus how these pipeline stages or <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> functions are connected together.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><strong>The best way to design a pipeline is to:</strong></p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><strong>write down the file names of the data as it flows across your pipeline</strong></li>
-<li><strong>write down the names of functions which transforms the data at each stage of the pipeline.</strong></li>
-</ul>
-</div></blockquote>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="task-functions-as-recipes">
-<h2>Task functions as recipes<a class="headerlink" href="#task-functions-as-recipes" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Each <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function of the pipeline is a recipe or
-<a class="reference external" href="http://www.gnu.org/software/make/manual/make.html#Rule-Introduction">rule</a>
-which can be applied repeatedly to our data.</p>
-<p>For example, one can have</p>
-<blockquote>
-<div><ul class="simple">
-<li>a <tt class="docutils literal"><span class="pre">compile()</span></tt> <em>task</em> which will compile any number of source code files, or</li>
-<li>a <tt class="docutils literal"><span class="pre">count_lines()</span></tt> <em>task</em> which will count the number of lines in any file or</li>
-<li>an <tt class="docutils literal"><span class="pre">align_dna()</span></tt> <em>task</em> which will align the DNA of many chromosomes.</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="transform-is-a-1-to-1-operation">
-<span id="index-1"></span><h2><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> is a 1 to 1 operation<a class="headerlink" href="#transform-is-a-1-to-1-operation" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">@transform</span></tt> is a 1:1 operation because for each input, it generates one output.</p>
-<a class="reference internal image-reference" href="../../_images/transform_1_to_1_example.png"><img alt="../../_images/transform_1_to_1_example.png" src="../../_images/transform_1_to_1_example.png" style="width: 535.5px; height: 371.0px;" /></a>
-<p>This is obvious when you count the number of jobs at each step. In our example pipeline, there are always
-three jobs moving through in step at each stage (<a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>).</p>
-<p>Each <strong>Input</strong> or <strong>Output</strong> is not limited, however, to a single filename. Each job can accept, for example,
-a pair of files as its <strong>Input</strong>, or generate more than one file or a dictionary or numbers as its <strong>Output</strong>.</p>
-<p>When each job outputs a pair of files, this does not generate two jobs downstream. It just means that the successive
-<a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> in the pipeline will receive a list or tuple of files as its input parameter.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>The different sort of decorators in Ruffus determine the <em>topology</em> of your pipeline,
-i.e. how the jobs from different tasks are linked together seamlessly.</p>
-<p><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> always generates one <strong>Output</strong> for one <strong>Input</strong>.</p>
-<p>In the later parts of the tutorial, we will encounter more decorators which can <em>split up</em>, or <em>join together</em> or <em>group</em> inputs.</p>
-<p class="last">In other words, using other decorators <strong>Input</strong> and <strong>Output</strong>  can have <strong>many to one</strong>, <strong>many to many</strong> etc. relationships.</p>
-</div>
-</div></blockquote>
-<div class="section" id="a-pair-of-files-as-the-input">
-<h3>A pair of files as the <strong>Input</strong><a class="headerlink" href="#a-pair-of-files-as-the-input" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>Let us rewrite our previous example so that the <strong>Input</strong> of the first task
-are <a class="reference external" href="http://en.wikipedia.org/wiki/DNA_sequencing_theory#Pairwise_end-sequencing">matching pairs</a>
-of DNA sequence files, processed in tandem.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="n">starting_files</span> <span class="o">=</span> <span class="p">[(</span><span class="s">"a.1.fastq"</span><span class="p">,</span> <span class="s">"a.2.fastq"</span><span class="p">),</span>
-                  <span class="p">(</span><span class="s">"a.1.fastq"</span><span class="p">,</span> <span class="s">"a.2.fastq"</span><span class="p">),</span>
-                  <span class="p">(</span><span class="s">"a.1.fastq"</span><span class="p">,</span> <span class="s">"a.2.fastq"</span><span class="p">)]</span>
-<span class="hll">
-</span><span class="hll"><span class="c">#</span>
-</span><span class="hll"><span class="c">#   STAGE 1 fasta->sam</span>
-</span><span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">starting_files</span><span class="p">,</span>                     <span class="c"># Input = starting files</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".1.fastq"</span><span class="p">),</span>                <span class="c">#         suffix = .1.fastq</span>
-            <span class="s">".sam"</span><span class="p">)</span>                            <span class="c"># Output  suffix = .sam</span>
-<span class="k">def</span> <span class="nf">map_dna_sequence</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span>
-                    <span class="n">output_file</span><span class="p">):</span>
-    <span class="c"># remember there are two input files now</span>
-    <span class="n">ii1</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_files</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-<span class="hll">    <span class="n">ii2</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_files</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-</span><span class="hll">    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</span></pre></div>
-</div>
-</div></blockquote>
-<p>The only changes are to the first task:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="go">pipeline_run()</span>
-<span class="go">    Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed</span>
-<span class="go">    Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed</span>
-<span class="go">    Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed</span>
-<span class="go">Completed Task = map_dna_sequence</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><a class="reference internal" href="../../decorators/indicator_objects.html#decorators-suffix"><em>suffix</em></a> always matches only the first file name in each <strong>Input</strong>.</p>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="input-and-output-parameters">
-<span id="index-2"></span><h2><strong>Input</strong> and <strong>Output</strong> parameters<a class="headerlink" href="#input-and-output-parameters" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><strong>Ruffus</strong> chains together different tasks by taking the <strong>Output</strong> from one job
-and plugging it automatically as the <strong>Input</strong> of the next.</p>
-<p>The first two parameters of each job are the <strong>Input</strong> and <strong>Output</strong> parameters respectively.</p>
-<p>In the above example, we have:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [a.bam -> a.statistics, use_linear_model] completed</span>
-<span class="go">    Job  = [b.bam -> b.statistics, use_linear_model] completed</span>
-<span class="go">    Job  = [c.bam -> c.statistics, use_linear_model] completed</span>
-<span class="go">Completed Task = summarise_bam_file</span>
-</pre></div>
-</div>
-<table border="1" class="docutils">
-<caption>Parameters for <tt class="docutils literal"><span class="pre">summarise_bam_file()</span></tt></caption>
-<colgroup>
-<col width="20%" />
-<col width="25%" />
-<col width="56%" />
-</colgroup>
-<thead valign="bottom">
-<tr class="row-odd"><th class="head"><strong>Inputs</strong></th>
-<th class="head"><strong>Outputs</strong></th>
-<th class="head"><strong>Extra</strong></th>
-</tr>
-</thead>
-<tbody valign="top">
-<tr class="row-even"><td><tt class="docutils literal"><span class="pre">"a.bam"</span></tt></td>
-<td><tt class="docutils literal"><span class="pre">"a.statistics"</span></tt></td>
-<td><tt class="docutils literal"><span class="pre">"use_linear_model"</span></tt></td>
-</tr>
-<tr class="row-odd"><td><tt class="docutils literal"><span class="pre">"b.bam"</span></tt></td>
-<td><tt class="docutils literal"><span class="pre">"b.statistics"</span></tt></td>
-<td><tt class="docutils literal"><span class="pre">"use_linear_model"</span></tt></td>
-</tr>
-<tr class="row-even"><td><tt class="docutils literal"><span class="pre">"c.bam"</span></tt></td>
-<td><tt class="docutils literal"><span class="pre">"c.statistics"</span></tt></td>
-<td><tt class="docutils literal"><span class="pre">"use_linear_model"</span></tt></td>
-</tr>
-</tbody>
-</table>
-</div></blockquote>
-<p><strong>Extra</strong> parameters are for the consumption of <tt class="docutils literal"><span class="pre">summarise_bam_file()</span></tt> and will not passed to the next task.</p>
-<p>Ruffus was designed for pipelines which save intermediate data in files. This is not
-compulsory but saving your data in files at each step provides many advantages:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Ruffus can use file system time stamps to check if your pipeline is up to date</li>
-<li>Your data is persistent across runs</li>
-<li>This is a good way to pass large amounts of data across processes and computational nodes</li>
-</ol>
-</div></blockquote>
-<p>Nevertheless, <em>all</em> the <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> parameters can include anything which suits your workflow, from lists of files, to numbers,
-sets or tuples. <em>Ruffus</em> imposes few constraints on what <em>you</em>
-would like to send to each stage of your pipeline.</p>
-<p><em>Ruffus</em> does, however, assume that if the <strong>Input</strong> and <strong>Output</strong> parameter contains strings, these will be interpreted as file names
-required by and produced by that job. As we shall see, the modification times of these file names
-indicate whether that part of the pipeline is up to date or needs to be rerun.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 2</strong>: Transforming data in a pipeline with <tt class="docutils literal"><span class="pre">@transform</span></tt></a><ul>
-<li><a class="reference internal" href="#review">Review</a></li>
-<li><a class="reference internal" href="#task-functions-as-recipes">Task functions as recipes</a></li>
-<li><a class="reference internal" href="#transform-is-a-1-to-1-operation"><tt class="docutils literal"><span class="pre">@transform</span></tt> is a 1 to 1 operation</a><ul>
-<li><a class="reference internal" href="#a-pair-of-files-as-the-input">A pair of files as the <strong>Input</strong></a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#input-and-output-parameters"><strong>Input</strong> and <strong>Output</strong> parameters</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="introduction.html"
-                        title="previous chapter"><strong>Chapter 1</strong>: An introduction to basic <em>Ruffus</em> syntax</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="transform_in_parallel.html"
-                        title="next chapter"><strong>Chapter 3</strong>: More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data</a></p>
-  <h3>This Page</h3>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
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-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-            
-  <div class="section" id="new-manual-introduction-chapter-num-python-code-for-transforming-data-in-a-pipeline-with-transform">
-<span id="new-manual-transform-code"></span><h1><strong>Chapter 1</strong>: Python Code for Transforming data in a pipeline with <tt class="docutils literal"><span class="pre">@transform</span></tt><a class="headerlink" href="#new-manual-introduction-chapter-num-python-code-for-transforming-data-in-a-pipeline-with-transform" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform syntax in detail</em></a></li>
-<li>Back to <strong>Chapter 2</strong>: <a class="reference internal" href="transform.html#new-manual-transform"><em>Transforming data in a pipeline with @transform</em></a></li>
-</ul>
-</div>
-<div class="section" id="your-first-ruffus-script">
-<h2>Your first Ruffus script<a class="headerlink" href="#your-first-ruffus-script" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   The starting data files would normally exist beforehand!</span>
-<span class="c">#       We create some empty files for this example</span>
-<span class="c">#</span>
-<span class="n">starting_files</span> <span class="o">=</span> <span class="p">[(</span><span class="s">"a.1.fastq"</span><span class="p">,</span> <span class="s">"a.2.fastq"</span><span class="p">),</span>
-                  <span class="p">(</span><span class="s">"b.1.fastq"</span><span class="p">,</span> <span class="s">"b.2.fastq"</span><span class="p">),</span>
-                  <span class="p">(</span><span class="s">"c.1.fastq"</span><span class="p">,</span> <span class="s">"c.2.fastq"</span><span class="p">)]</span>
-
-
-<span class="k">for</span> <span class="n">ff_pair</span> <span class="ow">in</span> <span class="n">starting_files</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">ff_pair</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">ff_pair</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#</span>
-<span class="c">#   STAGE 1 fasta->sam</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">starting_files</span><span class="p">,</span>                     <span class="c"># Input = starting files</span>
-           <span class="n">suffix</span><span class="p">(</span><span class="s">".1.fastq"</span><span class="p">),</span>                 <span class="c">#         suffix = .1.fastq</span>
-           <span class="s">".sam"</span><span class="p">)</span>                             <span class="c"># Output  suffix = .sam</span>
-<span class="k">def</span> <span class="nf">map_dna_sequence</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span>
-                    <span class="n">output_file</span><span class="p">):</span>
-    <span class="c"># remember there are two input files now</span>
-    <span class="n">ii1</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_files</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-    <span class="n">ii2</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_files</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   STAGE 2 sam->bam</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">map_dna_sequence</span><span class="p">,</span>                   <span class="c"># Input = previous stage</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".sam"</span><span class="p">),</span>                    <span class="c">#         suffix = .sam</span>
-            <span class="s">".bam"</span><span class="p">)</span>                            <span class="c"># Output  suffix = .bam</span>
-<span class="k">def</span> <span class="nf">compress_sam_file</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                      <span class="n">output_file</span><span class="p">):</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#</span>
-<span class="c">#   STAGE 3 bam->statistics</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">compress_sam_file</span><span class="p">,</span>                  <span class="c"># Input = previous stage</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".bam"</span><span class="p">),</span>                    <span class="c">#         suffix = .bam</span>
-            <span class="s">".statistics"</span><span class="p">,</span>                     <span class="c"># Output  suffix = .statistics</span>
-            <span class="s">"use_linear_model"</span><span class="p">)</span>                <span class="c"># Extra statistics parameter</span>
-<span class="k">def</span> <span class="nf">summarise_bam_file</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                       <span class="n">output_file</span><span class="p">,</span>
-                       <span class="n">extra_stats_parameter</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Sketch of real analysis function</span>
-<span class="sd">    """</span>
-    <span class="n">ii</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">)</span>
-    <span class="n">oo</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">()</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">()</span>
-<span class="go">    Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed</span>
-<span class="go">    Job  = [[b.1.fastq, b.2.fastq] -> b.sam] completed</span>
-<span class="go">    Job  = [[c.1.fastq, c.2.fastq] -> c.sam] completed</span>
-<span class="go">Completed Task = map_dna_sequence</span>
-<span class="go">    Job  = [a.sam -> a.bam] completed</span>
-<span class="go">    Job  = [b.sam -> b.bam] completed</span>
-<span class="go">    Job  = [c.sam -> c.bam] completed</span>
-<span class="go">Completed Task = compress_sam_file</span>
-<span class="go">    Job  = [a.bam -> a.statistics, use_linear_model] completed</span>
-<span class="go">    Job  = [b.bam -> b.statistics, use_linear_model] completed</span>
-<span class="go">    Job  = [c.bam -> c.statistics, use_linear_model] completed</span>
-<span class="go">Completed Task = summarise_bam_file</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
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-                        title="next chapter"><strong>Chapter 3</strong>: Python Code for More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data</a></p>
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-  <div class="section" id="new-manual-transform-in-parallel-chapter-num-more-on-transform-ing-data">
-<span id="new-manual-transform-in-parallel"></span><span id="index-0"></span><h1><strong>Chapter 3</strong>: More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data<a class="headerlink" href="#new-manual-transform-in-parallel-chapter-num-more-on-transform-ing-data" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a>  syntax</li>
-</ul>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="transform_in_parallel_code.html#new-manual-transform-in-parallel-code"><em>Chapter 3: Python Code for More on @transform-ing data</em></a></li>
-</ul>
-</div>
-<div class="section" id="review">
-<h2>Review<a class="headerlink" href="#review" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><a class="reference internal image-reference" href="../../_images/theoretical_pipeline_schematic.png"><img alt="../../_images/theoretical_pipeline_schematic.png" src="../../_images/theoretical_pipeline_schematic.png" style="width: 610.0px; height: 71.0px;" /></a>
-<p>Computational pipelines transform your data in stages until the final result is produced.
-<em>Ruffus</em> automates the plumbing in your pipeline. You supply the python functions which perform the data transformation,
-and tell <em>Ruffus</em> how these pipeline stages or <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> functions are connected together.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><strong>The best way to design a pipeline is to:</strong></p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><strong>write down the file names of the data as it flows across your pipeline</strong></li>
-<li><strong>write down the names of functions which transforms the data at each stage of the pipeline.</strong></li>
-</ul>
-</div></blockquote>
-</div>
-<p><a class="reference internal" href="introduction.html#new-manual-introduction"><em>Chapter 1: An introduction to basic Ruffus syntax</em></a> described the bare bones of a simple <em>Ruffus</em> pipeline.</p>
-<p>Using the <em>Ruffus</em> <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> decorator, we were able to
-specify the data files moving through our pipeline so that our specified task functions
-could be invoked.</p>
-<p>This may seem like a lot of effort and complication for something so simple: a couple of
-simple python function calls we could have invoked ourselves.
-However, By letting <em>Ruffus</em> manage your pipeline parameters, you will get the following features
-for free:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Only out-of-date parts of the pipeline will be re-run</li>
-<li>Multiple jobs can be run in parallel (on different processors if possible)</li>
-<li>Pipeline stages can be chained together automatically. This means you can apply your
-pipeline just as easily to 1000 files as to 3.</li>
-</ol>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="running-pipelines-in-parallel">
-<h2>Running pipelines in parallel<a class="headerlink" href="#running-pipelines-in-parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Even though three sets of files have been specified for our initial pipeline, and they can be
-processed completely independently, by default  <em>Ruffus</em> runs each of them serially in succession.</p>
-<p>To ask <em>Ruffus</em> to run them in parallel, all you have to do is to add a <tt class="docutils literal"><span class="pre">multiprocess</span></tt> parameter to <tt class="docutils literal"><span class="pre">pipeline_run</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>In this case, we are telling <em>Ruffus</em> to run a maximum of 5 jobs at the same time. Since we only have
-three sets of data, that is as much parallelism as we are going to get...</p>
-</div></blockquote>
-</div>
-<div class="section" id="up-to-date-jobs-are-not-re-run-unnecessarily">
-<span id="new-manual-only-rerun-out-of-date"></span><h2>Up-to-date jobs are not re-run unnecessarily<a class="headerlink" href="#up-to-date-jobs-are-not-re-run-unnecessarily" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>A job will be run only if the output file timestamps are out of date.
-If you ran our example code a second time, nothing would happen because all the work is already complete.</p>
-<p>We can check the details by asking <em>Ruffus</em> for more <tt class="docutils literal"><span class="pre">verbose</span></tt> output</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">(</span><span class="n">verbose</span> <span class="o">=</span> <span class="mi">4</span><span class="p">)</span>
-<span class="go">  Task = map_dna_sequence</span>
-<span class="go">    All jobs up to date</span>
-<span class="go">  Task = compress_sam_file</span>
-<span class="go">    All jobs up to date</span>
-<span class="go">  Task = summarise_bam_file</span>
-<span class="go">    All jobs up to date</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>Nothing happens because:</dt>
-<dd><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">a.sam</span></tt> was created later than <tt class="docutils literal"><span class="pre">a.1.fastq</span></tt> and <tt class="docutils literal"><span class="pre">a.2.fastq</span></tt>, and</li>
-<li><tt class="docutils literal"><span class="pre">a.bam</span></tt> was created later than <tt class="docutils literal"><span class="pre">a.sam</span></tt> and</li>
-<li><tt class="docutils literal"><span class="pre">a.statistics</span></tt> was created later than <tt class="docutils literal"><span class="pre">a.bam</span></tt>.</li>
-</ul>
-</dd>
-</dl>
-<p>and so on...</p>
-<dl class="docutils">
-<dt>Let us see what happens if we recreated the file <tt class="docutils literal"><span class="pre">a.1.fastq</span></tt> so that it appears as if 1 out of the original data files is out of date</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">open</span><span class="p">(</span><span class="s">"a.1.fastq"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="n">pipeline_run</span><span class="p">(</span><span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>The up to date jobs are cleverly ignored and only the out of date files are reprocessed.</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="go"> >>> open("a.1.fastq", "w")</span>
-<span class="go"> >>> pipeline_run(verbose=2)</span>
-<span class="hll"><span class="go">     Job  = [[b.1.fastq, b.2.fastq] -> b.sam] # unnecessary: already up to date</span>
-</span><span class="hll"><span class="go">     Job  = [[c.1.fastq, c.2.fastq] -> c.sam] # unnecessary: already up to date</span>
-</span><span class="go">     Job  = [[a.1.fastq, a.2.fastq] -> a.sam] completed</span>
-<span class="go"> Completed Task = map_dna_sequence</span>
-<span class="hll"><span class="go">     Job  = [b.sam -> b.bam] # unnecessary: already up to date</span>
-</span><span class="hll"><span class="go">     Job  = [c.sam -> c.bam] # unnecessary: already up to date</span>
-</span><span class="go">     Job  = [a.sam -> a.bam] completed</span>
-<span class="go"> Completed Task = compress_sam_file</span>
-<span class="hll"><span class="go">     Job  = [b.bam -> b.statistics, use_linear_model] # unnecessary: already up to date</span>
-</span><span class="hll"><span class="go">     Job  = [c.bam -> c.statistics, use_linear_model] # unnecessary: already up to date</span>
-</span><span class="go">     Job  = [a.bam -> a.statistics, use_linear_model] completed</span>
-<span class="go"> Completed Task = summarise_bam_file</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="defining-pipeline-tasks-out-of-order">
-<span id="new-manual-output-from"></span><span id="index-1"></span><h2>Defining pipeline tasks out of order<a class="headerlink" href="#defining-pipeline-tasks-out-of-order" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>The examples so far assumes that all your pipelined tasks are defined in order.
-(<tt class="docutils literal"><span class="pre">first_task</span></tt> before <tt class="docutils literal"><span class="pre">second_task</span></tt>). This is usually the most sensible way to arrange your code.</p>
-<p>If you wish to refer to tasks which are not yet defined, you can do so by quoting the function name as a string and wrapping
-it with the <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-indicator-objects"><em>indicator class</em></a> <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-output-from"><em>output_from(...)</em></a> so that <em>Ruffus</em>
-knowns this is a <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> name, not a file name</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre> <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#   second task</span>
- <span class="c">#</span>
-<span class="hll"> <span class="c">#   task name string wrapped in output_from(...)</span>
-</span> <span class="nd">@transform</span><span class="p">(</span><span class="n">output_from</span><span class="p">(</span><span class="s">"first_task"</span><span class="p">),</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-     <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#   first task</span>
- <span class="c">#</span>
- <span class="nd">@transform</span><span class="p">(</span><span class="n">first_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                         <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                          <span class="s">".output.extra.1"</span><span class="p">],</span>
-                        <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                 <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-     <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_file_pair</span><span class="p">:</span>
-         <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-             <span class="k">pass</span>
-
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#       Run</span>
- <span class="c">#</span>
- <span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>You can also refer to tasks (functions) in other modules, in which case the full
-qualified name must be used:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">output_from</span><span class="p">(</span><span class="s">"other_module.first_task"</span><span class="p">),</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="multiple-dependencies">
-<span id="new-manual-transform-multiple-dependencies"></span><span id="index-2"></span><h2>Multiple dependencies<a class="headerlink" href="#multiple-dependencies" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Each task can depend on more than one antecedent simply by chaining to a list in <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a></p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre> <span class="c">#</span>
-<span class="hll"> <span class="c"># third_task depends on both first_task() and second_task()</span>
-</span> <span class="c">#</span>
- <span class="nd">@transform</span><span class="p">([</span><span class="n">first_task</span><span class="p">,</span> <span class="n">second_task</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">third_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-     <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><tt class="docutils literal"><span class="pre">third_task()</span></tt> depends on and follows both <tt class="docutils literal"><span class="pre">first_task()</span></tt> and <tt class="docutils literal"><span class="pre">second_task()</span></tt>. However, these latter two tasks are independent of each other
-and can and will run in parallel. This can be clearly shown for our example if we added a little randomness to the run time of each job:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">())</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The execution of <tt class="docutils literal"><span class="pre">first_task()</span></tt> and <tt class="docutils literal"><span class="pre">second_task()</span></tt> jobs will be interleaved and they finish in no particular order:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">third_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">6</span><span class="p">)</span>
-<span class="go">    Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = second_task</span>
-<span class="go">    Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">See the <a class="reference internal" href="transform_in_parallel_code.html#new-manual-transform-multiple-dependencies-code"><em>example code</em></a></p>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="follows">
-<span id="new-manual-follows"></span><span id="index-3"></span><h2><a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows</em></a><a class="headerlink" href="#follows" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If there is some extrinsic reason one non-dependent task has to precede the other, then this can be specified explicitly using <a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows</em></a>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre> <span class="c">#</span>
-<span class="hll"> <span class="c">#   @follows specifies a preceding task</span>
-</span> <span class="c">#</span>
- <span class="nd">@follows</span><span class="p">(</span><span class="s">"first_task"</span><span class="p">)</span>
- <span class="nd">@transform</span><span class="p">(</span><span class="n">second_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                         <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                          <span class="s">".output.extra.1"</span><span class="p">],</span>
-                        <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                 <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p><a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows</em></a> specifies either a preceding task (e.g. <tt class="docutils literal"><span class="pre">first_task</span></tt>), or if
-it has not yet been defined, the name (as a string) of a task function (e.g. <tt class="docutils literal"><span class="pre">"first_task"</span></tt>).</p>
-<p>With the addition of <a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows</em></a>, all the jobs
-of <tt class="docutils literal"><span class="pre">second_task()</span></tt> start <em>after</em> those from <tt class="docutils literal"><span class="pre">first_task()</span></tt> have finished:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">third_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">6</span><span class="p">)</span>
-<span class="go">    Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = first_task</span>
-<span class="go">    Job  = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = second_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="making-directories-automatically-with-follows-and-mkdir">
-<span id="new-manual-follows-mkdir"></span><span id="index-4"></span><h2>Making directories automatically with <a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows</em></a> and  <a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>mkdir</em></a><a class="headerlink" href="#making-directories-automatically-with-follows-and-mkdir" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows</em></a> is also useful for making sure one or more destination directories
-exist before a task is run.</p>
-<p><em>Ruffus</em> provides special syntax to support this, using the special
-<a class="reference internal" href="../../decorators/mkdir.html#decorators-mkdir"><em>mkdir</em></a> indicator class. For example:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="hll"><span class="c">#   @follows specifies both a preceding task and a directory name</span>
-</span><span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="s">"first_task"</span><span class="p">,</span> <span class="n">mkdir</span><span class="p">(</span><span class="s">"output/results/here"</span><span class="p">))</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">second_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                        <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                         <span class="s">".output.extra.1"</span><span class="p">],</span>
-                       <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Before <tt class="docutils literal"><span class="pre">second_task()</span></tt> is run, the <tt class="docutils literal"><span class="pre">output/results/here</span></tt> directory will be created if necessary.</p>
-</div></blockquote>
-</div>
-<div class="section" id="globs-in-the-input-parameter">
-<span id="new-manual-globs-as-input"></span><span id="index-5"></span><h2>Globs in the <strong>Input</strong> parameter<a class="headerlink" href="#globs-in-the-input-parameter" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><ul class="simple">
-<li>As a syntactic convenience, <em>Ruffus</em> also allows you to specify a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> pattern (e.g. <tt class="docutils literal"><span class="pre">*.txt</span></tt>) in the
-<strong>Input</strong> parameter.</li>
-<li><a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns will be automatically specify all matching file names as the <strong>Input</strong>.</li>
-<li>Any strings within <strong>Input</strong> which contain the letters: <tt class="docutils literal"><span class="pre">*?[]</span></tt> will be treated as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> pattern.</li>
-</ul>
-<p>The first function in our initial <em>Ruffus</em> pipeline example could have been written as:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c">#</span>
-<span class="c">#   STAGE 1 fasta->sam</span>
-<span class="c">#</span>
-<span class="hll"><span class="nd">@transform</span><span class="p">(</span><span class="s">"*.fasta"</span><span class="p">,</span>                          <span class="c"># Input = glob</span>
-</span>            <span class="n">suffix</span><span class="p">(</span><span class="s">".fasta"</span><span class="p">),</span>                  <span class="c">#         suffix = .fasta</span>
-            <span class="s">".sam"</span><span class="p">)</span>                            <span class="c"># Output  suffix = .sam</span>
-<span class="k">def</span> <span class="nf">map_dna_sequence</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                    <span class="n">output_file</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="mixing-tasks-and-globs-in-the-input-parameter">
-<span id="index-6"></span><h2>Mixing Tasks and Globs in the <strong>Input</strong> parameter<a class="headerlink" href="#mixing-tasks-and-globs-in-the-input-parameter" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> patterns, references to tasks and file names strings
-can be mixed freely in (nested) python lists and tuples in the <strong>Input</strong> parameter.</p>
-<p>For example, a task function can chain to the <strong>Output</strong> from multiple upstream tasks:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">([</span><span class="n">task1</span><span class="p">,</span> <span class="n">task2</span><span class="p">,</span>                      <span class="c"># Input = multiple tasks</span>
-            <span class="s">"aa*.fasta"</span><span class="p">,</span>                               <span class="o">+</span> <span class="nb">all</span> <span class="n">files</span> <span class="n">matching</span> <span class="n">glob</span>
-            <span class="s">"zz.fasta"</span><span class="p">]</span>                                <span class="o">+</span> <span class="nb">file</span> <span class="n">name</span>
-            <span class="n">suffix</span><span class="p">(</span><span class="s">".fasta"</span><span class="p">),</span>                  <span class="c">#         suffix = .fasta</span>
-            <span class="s">".sam"</span><span class="p">)</span>                            <span class="c"># Output  suffix = .sam</span>
-<span class="k">def</span> <span class="nf">map_dna_sequence</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span>
-                    <span class="n">output_file</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>In all cases, <em>Ruffus</em> tries to do the right thing, and to make the simple or
-obvious case require the simplest, least onerous syntax.</p>
-<p>If sometimes <em>Ruffus</em> does not behave the way you expect, please write to the authors:
-it may be a bug!</p>
-<p><a class="reference internal" href="pipeline_printout.html#new-manual-pipeline-printout"><em>Chapter 5: Understanding how your pipeline works with pipeline_printout(...)</em></a>  and
-<a class="reference internal" href="command_line.html#new-manual-cmdline"><em>Chapter 6: Running Ruffus from the command line with ruffus.cmdline</em></a> will show you how to
-to make sure that your intentions are reflected in <em>Ruffus</em> code.</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 3</strong>: More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data</a><ul>
-<li><a class="reference internal" href="#review">Review</a></li>
-<li><a class="reference internal" href="#running-pipelines-in-parallel">Running pipelines in parallel</a></li>
-<li><a class="reference internal" href="#up-to-date-jobs-are-not-re-run-unnecessarily">Up-to-date jobs are not re-run unnecessarily</a></li>
-<li><a class="reference internal" href="#defining-pipeline-tasks-out-of-order">Defining pipeline tasks out of order</a></li>
-<li><a class="reference internal" href="#multiple-dependencies">Multiple dependencies</a></li>
-<li><a class="reference internal" href="#follows"><tt class="docutils literal"><span class="pre">@follows</span></tt></a></li>
-<li><a class="reference internal" href="#making-directories-automatically-with-follows-and-mkdir">Making directories automatically with <tt class="docutils literal"><span class="pre">@follows</span></tt> and  <tt class="docutils literal"><span class="pre">mkdir</span></tt></a></li>
-<li><a class="reference internal" href="#globs-in-the-input-parameter">Globs in the <strong>Input</strong> parameter</a></li>
-<li><a class="reference internal" href="#mixing-tasks-and-globs-in-the-input-parameter">Mixing Tasks and Globs in the <strong>Input</strong> parameter</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="transform.html"
-                        title="previous chapter"><strong>Chapter 2</strong>: Transforming data in a pipeline with <tt class="docutils literal"><span class="pre">@transform</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="originate.html"
-                        title="next chapter"><strong>Chapter 4</strong>: Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt></a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-           rel="nofollow">Show Source</a></li>
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
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-            
-  <div class="section" id="new-manual-transform-in-parallel-chapter-num-python-code-for-more-on-transform-ing-data">
-<span id="new-manual-transform-in-parallel-code"></span><h1><strong>Chapter 3</strong>: Python Code for More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data<a class="headerlink" href="#new-manual-transform-in-parallel-chapter-num-python-code-for-more-on-transform-ing-data" title="Permalink to this headline">¶</a></h1>
-<div class="admonition seealso">
-<p class="first admonition-title">See also</p>
-<ul class="last simple">
-<li><a class="reference internal" href="manual_contents.html#new-manual-table-of-contents"><em>Manual Table of Contents</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform syntax in detail</em></a></li>
-<li>Back to <strong>Chapter 3</strong>: <a class="reference internal" href="transform_in_parallel.html#new-manual-transform-in-parallel"><em>More on @transform-ing data and @originate</em></a></li>
-</ul>
-</div>
-<div class="section" id="producing-several-items-files-per-job">
-<h2>Producing several items / files per job<a class="headerlink" href="#producing-several-items-files-per-job" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   Create pairs of input files</span>
-<span class="c">#</span>
-<span class="n">first_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                     <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-                     <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-                     <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">],</span>
-                    <span class="p">]</span>
-
-<span class="k">for</span> <span class="n">input_file_pairs</span> <span class="ow">in</span> <span class="n">first_task_params</span><span class="p">:</span>
-    <span class="k">for</span> <span class="n">input_file</span> <span class="ow">in</span> <span class="n">input_file_pairs</span><span class="p">:</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   first task</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                        <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                         <span class="s">".output.extra.1"</span><span class="p">],</span>
-                       <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_file_pair</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-            <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   second task</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="section" id="resulting-output">
-<h3>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-<span class="go">    Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = first_task</span>
-<span class="go">    Job  = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed</span>
-<span class="go">    Job  = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed</span>
-<span class="go">    Job  = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed</span>
-<span class="go">Completed Task = second_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="defining-tasks-function-out-of-order">
-<h2>Defining tasks function out of order<a class="headerlink" href="#defining-tasks-function-out-of-order" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre> <span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#   Create pairs of input files</span>
- <span class="c">#</span>
- <span class="n">first_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                      <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-                      <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-                      <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">],</span>
-                     <span class="p">]</span>
-
- <span class="k">for</span> <span class="n">input_file_pairs</span> <span class="ow">in</span> <span class="n">first_task_params</span><span class="p">:</span>
-     <span class="k">for</span> <span class="n">input_file</span> <span class="ow">in</span> <span class="n">input_file_pairs</span><span class="p">:</span>
-         <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#   second task defined first</span>
- <span class="c">#</span>
-<span class="hll"> <span class="c">#   task name string wrapped in output_from(...)</span>
-</span> <span class="nd">@transform</span><span class="p">(</span><span class="n">output_from</span><span class="p">(</span><span class="s">"first_task"</span><span class="p">),</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-     <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#   first task</span>
- <span class="c">#</span>
- <span class="nd">@transform</span><span class="p">(</span><span class="n">first_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                         <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                          <span class="s">".output.extra.1"</span><span class="p">],</span>
-                        <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                 <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-     <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_file_pair</span><span class="p">:</span>
-         <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-             <span class="k">pass</span>
-
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#       Run</span>
- <span class="c">#</span>
- <span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="section" id="id1">
-<h3>Resulting Output<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-<span class="go">    Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = first_task</span>
-<span class="go">    Job  = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed</span>
-<span class="go">    Job  = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed</span>
-<span class="go">    Job  = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed</span>
-<span class="go">Completed Task = second_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="multiple-dependencies">
-<span id="new-manual-transform-multiple-dependencies-code"></span><h2>Multiple dependencies<a class="headerlink" href="#multiple-dependencies" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre> <span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
- <span class="kn">import</span> <span class="nn">time</span>
- <span class="kn">import</span> <span class="nn">random</span>
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#   Create pairs of input files</span>
- <span class="c">#</span>
- <span class="n">first_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                      <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-                      <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-                      <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">],</span>
-                     <span class="p">]</span>
- <span class="n">second_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                      <span class="p">[</span><span class="s">'job4.a.start'</span><span class="p">,</span> <span class="s">'job4.b.start'</span><span class="p">],</span>
-                      <span class="p">[</span><span class="s">'job5.a.start'</span><span class="p">,</span> <span class="s">'job5.b.start'</span><span class="p">],</span>
-                      <span class="p">[</span><span class="s">'job6.a.start'</span><span class="p">,</span> <span class="s">'job6.b.start'</span><span class="p">],</span>
-                     <span class="p">]</span>
-
- <span class="k">for</span> <span class="n">input_file_pairs</span> <span class="ow">in</span> <span class="n">first_task_params</span> <span class="o">+</span> <span class="n">second_task_params</span><span class="p">:</span>
-     <span class="k">for</span> <span class="n">input_file</span> <span class="ow">in</span> <span class="n">input_file_pairs</span><span class="p">:</span>
-         <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#   first task</span>
- <span class="c">#</span>
- <span class="nd">@transform</span><span class="p">(</span><span class="n">first_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                         <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                          <span class="s">".output.extra.1"</span><span class="p">],</span>
-                        <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                 <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-     <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_file_pair</span><span class="p">:</span>
-         <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-             <span class="k">pass</span>
-     <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">())</span>
-
-
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#   second task</span>
- <span class="c">#</span>
- <span class="nd">@transform</span><span class="p">(</span><span class="n">second_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                         <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                          <span class="s">".output.extra.1"</span><span class="p">],</span>
-                        <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                 <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-     <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_file_pair</span><span class="p">:</span>
-         <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-             <span class="k">pass</span>
-     <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">())</span>
-
-
-<span class="hll"> <span class="c">#---------------------------------------------------------------</span>
-</span> <span class="c">#</span>
- <span class="c">#   third task</span>
- <span class="c">#</span>
- <span class="c">#       depends on both first_task() and second_task()</span>
- <span class="nd">@transform</span><span class="p">([</span><span class="n">first_task</span><span class="p">,</span> <span class="n">second_task</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
- <span class="k">def</span> <span class="nf">third_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-     <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
- <span class="c">#---------------------------------------------------------------</span>
- <span class="c">#</span>
- <span class="c">#       Run</span>
- <span class="c">#</span>
- <span class="n">pipeline_run</span><span class="p">([</span><span class="n">third_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">6</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="section" id="id2">
-<h3>Resulting Output<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">third_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">6</span><span class="p">)</span>
-<span class="go">    Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = second_task</span>
-<span class="go">    Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = first_task</span>
-<span class="go">    Job  = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed</span>
-<span class="go">    Job  = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed</span>
-<span class="go">    Job  = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed</span>
-<span class="go">    Job  = [[job4.a.output.1, job4.a.output.extra.1] -> job4.a.output2] completed</span>
-<span class="go">    Job  = [[job5.a.output.1, job5.a.output.extra.1] -> job5.a.output2] completed</span>
-<span class="go">    Job  = [[job6.a.output.1, job6.a.output.extra.1] -> job6.a.output2] completed</span>
-<span class="go">Completed Task = third_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-<div class="section" id="multiple-dependencies-after-follows">
-<h2>Multiple dependencies after @follows<a class="headerlink" href="#multiple-dependencies-after-follows" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">time</span>
-<span class="kn">import</span> <span class="nn">random</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   Create pairs of input files</span>
-<span class="c">#</span>
-<span class="n">first_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                     <span class="p">[</span><span class="s">'job1.a.start'</span><span class="p">,</span> <span class="s">'job1.b.start'</span><span class="p">],</span>
-                     <span class="p">[</span><span class="s">'job2.a.start'</span><span class="p">,</span> <span class="s">'job2.b.start'</span><span class="p">],</span>
-                     <span class="p">[</span><span class="s">'job3.a.start'</span><span class="p">,</span> <span class="s">'job3.b.start'</span><span class="p">],</span>
-                    <span class="p">]</span>
-<span class="n">second_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                     <span class="p">[</span><span class="s">'job4.a.start'</span><span class="p">,</span> <span class="s">'job4.b.start'</span><span class="p">],</span>
-                     <span class="p">[</span><span class="s">'job5.a.start'</span><span class="p">,</span> <span class="s">'job5.b.start'</span><span class="p">],</span>
-                     <span class="p">[</span><span class="s">'job6.a.start'</span><span class="p">,</span> <span class="s">'job6.b.start'</span><span class="p">],</span>
-                    <span class="p">]</span>
-
-<span class="k">for</span> <span class="n">input_file_pairs</span> <span class="ow">in</span> <span class="n">first_task_params</span> <span class="o">+</span> <span class="n">second_task_params</span><span class="p">:</span>
-    <span class="k">for</span> <span class="n">input_file</span> <span class="ow">in</span> <span class="n">input_file_pairs</span><span class="p">:</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   first task</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                        <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-<span class="hll">                         <span class="s">".output.extra.1"</span><span class="p">],</span>
-</span>                       <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_file_pair</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-            <span class="k">pass</span>
-    <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">())</span>
-
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   second task</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="s">"first_task"</span><span class="p">)</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">second_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".start"</span><span class="p">),</span>
-                        <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                         <span class="s">".output.extra.1"</span><span class="p">],</span>
-                       <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pair</span><span class="p">,</span>
-                <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_file_pair</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span>
-            <span class="k">pass</span>
-    <span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">())</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   third task</span>
-<span class="c">#</span>
-<span class="c">#       depends on both first_task() and second_task()</span>
-<span class="nd">@transform</span><span class="p">([</span><span class="n">first_task</span><span class="p">,</span> <span class="n">second_task</span><span class="p">],</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">third_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">):</span> <span class="k">pass</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">third_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">6</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="section" id="resulting-output-first-task-completes-before-second-task">
-<h3>Resulting Output: <tt class="docutils literal"><span class="pre">first_task</span></tt> completes before <tt class="docutils literal"><span class="pre">second_task</span></tt><a class="headerlink" href="#resulting-output-first-task-completes-before-second-task" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">third_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">6</span><span class="p">)</span>
-<span class="go">    Job  = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = first_task</span>
-<span class="go">    Job  = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = second_task</span>
-<span class="go">    Job  = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed</span>
-<span class="go">    Job  = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed</span>
-<span class="go">    Job  = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed</span>
-<span class="go">    Job  = [[job4.a.output.1, job4.a.output.extra.1] -> job4.a.output2] completed</span>
-<span class="go">    Job  = [[job5.a.output.1, job5.a.output.extra.1] -> job5.a.output2] completed</span>
-<span class="go">    Job  = [[job6.a.output.1, job6.a.output.extra.1] -> job6.a.output2] completed</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#"><strong>Chapter 3</strong>: Python Code for More on <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data</a><ul>
-<li><a class="reference internal" href="#producing-several-items-files-per-job">Producing several items / files per job</a><ul>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#defining-tasks-function-out-of-order">Defining tasks function out of order</a><ul>
-<li><a class="reference internal" href="#id1">Resulting Output</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#multiple-dependencies">Multiple dependencies</a><ul>
-<li><a class="reference internal" href="#id2">Resulting Output</a></li>
-</ul>
-</li>
-<li><a class="reference internal" href="#multiple-dependencies-after-follows">Multiple dependencies after @follows</a><ul>
-<li><a class="reference internal" href="#resulting-output-first-task-completes-before-second-task">Resulting Output: <tt class="docutils literal"><span class="pre">first_task</span></tt> completes before <tt class="docutils literal"><span class="pre">second_task</span></tt></a></li>
-</ul>
-</li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="transform_code.html"
-                        title="previous chapter"><strong>Chapter 1</strong>: Python Code for Transforming data in a pipeline with <tt class="docutils literal"><span class="pre">@transform</span></tt></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="originate_code.html"
-                        title="next chapter"><strong>Chapter 4</strong>: Python Code for Creating files with <tt class="docutils literal"><span class="pre">@originate</span></tt></a></p>
-  <h3>This Page</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
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-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
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-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-  <div class="section" id="a-simple-tutorial-8-steps-to-ruffus">
-<span id="simple-tutorial"></span><h1>A simple tutorial: 8 steps to <em>Ruffus</em><a class="headerlink" href="#a-simple-tutorial-8-steps-to-ruffus" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="table-of-contents">
-<h2>Table of Contents<a class="headerlink" href="#table-of-contents" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="features">
-<h3>Features<a class="headerlink" href="#features" title="Permalink to this headline">¶</a></h3>
-<p>The <strong>Ruffus</strong> provides automatic support for</p>
-<blockquote>
-<div><blockquote>
-<div><ul class="simple">
-<li>Managing dependencies</li>
-<li>Parallel jobs</li>
-<li>Re-starting from arbitrary points, especially after errors</li>
-<li>Display of the pipeline as a flowchart</li>
-<li>Reporting</li>
-</ul>
-</div></blockquote>
-<div class="line-block">
-<div class="line">This tutorial has seven steps which cover all the core functionality of <em>Ruffus</em>.</div>
-<div class="line">Don’t worry if steps 1 and 2 seem a bit slow: Once you get used to <strong>Ruffus</strong>
-steps 4-8 will be a breeze.</div>
-</div>
-<p>You can click on “previous” and “next” at the top and bottom of each page to
-navigate through the tutorial.</p>
-</div></blockquote>
-</div>
-<div class="section" id="the-first-steps-1-4">
-<h3>The first steps (1-4)<a class="headerlink" href="#the-first-steps-1-4" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The first half of the tutorial will show you how to:</p>
-<ol class="arabic simple">
-<li><a class="reference internal" href="step1_follows.html#simple-tutorial-1st-step"><em>Chain tasks (functions) together into a pipeline</em></a></li>
-<li><a class="reference internal" href="step2.html#simple-tutorial-2nd-step"><em>Provide parameters to run jobs in parallel</em></a></li>
-<li><a class="reference internal" href="step3_run_pipeline.html#simple-tutorial-3rd-step"><em>Tracing through your new pipeline</em></a></li>
-<li><a class="reference internal" href="step4_run_pipeline_graphically.html#simple-tutorial-4th-step-graphical"><em>Using flowcharts</em></a></li>
-</ol>
-</div></blockquote>
-</div>
-<div class="section" id="a-worked-example-steps-5-8">
-<h3>A worked example (steps 5-8)<a class="headerlink" href="#a-worked-example-steps-5-8" title="Permalink to this headline">¶</a></h3>
-<blockquote>
-<div><p>The second half of the tutorial is a worked example to calculate
-the sample variance of 10,000 random numbers. This shows you how to:</p>
-<ol class="arabic simple" start="5">
-<li><a class="reference internal" href="step5_split.html#simple-tutorial-5th-step"><em>Split up a large problem into smaller chunks</em></a></li>
-<li><a class="reference internal" href="step6_transform.html#simple-tutorial-6th-step"><em>Calculate partial solutions in parallel</em></a></li>
-<li><a class="reference internal" href="step7_merge.html#simple-tutorial-7th-step"><em>Re-combine the partial solutions into the final result</em></a></li>
-<li><a class="reference internal" href="step8_posttask.html#simple-tutorial-8th-step"><em>Automatically signal the completion of each step of our pipeline</em></a></li>
-</ol>
-<p>This covers the core functionality of <em>Ruffus</em>.</p>
-</div></blockquote>
-</div>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">A simple tutorial: 8 steps to <em>Ruffus</em></a><ul>
-<li><a class="reference internal" href="#table-of-contents">Table of Contents</a><ul>
-<li><a class="reference internal" href="#features">Features</a></li>
-<li><a class="reference internal" href="#the-first-steps-1-4">The first steps (1-4)</a></li>
-<li><a class="reference internal" href="#a-worked-example-steps-5-8">A worked example (steps 5-8)</a></li>
-</ul>
-</li>
-</ul>
-</li>
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-  <h4>Previous topic</h4>
-  <p class="topless"><a href="../../recipes.html"
-                        title="previous chapter">Recipes</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step1_follows.html"
-                        title="next chapter">Step 1: An introduction to Ruffus pipelines</a></p>
-  <h3>This Page</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
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diff --git a/doc/_build/html/tutorials/simple_tutorial/simple_tutorial_code.html b/doc/_build/html/tutorials/simple_tutorial/simple_tutorial_code.html
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-        <div class="bodywrapper">
-          <div class="body">
-            
-  <div class="section" id="code-for-the-simple-tutorial-8-steps-to-ruffus">
-<span id="simple-tutorial-code"></span><h1>Code for the simple tutorial: 8 steps to <em>Ruffus</em><a class="headerlink" href="#code-for-the-simple-tutorial-8-steps-to-ruffus" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>A simple tutorial</em></a></li>
-</ul>
-</div></blockquote>
-<div class="section" id="table-of-contents">
-<h2>Table of Contents<a class="headerlink" href="#table-of-contents" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><a class="reference internal" href="step1_follows.html#simple-tutorial-1st-step"><em>Chain tasks (functions) together into a pipeline</em></a>
-<a class="reference internal" href="step2.html#simple-tutorial-2nd-step"><em>Provide parameters to run jobs in parallel</em></a>
-<a class="reference internal" href="step3_run_pipeline.html#simple-tutorial-3rd-step"><em>Tracing through your new pipeline</em></a>
-<a class="reference internal" href="step4_run_pipeline_graphically.html#simple-tutorial-4th-step-graphical"><em>Using flowcharts</em></a>
-<a class="reference internal" href="step5_split.html#simple-tutorial-5th-step"><em>Split up a large problem into smaller chunks</em></a>
-<a class="reference internal" href="step6_transform.html#simple-tutorial-6th-step"><em>Calculate partial solutions in parallel</em></a>
-<a class="reference internal" href="step7_merge.html#simple-tutorial-7th-step"><em>Re-combine the partial solutions into the final result</em></a>
-<a class="reference internal" href="step8_posttask.html#simple-tutorial-8th-step"><em>Automatically signal the completion of each step of our pipeline</em></a></div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
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-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for the simple tutorial: 8 steps to <em>Ruffus</em></a><ul>
-<li><a class="reference internal" href="#table-of-contents">Table of Contents</a></li>
-</ul>
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-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="../manual/manual_code.html"
-                        title="previous chapter">Code for the manual tutorial</a></p>
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-                        title="next chapter">Ruffus Decorators</a></p>
-  <h3>This Page</h3>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
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-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
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-  <blockquote id="simple-tutorial-1st-step">
-<div><ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-</ul>
-</div></blockquote>
-<div class="section" id="step-1-an-introduction-to-ruffus-pipelines">
-<h1>Step 1: An introduction to Ruffus pipelines<a class="headerlink" href="#step-1-an-introduction-to-ruffus-pipelines" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="overview">
-<h2>Overview<a class="headerlink" href="#overview" title="Permalink to this headline">¶</a></h2>
-<blockquote>
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-</svg><p>Computational pipelines transform your data in stages until the final result is produced. One easy way to understand pipelines is by imagining your data flowing across a series of pipes until it reaches its final destination. Even quite complicated processes can be simplified if we broke things down into simple stages. Of course, it helps if we can visualise the whole process.</p>
-<p>Ruffus is a way of automating the plumbing in your pipeline: You supply the python functions which perform the data transformation, and tell Ruffus how these pipeline <tt class="docutils literal"><span class="pre">task</span></tt> functions are connected up. Ruffus will make sure that the right data flows down your pipeline in the right way at the right time.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Ruffus refers to each stage of your pipeline as a <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a>.</p>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="a-gentle-introduction-to-ruffus-syntax">
-<h2>A gentle introduction to Ruffus syntax<a class="headerlink" href="#a-gentle-introduction-to-ruffus-syntax" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="line-block">
-<div class="line">Let us start with the usual “Hello World” programme.</div>
-<div class="line">We have the following two python functions which
-we would like to turn into an automatic pipeline:</div>
-</div>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="k">def</span> <span class="nf">first_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"Hello "</span>
-
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"world"</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The simplest <strong>Ruffus</strong> pipeline would look like this:</p>
-<blockquote>
-<div></div></blockquote>
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-The role of <strong>Ruffus</strong> is to make sure these functions are called in the right order,
-with the right parameters, running in parallel using multiprocessing if desired.</p>
-<p>There are three simple parts to building a <strong>ruffus</strong> pipeline</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>importing ruffus</li>
-<li>“Decorating” functions which are part of the pipeline</li>
-<li>Running the pipeline!</li>
-</ol>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="decorators">
-<span id="index-0"></span><h2>“Decorators”<a class="headerlink" href="#decorators" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>You need to tag or <a class="reference internal" href="../../glossary.html#term-decorator"><em class="xref std std-term">decorator</em></a> existing code to tell <strong>Ruffus</strong> that they are part
-of the pipeline.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>python <a class="reference internal" href="../../glossary.html#term-decorator"><em class="xref std std-term">decorator</em></a>s are ways to tag or mark out functions.</p>
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-<div class="line">Multiple <a class="reference internal" href="../../glossary.html#term-decorator"><em class="xref std std-term">decorator</em></a>s can be used for each <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function to add functionality
-to <em>Ruffus</em> pipeline functions.</div>
-<div class="line">However, the decorated python functions can still be
-called normally, outside of <em>Ruffus</em>.</div>
-<div class="line"><em>Ruffus</em> <a class="reference internal" href="../../glossary.html#term-decorator"><em class="xref std std-term">decorator</em></a>s can be added to (stacked on top of) any function in any order.</div>
-</div>
-<ul class="simple">
-<li><a class="reference internal" href="../manual/follows.html#manual-follows"><em>More on @follows in the in the Ruffus `Manual</em></a></li>
-<li><a class="reference internal" href="../../decorators/follows.html#decorators-follows"><em>@follows syntax in detail</em></a></li>
-</ul>
-</div></blockquote>
-</div>
-<div class="section" id="running-the-pipeline">
-<span id="index-1"></span><h2>Running the pipeline<a class="headerlink" href="#running-the-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>We run the pipeline by specifying the <strong>last</strong> stage (<a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function) of your pipeline.
-Ruffus will know what other functions this depends on, following the appropriate chain of
-dependencies automatically, making sure that the entire pipeline is up-to-date.</p>
-<p>Because <tt class="docutils literal"><span class="pre">second_task</span></tt> depends on <tt class="docutils literal"><span class="pre">first_task</span></tt>, both functions are executed in order.</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Ruffus by default prints out the <tt class="docutils literal"><span class="pre">verbose</span></tt> progress through the pipelined code,
-interleaved with the <strong>Hello</strong> printed by <tt class="docutils literal"><span class="pre">first_task</span></tt> and <strong>World</strong> printed
-by <tt class="docutils literal"><span class="pre">second_task</span></tt>.</p>
-<blockquote>
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-
-
-          </div>
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-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Step 1: An introduction to Ruffus pipelines</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#a-gentle-introduction-to-ruffus-syntax">A gentle introduction to Ruffus syntax</a></li>
-<li><a class="reference internal" href="#decorators">“Decorators”</a></li>
-<li><a class="reference internal" href="#running-the-pipeline">Running the pipeline</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="simple_tutorial.html"
-                        title="previous chapter">A simple tutorial: 8 steps to <em>Ruffus</em></a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step2.html"
-                        title="next chapter">Step 2: <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data in a pipeline</a></p>
-  <h3>This Page</h3>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
-        </ul>
-
-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
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-  <span class="target" id="simple-tutorial-2nd-step"></span><div class="section" id="step-2-transform-ing-data-in-a-pipeline">
-<span id="index-0"></span><h1>Step 2: <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data in a pipeline<a class="headerlink" href="#step-2-transform-ing-data-in-a-pipeline" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform syntax in detail</em></a></li>
-</ul>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="step2_code.html#simple-tutorial-2nd-step-code"><em>Python Code for step 2</em></a></li>
-</ul>
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-</svg><p>Computational pipelines transform your data in stages until the final result is produced.
-Ruffus automates the plumbing in your pipeline. You supply the python functions which perform the data transformation,
-and tell Ruffus how these pipeline stages or <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> functions are connected together.</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><strong>The best way to design a pipeline is to:</strong></p>
-<blockquote class="last">
-<div><ul class="simple">
-<li><strong>write down the file names of the data as it flows across your pipeline</strong></li>
-<li><strong>write down the names of functions which transforms the data at each stage of the pipeline.</strong></li>
-</ul>
-</div></blockquote>
-</div>
-<p>By letting <strong>Ruffus</strong> manage your pipeline parameters, you will get the following features
-for free:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>only out-of-date parts of the pipeline will be re-run</li>
-<li>multiple jobs can be run in parallel (on different processors if possible)</li>
-<li>pipeline stages can be chained together automatically</li>
-</ol>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="transform">
-<h2>@transform<a class="headerlink" href="#transform" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Let us start with the simplest pipeline with a single <em>input</em> data file <strong>transform</strong>ed
-into a single <em>output</em> file. We will add some arbitrary extra parameters as well.</p>
-<p>The <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> decorator tells Ruffus that this
-task function <strong>transforms</strong> each and every piece of input data into a corresponding output.</p>
-<blockquote>
-<div>In other words, inputs and outputs have a <strong>1 to 1</strong> relationship.</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>In the second part of the tutorial, we will encounter more decorators which can <em>split up</em>, or <em>join together</em> or <em>group</em> inputs.</p>
-<blockquote class="last">
-<div>In other words, inputs and output can have <strong>many to one</strong>, <strong>many to many</strong> etc. relationships.</div></blockquote>
-</div>
-<p>Let us provide <strong>input</strong>s and <strong>output</strong>s to our new pipeline:</p>
-<blockquote>
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-  <text x="22.156881" y="166.77328" transform="scale(1.0042467,0.99577126)" id="text3319" xml:space="preserve" style="font-size:9.89657974px;font-family:monospace"><tspan id="tspan3321" style="fill:#808080">#   make sure the input file is there</tspan></text>
-  <text x="22.156881" y="180.20436" transform="scale(1.0042467,0.99577126)" id="text3323" xml:space="preserve" style="font-size:9.89657974px;font-family:monospace"><tspan id="tspan3325" style="fill:#007020">open</tspan>('job1.input', "w")</text>
-  <text x="22.156881" y="199.1844" transform="scale(1.0042467,0.99577126)" id="text3329" xml:space="preserve" style="font-size:9.89657974px;font-family:monospace">pipeline_run([first_task])</text>
-  <path d="m 11.798134,17.75418 0,40.879392 11.506636,16.489166" id="path3696" style="fill:none;stroke:#ff0000;stroke-width:1.25536001;stroke-linecap:butt;stroke-linejoin:bevel;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-end:url(#Arrow2Mend)" />
-</svg><p>The <tt class="docutils literal"><span class="pre">@transform</span></tt> decorator tells Ruffus to generate the appropriate arguments for our python function:</p>
-<blockquote>
-<div><ul class="simple">
-<li>The input file name is as given: <tt class="docutils literal"><span class="pre">job1.input</span></tt></li>
-<li>The output file name is the input file name with its <strong>suffix</strong> of <tt class="docutils literal"><span class="pre">.input</span></tt> replaced with <tt class="docutils literal"><span class="pre">.output1</span></tt></li>
-<li>There are two extra parameters, a string and a number.</li>
-</ul>
-</div></blockquote>
-<p>This is exactly equivalent to the following function call:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">first_task</span><span class="p">(</span><span class="s">'job1.input'</span><span class="p">,</span> <span class="s">'job1.output1'</span><span class="p">,</span> <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Even though this (empty) function doesn’t do anything just yet, the output from <strong>Ruffus</strong> <tt class="docutils literal"><span class="pre">pipeline_run</span></tt> will show that that this part of the pipeline completed successfully:</p>
-<blockquote>
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-    <text x="92.396126" y="13.742188" id="text3643" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Inputs</text>
-    <text x="193.83928" y="13.742188" id="text3673" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Outputs</text>
-    <text x="256.93237" y="13.742188" id="text3657" style="font-size:12px;fill:#00a14b;font-family:ArialMT">Extra parameters</text>
-    <text x="9.3237839" y="40.037392" id="text3040" xml:space="preserve" style="font-size:10.32079887px;font-family:monospace"><tspan id="tspan3042" style="font-weight:bold;fill:#ff0000">>>></tspan> pipeline_run([first_task])</text>
-    <text x="9.3237839" y="54.044189" id="text3046" xml:space="preserve" style="font-size:10.32079887px;font-family:monospace">    Job  <tspan id="tspan3048" style="fill:#666666">=</tspan> [job1<tspan id="tspan3050" style="fill:#666666">.</tspan>input <tspan id="tspan3052" style="fill:#666666">-></tspan> job1<tspan id="tspan3056" style="fill:#666666">.</tspan>output1,</text>
-    <text x="58.633194" y="67.193367" id="text3160" xml:space="preserve" style="font-size:10.32079887px;font-family:monospace">    some_extra.string.for_example, 14] completed</text>
-    <text x="9.3237839" y="82.432899" id="text3058" xml:space="preserve" style="font-size:10.32079887px;font-family:monospace">Completed Task <tspan id="tspan3060" style="fill:#666666">=</tspan> first_task</text>
-    </svg></div></blockquote>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="task-functions-as-recipes">
-<h2>Task functions as recipes<a class="headerlink" href="#task-functions-as-recipes" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>This may seem like a lot of effort and complication for something so simple: a normal python function call.
-However, now that we have annotated a task, we can start using it as part of our computational pipeline:</p>
-<p>Each <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> function of the pipeline is a recipe or
-<a class="reference external" href="http://www.gnu.org/software/make/manual/make.html#Rule-Introduction">rule</a>
-which can be applied repeatedly to our data.</p>
-<p>For example, one can have</p>
-<blockquote>
-<div><ul class="simple">
-<li>a <tt class="docutils literal"><span class="pre">compile()</span></tt> <em>task</em> which will compile any number of source code files, or</li>
-<li>a <tt class="docutils literal"><span class="pre">count_lines()</span></tt> <em>task</em> which will count the number of lines in any file or</li>
-<li>an <tt class="docutils literal"><span class="pre">align_dna()</span></tt> <em>task</em> which will align the DNA of many chromosomes.</li>
-</ul>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p><strong>Key Ruffus Terminology</strong>:</p>
-<p>A  <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> is an annotated python function which represents a recipe or stage of your pipeline.</p>
-<p>A  <a class="reference internal" href="../../glossary.html#term-job"><em class="xref std std-term">job</em></a> is each time your recipe is applied to a piece of data, i.e. each time Ruffus calls your function.</p>
-<p class="last">Each <strong>task</strong> or pipeline recipe can thus have many <strong>jobs</strong> each of which can work in parallel on different data.</p>
-</div>
-<p>In the original example, we have made a single output file by supplying a single input parameter.
-We shall use much the same syntax to apply the same recipe to <em>multiple</em> input files.
-Instead of providing a single <em>input</em>, and a single <em>output</em>, we are going to specify
-the parameters for <em>three</em> jobs at once:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="c"># previously,</span>
-<span class="c"># first_task_params = 'job1.input'</span>
-<span class="n">first_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="s">'job1.input'</span><span class="p">,</span>
-                    <span class="s">'job2.input'</span>
-                    <span class="s">'job3.input'</span>
-                    <span class="p">]</span>
-
-<span class="c"># make sure the input files are there</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">'job1.input'</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">'job2.input'</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">'job3.input'</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">first_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>Just by changing the inputs from a single file to a list of three files, we now have a pipeline which runs independently on three pieces of data.
-The results should look familiar:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">first_task</span><span class="p">])</span>
-<span class="go">    Job  = [job1.input -> job1.output1,</span>
-<span class="go">            some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [job2.input -> job2.output1,</span>
-<span class="go">            some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [job3.input -> job3.output1,</span>
-<span class="go">            some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = first_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="multiple-steps">
-<h2>Multiple steps<a class="headerlink" href="#multiple-steps" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Best of all, it is easy to add another step to our initial pipeline.</p>
-<p>We have to</p>
-<blockquote>
-<div><ul class="simple">
-<li>add another <tt class="docutils literal"><span class="pre">@transform</span></tt> decorated function (<tt class="docutils literal"><span class="pre">second_task()</span></tt>),</li>
-<li>specify <tt class="docutils literal"><span class="pre">first_task()</span></tt> as the source:</li>
-<li>use a <tt class="docutils literal"><span class="pre">suffix</span></tt> which matches the output from <tt class="docutils literal"><span class="pre">first_task()</span></tt></li>
-</ul>
-<div class="highlight-python"><div class="highlight"><pre><span class="nd">@transform</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="c"># make output file</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-</pre></div>
-</div>
-<ul class="simple">
-<li>call <tt class="docutils literal"><span class="pre">pipeline_run()</span></tt> with the correct final task (<tt class="docutils literal"><span class="pre">second_task()</span></tt>)</li>
-</ul>
-</div></blockquote>
-<p>The full source code can be found <a class="reference internal" href="step2_code.html#simple-tutorial-2nd-step-code"><em>here</em></a></p>
-<p>With very little effort, we now have three independent pieces of information coursing through our pipeline.
-Because <tt class="docutils literal"><span class="pre">second_task()</span></tt> <em>transforms</em> the output from <tt class="docutils literal"><span class="pre">first_task()</span></tt>, it magically knows its dependencies and
-that it too has to work on three jobs.</p>
-</div></blockquote>
-</div>
-<div class="section" id="multi-tasking">
-<h2>Multi-tasking<a class="headerlink" href="#multi-tasking" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Though, three jobs have been specified in parallel, <strong>Ruffus</strong> defaults to running
-each of them successively. With modern CPUs, it is often a lot faster to run parts
-of your pipeline in parallel, all at the same time.</p>
-<p>To do this, all you have to do is to add a multiprocess parameter to pipeline_run:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">],</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>In this case, ruffus will try to run up to 5 jobs at the same time. Since our second
-task only has three jobs, these will be started simultaneously.</p>
-</div></blockquote>
-</div>
-<div class="section" id="up-to-date-jobs-are-not-re-run-unnecessarily">
-<h2>Up-to-date jobs are not re-run unnecessarily<a class="headerlink" href="#up-to-date-jobs-are-not-re-run-unnecessarily" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>A job will be run only if the output file timestamps are out of date.
-If you ran the same code a second time,</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<dl class="docutils">
-<dt>Nothing would happen because:</dt>
-<dd><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">job1.output2</span></tt> is more recent than <tt class="docutils literal"><span class="pre">job1.output1</span></tt> and</li>
-<li><tt class="docutils literal"><span class="pre">job2.output2</span></tt> is more recent than <tt class="docutils literal"><span class="pre">job2.output1</span></tt> and</li>
-<li><tt class="docutils literal"><span class="pre">job3.output2</span></tt> is more recent than <tt class="docutils literal"><span class="pre">job3.output1</span></tt>.</li>
-</ul>
-</dd>
-<dt>Let us see what happens when just 1 out of 3 pieces of data is modified</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="nb">open</span><span class="p">(</span><span class="s">"job1.input1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>You would see that only the out of date jobs (highlighted) have been re-run:</p>
-<blockquote>
-<div><div class="highlight-pycon"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">multiprocess</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-<span class="hll"><span class="go">    Job  = [job1.input -> job1.output1, some_extra.string.for_example, 14] completed</span>
-</span><span class="go">    Job  = [job3.input -> job3.output1, some_extra.string.for_example, 14] unnecessary: already up to date</span>
-<span class="go">    Job  = [job2.input -> job2.output1, some_extra.string.for_example, 14] unnecessary: already up to date</span>
-<span class="go">Completed Task = first_task</span>
-<span class="hll"><span class="go">    Job  = [job1.output1 -> job1.output2] completed</span>
-</span><span class="go">    Job  = [job2.output1 -> job2.output2] unnecessary: already up to date</span>
-<span class="go">    Job  = [job3.output1 -> job3.output2] unnecessary: already up to date</span>
-<span class="go">Completed Task = second_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="intermediate-files">
-<span id="index-1"></span><h2>Intermediate files<a class="headerlink" href="#intermediate-files" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>In the above examples, the <em>input</em> and <em>output</em> parameters are file names.
-Ruffus was designed for pipelines which save intermediate data in files. This is not
-compulsory but saving your data in files at each step provides a few advantages:</p>
-<blockquote>
-<div><ol class="arabic simple">
-<li>Ruffus can use file system time stamps to check if your pipeline is up to date</li>
-<li>Your data is persistent across runs</li>
-<li>This is a good way to pass large amounts of data across processes and computational nodes</li>
-</ol>
-</div></blockquote>
-<p>Otherwise, task parameters could be all sorts of data, from lists of files, to numbers,
-sets or tuples. Ruffus imposes few constraints on what <em>you</em>
-would like to send to each stage of your pipeline.</p>
-<p><strong>Ruffus</strong> does, however, assume that all strings in your <em>input</em> and <em>output</em>
-parameters represent file names.</p>
-<p><em>input</em> parameters which contains a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a> pattern (e.g. <tt class="docutils literal"><span class="pre">*.txt</span></tt>) are expanded to the matching file names.</p>
-</div></blockquote>
-</div>
-<div class="section" id="transform-is-a-1-to-1-operation">
-<h2>@transform is a 1 to 1 operation<a class="headerlink" href="#transform-is-a-1-to-1-operation" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><tt class="docutils literal"><span class="pre">@transform</span></tt> is a 1:1 operation because it keeps the number of jobs constant
-entering and leaving the task. Each job can accept, for example, a pair of files as its input,
-or generate more than one output files.</p>
-<dl class="docutils">
-<dt>Let us see this in action using the previous example:</dt>
-<dd><ul class="first">
-<li><p class="first"><tt class="docutils literal"><span class="pre">first_task_params</span></tt> is changed to 3 <em>pairs</em> of file names</p>
-</li>
-<li><dl class="first docutils">
-<dt><tt class="docutils literal"><span class="pre">@transform</span></tt> for <tt class="docutils literal"><span class="pre">first_task</span></tt> is modified to produce <em>pairs</em> of file names</dt>
-<dd><ul class="first last simple">
-<li><tt class="docutils literal"><span class="pre">.output.1</span></tt></li>
-<li><tt class="docutils literal"><span class="pre">.output.extra.1</span></tt></li>
-</ul>
-</dd>
-</dl>
-</li>
-</ul>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   Create pairs of input files</span>
-<span class="c">#</span>
-<span class="n">first_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                     <span class="p">[</span><span class="s">'job1.a.input'</span><span class="p">,</span> <span class="s">'job1.b.input'</span><span class="p">],</span>
-                     <span class="p">[</span><span class="s">'job2.a.input'</span><span class="p">,</span> <span class="s">'job2.b.input'</span><span class="p">],</span>
-                     <span class="p">[</span><span class="s">'job3.a.input'</span><span class="p">,</span> <span class="s">'job3.b.input'</span><span class="p">],</span>
-                    <span class="p">]</span>
-
-<span class="k">for</span> <span class="n">input_file_pairs</span> <span class="ow">in</span> <span class="n">first_task_params</span><span class="p">:</span>
-    <span class="k">for</span> <span class="n">input_file</span> <span class="ow">in</span> <span class="n">input_file_pairs</span><span class="p">:</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   first task</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".input"</span><span class="p">),</span>
-                        <span class="p">[</span><span class="s">".output.1"</span><span class="p">,</span>
-                         <span class="s">".output.extra.1"</span><span class="p">],</span>
-                       <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file_pairs</span><span class="p">,</span>
-                <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-    <span class="c"># make both pairs of output files</span>
-    <span class="k">for</span> <span class="n">output_file</span> <span class="ow">in</span> <span class="n">output_file_pairs</span><span class="p">:</span>
-        <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   second task</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output.1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_files</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="c"># make output file</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-</pre></div>
-</div>
-<p>This gives the following results:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">pipeline_task</span><span class="p">])</span>
-</pre></div>
-</div>
-<p class="last">We see that apart from having a file pair where previously there was a single file,
-little else has changed. We still have three pieces of data going through the
-pipeline in three parallel jobs.</p>
-</dd>
-</dl>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Step 2: <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data in a pipeline</a><ul>
-<li><a class="reference internal" href="#overview">Overview</a></li>
-<li><a class="reference internal" href="#transform">@transform</a></li>
-<li><a class="reference internal" href="#task-functions-as-recipes">Task functions as recipes</a></li>
-<li><a class="reference internal" href="#multiple-steps">Multiple steps</a></li>
-<li><a class="reference internal" href="#multi-tasking">Multi-tasking</a></li>
-<li><a class="reference internal" href="#up-to-date-jobs-are-not-re-run-unnecessarily">Up-to-date jobs are not re-run unnecessarily</a></li>
-<li><a class="reference internal" href="#intermediate-files">Intermediate files</a></li>
-<li><a class="reference internal" href="#transform-is-a-1-to-1-operation">@transform is a 1 to 1 operation</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step1_follows.html"
-                        title="previous chapter">Step 1: An introduction to Ruffus pipelines</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step3_run_pipeline.html"
-                        title="next chapter">Step 3: Understanding how your pipeline works</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/simple_tutorial/step2.txt"
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-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-  <div class="section" id="code-for-step-2-passing-parameters-to-the-pipeline">
-<span id="simple-tutorial-2nd-step-code"></span><h1>Code for Step 2: Passing parameters to the pipeline<a class="headerlink" href="#code-for-step-2-passing-parameters-to-the-pipeline" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Up</em></a></li>
-<li><a class="reference internal" href="step2.html#simple-tutorial-2nd-step"><em>Back</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform syntax</em></a> in detail</li>
-</ul>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#   Create input files</span>
-<span class="c">#</span>
-<span class="n">first_task_params</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="s">'job1.input'</span><span class="p">,</span>
-                    <span class="s">'job2.input'</span><span class="p">,</span>
-                    <span class="s">'job3.input'</span>
-                    <span class="p">]</span>
-
-<span class="k">for</span> <span class="n">input_file</span> <span class="ow">in</span> <span class="n">first_task_params</span><span class="p">:</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   first task</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task_params</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".input"</span><span class="p">),</span> <span class="s">".output1"</span><span class="p">,</span>
-                       <span class="s">"some_extra.string.for_example"</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span>
-                <span class="n">extra_parameter_str</span><span class="p">,</span> <span class="n">extra_parameter_num</span><span class="p">):</span>
-    <span class="c"># make output file</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   second task</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">first_task</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".output1"</span><span class="p">),</span> <span class="s">".output2"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="c"># make output file</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-</pre></div>
-</div>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-<span class="go">    Job  = [job1.input -> job1.output1, some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [job2.input -> job2.output1, some_extra.string.for_example, 14] completed</span>
-<span class="go">    Job  = [job3.input -> job3.output1, some_extra.string.for_example, 14] completed</span>
-<span class="go">Completed Task = first_task</span>
-<span class="go">    Job  = [job1.output1 -> job1.output2] completed</span>
-<span class="go">    Job  = [job2.output1 -> job2.output2] completed</span>
-<span class="go">    Job  = [job3.output1 -> job3.output2] completed</span>
-<span class="go">Completed Task = second_task</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
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-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Step 2: Passing parameters to the pipeline</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="../manual/transform_code.html"
-                        title="previous chapter">Code for Chapter 6: Applying the same recipe to create many different files</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step3_run_pipeline_code.html"
-                        title="next chapter">Code for Step 3: Displaying the pipeline visually</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/simple_tutorial/step2_code.txt"
-           rel="nofollow">Show Source</a></li>
-  </ul>
-    
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-    <form class="search" action="../../search.html" method="get">
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
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-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
-    </ul>
-
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-  <div class="section" id="step-3-understanding-how-your-pipeline-works">
-<span id="simple-tutorial-3rd-step"></span><h1>Step 3: Understanding how your pipeline works<a class="headerlink" href="#step-3-understanding-how-your-pipeline-works" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions"><em>pipeline functions</em></a> in detail</li>
-</ul>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="step3_run_pipeline_code.html#simple-tutorial-3nd-step-code"><em>Python Code for step 3</em></a></li>
-</ul>
-</div>
-<p id="index-0">The trickiest part of developing pipelines is understanding how your
-data flows through the pipeline.</p>
-<p>Parameters and files are passed from one task to another down the chain
-of pipelined functions.</p>
-<p>Whether you are learning how to use <strong>ruffus</strong>, or trying out a new
-feature in <strong>ruffus</strong>, or just have a horrendously complicated pipeline
-to debug (we have colleagues with >100 criss-crossing pipelined stages),
-your best friend is <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a></p>
-<div class="section" id="printing-out-which-jobs-will-be-run">
-<h2>Printing out which jobs will be run<a class="headerlink" href="#printing-out-which-jobs-will-be-run" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> takes the same parameters as pipeline_run but just prints
-the tasks which are and are not up-to-date.</p>
-<p>The <tt class="docutils literal"><span class="pre">verbose</span></tt> parameter controls how much detail is displayed.</p>
-<p>Let us take the two step <a class="reference internal" href="step3_run_pipeline_code.html#simple-tutorial-3nd-step-code"><em>pipelined code</em></a> we have previously written,
-but call <a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-printout"><em>pipeline_printout(...)</em></a> instead of
-<a class="reference internal" href="../../pipeline_functions.html#pipeline-functions-pipeline-run"><em>pipeline_run(...)</em></a>.
-This lists the tasks which will be run in the pipeline:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_pipeline_printout11.png" src="../../_images/simple_tutorial_pipeline_printout11.png" />
-</div></blockquote>
-<p>To see the input and output parameters of each job in the pipeline, we can increase the verbosity from the default (1) to 3:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_pipeline_printout21.png" src="../../_images/simple_tutorial_pipeline_printout21.png" />
-</div></blockquote>
-<dl class="docutils">
-<dt>This is very useful for checking that the input and output parameters have been specified</dt>
-<dd>correctly.</dd>
-</dl>
-</div></blockquote>
-</div>
-<div class="section" id="determining-which-jobs-are-out-of-date-or-not">
-<h2>Determining which jobs are out-of-date or not<a class="headerlink" href="#determining-which-jobs-are-out-of-date-or-not" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>It is often useful to see which tasks are or are not up-to-date. For example, if we
-were to run the pipeline in full, and then modify one of the intermediate files, the
-pipeline would be partially out of date.</p>
-<p>Let us start by run the pipeline in full but then modify <tt class="docutils literal"><span class="pre">job1.stage</span></tt> so that the second task is no longer up-to-date:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-
-<span class="c"># modify job1.stage1</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"job1.stage1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>At a verbosity of 5, even jobs which are up-to-date will be displayed.
-We can now see that the there is only one job in <tt class="docutils literal"><span class="pre">second_task(...)</span></tt> which needs to be re-run
-because <tt class="docutils literal"><span class="pre">job1.stage1</span></tt> has been modified after <tt class="docutils literal"><span class="pre">job1.stage2</span></tt> (highlighted in blue):</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_pipeline_printout31.png" src="../../_images/simple_tutorial_pipeline_printout31.png" />
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
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-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Step 3: Understanding how your pipeline works</a><ul>
-<li><a class="reference internal" href="#printing-out-which-jobs-will-be-run">Printing out which jobs will be run</a></li>
-<li><a class="reference internal" href="#determining-which-jobs-are-out-of-date-or-not">Determining which jobs are out-of-date or not</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step2.html"
-                        title="previous chapter">Step 2: <tt class="docutils literal"><span class="pre">@transform</span></tt>-ing data in a pipeline</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step4_run_pipeline_graphically.html"
-                        title="next chapter">Step 4: Displaying the pipeline visually</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
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-            <li><a href="../../decorators/transform_ex.html">@transform (add_inputs) </a>          </li>
-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-<span id="simple-tutorial-3nd-step-code"></span><h1>Code for Step 3: Displaying the pipeline visually<a class="headerlink" href="#code-for-step-3-displaying-the-pipeline-visually" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions"><em>pipeline functions</em></a> in detail</li>
-<li><a class="reference internal" href="step3_run_pipeline.html#simple-tutorial-3rd-step"><em>Back to Step 3</em></a></li>
-</ul>
-<div class="section" id="display-the-initial-state-of-the-pipeline">
-<h2>Display the initial state of the pipeline<a class="headerlink" href="#display-the-initial-state-of-the-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   first task</span>
-<span class="c">#</span>
-<span class="n">task1_param</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="bp">None</span><span class="p">,</span> <span class="s">'job1.stage1'</span><span class="p">],</span> <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="bp">None</span><span class="p">,</span> <span class="s">'job2.stage1'</span><span class="p">],</span> <span class="c"># 2nd job</span>
-              <span class="p">]</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">task1_param</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">no_input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c"># pretend we have worked hard</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   second task</span>
-<span class="c">#</span>
-<span class="n">task2_param</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="s">'job1.stage1'</span><span class="p">,</span> <span class="s">"job1.stage2"</span><span class="p">,</span> <span class="s">"    1st_job"</span><span class="p">],</span> <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="s">'job2.stage1'</span><span class="p">,</span> <span class="s">"job2.stage2"</span><span class="p">,</span> <span class="s">"    2nd_job"</span><span class="p">],</span> <span class="c"># 2nd job</span>
-              <span class="p">]</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">first_task</span><span class="p">)</span>
-<span class="nd">@files</span><span class="p">(</span><span class="n">task2_param</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">extra_parameter</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">print</span> <span class="n">extra_parameter</span>
-
-<span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">])</span>
-
-<span class="go">    Task = first_task</span>
-<span class="go">           Job = [None -> job1.stage1]</span>
-<span class="go">           Job = [None -> job2.stage1]</span>
-
-<span class="go">    Task = second_task</span>
-<span class="go">           Job = [job1.stage1 -> job1.stage2,     1st_job]</span>
-<span class="go">           Job = [job2.stage1 -> job2.stage2,     2nd_job]</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="display-the-partially-up-to-date-pipeline">
-<h2>Display the partially up-to-date pipeline<a class="headerlink" href="#display-the-partially-up-to-date-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Run the pipeline, modify <tt class="docutils literal"><span class="pre">job1.stage</span></tt> so that the second task is no longer up-to-date
-and printout the pipeline stage again:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-
-<span class="c"># modify job1.stage1</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"job1.stage1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-</pre></div>
-</div>
-<p>At a verbosity of 5, even jobs which are up-to-date will be displayed:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_printout</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="p">[</span><span class="n">second_task</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
-<span class="go">________________________________________</span>
-<span class="go">Tasks which are up-to-date:</span>
-
-<span class="go">Task = first_task</span>
-<span class="go">       Job = [None</span>
-<span class="go">             ->job1.stage1]</span>
-<span class="go">         Job up-to-date</span>
-<span class="go">       Job = [None</span>
-<span class="go">             ->job2.stage1]</span>
-<span class="go">         Job up-to-date</span>
-
-
-<span class="go">________________________________________</span>
-<span class="go">Tasks which will be run:</span>
-
-<span class="go">Task = second_task</span>
-<span class="go">       Job = [job1.stage1</span>
-<span class="go">             ->job1.stage2,     1st_job]</span>
-<span class="go">         Job needs update: Need update file times= [[(1269025787.0, 'job1.stage1')], [(1269025785.0,</span>
-<span class="go">               'job1.stage2')]]</span>
-<span class="go">       Job = [job2.stage1</span>
-<span class="go">             ->job2.stage2,     2nd_job]</span>
-<span class="go">         Job up-to-date</span>
-
-<span class="go">________________________________________</span>
-</pre></div>
-</div>
-<p>We can now see that the there is only one job in “second_task” which needs to be re-run
-because ‘job1.stage1’ has been modified after ‘job1.stage2’</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Step 3: Displaying the pipeline visually</a><ul>
-<li><a class="reference internal" href="#display-the-initial-state-of-the-pipeline">Display the initial state of the pipeline</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-<li><a class="reference internal" href="#display-the-partially-up-to-date-pipeline">Display the partially up-to-date pipeline</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step2_code.html"
-                        title="previous chapter">Code for Step 2: Passing parameters to the pipeline</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step4_run_pipeline_graphically_code.html"
-                        title="next chapter">Code for Step 4: Displaying the pipeline visually</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/simple_tutorial/step3_run_pipeline_code.txt"
-           rel="nofollow">Show Source</a></li>
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-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
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-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="../../todo.html">Future plans</a>
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-            
-  <div class="section" id="step-4-displaying-the-pipeline-visually">
-<span id="simple-tutorial-4th-step-graphical"></span><h1>Step 4: Displaying the pipeline visually<a class="headerlink" href="#step-4-displaying-the-pipeline-visually" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions"><em>pipeline functions</em></a> in detail</li>
-</ul>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="step4_run_pipeline_graphically_code.html#simple-tutorial-4th-step-graphical-code"><em>Python Code for step 4</em></a></li>
-</ul>
-</div>
-<span class="target" id="index-0"></span><div class="section" id="printing-out-a-flowchart-of-our-pipeline">
-<span id="index-1"></span><h2>Printing out a flowchart of our pipeline<a class="headerlink" href="#printing-out-a-flowchart-of-our-pipeline" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>It is all very well being able to trace the data flow through the pipeline.
-Sometimes, however, we need a bit of eye-candy.</p>
-<table border="1" class="borderless docutils">
-<colgroup>
-<col width="1%" />
-<col width="99%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><img alt="../../_images/simple_tutorial_step4.png" class="first last" src="../../_images/simple_tutorial_step4.png" />
-</td>
-<td><blockquote class="first last">
-<div><dl class="docutils">
-<dt>We can see this flowchart of our fledgling pipeline by executing:</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="n">pipeline_printout_graph</span> <span class="p">(</span>   <span class="s">'flowchart.svg'</span><span class="p">,</span>
-                            <span class="s">'svg'</span><span class="p">,</span>
-                            <span class="p">[</span><span class="n">second_task</span><span class="p">],</span>
-                            <span class="n">no_key_legend</span> <span class="o">=</span> <span class="bp">False</span><span class="p">)</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>Flowcharts can be printed in a large number of formats including jpg, svg,
-png and pdf provided that the <tt class="docutils literal"><span class="pre">dot</span></tt> programme from
-<a class="reference external" href="http://www.graphviz.org/">Graphviz</a> is installed.</p>
-<p>For this simple case, we have ommitted the legend key which distinguishes between the
-different states of the various tasks. (See below for the legend key.)</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-</div></blockquote>
-</div>
-<div class="section" id="horribly-complicated-pipelines">
-<h2>Horribly complicated pipelines!<a class="headerlink" href="#horribly-complicated-pipelines" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Flowcharts are especially useful if you have really complicated pipelines, such as</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_complex_flowchart1.png" src="../../_images/simple_tutorial_complex_flowchart1.png" />
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="circular-dependency-errors-in-pipelines">
-<h2>Circular dependency errors in pipelines!<a class="headerlink" href="#circular-dependency-errors-in-pipelines" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Especially, if the pipeline is not set up properly, and vicious circular dependencies
-are present:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_complex_flowchart_error1.png" src="../../_images/simple_tutorial_complex_flowchart_error1.png" />
-</div></blockquote>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Step 4: Displaying the pipeline visually</a><ul>
-<li><a class="reference internal" href="#printing-out-a-flowchart-of-our-pipeline">Printing out a flowchart of our pipeline</a></li>
-<li><a class="reference internal" href="#horribly-complicated-pipelines">Horribly complicated pipelines!</a></li>
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-  <div class="section" id="code-for-step-4-displaying-the-pipeline-visually">
-<span id="simple-tutorial-4th-step-graphical-code"></span><h1>Code for Step 4: Displaying the pipeline visually<a class="headerlink" href="#code-for-step-4-displaying-the-pipeline-visually" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../pipeline_functions.html#pipeline-functions"><em>pipeline functions</em></a> in detail</li>
-<li><a class="reference internal" href="step4_run_pipeline_graphically.html#simple-tutorial-4th-step-graphical"><em>Back to Step 4</em></a></li>
-</ul>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">time</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   first task</span>
-<span class="c">#</span>
-<span class="n">task1_param</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="bp">None</span><span class="p">,</span> <span class="s">'job1.stage1'</span><span class="p">],</span> <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="bp">None</span><span class="p">,</span> <span class="s">'job2.stage1'</span><span class="p">],</span> <span class="c"># 2nd job</span>
-              <span class="p">]</span>
-
-<span class="nd">@files</span><span class="p">(</span><span class="n">task1_param</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">first_task</span><span class="p">(</span><span class="n">no_input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   second task</span>
-<span class="c">#</span>
-<span class="n">task2_param</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="p">[</span> <span class="s">'job1.stage1'</span><span class="p">,</span> <span class="s">"job1.stage2"</span><span class="p">,</span> <span class="s">"    1st_job"</span><span class="p">],</span> <span class="c"># 1st job</span>
-                    <span class="p">[</span> <span class="s">'job2.stage1'</span><span class="p">,</span> <span class="s">"job2.stage2"</span><span class="p">,</span> <span class="s">"    2nd_job"</span><span class="p">],</span> <span class="c"># 2nd job</span>
-              <span class="p">]</span>
-
-<span class="nd">@follows</span><span class="p">(</span><span class="n">first_task</span><span class="p">)</span>
-<span class="nd">@files</span><span class="p">(</span><span class="n">task2_param</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">second_task</span><span class="p">(</span><span class="n">input_file</span><span class="p">,</span> <span class="n">output_file</span><span class="p">,</span> <span class="n">extra_parameter</span><span class="p">):</span>
-    <span class="nb">open</span><span class="p">(</span><span class="n">output_file</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">print</span> <span class="n">extra_parameter</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Show flow chart and tasks before running the pipeline</span>
-<span class="c">#</span>
-<span class="k">print</span> <span class="s">"Show flow chart and tasks before running the pipeline"</span>
-<span class="n">pipeline_printout_graph</span> <span class="p">(</span> <span class="nb">open</span><span class="p">(</span><span class="s">"flowchart_before.png"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">),</span>
-                         <span class="s">"png"</span><span class="p">,</span>
-                         <span class="p">[</span><span class="n">second_task</span><span class="p">],</span>
-                         <span class="n">no_key_legend</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">second_task</span><span class="p">])</span>
-
-
-<span class="c"># modify job1.stage1</span>
-<span class="nb">open</span><span class="p">(</span><span class="s">"job1.stage1"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Show flow chart and tasks after running the pipeline</span>
-<span class="c">#</span>
-<span class="k">print</span> <span class="s">"Show flow chart and tasks after running the pipeline"</span>
-<span class="n">pipeline_printout_graph</span> <span class="p">(</span> <span class="nb">open</span><span class="p">(</span><span class="s">"flowchart_after.png"</span><span class="p">,</span> <span class="s">"w"</span><span class="p">),</span>
-                         <span class="s">"png"</span><span class="p">,</span>
-                         <span class="p">[</span><span class="n">second_task</span><span class="p">],</span>
-                         <span class="n">no_key_legend</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-flowcharts">
-<h2>Resulting Flowcharts<a class="headerlink" href="#resulting-flowcharts" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><table border="1" class="docutils">
-<colgroup>
-<col width="46%" />
-<col width="54%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><a class="first reference internal image-reference" href="../../_images/simple_tutorial_stage4_before.png"><img alt="Before running the pipeline" class="align-center" src="../../_images/simple_tutorial_stage4_before.png" style="width: 103.0px; height: 94.5px;" /></a>
-<p class="last centered">
-<strong>Before</strong></p></td>
-<td><a class="first reference internal image-reference" href="../../_images/simple_tutorial_stage4_after.png"><img alt="After running the pipeline" class="align-center" src="../../_images/simple_tutorial_stage4_after.png" style="width: 103.0px; height: 98.5px;" /></a>
-<p class="last centered">
-<strong>After</strong></p></td>
-</tr>
-</tbody>
-</table>
-<table border="1" class="docutils">
-<colgroup>
-<col width="100%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><a class="first reference internal image-reference" href="../../_images/tutorial_key.jpg"><img alt="Legend key" class="align-center" src="../../_images/tutorial_key.jpg" style="width: 722.25px; height: 78.75px;" /></a>
-<p class="last centered">
-<strong>Legend</strong></p></td>
-</tr>
-</tbody>
-</table>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Step 4: Displaying the pipeline visually</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-flowcharts">Resulting Flowcharts</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step3_run_pipeline_code.html"
-                        title="previous chapter">Code for Step 3: Displaying the pipeline visually</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step5_split_code.html"
-                        title="next chapter">Code for Step 5: Splitting up large tasks / files</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
-    <li><a href="../../_sources/tutorials/simple_tutorial/step4_run_pipeline_graphically_code.txt"
-           rel="nofollow">Show Source</a></li>
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-    Enter search terms or a module, class or function name.
-    </p>
-</div>
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
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-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="../../decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
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-    
-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="../../decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="../../decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
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-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
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-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
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-            
-  <span class="target" id="tutorial-split"><span id="simple-tutorial-5th-step"></span></span><div class="section" id="step-5-splitting-up-large-tasks-files">
-<span id="index-0"></span><h1>Step 5: Splitting up large tasks / files<a class="headerlink" href="#step-5-splitting-up-large-tasks-files" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split in detail</em></a></li>
-</ul>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="step5_split_code.html#simple-tutorial-5th-step-code"><em>Python Code for step 5</em></a></li>
-</ul>
-</div>
-<div class="line-block">
-<div class="line">The second half of this tutorial is a worked example to calculate
-the sample variance of 10,000 random numbers.</div>
-<div class="line">This is similar to many computational projects: we are tackling a big problem
-by splitting it up into many tiny problems solved in parallel. We can then
-merge our piecemeal solutions into our final answer. These
-<a class="reference external" href="http://en.wikipedia.org/wiki/Embarrassingly_parallel">embarassingly parallel</a>
-problems motivated the original design of <strong>Ruffus</strong>.</div>
-</div>
-<p><strong>Ruffus</strong> has three dedicated decorators to handle these problems with ease:</p>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> to break up the big problem</li>
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@transfrom</em></a> to solve the parts in parallel</li>
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@merge</em></a> to merge our piecemeal solutions into the final answer.</li>
-</ul>
-</div></blockquote>
-</div></blockquote>
-<div class="section" id="splitting-up-a-long-list-of-random-numbers-to-calculate-their-variance">
-<h2>Splitting up a long list of random numbers to calculate their variance<a class="headerlink" href="#splitting-up-a-long-list-of-random-numbers-to-calculate-their-variance" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><table border="1" class="borderless docutils">
-<colgroup>
-<col width="1%" />
-<col width="99%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><p class="first centered">
-<strong>Step 5 from:</strong></p><img alt="../../_images/simple_tutorial_step5.png" class="last" src="../../_images/simple_tutorial_step5.png" />
-</td>
-<td><blockquote class="first last">
-<div><p>Suppose we had a list of 100,000 random numbers in the file <tt class="docutils literal"><span class="pre">random_numbers.list</span></tt>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">random</span>
-<span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">'random_numbers.list'</span><span class="p">,</span> <span class="s">'w'</span><span class="p">)</span>
-<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">NUMBER_OF_RANDOMS</span><span class="p">):</span>
-    <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">'</span><span class="si">%g</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mf">100.0</span><span class="p">))</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>We might want to calculate the sample variance more quickly by splitting them
-into <tt class="docutils literal"><span class="pre">NNN</span></tt> parcels of 1000 numbers each and working on them in parallel.
-In this case we known that <tt class="docutils literal"><span class="pre">NNN</span> <span class="pre">==</span> <span class="pre">100</span></tt> but usually the number of resulting files
-is only apparent after we have finished processing our starting file.</p>
-</div></blockquote>
-</td>
-</tr>
-</tbody>
-</table>
-<p>Our pipeline function needs to take the random numbers file <tt class="docutils literal"><span class="pre">random_numbers.list</span></tt>,
-read the random numbers from it, and write to a new file every 100 lines.</p>
-<p>The <em>Ruffus</em> decorator <a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split</em></a> is designed specifically for
-splitting up input into an indeterminate <tt class="docutils literal"><span class="pre">NNN</span></tt> number of output files:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_split1.png" src="../../_images/simple_tutorial_split1.png" />
-</div></blockquote>
-<p>Ruffus will set</p>
-<blockquote>
-<div><div class="line-block">
-<div class="line"><tt class="docutils literal"><span class="pre">input_file_name</span></tt> to <tt class="docutils literal"><span class="pre">"random_numbers.list"</span></tt></div>
-<div class="line"><tt class="docutils literal"><span class="pre">output_files</span></tt> to all files which match <tt class="docutils literal"><span class="pre">*.chunks</span></tt> (i.e. <tt class="docutils literal"><span class="pre">"1.chunks"</span></tt>, <tt class="docutils literal"><span class="pre">"2.chunks"</span></tt> etc.).</div>
-</div>
-</div></blockquote>
-<p>The first time you run this function <tt class="docutils literal"><span class="pre">*.chunks</span></tt> will return an empty list because
-no <tt class="docutils literal"><span class="pre">.chunks</span></tt> files have been created, resulting in the following:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">step_5_split_numbers_into_chunks</span> <span class="p">(</span><span class="s">"random_numbers.list"</span><span class="p">,</span> <span class="p">[])</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>After that <tt class="docutils literal"><span class="pre">*.chunks</span></tt> will match the list of current <tt class="docutils literal"><span class="pre">.chunks</span></tt> files created by
-the previous pipeline run. Some of these files will be out of date or superfluous.
-These file names are usually only useful for removing detritus from previous runs
-(have a look at <a class="reference internal" href="step5_split_code.html#simple-tutorial-5th-step-code"><em>step_5_split_numbers_into_chunks(...)</em></a>).</p>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>The great value of specifying correctly the list of <em>output</em> files will become apparent in the next
-step of this tutorial when we shall see how pipeline tasks can be “chained” together conveniently.</p>
-<p>Remember to specify <tt class="docutils literal"><span class="pre">globs</span></tt> patterns which match <em>all</em> the files you are splitting up. You can
-cover different directories, or groups of file names by using a list of <tt class="docutils literal"><span class="pre">globs</span></tt>:
-e.g.</p>
-<div class="last highlight-python"><div class="highlight"><pre><span class="nd">@split</span><span class="p">(</span><span class="s">"input.file"</span><span class="p">,</span> <span class="p">[</span><span class="s">'a*.bits'</span><span class="p">,</span> <span class="s">'b*.pieces'</span><span class="p">,</span> <span class="s">'somewhere_else/c*.stuff'</span><span class="p">])</span>
-<span class="k">def</span> <span class="nf">split_function</span> <span class="p">(</span><span class="n">input_filename</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="s">"Code to split up 'input.file'"</span>
-</pre></div>
-</div>
-</div>
-</div></blockquote>
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-</div>
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-  <ul>
-<li><a class="reference internal" href="#">Step 5: Splitting up large tasks / files</a><ul>
-<li><a class="reference internal" href="#splitting-up-a-long-list-of-random-numbers-to-calculate-their-variance">Splitting up a long list of random numbers to calculate their variance</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step4_run_pipeline_graphically.html"
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
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-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-            
-  <span class="target" id="simple-tutorial-5th-step-code"></span><div class="section" id="code-for-step-5-splitting-up-large-tasks-files">
-<h1>Code for Step 5: Splitting up large tasks / files<a class="headerlink" href="#code-for-step-5-splitting-up-large-tasks-files" title="Permalink to this headline">¶</a></h1>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/split.html#decorators-split"><em>@split in detail</em></a></li>
-<li><a class="reference internal" href="step5_split.html#simple-tutorial-5th-step"><em>back to step 5</em></a></li>
-</ul>
-</div></blockquote>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">NUMBER_OF_RANDOMS</span> <span class="o">=</span> <span class="mi">10000</span>
-<span class="n">CHUNK_SIZE</span> <span class="o">=</span> <span class="mi">1000</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">time</span>
-
-<span class="kn">import</span> <span class="nn">random</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Create random numbers</span>
-<span class="c">#</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"random_numbers.list"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_random_numbers</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">NUMBER_OF_RANDOMS</span><span class="p">):</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%g</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mf">100.0</span><span class="p">))</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Split initial file</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">create_random_numbers</span><span class="p">)</span>
-<span class="nd">@split</span><span class="p">(</span><span class="s">"random_numbers.list"</span><span class="p">,</span> <span class="s">"*.chunks"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_5_split_numbers_into_chunks</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        Splits random numbers file into XXX files of CHUNK_SIZE each</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   clean up files from previous runs</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s">"*.chunks"</span><span class="p">):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   create new file every CHUNK_SIZE lines and</span>
-    <span class="c">#       copy each line into current file</span>
-    <span class="c">#</span>
-    <span class="n">output_file</span> <span class="o">=</span> <span class="bp">None</span>
-    <span class="n">cnt_files</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)):</span>
-        <span class="k">if</span> <span class="n">i</span> <span class="o">%</span> <span class="n">CHUNK_SIZE</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="n">cnt_files</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.chunks"</span> <span class="o">%</span> <span class="n">cnt_files</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">step_5_split_numbers_into_chunks</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">step_5_split_numbers_into_chunks</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
-
-<span class="go">    Start Task = create_random_numbers</span>
-
-<span class="go">        Job = [None -> random_numbers.list] Missing file random_numbers.list</span>
-<span class="go">        Job = [None -> random_numbers.list] completed</span>
-<span class="go">    Completed Task = create_random_numbers</span>
-<span class="go">    Start Task = step_5_split_numbers_into_chunks</span>
-<span class="go">    Splits random numbers file into XXX files of CHUNK_SIZE each</span>
-<span class="go">        Job = [random_numbers.list -> *.chunks] Missing output file</span>
-<span class="go">        Job = [random_numbers.list -> *.chunks] completed</span>
-<span class="go">    Completed Task = step_5_split_numbers_into_chunks</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
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-  <ul>
-<li><a class="reference internal" href="#">Code for Step 5: Splitting up large tasks / files</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step4_run_pipeline_graphically_code.html"
-                        title="previous chapter">Code for Step 4: Displaying the pipeline visually</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step6_transform_code.html"
-                        title="next chapter">Code for Step 6: Running jobs in parallel</a></p>
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-        </ul>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
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-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
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-            
-  <span class="target" id="tutorial-transform"><span id="simple-tutorial-6th-step"></span></span><div class="section" id="step-6-running-jobs-in-parallel">
-<span id="index-0"></span><h1>Step 6: Running jobs in parallel<a class="headerlink" href="#step-6-running-jobs-in-parallel" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform in detail</em></a></li>
-</ul>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="step6_transform_code.html#simple-tutorial-6th-step-code"><em>Python Code for step 6</em></a></li>
-</ul>
-</div>
-<div class="section" id="calculating-sums-and-sum-of-squares-in-parallel">
-<h2>Calculating sums and sum of squares in parallel<a class="headerlink" href="#calculating-sums-and-sum-of-squares-in-parallel" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>Now that we have many smaller lists of numbers in separate files, we can calculate their sums and
-sum of squares in parallel.</p>
-<p>All we need is a function which takes a <tt class="docutils literal"><span class="pre">*.chunk</span></tt> file, reads the numbers, calculates
-the answers and writes them back out to a corresponding <tt class="docutils literal"><span class="pre">*.sums</span></tt> file.</p>
-<p><em>Ruffus</em> magically takes care of applying this task function to all the different
-data files in parallel.</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_transform1.png" src="../../_images/simple_tutorial_transform1.png" />
-</div></blockquote>
-<div class="line-block">
-<div class="line">The first thing to note about this example is that the <em>input</em> files are not specified
-as a <a class="reference external" href="http://docs.python.org/library/glob.html"><cite>glob</cite></a>  (e.g. <tt class="docutils literal"><span class="pre">*.chunk</span></tt>) but as the preceding task.</div>
-<div class="line"><em>Ruffus</em> will take all
-the files produced by <tt class="docutils literal"><span class="pre">step_5_split_numbers_into_chunks()</span></tt> and feed them as the <em>input</em>
-into step 6.</div>
-</div>
-<p>This handy shortcut also means that <strong>Ruffus</strong> knows that <tt class="docutils literal"><span class="pre">step_6_calculate_sum_of_squares</span></tt>
-depends on <tt class="docutils literal"><span class="pre">step_5_split_numbers_into_chunks</span></tt> and an additional <tt class="docutils literal"><span class="pre">@follows</span></tt> directive
-is unnecessary.</p>
-<p>The use of <a class="reference internal" href="../../decorators/transform_ex.html#decorators-transform-suffix-string"><em>suffix</em></a> within the decorator tells
-<em>Ruffus</em> to take all <em>input</em> files with the <tt class="docutils literal"><span class="pre">.chunks</span></tt> suffix and substitute a <tt class="docutils literal"><span class="pre">.sums</span></tt>
-suffix to generate the corresponding <em>output</em> file name.</p>
-<dl class="docutils">
-<dt>Thus if <tt class="docutils literal"><span class="pre">step_5_split_numbers_into_chunks</span></tt> created</dt>
-<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="s">"1.chunks"</span>
-<span class="s">"2.chunks"</span>
-<span class="s">"3.chunks"</span>
-</pre></div>
-</div>
-</dd>
-</dl>
-<p>This would result in the following function calls:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">step_6_calculate_sum_of_squares</span> <span class="p">(</span><span class="s">"1.chunk"</span><span class="p">,</span> <span class="s">"1.sums"</span><span class="p">)</span>
-<span class="n">step_6_calculate_sum_of_squares</span> <span class="p">(</span><span class="s">"2.chunk"</span><span class="p">,</span> <span class="s">"2.sums"</span><span class="p">)</span>
-<span class="n">step_6_calculate_sum_of_squares</span> <span class="p">(</span><span class="s">"3.chunk"</span><span class="p">,</span> <span class="s">"3.sums"</span><span class="p">)</span>
-
-<span class="c"># etc...</span>
-</pre></div>
-</div>
-</div></blockquote>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">It is possible to generate <em>output</em> filenames using more powerful regular expressions
-as well. See the <a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform</em></a> syntax documentation for more details.</p>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Step 6: Running jobs in parallel</a><ul>
-<li><a class="reference internal" href="#calculating-sums-and-sum-of-squares-in-parallel">Calculating sums and sum of squares in parallel</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step5_split.html"
-                        title="previous chapter">Step 5: Splitting up large tasks / files</a></p>
-  <h4>Next topic</h4>
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-  <div class="section" id="code-for-step-6-running-jobs-in-parallel">
-<span id="simple-tutorial-6th-step-code"></span><h1>Code for Step 6: Running jobs in parallel<a class="headerlink" href="#code-for-step-6-running-jobs-in-parallel" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/transform.html#decorators-transform"><em>@transform in detail</em></a></li>
-<li><a class="reference internal" href="step6_transform.html#simple-tutorial-6th-step"><em>back to step 6</em></a></li>
-</ul>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">NUMBER_OF_RANDOMS</span> <span class="o">=</span> <span class="mi">10000</span>
-<span class="n">CHUNK_SIZE</span> <span class="o">=</span> <span class="mi">1000</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">time</span>
-
-<span class="kn">import</span> <span class="nn">random</span>
-<span class="kn">import</span> <span class="nn">glob</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Create random numbers</span>
-<span class="c">#</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"random_numbers.list"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_random_numbers</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">NUMBER_OF_RANDOMS</span><span class="p">):</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%g</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mf">100.0</span><span class="p">))</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Split initial file</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">create_random_numbers</span><span class="p">)</span>
-<span class="nd">@split</span><span class="p">(</span><span class="s">"random_numbers.list"</span><span class="p">,</span> <span class="s">"*.chunks"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_5_split_numbers_into_chunks</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        Splits random numbers file into XXX files of CHUNK_SIZE each</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   clean up files from previous runs</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s">"*.chunks"</span><span class="p">):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#</span>
-    <span class="c">#   create new file every CHUNK_SIZE lines and</span>
-    <span class="c">#       copy each line into current file</span>
-    <span class="c">#</span>
-    <span class="n">output_file</span> <span class="o">=</span> <span class="bp">None</span>
-    <span class="n">cnt_files</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)):</span>
-        <span class="k">if</span> <span class="n">i</span> <span class="o">%</span> <span class="n">CHUNK_SIZE</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="n">cnt_files</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.chunks"</span> <span class="o">%</span> <span class="n">cnt_files</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate sum and sum of squares for each chunk file</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">step_5_split_numbers_into_chunks</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".chunks"</span><span class="p">),</span> <span class="s">".sums"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_6_calculate_sum_of_squares</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">output</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">]</span>
-    <span class="n">cnt_values</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">):</span>
-        <span class="n">cnt_values</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="n">val</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">rstrip</span><span class="p">())</span>
-        <span class="n">sum_squared</span> <span class="o">+=</span> <span class="n">val</span> <span class="o">*</span> <span class="n">val</span>
-        <span class="nb">sum</span> <span class="o">+=</span> <span class="n">val</span>
-    <span class="n">output</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="n">sum_squared</span><span class="p">),</span> <span c [...]
-
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">step_6_calculate_sum_of_squares</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">pipeline_run</span><span class="p">([</span><span class="n">step_6_calculate_sum_of_squares</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-<span class="go">    Job = [None -> random_numbers.list] unnecessary: already up to date</span>
-<span class="go">Completed Task = create_random_numbers</span>
-<span class="go">    Job = [random_numbers.list -> *.chunks] unnecessary: already up to date</span>
-<span class="go">Completed Task = step_5_split_numbers_into_chunks</span>
-<span class="go">    Job = [6.chunks -> 6.sums] completed</span>
-<span class="go">    Job = [1.chunks -> 1.sums] completed</span>
-<span class="go">    Job = [4.chunks -> 4.sums] completed</span>
-<span class="go">    Job = [7.chunks -> 7.sums] completed</span>
-<span class="go">    Job = [2.chunks -> 2.sums] completed</span>
-<span class="go">    Job = [9.chunks -> 9.sums] completed</span>
-<span class="go">    Job = [10.chunks -> 10.sums] completed</span>
-<span class="go">    Job = [3.chunks -> 3.sums] completed</span>
-<span class="go">    Job = [5.chunks -> 5.sums] completed</span>
-<span class="go">    Job = [8.chunks -> 8.sums] completed</span>
-<span class="go">Completed Task = step_6_calculate_sum_of_squares</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
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-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Step 6: Running jobs in parallel</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step5_split_code.html"
-                        title="previous chapter">Code for Step 5: Splitting up large tasks / files</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="step7_merge_code.html"
-                        title="next chapter">Code for Step 7: Merging results back together</a></p>
-  <h3>This Page</h3>
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-  <span class="target" id="simple-tutorial-7th-step"></span><div class="section" id="step-7-merging-results-back-together">
-<span id="index-0"></span><h1>Step 7: Merging results back together<a class="headerlink" href="#step-7-merging-results-back-together" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge in detail</em></a></li>
-</ul>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="step7_merge_code.html#simple-tutorial-7th-step-code"><em>Python Code for step 7</em></a></li>
-</ul>
-</div>
-<p>Now that we have all the partial solutions in <tt class="docutils literal"><span class="pre">*.sums</span></tt>, we can merge them
-together to generate the final answer: the variance of all 100,000 random
-numbers.</p>
-<div class="section" id="calculating-variances-from-the-sums-and-sum-of-squares-of-all-chunks">
-<h2>Calculating variances from the sums and sum of squares of all chunks<a class="headerlink" href="#calculating-variances-from-the-sums-and-sum-of-squares-of-all-chunks" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>If we add up all the sums, and sum of squares we calculated previously, we can
-obtain the variance as follows:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">variance</span> <span class="o">=</span> <span class="p">(</span><span class="n">sum_squared</span> <span class="o">-</span> <span class="nb">sum</span> <span class="o">*</span> <span class="nb">sum</span> <span class="o">/</span> <span class="n">N</span><span class="p">)</span><span class="o">/</span><span class="n">N</span>
-</pre></div>
-</div>
-<p>where <tt class="docutils literal"><span class="pre">N</span></tt> is the number of values</p>
-<p>See the <a class="reference external" href="http://en.wikipedia.org/wiki/Algorithms_for_calculating_variance">wikipedia</a> entry for a discussion of
-why this is a very naive approach!</p>
-<p>To do this, all we have to do is merge together all the values in <tt class="docutils literal"><span class="pre">*.sums</span></tt>, i.e.
-add up the <tt class="docutils literal"><span class="pre">sums</span></tt> and <tt class="docutils literal"><span class="pre">sum_squared</span></tt> for each chunk. We can then apply the above (naive) formula.</p>
-<p>Merging files is straightforward in <strong>Ruffus</strong>:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_merge1.png" src="../../_images/simple_tutorial_merge1.png" />
-</div></blockquote>
-<p>The <a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge</em></a> decorator tells <em>Ruffus</em> to take all the files from the step 6 task (i.e. <tt class="docutils literal"><span class="pre">*.sums</span></tt>),
-and produced a merged file in the form of <tt class="docutils literal"><span class="pre">"variance.result"</span></tt>.</p>
-<dl class="docutils">
-<dt>Thus if <tt class="docutils literal"><span class="pre">step_6_calculate_sum_of_squares</span></tt> created</dt>
-<dd><div class="first last line-block">
-<div class="line"><tt class="docutils literal"><span class="pre">1.sums</span></tt> and</div>
-<div class="line"><tt class="docutils literal"><span class="pre">2.sums</span></tt> etc.</div>
-</div>
-</dd>
-</dl>
-<p>This would result in the following function call:</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_merge2.png" src="../../_images/simple_tutorial_merge2.png" />
-</div></blockquote>
-<p>The final result is, of course, in <tt class="docutils literal"><span class="pre">"variance.result"</span></tt>.</p>
-</div></blockquote>
-</div>
-</div>
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-  <ul>
-<li><a class="reference internal" href="#">Step 7: Merging results back together</a><ul>
-<li><a class="reference internal" href="#calculating-variances-from-the-sums-and-sum-of-squares-of-all-chunks">Calculating variances from the sums and sum of squares of all chunks</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step6_transform.html"
-                        title="previous chapter">Step 6: Running jobs in parallel</a></p>
-  <h4>Next topic</h4>
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-                        title="next chapter">Step 8: Signal the completion of each stage of our pipeline</a></p>
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-<span id="simple-tutorial-7th-step-code"></span><h1>Code for Step 7: Merging results back together<a class="headerlink" href="#code-for-step-7-merging-results-back-together" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/merge.html#decorators-merge"><em>@merge in detail</em></a></li>
-<li><a class="reference internal" href="step7_merge.html#simple-tutorial-7th-step"><em>back to step 7</em></a></li>
-</ul>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">NUMBER_OF_RANDOMS</span> <span class="o">=</span> <span class="mi">10000</span>
-<span class="n">CHUNK_SIZE</span> <span class="o">=</span> <span class="mi">1000</span>
-
-
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">import</span> <span class="nn">time</span>
-
-<span class="kn">import</span> <span class="nn">random</span>
-<span class="kn">import</span> <span class="nn">glob</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Create random numbers</span>
-<span class="c">#</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="s">"random_numbers.list"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_random_numbers</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">NUMBER_OF_RANDOMS</span><span class="p">):</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%g</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mf">100.0</span><span class="p">))</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Split initial file</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">create_random_numbers</span><span class="p">)</span>
-<span class="nd">@split</span><span class="p">(</span><span class="s">"random_numbers.list"</span><span class="p">,</span> <span class="s">"*.chunks"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_5_split_numbers_into_chunks</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        Splits random numbers file into XXX files of CHUNK_SIZE each</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   clean up files from previous runs</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s">"*.chunks"</span><span class="p">):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   create new file every CHUNK_SIZE lines and</span>
-    <span class="c">#       copy each line into current file</span>
-    <span class="c">#</span>
-    <span class="n">output_file</span> <span class="o">=</span> <span class="bp">None</span>
-    <span class="n">cnt_files</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)):</span>
-        <span class="k">if</span> <span class="n">i</span> <span class="o">%</span> <span class="n">CHUNK_SIZE</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="n">cnt_files</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s">"</span><span class="si">%d</span><span class="s">.chunks"</span> <span class="o">%</span> <span class="n">cnt_files</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate sum and sum of squares for each chunk file</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">step_5_split_numbers_into_chunks</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".chunks"</span><span class="p">),</span> <span class="s">".sums"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_6_calculate_sum_of_squares</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">output</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">]</span>
-    <span class="n">cnt_values</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">):</span>
-        <span class="n">cnt_values</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="n">val</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">rstrip</span><span class="p">())</span>
-        <span class="n">sum_squared</span> <span class="o">+=</span> <span class="n">val</span> <span class="o">*</span> <span class="n">val</span>
-        <span class="nb">sum</span> <span class="o">+=</span> <span class="n">val</span>
-    <span class="n">output</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="n">sum_squared</span><span class="p">),</span> <span c [...]
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate sum and sum of squares for each chunk</span>
-<span class="c">#</span>
-<span class="nd">@merge</span><span class="p">(</span><span class="n">step_6_calculate_sum_of_squares</span><span class="p">,</span> <span class="s">"variance.result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_7_calculate_variance</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Calculate variance naively</span>
-<span class="sd">    """</span>
-    <span class="n">output</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   initialise variables</span>
-    <span class="c">#</span>
-    <span class="n">all_sum_squared</span> <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="n">all_sum</span>         <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="n">all_cnt_values</span>  <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="c">#</span>
-    <span class="c"># added up all the sum_squared, and sum and cnt_values from all the chunks</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">input_file_name</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span><span class="p">,</span> <span class="n">cnt_values</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">())</span>
-        <span class="n">all_sum_squared</span> <span class="o">+=</span> <span class="n">sum_squared</span>
-        <span class="n">all_sum</span>         <span class="o">+=</span> <span class="nb">sum</span>
-        <span class="n">all_cnt_values</span>  <span class="o">+=</span> <span class="n">cnt_values</span>
-    <span class="n">all_mean</span> <span class="o">=</span> <span class="n">all_sum</span> <span class="o">/</span> <span class="n">all_cnt_values</span>
-    <span class="n">variance</span> <span class="o">=</span> <span class="p">(</span><span class="n">all_sum_squared</span> <span class="o">-</span> <span class="n">all_sum</span> <span class="o">*</span> <span class="n">all_mean</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">all_cnt_values</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   print output</span>
-    <span class="c">#</span>
-    <span class="k">print</span> <span class="o">>></span><span class="n">output</span><span class="p">,</span> <span class="n">variance</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">step_7_calculate_variance</span><span class="p">],</span> <span class="p">[</span><span class="n">create_random_numbers</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><pre>pipeline_run([step_7_calculate_variance], [create_random_numbers], verbose = 1)
-    Job = [None -> random_numbers.list] completed
-Completed Task = create_random_numbers
-    Job = [random_numbers.list -> *.chunks] completed
-Completed Task = step_5_split_numbers_into_chunks
-    Job = [6.chunks -> 6.sums] completed
-    Job = [1.chunks -> 1.sums] completed
-    Job = [4.chunks -> 4.sums] completed
-    Job = [7.chunks -> 7.sums] completed
-    Job = [2.chunks -> 2.sums] completed
-    Job = [9.chunks -> 9.sums] completed
-    Job = [10.chunks -> 10.sums] completed
-    Job = [3.chunks -> 3.sums] completed
-    Job = [5.chunks -> 5.sums] completed
-    Job = [8.chunks -> 8.sums] completed
-Completed Task = step_6_calculate_sum_of_squares
-    Job = [[6.sums, 5.sums, 1.sums, 4.sums, 3.sums, 2.sums, 8.sums, 7.sums, 10.sums, 9.sums] -> variance.result] completed
-Completed Task = step_7_calculate_variance</pre>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
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-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Step 7: Merging results back together</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step6_transform_code.html"
-                        title="previous chapter">Code for Step 6: Running jobs in parallel</a></p>
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-        <h4 >Pipeline functions</h4>
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-  <div class="section" id="step-8-signal-the-completion-of-each-stage-of-our-pipeline">
-<span id="simple-tutorial-8th-step"></span><span id="index-0"></span><h1>Step 8: Signal the completion of each stage of our pipeline<a class="headerlink" href="#step-8-signal-the-completion-of-each-stage-of-our-pipeline" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> in detail</li>
-</ul>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p>Remember to look at the example code:</p>
-<ul class="last simple">
-<li><a class="reference internal" href="step8_posttask_code.html#simple-tutorial-8th-step-code"><em>Python Code for step 8</em></a></li>
-</ul>
-</div>
-<p>Let us finish by celebrating the success of our modest pipeline example.</p>
-<div class="section" id="running-some-code-to-show-that-a-stage-of-the-pipeline-has-finished">
-<h2>Running some code to show that a stage of the pipeline has finished<a class="headerlink" href="#running-some-code-to-show-that-a-stage-of-the-pipeline-has-finished" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>A common requirement is to take some extra action when a particular
-<a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> or stage of a pipeline is complete.</p>
-<p>This can range from printing out some message, or <tt class="docutils literal"><span class="pre">touching</span></tt> some sentinel file,
-to emailing the author.</p>
-<p>This is particular useful if the <a class="reference internal" href="../../glossary.html#term-task"><em class="xref std std-term">task</em></a> is a recipe apply to an unspecified number
-of parameters in parallel in different <a class="reference internal" href="../../glossary.html#term-job"><em class="xref std std-term">job</em></a>s</p>
-<p>The “extra action” can be added to a <em>Ruffus</em> pipeline using the <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a>
-decorator.</p>
-<p>Let us print a “hooray” message to show that we have finished calculating variances.</p>
-<blockquote>
-<div><img alt="../../_images/simple_tutorial_posttask.png" src="../../_images/simple_tutorial_posttask.png" />
-</div></blockquote>
-<p>This is such a short function, we can even write it in-line:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@posttask</span><span class="p">(</span><span class="k">lambda</span><span class="p">:</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"hooray</span><span class="se">\n</span><span class="s">"</span><span class="p">))</span>
-<span class="nd">@merge</span><span class="p">(</span><span class="n">step_6_calculate_sum_of_squares</span><span class="p">,</span> <span class="s">"variance.result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_7_calculate_variance</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="touching-a-sentinel-file-after-finishing-a-pipeline-stage">
-<span id="index-1"></span><h2><em>Touching</em> a sentinel file after finishing a pipeline stage<a class="headerlink" href="#touching-a-sentinel-file-after-finishing-a-pipeline-stage" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="line-block">
-<div class="line">Very often we would like to mark the competion of a pipeline stage by using the
-date/time stamp of a “sentinel” file.</div>
-<div class="line">This is such a common requirement that <em>Ruffus</em> even has special syntax for this
-in the form of <a class="reference internal" href="../../decorators/indicator_objects.html#decorators-touch-file"><em>touch_file</em></a>.</div>
-</div>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@posttask</span><span class="p">(</span><span class="n">touch_file</span><span class="p">(</span><span class="s">"sentinel_flag"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">your_pipeline_function</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-<p>The file <tt class="docutils literal"><span class="pre">sentinel_flag</span></tt> will be created (if it did not exist) or its
-date/time stamp changed to the current time whenever this stage of the pipeline is
-completed.</p>
-</div></blockquote>
-</div>
-<div class="section" id="adding-several-post-task-actions">
-<h2>Adding several post task actions<a class="headerlink" href="#adding-several-post-task-actions" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>You can, of course, add more than one different action to be taken on completion of the
-task, either by stacking up <a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask</em></a> decorators or by including
-several functions in the same <strong>@posttask</strong>:</p>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="nd">@posttask</span><span class="p">(</span><span class="n">print_hooray</span><span class="p">,</span> <span class="n">print_whopee</span><span class="p">)</span>
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">touch_file</span><span class="p">(</span><span class="s">"sentinel_flag"</span><span class="p">))</span>
-<span class="k">def</span> <span class="nf">your_pipeline_function</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="s">""</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div></blockquote>
-</div>
-<div class="section" id="finding-out-more-about-ruffus">
-<h2>Finding out more about <strong>Ruffus</strong><a class="headerlink" href="#finding-out-more-about-ruffus" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><p>This wraps up our short tutorial on the <strong>Ruffus</strong>.</p>
-<p>Here are a few useful topics you may be interested in:</p>
-<blockquote>
-<div><ul class="simple">
-<li><a class="reference internal" href="../manual/collate.html#manual-collate"><em>How to summarise disparate input by category</em></a></li>
-<li><a class="reference internal" href="../manual/logging.html#manual-logging"><em>How to log pipeline progress</em></a></li>
-<li><a class="reference internal" href="../manual/exceptions.html#manual-exceptions"><em>How exceptions are handled</em></a></li>
-</ul>
-</div></blockquote>
-<p>To find out more about <strong>Ruffus</strong>, you can read the <a class="reference internal" href="../manual/manual_introduction.html#manual-introduction"><em>manual</em></a>
-or just start using <strong>Ruffus</strong>.</p>
-<p>Email the authors at ruffus_lib at llew.org.uk if you have any comments or suggestions.</p>
-<p>Happy pipelining!</p>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
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-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Step 8: Signal the completion of each stage of our pipeline</a><ul>
-<li><a class="reference internal" href="#running-some-code-to-show-that-a-stage-of-the-pipeline-has-finished">Running some code to show that a stage of the pipeline has finished</a></li>
-<li><a class="reference internal" href="#touching-a-sentinel-file-after-finishing-a-pipeline-stage"><em>Touching</em> a sentinel file after finishing a pipeline stage</a></li>
-<li><a class="reference internal" href="#adding-several-post-task-actions">Adding several post task actions</a></li>
-<li><a class="reference internal" href="#finding-out-more-about-ruffus">Finding out more about <strong>Ruffus</strong></a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step7_merge.html"
-                        title="previous chapter">Step 7: Merging results back together</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="../manual/dependencies_code.html"
-                        title="next chapter">Code for Chapter 9: Checking dependencies to run tasks in order</a></p>
-  <h3>This Page</h3>
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-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
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-  <div class="section" id="code-for-step-8-signal-the-completion-of-each-stage-of-our-pipeline">
-<span id="simple-tutorial-8th-step-code"></span><h1>Code for Step 8: Signal the completion of each stage of our pipeline<a class="headerlink" href="#code-for-step-8-signal-the-completion-of-each-stage-of-our-pipeline" title="Permalink to this headline">¶</a></h1>
-<ul class="simple">
-<li><a class="reference internal" href="simple_tutorial.html#simple-tutorial"><em>Simple tutorial overview</em></a></li>
-<li><a class="reference internal" href="../../decorators/posttask.html#decorators-posttask"><em>@posttask in detail</em></a></li>
-<li><a class="reference internal" href="step8_posttask.html#simple-tutorial-8th-step"><em>back to step 8</em></a></li>
-</ul>
-<div class="section" id="code">
-<h2>Code<a class="headerlink" href="#code" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><div class="highlight"><pre><span class="n">NUMBER_OF_RANDOMS</span> <span class="o">=</span> <span class="mi">10000</span>
-<span class="n">CHUNK_SIZE</span> <span class="o">=</span> <span class="mi">1000</span>
-<span class="n">working_dir</span> <span class="o">=</span> <span class="s">"temp_tutorial8/"</span>
-
-
-
-<span class="kn">import</span> <span class="nn">time</span><span class="o">,</span> <span class="nn">sys</span><span class="o">,</span> <span class="nn">os</span>
-<span class="kn">from</span> <span class="nn">ruffus</span> <span class="kn">import</span> <span class="o">*</span>
-
-<span class="kn">import</span> <span class="nn">random</span>
-<span class="kn">import</span> <span class="nn">glob</span>
-
-
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Create random numbers</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">mkdir</span><span class="p">(</span><span class="n">working_dir</span><span class="p">))</span>
-<span class="nd">@files</span><span class="p">(</span><span class="bp">None</span><span class="p">,</span> <span class="n">working_dir</span> <span class="o">+</span> <span class="s">"random_numbers.list"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">create_random_numbers</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">NUMBER_OF_RANDOMS</span><span class="p">):</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%g</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">random</span><span class="p">()</span> <span class="o">*</span> <span class="mf">100.0</span><span class="p">))</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Split initial file</span>
-<span class="c">#</span>
-<span class="nd">@follows</span><span class="p">(</span><span class="n">create_random_numbers</span><span class="p">)</span>
-<span class="nd">@split</span><span class="p">(</span><span class="n">working_dir</span> <span class="o">+</span> <span class="s">"random_numbers.list"</span><span class="p">,</span> <span class="n">working_dir</span> <span class="o">+</span> <span class="s">"*.chunks"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_5_split_numbers_into_chunks</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_files</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">        Splits random numbers file into XXX files of CHUNK_SIZE each</span>
-<span class="sd">    """</span>
-    <span class="c">#</span>
-    <span class="c">#   clean up files from previous runs</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s">"*.chunks"</span><span class="p">):</span>
-        <span class="n">os</span><span class="o">.</span><span class="n">unlink</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   create new file every CHUNK_SIZE lines and</span>
-    <span class="c">#       copy each line into current file</span>
-    <span class="c">#</span>
-    <span class="n">output_file</span> <span class="o">=</span> <span class="bp">None</span>
-    <span class="n">cnt_files</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)):</span>
-        <span class="k">if</span> <span class="n">i</span> <span class="o">%</span> <span class="n">CHUNK_SIZE</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="n">cnt_files</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">output_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">working_dir</span> <span class="o">+</span> <span class="s">"</span><span class="si">%d</span><span class="s">.chunks"</span> <span class="o">%</span> <span class="n">cnt_files</span><span class="p">,</span> <span class="s">"w"</span><span class="p">)</span>
-        <span class="n">output_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate sum and sum of squares for each chunk file</span>
-<span class="c">#</span>
-<span class="nd">@transform</span><span class="p">(</span><span class="n">step_5_split_numbers_into_chunks</span><span class="p">,</span> <span class="n">suffix</span><span class="p">(</span><span class="s">".chunks"</span><span class="p">),</span> <span class="s">".sums"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_6_calculate_sum_of_squares</span> <span class="p">(</span><span class="n">input_file_name</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="n">output</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">]</span>
-    <span class="n">cnt_values</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">):</span>
-        <span class="n">cnt_values</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="n">val</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">rstrip</span><span class="p">())</span>
-        <span class="n">sum_squared</span> <span class="o">+=</span> <span class="n">val</span> <span class="o">*</span> <span class="n">val</span>
-        <span class="nb">sum</span> <span class="o">+=</span> <span class="n">val</span>
-    <span class="n">output</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="si">%d</span><span class="se">\n</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">repr</span><span class="p">(</span><span class="n">sum_squared</span><span class="p">),</span> <span c [...]
-
-
-<span class="k">def</span> <span class="nf">print_hooray_again</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"hooray again"</span>
-
-<span class="k">def</span> <span class="nf">print_whoppee_again</span><span class="p">():</span>
-    <span class="k">print</span> <span class="s">"whoppee again"</span>
-
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#   Calculate sum and sum of squares for each chunk</span>
-<span class="c">#</span>
-<span class="nd">@posttask</span><span class="p">(</span><span class="k">lambda</span><span class="p">:</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">"hooray</span><span class="se">\n</span><span class="s">"</span><span class="p">))</span>
-<span class="nd">@posttask</span><span class="p">(</span><span class="n">print_hooray_again</span><span class="p">,</span> <span class="n">print_whoppee_again</span><span class="p">,</span> <span class="n">touch_file</span><span class="p">(</span><span class="s">"done"</span><span class="p">))</span>
-<span class="nd">@merge</span><span class="p">(</span><span class="n">step_6_calculate_sum_of_squares</span><span class="p">,</span> <span class="s">"variance.result"</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">step_7_calculate_variance</span> <span class="p">(</span><span class="n">input_file_names</span><span class="p">,</span> <span class="n">output_file_name</span><span class="p">):</span>
-    <span class="sd">"""</span>
-<span class="sd">    Calculate variance naively</span>
-<span class="sd">    """</span>
-    <span class="n">output</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">output_file_name</span><span class="p">,</span>  <span class="s">"w"</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   initialise variables</span>
-    <span class="c">#</span>
-    <span class="n">all_sum_squared</span> <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="n">all_sum</span>         <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="n">all_cnt_values</span>  <span class="o">=</span> <span class="mf">0.0</span>
-    <span class="c">#</span>
-    <span class="c"># added up all the sum_squared, and sum and cnt_values from all the chunks</span>
-    <span class="c">#</span>
-    <span class="k">for</span> <span class="n">input_file_name</span> <span class="ow">in</span> <span class="n">input_file_names</span><span class="p">:</span>
-        <span class="n">sum_squared</span><span class="p">,</span> <span class="nb">sum</span><span class="p">,</span> <span class="n">cnt_values</span> <span class="o">=</span> <span class="nb">map</span><span class="p">(</span><span class="nb">float</span><span class="p">,</span> <span class="nb">open</span><span class="p">(</span><span class="n">input_file_name</span><span class="p">)</span><span class="o">.</span><span class="n">readlines</span><span class="p">())</span>
-        <span class="n">all_sum_squared</span> <span class="o">+=</span> <span class="n">sum_squared</span>
-        <span class="n">all_sum</span>         <span class="o">+=</span> <span class="nb">sum</span>
-        <span class="n">all_cnt_values</span>  <span class="o">+=</span> <span class="n">cnt_values</span>
-    <span class="n">all_mean</span> <span class="o">=</span> <span class="n">all_sum</span> <span class="o">/</span> <span class="n">all_cnt_values</span>
-    <span class="n">variance</span> <span class="o">=</span> <span class="p">(</span><span class="n">all_sum_squared</span> <span class="o">-</span> <span class="n">all_sum</span> <span class="o">*</span> <span class="n">all_mean</span><span class="p">)</span><span class="o">/</span><span class="p">(</span><span class="n">all_cnt_values</span><span class="p">)</span>
-    <span class="c">#</span>
-    <span class="c">#   print output</span>
-    <span class="c">#</span>
-    <span class="k">print</span> <span class="o">>></span><span class="n">output</span><span class="p">,</span> <span class="n">variance</span>
-
-<span class="c">#---------------------------------------------------------------</span>
-<span class="c">#</span>
-<span class="c">#       Run</span>
-<span class="c">#</span>
-<span class="n">pipeline_run</span><span class="p">([</span><span class="n">step_7_calculate_variance</span><span class="p">],</span> <span class="n">verbose</span> <span class="o">=</span> <span class="mi">1</span><span class="p">)</span>
-</pre></div>
-</div>
-</div></blockquote>
-</div>
-<div class="section" id="resulting-output">
-<h2>Resulting Output<a class="headerlink" href="#resulting-output" title="Permalink to this headline">¶</a></h2>
-<blockquote>
-<div><div class="highlight-python"><pre>>> pipeline_run([step_7_calculate_variance], verbose = 1)
-    Make directories [temp_tutorial8/] completed
-Completed Task = create_random_numbers_mkdir_1
-    Job = [None -> temp_tutorial8/random_numbers.list] completed
-Completed Task = create_random_numbers
-    Job = [temp_tutorial8/random_numbers.list -> temp_tutorial8/*.chunks] completed
-Completed Task = step_5_split_numbers_into_chunks
-    Job = [temp_tutorial8/1.chunks -> temp_tutorial8/1.sums] completed
-    Job = [temp_tutorial8/10.chunks -> temp_tutorial8/10.sums] completed
-    Job = [temp_tutorial8/2.chunks -> temp_tutorial8/2.sums] completed
-    Job = [temp_tutorial8/3.chunks -> temp_tutorial8/3.sums] completed
-    Job = [temp_tutorial8/4.chunks -> temp_tutorial8/4.sums] completed
-    Job = [temp_tutorial8/5.chunks -> temp_tutorial8/5.sums] completed
-    Job = [temp_tutorial8/6.chunks -> temp_tutorial8/6.sums] completed
-    Job = [temp_tutorial8/7.chunks -> temp_tutorial8/7.sums] completed
-    Job = [temp_tutorial8/8.chunks -> temp_tutorial8/8.sums] completed
-    Job = [temp_tutorial8/9.chunks -> temp_tutorial8/9.sums] completed
-Completed Task = step_6_calculate_sum_of_squares
-    Job = [[temp_tutorial8/1.sums, temp_tutorial8/10.sums, temp_tutorial8/2.sums, temp_tutorial8/3.sums, temp_tutorial8/4.sums, temp_tutorial8/5.sums, temp_tutorial8/6.sums, temp_tutorial8/7.sums, temp_tutorial8/8.sums, temp_tutorial8/9.sums] -> variance.result] completed
-hooray again
-whoppee again
-hooray
-Completed Task = step_7_calculate_variance</pre>
-</div>
-</div></blockquote>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../../contents.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Code for Step 8: Signal the completion of each stage of our pipeline</a><ul>
-<li><a class="reference internal" href="#code">Code</a></li>
-<li><a class="reference internal" href="#resulting-output">Resulting Output</a></li>
-</ul>
-</li>
-</ul>
-
-  <h4>Previous topic</h4>
-  <p class="topless"><a href="step7_merge_code.html"
-                        title="previous chapter">Code for Step 7: Merging results back together</a></p>
-  <h3>This Page</h3>
-  <ul class="this-page-menu">
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-    <h3> Quick Reference:</h3>
-    <ul>
-        <h4><a href="../../decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/originate.html">@originate</a>                           </li>
-            <li><a href="../../decorators/split.html">@split</a>                                   </li>
-            <li><a href="../../decorators/transform.html">@transform</a>                           </li>
-            <li><a href="../../decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="../../decorators/decorators.html#advanced">Advanced</a></h4>   
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-            <li><a href="../../decorators/subdivide.html">@subdivide</a>                           </li>
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-            <li><a href="../../decorators/collate.html">@collate</a>                               </li>
-            <li><a href="../../decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
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-            <li><a href="../../decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="../../decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="../../decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="../../decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="../../decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
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-        <h4><a href="../../decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="../../decorators/product.html">@product </a>                              </li>
-            <li><a href="../../decorators/permutations.html">@permutations </a>                    </li>
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-        <h4><a href="../../decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="../../decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="../../decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="../../decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="../../decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="../../pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="../../drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
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-  <div class="section" id="why-ruffus">
-<span id="design-why-ruffus"></span><span id="index-0"></span><h1>Why <em>Ruffus</em>?<a class="headerlink" href="#why-ruffus" title="Permalink to this headline">¶</a></h1>
-<p><strong>Cylindrophis ruffus</strong> is the name of the
-<a class="reference external" href="http://en.wikipedia.org/wiki/Cylindrophis_ruffus">red-tailed pipe snake</a> (bad python-y pun)
-which can be found in <a class="reference external" href="http://www.discoverhongkong.com/eng/index.html">Hong Kong</a> where the original author comes from.</p>
-<p><em>Ruffus</em> is a shy creature, and pretends to be a cobra or a <a class="reference external" href="http://en.wikipedia.org/wiki/File:Bandedkrait.jpg">banded krait</a> by putting up its red tail and ducking its
-head in its coils when startled.</p>
-<table border="1" class="docutils">
-<colgroup>
-<col width="28%" />
-<col width="72%" />
-</colgroup>
-<tbody valign="top">
-<tr class="row-odd"><td><img alt="_images/wikimedia_cyl_ruffus.jpg" class="first last" src="_images/wikimedia_cyl_ruffus.jpg" />
-</td>
-<td><a class="first last reference internal image-reference" href="_images/wikimedia_bandedkrait.jpg"><img alt="_images/wikimedia_bandedkrait.jpg" src="_images/wikimedia_bandedkrait.jpg" style="width: 462.0px; height: 346.5px;" /></a>
-</td>
-</tr>
-<tr class="row-even"><td><ul class="first last simple">
-<li>Not venomous</li>
-<li><a class="reference external" href="http://en.wikipedia.org/wiki/Mostly_Harmless">Mostly Harmless</a></li>
-</ul>
-</td>
-<td><ul class="first last simple">
-<li>Deadly poisonous</li>
-<li><a class="reference external" href="http://en.wikipedia.org/wiki/List_of_races_and_species_in_The_Hitchhiker's_Guide_to_the_Galaxy#Ravenous_Bugblatter_Beast_of_Traal">Seriously unfriendly</a></li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-<p>Be careful not to step on one when running down country park lanes at full speed
-in Hong Kong: this snake is a <a class="reference external" href="http://www.hkras.org/eng/info/hkspp.htm">rare breed</a>!</p>
-<p><em>Ruffus</em> does most of its work at night and sleeps during the day: typical of many (but alas not all) python programmers!</p>
-<p>The original <a class="reference external" href="http://upload.wikimedia.org/wikipedia/commons/a/a1/Cyl_ruffus_061212_2025_tdp.jpg">red-tail pipe</a> and <a class="reference external" href="http://en.wikipedia.org/wiki/File:AB_054_Banded_Krait.JPG">banded krait</a> images are from wikimedia.</p>
-</div>
-
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-          </div>
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-      <div class="sphinxsidebar">
-        <div class="sphinxsidebarwrapper">
-  <h4>Previous topic</h4>
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-  <p class="topless"><a href="examples/bioinformatics/index.html"
-                        title="next chapter">Construction of a simple pipeline to run BLAST jobs</a></p>
-  <h3>This Page</h3>
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-    <li><a href="_sources/why_ruffus.txt"
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-    Enter search terms or a module, class or function name.
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-    <h3> Quick Reference:</h3>
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-        <h4><a href="decorators/decorators.html#core">Core:</a></h4>   
-        <ul>
-            <li><a href="decorators/originate.html">@originate</a>                           </li>
-            <li><a href="decorators/split.html">@split</a>                                   </li>
-            <li><a href="decorators/transform.html">@transform</a>                           </li>
-            <li><a href="decorators/merge.html">@merge</a>                                   </li>
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-        <h4><a href="decorators/decorators.html#advanced">Advanced</a></h4>   
-        <ul>
-            <li><a href="decorators/subdivide.html">@subdivide</a>                           </li>
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-            <li><a href="decorators/collate.html">@collate</a>                               </li>
-            <li><a href="decorators/collate_ex.html">@collate (add_inputs)</a>               </li>
-            <li><a href="decorators/graphviz.html">@graphviz</a>                             </li>
-            <li><a href="decorators/mkdir.html">@mkdir</a>                                   </li>
-            <li><a href="decorators/follows.html">@follows / mkdir</a>                       </li>
-            <li><a href="decorators/posttask.html">@posttask touch_file</a>                  </li>
-            <li><a href="decorators/active_if.html">@active_if</a>                           </li>
-            <li><a href="decorators/jobs_limit.html">@jobs_limit</a>                         </li>
-        </ul>
-    
-        <h4><a href="decorators/decorators.html#combinatorics">Combinatorial:</a></h4>   
-        <ul>
-            <li><a href="decorators/product.html">@product </a>                              </li>
-            <li><a href="decorators/permutations.html">@permutations </a>                    </li>
-            <li><a href="decorators/combinations.html">@combinations </a>                    </li>
-            <li><a href="decorators/combinations_with_replacement.html">@combinations_ _with_replacement </a>                    </li>
-        </ul>
-
-                        
-        <h4><a href="decorators/decorators.html#esoteric">Esoteric</a></h4>   
-        <ul>
-            <li><a href="decorators/files_ex.html">@files (on the fly)</a>                   </li>
-            <li><a href="decorators/parallel.html">@parallel</a>                             </li>
-            <li><a href="decorators/check_if_uptodate.html">@check_if_uptodate</a>           </li>
-        </ul>
-
-
-        <h4 ><a href="decorators/indicator_objects.html">Indicator objects</a></h4>
-        <h4 >Pipeline functions</h4>
-        <ul>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-run">pipeline_run</a>                       </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout">pipeline_printout</a>                      </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-printout-graph">pipeline_printout_graph</a>          </li>
-            <li><a href="pipeline_functions.html#pipeline-functions-pipeline-get-task-names">pipeline_get_task_names</a>          </li>
-            <li><a href="drmaa_wrapper_functions.html#drmaa-wrapper-functions-drmaa_wrapper-run_job">drmaa_wrapper.run_job</a>          </li>
-        </ul>
-
-         <a href="todo.html">Future plans</a>
-    </ul>
-
-        </div>
-      </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="genindex.html" title="General Index"
-             >index</a></li>
-        <li class="right" >
-          <a href="examples/bioinformatics/index.html" title="Construction of a simple pipeline to run BLAST jobs"
-             >next</a> |</li>
-        <li class="right" >
-          <a href="gallery.html" title="Hall of Fame: User contributed flowcharts"
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-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
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\ No newline at end of file
diff --git a/doc/_build/latex/Makefile b/doc/_build/latex/Makefile
deleted file mode 100644
index 6b87ad8..0000000
--- a/doc/_build/latex/Makefile
+++ /dev/null
@@ -1,66 +0,0 @@
-# Makefile for Sphinx LaTeX output
-
-ALLDOCS = $(basename $(wildcard *.tex))
-ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
-ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
-
-# Prefix for archive names
-ARCHIVEPRREFIX =
-# Additional LaTeX options
-LATEXOPTS =
-
-all: $(ALLPDF)
-all-pdf: $(ALLPDF)
-all-dvi: $(ALLDVI)
-all-ps: all-dvi
-	for f in *.dvi; do dvips $$f; done
-
-all-pdf-ja:
-	for f in *.pdf *.png *.gif *.jpg *.jpeg; do extractbb $$f; done
-	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
-	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
-	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
-	-for f in *.idx; do mendex -U -f -d "`basename $$f .idx`.dic" -s python.ist $$f; done
-	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
-	for f in *.tex; do platex -kanji=utf8 $(LATEXOPTS) $$f; done
-	for f in *.dvi; do dvipdfmx $$f; done
-
-zip: all-$(FMT)
-	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
-	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
-	zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
-	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
-
-tar: all-$(FMT)
-	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
-	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
-	tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
-	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
-
-bz2: tar
-	bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
-
-# The number of LaTeX runs is quite conservative, but I don't expect it
-# to get run often, so the little extra time won't hurt.
-%.dvi: %.tex
-	latex $(LATEXOPTS) '$<'
-	latex $(LATEXOPTS) '$<'
-	latex $(LATEXOPTS) '$<'
-	-makeindex -s python.ist '$(basename $<).idx'
-	latex $(LATEXOPTS) '$<'
-	latex $(LATEXOPTS) '$<'
-
-%.pdf: %.tex
-	pdflatex $(LATEXOPTS) '$<'
-	pdflatex $(LATEXOPTS) '$<'
-	pdflatex $(LATEXOPTS) '$<'
-	-makeindex -s python.ist '$(basename $<).idx'
-	pdflatex $(LATEXOPTS) '$<'
-	pdflatex $(LATEXOPTS) '$<'
-
-clean:
-	rm -f *.dvi *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla
-
-.PHONY: all all-pdf all-dvi all-ps clean
-.PHONY: all-pdf-ja
-
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diff --git a/doc/_build/latex/fncychap.sty b/doc/_build/latex/fncychap.sty
deleted file mode 100644
index 9a56c04..0000000
--- a/doc/_build/latex/fncychap.sty
+++ /dev/null
@@ -1,683 +0,0 @@
-%%% Copyright   Ulf A. Lindgren
-%%%
-%%% Note        Premission is granted to modify this file under
-%%%             the condition that it is saved using another
-%%%             file and package name.
-%%%
-%%% Revision    1.1 (1997)
-%%%
-%%%             Jan. 8th Modified package name base date option
-%%%             Jan. 22th Modified FmN and FmTi for error in book.cls
-%%%                  \MakeUppercase{#}->{\MakeUppercase#}
-%%%             Apr. 6th Modified Lenny option to prevent undesired 
-%%%                  skip of line.
-%%%             Nov. 8th Fixed \@chapapp for AMS
-%%%
-%%% Revision    1.2 (1998)
-%%%
-%%%             Feb. 11th Fixed appendix problem related to Bjarne
-%%%             Aug. 11th Fixed problem related to 11pt and 12pt 
-%%%                  suggested by Tomas Lundberg. THANKS!
-%%%
-%%% Revision    1.3 (2004)
-%%%             Sep. 20th problem with frontmatter, mainmatter and
-%%%                  backmatter, pointed out by Lapo Mori
-%%%
-%%% Revision    1.31 (2004)
-%%%             Sep. 21th problem with the Rejne definition streched text
-%%%                  caused ugly gaps in the vrule aligned with the title
-%%%                  text. Kindly pointed out to me by Hendri Adriaens
-%%%
-%%% Revision    1.32 (2005)
-%%%             Jun. 23th compatibility problem with the KOMA class 'scrbook.cls'
-%%%                  a remedy is a redefinition of '\@schapter' in
-%%%                  line with that used in KOMA. The problem was pointed
-%%%                  out to me by Mikkel Holm Olsen
-%%%
-%%% Revision    1.33 (2005)
-%%%             Aug. 9th misspelled ``TWELV'' corrected, the error was pointed
-%%%                  out to me by George Pearson
-%%%
-%%% Revision    1.34 (2007)
-%%%             Added an alternative to Lenny provided by Peter
-%%%             Osborne (2005-11-28)
-%%%             Corrected front, main and back matter, based on input
-%%%             from Bas van Gils (2006-04-24)
-%%%             Jul. 30th Added Bjornstrup option provided by Jean-Marc
-%%%             Francois (2007-01-05).
-%%%             Reverted to \MakeUppercase{#} see rev 1.1, solved
-%%%             problem with MakeUppercase and MakeLowercase pointed
-%%%             out by Marco Feuerstein  (2007-06-06) 
-
-
-%%% Last modified   Jul. 2007
-
-\NeedsTeXFormat{LaTeX2e}[1995/12/01]
-\ProvidesPackage{fncychap}
-             [2007/07/30 v1.34
-                 LaTeX package (Revised chapters)]
-
-%%%% For conditional inclusion of color
-\newif\ifusecolor
-\usecolorfalse
-
-
-
-%%%% DEFINITION OF Chapapp variables
-\newcommand{\CNV}{\huge\bfseries}
-\newcommand{\ChNameVar}[1]{\renewcommand{\CNV}{#1}}
-
-
-%%%% DEFINITION OF TheChapter variables
-\newcommand{\CNoV}{\huge\bfseries}
-\newcommand{\ChNumVar}[1]{\renewcommand{\CNoV}{#1}}
-
-\newif\ifUCN
-\UCNfalse
-\newif\ifLCN
-\LCNfalse
-\def\ChNameLowerCase{\LCNtrue\UCNfalse}
-\def\ChNameUpperCase{\UCNtrue\LCNfalse}
-\def\ChNameAsIs{\UCNfalse\LCNfalse}
-
-%%%%% Fix for AMSBook 971008
-
-\@ifundefined{@chapapp}{\let\@chapapp\chaptername}{}
-
-
-%%%%% Fix for Bjarne and appendix 980211
-
-\newif\ifinapp
-\inappfalse
-\renewcommand\appendix{\par
-  \setcounter{chapter}{0}%
-  \setcounter{section}{0}%
-  \inapptrue%
-  \renewcommand\@chapapp{\appendixname}%
-  \renewcommand\thechapter{\@Alph\c at chapter}}
-
-%%%%% Fix for frontmatter, mainmatter, and backmatter 040920
-
-\@ifundefined{@mainmatter}{\newif\if at mainmatter \@mainmattertrue}{}
-
-%%%%%
-
-
-
-\newcommand{\FmN}[1]{%
-\ifUCN
-   {\MakeUppercase{#1}}\LCNfalse
-\else
-   \ifLCN
-      {\MakeLowercase{#1}}\UCNfalse
-   \else #1
-   \fi
-\fi}
-
-
-%%%% DEFINITION OF Title variables
-\newcommand{\CTV}{\Huge\bfseries}
-\newcommand{\ChTitleVar}[1]{\renewcommand{\CTV}{#1}}
-
-%%%% DEFINITION OF the basic rule width
-\newlength{\RW}
-\setlength{\RW}{1pt}
-\newcommand{\ChRuleWidth}[1]{\setlength{\RW}{#1}}
-
-\newif\ifUCT
-\UCTfalse
-\newif\ifLCT
-\LCTfalse
-\def\ChTitleLowerCase{\LCTtrue\UCTfalse}
-\def\ChTitleUpperCase{\UCTtrue\LCTfalse}
-\def\ChTitleAsIs{\UCTfalse\LCTfalse}
-\newcommand{\FmTi}[1]{%
-\ifUCT
-   {\MakeUppercase{#1}}\LCTfalse
-\else
-   \ifLCT
-      {\MakeLowercase{#1}}\UCTfalse
-   \else {#1}
-   \fi
-\fi}
-
-
-
-\newlength{\mylen}
-\newlength{\myhi}
-\newlength{\px}
-\newlength{\py}
-\newlength{\pyy}
-\newlength{\pxx}
-
-
-\def\mghrulefill#1{\leavevmode\leaders\hrule\@height #1\hfill\kern\z@}
-
-\newcommand{\DOCH}{%
-  \CNV\FmN{\@chapapp}\space \CNoV\thechapter
-  \par\nobreak
-  \vskip 20\p@
-  }
-\newcommand{\DOTI}[1]{%
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@
-    }
-\newcommand{\DOTIS}[1]{%
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@
-    }
-
-%%%%%% SONNY DEF
-
-\DeclareOption{Sonny}{%
-  \ChNameVar{\Large\sf}
-  \ChNumVar{\Huge}
-  \ChTitleVar{\Large\sf}
-  \ChRuleWidth{0.5pt}
-  \ChNameUpperCase
-  \renewcommand{\DOCH}{%
-    \raggedleft
-    \CNV\FmN{\@chapapp}\space \CNoV\thechapter
-    \par\nobreak
-    \vskip 40\p@}
-  \renewcommand{\DOTI}[1]{%
-    \CTV\raggedleft\mghrulefill{\RW}\par\nobreak
-    \vskip 5\p@
-    \CTV\FmTi{#1}\par\nobreak
-    \mghrulefill{\RW}\par\nobreak
-    \vskip 40\p@}
-  \renewcommand{\DOTIS}[1]{%
-    \CTV\raggedleft\mghrulefill{\RW}\par\nobreak
-    \vskip 5\p@
-    \CTV\FmTi{#1}\par\nobreak
-    \mghrulefill{\RW}\par\nobreak
-    \vskip 40\p@}
-}
-
-%%%%%% LENNY DEF
-
-\DeclareOption{Lenny}{%
-
-  \ChNameVar{\fontsize{14}{16}\usefont{OT1}{phv}{m}{n}\selectfont}
-  \ChNumVar{\fontsize{60}{62}\usefont{OT1}{ptm}{m}{n}\selectfont}
-  \ChTitleVar{\Huge\bfseries\rm}
-  \ChRuleWidth{1pt}
-  \renewcommand{\DOCH}{%
-    \settowidth{\px}{\CNV\FmN{\@chapapp}}
-    \addtolength{\px}{2pt}
-    \settoheight{\py}{\CNV\FmN{\@chapapp}}
-    \addtolength{\py}{1pt}
-
-    \settowidth{\mylen}{\CNV\FmN{\@chapapp}\space\CNoV\thechapter}
-    \addtolength{\mylen}{1pt}
-    \settowidth{\pxx}{\CNoV\thechapter}
-    \addtolength{\pxx}{-1pt}
-
-    \settoheight{\pyy}{\CNoV\thechapter}
-    \addtolength{\pyy}{-2pt}
-    \setlength{\myhi}{\pyy}
-    \addtolength{\myhi}{-1\py}
-    \par
-    \parbox[b]{\textwidth}{%
-    \rule[\py]{\RW}{\myhi}%
-    \hskip -\RW%
-    \rule[\pyy]{\px}{\RW}%
-    \hskip -\px%
-    \raggedright%
-    \CNV\FmN{\@chapapp}\space\CNoV\thechapter%
-    \hskip1pt%
-    \mghrulefill{\RW}%
-    \rule{\RW}{\pyy}\par\nobreak%
-    \vskip -\baselineskip%
-    \vskip -\pyy%
-    \hskip \mylen%
-    \mghrulefill{\RW}\par\nobreak%
-    \vskip \pyy}%
-    \vskip 20\p@}
- 
-
-  \renewcommand{\DOTI}[1]{%
-    \raggedright
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@}
-
-  \renewcommand{\DOTIS}[1]{%
-    \raggedright
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@}
- }
-
-%%%%%% Peter Osbornes' version of LENNY DEF
-
-\DeclareOption{PetersLenny}{%
-
-% five new lengths 
-\newlength{\bl}                           %  bottom left   : orig \space
-\setlength{\bl}{6pt}
-\newcommand{\BL}[1]{\setlength{\bl}{#1}}
-\newlength{\br}                           %  bottom right  : orig 1pt
-\setlength{\br}{1pt}
-\newcommand{\BR}[1]{\setlength{\br}{#1}}
-\newlength{\tl}                           %  top left      : orig 2pt
-\setlength{\tl}{2pt}
-\newcommand{\TL}[1]{\setlength{\tl}{#1}}
-\newlength{\trr}                           %  top right      :orig 1pt 
-\setlength{\trr}{1pt}
-\newcommand{\TR}[1]{\setlength{\trr}{#1}}
-\newlength{\blrule}                           %  top right      :orig 1pt 
-\setlength{\trr}{0pt}
-\newcommand{\BLrule}[1]{\setlength{\blrule}{#1}}
-
-
-  \ChNameVar{\fontsize{14}{16}\usefont{OT1}{phv}{m}{n}\selectfont}
-  \ChNumVar{\fontsize{60}{62}\usefont{OT1}{ptm}{m}{n}\selectfont}
-  \ChTitleVar{\Huge\bfseries\rm}
-  \ChRuleWidth{1pt}
-\renewcommand{\DOCH}{%
-
-
-%%%%%%%                                   tweaks for 1--9 and A--Z
-\ifcase\c at chapter\relax%
-\or\BL{-3pt}\TL{-4pt}\BR{0pt}\TR{-6pt}%1
-\or\BL{0pt}\TL{-4pt}\BR{2pt}\TR{-4pt}%2
-\or\BL{0pt}\TL{-4pt}\BR{2pt}\TR{-4pt}%3
-\or\BL{0pt}\TL{5pt}\BR{2pt}\TR{-4pt}%4
-\or\BL{0pt}\TL{3pt}\BR{2pt}\TR{-4pt}%5
-\or\BL{-1pt}\TL{0pt}\BR{2pt}\TR{-2pt}%6
-\or\BL{0pt}\TL{-3pt}\BR{2pt}\TR{-2pt}%7
-\or\BL{0pt}\TL{-3pt}\BR{2pt}\TR{-2pt}%8
-\or\BL{0pt}\TL{-3pt}\BR{-4pt}\TR{-2pt}%9
-\or\BL{-3pt}\TL{-3pt}\BR{2pt}\TR{-7pt}%10
-\or\BL{-6pt}\TL{-6pt}\BR{0pt}\TR{-9pt}%11
-\or\BL{-6pt}\TL{-6pt}\BR{2pt}\TR{-7pt}%12
-\or\BL{-5pt}\TL{-5pt}\BR{0pt}\TR{-9pt}%13
-\or\BL{-6pt}\TL{-6pt}\BR{0pt}\TR{-9pt}%14
-\or\BL{-3pt}\TL{-3pt}\BR{3pt}\TR{-6pt}%15
-\or\BL{-3pt}\TL{-3pt}\BR{3pt}\TR{-6pt}%16
-\or\BL{-5pt}\TL{-3pt}\BR{-8pt}\TR{-6pt}%17
-\or\BL{-5pt}\TL{-5pt}\BR{0pt}\TR{-9pt}%18
-\or\BL{-3pt}\TL{-3pt}\BR{-6pt}\TR{-9pt}%19
-\or\BL{0pt}\TL{0pt}\BR{0pt}\TR{-5pt}%20
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-
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-\or\BL{0pt}\TL{14pt}\BR{5pt}\TR{-19pt}%A
-\or\BL{0pt}\TL{-5pt}\BR{-3pt}\TR{-8pt}%B
-\or\BL{-3pt}\TL{-2pt}\BR{1pt}\TR{-6pt}\BLrule{0pt}%C
-\or\BL{0pt}\TL{-5pt}\BR{-3pt}\TR{-8pt}\BLrule{0pt}%D
-\or\BL{0pt}\TL{-5pt}\BR{2pt}\TR{-3pt}%E
-\or\BL{0pt}\TL{-5pt}\BR{-10pt}\TR{-1pt}%F
-\or\BL{-3pt}\TL{0pt}\BR{0pt}\TR{-7pt}%G
-\or\BL{0pt}\TL{-5pt}\BR{3pt}\TR{-1pt}%H
-\or\BL{0pt}\TL{-5pt}\BR{3pt}\TR{-1pt}%I
-\or\BL{2pt}\TL{0pt}\BR{-3pt}\TR{1pt}%J
-\or\BL{0pt}\TL{-5pt}\BR{3pt}\TR{-1pt}%K
-\or\BL{0pt}\TL{-5pt}\BR{2pt}\TR{-19pt}%L
-\or\BL{0pt}\TL{-5pt}\BR{3pt}\TR{-1pt}%M
-\or\BL{0pt}\TL{-5pt}\BR{-2pt}\TR{-1pt}%N
-\or\BL{-3pt}\TL{-2pt}\BR{-3pt}\TR{-11pt}%O
-\or\BL{0pt}\TL{-5pt}\BR{-9pt}\TR{-3pt}%P
-\or\BL{-3pt}\TL{-2pt}\BR{-3pt}\TR{-11pt}%Q
-\or\BL{0pt}\TL{-5pt}\BR{4pt}\TR{-8pt}%R
-\or\BL{-2pt}\TL{-2pt}\BR{-2pt}\TR{-7pt}%S
-\or\BL{-3pt}\TL{0pt}\BR{-5pt}\TR{4pt}\BLrule{8pt}%T
-\or\BL{-7pt}\TL{-11pt}\BR{-5pt}\TR{-7pt}\BLrule{0pt}%U
-\or\BL{-14pt}\TL{-5pt}\BR{-14pt}\TR{-1pt}\BLrule{14pt}%V
-\or\BL{-10pt}\TL{-9pt}\BR{-13pt}\TR{-3pt}\BLrule{7pt}%W
-\or\BL{0pt}\TL{-5pt}\BR{3pt}\TR{-1pt}\BLrule{0pt}%X
-\or\BL{-6pt}\TL{-4pt}\BR{-7pt}\TR{1pt}\BLrule{7pt}%Y
-\or\BL{0pt}\TL{-5pt}\BR{3pt}\TR{-1pt}\BLrule{0pt}%Z
-\fi\fi
-%%%%%%%
-    \settowidth{\px}{\CNV\FmN{\@chapapp}}
-    \addtolength{\px}{\tl}        %MOD change 2pt to \tl
-    \settoheight{\py}{\CNV\FmN{\@chapapp}}
-    \addtolength{\py}{1pt}
-
-    \settowidth{\mylen}{\CNV\FmN{\@chapapp}\space\CNoV\thechapter}
-    \addtolength{\mylen}{\trr}% MOD change 1pt to \tr
-    \settowidth{\pxx}{\CNoV\thechapter}
-    \addtolength{\pxx}{-1pt}
-
-    \settoheight{\pyy}{\CNoV\thechapter}
-    \addtolength{\pyy}{-2pt}
-    \setlength{\myhi}{\pyy}
-    \addtolength{\myhi}{-1\py}
-    \par
-    \parbox[b]{\textwidth}{%
-    \rule[\py]{\RW}{\myhi}%
-    \hskip -\RW%
-    \rule[\pyy]{\px}{\RW}% 
-    \hskip -\px%
-    \raggedright%
-    \CNV\FmN{\@chapapp}\rule{\blrule}{\RW}\hskip\bl\CNoV\thechapter%MOD 
-%    \CNV\FmN{\@chapapp}\space\CNoV\thechapter                     %ORIGINAL
-    \hskip\br%                           %MOD 1pt to \br
-    \mghrulefill{\RW}% 
-    \rule{\RW}{\pyy}\par\nobreak% 
-    \vskip -\baselineskip%
-    \vskip -\pyy%
-    \hskip \mylen%
-    \mghrulefill{\RW}\par\nobreak%
-    \vskip \pyy}%
-    \vskip 20\p@}
- 
-
-  \renewcommand{\DOTI}[1]{%
-    \raggedright
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@}
-
-  \renewcommand{\DOTIS}[1]{%
-    \raggedright
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@}
- }
-
-
-%
-
-
-%%%%%% BJORNSTRUP DEF
-
-\DeclareOption{Bjornstrup}{%
-  \usecolortrue
-  % pzc (Zapf Chancelery) is nice.  ppl (Palatino) is cool too.
-  \ChNumVar{\fontsize{76}{80}\usefont{OT1}{pzc}{m}{n}\selectfont}
-  \ChTitleVar{\raggedleft\Large\sffamily\bfseries}
-
-  \setlength{\myhi}{10pt}         % Space between grey box border and text
-  \setlength{\mylen}{\textwidth}
-  \addtolength{\mylen}{-2\myhi}
-  \renewcommand{\DOCH}{%
-    \settowidth{\py}{\CNoV\thechapter}
-    \addtolength{\py}{-10pt}      % Amount of space by which the
-%                                  % number is shifted right
-    \fboxsep=0pt%
-    \colorbox[gray]{.85}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}%
-    \kern-\py\raise20pt%
-    \hbox{\color[gray]{.5}\CNoV\thechapter}\\%
-  }
-  
-  \renewcommand{\DOTI}[1]{%
-    \nointerlineskip\raggedright%
-    \fboxsep=\myhi%
-    \vskip-1ex%
-    \colorbox[gray]{.85}{\parbox[t]{\mylen}{\CTV\FmTi{#1}}}\par\nobreak%
-    \vskip 40\p@%
-  }
-
-  \renewcommand{\DOTIS}[1]{%
-    \fboxsep=0pt
-    \colorbox[gray]{.85}{\rule{0pt}{40pt}\parbox[b]{\textwidth}{\hfill}}\\%
-    \nointerlineskip\raggedright%
-    \fboxsep=\myhi%
-    \colorbox[gray]{.85}{\parbox[t]{\mylen}{\CTV\FmTi{#1}}}\par\nobreak%
-    \vskip 40\p@%
-  }
-}
-
-
-%%%%%%% GLENN DEF
-
-
-\DeclareOption{Glenn}{%
-  \ChNameVar{\bfseries\Large\sf}
-  \ChNumVar{\Huge}
-  \ChTitleVar{\bfseries\Large\rm}
-  \ChRuleWidth{1pt}
-  \ChNameUpperCase
-  \ChTitleUpperCase
-  \renewcommand{\DOCH}{%
-    \settoheight{\myhi}{\CTV\FmTi{Test}}
-    \setlength{\py}{\baselineskip}
-    \addtolength{\py}{\RW}
-    \addtolength{\py}{\myhi}
-    \setlength{\pyy}{\py}
-    \addtolength{\pyy}{-1\RW}
-     
-    \raggedright
-    \CNV\FmN{\@chapapp}\space\CNoV\thechapter
-    \hskip 3pt\mghrulefill{\RW}\rule[-1\pyy]{2\RW}{\py}\par\nobreak}
-
-  \renewcommand{\DOTI}[1]{%
-    \addtolength{\pyy}{-4pt}
-    \settoheight{\myhi}{\CTV\FmTi{#1}}
-    \addtolength{\myhi}{\py}
-    \addtolength{\myhi}{-1\RW}
-    \vskip -1\pyy
-    \rule{2\RW}{\myhi}\mghrulefill{\RW}\hskip 2pt
-    \raggedleft\CTV\FmTi{#1}\par\nobreak
-    \vskip 80\p@}
-
-\newlength{\backskip}
-  \renewcommand{\DOTIS}[1]{%
-%    \setlength{\py}{10pt}
-%    \setlength{\pyy}{\py}
-%    \addtolength{\pyy}{\RW}
-%    \setlength{\myhi}{\baselineskip}
-%    \addtolength{\myhi}{\pyy}
-%    \mghrulefill{\RW}\rule[-1\py]{2\RW}{\pyy}\par\nobreak
-%    \addtolength{}{}
-%\vskip -1\baselineskip
-%    \rule{2\RW}{\myhi}\mghrulefill{\RW}\hskip 2pt
-%    \raggedleft\CTV\FmTi{#1}\par\nobreak
-%    \vskip 60\p@}
-%% Fix suggested by Tomas Lundberg
-    \setlength{\py}{25pt}  % eller vad man vill
-    \setlength{\pyy}{\py}
-    \setlength{\backskip}{\py}
-    \addtolength{\backskip}{2pt}
-    \addtolength{\pyy}{\RW}
-    \setlength{\myhi}{\baselineskip}
-    \addtolength{\myhi}{\pyy}
-    \mghrulefill{\RW}\rule[-1\py]{2\RW}{\pyy}\par\nobreak
-    \vskip -1\backskip
-    \rule{2\RW}{\myhi}\mghrulefill{\RW}\hskip 3pt %
-    \raggedleft\CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@}
- }
-
-%%%%%%% CONNY DEF
-
-\DeclareOption{Conny}{%
-  \ChNameUpperCase
-  \ChTitleUpperCase  
-  \ChNameVar{\centering\Huge\rm\bfseries}
-  \ChNumVar{\Huge}
-  \ChTitleVar{\centering\Huge\rm}
-  \ChRuleWidth{2pt}
-
-  \renewcommand{\DOCH}{%
-    \mghrulefill{3\RW}\par\nobreak
-    \vskip -0.5\baselineskip
-    \mghrulefill{\RW}\par\nobreak
-    \CNV\FmN{\@chapapp}\space \CNoV\thechapter
-    \par\nobreak
-    \vskip -0.5\baselineskip
-   }
-  \renewcommand{\DOTI}[1]{%
-    \mghrulefill{\RW}\par\nobreak
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 60\p@
-    }
-  \renewcommand{\DOTIS}[1]{%
-    \mghrulefill{\RW}\par\nobreak
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 60\p@
-    }
-  }
-
-%%%%%%% REJNE DEF
-
-\DeclareOption{Rejne}{%
-
-  \ChNameUpperCase
-  \ChTitleUpperCase  
-  \ChNameVar{\centering\Large\rm}
-  \ChNumVar{\Huge}
-  \ChTitleVar{\centering\Huge\rm}
-  \ChRuleWidth{1pt}
-  \renewcommand{\DOCH}{%
-    \settoheight{\py}{\CNoV\thechapter}
-    \parskip=0pt plus 1pt % Set parskip to default, just in case v1.31
-    \addtolength{\py}{-1pt}
-    \CNV\FmN{\@chapapp}\par\nobreak
-    \vskip 20\p@
-    \setlength{\myhi}{2\baselineskip}
-    \setlength{\px}{\myhi}
-    \addtolength{\px}{-1\RW}
-    \rule[-1\px]{\RW}{\myhi}\mghrulefill{\RW}\hskip
-    10pt\raisebox{-0.5\py}{\CNoV\thechapter}\hskip 10pt\mghrulefill{\RW}\rule[-1\px]{\RW}{\myhi}\par\nobreak
-     \vskip -3\p@% Added -2pt vskip to correct for streched text v1.31
-    }
-  \renewcommand{\DOTI}[1]{%
-    \setlength{\mylen}{\textwidth}
-    \parskip=0pt plus 1pt % Set parskip to default, just in case v1.31
-    \addtolength{\mylen}{-2\RW}
-    {\vrule width\RW}\parbox{\mylen}{\CTV\FmTi{#1}}{\vrule width\RW}\par\nobreak%
-    \vskip -3pt\rule{\RW}{2\baselineskip}\mghrulefill{\RW}\rule{\RW}{2\baselineskip}%
-    \vskip 60\p@% Added -2pt in vskip to correct for streched text v1.31
-    }
-  \renewcommand{\DOTIS}[1]{%
-    \setlength{\py}{\fboxrule}
-    \setlength{\fboxrule}{\RW}
-    \setlength{\mylen}{\textwidth}
-    \addtolength{\mylen}{-2\RW}
-    \fbox{\parbox{\mylen}{\vskip 2\baselineskip\CTV\FmTi{#1}\par\nobreak\vskip \baselineskip}} 
-    \setlength{\fboxrule}{\py}
-    \vskip 60\p@
-    }
-  }
-
-
-%%%%%%% BJARNE DEF
-
-\DeclareOption{Bjarne}{%
-  \ChNameUpperCase
-  \ChTitleUpperCase  
-  \ChNameVar{\raggedleft\normalsize\rm}
-  \ChNumVar{\raggedleft \bfseries\Large}
-  \ChTitleVar{\raggedleft \Large\rm}
-  \ChRuleWidth{1pt}
-
-
-%% Note thechapter -> c at chapter fix appendix bug
-%% Fixed misspelled 12
-
-  \newcounter{AlphaCnt}
-  \newcounter{AlphaDecCnt}
-  \newcommand{\AlphaNo}{%
-    \ifcase\number\theAlphaCnt
-      \ifnum\c at chapter=0
-        ZERO\else{}\fi
-    \or ONE\or TWO\or THREE\or FOUR\or FIVE
-    \or SIX\or SEVEN\or EIGHT\or NINE\or TEN
-    \or ELEVEN\or TWELVE\or THIRTEEN\or FOURTEEN\or FIFTEEN
-    \or SIXTEEN\or SEVENTEEN\or EIGHTEEN\or NINETEEN\fi
-}
-
-  \newcommand{\AlphaDecNo}{%
-    \setcounter{AlphaDecCnt}{0}
-    \@whilenum\number\theAlphaCnt>0\do
-      {\addtocounter{AlphaCnt}{-10}
-       \addtocounter{AlphaDecCnt}{1}}
-     \ifnum\number\theAlphaCnt=0
-     \else
-       \addtocounter{AlphaDecCnt}{-1}
-       \addtocounter{AlphaCnt}{10}
-     \fi
-     
-     
-    \ifcase\number\theAlphaDecCnt\or TEN\or TWENTY\or THIRTY\or
-    FORTY\or FIFTY\or SIXTY\or SEVENTY\or EIGHTY\or NINETY\fi
-    }
-  \newcommand{\TheAlphaChapter}{%
-    
-    \ifinapp 
-      \thechapter
-    \else
-      \setcounter{AlphaCnt}{\c at chapter}
-      \ifnum\c at chapter<20
-        \AlphaNo
-      \else
-        \AlphaDecNo\AlphaNo
-      \fi
-    \fi
-    }  
-  \renewcommand{\DOCH}{%
-    \mghrulefill{\RW}\par\nobreak
-    \CNV\FmN{\@chapapp}\par\nobreak 
-    \CNoV\TheAlphaChapter\par\nobreak
-    \vskip -1\baselineskip\vskip 5pt\mghrulefill{\RW}\par\nobreak
-    \vskip 20\p@
-    }
-  \renewcommand{\DOTI}[1]{%
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@
-    }
-  \renewcommand{\DOTIS}[1]{%
-    \CTV\FmTi{#1}\par\nobreak
-    \vskip 40\p@
-    }
-}
-
-\DeclareOption*{%
-  \PackageWarning{fancychapter}{unknown style option}
-  }
-
-\ProcessOptions* \relax
-
-\ifusecolor
-  \RequirePackage{color} 
-\fi
-\def\@makechapterhead#1{%
-  \vspace*{50\p@}%
-  {\parindent \z@ \raggedright \normalfont
-    \ifnum \c at secnumdepth >\m at ne
-      \if at mainmatter%%%%% Fix for frontmatter, mainmatter, and backmatter 040920
-        \DOCH
-      \fi
-    \fi
-    \interlinepenalty\@M
-    \if at mainmatter%%%%% Fix for frontmatter, mainmatter, and backmatter 060424
-      \DOTI{#1}%
-    \else%
-      \DOTIS{#1}%
-    \fi
-  }}
-
-
-%%% Begin: To avoid problem with scrbook.cls (fncychap version 1.32)
-
-%%OUT:
-%\def\@schapter#1{\if at twocolumn
-%                   \@topnewpage[\@makeschapterhead{#1}]%
-%                 \else
-%                   \@makeschapterhead{#1}%
-%                   \@afterheading
-%                 \fi}
-
-%%IN:
-\def\@schapter#1{%
-\if at twocolumn%
-  \@makeschapterhead{#1}%
-\else%
-  \@makeschapterhead{#1}%
-  \@afterheading%
-\fi}
-
-%%% End: To avoid problem with scrbook.cls (fncychap version 1.32)
-
-\def\@makeschapterhead#1{%
-  \vspace*{50\p@}%
-  {\parindent \z@ \raggedright
-    \normalfont
-    \interlinepenalty\@M
-    \DOTIS{#1}
-    \vskip 40\p@
-  }}
-
-\endinput
-
-
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diff --git a/doc/_build/latex/gallery_snp_annotation_consequences.png b/doc/_build/latex/gallery_snp_annotation_consequences.png
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diff --git a/doc/_build/latex/history_html_flowchart.png b/doc/_build/latex/history_html_flowchart.png
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diff --git a/doc/_build/latex/pretty_flowchart.png b/doc/_build/latex/pretty_flowchart.png
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diff --git a/doc/_build/latex/python.ist b/doc/_build/latex/python.ist
deleted file mode 100644
index 9ffa0f9..0000000
--- a/doc/_build/latex/python.ist
+++ /dev/null
@@ -1,11 +0,0 @@
-line_max 100
-headings_flag 1
-heading_prefix "  \\bigletter "
-
-preamble "\\begin{theindex}
-\\def\\bigletter#1{{\\Large\\sffamily#1}\\nopagebreak\\vspace{1mm}}
-
-"
-
-symhead_positive "{Symbols}"
-numhead_positive "{Numbers}"
diff --git a/doc/_build/latex/ruffus.aux b/doc/_build/latex/ruffus.aux
deleted file mode 100644
index 84ae53d..0000000
--- a/doc/_build/latex/ruffus.aux
+++ /dev/null
@@ -1,1937 +0,0 @@
-\relax 
-\providecommand\hyper at newdestlabel[2]{}
-\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
-\HyperFirstAtBeginDocument{\ifx\hyper at anchor\@undefined
-\global\let\oldcontentsline\contentsline
-\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
-\global\let\oldnewlabel\newlabel
-\gdef\newlabel#1#2{\newlabelxx{#1}#2}
-\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
-\AtEndDocument{\ifx\hyper at anchor\@undefined
-\let\contentsline\oldcontentsline
-\let\newlabel\oldnewlabel
-\fi}
-\fi}
-\global\let\hyper at last\relax 
-\gdef\HyperFirstAtBeginDocument#1{#1}
-\providecommand\HyField at AuxAddToFields[1]{}
-\providecommand\HyField at AuxAddToCoFields[2]{}
-\select at language{english}
-\@writefile{toc}{\select at language{english}}
-\@writefile{lof}{\select at language{english}}
-\@writefile{lot}{\select at language{english}}
-\newlabel{contents::doc}{{}{1}{}{section*.2}{}}
-\@writefile{toc}{\contentsline {chapter}{\numberline {1}Start Here:}{1}{chapter.1}}
-\@writefile{lof}{\addvspace {10\p@ }}
-\@writefile{lot}{\addvspace {10\p@ }}
-\newlabel{contents:glob}{{1}{1}{Start Here:}{chapter.1}{}}
-\newlabel{contents:ruffus-documentation}{{1}{1}{Start Here:}{chapter.1}{}}
-\newlabel{contents:start-here}{{1}{1}{Start Here:}{chapter.1}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {1.1}Installation}{1}{section.1.1}}
-\newlabel{installation:installation}{{1.1}{1}{Installation}{section.1.1}{}}
-\newlabel{installation::doc}{{1.1}{1}{Installation}{section.1.1}{}}
-\newlabel{installation:id1}{{1.1}{1}{Installation}{section.1.1}{}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {1.1.1}The easy way}{1}{subsection.1.1.1}}
-\newlabel{installation:the-easy-way}{{1.1.1}{1}{The easy way}{subsection.1.1.1}{}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {1.1.2}The most up-to-date code:}{1}{subsection.1.1.2}}
-\newlabel{installation:the-most-up-to-date-code}{{1.1.2}{1}{The most up-to-date code:}{subsection.1.1.2}{}}
-\@writefile{toc}{\contentsline {subsubsection}{Graphical flowcharts}{1}{subsubsection*.3}}
-\newlabel{installation:graphical-flowcharts}{{1.1.2}{1}{Graphical flowcharts}{subsubsection*.3}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {1.2}\textbf  {Ruffus} Manual: List of Chapters and Example code}{2}{section.1.2}}
-\newlabel{tutorials/new_tutorial/manual_contents:ruffus-manual-list-of-chapters-and-example-code}{{1.2}{2}{\textbf {Ruffus} Manual: List of Chapters and Example code}{section.1.2}{}}
-\newlabel{tutorials/new_tutorial/manual_contents::doc}{{1.2}{2}{\textbf {Ruffus} Manual: List of Chapters and Example code}{section.1.2}{}}
-\newlabel{tutorials/new_tutorial/manual_contents:new-manual-table-of-contents}{{1.2}{2}{\textbf {Ruffus} Manual: List of Chapters and Example code}{section.1.2}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {1.3}\textbf  {Chapter 1}: An introduction to basic \emph  {Ruffus} syntax}{3}{section.1.3}}
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-\newlabel{decorators/transform:decorators-transform-tasks-or-file-names}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.373}{}}
-\newlabel{decorators/transform:decorators-transform-suffix-string}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.374}{}}
-\newlabel{decorators/transform:decorators-transform-matching-regex}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.375}{}}
-\newlabel{decorators/transform:decorators-transform-matching-formatter}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.376}{}}
-\newlabel{decorators/transform:decorators-transform-output-pattern}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.377}{}}
-\newlabel{decorators/transform:decorators-transform-extra-parameters}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.378}{}}
-\newlabel{decorators/merge:decorators-merge}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.379}{}}
-\newlabel{decorators/merge:decorators-merge-tasks-or-file-names}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.380}{}}
-\newlabel{decorators/merge:tasks-or-file-names}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.381}{}}
-\newlabel{decorators/merge:decorators-merge-extra-parameters}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.382}{}}
-\newlabel{decorators/merge:extra-parameters}{{4.1.6}{237}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.383}{}}
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-\newlabel{decorators/merge:merge}{{4.1.7}{237}{@merge}{subsection.4.1.7}{}}
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-\newlabel{decorators/merge:merge-tasks-or-file-names-output-file-extra-parameters}{{4.1.7}{237}{\emph {@merge} ( \emph {tasks\_or\_file\_names}, \emph {output\_file}, {[}\emph {extra\_parameters},...{]} )}{subsubsection*.384}{}}
-\newlabel{decorators/merge:decorators-merge-tasks-or-file-names}{{4.1.7}{237}{\emph {@merge} ( \emph {tasks\_or\_file\_names}, \emph {output\_file}, {[}\emph {extra\_parameters},...{]} )}{section*.385}{}}
-\newlabel{decorators/merge:decorators-merge-output-file}{{4.1.7}{237}{\emph {@merge} ( \emph {tasks\_or\_file\_names}, \emph {output\_file}, {[}\emph {extra\_parameters},...{]} )}{section*.386}{}}
-\newlabel{decorators/merge:decorators-merge-extra-parameters}{{4.1.7}{237}{\emph {@merge} ( \emph {tasks\_or\_file\_names}, \emph {output\_file}, {[}\emph {extra\_parameters},...{]} )}{section*.387}{}}
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-\newlabel{decorators/subdivide:output-pattern}{{4.1.8}{239}{@subdivide}{section*.394}{}}
-\newlabel{decorators/subdivide:decorators-subdivide-matching-regex}{{4.1.8}{239}{@subdivide}{section*.395}{}}
-\newlabel{decorators/subdivide:matching-regex}{{4.1.8}{239}{@subdivide}{section*.396}{}}
-\newlabel{decorators/subdivide:decorators-subdivide-matching-formatter}{{4.1.8}{239}{@subdivide}{section*.397}{}}
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-\newlabel{decorators/subdivide:input-pattern-or-glob}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{subsubsection*.399}{}}
-\newlabel{decorators/subdivide:decorators-subdivide-input-pattern-or-glob}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} ) [...]
-\newlabel{decorators/subdivide:subdivide-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-inputs-input-pattern-or-glob-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph { [...]
-\newlabel{decorators/subdivide:decorators-subdivide-tasks-or-file-names}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{ [...]
-\newlabel{decorators/subdivide:decorators-subdivide-matching-regex}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{secti [...]
-\newlabel{decorators/subdivide:decorators-subdivide-matching-formatter}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{s [...]
-\newlabel{decorators/subdivide:decorators-subdivide-output-pattern}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{secti [...]
-\newlabel{decorators/subdivide:decorators-subdivide-input-pattern-or-glob}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} ) [...]
-\newlabel{decorators/subdivide:decorators-subdivide-extra-parameters}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{sec [...]
-\newlabel{decorators/transform_ex:decorators-transform-ex}{{4.1.8}{239}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.406}{}}
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-\newlabel{decorators/transform_ex:transform-with-add-inputs-and-inputs}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{subsection.4.1.9}{}}
-\newlabel{decorators/transform_ex::doc}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{subsection.4.1.9}{}}
-\newlabel{decorators/transform_ex:decorators-transform-tasks-or-file-names}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.407}{}}
-\newlabel{decorators/transform_ex:tasks-or-file-names}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.408}{}}
-\newlabel{decorators/transform_ex:decorators-transform-extra-parameters}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.409}{}}
-\newlabel{decorators/transform_ex:extra-parameters}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.410}{}}
-\newlabel{decorators/transform_ex:decorators-transform-output-pattern}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.411}{}}
-\newlabel{decorators/transform_ex:output-pattern}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.412}{}}
-\newlabel{decorators/transform_ex:decorators-transform-input-pattern-or-glob}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.413}{}}
-\newlabel{decorators/transform_ex:input-pattern-or-glob}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.414}{}}
-\newlabel{decorators/transform_ex:decorators-transform-matching-regex}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.415}{}}
-\newlabel{decorators/transform_ex:matching-regex}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.416}{}}
-\newlabel{decorators/transform_ex:decorators-transform-matching-formatter}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.417}{}}
-\newlabel{decorators/transform_ex:matching-formatter}{{4.1.9}{239}{@transform with \texttt {add\_inputs} and \texttt {inputs}}{section*.418}{}}
-\@writefile{toc}{\contentsline {subsubsection}{\emph  {@transform} ( \emph  {tasks\_or\_file\_names}, \emph  {suffix}\emph  {(}\emph  {suffix\_string}\emph  {)}\textbar {} \emph  {regex}\emph  {(}\emph  {matching\_regex}\emph  {)} \textbar {} \emph  {formatter}\emph  {(}\emph  {matching\_formatter}\emph  {)}, \emph  {inputs} \textbar {} \emph  {add\_inputs}\emph  {(}\emph  {input\_pattern\_or\_glob}\emph  {)}, \emph  {output\_pattern}, {[}\emph  {extra\_parameters},...{]} )}{239}{subsubs [...]
-\newlabel{decorators/transform_ex:suffix-string}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{subsubsection*.419}{}}
-\newlabel{decorators/transform_ex:transform-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-inputs-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textb [...]
-\newlabel{decorators/transform_ex:decorators-transform-suffix-string}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]}  [...]
-\newlabel{decorators/transform_ex:decorators-transform-tasks-or-file-names}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},. [...]
-\newlabel{decorators/transform_ex:decorators-transform-suffix-string}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]}  [...]
-\newlabel{decorators/transform_ex:decorators-transform-matching-regex}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} [...]
-\newlabel{decorators/transform_ex:decorators-transform-matching-formatter}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},.. [...]
-\newlabel{decorators/transform_ex:decorators-transform-input-pattern-or-glob}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters} [...]
-\newlabel{decorators/transform_ex:decorators-transform-output-pattern}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} [...]
-\newlabel{decorators/transform_ex:decorators-transform-extra-parameters}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{ [...]
-\newlabel{decorators/collate:decorators-collate}{{4.1.9}{239}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{section*.427}{}}
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-\newlabel{decorators/collate:decorators-collate-tasks-or-file-names}{{4.1.10}{239}{@collate}{section*.428}{}}
-\newlabel{decorators/collate:tasks-or-file-names}{{4.1.10}{239}{@collate}{section*.429}{}}
-\newlabel{decorators/collate:decorators-collate-extra-parameters}{{4.1.10}{239}{@collate}{section*.430}{}}
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-\newlabel{decorators/collate:decorators-collate-output-pattern}{{4.1.10}{239}{@collate}{section*.432}{}}
-\newlabel{decorators/collate:output-pattern}{{4.1.10}{239}{@collate}{section*.433}{}}
-\newlabel{decorators/collate:decorators-collate-matching-regex}{{4.1.10}{239}{@collate}{section*.434}{}}
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-\newlabel{decorators/files_re:decorators-files-re-output-pattern}{{4.1.26}{245}{Legacy design now deprecated. We suggest using \emph {@transform()} instead}{section*.599}{}}
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-\newlabel{task:ruffus.task.transform_param_factory}{{4.2.1}{249}{Parameter factories:}{section*.616}{}}
-\newlabel{task:ruffus.task.files_param_factory}{{4.2.1}{250}{Parameter factories:}{section*.617}{}}
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-\newlabel{proxy_logger:example-3}{{4.2.2}{251}{Example 3}{paragraph*.634}{}}
-\@writefile{toc}{\contentsline {paragraph}{To use:}{252}{paragraph*.635}}
-\newlabel{proxy_logger:to-use}{{4.2.2}{252}{To use:}{paragraph*.635}{}}
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diff --git a/doc/_build/latex/ruffus.idx b/doc/_build/latex/ruffus.idx
deleted file mode 100644
index 25b519b..0000000
--- a/doc/_build/latex/ruffus.idx
+++ /dev/null
@@ -1,270 +0,0 @@
-\indexentry{overview!Tutorial|hyperpage}{3}
-\indexentry{Tutorial!overview|hyperpage}{3}
-\indexentry{importing ruffus|hyperpage}{4}
-\indexentry{pipeline\_run!Tutorial|hyperpage}{8}
-\indexentry{Tutorial!pipeline\_run|hyperpage}{8}
-\indexentry{transform!Tutorial|hyperpage}{8}
-\indexentry{Tutorial!transform|hyperpage}{8}
-\indexentry{one to one @transform!Tutorial|hyperpage}{9}
-\indexentry{Tutorial!one to one @transform|hyperpage}{9}
-\indexentry{input / output parameters!Tutorial|hyperpage}{10}
-\indexentry{Tutorial!input / output parameters|hyperpage}{10}
-\indexentry{transforming in parallel!Tutorial|hyperpage}{11}
-\indexentry{Tutorial!transforming in parallel|hyperpage}{11}
-\indexentry{output\_from!referring to functions before they are defined|hyperpage}{13}
-\indexentry{referring to functions before they are defined!output\_from|hyperpage}{13}
-\indexentry{output\_from!defining tasks out of order|hyperpage}{13}
-\indexentry{defining tasks out of order!output\_from|hyperpage}{13}
-\indexentry{@transform!multiple dependencies|hyperpage}{14}
-\indexentry{multiple dependencies!@transform|hyperpage}{14}
-\indexentry{@follow!imposing order with|hyperpage}{14}
-\indexentry{imposing order with!@follow|hyperpage}{14}
-\indexentry{@follows!mkdir (Manual)|hyperpage}{15}
-\indexentry{mkdir!@follows (Manual)|hyperpage}{15}
-\indexentry{inputs parameters!globs|hyperpage}{15}
-\indexentry{globs!inputs parameters|hyperpage}{15}
-\indexentry{globs in input parameters!Tutorial|hyperpage}{15}
-\indexentry{Tutorial!globs in input parameters|hyperpage}{15}
-\indexentry{Mixing tasks, globs and file names!Tutorial|hyperpage}{15}
-\indexentry{Tutorial!Mixing tasks, globs and file names|hyperpage}{15}
-\indexentry{originate!Tutorial|hyperpage}{16}
-\indexentry{Tutorial!originate|hyperpage}{16}
-\indexentry{pipeline\_printout!Tutorial|hyperpage}{17}
-\indexentry{Tutorial!pipeline\_printout|hyperpage}{17}
-\indexentry{command line!Tutorial|hyperpage}{20}
-\indexentry{Tutorial!command line|hyperpage}{20}
-\indexentry{pipeline\_printout\_graph!Tutorial|hyperpage}{25}
-\indexentry{Tutorial!pipeline\_printout\_graph|hyperpage}{25}
-\indexentry{formatter!Tutorial|hyperpage}{29}
-\indexentry{Tutorial!formatter|hyperpage}{29}
-\indexentry{suffix!Tutorial|hyperpage}{29}
-\indexentry{Tutorial!suffix|hyperpage}{29}
-\indexentry{regex!Tutorial|hyperpage}{29}
-\indexentry{Tutorial!regex|hyperpage}{29}
-\indexentry{output file names!Tutorial|hyperpage}{29}
-\indexentry{Tutorial!output file names|hyperpage}{29}
-\indexentry{mkdir!Tutorial|hyperpage}{37}
-\indexentry{Tutorial!mkdir|hyperpage}{37}
-\indexentry{Up to date!Tutorial|hyperpage}{39}
-\indexentry{Tutorial!Up to date|hyperpage}{39}
-\indexentry{Task completion!Tutorial|hyperpage}{39}
-\indexentry{Tutorial!Task completion|hyperpage}{39}
-\indexentry{Exceptions!Tutorial|hyperpage}{39}
-\indexentry{Tutorial!Exceptions|hyperpage}{39}
-\indexentry{Interrupted Pipeline!Tutorial|hyperpage}{39}
-\indexentry{Tutorial!Interrupted Pipeline|hyperpage}{39}
-\indexentry{Tutorial!interrupting tasks|hyperpage}{40}
-\indexentry{interrupting tasks!Tutorial|hyperpage}{40}
-\indexentry{Tutorial!Regenerating the checkpoint file|hyperpage}{43}
-\indexentry{Regenerating the checkpoint file!Tutorial|hyperpage}{43}
-\indexentry{rules!for rerunning jobs|hyperpage}{43}
-\indexentry{for rerunning jobs!rules|hyperpage}{43}
-\indexentry{Exception!Missing input files|hyperpage}{43}
-\indexentry{Missing input files!Exception|hyperpage}{43}
-\indexentry{Manual!Timestamp resolution|hyperpage}{44}
-\indexentry{Timestamp resolution!Manual|hyperpage}{44}
-\indexentry{Manual!flag files|hyperpage}{44}
-\indexentry{flag files!Manual|hyperpage}{44}
-\indexentry{decorators\_compendium!Tutorial|hyperpage}{44}
-\indexentry{Tutorial!decorators\_compendium|hyperpage}{44}
-\indexentry{split!Tutorial|hyperpage}{47}
-\indexentry{Tutorial!split|hyperpage}{47}
-\indexentry{merge!Tutorial|hyperpage}{51}
-\indexentry{Tutorial!merge|hyperpage}{51}
-\indexentry{multiprocessing!Tutorial|hyperpage}{52}
-\indexentry{Tutorial!multiprocessing|hyperpage}{52}
-\indexentry{pipeline\_run(multiprocess)!Tutorial|hyperpage}{53}
-\indexentry{Tutorial!pipeline\_run(multiprocess)|hyperpage}{53}
-\indexentry{data sharing across processes!Tutorial|hyperpage}{53}
-\indexentry{Tutorial!data sharing across processes|hyperpage}{53}
-\indexentry{@jobs\_limit!Tutorial|hyperpage}{53}
-\indexentry{Tutorial!@jobs\_limit|hyperpage}{53}
-\indexentry{pipeline\_run touch mode!Tutorial|hyperpage}{55}
-\indexentry{Tutorial!pipeline\_run touch mode|hyperpage}{55}
-\indexentry{touch mode pipeline\_run!Tutorial|hyperpage}{55}
-\indexentry{Tutorial!touch mode pipeline\_run|hyperpage}{55}
-\indexentry{logging!Tutorial|hyperpage}{56}
-\indexentry{Tutorial!logging|hyperpage}{56}
-\indexentry{pipeline\_run verbosity!Tutorial|hyperpage}{57}
-\indexentry{Tutorial!pipeline\_run verbosity|hyperpage}{57}
-\indexentry{logging with ruffus.cmdline!Tutorial|hyperpage}{57}
-\indexentry{Tutorial!logging with ruffus.cmdline|hyperpage}{57}
-\indexentry{logging customising!Tutorial|hyperpage}{57}
-\indexentry{Tutorial!logging customising|hyperpage}{57}
-\indexentry{logging your own message!Tutorial|hyperpage}{58}
-\indexentry{Tutorial!logging your own message|hyperpage}{58}
-\indexentry{@subdivide!Tutorial|hyperpage}{59}
-\indexentry{Tutorial!@subdivide|hyperpage}{59}
-\indexentry{@collate!Tutorial|hyperpage}{59}
-\indexentry{Tutorial!@collate|hyperpage}{59}
-\indexentry{combinatorics!Tutorial|hyperpage}{62}
-\indexentry{Tutorial!combinatorics|hyperpage}{62}
-\indexentry{@active\_if!Tutorial|hyperpage}{68}
-\indexentry{Tutorial!@active\_if|hyperpage}{68}
-\indexentry{posttask!Tutorial|hyperpage}{71}
-\indexentry{Tutorial!posttask|hyperpage}{71}
-\indexentry{@posttask!touchfile (Manual)|hyperpage}{71}
-\indexentry{touchfile !@posttask (Manual)|hyperpage}{71}
-\indexentry{inputs!Tutorial|hyperpage}{72}
-\indexentry{Tutorial!inputs|hyperpage}{72}
-\indexentry{add\_inputs!Tutorial|hyperpage}{72}
-\indexentry{Tutorial!add\_inputs|hyperpage}{72}
-\indexentry{string substiution for inputs!Tutorial|hyperpage}{72}
-\indexentry{Tutorial!string substiution for inputs|hyperpage}{72}
-\indexentry{on\_the\_fly!Tutorial|hyperpage}{75}
-\indexentry{Tutorial!on\_the\_fly|hyperpage}{75}
-\indexentry{@files!Tutorial on-the-fly parameter generation|hyperpage}{76}
-\indexentry{Tutorial on-the-fly parameter generation!@files|hyperpage}{76}
-\indexentry{@parallel!Tutorial|hyperpage}{78}
-\indexentry{Tutorial!@parallel|hyperpage}{78}
-\indexentry{check\_if\_uptodate!Tutorial|hyperpage}{79}
-\indexentry{Tutorial!check\_if\_uptodate|hyperpage}{79}
-\indexentry{flowchart colours!Tutorial|hyperpage}{80}
-\indexentry{Tutorial!flowchart colours|hyperpage}{80}
-\indexentry{Checking dependencies!Tutorial|hyperpage}{81}
-\indexentry{Tutorial!Checking dependencies|hyperpage}{81}
-\indexentry{exceptions!Tutorial|hyperpage}{82}
-\indexentry{Tutorial!exceptions|hyperpage}{82}
-\indexentry{signalling|hyperpage}{84}
-\indexentry{interrupts|hyperpage}{84}
-\indexentry{break|hyperpage}{84}
-\indexentry{errors|hyperpage}{84}
-\indexentry{exceptions|hyperpage}{84}
-\indexentry{multiple errors|hyperpage}{84}
-\indexentry{Ruffus names list!Tutorial|hyperpage}{85}
-\indexentry{Tutorial!Ruffus names list|hyperpage}{85}
-\indexentry{deprecated @files!Tutorial|hyperpage}{87}
-\indexentry{Tutorial!deprecated @files|hyperpage}{87}
-\indexentry{@files!Manual|hyperpage}{87}
-\indexentry{Manual!@files|hyperpage}{87}
-\indexentry{@files!in parallel|hyperpage}{88}
-\indexentry{in parallel!@files|hyperpage}{88}
-\indexentry{@files!check if up to date|hyperpage}{89}
-\indexentry{check if up to date!@files|hyperpage}{89}
-\indexentry{deprecated @files\_re!Tutorial|hyperpage}{90}
-\indexentry{Tutorial!deprecated @files\_re|hyperpage}{90}
-\indexentry{combine!Manual|hyperpage}{90}
-\indexentry{Manual!combine|hyperpage}{90}
-\indexentry{flowchart colours!Tutorial|hyperpage}{136}
-\indexentry{Tutorial!flowchart colours|hyperpage}{136}
-\indexentry{pipeline functions!pipeline\_run|hyperpage}{145}
-\indexentry{pipeline\_run!Run pipeline|hyperpage}{145}
-\indexentry{Run pipeline!pipeline\_run|hyperpage}{145}
-\indexentry{pipeline functions!pipeline\_run|hyperpage}{147}
-\indexentry{pipeline\_printout!Printout simulated run of the pipeline|hyperpage}{147}
-\indexentry{Printout simulated run of the pipeline!pipeline\_printout|hyperpage}{147}
-\indexentry{pipeline functions!pipeline\_printout\_graph|hyperpage}{148}
-\indexentry{pipeline\_printout\_graph!print flowchart representation of pipeline functions|hyperpage}{148}
-\indexentry{print flowchart representation of pipeline functions!pipeline\_printout\_graph|hyperpage}{148}
-\indexentry{pipeline functions!pipeline\_get\_task\_names|hyperpage}{151}
-\indexentry{pipeline\_get\_task\_names!print list of task names without running the pipeline|hyperpage}{151}
-\indexentry{print list of task names without running the pipeline!pipeline\_get\_task\_names|hyperpage}{151}
-\indexentry{drmaa !run\_job|hyperpage}{151}
-\indexentry{run\_job!Run drmaa|hyperpage}{151}
-\indexentry{Run drmaa!run\_job|hyperpage}{151}
-\indexentry{Design!Ruffus|hyperpage}{155}
-\indexentry{Ruffus!Design|hyperpage}{155}
-\indexentry{Design!Comparison of Ruffus with alternatives|hyperpage}{159}
-\indexentry{Comparison of Ruffus with alternatives!Design|hyperpage}{159}
-\indexentry{Acknowledgements|hyperpage}{159}
-\indexentry{task|hyperindexformat{\textbf}}{200}
-\indexentry{job|hyperindexformat{\textbf}}{200}
-\indexentry{decorator|hyperindexformat{\textbf}}{201}
-\indexentry{generator|hyperindexformat{\textbf}}{201}
-\indexentry{Ruffus!Etymology|hyperpage}{204}
-\indexentry{Etymology!Ruffus|hyperpage}{204}
-\indexentry{Ruffus!Name origins|hyperpage}{204}
-\indexentry{Name origins!Ruffus|hyperpage}{204}
-\indexentry{Indicator Object (Disambiguating parameters)|hyperpage}{228}
-\indexentry{formatter!Indicator Object (Disambiguating parameters)|hyperpage}{228}
-\indexentry{Indicator Object (Disambiguating parameters)!formatter|hyperpage}{228}
-\indexentry{suffix!Indicator Object (Disambiguating parameters)|hyperpage}{231}
-\indexentry{Indicator Object (Disambiguating parameters)!suffix|hyperpage}{231}
-\indexentry{regex!Indicator Object (Disambiguating parameters)|hyperpage}{231}
-\indexentry{Indicator Object (Disambiguating parameters)!regex|hyperpage}{231}
-\indexentry{add\_inputs!Indicator Object (Adding additional input parameters)|hyperpage}{232}
-\indexentry{Indicator Object (Adding additional input parameters)!add\_inputs|hyperpage}{232}
-\indexentry{inputs!Indicator Object (Replacing input parameters)|hyperpage}{233}
-\indexentry{Indicator Object (Replacing input parameters)!inputs|hyperpage}{233}
-\indexentry{@follows!mkdir (Syntax)|hyperpage}{234}
-\indexentry{mkdir!@follows (Syntax)|hyperpage}{234}
-\indexentry{Indicator Object (Disambiguating parameters)!mkdir|hyperpage}{234}
-\indexentry{@posttask!touch\_file (Syntax)|hyperpage}{234}
-\indexentry{touch\_file!@posttask (Syntax)|hyperpage}{234}
-\indexentry{Indicator Object (Disambiguating parameters)!touch\_file|hyperpage}{234}
-\indexentry{output\_from!Indicator Object (Disambiguating parameters)|hyperpage}{234}
-\indexentry{Indicator Object (Disambiguating parameters)!output\_from|hyperpage}{234}
-\indexentry{@files\_re!combine (Deprecated Syntax)|hyperpage}{235}
-\indexentry{combine!@follows (Deprecated Syntax)|hyperpage}{235}
-\indexentry{Indicator Object (Disambiguating parameters)!combine|hyperpage}{235}
-\indexentry{@originate!Syntax|hyperpage}{237}
-\indexentry{Syntax!@originate|hyperpage}{237}
-\indexentry{@split!Syntax|hyperpage}{237}
-\indexentry{Syntax!@split|hyperpage}{237}
-\indexentry{@transform!Syntax|hyperpage}{237}
-\indexentry{Syntax!@transform|hyperpage}{237}
-\indexentry{@merge!Syntax|hyperpage}{237}
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-\indexentry{pipeline\_printout() (in module ruffus.task)|hyperpage}{247}
-\indexentry{pipeline\_printout\_graph() (in module ruffus.task)|hyperpage}{248}
-\indexentry{t\_black\_hole\_logger (class in ruffus.task)|hyperpage}{249}
-\indexentry{t\_stderr\_logger (class in ruffus.task)|hyperpage}{249}
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-\indexentry{files\_param\_factory() (in module ruffus.task)|hyperpage}{250}
-\indexentry{args\_param\_factory() (in module ruffus.task)|hyperpage}{250}
-\indexentry{split\_param\_factory() (in module ruffus.task)|hyperpage}{250}
-\indexentry{job\_wrapper\_generic() (in module ruffus.task)|hyperpage}{250}
-\indexentry{job\_wrapper\_io\_files() (in module ruffus.task)|hyperpage}{250}
-\indexentry{job\_wrapper\_mkdir() (in module ruffus.task)|hyperpage}{250}
-\indexentry{needs\_update\_check\_modify\_time() (in module ruffus.task)|hyperpage}{250}
-\indexentry{needs\_update\_check\_directory\_missing() (in module ruffus.task)|hyperpage}{250}
-\indexentry{ruffus.proxy\_logger (module)|hyperpage}{251}
-\indexentry{make\_shared\_logger\_and\_proxy() (in module ruffus.proxy\_logger)|hyperpage}{252}
-\indexentry{setup\_std\_shared\_logger() (in module ruffus.proxy\_logger)|hyperpage}{252}
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diff --git a/doc/_build/latex/ruffus.out b/doc/_build/latex/ruffus.out
deleted file mode 100644
index b7c99fb..0000000
--- a/doc/_build/latex/ruffus.out
+++ /dev/null
@@ -1,77 +0,0 @@
-\BOOKMARK [0][-]{chapter.1}{Start Here:}{}% 1
-\BOOKMARK [1][-]{section.1.1}{Installation}{chapter.1}% 2
-\BOOKMARK [1][-]{section.1.2}{Ruffus Manual: List of Chapters and Example code}{chapter.1}% 3
-\BOOKMARK [1][-]{section.1.3}{Chapter 1: An introduction to basic Ruffus syntax}{chapter.1}% 4
-\BOOKMARK [1][-]{section.1.4}{Chapter 2: Transforming data in a pipeline with @transform}{chapter.1}% 5
-\BOOKMARK [1][-]{section.1.5}{Chapter 3: More on @transform-ing data}{chapter.1}% 6
-\BOOKMARK [1][-]{section.1.6}{Chapter 4: Creating files with @originate}{chapter.1}% 7
-\BOOKMARK [1][-]{section.1.7}{Chapter 5: Understanding how your pipeline works with pipeline\137printout\(...\)}{chapter.1}% 8
-\BOOKMARK [1][-]{section.1.8}{Chapter 6: Running Ruffus from the command line with ruffus.cmdline}{chapter.1}% 9
-\BOOKMARK [1][-]{section.1.9}{Chapter 7: Displaying the pipeline visually with pipeline\137printout\137graph\(...\)}{chapter.1}% 10
-\BOOKMARK [1][-]{section.1.10}{Chapter 8: Specifying output file names with formatter\(\) and regex\(\)}{chapter.1}% 11
-\BOOKMARK [1][-]{section.1.11}{Chapter 9: Preparing directories for output with @mkdir\(\)}{chapter.1}% 12
-\BOOKMARK [1][-]{section.1.12}{Chapter 10: Checkpointing: Interrupted Pipelines and Exceptions}{chapter.1}% 13
-\BOOKMARK [1][-]{section.1.13}{Chapter 11: Pipeline topologies and a compendium of Ruffus decorators}{chapter.1}% 14
-\BOOKMARK [1][-]{section.1.14}{Chapter 12: Splitting up large tasks / files with @split}{chapter.1}% 15
-\BOOKMARK [1][-]{section.1.15}{Chapter 13: @merge multiple input into a single result}{chapter.1}% 16
-\BOOKMARK [1][-]{section.1.16}{Chapter 14: Multiprocessing, drmaa and Computation Clusters}{chapter.1}% 17
-\BOOKMARK [1][-]{section.1.17}{Chapter 15: Logging progress through a pipeline}{chapter.1}% 18
-\BOOKMARK [1][-]{section.1.18}{Chapter 16: @subdivide tasks to run efficiently and regroup with @collate}{chapter.1}% 19
-\BOOKMARK [1][-]{section.1.19}{Chapter 17: @combinations, @permutations and all versus all @product}{chapter.1}% 20
-\BOOKMARK [1][-]{section.1.20}{Chapter 18: Turning parts of the pipeline on and off at runtime with @active\137if}{chapter.1}% 21
-\BOOKMARK [1][-]{section.1.21}{Chapter 19: Signal the completion of each stage of our pipeline with @posttask}{chapter.1}% 22
-\BOOKMARK [1][-]{section.1.22}{Chapter 20: Manipulating task inputs via string substitution using inputs\(\) and add\137inputs\(\)}{chapter.1}% 23
-\BOOKMARK [1][-]{section.1.23}{Chapter 21: Esoteric: Generating parameters on the fly with @files}{chapter.1}% 24
-\BOOKMARK [1][-]{section.1.24}{Chapter 22: Esoteric: Running jobs in parallel without files using @parallel}{chapter.1}% 25
-\BOOKMARK [1][-]{section.1.25}{Chapter 23: Esoteric: Writing custom functions to decide which jobs are up to date with @check\137if\137uptodate}{chapter.1}% 26
-\BOOKMARK [1][-]{section.1.26}{Appendix 1: Flow Chart Colours with pipeline\137printout\137graph\(...\)}{chapter.1}% 27
-\BOOKMARK [1][-]{section.1.27}{Appendix 2: How dependency is checked}{chapter.1}% 28
-\BOOKMARK [1][-]{section.1.28}{Appendix 3: Exceptions thrown inside pipelines}{chapter.1}% 29
-\BOOKMARK [1][-]{section.1.29}{Appendix 4: Names exported from Ruffus}{chapter.1}% 30
-\BOOKMARK [1][-]{section.1.30}{Appendix 5: @files: Deprecated syntax}{chapter.1}% 31
-\BOOKMARK [1][-]{section.1.31}{Appendix 6: @files\137re: Deprecated syntax using regular expressions}{chapter.1}% 32
-\BOOKMARK [1][-]{section.1.32}{Chapter 1: Python Code for An introduction to basic Ruffus syntax}{chapter.1}% 33
-\BOOKMARK [1][-]{section.1.33}{Chapter 1: Python Code for Transforming data in a pipeline with @transform}{chapter.1}% 34
-\BOOKMARK [1][-]{section.1.34}{Chapter 3: Python Code for More on @transform-ing data}{chapter.1}% 35
-\BOOKMARK [1][-]{section.1.35}{Chapter 4: Python Code for Creating files with @originate}{chapter.1}% 36
-\BOOKMARK [1][-]{section.1.36}{Chapter 5: Python Code for Understanding how your pipeline works with pipeline\137printout\(...\)}{chapter.1}% 37
-\BOOKMARK [1][-]{section.1.37}{Chapter 7: Python Code for Displaying the pipeline visually with pipeline\137printout\137graph\(...\)}{chapter.1}% 38
-\BOOKMARK [1][-]{section.1.38}{Chapter 8: Python Code for Specifying output file names with formatter\(\) and regex\(\)}{chapter.1}% 39
-\BOOKMARK [1][-]{section.1.39}{Chapter 9: Python Code for Preparing directories for output with @mkdir\(\)}{chapter.1}% 40
-\BOOKMARK [1][-]{section.1.40}{Chapter 10: Python Code for Checkpointing: Interrupted Pipelines and Exceptions}{chapter.1}% 41
-\BOOKMARK [1][-]{section.1.41}{Chapter 12: Python Code for Splitting up large tasks / files with @split}{chapter.1}% 42
-\BOOKMARK [1][-]{section.1.42}{Chapter 13: Python Code for @merge multiple input into a single result}{chapter.1}% 43
-\BOOKMARK [1][-]{section.1.43}{Chapter 14: Python Code for Multiprocessing, drmaa and Computation Clusters}{chapter.1}% 44
-\BOOKMARK [1][-]{section.1.44}{Chapter 15: Python Code for Logging progress through a pipeline}{chapter.1}% 45
-\BOOKMARK [1][-]{section.1.45}{Chapter 16: Python Code for @subdivide tasks to run efficiently and regroup with @collate}{chapter.1}% 46
-\BOOKMARK [1][-]{section.1.46}{Chapter 17: Python Code for @combinations, @permutations and all versus all @product}{chapter.1}% 47
-\BOOKMARK [1][-]{section.1.47}{Chapter 20: Python Code for Manipulating task inputs via string substitution using inputs\(\) and add\137inputs\(\)}{chapter.1}% 48
-\BOOKMARK [1][-]{section.1.48}{Chapter 21: Esoteric: Python Code for Generating parameters on the fly with @files}{chapter.1}% 49
-\BOOKMARK [1][-]{section.1.49}{Appendix 1: Python code for Flow Chart Colours with pipeline\137printout\137graph\(...\)}{chapter.1}% 50
-\BOOKMARK [0][-]{chapter.2}{Overview:}{}% 51
-\BOOKMARK [1][-]{section.2.1}{Cheat Sheet}{chapter.2}% 52
-\BOOKMARK [1][-]{section.2.2}{Pipeline functions}{chapter.2}% 53
-\BOOKMARK [1][-]{section.2.3}{drmaa functions}{chapter.2}% 54
-\BOOKMARK [1][-]{section.2.4}{Installation}{chapter.2}% 55
-\BOOKMARK [1][-]{section.2.5}{Design \046 Architecture}{chapter.2}% 56
-\BOOKMARK [1][-]{section.2.6}{Major Features added to Ruffus}{chapter.2}% 57
-\BOOKMARK [1][-]{section.2.7}{Fixed Bugs}{chapter.2}% 58
-\BOOKMARK [1][-]{section.2.8}{Future Changes to Ruffus}{chapter.2}% 59
-\BOOKMARK [1][-]{section.2.9}{Planned Improvements to Ruffus}{chapter.2}% 60
-\BOOKMARK [1][-]{section.2.10}{Implementation Tips}{chapter.2}% 61
-\BOOKMARK [1][-]{section.2.11}{Implementation notes}{chapter.2}% 62
-\BOOKMARK [1][-]{section.2.12}{FAQ}{chapter.2}% 63
-\BOOKMARK [1][-]{section.2.13}{Glossary}{chapter.2}% 64
-\BOOKMARK [1][-]{section.2.14}{Hall of Fame: User contributed flowcharts}{chapter.2}% 65
-\BOOKMARK [1][-]{section.2.15}{Why Ruffus?}{chapter.2}% 66
-\BOOKMARK [0][-]{chapter.3}{Examples}{}% 67
-\BOOKMARK [1][-]{section.3.1}{Construction of a simple pipeline to run BLAST jobs}{chapter.3}% 68
-\BOOKMARK [1][-]{section.3.2}{Part 2: A slightly more practical pipeline to run blasts jobs}{chapter.3}% 69
-\BOOKMARK [1][-]{section.3.3}{Ruffus code}{chapter.3}% 70
-\BOOKMARK [1][-]{section.3.4}{Ruffus code}{chapter.3}% 71
-\BOOKMARK [1][-]{section.3.5}{Example code for FAQ Good practices: ``What is the best way of handling data in file pairs \(or triplets etc.\)?''}{chapter.3}% 72
-\BOOKMARK [0][-]{chapter.4}{Reference:}{}% 73
-\BOOKMARK [1][-]{section.4.1}{Decorators}{chapter.4}% 74
-\BOOKMARK [1][-]{section.4.2}{Modules:}{chapter.4}% 75
-\BOOKMARK [0][-]{chapter.5}{Indices and tables}{}% 76
-\BOOKMARK [0][-]{section*.640}{Python Module Index}{}% 77
diff --git a/doc/_build/latex/ruffus.pdf b/doc/_build/latex/ruffus.pdf
deleted file mode 100644
index 68836b8..0000000
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diff --git a/doc/_build/latex/ruffus.tex b/doc/_build/latex/ruffus.tex
deleted file mode 100644
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--- a/doc/_build/latex/ruffus.tex
+++ /dev/null
@@ -1,21827 +0,0 @@
-% Generated by Sphinx.
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-
-\title{ruffus Documentation}
-\date{August 06, 2014}
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-
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-\chapter{Start Here:}
-\label{contents:glob}\label{contents:ruffus-documentation}\label{contents:start-here}
-
-\section{Installation}
-\label{installation:installation}\label{installation::doc}\label{installation:id1}
-\code{Ruffus} is a lightweight python module for building computational pipelines.
-
-
-\subsection{The easy way}
-\label{installation:the-easy-way}\begin{quote}
-
-\emph{Ruffus} is available as an
-\href{http://peak.telecommunity.com/DevCenter/EasyInstall}{easy-install} -able package
-on the \href{http://pypi.python.org/pypi/Sphinx}{Python Package Index}.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-sudo pip install ruffus --upgrade
-\end{Verbatim}
-
-This may also work for older installations
-\begin{enumerate}
-\item {} 
-Install setuptools:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-wget peak.telecommunity.com/dist/ez\_setup.py
-sudo python ez\_setup.py
-\end{Verbatim}
-
-\item {} 
-Install \emph{Ruffus} automatically:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-easy\_install -U ruffus
-\end{Verbatim}
-
-\end{enumerate}
-\end{quote}
-
-
-\subsection{The most up-to-date code:}
-\label{installation:the-most-up-to-date-code}\begin{itemize}
-\item {} 
-\href{https://pypi.python.org/pypi/ruffus}{Download the latest sources} or
-
-\item {} 
-Check out the latest code from Google using git:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-git clone https://bunbun68@code.google.com/p/ruffus/ .
-\end{Verbatim}
-
-\item {} 
-Bleeding edge Ruffus development takes place on github:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-git clone git at github.com:bunbun/ruffus.git .
-\end{Verbatim}
-
-\item {} 
-To install after downloading, change to the , type:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-python ./setup.py install
-\end{Verbatim}
-
-\end{itemize}
-
-
-\subsubsection{Graphical flowcharts}
-\label{installation:graphical-flowcharts}\begin{quote}
-
-\textbf{Ruffus} relies on the \code{dot} programme from \href{http://www.graphviz.org/}{Graphviz}
-(``Graph visualisation'') to make pretty flowchart representations of your pipelines in multiple
-graphical formats (e.g. \code{png}, \code{jpg}). The crossplatform Graphviz package can be
-\href{http://www.graphviz.org/Download.php}{downloaded here} for Windows,
-Linux, Macs and Solaris. Some Linux
-distributions may include prebuilt packages.
-\begin{description}
-\item[{For Fedora, try}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-yum list 'graphviz*'
-\end{Verbatim}
-
-\item[{For ubuntu / Debian, try}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-sudo apt-get install graphviz
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-
-\section{\textbf{Ruffus} Manual: List of Chapters and Example code}
-\label{tutorials/new_tutorial/manual_contents:ruffus-manual-list-of-chapters-and-example-code}\label{tutorials/new_tutorial/manual_contents::doc}\label{tutorials/new_tutorial/manual_contents:new-manual-table-of-contents}\begin{quote}
-
-Download as \code{pdf}.
-\begin{itemize}
-\item {} 
-\textbf{Chapter 1}: {\hyperref[tutorials/new_tutorial/introduction:new-manual-introduction]{\emph{An introduction to basic Ruffus syntax}}}
-
-\item {} 
-\textbf{Chapter 2}: {\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{Transforming data in a pipeline with @transform}}}
-
-\item {} 
-\textbf{Chapter 3}: {\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-transform-in-parallel]{\emph{More on @transform-ing data}}}
-
-\item {} 
-\textbf{Chapter 4}: {\hyperref[tutorials/new_tutorial/originate:new-manual-originate]{\emph{Creating files with @originate}}}
-
-\item {} 
-\textbf{Chapter 5}: {\hyperref[tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout]{\emph{Understanding how your pipeline works with pipeline\_printout()}}}
-
-\item {} 
-\textbf{Chapter 6}: {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline]{\emph{Running Ruffus from the command line with ruffus.cmdline}}}
-
-\item {} 
-\textbf{Chapter 7}: {\hyperref[tutorials/new_tutorial/pipeline_printout_graph:new-manual-pipeline-printout-graph]{\emph{Displaying the pipeline visually with pipeline\_printout\_graph()}}}
-
-\item {} 
-\textbf{Chapter 8}: {\hyperref[tutorials/new_tutorial/output_file_names:new-manual-output-file-names]{\emph{Specifying output file names with formatter() and regex()}}}
-
-\item {} 
-\textbf{Chapter 9}: {\hyperref[tutorials/new_tutorial/mkdir:new-manual-mkdir]{\emph{Preparing directories for output with @mkdir}}}
-
-\item {} 
-\textbf{Chapter 10}: {\hyperref[tutorials/new_tutorial/checkpointing:new-manual-checkpointing]{\emph{Checkpointing: Interrupted Pipelines and Exceptions}}}
-
-\item {} 
-\textbf{Chapter 11}: {\hyperref[tutorials/new_tutorial/decorators_compendium:new-manual-decorators-compendium]{\emph{Pipeline topologies and a compendium of Ruffus decorators}}}
-
-\item {} 
-\textbf{Chapter 12}: {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{Splitting up large tasks / files with @split}}}
-
-\item {} 
-\textbf{Chapter 13}: {\hyperref[tutorials/new_tutorial/merge:new-manual-merge]{\emph{@merge multiple input into a single result}}}
-
-\item {} 
-\textbf{Chapter 15}: {\hyperref[tutorials/new_tutorial/logging:new-manual-logging]{\emph{Logging progress through a pipeline}}}
-
-\item {} 
-\textbf{Chapter 14}: {\hyperref[tutorials/new_tutorial/multiprocessing:new-manual-multiprocessing]{\emph{Multiprocessing, drmaa and Computation Clusters}}}
-
-\item {} 
-\textbf{Chapter 16}: {\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-subdivide-collate]{\emph{@subdivide tasks to run efficiently and regroup with @collate}}}
-
-\item {} 
-\textbf{Chapter 17}: {\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinatorics]{\emph{@combinations, @permutations and all versus all @product}}}
-
-\item {} 
-\textbf{Chapter 18}: {\hyperref[tutorials/new_tutorial/active_if:new-manual-active-if]{\emph{Turning parts of the pipeline on and off at runtime with @active\_if}}}
-
-\item {} 
-\textbf{Chapter 20}: {\hyperref[tutorials/new_tutorial/inputs:new-manual-inputs]{\emph{Manipulating task inputs via string substitution with inputs() and add\_inputs()}}}
-
-\item {} 
-\textbf{Chapter 19}: {\hyperref[tutorials/new_tutorial/posttask:new-manual-posttask]{\emph{Signal the completion of each stage of our pipeline with @posttask}}}
-
-\item {} 
-\textbf{Chapter 21}: {\hyperref[tutorials/new_tutorial/onthefly:new-manual-on-the-fly]{\emph{Esoteric: Generating parameters on the fly with @files}}}
-
-\item {} 
-\textbf{Chapter 22}: {\hyperref[tutorials/new_tutorial/parallel:new-manual-deprecated-parallel]{\emph{Esoteric: Running jobs in parallel without files using @parallel}}}
-
-\item {} 
-\textbf{Chapter 23}: {\hyperref[tutorials/new_tutorial/check_if_uptodate:new-manual-check-if-uptodate]{\emph{Esoteric: Writing custom functions to decide which jobs are up to date with @check\_if\_uptodate}}}
-
-\item {} 
-\textbf{Appendix 1} {\hyperref[tutorials/new_tutorial/flowchart_colours:new-manual-flowchart-colours]{\emph{Flow Chart Colours with pipeline\_printout\_graph}}}
-
-\item {} 
-\textbf{Appendix 2} {\hyperref[tutorials/new_tutorial/dependencies:new-manual-dependencies]{\emph{Under the hood: How dependency works}}}
-
-\item {} 
-\textbf{Appendix 3} {\hyperref[tutorials/new_tutorial/exceptions:new-manual-exceptions]{\emph{Exceptions thrown inside pipelines}}}
-
-\item {} 
-\textbf{Appendix 4} {\hyperref[tutorials/new_tutorial/list_of_ruffus_names:new-manual-ruffus-names]{\emph{Names (keywords) exported from Ruffus}}}
-
-\item {} 
-\textbf{Appendix 5}: {\hyperref[tutorials/new_tutorial/deprecated_files:new-manual-deprecated-files]{\emph{Legacy and deprecated syntax @files}}}
-
-\item {} 
-\textbf{Appendix 6}: {\hyperref[tutorials/new_tutorial/deprecated_files_re:new-manual-deprecated-files-re]{\emph{Legacy and deprecated syntax @files\_re}}}
-
-\end{itemize}
-\end{quote}
-
-\textbf{Ruffus} Manual: List of Example Code for Each Chapter:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/introduction_code:new-manual-introduction-code]{\emph{Chapter 1: Python Code for An introduction to basic Ruffus syntax}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/transform_code:new-manual-transform-code]{\emph{Chapter 1: Python Code for Transforming data in a pipeline with @transform}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/transform_in_parallel_code:new-manual-transform-in-parallel-code]{\emph{Chapter 3: Python Code for More on @transform-ing data}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/originate_code:new-manual-originate-code]{\emph{Chapter 4: Python Code for Creating files with @originate}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/pipeline_printout_code:new-manual-pipeline-printout-code]{\emph{Chapter 5: Python Code for Understanding how your pipeline works with pipeline\_printout(...)}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/pipeline_printout_graph_code:new-manual-pipeline-printout-graph-code]{\emph{Chapter 7: Python Code for Displaying the pipeline visually with pipeline\_printout\_graph(...)}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/output_file_names_code:new-manual-output-file-names-code]{\emph{Chapter 8: Python Code for Specifying output file names with formatter() and regex()}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/mkdir_code:new-manual-mkdir-code]{\emph{Chapter 9: Python Code for Preparing directories for output with @mkdir()}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/checkpointing_code:new-manual-checkpointing-code]{\emph{Chapter 10: Python Code for Checkpointing: Interrupted Pipelines and Exceptions}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/split_code:new-manual-split-code]{\emph{Chapter 12: Python Code for Splitting up large tasks / files with @split}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/merge_code:new-manual-merge-code]{\emph{Chapter 13: Python Code for  @merge multiple input into a single result}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/multiprocessing_code:new-manual-multiprocessing-code]{\emph{Chapter 14: Python Code for Multiprocessing, drmaa and Computation Clusters}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/logging_code:new-manual-logging-code]{\emph{Chapter 15: Python Code for Logging progress through a pipeline}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/subdivide_collate_code:new-manual-subdivide-collate-code]{\emph{Chapter 16: Python Code for @subdivide tasks to run efficiently and regroup with @collate}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/combinatorics_code:new-manual-combinatorics-code]{\emph{Chapter 17: Python Code for @combinations, @permutations and all versus all @product}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/inputs_code:new-manual-inputs-code]{\emph{Chapter 20: Python Code for Manipulating task inputs via string substitution using inputs()  and  add\_inputs()}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/onthefly_code:new-manual-on-the-fly-code]{\emph{Chapter 21: Esoteric: Python Code for Generating parameters on the fly with @files}}}
-
-\end{itemize}
-
-
-
-
-
-\index{overview!Tutorial}\index{Tutorial!overview}
-
-\section{\textbf{Chapter 1}: An introduction to basic \emph{Ruffus} syntax}
-\label{tutorials/new_tutorial/introduction:new-manual-introduction}\label{tutorials/new_tutorial/introduction:index-0}\label{tutorials/new_tutorial/introduction::doc}\label{tutorials/new_tutorial/introduction:new-manual-introduction-chapter-num-an-introduction-to-basic-ruffus-syntax}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/introduction:overview}\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{theoretical_pipeline_schematic.png}}
-
-Computational pipelines transform your data in stages until the final result is produced.
-One easy way to understand pipelines is by imagining your data flowing across a series of
-pipes until it reaches its final destination. Even quite complicated processes can be
-broken into simple stages. Of course, it helps to visualise the whole process.
-
-\emph{Ruffus} is a way of automating the plumbing in your pipeline: You supply the python functions
-which perform the data transformation, and tell \emph{Ruffus} how these pipeline \code{task} functions
-are connected up. \emph{Ruffus} will make sure that the right data flows down your pipeline in the
-right way at the right time.
-
-\begin{notice}{note}{Note:}
-\emph{Ruffus} refers to each stage of your pipeline as a {\hyperref[glossary:term-task]{\emph{task}}}.
-\end{notice}
-\end{quote}
-\phantomsection\label{tutorials/new_tutorial/introduction:new-manual-introduction-import}
-\index{importing ruffus}
-
-\subsection{Importing \emph{Ruffus}}
-\label{tutorials/new_tutorial/introduction:index-1}\label{tutorials/new_tutorial/introduction:importing-ruffus}\begin{quote}
-
-The most convenient way to use \emph{Ruffus} is to import the various names directly:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\end{Verbatim}
-\end{quote}
-
-This will allow \emph{Ruffus} terms to be used directly in your code. This is also
-the style we have adopted for this manual.
-\begin{description}
-\item[{If any of these clash with names in your code, you can use qualified names instead:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{ruffus}
-
-\PYG{n}{ruffus}\PYG{o}{.}\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{...}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\emph{Ruffus} uses only standard python syntax.
-
-There is no need to install anything extra or to have your script ``preprocessed'' to run
-your pipeline.
-\end{quote}
-
-
-\subsection{\emph{Ruffus} decorators}
-\label{tutorials/new_tutorial/introduction:ruffus-decorators}\begin{quote}
-
-To let \emph{Ruffus} know that which python functions are part of your pipeline,
-they need to be tagged or annotated using
-\emph{Ruffus} \href{https://docs.python.org/2/glossary.html\#term-decorator}{decorators} .
-
-\href{https://docs.python.org/2/glossary.html\#term-decorator}{Decorators} have been part of the Python language since version 2.4.
-Common examples from the standard library include \href{https://docs.python.org/2/library/functions.html\#staticmethod}{@staticmethod} and
-\href{https://docs.python.org/2/library/functions.html\#classmethod}{classmethod}.
-
-\href{https://docs.python.org/2/glossary.html\#term-decorator}{decorators}  start with a \code{@}
-prefix, and take a number of parameters in parenthesis, much like in a function call.
-
-\href{https://docs.python.org/2/glossary.html\#term-decorator}{decorators}   are placed before a normal python function.
-\begin{quote}
-
-\includegraphics{tutorial_step1_decorator_syntax.png}
-\end{quote}
-
-Multiple decorators can be stacked as necessary in whichever order:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{first\PYGZus{}task}\PYG{p}{)}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{another\PYGZus{}task}\PYG{p}{)}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{n+nb}{range}\PYG{p}{(}\PYG{l+m+mi}{5}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-\emph{Ruffus} \href{https://docs.python.org/2/glossary.html\#term-decorator}{decorators} do not
-otherwise alter the underlying function. These can still be called normally.
-\end{quote}
-
-
-\subsection{Your first \emph{Ruffus} pipeline}
-\label{tutorials/new_tutorial/introduction:your-first-ruffus-pipeline}
-
-\subsubsection{1. Write down the file names}
-\label{tutorials/new_tutorial/introduction:write-down-the-file-names}\begin{quote}
-
-\emph{Ruffus} is designed for data moving through a computational pipeline as a series of files.
-
-It is also possible to use \emph{Ruffus} pipelines without using intermediate data files but for your
-first efforts, it is probably best not to subvert its canonical design.
-
-The first thing when designing a new \emph{Ruffus} pipeline is to sketch out the set of file names for
-the pipeline on paper:
-\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{tutorial_ruffus_files.jpg}}
-\end{quote}
-\begin{description}
-\item[{Here we have a number of DNA sequence files (\code{*.fasta})}] \leavevmode\begin{enumerate}
-\item {} 
-mapped to a genome (\code{*.sam}), and
-
-\item {} 
-compressed (\code{*.bam}) before being
-
-\item {} 
-summarised statistically (\code{*.statistics})
-
-\end{enumerate}
-
-\end{description}
-
-The first striking thing is that all of the files following the same \textbf{consistent naming scheme}.
-
-\begin{notice}{note}{Note:}
-\DUspan{highlight-red}{The most important part of a Ruffus pipeline is to have a consistent naming scheme for your files.}
-
-This allows you to build sane pipelines.
-\end{notice}
-
-In this case, each of the files at the same stage share the same file extension, e.g. (\code{.sam}).
-This is usually the simplest and most sensible choice. (We shall see in later chapters
-that \emph{Ruffus} supports more complicated naming patterns so long as they are consistent.)
-\end{quote}
-
-
-\subsubsection{2. Write the python functions for each stage}
-\label{tutorials/new_tutorial/introduction:write-the-python-functions-for-each-stage}\begin{quote}
-
-Next, we can sketch out the python functions which do the actual work for the pipeline.
-\begin{quote}
-
-\begin{notice}{note}{Note:}\begin{enumerate}
-\item {} 
-\DUspan{highlight-red}{These are normal python functions with the important proviso that}
-\begin{quote}
-\begin{enumerate}
-\item {} 
-The first parameter contains the \textbf{Input} (file names)
-
-\item {} 
-The second parameter contains the \textbf{Output} (file names)
-
-\end{enumerate}
-
-You can otherwise supply as many parameters as is required.
-\end{quote}
-
-\item {} 
-\DUspan{highlight-red}{Each python function should only take a} \emph{Single} \textbf{Input} at a time
-\begin{quote}
-
-All the parallelism in your pipeline should be handled by \emph{Ruffus}. Make sure
-each function analyses one thing at a time.
-\end{quote}
-
-\end{enumerate}
-\end{notice}
-\end{quote}
-
-\emph{Ruffus} refers to a pipelined function as a {\hyperref[glossary:term-task]{\emph{task}}}.
-
-The code for our three task functions look something like:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 1 fasta\PYGZhy{}\PYGZgt{}sam}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{def} \PYG{n+nf}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}               \PYG{c}{\PYGZsh{} 1st parameter is Input}
-                    \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}              \PYG{c}{\PYGZsh{} 2nd parameter is Output}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Sketch of real mapping function}
-\PYG{l+s+sd}{    We can do the mapping ourselves}
-\PYG{l+s+sd}{        or call some other programme:}
-\PYG{l+s+sd}{            os.system(\PYGZdq{}stampy \PYGZpc{}s \PYGZpc{}s...\PYGZdq{} \PYGZpc{} (input\PYGZus{}file, output\PYGZus{}file))}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 2 sam\PYGZhy{}\PYGZgt{}bam}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{def} \PYG{n+nf}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}              \PYG{c}{\PYGZsh{} Input  parameter}
-                      \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}            \PYG{c}{\PYGZsh{} Output parameter}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Sketch of real compression function}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 3 bam\PYGZhy{}\PYGZgt{}statistics}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{def} \PYG{n+nf}{summarise\PYGZus{}bam\PYGZus{}file}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}             \PYG{c}{\PYGZsh{} Input  parameter}
-                       \PYG{n}{output\PYGZus{}file}\PYG{p}{,}            \PYG{c}{\PYGZsh{} Output parameter}
-                       \PYG{n}{extra\PYGZus{}stats\PYGZus{}parameter}\PYG{p}{)}\PYG{p}{:} \PYG{c}{\PYGZsh{} Any number of extra parameters as required}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Sketch of real analysis function}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-If we were calling our functions manually, without the benefit of \emph{Ruffus}, we would need
-the following sequence of calls:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} STAGE 1}
-\PYG{n}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} STAGE 2}
-\PYG{n}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} STAGE 3}
-\PYG{n}{summarise\PYGZus{}bam\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.statistics}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{summarise\PYGZus{}bam\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.statistics}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{summarise\PYGZus{}bam\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.statistics}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{3. Link the python functions into a pipeline}
-\label{tutorials/new_tutorial/introduction:link-the-python-functions-into-a-pipeline}\begin{quote}
-
-\emph{Ruffus} makes exactly the same function calls on your behalf. However, first, we need to
-tell \emph{Ruffus} what the arguments should be for each of the function calls.
-\begin{itemize}
-\item {} 
-The \textbf{Input} is easy: This is either the starting file set (\code{*.fasta}) or whatever is produced
-by the previous stage.
-
-\item {} 
-The \textbf{Output} file name is the same as the \textbf{Input} but with the appropriate extension.
-
-\end{itemize}
-
-These are specified using the \emph{Ruffus} {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} decorator as follows:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n}{starting\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 1 fasta\PYGZhy{}\PYGZgt{}sam}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{starting\PYGZus{}files}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} Input = starting files}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                  \PYG{c}{\PYGZsh{}         suffix = .fasta}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                            \PYG{c}{\PYGZsh{} Output  suffix = .sam}
-\PYG{k}{def} \PYG{n+nf}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                    \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 2 sam\PYGZhy{}\PYGZgt{}bam}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{,}                   \PYG{c}{\PYGZsh{} Input = previous stage}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{}         suffix = .sam}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                            \PYG{c}{\PYGZsh{} Output  suffix = .bam}
-\PYG{k}{def} \PYG{n+nf}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                      \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 3 bam\PYGZhy{}\PYGZgt{}statistics}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{,}                  \PYG{c}{\PYGZsh{} Input = previous stage}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{}         suffix = .bam}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.statistics}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} Output  suffix = .statistics}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{use\PYGZus{}linear\PYGZus{}model}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                \PYG{c}{\PYGZsh{} Extra statistics parameter}
-\PYG{k}{def} \PYG{n+nf}{summarise\PYGZus{}bam\PYGZus{}file}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                       \PYG{n}{output\PYGZus{}file}\PYG{p}{,}
-                       \PYG{n}{extra\PYGZus{}stats\PYGZus{}parameter}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Sketch of real analysis function}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{4. @transform syntax}
-\label{tutorials/new_tutorial/introduction:transform-syntax}\begin{quote}
-\begin{enumerate}
-\item {} 
-\begin{DUlineblock}{0em}
-\item[] The 1st parameter for {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} is the \textbf{Input}.
-\item[] This is either the set of starting data or the name of the previous pipeline function.
-\item[] \emph{Ruffus} \emph{chains} together the stages of a pipeline by linking the \textbf{Output} of the previous stage into the \textbf{Input} of the next.
-\end{DUlineblock}
-
-\item {} 
-\begin{DUlineblock}{0em}
-\item[] The 2nd parameter is the current {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}}
-\item[] (i.e. our \textbf{Input} file extensions of \code{".fasta"} or  \code{".sam"} or  \code{".bam"})
-\end{DUlineblock}
-
-\item {} 
-\begin{DUlineblock}{0em}
-\item[] The 3rd parameter is what we want our \textbf{Output} file name to be after {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} string substitution (e.g. \code{.fasta - \textgreater{} .sam}).
-\item[] This works because we are using a sane naming scheme for our data files.
-\end{DUlineblock}
-
-\item {} 
-Other parameters can be passed to \code{@transform} and they will be forwarded to our python
-pipeline function.
-
-\end{enumerate}
-
-The functions that do the actual work of each stage of the pipeline remain unchanged.
-The role of \emph{Ruffus} is to make sure each is called in the right order,
-with the right parameters, running in parallel (using multiprocessing if desired).
-\end{quote}
-
-\index{pipeline\_run!Tutorial}\index{Tutorial!pipeline\_run}
-
-\subsubsection{5. Run the pipeline!}
-\label{tutorials/new_tutorial/introduction:run-the-pipeline}\label{tutorials/new_tutorial/introduction:index-2}\label{tutorials/new_tutorial/introduction:new-manual-pipeline-run}\begin{quote}
-
-\begin{notice}{note}{Note:}
-\textbf{Key Ruffus Terminology}:
-
-A  {\hyperref[glossary:term-task]{\emph{task}}} is an annotated python function which represents a recipe or stage of your pipeline.
-
-A  {\hyperref[glossary:term-job]{\emph{job}}} is each time your recipe is applied to a piece of data, i.e. each time \emph{Ruffus} calls your function.
-
-Each \textbf{task} or pipeline recipe can thus have many \textbf{jobs} each of which can work in parallel on different data.
-\end{notice}
-
-Now we can run the pipeline with the \emph{Ruffus} function {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-This produces three sets of results in parallel, as you might expect:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [a.fasta \PYGZhy{}\PYGZgt{} a.sam] completed}
-\PYG{g+go}{    Job  = [b.fasta \PYGZhy{}\PYGZgt{} b.sam] completed}
-\PYG{g+go}{    Job  = [c.fasta \PYGZhy{}\PYGZgt{} c.sam] completed}
-\PYG{g+go}{Completed Task = map\PYGZus{}dna\PYGZus{}sequence}
-\PYG{g+go}{    Job  = [a.sam \PYGZhy{}\PYGZgt{} a.bam] completed}
-\PYG{g+go}{    Job  = [b.sam \PYGZhy{}\PYGZgt{} b.bam] completed}
-\PYG{g+go}{    Job  = [c.sam \PYGZhy{}\PYGZgt{} c.bam] completed}
-\PYG{g+go}{Completed Task = compress\PYGZus{}sam\PYGZus{}file}
-\PYG{g+go}{    Job  = [a.bam \PYGZhy{}\PYGZgt{} a.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{    Job  = [b.bam \PYGZhy{}\PYGZgt{} b.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{    Job  = [c.bam \PYGZhy{}\PYGZgt{} c.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{Completed Task = summarise\PYGZus{}bam\PYGZus{}file}
-\end{Verbatim}
-\end{quote}
-
-To work out which functions to call, {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}}
-finds the \textbf{last} {\hyperref[glossary:term-task]{\emph{task}}} function of your pipeline, then
-works out all the other functions this depends on, working backwards up the chain of
-dependencies automatically.
-
-We can specify this end point of your pipeline explicitly:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{target\PYGZus{}tasks} \PYG{o}{=} \PYG{p}{[}\PYG{n}{summarise\PYGZus{}bam\PYGZus{}file}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-This allows us to only run part of the pipeline, for example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{target\PYGZus{}tasks} \PYG{o}{=} \PYG{p}{[}\PYG{n}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\begin{notice}{note}{Note:}
-The {\hyperref[tutorials/new_tutorial/introduction_code:new-manual-introduction-code]{\emph{example code}}} can be copied and pasted into a python
-command shell.
-\end{notice}
-
-\index{transform!Tutorial}\index{Tutorial!transform}
-
-\section{\textbf{Chapter 2}: Transforming data in a pipeline with \emph{@transform}}
-\label{tutorials/new_tutorial/transform:index-0}\label{tutorials/new_tutorial/transform:new-manual-transform-chapter-num-transforming-data-in-a-pipeline-with-transform}\label{tutorials/new_tutorial/transform::doc}\label{tutorials/new_tutorial/transform:new-manual-transform}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} syntax
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/transform_code:new-manual-transform-code]{\emph{Chapter 1: Python Code for Transforming data in a pipeline with @transform}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Review}
-\label{tutorials/new_tutorial/transform:review}\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{theoretical_pipeline_schematic.png}}
-
-Computational pipelines transform your data in stages until the final result is produced.
-Ruffus automates the plumbing in your pipeline. You supply the python functions which perform the data transformation,
-and tell Ruffus how these pipeline stages or {\hyperref[glossary:term-task]{\emph{task}}} functions are connected together.
-
-\begin{notice}{note}{Note:}
-\textbf{The best way to design a pipeline is to:}
-\begin{itemize}
-\item {} 
-\textbf{write down the file names of the data as it flows across your pipeline}
-
-\item {} 
-\textbf{write down the names of functions which transforms the data at each stage of the pipeline.}
-
-\end{itemize}
-\end{notice}
-\end{quote}
-
-
-\subsection{Task functions as recipes}
-\label{tutorials/new_tutorial/transform:task-functions-as-recipes}\begin{quote}
-
-Each {\hyperref[glossary:term-task]{\emph{task}}} function of the pipeline is a recipe or
-\href{http://www.gnu.org/software/make/manual/make.html\#Rule-Introduction}{rule}
-which can be applied repeatedly to our data.
-
-For example, one can have
-\begin{itemize}
-\item {} 
-a \code{compile()} \emph{task} which will compile any number of source code files, or
-
-\item {} 
-a \code{count\_lines()} \emph{task} which will count the number of lines in any file or
-
-\item {} 
-an \code{align\_dna()} \emph{task} which will align the DNA of many chromosomes.
-
-\end{itemize}
-\end{quote}
-
-\index{one to one @transform!Tutorial}\index{Tutorial!one to one @transform}
-
-\subsection{\emph{@transform} is a 1 to 1 operation}
-\label{tutorials/new_tutorial/transform:transform-is-a-1-to-1-operation}\label{tutorials/new_tutorial/transform:index-1}\begin{quote}
-
-\code{@transform} is a 1:1 operation because for each input, it generates one output.
-
-\scalebox{0.500000}{\includegraphics{transform_1_to_1_example.png}}
-
-This is obvious when you count the number of jobs at each step. In our example pipeline, there are always
-three jobs moving through in step at each stage ({\hyperref[glossary:term-task]{\emph{task}}}).
-
-Each \textbf{Input} or \textbf{Output} is not limited, however, to a single filename. Each job can accept, for example,
-a pair of files as its \textbf{Input}, or generate more than one file or a dictionary or numbers as its \textbf{Output}.
-
-When each job outputs a pair of files, this does not generate two jobs downstream. It just means that the successive
-{\hyperref[glossary:term-task]{\emph{task}}} in the pipeline will receive a list or tuple of files as its input parameter.
-
-\begin{notice}{note}{Note:}
-The different sort of decorators in Ruffus determine the \emph{topology} of your pipeline,
-i.e. how the jobs from different tasks are linked together seamlessly.
-
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} always generates one \textbf{Output} for one \textbf{Input}.
-
-In the later parts of the tutorial, we will encounter more decorators which can \emph{split up}, or \emph{join together} or \emph{group} inputs.
-
-In other words, using other decorators \textbf{Input} and \textbf{Output}  can have \textbf{many to one}, \textbf{many to many} etc. relationships.
-\end{notice}
-\end{quote}
-
-
-\subsubsection{A pair of files as the \textbf{Input}}
-\label{tutorials/new_tutorial/transform:a-pair-of-files-as-the-input}\begin{quote}
-
-Let us rewrite our previous example so that the \textbf{Input} of the first task
-are \href{http://en.wikipedia.org/wiki/DNA\_sequencing\_theory\#Pairwise\_end-sequencing}{matching pairs}
-of DNA sequence files, processed in tandem.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n}{starting\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.2.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                  \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.2.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                  \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.2.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{]}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 1 fasta\PYGZhy{}\PYGZgt{}sam}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{starting\PYGZus{}files}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} Input = starting files}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                \PYG{c}{\PYGZsh{}         suffix = .1.fastq}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                            \PYG{c}{\PYGZsh{} Output  suffix = .sam}
-\PYG{k}{def} \PYG{n+nf}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,}
-                    \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} remember there are two input files now}
-    \PYG{n}{ii1} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{)}
-    \PYG{n}{ii2} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-The only changes are to the first task:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+go}{pipeline\PYGZus{}run()}
-\PYG{g+go}{    Job  = [[a.1.fastq, a.2.fastq] \PYGZhy{}\PYGZgt{} a.sam] completed}
-\PYG{g+go}{    Job  = [[a.1.fastq, a.2.fastq] \PYGZhy{}\PYGZgt{} a.sam] completed}
-\PYG{g+go}{    Job  = [[a.1.fastq, a.2.fastq] \PYGZhy{}\PYGZgt{} a.sam] completed}
-\PYG{g+go}{Completed Task = map\PYGZus{}dna\PYGZus{}sequence}
-\end{Verbatim}
-\end{quote}
-
-{\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} always matches only the first file name in each \textbf{Input}.
-\end{quote}
-
-\index{input / output parameters!Tutorial}\index{Tutorial!input / output parameters}
-
-\subsection{\textbf{Input} and \textbf{Output} parameters}
-\label{tutorials/new_tutorial/transform:input-and-output-parameters}\label{tutorials/new_tutorial/transform:index-2}\begin{quote}
-
-\textbf{Ruffus} chains together different tasks by taking the \textbf{Output} from one job
-and plugging it automatically as the \textbf{Input} of the next.
-
-The first two parameters of each job are the \textbf{Input} and \textbf{Output} parameters respectively.
-
-In the above example, we have:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [a.bam \PYGZhy{}\PYGZgt{} a.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{    Job  = [b.bam \PYGZhy{}\PYGZgt{} b.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{    Job  = [c.bam \PYGZhy{}\PYGZgt{} c.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{Completed Task = summarise\PYGZus{}bam\PYGZus{}file}
-\end{Verbatim}
-
-
-\begin{threeparttable}
-\capstart\caption{Parameters for summarise\_bam\_file()}
-
-\begin{tabulary}{\linewidth}{|L|L|L|}
-\hline
-\textbf{\relax 
-\textbf{Inputs}
-} & \textbf{\relax 
-\textbf{Outputs}
-} & \textbf{\relax 
-\textbf{Extra}
-}\\\hline
-
-\code{"a.bam"}
- & 
-\code{"a.statistics"}
- & 
-\code{"use\_linear\_model"}
-\\\hline
-
-\code{"b.bam"}
- & 
-\code{"b.statistics"}
- & 
-\code{"use\_linear\_model"}
-\\\hline
-
-\code{"c.bam"}
- & 
-\code{"c.statistics"}
- & 
-\code{"use\_linear\_model"}
-\\\hline
-\end{tabulary}
-
-\end{threeparttable}
-
-\end{quote}
-
-\textbf{Extra} parameters are for the consumption of \code{summarise\_bam\_file()} and will not passed to the next task.
-
-Ruffus was designed for pipelines which save intermediate data in files. This is not
-compulsory but saving your data in files at each step provides many advantages:
-\begin{enumerate}
-\item {} 
-Ruffus can use file system time stamps to check if your pipeline is up to date
-
-\item {} 
-Your data is persistent across runs
-
-\item {} 
-This is a good way to pass large amounts of data across processes and computational nodes
-
-\end{enumerate}
-
-Nevertheless, \emph{all} the {\hyperref[glossary:term-task]{\emph{task}}} parameters can include anything which suits your workflow, from lists of files, to numbers,
-sets or tuples. \emph{Ruffus} imposes few constraints on what \emph{you}
-would like to send to each stage of your pipeline.
-
-\emph{Ruffus} does, however, assume that if the \textbf{Input} and \textbf{Output} parameter contains strings, these will be interpreted as file names
-required by and produced by that job. As we shall see, the modification times of these file names
-indicate whether that part of the pipeline is up to date or needs to be rerun.
-\end{quote}
-
-\index{transforming in parallel!Tutorial}\index{Tutorial!transforming in parallel}
-
-\section{\textbf{Chapter 3}: More on \texttt{@transform}-ing data}
-\label{tutorials/new_tutorial/transform_in_parallel:new-manual-transform-in-parallel-chapter-num-more-on-transform-ing-data}\label{tutorials/new_tutorial/transform_in_parallel:index-0}\label{tutorials/new_tutorial/transform_in_parallel::doc}\label{tutorials/new_tutorial/transform_in_parallel:new-manual-transform-in-parallel}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}  syntax
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/transform_in_parallel_code:new-manual-transform-in-parallel-code]{\emph{Chapter 3: Python Code for More on @transform-ing data}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Review}
-\label{tutorials/new_tutorial/transform_in_parallel:review}\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{theoretical_pipeline_schematic.png}}
-
-Computational pipelines transform your data in stages until the final result is produced.
-\emph{Ruffus} automates the plumbing in your pipeline. You supply the python functions which perform the data transformation,
-and tell \emph{Ruffus} how these pipeline stages or {\hyperref[glossary:term-task]{\emph{task}}} functions are connected together.
-
-\begin{notice}{note}{Note:}
-\textbf{The best way to design a pipeline is to:}
-\begin{itemize}
-\item {} 
-\textbf{write down the file names of the data as it flows across your pipeline}
-
-\item {} 
-\textbf{write down the names of functions which transforms the data at each stage of the pipeline.}
-
-\end{itemize}
-\end{notice}
-
-{\hyperref[tutorials/new_tutorial/introduction:new-manual-introduction]{\emph{Chapter 1: An introduction to basic Ruffus syntax}}} described the bare bones of a simple \emph{Ruffus} pipeline.
-
-Using the \emph{Ruffus} {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} decorator, we were able to
-specify the data files moving through our pipeline so that our specified task functions
-could be invoked.
-
-This may seem like a lot of effort and complication for something so simple: a couple of
-simple python function calls we could have invoked ourselves.
-However, By letting \emph{Ruffus} manage your pipeline parameters, you will get the following features
-for free:
-\begin{enumerate}
-\item {} 
-Only out-of-date parts of the pipeline will be re-run
-
-\item {} 
-Multiple jobs can be run in parallel (on different processors if possible)
-
-\item {} 
-Pipeline stages can be chained together automatically. This means you can apply your
-pipeline just as easily to 1000 files as to 3.
-
-\end{enumerate}
-\end{quote}
-
-
-\subsection{Running pipelines in parallel}
-\label{tutorials/new_tutorial/transform_in_parallel:running-pipelines-in-parallel}\begin{quote}
-
-Even though three sets of files have been specified for our initial pipeline, and they can be
-processed completely independently, by default  \emph{Ruffus} runs each of them serially in succession.
-
-To ask \emph{Ruffus} to run them in parallel, all you have to do is to add a \code{multiprocess} parameter to \code{pipeline\_run}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-In this case, we are telling \emph{Ruffus} to run a maximum of 5 jobs at the same time. Since we only have
-three sets of data, that is as much parallelism as we are going to get...
-\end{quote}
-
-
-\subsection{Up-to-date jobs are not re-run unnecessarily}
-\label{tutorials/new_tutorial/transform_in_parallel:new-manual-only-rerun-out-of-date}\label{tutorials/new_tutorial/transform_in_parallel:up-to-date-jobs-are-not-re-run-unnecessarily}\begin{quote}
-
-A job will be run only if the output file timestamps are out of date.
-If you ran our example code a second time, nothing would happen because all the work is already complete.
-
-We can check the details by asking \emph{Ruffus} for more \code{verbose} output
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-\PYG{g+go}{  Task = map\PYGZus{}dna\PYGZus{}sequence}
-\PYG{g+go}{    All jobs up to date}
-\PYG{g+go}{  Task = compress\PYGZus{}sam\PYGZus{}file}
-\PYG{g+go}{    All jobs up to date}
-\PYG{g+go}{  Task = summarise\PYGZus{}bam\PYGZus{}file}
-\PYG{g+go}{    All jobs up to date}
-\end{Verbatim}
-\end{quote}
-\begin{description}
-\item[{Nothing happens because:}] \leavevmode\begin{itemize}
-\item {} 
-\code{a.sam} was created later than \code{a.1.fastq} and \code{a.2.fastq}, and
-
-\item {} 
-\code{a.bam} was created later than \code{a.sam} and
-
-\item {} 
-\code{a.statistics} was created later than \code{a.bam}.
-
-\end{itemize}
-
-\end{description}
-
-and so on...
-\begin{description}
-\item[{Let us see what happens if we recreated the file \code{a.1.fastq} so that it appears as if 1 out of the original data files is out of date}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-The up to date jobs are cleverly ignored and only the out of date files are reprocessed.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+go}{ \PYGZgt{}\PYGZgt{}\PYGZgt{} open(\PYGZdq{}a.1.fastq\PYGZdq{}, \PYGZdq{}w\PYGZdq{})}
-\PYG{g+go}{ \PYGZgt{}\PYGZgt{}\PYGZgt{} pipeline\PYGZus{}run(verbose=2)}
-\PYG{g+go}{     Job  = [[b.1.fastq, b.2.fastq] \PYGZhy{}\PYGZgt{} b.sam] \PYGZsh{} unnecessary: already up to date}
-\PYG{g+go}{     Job  = [[c.1.fastq, c.2.fastq] \PYGZhy{}\PYGZgt{} c.sam] \PYGZsh{} unnecessary: already up to date}
-\PYG{g+go}{     Job  = [[a.1.fastq, a.2.fastq] \PYGZhy{}\PYGZgt{} a.sam] completed}
-\PYG{g+go}{ Completed Task = map\PYGZus{}dna\PYGZus{}sequence}
-\PYG{g+go}{     Job  = [b.sam \PYGZhy{}\PYGZgt{} b.bam] \PYGZsh{} unnecessary: already up to date}
-\PYG{g+go}{     Job  = [c.sam \PYGZhy{}\PYGZgt{} c.bam] \PYGZsh{} unnecessary: already up to date}
-\PYG{g+go}{     Job  = [a.sam \PYGZhy{}\PYGZgt{} a.bam] completed}
-\PYG{g+go}{ Completed Task = compress\PYGZus{}sam\PYGZus{}file}
-\PYG{g+go}{     Job  = [b.bam \PYGZhy{}\PYGZgt{} b.statistics, use\PYGZus{}linear\PYGZus{}model] \PYGZsh{} unnecessary: already up to date}
-\PYG{g+go}{     Job  = [c.bam \PYGZhy{}\PYGZgt{} c.statistics, use\PYGZus{}linear\PYGZus{}model] \PYGZsh{} unnecessary: already up to date}
-\PYG{g+go}{     Job  = [a.bam \PYGZhy{}\PYGZgt{} a.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{ Completed Task = summarise\PYGZus{}bam\PYGZus{}file}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{output\_from!referring to functions before they are defined}\index{referring to functions before they are defined!output\_from}\index{output\_from!defining tasks out of order}\index{defining tasks out of order!output\_from}
-
-\subsection{Defining pipeline tasks out of order}
-\label{tutorials/new_tutorial/transform_in_parallel:new-manual-output-from}\label{tutorials/new_tutorial/transform_in_parallel:index-1}\label{tutorials/new_tutorial/transform_in_parallel:defining-pipeline-tasks-out-of-order}\begin{quote}
-
-The examples so far assumes that all your pipelined tasks are defined in order.
-(\code{first\_task} before \code{second\_task}). This is usually the most sensible way to arrange your code.
-
-If you wish to refer to tasks which are not yet defined, you can do so by quoting the function name as a string and wrapping
-it with the {\hyperref[decorators/indicator_objects:decorators-indicator-objects]{\emph{indicator class}}} {\hyperref[decorators/indicator_objects:decorators-output-from]{\emph{output\_from(...)}}} so that \emph{Ruffus}
-knowns this is a {\hyperref[glossary:term-task]{\emph{task}}} name, not a file name
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   second task}
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   task name string wrapped in output\PYGZus{}from(...)}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{output\PYGZus{}from}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{first\PYGZus{}task}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   first task}
- \PYG{c}{\PYGZsh{}}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                         \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                          \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                        \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                 \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{:}
-         \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-             \PYG{k}{pass}
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}       Run}
- \PYG{c}{\PYGZsh{}}
- \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-You can also refer to tasks (functions) in other modules, in which case the full
-qualified name must be used:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{output\PYGZus{}from}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{other\PYGZus{}module.first\PYGZus{}task}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{@transform!multiple dependencies}\index{multiple dependencies!@transform}
-
-\subsection{Multiple dependencies}
-\label{tutorials/new_tutorial/transform_in_parallel:new-manual-transform-multiple-dependencies}\label{tutorials/new_tutorial/transform_in_parallel:index-2}\label{tutorials/new_tutorial/transform_in_parallel:multiple-dependencies}\begin{quote}
-
-Each task can depend on more than one antecedent simply by chaining to a list in {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{} third\PYGZus{}task depends on both first\PYGZus{}task() and second\PYGZus{}task()}
- \PYG{c}{\PYGZsh{}}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{n}{first\PYGZus{}task}\PYG{p}{,} \PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{third\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-\end{Verbatim}
-\end{quote}
-
-\code{third\_task()} depends on and follows both \code{first\_task()} and \code{second\_task()}. However, these latter two tasks are independent of each other
-and can and will run in parallel. This can be clearly shown for our example if we added a little randomness to the run time of each job:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{n}{random}\PYG{o}{.}\PYG{n}{random}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-The execution of \code{first\_task()} and \code{second\_task()} jobs will be interleaved and they finish in no particular order:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{third\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{6}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[job3.a.start, job3.b.start] \PYGZhy{}\PYGZgt{} [job3.a.output.1, job3.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job6.a.start, job6.b.start] \PYGZhy{}\PYGZgt{} [job6.a.output.1, job6.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job1.a.start, job1.b.start] \PYGZhy{}\PYGZgt{} [job1.a.output.1, job1.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job4.a.start, job4.b.start] \PYGZhy{}\PYGZgt{} [job4.a.output.1, job4.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job5.a.start, job5.b.start] \PYGZhy{}\PYGZgt{} [job5.a.output.1, job5.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = second\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job2.a.start, job2.b.start] \PYGZhy{}\PYGZgt{} [job2.a.output.1, job2.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\end{Verbatim}
-\end{quote}
-
-\begin{notice}{note}{Note:}
-See the {\hyperref[tutorials/new_tutorial/transform_in_parallel_code:new-manual-transform-multiple-dependencies-code]{\emph{example code}}}
-\end{notice}
-\end{quote}
-
-\index{@follow!imposing order with}\index{imposing order with!@follow}
-
-\subsection{\emph{@follows}}
-\label{tutorials/new_tutorial/transform_in_parallel:follows}\label{tutorials/new_tutorial/transform_in_parallel:new-manual-follows}\label{tutorials/new_tutorial/transform_in_parallel:index-3}\begin{quote}
-
-If there is some extrinsic reason one non-dependent task has to precede the other, then this can be specified explicitly using {\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   @follows specifies a preceding task}
- \PYG{c}{\PYGZsh{}}
- \PYG{n+nd}{@follows}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{first\PYGZus{}task}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{second\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                         \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                          \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                        \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                 \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-\end{Verbatim}
-\end{quote}
-
-{\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}} specifies either a preceding task (e.g. \code{first\_task}), or if
-it has not yet been defined, the name (as a string) of a task function (e.g. \code{"first\_task"}).
-
-With the addition of {\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}}, all the jobs
-of \code{second\_task()} start \emph{after} those from \code{first\_task()} have finished:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{third\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{6}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[job2.a.start, job2.b.start] \PYGZhy{}\PYGZgt{} [job2.a.output.1, job2.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job3.a.start, job3.b.start] \PYGZhy{}\PYGZgt{} [job3.a.output.1, job3.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job1.a.start, job1.b.start] \PYGZhy{}\PYGZgt{} [job1.a.output.1, job1.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = first\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job4.a.start, job4.b.start] \PYGZhy{}\PYGZgt{} [job4.a.output.1, job4.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job6.a.start, job6.b.start] \PYGZhy{}\PYGZgt{} [job6.a.output.1, job6.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job5.a.start, job5.b.start] \PYGZhy{}\PYGZgt{} [job5.a.output.1, job5.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = second\PYGZus{}task}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{@follows!mkdir (Manual)}\index{mkdir!@follows (Manual)}
-
-\subsection{Making directories automatically with \emph{@follows} and  \emph{mkdir}}
-\label{tutorials/new_tutorial/transform_in_parallel:index-4}\label{tutorials/new_tutorial/transform_in_parallel:new-manual-follows-mkdir}\label{tutorials/new_tutorial/transform_in_parallel:making-directories-automatically-with-follows-and-mkdir}\begin{quote}
-
-{\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}} is also useful for making sure one or more destination directories
-exist before a task is run.
-
-\emph{Ruffus} provides special syntax to support this, using the special
-{\hyperref[decorators/mkdir:decorators-mkdir]{\emph{mkdir}}} indicator class. For example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   @follows specifies both a preceding task and a directory name}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{first\PYGZus{}task}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{mkdir}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output/results/here}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{second\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-\end{Verbatim}
-\end{quote}
-
-Before \code{second\_task()} is run, the \code{output/results/here} directory will be created if necessary.
-\end{quote}
-
-\index{inputs parameters!globs}\index{globs!inputs parameters}\index{globs in input parameters!Tutorial}\index{Tutorial!globs in input parameters}
-
-\subsection{Globs in the \textbf{Input} parameter}
-\label{tutorials/new_tutorial/transform_in_parallel:globs-in-the-input-parameter}\label{tutorials/new_tutorial/transform_in_parallel:index-5}\label{tutorials/new_tutorial/transform_in_parallel:new-manual-globs-as-input}\begin{quote}
-\begin{itemize}
-\item {} 
-As a syntactic convenience, \emph{Ruffus} also allows you to specify a \href{http://docs.python.org/library/glob.html}{\emph{glob}} pattern (e.g. \code{*.txt}) in the
-\textbf{Input} parameter.
-
-\item {} 
-\href{http://docs.python.org/library/glob.html}{\emph{glob}} patterns will be automatically specify all matching file names as the \textbf{Input}.
-
-\item {} 
-Any strings within \textbf{Input} which contain the letters: \code{*?{[}{]}} will be treated as a \href{http://docs.python.org/library/glob.html}{\emph{glob}} pattern.
-
-\end{itemize}
-
-The first function in our initial \emph{Ruffus} pipeline example could have been written as:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 1 fasta\PYGZhy{}\PYGZgt{}sam}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                          \PYG{c}{\PYGZsh{} Input = glob}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                  \PYG{c}{\PYGZsh{}         suffix = .fasta}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                            \PYG{c}{\PYGZsh{} Output  suffix = .sam}
-\PYG{k}{def} \PYG{n+nf}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                    \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{Mixing tasks, globs and file names!Tutorial}\index{Tutorial!Mixing tasks, globs and file names}
-
-\subsection{Mixing Tasks and Globs in the \textbf{Input} parameter}
-\label{tutorials/new_tutorial/transform_in_parallel:index-6}\label{tutorials/new_tutorial/transform_in_parallel:mixing-tasks-and-globs-in-the-input-parameter}\begin{quote}
-
-\href{http://docs.python.org/library/glob.html}{\emph{glob}} patterns, references to tasks and file names strings
-can be mixed freely in (nested) python lists and tuples in the \textbf{Input} parameter.
-
-For example, a task function can chain to the \textbf{Output} from multiple upstream tasks:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{n}{task1}\PYG{p}{,} \PYG{n}{task2}\PYG{p}{,}                      \PYG{c}{\PYGZsh{} Input = multiple tasks}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{aa*.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                               \PYG{o}{+} \PYG{n+nb}{all} \PYG{n}{files} \PYG{n}{matching} \PYG{n}{glob}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{zz.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}                                \PYG{o}{+} \PYG{n+nb}{file} \PYG{n}{name}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                  \PYG{c}{\PYGZsh{}         suffix = .fasta}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                            \PYG{c}{\PYGZsh{} Output  suffix = .sam}
-\PYG{k}{def} \PYG{n+nf}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                    \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-In all cases, \emph{Ruffus} tries to do the right thing, and to make the simple or
-obvious case require the simplest, least onerous syntax.
-
-If sometimes \emph{Ruffus} does not behave the way you expect, please write to the authors:
-it may be a bug!
-
-{\hyperref[tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout]{\emph{Chapter 5: Understanding how your pipeline works with pipeline\_printout(...)}}}  and
-{\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline]{\emph{Chapter 6: Running Ruffus from the command line with ruffus.cmdline}}} will show you how to
-to make sure that your intentions are reflected in \emph{Ruffus} code.
-\end{quote}
-
-\index{originate!Tutorial}\index{Tutorial!originate}
-
-\section{\textbf{Chapter 4}: Creating files with \texttt{@originate}}
-\label{tutorials/new_tutorial/originate:index-0}\label{tutorials/new_tutorial/originate:new-manual-originate}\label{tutorials/new_tutorial/originate:new-manual-originate-chapter-num-creating-files-with-originate}\label{tutorials/new_tutorial/originate::doc}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/originate:decorators-originate]{\emph{@originate syntax in detail}}}
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/originate_code:new-manual-originate-code]{\emph{Chapter 4: Python Code for Creating files with @originate}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Simplifying our example with \emph{@originate}}
-\label{tutorials/new_tutorial/originate:simplifying-our-example-with-originate}\begin{quote}
-
-Our previous pipeline example started off with a set of files which we had to create first.
-
-This is a common task: pipelines have to start \emph{somewhere}.
-
-Ideally, though, we would only want to create these starting files if they didn't already exist. In other words, we want a sort of \code{@transform} which makes files from nothing (\code{None}?).
-
-This is exactly what {\hyperref[decorators/originate:decorators-originate]{\emph{@originate}}} helps you to do.
-
-Rewriting our pipeline with {\hyperref[decorators/originate:decorators-originate]{\emph{@originate}}} gives the following three steps:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} create both files as necessary}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   second task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-    Job  = [None -\textgreater{} [job1.a.start, job1.b.start]] completed
-    Job  = [None -\textgreater{} [job2.a.start, job2.b.start]] completed
-    Job  = [None -\textgreater{} [job3.a.start, job3.b.start]] completed
-Completed Task = create\_initial\_file\_pairs
-    Job  = [[job1.a.start, job1.b.start] -\textgreater{} job1.a.output.1] completed
-    Job  = [[job2.a.start, job2.b.start] -\textgreater{} job2.a.output.1] completed
-    Job  = [[job3.a.start, job3.b.start] -\textgreater{} job3.a.output.1] completed
-Completed Task = first\_task
-    Job  = [job1.a.output.1 -\textgreater{} job1.a.output.2] completed
-    Job  = [job2.a.output.1 -\textgreater{} job2.a.output.2] completed
-    Job  = [job3.a.output.1 -\textgreater{} job3.a.output.2] completed
-Completed Task = second\_task
-\end{Verbatim}
-\end{quote}
-
-\index{pipeline\_printout!Tutorial}\index{Tutorial!pipeline\_printout}
-
-\section{\textbf{Chapter 5}: Understanding how your pipeline works with \emph{pipeline\_printout(...)}}
-\label{tutorials/new_tutorial/pipeline_printout:index-0}\label{tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout}\label{tutorials/new_tutorial/pipeline_printout::doc}\label{tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout-chapter-num-understanding-how-your-pipeline-works-with-pipeline-printout}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}} syntax
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/pipeline_printout_code:new-manual-pipeline-printout-code]{\emph{Python Code for this chapter}}}
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}\begin{itemize}
-\item {} 
-\textbf{Whether you are learning or developing ruffus pipelines, your best friend is} {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}}
-\textbf{This shows the exact parameters and files as they are passed through the pipeline.}
-
-\item {} 
-\textbf{We also} \emph{strongly} \textbf{recommend you use the} \code{Ruffus.cmdline} \textbf{convenience module which}
-\textbf{will take care of all the command line arguments for you. See} {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline]{\emph{Chapter 6: Running Ruffus from the command line with ruffus.cmdline}}}.
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Printing out which jobs will be run}
-\label{tutorials/new_tutorial/pipeline_printout:printing-out-which-jobs-will-be-run}\begin{quote}
-
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}} takes the same parameters as pipeline\_run but just prints
-the tasks which are and are not up-to-date.
-
-The \code{verbose} parameter controls how much detail is displayed.
-
-Let us take the pipelined code we previously wrote in
-\textbf{Chapter 3} {\hyperref[tutorials/new_tutorial/transform_in_parallel_code:new-manual-transform-in-parallel-code]{\emph{More on @transform-ing data and @originate}}}
-but call {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}} instead of
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(...)}}}.
-This lists the tasks which will be run in the pipeline:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{import} \PYG{n+nn}{sys}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which will be run:}
-
-\PYG{g+go}{Task = create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}
-\PYG{g+go}{Task = first\PYGZus{}task}
-\PYG{g+go}{Task = second\PYGZus{}task}
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\end{Verbatim}
-\end{quote}
-
-To see the input and output parameters of each job in the pipeline, try increasing the verbosity from the default (\code{1}) to \code{3}
-(See {\hyperref[tutorials/new_tutorial/pipeline_printout_code:new-manual-pipeline-printout-code]{\emph{code}}})
-
-This is very useful for checking that the input and output parameters have been specified correctly.
-\end{quote}
-
-
-\subsection{Determining which jobs are out-of-date or not}
-\label{tutorials/new_tutorial/pipeline_printout:determining-which-jobs-are-out-of-date-or-not}\begin{quote}
-
-It is often useful to see which tasks are or are not up-to-date. For example, if we
-were to run the pipeline in full, and then modify one of the intermediate files, the
-pipeline would be partially out of date.
-
-Let us start by run the pipeline in full but then modify \code{job1.a.output.1} so that the second task appears out-of-date:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} \PYGZdq{}touch\PYGZdq{} job1.stage1}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{job1.a.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{close}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Run {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}} with a verbosity of \code{5}.
-
-This will tell you exactly why \code{second\_task(...)} needs to be re-run:
-because \code{job1.a.output.1} has a file modification time \emph{after} \code{job1.a.output.2} (highlighted):
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which are up\PYGZhy{}to\PYGZhy{}date:}
-
-\PYG{g+go}{Task = create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}
-\PYG{g+go}{Task = first\PYGZus{}task}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which will be run:}
-
-\PYG{g+go}{Task = second\PYGZus{}task}
-\PYG{g+go}{       Job  = [job1.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.a.output.2]}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} File modification times shown for out of date files}
-\PYG{g+go}{         Job needs update:}
-\PYG{g+go}{         Input files:}
-\PYG{g+go}{          * 22 Jul 2014 15:29:19.33: job1.a.output.1}
-\PYG{g+go}{         Output files:}
-\PYG{g+go}{          * 22 Jul 2014 15:29:07.53: job1.a.output.2}
-
-\PYG{g+go}{       Job  = [job2.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.a.output.2]}
-\PYG{g+go}{       Job  = [job3.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.a.output.2]}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\end{Verbatim}
-\end{quote}
-
-N.B. At a verbosity of 5, even jobs which are up-to-date in \code{second\_task} are displayed.
-\end{quote}
-
-
-\subsection{Verbosity levels}
-\label{tutorials/new_tutorial/pipeline_printout:verbosity-levels}\begin{quote}
-
-The verbosity levels for {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}} and {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(...)}}}
-can be specified from \code{verbose = 0} (print out nothing) to the extreme verbosity of \code{verbose=6}.  A verbosity of above 10 is reserved for the internal
-debugging of Ruffus
-\begin{itemize}
-\item {} 
-level \textbf{0} : \emph{nothing}
-
-\item {} 
-level \textbf{1} : \emph{Out-of-date Task names}
-
-\item {} 
-level \textbf{2} : \emph{All Tasks (including any task function docstrings)}
-
-\item {} 
-level \textbf{3} : \emph{Out-of-date Jobs in Out-of-date Tasks, no explanation}
-
-\item {} 
-level \textbf{4} : \emph{Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings}
-
-\item {} 
-level \textbf{5} : \emph{All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)}
-
-\item {} 
-level \textbf{6} : \emph{All jobs in All Tasks whether out of date or not}
-
-\item {} 
-level \textbf{10}: \emph{logs messages useful only for debugging ruffus pipeline code}
-
-\end{itemize}
-\end{quote}
-
-
-\subsection{Abbreviating long file paths with \texttt{verbose\_abbreviated\_path}}
-\label{tutorials/new_tutorial/pipeline_printout:abbreviating-long-file-paths-with-verbose-abbreviated-path}\label{tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout-verbose-abbreviated-path}\begin{quote}
-
-Pipelines often produce interminable lists of deeply nested filenames. It would be nice to be able to abbreviate this
-to just enough information to follow the progress.
-
-The \code{verbose\_abbreviated\_path} parameter specifies that   {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}} and {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(...)}}} only display
-\begin{quote}
-\begin{enumerate}
-\item {} 
-the \code{NNN} th top level sub-directories to be included, or that
-
-\item {} 
-the message to be truncated to a specified \code{{}`MMM} characters (to fit onto a line, for example). \code{MMM} is specified by setting \code{verbose\_abbreviated\_path = -MMM}, i.e. negative values.
-
-Note that the number of characters specified is just the separate lengths of the input and output parameters,
-not the entire indented line. You many need to specify a smaller limit that you expect (e.g. \code{60} rather than \emph{80})
-
-\end{enumerate}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{n}{NNN}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{n}{MMM}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\code{verbose\_abbreviated\_path} defaults to \code{2}
-
-For example:
-\begin{quote}
-
-Given \code{{[}"aa/bb/cc/dddd.txt", "aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt"{]}}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{c}{\PYGZsh{} Original relative paths}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[aa/bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
- \PYG{c}{\PYGZsh{} Full abspath}
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{l+m+mi}{0}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[/test/ruffus/src/aa/bb/cc/dddd.txt, /test/ruffus/src/aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
- \PYG{c}{\PYGZsh{} Specifed level of nested directories}
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{l+m+mi}{1}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[.../dddd.txt, .../gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{l+m+mi}{2}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[.../cc/dddd.txt, .../ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{l+m+mi}{3}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[.../bb/cc/dddd.txt, .../eeee/ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
-
- \PYG{c}{\PYGZsh{} Truncated to MMM characters}
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{60}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZlt{}???\PYGZgt{} /bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Getting a list of all tasks in a pipeline}
-\label{tutorials/new_tutorial/pipeline_printout:getting-a-list-of-all-tasks-in-a-pipeline}\begin{quote}
-
-If you just wanted a list of all tasks (Ruffus decorated function names), then you can
-just run Run {\hyperref[pipeline_functions:pipeline-functions-pipeline-get-task-names]{\emph{pipeline\_get\_task\_names(...)}}}.
-
-This doesn't touch any pipeline code or even check to see if the pipeline is connected up properly.
-
-However, it is sometimes useful to allow users at the command line to choose from a list of
-possible tasks as a target.
-\end{quote}
-
-\index{command line!Tutorial}\index{Tutorial!command line}
-
-\section{\textbf{Chapter 6}: Running \emph{Ruffus} from the command line with ruffus.cmdline}
-\label{tutorials/new_tutorial/command_line:new-manual-cmdline-chapter-num-running-ruffus-from-the-command-line-with-ruffus-cmdline}\label{tutorials/new_tutorial/command_line:index-0}\label{tutorials/new_tutorial/command_line::doc}\label{tutorials/new_tutorial/command_line:new-manual-cmdline}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual table of Contents}}}
-
-\end{itemize}
-
-
-
-We find that much of our \emph{Ruffus} pipeline code is built on the same template and this is generally
-a good place to start developing a new pipeline.
-
-From version 2.4, \emph{Ruffus} includes an optional \code{Ruffus.cmdline} module that provides
-support for a set of common command line arguments. This makes writing \emph{Ruffus} pipelines much more pleasant.
-\phantomsection\label{tutorials/new_tutorial/command_line:new-manual-cmdline-get-argparse}\phantomsection\label{tutorials/new_tutorial/command_line:new-manual-cmdline-run}
-
-\subsection{Template for argparse}
-\label{tutorials/new_tutorial/command_line:template-for-argparse}\label{tutorials/new_tutorial/command_line:new-manual-cmdline-run}\label{tutorials/new_tutorial/command_line:new-manual-cmdline-setup-logging}\label{tutorials/new_tutorial/command_line:new-manual-cmdline-get-argparse}\begin{quote}
-
-All you need to do is copy these 6 lines
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{ruffus.cmdline} \PYG{k+kn}{as} \PYG{n+nn}{cmdline}
-
-\PYG{n}{parser} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{get\PYGZus{}argparse}\PYG{p}{(}\PYG{n}{description}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{WHAT DOES THIS PIPELINE DO?}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}   \PYGZlt{}\PYGZlt{}\PYGZlt{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{} add your own command line options like \PYGZhy{}\PYGZhy{}input\PYGZus{}file here}
-\PYG{c}{\PYGZsh{} parser.add\PYGZus{}argument(\PYGZdq{}\PYGZhy{}\PYGZhy{}input\PYGZus{}file\PYGZdq{})}
-
-\PYG{n}{options} \PYG{o}{=} \PYG{n}{parser}\PYG{o}{.}\PYG{n}{parse\PYGZus{}args}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}  standard python logger which can be synchronised across concurrent Ruffus tasks}
-\PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{setup\PYGZus{}logging} \PYG{p}{(}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{log\PYGZus{}file}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}   \PYGZlt{}\PYGZlt{}\PYGZlt{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}  pipelined functions go here}
-
-\PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{run} \PYG{p}{(}\PYG{n}{options}\PYG{p}{)}
-\end{Verbatim}
-
-You are recommended to use the standard \href{http://docs.python.org/2.7/library/argparse.html}{argparse} module
-but the deprecated \href{http://docs.python.org/2.7/library/optparse.html}{optparse} module works as well. (See {\hyperref[tutorials/new_tutorial/command_line:code-template-optparse]{\emph{below}}} for the template)
-\end{quote}
-
-
-\subsection{Command Line Arguments}
-\label{tutorials/new_tutorial/command_line:command-line-arguments}\begin{quote}
-
-\code{Ruffus.cmdline} by default provides these predefined options:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYGZhy{}v, \PYGZhy{}\PYGZhy{}verbose
-    \PYGZhy{}\PYGZhy{}version
-\PYGZhy{}L, \PYGZhy{}\PYGZhy{}log\PYGZus{}file
-
-    \PYG{c}{\PYGZsh{} tasks}
-\PYGZhy{}T, \PYGZhy{}\PYGZhy{}target\PYGZus{}tasks
-    \PYGZhy{}\PYGZhy{}forced\PYGZus{}tasks
-\PYGZhy{}j, \PYGZhy{}\PYGZhy{}jobs
-    \PYGZhy{}\PYGZhy{}use\PYGZus{}threads
-
-
-    \PYG{c}{\PYGZsh{} printout}
-\PYGZhy{}n, \PYGZhy{}\PYGZhy{}just\PYGZus{}print
-
-    \PYG{c}{\PYGZsh{} flow chart}
-    \PYGZhy{}\PYGZhy{}flowchart
-    \PYGZhy{}\PYGZhy{}key\PYGZus{}legend\PYGZus{}in\PYGZus{}graph
-    \PYGZhy{}\PYGZhy{}draw\PYGZus{}graph\PYGZus{}horizontally
-    \PYGZhy{}\PYGZhy{}flowchart\PYGZus{}format
-
-
-    \PYG{c}{\PYGZsh{} check sum}
-    \PYGZhy{}\PYGZhy{}touch\PYGZus{}files\PYGZus{}only
-    \PYGZhy{}\PYGZhy{}checksum\PYGZus{}file\PYGZus{}name
-    \PYGZhy{}\PYGZhy{}recreate\PYGZus{}database
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{1) Logging}
-\label{tutorials/new_tutorial/command_line:logging}\begin{quote}
-
-The script provides for logging both to the command line:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-myscript \PYGZhy{}v
-myscript \PYGZhy{}\PYGZhy{}verbose
-\end{Verbatim}
-\end{quote}
-
-and an optional log file:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} keep tabs on yourself}
-myscript \PYGZhy{}\PYGZhy{}log\PYGZus{}file /var/log/secret.logbook
-\end{Verbatim}
-\end{quote}
-
-Logging is ignored if neither \code{-{-}verbose} or \code{-{-}log\_file} are specified on the command line
-
-\code{Ruffus.cmdline} automatically allows you to write to a shared log file via a proxy from multiple processes.
-However, you do need to use \code{logging\_mutex} for the log files to be synchronised properly across different jobs:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{with} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{:}
-
-    \PYG{n}{logger\PYGZus{}proxy}\PYG{o}{.}\PYG{n}{info}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Look Ma. No hands}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Logging is set up so that you can write
-\end{quote}
-
-
-\subsubsection{A) Only to the log file:}
-\label{tutorials/new_tutorial/command_line:a-only-to-the-log-file}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{logger}\PYG{o}{.}\PYG{n}{info}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{A message}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{B) Only to the display:}
-\label{tutorials/new_tutorial/command_line:b-only-to-the-display}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{logger}\PYG{o}{.}\PYG{n}{debug}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{A message}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{C) To both simultaneously:}
-\label{tutorials/new_tutorial/command_line:c-to-both-simultaneously}\label{tutorials/new_tutorial/command_line:new-manual-cmdline-message}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.cmdline} \PYG{k+kn}{import} \PYG{n}{MESSAGE}
-
-\PYG{n}{logger}\PYG{o}{.}\PYG{n}{log}\PYG{p}{(}\PYG{n}{MESSAGE}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{A message}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{2) Tracing pipeline progress}
-\label{tutorials/new_tutorial/command_line:tracing-pipeline-progress}\begin{quote}
-
-This is extremely useful for understanding what is happening with your pipeline, what tasks and which
-jobs are up-to-date etc.
-
-See {\hyperref[tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout]{\emph{Chapter 5: Understanding how your pipeline works with pipeline\_printout(...)}}}
-
-To trace the pipeline, call script with the following options
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} well\PYGZhy{}mannered, reserved}
-myscript \PYGZhy{}\PYGZhy{}just\PYGZus{}print
-myscript \PYGZhy{}n
-
-or
-
-\PYG{c}{\PYGZsh{} extremely loquacious}
-myscript \PYGZhy{}\PYGZhy{}just\PYGZus{}print \PYGZhy{}\PYGZhy{}verbose 5
-myscript \PYGZhy{}n \PYGZhy{}v5
-\end{Verbatim}
-\end{quote}
-
-Increasing levels of verbosity (\code{-{-}verbose} to \code{-{-}verbose 5}) provide more detailed output
-\end{quote}
-
-
-\subsection{3) Printing a flowchart}
-\label{tutorials/new_tutorial/command_line:printing-a-flowchart}\begin{quote}
-
-This is the subject of {\hyperref[tutorials/new_tutorial/pipeline_printout_graph:new-manual-pipeline-printout-graph]{\emph{Chapter 7: Displaying the pipeline visually with pipeline\_printout\_graph(...)}}}.
-
-Flowcharts can be specified using the following option:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-myscript \PYGZhy{}\PYGZhy{}flowchart xxxchart.svg
-\end{Verbatim}
-\end{quote}
-
-The extension of the flowchart file indicates what format the flowchart should take,
-for example, \code{svg}, \code{jpg} etc.
-
-Override with \code{-{-}flowchart\_format}
-\end{quote}
-
-
-\subsection{4) Running in parallel on multiple processors}
-\label{tutorials/new_tutorial/command_line:running-in-parallel-on-multiple-processors}\begin{quote}
-
-Optionally specify the number of parallel strands of execution and which is the last \emph{target} task to run.
-The pipeline will run starting from any out-of-date tasks which precede the \emph{target} and proceed no further
-beyond the \emph{target}.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-myscript \PYGZhy{}\PYGZhy{}jobs 15 \PYGZhy{}\PYGZhy{}target\PYGZus{}tasks \PYG{l+s+s2}{\PYGZdq{}final\PYGZus{}task\PYGZdq{}}
-myscript \PYGZhy{}j 15
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{5) Setup checkpointing so that \emph{Ruffus} knows which files are out of date}
-\label{tutorials/new_tutorial/command_line:setup-checkpointing-so-that-ruffus-knows-which-files-are-out-of-date}\begin{quote}
-
-The {\hyperref[tutorials/new_tutorial/checkpointing:new-manual-checkpointing]{\emph{checkpoint file}}} uses to the value set in the
-environment (\code{DEFAULT\_RUFFUS\_HISTORY\_FILE}).
-
-If this is not set, it will default to \code{.ruffus\_history.sqlite} in the current working directory.
-
-Either can be changed on the command line:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-myscript \PYGZhy{}\PYGZhy{}checksum\PYGZus{}file\PYGZus{}name mychecksum.sqlite
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Recreating checkpoints}
-\label{tutorials/new_tutorial/command_line:recreating-checkpoints}\begin{quote}
-
-Create or update the checkpoint file so that all existing files in completed jobs appear up to date
-
-Will stop sensibly if current state is incomplete or inconsistent
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{myscript} \PYG{o}{\PYGZhy{}}\PYG{o}{\PYGZhy{}}\PYG{n}{recreate\PYGZus{}database}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Touch files}
-\label{tutorials/new_tutorial/command_line:touch-files}\begin{quote}
-
-As far as possible, create empty files with the correct timestamp to make the pipeline appear up to date.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-myscript \PYGZhy{}\PYGZhy{}touch\PYGZus{}files\PYGZus{}only
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{6) Skipping specified options}
-\label{tutorials/new_tutorial/command_line:skipping-specified-options}\begin{quote}
-
-Note that particular options can be skipped (not added to the command line), if they conflict with your own options, for example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} see below for how to use get\PYGZus{}argparse}
-\PYG{n}{parser} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{get\PYGZus{}argparse}\PYG{p}{(}  \PYG{n}{description}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{WHAT DOES THIS PIPELINE DO?}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                                \PYG{c}{\PYGZsh{} Exclude the following options: \PYGZhy{}\PYGZhy{}log\PYGZus{}file \PYGZhy{}\PYGZhy{}key\PYGZus{}legend\PYGZus{}in\PYGZus{}graph}
-                                \PYG{n}{ignored\PYGZus{}args} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{log\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{key\PYGZus{}legend\PYGZus{}in\PYGZus{}graph}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{7) Specifying verbosity and abbreviating long paths}
-\label{tutorials/new_tutorial/command_line:specifying-verbosity-and-abbreviating-long-paths}\begin{quote}
-
-The verbosity can be specified on the command line
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-myscript \PYGZhy{}\PYGZhy{}verbose 5
-
-\PYG{c}{\PYGZsh{} verbosity of 5 + 1 = 6}
-myscript \PYGZhy{}\PYGZhy{}verbose 5 \PYGZhy{}\PYGZhy{}verbose
-
-\PYG{c}{\PYGZsh{} verbosity reset to 2}
-myscript \PYGZhy{}\PYGZhy{}verbose 5 \PYGZhy{}\PYGZhy{}verbose \PYGZhy{}\PYGZhy{}verbose 2
-\end{Verbatim}
-\end{quote}
-
-If the printed paths are too long, and need to be abbreviated, or alternatively, if you want see the full absolute paths of your input and output parameters,
-you can specify an extension to the verbosity. See the manual discussion of {\hyperref[tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout-verbose-abbreviated-path]{\emph{verbose\_abbreviated\_path}}} for
-more details. This is specified as \code{-{-}verbose VERBOSITY:VERBOSE\_ABBREVIATED\_PATH}. (No spaces!)
-
-For example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{c}{\PYGZsh{} verbosity of 4}
- myscript.py \PYGZhy{}\PYGZhy{}verbose 4
-
- \PYG{c}{\PYGZsh{} display three levels of nested directories}
- myscript.py \PYGZhy{}\PYGZhy{}verbose 4:3
-
- \PYG{c}{\PYGZsh{} restrict input and output parameters to 60 letters}
- myscript.py \PYGZhy{}\PYGZhy{}verbose 4:\PYGZhy{}60
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{8) Displaying the version}
-\label{tutorials/new_tutorial/command_line:displaying-the-version}\begin{quote}
-
-Note that the version for your script will default to \code{"\%(prog)s 1.0"} unless specified:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{parser} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{get\PYGZus{}argparse}\PYG{p}{(}  \PYG{n}{description}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{WHAT DOES THIS PIPELINE DO?}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                                \PYG{n}{version} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}programme.py v. 2.23}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Template for optparse}
-\label{tutorials/new_tutorial/command_line:code-template-optparse}\label{tutorials/new_tutorial/command_line:template-for-optparse}\begin{quote}
-
-deprecated since python 2.7
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Using optparse (new in python v 2.6)}
-\PYG{c}{\PYGZsh{}}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n}{parser} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{get\PYGZus{}optgparse}\PYG{p}{(}\PYG{n}{version}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZpc{}}\PYG{l+s}{prog 1.0}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{usage} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{    }\PYG{l+s}{\PYGZpc{}}\PYG{l+s}{prog [options]}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}   \PYGZlt{}\PYGZlt{}\PYGZlt{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{} add your own command line options like \PYGZhy{}\PYGZhy{}input\PYGZus{}file here}
-\PYG{c}{\PYGZsh{} parser.add\PYGZus{}option(\PYGZdq{}\PYGZhy{}i\PYGZdq{}, \PYGZdq{}\PYGZhy{}\PYGZhy{}input\PYGZus{}file\PYGZdq{}, dest=\PYGZdq{}input\PYGZus{}file\PYGZdq{}, help=\PYGZdq{}Input file\PYGZdq{})}
-
-\PYG{p}{(}\PYG{n}{options}\PYG{p}{,} \PYG{n}{remaining\PYGZus{}args}\PYG{p}{)} \PYG{o}{=} \PYG{n}{parser}\PYG{o}{.}\PYG{n}{parse\PYGZus{}args}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}  logger which can be passed to ruffus tasks}
-\PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{setup\PYGZus{}logging} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{this\PYGZus{}program}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{log\PYGZus{}file}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}   \PYGZlt{}\PYGZlt{}\PYGZlt{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}  pipelined functions go here}
-
-\PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{run} \PYG{p}{(}\PYG{n}{options}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{pipeline\_printout\_graph!Tutorial}\index{Tutorial!pipeline\_printout\_graph}
-
-\section{\textbf{Chapter 7}: Displaying the pipeline visually with \emph{pipeline\_printout\_graph(...)}}
-\label{tutorials/new_tutorial/pipeline_printout_graph:index-0}\label{tutorials/new_tutorial/pipeline_printout_graph:new-manual-pipeline-printout-graph-chapter-num-displaying-the-pipeline-visually-with-pipeline-printout-graph}\label{tutorials/new_tutorial/pipeline_printout_graph::doc}\label{tutorials/new_tutorial/pipeline_printout_graph:new-manual-pipeline-printout-graph}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph]{\emph{pipeline\_printout\_graph(...)}}} syntax
-
-\item {} 
-{\hyperref[decorators/graphviz:decorators-graphviz]{\emph{@graphviz(...)}}} syntax
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/pipeline_printout_graph_code:new-manual-pipeline-printout-graph-code]{\emph{Chapter 7: Python Code for Displaying the pipeline visually with pipeline\_printout\_graph(...)}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Printing out a flowchart of our pipeline}
-\label{tutorials/new_tutorial/pipeline_printout_graph:printing-out-a-flowchart-of-our-pipeline}\begin{quote}
-
-It is all very well being able to trace the data flow through the pipeline as text.
-Sometimes, however, we need a bit of eye-candy!
-
-We can see a flowchart for our fledgling pipeline by executing:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(}   \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{flowchart.svg}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                            \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{svg}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                            \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,}
-                            \PYG{n}{no\PYGZus{}key\PYGZus{}legend} \PYG{o}{=} \PYG{n+nb+bp}{False}\PYG{p}{)}
-\end{Verbatim}
-
-\scalebox{0.700000}{\includegraphics{simple_tutorial_stage5_flowchart.png}}
-\end{quote}
-
-Flowcharts can be printed in a large number of formats including \code{jpg}, \code{svg}, \code{png} and \code{pdf}.
-
-\begin{notice}{note}{Note:}
-Flowcharts rely on the \code{dot} programme from \href{http://www.graphviz.org/}{Graphviz}.
-
-Please make sure this is installed.
-\end{notice}
-
-There are 8 standard colour schemes, but you can further customise all the colours to your satisfaction:
-\begin{quote}
-
-\includegraphics{flowchart_colour_schemes.png}
-\end{quote}
-
-See {\hyperref[tutorials/new_tutorial/flowchart_colours:new-manual-flowchart-colours]{\emph{here}}} for example code.
-\end{quote}
-
-
-\subsection{Command line options made easier with \texttt{ruffus.cmdline}}
-\label{tutorials/new_tutorial/pipeline_printout_graph:command-line-options-made-easier-with-ruffus-cmdline}\begin{quote}
-
-If you are using \code{ruffus.cmdline}, then you can easily ask for a flowchart from the command line:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-your\PYGZus{}script.py \PYGZhy{}\PYGZhy{}flowchart pipeline\PYGZus{}flow\PYGZus{}chart.png
-\end{Verbatim}
-\end{quote}
-
-The output format is deduced from the extension but can be specified manually:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} specify format. Otherwise, deduced from the extension}
-your\PYGZus{}script.py \PYGZhy{}\PYGZhy{}flowchart pipeline\PYGZus{}flow\PYGZus{}chart.png \PYGZhy{}\PYGZhy{}flowchart\PYGZus{}format png
-\end{Verbatim}
-\end{quote}
-
-Print the flow chart horizontally or vertically...
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} flowchart proceeds from left to right , rather than from  top to bottom}
-your\PYGZus{}script.py \PYGZhy{}\PYGZhy{}flowchart pipeline\PYGZus{}flow\PYGZus{}chart.png \PYGZhy{}\PYGZhy{}draw\PYGZus{}graph\PYGZus{}horizontally
-\end{Verbatim}
-\end{quote}
-
-...with or without a key legend
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} Draw key legend}
-your\PYGZus{}script.py \PYGZhy{}\PYGZhy{}flowchart pipeline\PYGZus{}flow\PYGZus{}chart.png \PYGZhy{}\PYGZhy{}key\PYGZus{}legend\PYGZus{}in\PYGZus{}graph
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Horribly complicated pipelines!}
-\label{tutorials/new_tutorial/pipeline_printout_graph:horribly-complicated-pipelines}\begin{quote}
-
-Flowcharts are especially useful if you have really complicated pipelines, such as
-\begin{quote}
-
-\scalebox{0.700000}{\includegraphics{simple_tutorial_complex_flowchart.png}}
-\end{quote}
-\end{quote}
-
-
-\subsection{Circular dependency errors in pipelines!}
-\label{tutorials/new_tutorial/pipeline_printout_graph:circular-dependency-errors-in-pipelines}\begin{quote}
-
-Especially, if the pipeline is not set up properly, and vicious circular dependencies
-are present:
-\begin{quote}
-
-\scalebox{0.700000}{\includegraphics{simple_tutorial_complex_flowchart_error.png}}
-\end{quote}
-\end{quote}
-
-
-\subsection{\texttt{@graphviz}: Customising the appearance of each task}
-\label{tutorials/new_tutorial/pipeline_printout_graph:graphviz-customising-the-appearance-of-each-task}\begin{quote}
-
-The graphic for each task can be further customised as you please by adding
-\href{http://www.graphviz.org/doc/info/attrs.html}{graphviz attributes} such as the URL, shape, colour
-directly to that node using the decorator \code{{}`@graphviz}.
-
-For example, we can customise the graphic for \code{myTask()} to look like:
-\begin{quote}
-
-\scalebox{0.300000}{\includegraphics{history_html_flowchart2.png}}
-\end{quote}
-
-by adding the requisite attributes as follows:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@graphviz}\PYG{p}{(}\PYG{n}{URL}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{http://cnn.com}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{fillcolor} \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FFCCCC}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                \PYG{n}{color} \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF0000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{pencolor}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF0000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{fontcolor}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}4B6000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                \PYG{n}{label\PYGZus{}suffix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{???}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{label\PYGZus{}prefix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{What is this?\PYGZlt{}BR/\PYGZgt{} }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{n}{label} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZlt{}What \PYGZlt{}FONT COLOR=}\PYG{l+s+se}{\PYGZbs{}\PYGZdq{}}\PYG{l+s}{red}\PYG{l+s+se}{\PYGZbs{}\PYGZdq{}}\PYG{l+s}{\PYGZgt{}is\PYGZlt{}/FONT\PYGZgt{}this\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{n}{shape}\PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{component}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{height} \PYG{o}{=} \PYG{l+m+mf}{1.5}\PYG{p}{,} \PYG{n}{peripheries} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,}
-                \PYG{n}{style}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dashed}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task2}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   Can use dictionary if you wish...}
-\PYG{n}{graphviz\PYGZus{}params} \PYG{o}{=} \PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{URL}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{http://cnn.com}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF00FF}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{\PYGZcb{}}
-\PYG{n+nd}{@graphviz}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n}{graphviz\PYGZus{}params}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{myTask}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{,}\PYG{n}{output}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-You can even using HTML formatting in task names, including specifying line wraps (as in the above example),
-using the \code{label} parameter. However, HTML labels \textbf{must} be enclosed in \code{\textless{}} and \code{\textgreater{}}.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{label} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZlt{}Line \PYGZlt{}BR/\PYGZgt{} wrapped task\PYGZus{}name()\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-Otherwise, you can also opt to keep the task name and wrap it with a prefix and suffix:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{label\PYGZus{}suffix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{??? }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{label\PYGZus{}prefix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{: What is this?}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-\begin{description}
-\item[{The \code{URL} attribute allows the generation of clickable svg, and also client / server}] \leavevmode
-side image maps usable in web pages.
-See \href{http://www.graphviz.org/content/output-formats\#dimap}{Graphviz documentation}
-
-\end{description}
-\end{quote}
-
-\index{formatter!Tutorial}\index{Tutorial!formatter}\index{suffix!Tutorial}\index{Tutorial!suffix}\index{regex!Tutorial}\index{Tutorial!regex}\index{output file names!Tutorial}\index{Tutorial!output file names}
-
-\section{\textbf{Chapter 8}: Specifying output file names with \emph{formatter()} and \emph{regex()}}
-\label{tutorials/new_tutorial/output_file_names:new-manual-output-file-names-chapter-num-specifying-output-file-names-with-formatter-and-regex}\label{tutorials/new_tutorial/output_file_names:index-0}\label{tutorials/new_tutorial/output_file_names:new-manual-output-file-names}\label{tutorials/new_tutorial/output_file_names::doc}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}} syntax
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} syntax
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} syntax
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/output_file_names_code:new-manual-output-file-names-code]{\emph{Chapter 8: Python Code for Specifying output file names with formatter() and regex()}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Review}
-\label{tutorials/new_tutorial/output_file_names:review}\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{theoretical_pipeline_schematic.png}}
-
-Computational pipelines transform your data in stages until the final result is produced.
-The most straightforward way to use Ruffus is to hold the intermediate results after each stage
-in a series of files with related file names.
-
-Part of telling Ruffus how these pipeline stages or {\hyperref[glossary:term-task]{\emph{task}}} functions are connected
-together is to write simple rules for how to the file names for each stage follow on from each other.
-Ruffus helps you to specify these file naming rules.
-
-\begin{notice}{note}{Note:}
-\textbf{The best way to design a pipeline is to:}
-\begin{itemize}
-\item {} 
-\textbf{Write down the file names of the data as it flows across your pipeline.}
-Do these file names follow a \emph{pattern} ?
-
-\item {} 
-\textbf{Write down the names of functions which transforms the data at each stage of the pipeline.}
-
-\end{itemize}
-\end{notice}
-\end{quote}
-
-
-\subsection{A different file name \emph{suffix()} for each pipeline stage}
-\label{tutorials/new_tutorial/output_file_names:new-manual-suffix}\label{tutorials/new_tutorial/output_file_names:a-different-file-name-suffix-for-each-pipeline-stage}\begin{quote}
-
-The easiest and cleanest way to write Ruffus pipelines is to use a different suffix
-for each stage of your pipeline.
-
-We used this approach in {\hyperref[tutorials/new_tutorial/introduction:new-manual-introduction]{\emph{Chapter 1: An introduction to basic Ruffus syntax}}}  and in {\hyperref[tutorials/new_tutorial/transform_in_parallel_code:new-manual-transform-in-parallel-code]{\emph{code}}} from {\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-transform-in-parallel]{\emph{Chapter 3: More on @transform-ing data}}}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-    \PYG{c}{\PYGZsh{}Task Name:                  File suffices}
-    \PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}      \PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}
-    create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs            *.start
-    first\PYGZus{}task                           *.output.1
-    second\PYGZus{}task                          *.output.2
-\end{Verbatim}
-
-There is a long standing convention of using file suffices to denote file type: For example, a \textbf{``compile''} task might convert \textbf{source} files of type \code{*.c} to \textbf{object} files of type \code{*.o}.
-\begin{description}
-\item[{We can think of Ruffus tasks comprising :}] \leavevmode\begin{itemize}
-\item {} 
-recipes in \code{@transform(...)} for transforming file names: changing  \code{.c} to a \code{.o} (e.g. \code{AA.c -\textgreater{} AA.o} \code{BB.c -\textgreater{} BB.o})
-
-\item {} 
-recipes in a task function \code{def foo\_bar()} for transforming your data: from \textbf{source} \code{.c} to \textbf{object} \code{.o}
-
-\end{itemize}
-
-\end{description}
-
-Let us review the Ruffus syntax for doing this:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- at transform\PYG{o}{(} create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs,  \PYG{c}{\PYGZsh{} Input:   Name of previous task(s)}
-            suffix\PYG{o}{(}\PYG{l+s+s2}{\PYGZdq{}.start\PYGZdq{}}\PYG{o}{)},           \PYG{c}{\PYGZsh{} Matching suffix}
-            \PYG{l+s+s2}{\PYGZdq{}.output.1\PYGZdq{}}\PYG{o}{)}                \PYG{c}{\PYGZsh{} Replacement string}
-def first\PYGZus{}task\PYG{o}{(}input\PYGZus{}files, output\PYGZus{}file\PYG{o}{)}:
-    with open\PYG{o}{(}output\PYGZus{}file, \PYG{l+s+s2}{\PYGZdq{}w\PYGZdq{}}\PYG{o}{)}: pass
-\end{Verbatim}
-\end{quote}
-\begin{enumerate}
-\item {} 
-\textbf{Input}:
-\begin{quote}
-\begin{description}
-\item[{The first parameter for \code{@transform} can be a mixture of one or more:}] \leavevmode\begin{itemize}
-\item {} 
-previous tasks (e.g. \code{create\_initial\_file\_pairs})
-
-\item {} 
-file names (all python strings are treated as paths)
-
-\item {} 
-glob specifications (e.g \code{*.c}, \code{/my/path/*.foo})
-
-\end{itemize}
-
-\end{description}
-
-Each element provides an input for the task. So if the previous task \code{create\_initial\_file\_pairs} has five outputs, the next \code{@transform} task will accept
-these as five separate inputs leading to five independent jobs.
-\end{quote}
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}}:
-\begin{quote}
-
-The second parameter \code{suffix(".start")} must match the end of the first string in each input.
-For example, \code{create\_initial\_file\_pairs} produces the list \code{{[}'job1.a.start', 'job1.b.start'{]}}, then \code{suffix(".start")}  must matches the first string, i.e. \code{'job1.a.start'}.
-If the input is nested structure, this would be iterated through recursively to find the first string.
-
-\begin{notice}{note}{Note:}
-Inputs which do not match the suffix are discarded altogether.
-\end{notice}
-\end{quote}
-
-\item {} 
-\textbf{Replacement}:
-\begin{quote}
-
-The third parameter is the replacement for the suffix.
-The pair of input strings in the step3 example produces the following output parameter
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{input\PYGZus{}parameters}   \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}
-\PYG{n}{matching\PYGZus{}input}     \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}
-\PYG{n}{output\PYGZus{}parameter}   \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.output.1}\PYG{l+s}{\PYGZsq{}}
-\end{Verbatim}
-\end{quote}
-
-When the pipeline is run, this results in the following equivalent call to \code{first\_task(...)}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{first\PYGZus{}task}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.output.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{:}
-\end{Verbatim}
-\end{quote}
-
-The replacement parameter can itself be a list or any arbitrary complicated structure:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- at transform\PYG{o}{(}create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs,            \PYG{c}{\PYGZsh{} Input}
-            suffix\PYG{o}{(}\PYG{l+s+s2}{\PYGZdq{}.a.start\PYGZdq{}}\PYG{o}{)},                  \PYG{c}{\PYGZsh{} Matching suffix}
-            \PYG{o}{[}\PYG{l+s+s2}{\PYGZdq{}.output.a.1\PYGZdq{}}, \PYG{l+s+s2}{\PYGZdq{}.output.b.1\PYGZdq{}}, 45\PYG{o}{]}\PYG{o}{)}  \PYG{c}{\PYGZsh{} Replacement list}
-def first\PYGZus{}task\PYG{o}{(}input\PYGZus{}files, output\PYGZus{}parameters\PYG{o}{)}:
-    print \PYG{l+s+s2}{\PYGZdq{}input\PYGZus{}parameters = \PYGZdq{}}, input\PYGZus{}files
-    print \PYG{l+s+s2}{\PYGZdq{}output\PYGZus{}parameters = \PYGZdq{}}, output\PYGZus{}parameters
-\end{Verbatim}
-\end{quote}
-
-In which case, all the strings are used as replacements, other values are left untouched, and we obtain the following:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} job \PYGZsh{}1}
-\PYG{n+nv}{input}  \PYG{o}{=}  \PYG{o}{[}\PYG{l+s+s1}{\PYGZsq{}job1.a.start\PYGZsq{}},    \PYG{l+s+s1}{\PYGZsq{}job1.b.start\PYGZsq{}}\PYG{o}{]}
-\PYG{n+nv}{output} \PYG{o}{=}  \PYG{o}{[}\PYG{l+s+s1}{\PYGZsq{}job1.output.a.1\PYGZsq{}}, \PYG{l+s+s1}{\PYGZsq{}job1.output.b.1\PYGZsq{}}, 45\PYG{o}{]}
-
-\PYG{c}{\PYGZsh{} job \PYGZsh{}2}
-\PYG{n+nv}{input}  \PYG{o}{=}  \PYG{o}{[}\PYG{l+s+s1}{\PYGZsq{}job2.a.start\PYGZsq{}},    \PYG{l+s+s1}{\PYGZsq{}job2.b.start\PYGZsq{}}\PYG{o}{]}
-\PYG{n+nv}{output} \PYG{o}{=}  \PYG{o}{[}\PYG{l+s+s1}{\PYGZsq{}job2.output.a.1\PYGZsq{}}, \PYG{l+s+s1}{\PYGZsq{}job2.output.b.1\PYGZsq{}}, 45\PYG{o}{]}
-
-\PYG{c}{\PYGZsh{} job \PYGZsh{}3}
-\PYG{n+nv}{input}  \PYG{o}{=}  \PYG{o}{[}\PYG{l+s+s1}{\PYGZsq{}job3.a.start\PYGZsq{}},    \PYG{l+s+s1}{\PYGZsq{}job3.b.start\PYGZsq{}}\PYG{o}{]}
-\PYG{n+nv}{output} \PYG{o}{=}  \PYG{o}{[}\PYG{l+s+s1}{\PYGZsq{}job3.output.a.1\PYGZsq{}}, \PYG{l+s+s1}{\PYGZsq{}job3.output.b.1\PYGZsq{}}, 45\PYG{o}{]}
-\end{Verbatim}
-\end{quote}
-
-Note how task function is called with the value \code{45} \emph{verbatim} because it is not a string.
-\end{quote}
-
-\end{enumerate}
-\end{quote}
-
-
-\subsection{\emph{formatter()} manipulates pathnames and regular expression}
-\label{tutorials/new_tutorial/output_file_names:formatter-manipulates-pathnames-and-regular-expression}\label{tutorials/new_tutorial/output_file_names:new-manual-formatter}\begin{quote}
-
-{\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}} replacement is the cleanest and easiest way to generate suitable output file names for each stage in a pipeline.
-Often, however, we require more complicated manipulations to specify our file names.
-For example,
-\begin{itemize}
-\item {} 
-It is common to have to change directories from a \emph{data} directory to a \emph{working} directory as the first step of a pipeline.
-
-\item {} 
-Data management can be simplified by separate files from each pipeline stage into their own directory.
-
-\item {} 
-Information may have to be decoded from data file names, e.g. \code{"experiment373.IBM.03March2002.txt"}
-
-\end{itemize}
-
-Though {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} is much more powerful, the principle and syntax are the same:
-we take string elements from the \textbf{Input} and perform some replacements to generate the \textbf{Output} parameters.
-
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}}
-\begin{itemize}
-\item {} 
-Allows easy manipulation of path subcomponents in the style of \href{http://docs.python.org/2/library/os.path.html\#os.path.split}{os.path.split()}, and \href{http://docs.python.org/2/library/os.path.html\#os.path.basename}{os.path.basename}
-
-\item {} 
-Uses familiar python \href{http://docs.python.org/2/library/string.html\#string-formatting}{string.format} syntax (See \href{http://docs.python.org/2/library/string.html\#format-examples}{string.format examples}. )
-
-\item {} 
-Supports optional regular expression (\href{http://docs.python.org/2/library/re.html\#re.MatchObject.group}{re}) matches including named captures.
-
-\item {} 
-Can refer to any file path (i.e. python string) in each input and is not limited like {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}} to the first string.
-
-\item {} 
-Can even refer to individual letters within a match
-
-\end{itemize}
-\end{quote}
-
-
-\subsubsection{Path name components}
-\label{tutorials/new_tutorial/output_file_names:path-name-components}\begin{quote}
-
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} breaks down each input pathname into path name components which can then be recombined in whichever way by the replacement string.
-
-Given an example string of :
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{input\PYGZus{}string} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/directory/to/a/file.name.ext}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-the path components are:
-\begin{itemize}
-\item {} 
-\code{basename}: The \href{http://docs.python.org/2/library/os.path.html\#os.path.basename}{base name} \emph{excluding} \href{http://docs.python.org/2/library/os.path.html\#os.path.splitext}{extension}, \code{"file.name"}
-
-\item {} 
-\code{ext}     : The \href{http://docs.python.org/2/library/os.path.html\#os.path.splitext}{extension}, \code{".ext"}
-
-\item {} 
-\code{path}    : The \href{http://docs.python.org/2/library/os.path.html\#os.path.dirname}{dirname}, \code{"/directory/to/a"}
-
-\item {} 
-\code{subdir}  : A list of sub-directories in the \code{path} in reverse order, \code{{[}"a", "to", "directory", "/"{]}}
-
-\item {} 
-\code{subpath} : A list of descending sub-paths in reverse order, \code{{[}"/directory/to/a", "/directory/to", "/directory", "/"{]}}
-
-\end{itemize}
-\end{quote}
-
-The replacement string refers to these components by using python \href{http://docs.python.org/2/library/string.html\#string-formatting}{string.format} style curly braces. \code{"\{NAME\}"}
-
-We refer to an element from the Nth input string by index, for example:
-\begin{itemize}
-\item {} 
-\code{"\{ext{[}0{]}\}"}     is the extension of the first file name string in \textbf{Input}.
-
-\item {} 
-\code{"\{basename{[}1{]}\}"} is the basename of the second file name in \textbf{Input}.
-
-\item {} 
-\code{"\{basename{[}1{]}{[}0:3{]}\}"} are the first three letters from the basename of the second file name in \textbf{Input}.
-
-\end{itemize}
-
-\code{subdir}, \code{subpath} were designed to help you navigate directory hierachies with the minimum of fuss.
-For example, you might want to graft a hierachical path to another location:
-\code{"\{subpath{[}0{]}{[}2{]}\}/from/\{subdir{[}0{]}{[}0{]}\}/\{basename{[}0{]}\}"} neatly replaces just one directory (\code{"to"}) in the path with another  (\code{"from"}):
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{replacement\PYGZus{}string} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][2]\PYGZcb{}/from/\PYGZob{}subdir[0][0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{n}{input\PYGZus{}string}    \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/directory/to/a/file.name.ext}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{result\PYGZus{}string}   \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/directory/from/a/file.name.ext}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Filter and parse using regular expressions}
-\label{tutorials/new_tutorial/output_file_names:new-manual-formatter-regex}\label{tutorials/new_tutorial/output_file_names:filter-and-parse-using-regular-expressions}\begin{quote}
-
-\href{http://docs.python.org/2/library/re.html\#re.MatchObject.group}{Regular expression} matches can be used with the similar syntax.
-Our example string can be parsed using the following regular expression:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{input\PYGZus{}string} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/directory/to/a/file.name.ext}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{/directory/(.+)/(?P\PYGZlt{}MYFILENAME\PYGZgt{})}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.ext}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-We capture part of the path using \code{(.+)}, and the base name using \code{(?P\textless{}MYFILENAME\textgreater{})}.
-These \href{http://docs.python.org/2/library/re.html\#re.MatchObject.group}{matching subgroups} can be referred to by index
-but for greater clarity the second named capture can also be referred to by name, i.e. \code{\{MYFILENAME\}}.
-\end{quote}
-
-The regular expression components for the first string can thus be referred to as follows:
-\begin{itemize}
-\item {} 
-\code{\{0{[}0{]}\}}          : The entire match captured by index, \code{"/directory/to/a/file.name.ext"}
-
-\item {} 
-\code{\{1{[}0{]}\}}          : The first match captured by index, \code{"to/a"}
-
-\item {} 
-\code{\{2{[}0{]}\}}          : The second match captured by index, \code{"file.name"}
-
-\item {} 
-\code{\{MYFILENAME{[}0{]}\}} : The match captured by name, \code{"file.name"}
-
-\end{itemize}
-
-If each input consists of a list of paths such as \code{{[}'job1.a.start', 'job1.b.start', 'job1.c.start'{]}}, we can match each of them separately
-by using as many regular expressions as necessary. For example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{input\PYGZus{}string} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.c.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}
-\PYG{c}{\PYGZsh{} Regular expression matches for 1st, 2nd but not 3rd element}
-\PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.start\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Or if you only wanted regular expression matches for the second file name (string), pad with \code{None}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{input\PYGZus{}string} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.c.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}
-\PYG{c}{\PYGZsh{} Regular expression matches for 2nd but not 1st or 3rd elements}
-\PYG{n}{formatter}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.start\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Using \emph{@transform()} with \emph{formatter()}}
-\label{tutorials/new_tutorial/output_file_names:using-transform-with-formatter}\begin{quote}
-
-We can put these together in the following example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.c.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} create both files as necessary}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   formatter}
-\PYG{c}{\PYGZsh{}}
-
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} Input}
-
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job(?P\PYGZlt{}JOBNUMBER\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+).a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}           \PYG{c}{\PYGZsh{} Extract job number}
-                      \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job[123].b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                       \PYG{c}{\PYGZsh{} Match only \PYGZdq{}b\PYGZdq{} files}
-
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}             \PYG{c}{\PYGZsh{} Replacement list}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[1]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{45}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}parameters = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}files}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output\PYGZus{}parameters = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This produces:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+go}{input\PYGZus{}parameters  =  [\PYGZsq{}job1.a.start\PYGZsq{},}
-\PYG{g+go}{                      \PYGZsq{}job1.b.start\PYGZsq{}]}
-\PYG{g+go}{output\PYGZus{}parameters =  [\PYGZsq{}/home/lg/src/temp/jobs1.output.a.1\PYGZsq{},}
-\PYG{g+go}{                      \PYGZsq{}/home/lg/src/temp/jobs1.output.b.1\PYGZsq{}, 45]}
-
-\PYG{g+go}{input\PYGZus{}parameters  =  [\PYGZsq{}job2.a.start\PYGZsq{},}
-\PYG{g+go}{                      \PYGZsq{}job2.b.start\PYGZsq{}]}
-\PYG{g+go}{output\PYGZus{}parameters =  [\PYGZsq{}/home/lg/src/temp/jobs2.output.a.1\PYGZsq{},}
-\PYG{g+go}{                      \PYGZsq{}/home/lg/src/temp/jobs2.output.b.1\PYGZsq{}, 45]}
-\end{Verbatim}
-
-Notice that \code{job3} has \code{'job3.c.start'} as the second file.
-This fails to match the regular expression and is discarded.
-
-\begin{notice}{note}{Note:}
-Failed regular expression mismatches are ignored.
-
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} regular expressions are thus very useful in filtering out all
-files which do not match your specified criteria.
-
-If your some of your task inputs have a mixture of different file types, a simple \code{Formatter(".txt\$")}, for example, will make
-your code a lot simpler...
-\end{notice}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{string substitution for ``extra'' arguments}
-\label{tutorials/new_tutorial/output_file_names:string-substitution-for-extra-arguments}\begin{quote}
-
-The first two arguments for Ruffus task functions are special because they are the \textbf{Input} and \textbf{Output}
-parameters which link different stages of a pipeline.
-
-Python strings in these arguments are names of data files whose modification times indicate whether the pipeline is up to date or not.
-
-Other arguments to task functions are not passed down the pipeline but consumed.
-Any python strings they contain do not need to be file names. These extra arguments are very useful
-for passing data to pipelined tasks, such as shared values, loggers, programme options etc.
-
-One helpful feature is that strings in these extra arguments are also subject to {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} string substitution.
-This means you can leverage the parsing capabilities of Ruffus to decode any information about the pipeline data files,
-These might include the directories you are running in and parts of the file name.
-
-For example, if we would want to know which files go with which ``job number'' in the previous example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.c.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   print job number as an extra argument}
-\PYG{c}{\PYGZsh{}}
-
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} Input}
-
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job(?P\PYGZlt{}JOBNUMBER\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+).a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}           \PYG{c}{\PYGZsh{} Extract job number}
-                      \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job[123].b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                       \PYG{c}{\PYGZsh{} Match only \PYGZdq{}b\PYGZdq{} files}
-
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}             \PYG{c}{\PYGZsh{} Replacement list}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[1]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}JOBNUMBER[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}\PYG{p}{,} \PYG{n}{job\PYGZus{}number}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{n}{job\PYGZus{}number}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{:}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}files}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{1 : [\PYGZsq{}job1.a.start\PYGZsq{}, \PYGZsq{}job1.b.start\PYGZsq{}]}
-\PYG{g+go}{2 : [\PYGZsq{}job2.a.start\PYGZsq{}, \PYGZsq{}job2.b.start\PYGZsq{}]}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Changing directories using \emph{formatter()} in a zoo...}
-\label{tutorials/new_tutorial/output_file_names:changing-directories-using-formatter-in-a-zoo}\label{tutorials/new_tutorial/output_file_names:new-manual-output-file-names-formatter-zoo}\begin{quote}
-
-Here is a more fun example. We would like to feed the denizens of a zoo. Unfortunately, the file names for
-these are spread over several directories. Ideally, we would like their food supply to be grouped more
-sensibly. And, of course, we only want to feed the animals, not the plants.
-
-I have colour coded the input and output files for this task to show how we would like to rearrange them:
-\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{simple_tutorial_zoo_animals_formatter_example.jpg}}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   Make directories}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}
-            \PYG{c}{\PYGZsh{}   List of animals and plants}
-            \PYG{p}{[}    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.handreared.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.tame.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile/reptiles.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose/flowering.handreared.plants}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}   Put different animals in different directories depending on their clade}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}/\PYGZob{}tame[0]\PYGZcb{}.\PYGZob{}subdir[0][0]\PYGZcb{}.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subdir[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}tame[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Food for the \PYGZob{}tameness:11s\PYGZcb{} \PYGZob{}animal\PYGZus{}name:9s\PYGZcb{} = \PYGZob{}output\PYGZus{}file:90s\PYGZcb{} will be placed in \PYGZob{}new\PYGZus{}directory\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-We can see that the food for each animal are now grouped by clade in the same directory, which makes a lot more sense...
-
-Note how we used \code{subpath{[}0{]}{[}1{]}} to move down one level of the file path to build a new file name.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{Food for the wild        crocodile = ./reptiles/wild.crocodile.food will be placed in ./reptiles}
-\PYG{g+go}{Food for the tame        dog       = ./mammals/tame.dog.food        will be placed in ./mammals}
-\PYG{g+go}{Food for the wild        dog       = ./mammals/wild.dog.food        will be placed in ./mammals}
-\PYG{g+go}{Food for the handreared  lion      = ./mammals/handreared.lion.food will be placed in ./mammals}
-\PYG{g+go}{Food for the wild        lion      = ./mammals/wild.lion.food       will be placed in ./mammals}
-\PYG{g+go}{Food for the wild        tiger     = ./mammals/wild.tiger.food      will be placed in ./mammals}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{\emph{regex()} manipulates via regular expressions}
-\label{tutorials/new_tutorial/output_file_names:regex-manipulates-via-regular-expressions}\label{tutorials/new_tutorial/output_file_names:new-manual-regex}\begin{quote}
-
-If you are a hard core regular expressions fan, you may want to use {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} instead of {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}} or {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}}.
-
-\begin{notice}{note}{Note:}
-{\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} uses regular expressions like {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} but
-\begin{itemize}
-\item {} 
-It only matches the first file name in the input. As described above, {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} can match any one or more of the input filename strings.
-
-\item {} 
-It does not understand file paths so you may have to perform your own directory / file name parsing.
-
-\item {} 
-String replacement uses syntax borrowed from \href{http://docs.python.org/2/library/re.html\#re.sub}{re.sub()}, rather than building a result from parsed regular expression (and file path) components
-
-\end{itemize}
-
-In general {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} is more powerful and was introduced from version 2.4 is intended to be a more user friendly replacement for {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}}.
-\end{notice}
-
-Let us see how the previous zoo example looks with {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}}:
-\begin{quote}
-
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} code:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}   Put different animals in different directories depending on their clade}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}/\PYGZob{}tame[0]\PYGZcb{}.\PYGZob{}subdir[0][0]\PYGZcb{}.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subdir[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}tame[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Food for the \PYGZob{}tameness:11s\PYGZcb{} \PYGZob{}animal\PYGZus{}name:9s\PYGZcb{} = \PYGZob{}output\PYGZus{}file:90s\PYGZcb{} will be placed in \PYGZob{}new\PYGZus{}directory\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-
-{\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} code:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}   Put different animals in different directories depending on their clade}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                        \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*?/?)(}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+)/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}clade\PYGZgt{}/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}tame\PYGZgt{}.}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                            \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                             \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                                       \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                  \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Food for the \PYGZob{}tameness:11s\PYGZcb{} \PYGZob{}animal\PYGZus{}name:9s\PYGZcb{} = \PYGZob{}output\PYGZus{}file:90s\PYGZcb{} will be placed in \PYGZob{}new\PYGZus{}directory\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-The regular expression to parse the input file path safely was a bit hairy to write, and it is not
-clear that it handles all edge conditions (e.g. files in the root directory). Apart from that, if the
-limitations of {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} do not preclude its use, then the two approaches
-are not so different in practice.
-\end{quote}
-
-\index{mkdir!Tutorial}\index{Tutorial!mkdir}
-
-\section{\textbf{Chapter 9}: Preparing directories for output with \emph{@mkdir()}}
-\label{tutorials/new_tutorial/mkdir:index-0}\label{tutorials/new_tutorial/mkdir::doc}\label{tutorials/new_tutorial/mkdir:new-manual-mkdir-chapter-num-preparing-directories-for-output-with-mkdir}\label{tutorials/new_tutorial/mkdir:new-manual-mkdir}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/follows:decorators-follows]{\emph{@follows(mkdir()) syntax in detail}}}
-
-\item {} 
-{\hyperref[decorators/mkdir:decorators-mkdir]{\emph{@mkdir syntax in detail}}}
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/mkdir_code:new-manual-mkdir-code]{\emph{Chapter 9: Python Code for Preparing directories for output with @mkdir()}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/mkdir:overview}\begin{quote}
-
-In \textbf{Chapter 3}, we saw that we could use {\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-follows-mkdir]{\emph{@follows(mkdir())}}} to
-ensure that output directories exist:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   create\PYGZus{}new\PYGZus{}files() @follows mkdir}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{mkdir}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output/results/here}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output/results/here/a.start\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output/results/here/b.start\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}new\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-This ensures that the decorated task follows ({\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-follows-mkdir]{\emph{@follows}}}) the
-making of the specified directory (\code{mkdir()}).
-
-Sometimes, however, the \textbf{Output} is intended not for any single directory but a group
-of destinations depending on the parsed contents of \textbf{Input} paths.
-\end{quote}
-
-
-\subsection{Creating directories after string substitution in a zoo...}
-\label{tutorials/new_tutorial/mkdir:creating-directories-after-string-substitution-in-a-zoo}\begin{quote}
-
-You may remember {\hyperref[tutorials/new_tutorial/output_file_names:new-manual-output-file-names-formatter-zoo]{\emph{this example}}} from \textbf{Chapter 8}:
-
-We want to feed the denizens of a zoo. The original file names are spread over several directories and we
-group their food supply by the \emph{clade} of the animal in the following manner:
-\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{simple_tutorial_zoo_animals_formatter_example.jpg}}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}   Put different animals in different directories depending on their clade}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}/\PYGZob{}tame[0]\PYGZcb{}.\PYGZob{}subdir[0][0]\PYGZcb{}.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subdir[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}tame[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}40s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}90s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{} this blows up}
-    \PYG{c}{\PYGZsh{} open(output\PYGZus{}file, \PYGZdq{}w\PYGZdq{})}
-\end{Verbatim}
-\end{quote}
-
-The example code from \textbf{Chapter 8} is, however, incomplete. If we were to actually create the specified
-files we would realise that we had forgotten to create the destination directories \code{reptiles}, \code{mammals} first!
-\end{quote}
-
-
-\subsubsection{using \emph{formatter()}}
-\label{tutorials/new_tutorial/mkdir:using-formatter}\begin{quote}
-
-We could of course create directories manually.
-However, apart from being tedious and error prone, we have already gone to some lengths
-to parse out the diretories for {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}.
-Why don't we use the same logic to make the directories?
-
-Can you see the parallels between the syntax for {\hyperref[decorators/mkdir:decorators-mkdir]{\emph{@mkdir}}} and {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}?
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} create directories for each clade}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}    \PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{})                                \PYGZsh{} new\PYGZus{}directory}
-
-\PYG{c}{\PYGZsh{}   Put animals of each clade in the same directory}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}/\PYGZob{}tame[0]\PYGZcb{}.\PYGZob{}subdir[0][0]\PYGZcb{}.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subdir[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}tame[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}40s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}90s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{} this works now}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-See the {\hyperref[tutorials/new_tutorial/mkdir_code:new-manual-mkdir-code]{\emph{example code}}}
-\end{quote}
-
-
-\subsubsection{using \emph{regex()}}
-\label{tutorials/new_tutorial/mkdir:using-regex}\begin{quote}
-
-If you are particularly fond of using regular expression to parse file paths,
-you could also use {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} create directories for each clade}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}    \PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*?)/?(}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+)/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                             \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-
-\PYG{c}{\PYGZsh{}   Put animals of each clade in the same directory}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}/\PYGZob{}tame[0]\PYGZcb{}.\PYGZob{}subdir[0][0]\PYGZcb{}.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subdir[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}tame[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}40s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}90s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{} this works now}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{Up to date!Tutorial}\index{Tutorial!Up to date}\index{Task completion!Tutorial}\index{Tutorial!Task completion}\index{Exceptions!Tutorial}\index{Tutorial!Exceptions}\index{Interrupted Pipeline!Tutorial}\index{Tutorial!Interrupted Pipeline}
-
-\section{\textbf{Chapter 10}: Checkpointing: Interrupted Pipelines and Exceptions}
-\label{tutorials/new_tutorial/checkpointing:new-manual-checkpointing}\label{tutorials/new_tutorial/checkpointing:index-0}\label{tutorials/new_tutorial/checkpointing::doc}\label{tutorials/new_tutorial/checkpointing:new-manual-checkpointing-chapter-num-checkpointing-interrupted-pipelines-and-exceptions}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/checkpointing_code:new-manual-checkpointing-code]{\emph{Chapter 10: Python Code for Checkpointing: Interrupted Pipelines and Exceptions}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/checkpointing:overview}\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{theoretical_pipeline_schematic.png}}
-
-Computational pipelines transform your data in stages until the final result is produced.
-
-By default, \emph{Ruffus} uses file modification times for the \textbf{input} and \textbf{output} to determine
-whether each stage of a pipeline is up-to-date or not. But what happens when the task
-function is interrupted, whether from the command line or by error, half way through writing the output?
-
-In this case, the half-formed, truncated and corrupt \textbf{Output} file will look newer than its \textbf{Input} and hence up-to-date.
-\end{quote}
-
-\index{Tutorial!interrupting tasks}\index{interrupting tasks!Tutorial}
-
-\subsection{Interrupting tasks}
-\label{tutorials/new_tutorial/checkpointing:interrupting-tasks}\label{tutorials/new_tutorial/checkpointing:new-manual-interrupting-tasks}\label{tutorials/new_tutorial/checkpointing:index-1}\begin{quote}
-
-Let us try with an example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}\PYG{o}{,} \PYG{n+nn}{time}
-
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   long task to interrupt}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{long\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{ff}\PYG{p}{:}
-        \PYG{n}{ff}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Unfinished...}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-        \PYG{c}{\PYGZsh{} sleep for 2 seconds here so you can interrupt me}
-        \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Job started. Press \PYGZca{}C to interrupt me now...}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-        \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{)}
-        \PYG{n}{ff}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{Finished}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-        \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Job completed.}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{long\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-When this script runs, it pauses in the middle with this message:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-Job started. Press \textasciicircum{}C to interrupt me now...
-\end{Verbatim}
-
-If you interrupted the script by pressing Control-C at this point, you will see that \code{job1.output} contains only \code{Unfinished...}.
-However, if you should rerun the interrupted pipeline again, Ruffus ignores the corrupt, incomplete file:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{long\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\PYG{g+go}{Job started. Press \PYGZca{}C to interrupt me now...}
-\PYG{g+go}{Job completed}
-\end{Verbatim}
-\end{quote}
-
-And if you had run \code{pipeline\_printout}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{long\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{3}\PYG{p}{)}
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which will be run:}
-
-\PYG{g+go}{Task = long\PYGZus{}task}
-\PYG{g+go}{       Job  = [job1.start}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.output]}
-\PYG{g+go}{         \PYGZsh{} Job needs update: Previous incomplete run leftover: [job1.output]}
-\end{Verbatim}
-\end{quote}
-
-We can see that \emph{Ruffus} magically knows that the previous run was incomplete, and that \code{job1.output} is detritus that needs to be discarded.
-\end{quote}
-
-
-\subsection{Checkpointing: only log completed jobs}
-\label{tutorials/new_tutorial/checkpointing:checkpointing-only-log-completed-jobs}\label{tutorials/new_tutorial/checkpointing:new-manual-logging-completed-jobs}\begin{quote}
-
-All is revealed if you were to look in the working directory. \emph{Ruffus} has created a file called \code{.ruffus\_history.sqlite}.
-In this \href{https://sqlite.org/}{SQLite} database, \emph{Ruffus} logs only those files which are the result of a completed job,
-all other files are suspect.
-This file checkpoint database is a fail-safe, not a substitute for checking file modification times. If the \textbf{Input} or \textbf{Output} files are
-modified, the pipeline will rerun.
-
-By default, \emph{Ruffus} saves only file timestamps to the SQLite database but you can also add a checksum of the pipeline task function body or parameters.
-This behaviour can be controlled by setting the \code{checksum\_level} parameter
-in \code{pipeline\_run()}. For example, if you do not want to save any timestamps or checksums:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{checksum\PYGZus{}level} \PYG{o}{=} \PYG{l+m+mi}{0}\PYG{p}{)}
-
-\PYG{n}{CHECKSUM\PYGZus{}FILE\PYGZus{}TIMESTAMPS}      \PYG{o}{=} \PYG{l+m+mi}{0}     \PYG{c}{\PYGZsh{} only rerun when the file timestamps are out of date (classic mode)}
-\PYG{n}{CHECKSUM\PYGZus{}HISTORY\PYGZus{}TIMESTAMPS}   \PYG{o}{=} \PYG{l+m+mi}{1}     \PYG{c}{\PYGZsh{} Default: also rerun when the history shows a job as being out of date}
-\PYG{n}{CHECKSUM\PYGZus{}FUNCTIONS}            \PYG{o}{=} \PYG{l+m+mi}{2}     \PYG{c}{\PYGZsh{} also rerun when function body has changed}
-\PYG{n}{CHECKSUM\PYGZus{}FUNCTIONS\PYGZus{}AND\PYGZus{}PARAMS} \PYG{o}{=} \PYG{l+m+mi}{3}     \PYG{c}{\PYGZsh{} also rerun when function parameters or function body change}
-\end{Verbatim}
-\end{quote}
-
-\begin{notice}{note}{Note:}
-Checksums are calculated from the \href{http://docs.python.org/2/library/pickle.html}{pickled} string for the function code and parameters.
-If pickling fails, Ruffus will degrade gracefully to saving just the timestamp in the SQLite database.
-\end{notice}
-\end{quote}
-
-
-\subsection{Do not share the same checkpoint file across for multiple pipelines!}
-\label{tutorials/new_tutorial/checkpointing:new-manual-history-files-cannot-be-shared}\label{tutorials/new_tutorial/checkpointing:do-not-share-the-same-checkpoint-file-across-for-multiple-pipelines}\begin{quote}
-
-The name of the Ruffus python script is not saved in the checkpoint file along side timestamps and checksums.
-That means that you can rename your pipeline source code file without having to rerun the pipeline!
-The tradeoff is that if multiple pipelines are run from the same directory, and save their histories to the
-same SQlite database file, and if their file names overlap (all of these are bad ideas anyway!), this is
-bound to be a source of confusion.
-
-Luckily, the name and path of the checkpoint file can be also changed for each pipeline
-\end{quote}
-
-
-\subsection{Setting checkpoint file names}
-\label{tutorials/new_tutorial/checkpointing:new-manual-changing-history-file-name}\label{tutorials/new_tutorial/checkpointing:setting-checkpoint-file-names}\begin{quote}
-
-\begin{notice}{warning}{Warning:}
-Some file systems do not appear to support SQLite at all:
-
-There are reports that SQLite databases have \href{http://beets.radbox.org/blog/sqlite-nightmare.html}{file locking problems} on Lustre.
-
-The best solution would be to keep the SQLite database on an alternate compatible file system away from the working directory if possible.
-\end{notice}
-\end{quote}
-
-
-\subsubsection{environment variable \texttt{DEFAULT\_RUFFUS\_HISTORY\_FILE}}
-\label{tutorials/new_tutorial/checkpointing:environment-variable-default-ruffus-history-file}\begin{quote}
-
-The name of the checkpoint file is the value of the environment variable \code{DEFAULT\_RUFFUS\_HISTORY\_FILE}.
-\begin{quote}
-
-export DEFAULT\_RUFFUS\_HISTORY\_FILE=/some/where/.ruffus\_history.sqlite
-\end{quote}
-
-This gives considerable flexibility, and allows a system-wide policy to be set so that all Ruffus checkpoint files are set logically to particular paths.
-
-\begin{notice}{note}{Note:}
-It is your responsibility to make sure that the requisite destination directories for the checkpoint files exist beforehand!
-\end{notice}
-
-Where this is missing, the checkpoint file defaults to \code{.ruffus\_history.sqlite} in your working directory
-\end{quote}
-
-
-\subsubsection{Setting the checkpoint file name manually}
-\label{tutorials/new_tutorial/checkpointing:setting-the-checkpoint-file-name-manually}\begin{quote}
-
-This checkpoint file name can always be overridden as a parameter to Ruffus functions:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{history\PYGZus{}file} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{XXX}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{history\PYGZus{}file} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{XXX}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph}\PYG{p}{(}\PYG{n}{history\PYGZus{}file} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{XXX}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-There is also built in support in \code{Ruffus.cmdline}. So if you use this module, you can simply add to your command line:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} use a custom checkpoint file}
-myscript \PYGZhy{}\PYGZhy{}checksum\PYGZus{}file\PYGZus{}name .myscript.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-\end{quote}
-
-This takes precedence over everything else.
-\end{quote}
-
-
-\subsection{Useful checkpoint file name policies \texttt{DEFAULT\_RUFFUS\_HISTORY\_FILE}}
-\label{tutorials/new_tutorial/checkpointing:useful-checkpoint-file-name-policies-default-ruffus-history-file}\begin{quote}
-
-If the pipeline script is called \code{test/bin/scripts/run.me.py}, then these are the resulting checkpoint files locations:
-\end{quote}
-
-
-\subsubsection{Example 1: same directory, different name}
-\label{tutorials/new_tutorial/checkpointing:example-1-same-directory-different-name}\begin{quote}
-
-If the environment variable is:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{export }\PYG{n+nv}{DEFAULT\PYGZus{}RUFFUS\PYGZus{}HISTORY\PYGZus{}FILE}\PYG{o}{=}.\PYG{o}{\PYGZob{}}basename\PYG{o}{\PYGZcb{}}.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-
-Then the job checkpoint database for \code{run.me.py} will be \code{.run.me.ruffus\_history.sqlite}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-/test/bin/scripts/run.me.py
-/common/path/for/job\PYGZus{}history/scripts/.run.me.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Example 2: Different directory, same name}
-\label{tutorials/new_tutorial/checkpointing:example-2-different-directory-same-name}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{export }\PYG{n+nv}{DEFAULT\PYGZus{}RUFFUS\PYGZus{}HISTORY\PYGZus{}FILE}\PYG{o}{=}/common/path/for/job\PYGZus{}history/.\PYG{o}{\PYGZob{}}basename\PYG{o}{\PYGZcb{}}.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-/common/path/for/job\PYGZus{}history/.run.me.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Example 2: Different directory, same name but keep one level of subdirectory to disambiguate}
-\label{tutorials/new_tutorial/checkpointing:example-2-different-directory-same-name-but-keep-one-level-of-subdirectory-to-disambiguate}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{export }\PYG{n+nv}{DEFAULT\PYGZus{}RUFFUS\PYGZus{}HISTORY\PYGZus{}FILE}\PYG{o}{=}/common/path/for/job\PYGZus{}history/\PYG{o}{\PYGZob{}}subdir\PYG{o}{[}0\PYG{o}{]}\PYG{o}{\PYGZcb{}}/.\PYG{o}{\PYGZob{}}basename\PYG{o}{\PYGZcb{}}.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-/common/path/for/job\PYGZus{}history/scripts/.run.me.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Example 2: nested in common directory}
-\label{tutorials/new_tutorial/checkpointing:example-2-nested-in-common-directory}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{export }\PYG{n+nv}{DEFAULT\PYGZus{}RUFFUS\PYGZus{}HISTORY\PYGZus{}FILE}\PYG{o}{=}/common/path/for/job\PYGZus{}history/\PYG{o}{\PYGZob{}}path\PYG{o}{\PYGZcb{}}/.\PYG{o}{\PYGZob{}}basename\PYG{o}{\PYGZcb{}}.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-/common/path/for/job\PYGZus{}history/test/bin/scripts/.run.me.ruffus\PYGZus{}history.sqlite
-\end{Verbatim}
-\end{quote}
-
-\index{Tutorial!Regenerating the checkpoint file}\index{Regenerating the checkpoint file!Tutorial}
-
-\subsection{Regenerating the checkpoint file}
-\label{tutorials/new_tutorial/checkpointing:new-manual-regenerating-history-file}\label{tutorials/new_tutorial/checkpointing:regenerating-the-checkpoint-file}\label{tutorials/new_tutorial/checkpointing:index-2}\begin{quote}
-
-Occasionally you may need to re-generate the checkpoint file.
-
-This could be necessary:
-\begin{itemize}
-\item {} 
-because you are upgrading from a previous version of Ruffus without checkpoint file support
-
-\item {} 
-on the rare occasions when the SQLite file becomes corrupted and has to deleted
-
-\item {} 
-if you wish to circumvent the file checking of Ruffus after making some manual changes!
-
-\end{itemize}
-
-To do this, it is only necessary to call \code{pipeline\_run} appropriately:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{CHECKSUM\PYGZus{}REGENERATE} \PYG{o}{=} \PYG{l+m+mi}{2}
-\PYG{n}{pipeline}\PYG{p}{(}\PYG{n}{touch\PYGZus{}files\PYGZus{}only} \PYG{o}{=} \PYG{n}{CHECKSUM\PYGZus{}REGENERATE}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Similarly, if you are using \code{Ruffus.cmdline}, you can call:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-myscript \PYGZhy{}\PYGZhy{}recreate\PYGZus{}database
-\end{Verbatim}
-\end{quote}
-
-Note that this regenerates the checkpoint file to reflect the existing \emph{Input}, \emph{Output} files on disk.
-In other words, the onus is on you to make sure there are no half-formed, corrupt files. On the other hand,
-the pipeline does not need to have been previously run successfully for this to work. Essentially, Ruffus,
-pretends to run the pipeline, while logging all the files with consistent file modication times, stopping
-at the first tasks which appear out of date or incomplete.
-\end{quote}
-
-\index{rules!for rerunning jobs}\index{for rerunning jobs!rules}
-
-\subsection{Rules for determining if files are up to date}
-\label{tutorials/new_tutorial/checkpointing:new-manual-skip-up-to-date-rules}\label{tutorials/new_tutorial/checkpointing:rules-for-determining-if-files-are-up-to-date}\label{tutorials/new_tutorial/checkpointing:index-3}\begin{quote}
-
-The following simple rules are used by \emph{Ruffus}.
-\begin{enumerate}
-\item {} 
-The pipeline stage will be rerun if:
-\begin{itemize}
-\item {} 
-If any of the \textbf{Input} files are new (newer than the \textbf{Output} files)
-
-\item {} 
-If any of the \textbf{Output} files are missing
-
-\end{itemize}
-
-\item {} 
-In addition, it is possible to run jobs which create files from scratch.
-\begin{itemize}
-\item {} 
-If no \textbf{Input} file names are supplied, the job will only run if any \emph{output} file is missing.
-
-\end{itemize}
-
-\item {} 
-Finally, if no \textbf{Output} file names are supplied, the job will always run.
-
-\end{enumerate}
-\end{quote}
-
-\index{Exception!Missing input files}\index{Missing input files!Exception}
-
-\subsection{Missing files generate exceptions}
-\label{tutorials/new_tutorial/checkpointing:index-4}\label{tutorials/new_tutorial/checkpointing:missing-files-generate-exceptions}\begin{quote}
-
-If the \emph{inputs} files for a job are missing, the task function will have no way
-to produce its \emph{output}. In this case, a \code{MissingInputFileError} exception will be raised
-automatically. For example,
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-task.MissingInputFileError: No way to run job: Input file ['a.1'] does not exist
-for Job = ["a.1" -\textgreater{} "a.2", "A file"]
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{Manual!Timestamp resolution}\index{Timestamp resolution!Manual}
-
-\subsection{Caveats: Coarse Timestamp resolution}
-\label{tutorials/new_tutorial/checkpointing:index-5}\label{tutorials/new_tutorial/checkpointing:caveats-coarse-timestamp-resolution}\begin{quote}
-
-Note that modification times have precision to the nearest second under some older file systems
-(ext2/ext3?). This may be also be true for networked file systems.
-
-\emph{Ruffus} supplements the file system time resolution by independently recording the timestamp at
-full OS resolution (usually to at least the millisecond) at job completion, when presumably the \textbf{Output}
-files will have been created.
-
-However, \emph{Ruffus} only does this if the discrepancy between file time and system time is less than a second
-(due to poor file system timestamp resolution). If there are large mismatches between the two, due for example
-to network time slippage, misconfiguration etc, \emph{Ruffus} reverts to using the file system time and adds a one second
-delay between jobs (via \code{time.sleep()}) to make sure input and output file stamps are different.
-
-If you know that your filesystem has coarse-grained timestamp resolution, you can always revert to this very conservative behaviour,
-at the prices of some annoying 1s pauses, by setting {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(one\_second\_per\_job = True)}}}
-\end{quote}
-
-\index{Manual!flag files}\index{flag files!Manual}
-
-\subsection{Flag files: Checkpointing for the paranoid}
-\label{tutorials/new_tutorial/checkpointing:index-6}\label{tutorials/new_tutorial/checkpointing:flag-files-checkpointing-for-the-paranoid}\begin{quote}
-
-One other way of checkpointing your pipelines is to create an extra ``flag'' file as an additional
-\textbf{Output} file name. The flag file is only created or updated when everything else in the
-job has completed successifully and written to disk. A missing or out of date flag file then
-would be a sign for Ruffus that the task never completed properly in the first place.
-
-This used to be much the best way of performing checkpointing in Ruffus and is still
-the most bulletproof way of proceeding. For example, even the loss or corruption
-of the checkpoint file, would not affect things greatly.
-
-Nevertheless flag files are largely superfluous in modern \emph{Ruffus}.
-\end{quote}
-
-\index{decorators\_compendium!Tutorial}\index{Tutorial!decorators\_compendium}
-
-\section{\textbf{Chapter 11}: Pipeline topologies and a compendium of \emph{Ruffus} decorators}
-\label{tutorials/new_tutorial/decorators_compendium:index-0}\label{tutorials/new_tutorial/decorators_compendium:new-manual-decorators-compendium}\label{tutorials/new_tutorial/decorators_compendium:new-manual-decorators-compendium-chapter-num-pipeline-topologies-and-a-compendium-of-ruffus-decorators}\label{tutorials/new_tutorial/decorators_compendium::doc}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{decorators}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/decorators_compendium:overview}\begin{quote}
-
-Computational pipelines transform your data in stages until the final result is produced.
-
-You can visualise your pipeline data flowing like water down a system of pipes.
-\emph{Ruffus} has many ways of joining up your pipes to create different topologies.
-
-\begin{notice}{note}{Note:}
-\textbf{The best way to design a pipeline is to:}
-\begin{itemize}
-\item {} 
-\textbf{Write down the file names of the data as it flows across your pipeline.}
-
-\item {} 
-\textbf{Draw lines between the file names to show how they should be connected together.}
-
-\end{itemize}
-\end{notice}
-\end{quote}
-
-
-\subsection{\emph{@transform}}
-\label{tutorials/new_tutorial/decorators_compendium:transform}\begin{quote}
-
-So far, our data files have been flowing through our pipelines independently in lockstep.
-
-\scalebox{0.500000}{\includegraphics{bestiary_transform.png}}
-
-If we drew a graph of the data files moving through the pipeline, all of our flowcharts would look like something like this.
-
-The {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} decorator connects up your data files in 1 to 1 operations, ensuring that for every \textbf{Input}, a corresponding \textbf{Output} is
-generated, ready to got into the next pipeline stage. If we start with three sets of starting data, we would end up with three final sets of results.
-\end{quote}
-
-
-\subsection{A bestiary of \emph{Ruffus} decorators}
-\label{tutorials/new_tutorial/decorators_compendium:a-bestiary-of-ruffus-decorators}\begin{quote}
-
-Very often, we would like to transform our data in more complex ways, this is where other \emph{Ruffus} decorators come in.
-
-\scalebox{0.500000}{\includegraphics{bestiary_decorators.png}}
-\end{quote}
-
-
-\subsection{\emph{@originate}}
-\label{tutorials/new_tutorial/decorators_compendium:originate}\begin{itemize}
-\item {} 
-Introduced in \textbf{Chapter 3} {\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-transform-in-parallel]{\emph{More on @transform-ing data and @originate}}},
-{\hyperref[decorators/originate:decorators-originate]{\emph{@originate}}} generates \textbf{Output} files from scratch without the benefits of any \textbf{Input} files.
-
-\end{itemize}
-
-
-\subsection{\emph{@merge}}
-\label{tutorials/new_tutorial/decorators_compendium:merge}\begin{itemize}
-\item {} 
-A \textbf{many to one} operator.
-
-\item {} 
-The last decorator at the far right to the figure, {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} merges multiple \textbf{Input} into one \textbf{Output}.
-
-\end{itemize}
-
-
-\subsection{\emph{@split}}
-\label{tutorials/new_tutorial/decorators_compendium:split}\begin{itemize}
-\item {} 
-A  \textbf{one to many} operator,
-
-\item {} 
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}} is the evil twin of {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}}. It takes a single set of \textbf{Input} and splits them into multiple smaller pieces.
-
-\item {} 
-The best part of {\hyperref[decorators/split:decorators-split]{\emph{@split}}} is that we don't necessarily have to decide ahead of time \emph{how many} smaller pieces it should produce. If we have encounter a larger file,
-we might need to split it up into more fragments for greater parallelism.
-
-\item {} 
-Since {\hyperref[decorators/split:decorators-split]{\emph{@split}}} is a  \textbf{one to many} operator, if you pass it \textbf{many} inputs (e.g. via {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}, it performs an implicit {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} step to make one
-set of \textbf{Input} that you can redistribute into a different number of pieces. If you are looking to split \emph{each} \textbf{Input} into further smaller fragments, then you
-need {\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}
-
-\end{itemize}
-
-
-\subsection{\emph{@subdivide}}
-\label{tutorials/new_tutorial/decorators_compendium:subdivide}\begin{itemize}
-\item {} 
-A \textbf{many to even more} operator.
-
-\item {} 
-It takes each of multiple \textbf{Input}, and further subdivides them.
-
-\item {} 
-Uses {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}}, {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} or {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} to generate \textbf{Output} names from its \textbf{Input} files but like {\hyperref[decorators/split:decorators-split]{\emph{@split}}}, we don't have to decide ahead of time
-\emph{how many} smaller pieces each \textbf{Input} should be further divided into. For example, a large \textbf{Input} files might be subdivided into 7 pieces while the next job might,
-however, split its \textbf{Input} into just 4 pieces.
-
-\end{itemize}
-
-
-\subsection{\emph{@collate}}
-\label{tutorials/new_tutorial/decorators_compendium:collate}\begin{itemize}
-\item {} 
-A \textbf{many to fewer} operator.
-
-\item {} 
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} is the opposite twin of \code{subdivide}: it takes multiple \textbf{Output} and groups or collates them into bundles of \textbf{Output}.
-
-\item {} 
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} uses {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} or {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} to generate \textbf{Output} names.
-
-\item {} 
-All \textbf{Input} files which map to the same \textbf{Output} are grouped together into one job (one task function call) which
-produces one \textbf{Output}.
-
-\end{itemize}
-
-
-\subsection{Combinatorics}
-\label{tutorials/new_tutorial/decorators_compendium:combinatorics}\begin{quote}
-
-More rarely, we need to generate a set of \textbf{Output} based on a combination or permutation or product of the \textbf{Input}.
-
-For example, in bioinformatics, we might need to look for all instances of a set of genes in the genomes of a different number of species.
-In other words, we need to find the {\hyperref[decorators/product:decorators-product]{\emph{@product}}} of XXX genes x YYY species.
-
-\emph{Ruffus} provides decorators modelled on the ``Combinatoric generators'' in the Standard Python \href{http://docs.python.org/2/library/itertools.html}{itertools} library.
-
-To use combinatoric decorators, you need to explicitly include them from \emph{Ruffus}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{ruffus}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-\end{Verbatim}
-
-\scalebox{0.500000}{\includegraphics{bestiary_combinatorics.png}}
-\end{quote}
-
-
-\subsection{\emph{@product}}
-\label{tutorials/new_tutorial/decorators_compendium:product}\begin{itemize}
-\item {} 
-Given several sets of \textbf{Input}, it generates all versus all \textbf{Output}. For example, if there are four sets of \textbf{Input} files, {\hyperref[decorators/product:decorators-product]{\emph{@product}}} will generate \code{WWW x XXX x YYY x ZZZ} \textbf{Output}.
-
-\item {} 
-Uses {\hyperref[decorators/transform:decorators-transform]{\emph{formatter}}} to generate unique \textbf{Output} names from components parsed from \emph{any} parts of \emph{any} specified files in
-all \textbf{Input} sets. In the above example, this allows the generation of  \code{WWW x XXX x YYY x ZZZ} unique names.
-
-\end{itemize}
-
-
-\subsection{\emph{@combinations}}
-\label{tutorials/new_tutorial/decorators_compendium:combinations}\begin{itemize}
-\item {} 
-Given one set of \textbf{Input}, it generates the combinations of r-length tuples among them.
-
-\item {} 
-Uses {\hyperref[decorators/transform:decorators-transform]{\emph{formatter}}} to generate unique \textbf{Output} names from components parsed from \emph{any} parts of \emph{any} specified files in all \textbf{Input} sets.
-
-\item {} 
-For example, given \textbf{Input} called \code{A}, \code{B} and \code{C}, it will generate: \code{A-B},  \code{A-C},  \code{B-C}
-
-\item {} 
-The order of \textbf{Input} items is ignored so either \code{A-B} or \code{B-A} will be included, not both
-
-\item {} 
-Self-vs-self combinations (\code{A-A}) are excluded.
-
-\end{itemize}
-
-
-\subsection{\emph{@combinations\_with\_replacement}}
-\label{tutorials/new_tutorial/decorators_compendium:combinations-with-replacement}\begin{itemize}
-\item {} 
-Given one set of \textbf{Input}, it generates the combinations of r-length tuples among them but includes self-vs-self conbinations.
-
-\item {} 
-Uses {\hyperref[decorators/transform:decorators-transform]{\emph{formatter}}} to generate unique \textbf{Output} names from components parsed from \emph{any} parts of \emph{any} specified files in all \textbf{Input} sets.
-
-\item {} 
-For example, given \textbf{Input} called \code{A}, \code{B} and \code{C}, it will generate: \code{A-A}, \code{A-B},  \code{A-C}, \code{B-B}, \code{B-C},  \code{C-C}
-
-\end{itemize}
-
-
-\subsection{\emph{@permutations}}
-\label{tutorials/new_tutorial/decorators_compendium:permutations}\begin{itemize}
-\item {} 
-Given one set of \textbf{Input}, it generates the permutations of r-length tuples among them. This excludes self-vs-self combinations but includes all orderings (\code{A-B} and \code{B-A}).
-
-\item {} 
-Uses {\hyperref[decorators/transform:decorators-transform]{\emph{formatter}}} to generate unique \textbf{Output} names from components parsed from \emph{any} parts of \emph{any} specified files in all \textbf{Input} sets.
-
-\item {} 
-For example, given \textbf{Input} called \code{A}, \code{B} and \code{C}, it will generate: \code{A-A}, \code{A-B},  \code{A-C}, \code{B-A}, \code{B-C}, \code{C-A},  \code{C-B}
-
-\end{itemize}
-
-\index{split!Tutorial}\index{Tutorial!split}
-
-\section{\textbf{Chapter 12}: Splitting up large tasks / files with \textbf{@split}}
-\label{tutorials/new_tutorial/split:index-0}\label{tutorials/new_tutorial/split:new-manual-split}\label{tutorials/new_tutorial/split::doc}\label{tutorials/new_tutorial/split:new-manual-split-chapter-num-splitting-up-large-tasks-files-with-split}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}} syntax
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/split_code:new-manual-split-code]{\emph{Example code for this chapter}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/split:overview}\begin{quote}
-
-A common requirement in computational pipelines is to split up a large task into
-small jobs which can be run on different processors, (or sent to a computational
-cluster). Very often, the number of jobs depends dynamically on the size of the
-task, and cannot be known beforehand.
-
-\emph{Ruffus} uses the {\hyperref[decorators/split:decorators-split]{\emph{@split}}} decorator to indicate that
-the {\hyperref[glossary:term-task]{\emph{task}}} function will produce an indeterminate number of independent \emph{Outputs} from a single \emph{Input}.
-\end{quote}
-
-
-\subsection{Example: Calculate variance for a large list of numbers in parallel}
-\label{tutorials/new_tutorial/split:example-calculate-variance-for-a-large-list-of-numbers-in-parallel}\begin{quote}
-
-Suppose we wanted to calculate the \href{http://en.wikipedia.org/wiki/Variance}{variance} for
-100,000 numbers, how can we parallelise the calculation so that we can get an answer as
-speedily as possible?
-
-We need to
-\begin{itemize}
-\item {} 
-break down the problem into manageable chunks
-
-\item {} 
-solve these in parallel, possibly on a computational cluster and then
-
-\item {} 
-merge the partial solutions back together for a final result.
-
-\end{itemize}
-
-To complicate things, we usually do not want to hard-code the number of parallel chunks beforehand.
-The degree of parallelism is often only apparent as we process our data.
-
-\textbf{Ruffus} was designed to solve such problems which are common, for example, in bioinformatics and genomics.
-
-A flowchart for our variance problem might look like this:
-
-\scalebox{0.300000}{\includegraphics{manual_split_merge_example.jpg}}
-
-(In this toy example, we create our own starting data in \code{create\_random\_numbers()}.)
-\end{quote}
-
-
-\subsection{Output files for \emph{@split}}
-\label{tutorials/new_tutorial/split:output-files-for-split}\begin{quote}
-
-The \emph{Ruffus} decorator {\hyperref[decorators/split:decorators-split]{\emph{@split}}} is designed specifically with this run-time flexibility in mind:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n}{create\PYGZus{}random\PYGZus{}numbers}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}problem} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-This will split the incoming \code{input\_file\_names} into \code{NNN} number of \emph{outputs} where \code{NNN} is not predetermined:
-
-The \emph{output} (second) parameter of {\hyperref[decorators/split:decorators-split]{\emph{@split}}} often contains a \href{http://docs.python.org/library/glob.html}{\emph{glob}} pattern like the \code{*.chunks} above.
-
-Only \textbf{after} the task function has completed, will Ruffus match the \textbf{Output} parameter (\code{*.chunks})
-against the files which have been created by \code{split\_problem()} (e.g. \code{1.chunks}, \code{2.chunks}, \code{3.chunks})
-\end{quote}
-
-
-\subsection{Be careful in specifying  \textbf{Output} globs}
-\label{tutorials/new_tutorial/split:be-careful-in-specifying-output-globs}\begin{quote}
-
-Note that it is your responsibility to keep the \textbf{Output} specification tight enough so that Ruffus does not
-pick up extraneous files.
-
-You can specify multiple \href{http://docs.python.org/library/glob.html}{\emph{glob}} patterns to match \emph{all} the files which are the
-result of the splitting task function. These can even cover different directories,
-or groups of file names. This is a more extreme example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a*.bits}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b*.pieces}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{somewhere\PYGZus{}else/c*.stuff}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}function} \PYG{p}{(}\PYG{n}{input\PYGZus{}filename}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Code to split up }\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{input.file}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Clean up previous pipeline runs}
-\label{tutorials/new_tutorial/split:clean-up-previous-pipeline-runs}\begin{quote}
-
-Problem arise when the current directory contains results of previous pipeline runs.
-\begin{itemize}
-\item {} 
-For example, if the previous analysis involved a large data set, there might be 3 chunks: \code{1.chunks}, \code{2.chunks}, \code{3.chunks}.
-
-\item {} 
-In the current analysis, there might be a smaller data set which divides into only 2 chunks, \code{1.chunks} and \code{2.chunks}.
-
-\item {} 
-Unfortunately, \code{3.chunks} from the previous run is still hanging around and will be included erroneously by the glob \code{*.chunks}.
-
-\end{itemize}
-
-\begin{notice}{warning}{Warning:}
-\textbf{Your first duty in} {\hyperref[decorators/split:decorators-split]{\emph{@split}}} \textbf{tasks functions should be to clean up}
-\end{notice}
-
-To help you clean up thoroughly, Ruffus initialises the \textbf{output} parameter to all files which match specification.
-
-The first order of business is thus invariably to cleanup ( delete with \code{os.unlink}) all files in \textbf{Output}.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   split initial file}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n}{create\PYGZus{}random\PYGZus{}numbers}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}problem} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{        splits random numbers file into xxx files of chunk\PYGZus{}size each}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   clean up any files from previous runs}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}for ff in glob.glob(\PYGZdq{}*.chunks\PYGZdq{}):}
-    \PYG{k}{for} \PYG{n}{ff} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{ff}\PYG{p}{)}
-\end{Verbatim}
-
-(The first time you run the example code, \code{*.chunks} will initialise \code{output\_files} to an empty list. )
-\end{quote}
-
-
-\subsection{1 to many}
-\label{tutorials/new_tutorial/split:to-many}\label{tutorials/new_tutorial/split:new-manual-split-one-to-many}\begin{quote}
-
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}} is a one to many operator because its
-outputs are a list of \emph{independent} items.
-
-If {\hyperref[decorators/split:decorators-split]{\emph{@split}}} generates 5 files, then this will lead to 5 jobs downstream.
-
-This means we can just connect our old friend {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} to our pipeline
-and the results of {\hyperref[decorators/split:decorators-split]{\emph{@split}}} will be analysed in parallel. This code should look
-familiar:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Calculate sum and sum of squares for each chunk file}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{split\PYGZus{}problem}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{sum\PYGZus{}of\PYGZus{}squares} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-\end{quote}
-
-Which results in output like this:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[random\PYGZus{}numbers.list] \PYGZhy{}\PYGZgt{} *.chunks] completed}
-\PYG{g+go}{Completed Task = split\PYGZus{}problem}
-\PYG{g+go}{    Job  = [1.chunks \PYGZhy{}\PYGZgt{} 1.sums] completed}
-\PYG{g+go}{    Job  = [10.chunks \PYGZhy{}\PYGZgt{} 10.sums] completed}
-\PYG{g+go}{    Job  = [2.chunks \PYGZhy{}\PYGZgt{} 2.sums] completed}
-\PYG{g+go}{    Job  = [3.chunks \PYGZhy{}\PYGZgt{} 3.sums] completed}
-\PYG{g+go}{    Job  = [4.chunks \PYGZhy{}\PYGZgt{} 4.sums] completed}
-\PYG{g+go}{    Job  = [5.chunks \PYGZhy{}\PYGZgt{} 5.sums] completed}
-\PYG{g+go}{    Job  = [6.chunks \PYGZhy{}\PYGZgt{} 6.sums] completed}
-\PYG{g+go}{    Job  = [7.chunks \PYGZhy{}\PYGZgt{} 7.sums] completed}
-\PYG{g+go}{    Job  = [8.chunks \PYGZhy{}\PYGZgt{} 8.sums] completed}
-\PYG{g+go}{    Job  = [9.chunks \PYGZhy{}\PYGZgt{} 9.sums] completed}
-\PYG{g+go}{Completed Task = sum\PYGZus{}of\PYGZus{}squares}
-\end{Verbatim}
-\end{quote}
-
-Have a look at the {\hyperref[tutorials/new_tutorial/split_code:new-manual-split-code]{\emph{Example code for this chapter}}}
-\end{quote}
-
-
-\subsection{Nothing to many}
-\label{tutorials/new_tutorial/split:new-manual-split-nothing-to-many}\label{tutorials/new_tutorial/split:nothing-to-many}\begin{quote}
-
-Normally we would use {\hyperref[tutorials/new_tutorial/originate:new-manual-originate]{\emph{@originate}}} to create files from
-scratch, for example at the beginning of the pipeline.
-
-However, sometimes, it is not possible to determine ahead of time how many files you
-will be creating from scratch. {\hyperref[decorators/split:decorators-split]{\emph{@split}}} can also be useful even in such cases:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{random} \PYG{k+kn}{import} \PYG{n}{randint}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{os}
-
-\PYG{c}{\PYGZsh{} Create between 2 and 5 files}
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{no\PYGZus{}input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} cleanup first}
-    \PYG{k}{for} \PYG{n}{oo} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{oo}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{} make new files}
-    \PYG{k}{for} \PYG{n}{ii} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{randint}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{,}\PYG{l+m+mi}{5}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{ii}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.processed}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{process\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-Giving:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} *.start] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}initial\PYGZus{}files}
-\PYG{g+go}{    Job  = [0.start \PYGZhy{}\PYGZgt{} 0.processed] completed}
-\PYG{g+go}{    Job  = [1.start \PYGZhy{}\PYGZgt{} 1.processed] completed}
-\PYG{g+go}{Completed Task = process\PYGZus{}files}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{merge!Tutorial}\index{Tutorial!merge}
-
-\section{\textbf{Chapter 13}: \texttt{@merge} multiple input into a single result}
-\label{tutorials/new_tutorial/merge:index-0}\label{tutorials/new_tutorial/merge:new-manual-merge}\label{tutorials/new_tutorial/merge::doc}\label{tutorials/new_tutorial/merge:new-manual-merge-chapter-num-merge-multiple-input-into-a-single-result}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} syntax
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/merge_code:new-manual-merge-code]{\emph{Example code for this chapter}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Overview of \emph{@merge}}
-\label{tutorials/new_tutorial/merge:overview-of-merge}\begin{quote}
-
-The {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{previous chapter}}} explained how \textbf{Ruffus} allows large
-jobs to be split into small pieces with {\hyperref[decorators/split:decorators-split]{\emph{@split}}} and analysed
-in parallel using for example, our old friend {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}.
-
-Having done this, our next task is to recombine the fragments into a seamless whole.
-
-This is the role of the {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} decorator.
-\end{quote}
-
-
-\subsection{\emph{@merge}  is a many to one operator}
-\label{tutorials/new_tutorial/merge:merge-is-a-many-to-one-operator}\begin{quote}
-
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} tasks multiple \emph{inputs} and produces a single \emph{output}, \textbf{Ruffus}
-is again agnostic as to the sort of data contained within this single \emph{output}. It can be a single
-(string) file name, an arbitrary complicated nested structure with numbers, objects etc.
-Or even a list.
-
-The main thing is that downstream tasks will interpret this output as a single entity leading to a single
-job.
-
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}} and {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} are, in other words, about network topology.
-
-Because of this {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} is also very useful for summarising the progress
-in our pipeline. At key selected points, we can gather data from the multitude of data or disparate \emph{inputs}
-and {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} them to a single set of summaries.
-\end{quote}
-
-
-\subsection{Example: Combining partial solutions: Calculating variances}
-\label{tutorials/new_tutorial/merge:example-combining-partial-solutions-calculating-variances}\begin{quote}
-
-The {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{previous chapter}}} we had almost completed all the pieces of our flowchart:
-
-\scalebox{0.300000}{\includegraphics{manual_split_merge_example.jpg}}
-
-What remains is to take the partial solutions from the different \code{.sums} files
-and turn these into the variance as follows:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{variance} \PYG{o}{=} \PYG{p}{(}\PYG{n}{sum\PYGZus{}squared} \PYG{o}{\PYGZhy{}} \PYG{n+nb}{sum} \PYG{o}{*} \PYG{n+nb}{sum} \PYG{o}{/} \PYG{n}{N}\PYG{p}{)}\PYG{o}{/}\PYG{n}{N}
-\end{Verbatim}
-
-where \code{N} is the number of values
-
-See the \href{http://en.wikipedia.org/wiki/Algorithms\_for\_calculating\_variance}{wikipedia} entry for a discussion of
-why this is a very naive approach.
-\end{quote}
-
-To do this, all we have to do is iterate through all the values in \code{*.sums},
-add up the \code{sums} and \code{sum\_squared}, and apply the above (naive) formula.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   @merge files together}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@merge}\PYG{p}{(}\PYG{n}{sum\PYGZus{}of\PYGZus{}squares}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{variance.result}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{calculate\PYGZus{}variance} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Calculate variance naively}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   initialise variables}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{all\PYGZus{}sum\PYGZus{}squared} \PYG{o}{=} \PYG{l+m+mf}{0.0}
-    \PYG{n}{all\PYGZus{}sum}         \PYG{o}{=} \PYG{l+m+mf}{0.0}
-    \PYG{n}{all\PYGZus{}cnt\PYGZus{}values}  \PYG{o}{=} \PYG{l+m+mf}{0.0}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{} added up all the sum\PYGZus{}squared, and sum and cnt\PYGZus{}values from all the chunks}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{input\PYGZus{}file\PYGZus{}name} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-        \PYG{n}{sum\PYGZus{}squared}\PYG{p}{,} \PYG{n+nb}{sum}\PYG{p}{,} \PYG{n}{cnt\PYGZus{}values} \PYG{o}{=} \PYG{n+nb}{map}\PYG{p}{(}\PYG{n+nb}{float}\PYG{p}{,} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{o}{.}\PYG{n}{readlines}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-        \PYG{n}{all\PYGZus{}sum\PYGZus{}squared} \PYG{o}{+}\PYG{o}{=} \PYG{n}{sum\PYGZus{}squared}
-        \PYG{n}{all\PYGZus{}sum}         \PYG{o}{+}\PYG{o}{=} \PYG{n+nb}{sum}
-        \PYG{n}{all\PYGZus{}cnt\PYGZus{}values}  \PYG{o}{+}\PYG{o}{=} \PYG{n}{cnt\PYGZus{}values}
-    \PYG{n}{all\PYGZus{}mean} \PYG{o}{=} \PYG{n}{all\PYGZus{}sum} \PYG{o}{/} \PYG{n}{all\PYGZus{}cnt\PYGZus{}values}
-    \PYG{n}{variance} \PYG{o}{=} \PYG{p}{(}\PYG{n}{all\PYGZus{}sum\PYGZus{}squared} \PYG{o}{\PYGZhy{}} \PYG{n}{all\PYGZus{}sum} \PYG{o}{*} \PYG{n}{all\PYGZus{}mean}\PYG{p}{)}\PYG{o}{/}\PYG{p}{(}\PYG{n}{all\PYGZus{}cnt\PYGZus{}values}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   print output}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{variance}\PYG{p}{)}
-\end{Verbatim}
-
-This results in the following equivalent function call:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{calculate\PYGZus{}variance} \PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{3.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                     \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{4.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{5.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{6.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                     \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{7.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{8.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{9.sums, }\PYG{l+s}{\PYGZdq{}}\PYG{l+m+mf}{10.}\PYG{n}{sums}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{], }\PYG{l+s}{\PYGZdq{}}\PYG{n}{variance}\PYG{o}{.}\PYG{n}{result}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{)}
-\end{Verbatim}
-\end{quote}
-
-and the following display:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[1.sums, 10.sums, 2.sums, 3.sums, 4.sums, 5.sums, 6.sums, 7.sums, 8.sums, 9.sums] \PYGZhy{}\PYGZgt{} variance.result] completed}
-\PYG{g+go}{Completed Task = calculate\PYGZus{}variance}
-\end{Verbatim}
-\end{quote}
-
-The final result is in \code{variance.result}
-
-Have a look at the {\hyperref[tutorials/new_tutorial/merge_code:new-manual-merge-code]{\emph{complete example code for this chapter}}}.
-\end{quote}
-
-\index{multiprocessing!Tutorial}\index{Tutorial!multiprocessing}
-
-\section{\textbf{Chapter 14}: Multiprocessing, \texttt{drmaa} and Computation Clusters}
-\label{tutorials/new_tutorial/multiprocessing:index-0}\label{tutorials/new_tutorial/multiprocessing::doc}\label{tutorials/new_tutorial/multiprocessing:new-manual-multiprocessing}\label{tutorials/new_tutorial/multiprocessing:new-manual-multiprocessing-chapter-num-multiprocessing-drmaa-and-computation-clusters}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/jobs_limit:decorators-jobs-limit]{\emph{@jobs\_limit}}} syntax
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run()}}} syntax
-
-\item {} 
-{\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job]{\emph{drmaa\_wrapper.run\_job()}}} syntax
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/multiprocessing_code:new-manual-multiprocessing-code]{\emph{Chapter 14: Python Code for Multiprocessing, drmaa and Computation Clusters}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/multiprocessing:overview}
-\index{pipeline\_run(multiprocess)!Tutorial}\index{Tutorial!pipeline\_run(multiprocess)}
-
-\subsubsection{Multi Processing}
-\label{tutorials/new_tutorial/multiprocessing:multi-processing}\label{tutorials/new_tutorial/multiprocessing:index-1}\begin{quote}
-
-\emph{Ruffus} uses python \href{http://docs.python.org/library/multiprocessing.html}{multiprocessing} to run
-each job in a separate process.
-
-This means that jobs do \emph{not} necessarily complete in the order of the defined parameters.
-Task hierachies are, of course, inviolate: upstream tasks run before downstream, dependent tasks.
-
-Tasks that are independent (i.e. do not precede each other) may be run in parallel as well.
-
-The number of concurrent jobs can be set in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{parallel\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-If \code{multiprocess} is set to 1, then jobs will be run on a single process.
-\end{quote}
-
-\index{data sharing across processes!Tutorial}\index{Tutorial!data sharing across processes}
-
-\subsubsection{Data sharing}
-\label{tutorials/new_tutorial/multiprocessing:index-2}\label{tutorials/new_tutorial/multiprocessing:data-sharing}\begin{quote}
-
-Running jobs in separate processes allows \emph{Ruffus} to make full use of the multiple
-processors in modern computers. However, some \href{http://docs.python.org/library/multiprocessing.html\#multiprocessing-programming}{multiprocessing guidelines}
-should be borne in mind when writing \emph{Ruffus} pipelines. In particular:
-\begin{itemize}
-\item {} 
-Try not to pass large amounts of data between jobs, or at least be aware that this has to be marshalled
-across process boundaries.
-
-\item {} 
-Only data which can be \href{http://docs.python.org/library/pickle.html}{pickled} can be passed as
-parameters to \emph{Ruffus} task functions. Happily, that applies to almost any native Python data type.
-The use of the rare, unpicklable object will cause python to complain (fail) loudly when \emph{Ruffus} pipelines
-are run.
-
-\end{itemize}
-\end{quote}
-
-\index{@jobs\_limit!Tutorial}\index{Tutorial!@jobs\_limit}
-
-\subsection{Restricting parallelism with \emph{@jobs\_limit}}
-\label{tutorials/new_tutorial/multiprocessing:new-manual-jobs-limit}\label{tutorials/new_tutorial/multiprocessing:restricting-parallelism-with-jobs-limit}\label{tutorials/new_tutorial/multiprocessing:index-3}\begin{quote}
-
-Calling {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(multiprocess = NNN)}}} allows
-multiple jobs (from multiple independent tasks) to be run in parallel. However, there
-are some operations that consume so many resources that we might want them to run
-with less or no concurrency.
-
-For example, we might want to download some files via FTP but the server restricts
-requests from each IP address. Even if the rest of the pipeline is running 100 jobs in
-parallel, the FTP downloading must be restricted to 2 files at a time. We would really
-like to keep the pipeline running as is, but let this one operation run either serially,
-or with little concurrency.
-\begin{itemize}
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(multiprocess = NNN)}}} sets the pipeline-wide concurrency but
-
-\item {} 
-{\hyperref[decorators/jobs_limit:decorators-jobs-limit]{\emph{@jobs\_limit(MMM)}}} sets concurrency at \code{MMM} only for jobs in the decorated task.
-
-\end{itemize}
-
-The optional name (e.g. \code{@jobs\_limit(3, "ftp\_download\_limit")}) allows the same limit to
-be shared across multiple tasks. To be pedantic: a limit of \code{3} jobs at a time would be applied
-across all tasks which have a \code{@jobs\_limit} named \code{"ftp\_download\_limit"}.
-
-The {\hyperref[tutorials/new_tutorial/multiprocessing_code:new-manual-multiprocessing-code]{\emph{example code}}} uses up to 10 processes across the
-pipeline, but runs the \code{stage1\_big} and \code{stage1\_small} tasks 3 at a time (shared across
-both tasks). \code{stage2} jobs run 5 at a time.
-\end{quote}
-
-
-\subsection{Using \texttt{drmaa} to dispatch work to Computational Clusters or Grid engines from Ruffus jobs}
-\label{tutorials/new_tutorial/multiprocessing:using-drmaa-to-dispatch-work-to-computational-clusters-or-grid-engines-from-ruffus-jobs}\label{tutorials/new_tutorial/multiprocessing:new-manual-ruffus-drmaa-wrapper-run-job}\begin{quote}
-
-Ruffus has been widely used to manage work on computational clusters or grid engines. Though Ruffus
-task functions cannot (yet!) run natively and transparently on remote cluster nodes, it is trivial
-to dispatch work across the cluster.
-
-From version 2.4 onwards, Ruffus includes an optional helper module which interacts with
-\href{https://github.com/drmaa-python/drmaa-python}{python bindings} for the widely used \href{http://en.wikipedia.org/wiki/DRMAA}{drmaa}
-Open Grid Forum API specification. This allows jobs to dispatch work to a computational cluster and wait until it completes.
-
-Here are the necessary steps
-\end{quote}
-
-
-\subsubsection{1) Use a shared drmaa session:}
-\label{tutorials/new_tutorial/multiprocessing:use-a-shared-drmaa-session}\begin{quote}
-
-Before your pipeline runs:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   start shared drmaa session for all jobs / tasks in pipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{k+kn}{import} \PYG{n+nn}{drmaa}
-\PYG{n}{drmaa\PYGZus{}session} \PYG{o}{=} \PYG{n}{drmaa}\PYG{o}{.}\PYG{n}{Session}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{drmaa\PYGZus{}session}\PYG{o}{.}\PYG{n}{initialize}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-Cleanup after your pipeline completes:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   pipeline functions go here}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{if} \PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}} \PYG{o}{==} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZus{}\PYGZus{}main\PYGZus{}\PYGZus{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}
-    \PYG{n}{drmaa\PYGZus{}session}\PYG{o}{.}\PYG{n}{exit}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{2) import \texttt{ruffus.drmaa\_wrapper}}
-\label{tutorials/new_tutorial/multiprocessing:import-ruffus-drmaa-wrapper}\begin{quote}
-\begin{itemize}
-\item {} 
-The optional \code{ruffus.drmaa\_wrapper} module needs to be imported explicitly:
-
-\end{itemize}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} imported ruffus.drmaa\PYGZus{}wrapper explicitly}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.drmaa\PYGZus{}wrapper} \PYG{k+kn}{import} \PYG{n}{run\PYGZus{}job}\PYG{p}{,} \PYG{n}{error\PYGZus{}drmaa\PYGZus{}job}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{3) call \emph{drmaa\_wrapper.run\_job()}}
-\label{tutorials/new_tutorial/multiprocessing:call-drmaa-wrapper-run-job}\begin{quote}
-
-{\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job]{\emph{drmaa\_wrapper.run\_job()}}} dispatches the work to a cluster node within a normal Ruffus job and waits for completion
-
-This is the equivalent of \href{http://docs.python.org/2/library/os.html\#os.system}{os.system}  or
-\href{http://docs.python.org/2/library/subprocess.html\#subprocess.check\_call}{subprocess.check\_output} but the code will run remotely as specified:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-    \PYG{c}{\PYGZsh{} ruffus.drmaa\PYGZus{}wrapper.run\PYGZus{}job}
-    \PYG{n}{stdout\PYGZus{}res}\PYG{p}{,} \PYG{n}{stderr\PYGZus{}res}  \PYG{o}{=} \PYG{n}{run\PYGZus{}job}\PYG{p}{(}\PYG{n}{cmd\PYGZus{}str}           \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{touch }\PYG{l+s}{\PYGZdq{}} \PYG{o}{+} \PYG{n}{output\PYGZus{}file}\PYG{p}{,}
-                                      \PYG{n}{job\PYGZus{}name}          \PYG{o}{=} \PYG{n}{job\PYGZus{}name}\PYG{p}{,}
-                                      \PYG{n}{logger}            \PYG{o}{=} \PYG{n}{logger}\PYG{p}{,}
-                                      \PYG{n}{drmaa\PYGZus{}session}     \PYG{o}{=} \PYG{n}{drmaa\PYGZus{}session}\PYG{p}{,}
-                                      \PYG{n}{run\PYGZus{}locally}       \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{local\PYGZus{}run}\PYG{p}{,}
-                                      \PYG{n}{job\PYGZus{}other\PYGZus{}options} \PYG{o}{=} \PYG{n}{job\PYGZus{}other\PYGZus{}options}\PYG{p}{)}
-\end{Verbatim}
-
-The complete code is available {\hyperref[tutorials/new_tutorial/multiprocessing_code:using-ruffus-drmaa-wrapper]{\emph{here}}}
-\end{quote}
-\begin{itemize}
-\item {} 
-{\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job]{\emph{drmaa\_wrapper.run\_job()}}} is a convenience wrapper around the \href{https://github.com/drmaa-python/drmaa-python}{python drmaa bindings}
-\href{http://drmaa-python.readthedocs.org/en/latest/tutorials.html\#waiting-for-a-job}{RunJob} function.
-It takes care of writing drmaa \emph{job templates} for you.
-
-\item {} 
-Each call creates a separate drmaa \emph{job template}.
-
-\end{itemize}
-\end{quote}
-
-
-\subsubsection{4) Use multithread: \emph{pipeline\_run(multithread = NNN)}}
-\label{tutorials/new_tutorial/multiprocessing:use-multithread-pipeline-run-multithread-nnn}\begin{quote}
-
-\begin{notice}{warning}{Warning:}
-{\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job]{\emph{drmaa\_wrapper.run\_job()}}}
-\begin{quote}
-
-\textbf{requires} \code{pipeline\_run} {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{(multithread = NNN)}}}
-
-\textbf{and will not work with}  \code{pipeline\_run} {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{(multiprocess = NNN)}}}
-\end{quote}
-\end{notice}
-\begin{description}
-\item[{Using multithreading rather than multiprocessing}] \leavevmode\begin{itemize}
-\item {} 
-allows the drmaa session to be shared
-
-\item {} 
-prevents ``processing storms'' which lock up the queue submission node when hundreds or thousands of grid engine / cluster commands complete at the same time.
-
-\end{itemize}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run} \PYG{p}{(}\PYG{o}{.}\PYG{o}{.}\PYG{o}{.}\PYG{p}{,} \PYG{n}{multithread} \PYG{o}{=} \PYG{n}{NNN}\PYG{p}{,} \PYG{o}{.}\PYG{o}{.}\PYG{o}{.}\PYG{p}{)}
-\end{Verbatim}
-
-or if you are using ruffus.cmdline:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{run} \PYG{p}{(}\PYG{n}{options}\PYG{p}{,} \PYG{n}{multithread} \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{jobs}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-Normally multithreading reduces the amount of parallelism in python due to the python \href{http://en.wikipedia.org/wiki/Global\_Interpreter\_Lock}{Global interpreter Lock (GIL)}.
-However, as the work load is almost entirely on another computer (i.e. a cluster / grid engine node) with a separate python interpreter, any cost benefit calculations of this sort are moot.
-\end{quote}
-
-
-\subsubsection{5) Develop locally}
-\label{tutorials/new_tutorial/multiprocessing:develop-locally}\begin{quote}
-
-{\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job]{\emph{drmaa\_wrapper.run\_job()}}} provides two convenience parameters for developing grid engine pipelines:
-\begin{itemize}
-\item {} 
-commands can run locally, i.e. on the local machine rather than on cluster nodes:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{run\PYGZus{}job}\PYG{p}{(}\PYG{n}{cmd\PYGZus{}str}\PYG{p}{,} \PYG{n}{run\PYGZus{}locally} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\item {} 
-Output files can be \href{http://en.wikipedia.org/wiki/Touch\_(Unix)}{touch}ed, i.e. given the appearance of the work having being done without actually running the commands
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{run\PYGZus{}job}\PYG{p}{(}\PYG{n}{cmd\PYGZus{}str}\PYG{p}{,} \PYG{n}{touch\PYGZus{}only} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\end{itemize}
-\end{quote}
-
-\index{pipeline\_run touch mode!Tutorial}\index{Tutorial!pipeline\_run touch mode}\index{touch mode pipeline\_run!Tutorial}\index{Tutorial!touch mode pipeline\_run}
-
-\subsection{Forcing a pipeline to appear up to date}
-\label{tutorials/new_tutorial/multiprocessing:index-4}\label{tutorials/new_tutorial/multiprocessing:forcing-a-pipeline-to-appear-up-to-date}\label{tutorials/new_tutorial/multiprocessing:new-manual-pipeline-run-touch}\begin{quote}
-
-Sometimes, we \emph{know} that a pipeline has run to completion, that everything is up-to-date. However, Ruffus still insists on the basis
-of file modification times that you need to rerun.
-
-For example, sometimes a trivial accounting modification needs to be made to a data file.
-Even though you know that this changes nothing in practice, Ruffus will detect the modification and
-ask to rerun everything from that point forwards.
-
-One way to convince Ruffus that everything is fine is to manually \href{http://en.wikipedia.org/wiki/Touch\_(Unix)}{touch}
-all subsequent data files one by one in sequence so that the file timestamps follow the appropriate progression.
-
-You can also ask \emph{Ruffus} to do this automatically for you by running the pipeline in \href{http://en.wikipedia.org/wiki/Touch\_(Unix)}{touch}
-mode:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(} \PYG{n}{touch\PYGZus{}files\PYGZus{}only} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}} will run your pipeline script normally working backwards from any specified final target, or else the
-last task in the pipeline. It works out where it should begin running, i.e. with the first out-of-date data files.
-After that point, instead of calling your pipeline task functions, each missing or out-of-date file is
-\href{http://en.wikipedia.org/wiki/Touch\_(Unix)}{touch-ed} in turn so that the file modification dates
-follow on successively.
-
-This turns out to be useful way to check that your pipeline runs correctly by creating a series of dummy (empty files).
-However, \emph{Ruffus} does not know how to read your mind to know which files to create from {\hyperref[decorators/split:decorators-split]{\emph{@split}}} or
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}} tasks.
-
-Using {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline]{\emph{ruffus.cmdline}}} from version 2.4, you can just specify:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-your script \PYGZhy{}\PYGZhy{}touch\PYGZus{}files\PYGZus{}only \PYG{o}{[}\PYGZhy{}\PYGZhy{}other\PYGZus{}options\PYGZus{}of\PYGZus{}your\PYGZus{}own\PYGZus{}etc\PYG{o}{]}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{logging!Tutorial}\index{Tutorial!logging}
-
-\section{\textbf{Chapter 15}: Logging progress through a pipeline}
-\label{tutorials/new_tutorial/logging:new-manual-logging-chapter-num-logging-progress-through-a-pipeline}\label{tutorials/new_tutorial/logging:index-0}\label{tutorials/new_tutorial/logging::doc}\label{tutorials/new_tutorial/logging:new-manual-logging}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the {\hyperref[tutorials/new_tutorial/logging_code:new-manual-logging-code]{\emph{example code}}}
-\end{notice}
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/logging:overview}\begin{quote}
-
-There are two parts to logging with \textbf{Ruffus}:
-\begin{itemize}
-\item {} 
-Logging progress through the pipeline
-\begin{quote}
-
-This produces the sort of output displayed in this manual:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\PYG{g+go}{Task = parallel\PYGZus{}io\PYGZus{}task}
-\PYG{g+go}{    Job = [\PYGZdq{}a.1\PYGZdq{} \PYGZhy{}\PYGZgt{} \PYGZdq{}a.2\PYGZdq{}, \PYGZdq{}A file\PYGZdq{}] completed}
-\PYG{g+go}{    Job = [\PYGZdq{}b.1\PYGZdq{} \PYGZhy{}\PYGZgt{} \PYGZdq{}b.2\PYGZdq{}, \PYGZdq{}B file\PYGZdq{}] unnecessary: already up to date}
-\PYG{g+go}{Completed Task = parallel\PYGZus{}io\PYGZus{}task}
-\end{Verbatim}
-\end{quote}
-
-\item {} 
-Logging your own messages from within your pipelined functions.
-\begin{quote}
-
-Because \textbf{Ruffus} may run each task function in separate process on a separate
-CPU (multiprocessing), some attention has to be paid to how to send and
-synchronise your log messages across process boundaries.
-\end{quote}
-
-\end{itemize}
-
-We shall deal with these in turn.
-\end{quote}
-
-
-\subsection{Logging task/job completion}
-\label{tutorials/new_tutorial/logging:new-manual-logging-pipeline}\label{tutorials/new_tutorial/logging:logging-task-job-completion}\begin{quote}
-
-By default, \emph{Ruffus} logs each task and each job as it is completed to
-\href{http://docs.python.org/2/library/sys.html\#sys.stderr}{sys.stderr}.
-
-By default, Ruffus logs to \code{STDERR}: {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(logger = stderr\_logger)}}}.
-
-If you want to turn off all tracking messages as the pipeline runs, apart from setting \code{verbose = 0}, you
-can also use the aptly named Ruffus \code{black\_hole\_logger}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{logger} \PYG{o}{=} \PYG{n}{black\PYGZus{}hole\PYGZus{}logger}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{pipeline\_run verbosity!Tutorial}\index{Tutorial!pipeline\_run verbosity}
-
-\subsubsection{Controlling logging verbosity}
-\label{tutorials/new_tutorial/logging:controlling-logging-verbosity}\label{tutorials/new_tutorial/logging:index-1}\begin{quote}
-
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run()}}} currently has five levels of verbosity, set by the optional \code{verbose}
-parameter which defaults to 1:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-verbose = 0: nothing
-verbose = 1: logs completed jobs/tasks;
-verbose = 2: logs up to date jobs in incomplete tasks
-verbose = 3: logs reason for running job
-verbose = 4: logs messages useful only for debugging ruffus pipeline code
-\end{Verbatim}
-
-\code{verbose} \textgreater{} \code{5} are intended for debugging \textbf{Ruffus} by the developers and the details
-are liable to change from release to release
-\end{quote}
-\end{quote}
-
-\index{logging with ruffus.cmdline!Tutorial}\index{Tutorial!logging with ruffus.cmdline}
-
-\subsection{Use \emph{ruffus.cmdline}}
-\label{tutorials/new_tutorial/logging:use-ruffus-cmdline}\label{tutorials/new_tutorial/logging:index-2}\begin{quote}
-
-As always, it is easiest to use {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline]{\emph{ruffus.cmdline}}}.
-
-Set your script to
-\begin{quote}
-\begin{itemize}
-\item {} 
-write messages to \code{STDERR} with the \code{-{-}verbose} option and
-
-\item {} 
-to a log file with the \code{-{-}log\_file} option.
-
-\end{itemize}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
- \PYG{c}{\PYGZsh{}  Python logger which can be synchronised across concurrent Ruffus tasks}
- \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{setup\PYGZus{}logging} \PYG{p}{(}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{log\PYGZus{}file}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-
- \PYG{n+nd}{@transform}\PYG{p}{(} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{job1.input}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.input}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
- \PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{pass}
-
- \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{logger}\PYG{o}{=}\PYG{n}{logger}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{logging customising!Tutorial}\index{Tutorial!logging customising}
-
-\subsection{Customising logging}
-\label{tutorials/new_tutorial/logging:customising-logging}\label{tutorials/new_tutorial/logging:index-3}\begin{quote}
-
-You can also specify exactly how logging works by providing a \href{http://docs.python.org/library/logging.html}{logging} object
-to {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run()}}} .
-This log object should have \code{debug()} and \code{info()} methods.
-
-Instead of writing your own, it is usually more convenient to use the python
-\href{http://docs.python.org/library/logging.html}{logging}
-module which provides logging classes with rich functionality.
-
-The {\hyperref[tutorials/new_tutorial/logging_code:new-manual-logging-code]{\emph{example code}}} sets up a logger to a rotating set of files
-\end{quote}
-
-\index{logging your own message!Tutorial}\index{Tutorial!logging your own message}
-
-\subsection{Log your own messages}
-\label{tutorials/new_tutorial/logging:log-your-own-messages}\label{tutorials/new_tutorial/logging:index-4}\label{tutorials/new_tutorial/logging:new-manual-logging-per-job}\begin{quote}
-
-You need to take a little care when logging your custom messages \emph{within} your pipeline.
-\begin{itemize}
-\item {} 
-If your Ruffus pipeline may run in parallel, make sure that logging is synchronised.
-
-\item {} 
-If your Ruffus pipeline may run across separate processes, send your logging object across process boundaries.
-
-\end{itemize}
-
-\href{http://docs.python.org/library/logging.html}{logging} objects can not be
-\href{http://docs.python.org/library/pickle.html}{pickled} and shared naively across
-processes. Instead, we need to create proxies which forward the logging to a single
-shared log.
-
-The {\hyperref[proxy_logger:proxy-logger]{\emph{ruffus.proxy\_logger}}} module provides an easy way to share
-\href{http://docs.python.org/library/logging.html}{logging} objects among
-jobs. This requires just two simple steps:
-\end{quote}
-
-\begin{notice}{note}{Note:}\begin{itemize}
-\item {} 
-This is a good template for sharing \href{http://docs.python.org/2/library/pickle.html\#what-can-be-pickled-and-unpickled}{non-picklable objects}
-across processes.
-
-\end{itemize}
-\end{notice}
-
-
-\subsubsection{1. Set up logging}
-\label{tutorials/new_tutorial/logging:new-manual-sharing-proxy-object}\label{tutorials/new_tutorial/logging:set-up-logging}\begin{quote}
-
-Things are easiest if you are using \code{ruffus.cmdline}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}  standard python logger which can be synchronised across concurrent Ruffus tasks}
-\PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{setup\PYGZus{}logging} \PYG{p}{(}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{log\PYGZus{}file}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-\end{Verbatim}
-
-Otherwise, manually:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.proxy\PYGZus{}logger} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{p}{(}\PYG{n}{logger}\PYG{p}{,}
- \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)} \PYG{o}{=} \PYG{n}{make\PYGZus{}shared\PYGZus{}logger\PYGZus{}and\PYGZus{}proxy} \PYG{p}{(}\PYG{n}{setup\PYGZus{}std\PYGZus{}shared\PYGZus{}logger}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}logger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                                                \PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{file\PYGZus{}name}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/my/lg.log}\PYG{l+s}{\PYGZdq{}}\PYG{p}{\PYGZcb{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{2. Share the proxy}
-\label{tutorials/new_tutorial/logging:share-the-proxy}\begin{quote}
-
-Now, pass:
-\begin{itemize}
-\item {} 
-\code{logger} (which forwards logging calls across jobs) and
-
-\item {} 
-\code{logging\_mutex} (which prevents different jobs which are logging simultaneously
-from being jumbled up)
-
-\end{itemize}
-
-to each job:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{initial\PYGZus{}file}\PYG{p}{,}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.input}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} pass log and synchronisation as parameters}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,}
-            \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)}\PYG{p}{:}         \PYG{c}{\PYGZsh{} pass log and synchronisation as parameters}
-    \PYG{k}{pass}
-
-    \PYG{c}{\PYGZsh{} synchronise logging}
-    \PYG{k}{with} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{:}
-        \PYG{n}{logger}\PYG{o}{.}\PYG{n}{info}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Here we go logging...}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\index{@subdivide!Tutorial}\index{Tutorial!@subdivide}\index{@collate!Tutorial}\index{Tutorial!@collate}
-
-\section{\textbf{Chapter 16}: \emph{@subdivide} tasks to run efficiently and regroup with \emph{@collate}}
-\label{tutorials/new_tutorial/subdivide_collate:new-manual-subdivide-collate-chapter-num-subdivide-tasks-to-run-efficiently-and-regroup-with-collate}\label{tutorials/new_tutorial/subdivide_collate:index-0}\label{tutorials/new_tutorial/subdivide_collate::doc}\label{tutorials/new_tutorial/subdivide_collate:new-manual-subdivide-collate}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}} syntax
-
-\item {} 
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} syntax
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/subdivide_collate:overview}\begin{quote}
-
-In \textbf{Chapter 12} and \textbf{Chapter 13}, we saw how a large
-task can be {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{@split}}} into small jobs to be analysed efficiently
-in parallel. Ruffus can then {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{@merge}}} these back together
-to give a single, unified result.
-
-This assumes that your pipeline is processing one item at a time. Usually, however, we
-will have, for example, 10 large pieces of data in play, each of which has to be
-subdivided into smaller pieces for analysis before being put back together.
-
-This is the role of {\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}} and  {\hyperref[decorators/collate:decorators-collate]{\emph{@subdivide}}}.
-
-Like {\hyperref[decorators/split:decorators-split]{\emph{@split}}},  the number of output files
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}} produces for \emph{each} \textbf{Input} is not predetermined.
-
-On the other hand, these output files should be named in such a way that they can
-later be grouped back together later using {\hyperref[decorators/collate:decorators-collate]{\emph{@subdivide}}}.
-
-This will be clearer with some worked examples.
-\end{quote}
-
-
-\subsection{\emph{@subdivide} in parallel}
-\label{tutorials/new_tutorial/subdivide_collate:new-manual-subdivide}\label{tutorials/new_tutorial/subdivide_collate:subdivide-in-parallel}\begin{quote}
-
-Let us start from 3 files with varying number of lines. We wish to process these two
-lines at a time but we do not know ahead of time how long each file is:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{os}\PYG{o}{,} \PYG{n+nn}{random}\PYG{o}{,} \PYG{n+nn}{sys}
-
-\PYG{c}{\PYGZsh{} Create files a random number of lines}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}test\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{cnt\PYGZus{}lines} \PYG{o}{=} \PYG{n}{random}\PYG{o}{.}\PYG{n}{randint}\PYG{p}{(}\PYG{l+m+mi}{1}\PYG{p}{,}\PYG{l+m+mi}{3}\PYG{p}{)} \PYG{o}{*} \PYG{l+m+mi}{2}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:}
-        \PYG{k}{for} \PYG{n}{ii} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{cnt\PYGZus{}lines}\PYG{p}{)}\PYG{p}{:}
-            \PYG{n}{oo}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{data item = }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{ii}\PYG{p}{)}
-        \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{        }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ has }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{ lines}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{cnt\PYGZus{}lines}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   subdivide the input files into NNN fragment files of 2 lines each}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@subdivide}\PYG{p}{(} \PYG{n}{create\PYGZus{}test\PYGZus{}files}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}.*.fragment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{subdivide\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name\PYGZus{}stem}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   cleanup any previous results}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{oo} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{oo}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   Output files contain two lines each}
-    \PYG{c}{\PYGZsh{}       (new output files every even line)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{cnt\PYGZus{}output\PYGZus{}files} \PYG{o}{=} \PYG{l+m+mi}{0}
-    \PYG{k}{for} \PYG{n}{ii}\PYG{p}{,} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{enumerate}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{if} \PYG{n}{ii} \PYG{o}{\PYGZpc{}} \PYG{l+m+mi}{2} \PYG{o}{==} \PYG{l+m+mi}{0}\PYG{p}{:}
-            \PYG{n}{cnt\PYGZus{}output\PYGZus{}files} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-            \PYG{n}{output\PYGZus{}file\PYGZus{}name} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{.}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.fragment}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name\PYGZus{}stem}\PYG{p}{,} \PYG{n}{cnt\PYGZus{}output\PYGZus{}files}\PYG{p}{)}
-            \PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-            \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{        Subdivide }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}
-        \PYG{n}{output\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Analyse each fragment independently}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{subdivide\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.fragment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.analysed}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{analyse\PYGZus{}fragments}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{        Analysing }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:}
-        \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-            \PYG{n}{oo}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{analysed }\PYG{l+s}{\PYGZdq{}} \PYG{o}{+} \PYG{n}{line}\PYG{p}{)}
-\end{Verbatim}
-
-This produces the following output:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{1}\PYG{p}{)}
-\PYG{g+go}{        a.start has 2 lines}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} a.start] completed}
-\PYG{g+go}{        b.start has 6 lines}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} b.start] completed}
-\PYG{g+go}{        c.start has 6 lines}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} c.start] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}test\PYGZus{}files}
-
-\PYG{g+go}{        Subdivide a.start \PYGZhy{}\PYGZgt{} /home/lg/temp/a.1.fragment}
-\PYG{g+go}{    Job  = [a.start \PYGZhy{}\PYGZgt{} a.*.fragment, a] completed}
-
-\PYG{g+go}{        Subdivide b.start \PYGZhy{}\PYGZgt{} /home/lg/temp/b.1.fragment}
-\PYG{g+go}{        Subdivide b.start \PYGZhy{}\PYGZgt{} /home/lg/temp/b.2.fragment}
-\PYG{g+go}{        Subdivide b.start \PYGZhy{}\PYGZgt{} /home/lg/temp/b.3.fragment}
-\PYG{g+go}{    Job  = [b.start \PYGZhy{}\PYGZgt{} b.*.fragment, b] completed}
-
-\PYG{g+go}{        Subdivide c.start \PYGZhy{}\PYGZgt{} /home/lg/temp/c.1.fragment}
-\PYG{g+go}{        Subdivide c.start \PYGZhy{}\PYGZgt{} /home/lg/temp/c.2.fragment}
-\PYG{g+go}{        Subdivide c.start \PYGZhy{}\PYGZgt{} /home/lg/temp/c.3.fragment}
-\PYG{g+go}{    Job  = [c.start \PYGZhy{}\PYGZgt{} c.*.fragment, c] completed}
-
-\PYG{g+go}{Completed Task = subdivide\PYGZus{}files}
-
-\PYG{g+go}{        Analysing /home/lg/temp/a.1.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/a.1.analysed}
-\PYG{g+go}{    Job  = [a.1.fragment \PYGZhy{}\PYGZgt{} a.1.analysed] completed}
-\PYG{g+go}{        Analysing /home/lg/temp/b.1.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/b.1.analysed}
-\PYG{g+go}{    Job  = [b.1.fragment \PYGZhy{}\PYGZgt{} b.1.analysed] completed}
-
-\PYG{g+go}{    [ ...SEE EXAMPLE CODE FOR MORE LINES ...]}
-
-\PYG{g+go}{Completed Task = analyse\PYGZus{}fragments}
-\end{Verbatim}
-
-\code{a.start} has two lines and results in a single \code{.fragment} file,
-while there are 3 \code{b.*.fragment} files because it has 6 lines.
-Whatever their origin, all of the different fragment files are treated equally
-in \code{analyse\_fragments()} and processed (in parallel) in the same way.
-\end{quote}
-
-
-\subsection{Grouping using \emph{@collate}}
-\label{tutorials/new_tutorial/subdivide_collate:new-manual-collate}\label{tutorials/new_tutorial/subdivide_collate:grouping-using-collate}\begin{quote}
-
-All that is left in our example is to reassemble the analysed fragments back together into
-3 sets of results corresponding to the original 3 pieces of starting data.
-
-This is straightforward by eye: the file names all have the same pattern: \code{{[}abc{]}.*.analysed}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-a.1.analysed    -\textgreater{}   a.final\_result
-b.1.analysed    -\textgreater{}   b.final\_result
-b.2.analysed    -\textgreater{}   ..
-b.3.analysed    -\textgreater{}   ..
-c.1.analysed    -\textgreater{}   c.final\_result
-c.2.analysed    -\textgreater{}   ..
-\end{Verbatim}
-\end{quote}
-
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} does something similar:
-\begin{quote}
-\begin{enumerate}
-\item {} 
-Specify a string substitution e.g. \code{c.??.analysed  -\textgreater{} c.final\_result} and
-
-\item {} 
-Ask \emph{ruffus} to group together any \textbf{Input} (e.g. \code{c.1.analysed}, \code{c.2.analysed})
-that will result in the same \textbf{Output} (e.g. \code{c.final\_result})
-
-\end{enumerate}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   {}`{}`XXX.??.analysed  \PYGZhy{}\PYGZgt{} XXX.final\PYGZus{}result{}`{}`}
-\PYG{c}{\PYGZsh{}   Group results using original names}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@collate}\PYG{p}{(}   \PYG{n}{analyse\PYGZus{}fragments}\PYG{p}{,}
-
-            \PYG{c}{\PYGZsh{} split file name into [abc].NUMBER.analysed}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/(?P\PYGZlt{}NAME\PYGZgt{}[abc]+)}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.analysed\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}NAME[0]\PYGZcb{}.final\PYGZus{}result}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{recombine\PYGZus{}analyses}\PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:}
-        \PYG{k}{for} \PYG{n}{input\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-            \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{        Recombine }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-            \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-                \PYG{n}{oo}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-\end{Verbatim}
-
-This produces the following output:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+go}{        Recombine /home/lg/temp/a.1.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/a.final\PYGZus{}result}
-\PYG{g+go}{    Job  = [[a.1.analysed] \PYGZhy{}\PYGZgt{} a.final\PYGZus{}result] completed}
-\PYG{g+go}{        Recombine /home/lg/temp/b.1.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/b.final\PYGZus{}result}
-\PYG{g+go}{        Recombine /home/lg/temp/b.2.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/b.final\PYGZus{}result}
-\PYG{g+go}{        Recombine /home/lg/temp/b.3.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/b.final\PYGZus{}result}
-\PYG{g+go}{    Job  = [[b.1.analysed, b.2.analysed, b.3.analysed] \PYGZhy{}\PYGZgt{} b.final\PYGZus{}result] completed}
-\PYG{g+go}{        Recombine /home/lg/temp/c.1.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/c.final\PYGZus{}result}
-\PYG{g+go}{        Recombine /home/lg/temp/c.2.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/c.final\PYGZus{}result}
-\PYG{g+go}{        Recombine /home/lg/temp/c.3.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/c.final\PYGZus{}result}
-\PYG{g+go}{    Job  = [[c.1.analysed, c.2.analysed, c.3.analysed] \PYGZhy{}\PYGZgt{} c.final\PYGZus{}result] completed}
-\PYG{g+go}{Completed Task = recombine\PYGZus{}analyses}
-\end{Verbatim}
-\end{quote}
-
-\begin{notice}{warning}{Warning:}\begin{itemize}
-\item {} 
-\textbf{Input} file names are grouped together not in a guaranteed order.
-\begin{quote}
-
-For example, the fragment files may not be sent to \code{recombine\_analyses(input\_file\_names, ...)}
-in alphabetically or any other useful order.
-
-You may want to sort \textbf{Input} before concatenation.
-\end{quote}
-
-\item {} 
-All \textbf{Input} are grouped together if they have both the same \textbf{Output} \emph{and} \textbf{Extra}
-parameters. If any string substitution is specified in any of the other \textbf{Extra} parameters
-to {\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}, they must give the same answers for \textbf{Input}
-in the same group.
-
-\end{itemize}
-\end{notice}
-\end{quote}
-
-\index{combinatorics!Tutorial}\index{Tutorial!combinatorics}
-
-\section{\textbf{Chapter 17}: \emph{@combinations}, \emph{@permutations} and all versus all \emph{@product}}
-\label{tutorials/new_tutorial/combinatorics:index-0}\label{tutorials/new_tutorial/combinatorics:new-manual-combinatorics}\label{tutorials/new_tutorial/combinatorics::doc}\label{tutorials/new_tutorial/combinatorics:new-manual-combinatorics-chapter-num-combinations-permutations-and-all-versus-all-product}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}}
-
-\item {} 
-{\hyperref[decorators/combinations:decorators-combinations]{\emph{@combinations}}}
-
-\item {} 
-{\hyperref[decorators/permutations:decorators-permutations]{\emph{@permutations}}}
-
-\item {} 
-{\hyperref[decorators/product:decorators-product]{\emph{@product}}}
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}}
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/combinatorics_code:new-manual-combinatorics-code]{\emph{Chapter 17: Python Code for @combinations, @permutations and all versus all @product}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/combinatorics:overview}\begin{quote}
-
-A surprising number of computational problems involve some sort of all versus all calculations.
-Previously, this would have required all the parameters to be supplied using a custom function
-on the fly with {\hyperref[decorators/files_ex:decorators-files-on-the-fly]{\emph{@files}}}.
-
-From version 2.4, \emph{Ruffus} supports  {\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}},
-{\hyperref[decorators/combinations:decorators-combinations]{\emph{@combinations}}}, {\hyperref[decorators/permutations:decorators-permutations]{\emph{@permutations}}},
-{\hyperref[decorators/product:decorators-product]{\emph{@product}}}.
-
-These provide as far as possible all the functionality of the four combinatorics iterators
-from the standard python \href{http://docs.python.org/2/library/itertools.html}{itertools}
-functions of the same name.
-\end{quote}
-
-
-\subsection{Generating output with \emph{formatter()}}
-\label{tutorials/new_tutorial/combinatorics:generating-output-with-formatter}\begin{quote}
-
-String replacement always takes place via {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}}. Unfortunately,
-the other \emph{Ruffus} workhorses of  {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} and  {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}}
-do not have sufficient syntactic flexibility.
-
-Each combinatorics decorator deals with multiple sets of inputs whether this might be:
-\begin{itemize}
-\item {} 
-a self-self comparison (such as {\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}},
-{\hyperref[decorators/combinations:decorators-combinations]{\emph{@combinations}}}, {\hyperref[decorators/permutations:decorators-permutations]{\emph{@permutations}}}) or,
-
-\item {} 
-a self-other comparison ({\hyperref[decorators/product:decorators-product]{\emph{@product}}})
-
-\end{itemize}
-
-The replacement strings thus require an extra level of indirection to refer to
-parsed components.
-\begin{enumerate}
-\item {} 
-The first level refers to which \emph{set} of inputs.
-
-\item {} 
-The second level refers to which input file in any particular \emph{set} of inputs.
-
-\end{enumerate}
-
-For example, if the \emph{inputs} are  \textbf{{[}A1,A2{]},{[}B1,B2{]},{[}C1,C2{]} vs {[}P1,P2{]},{[}Q1,Q2{]},{[}R1,R2{]} vs {[}X1,X2{]},{[}Y1,Y2{]},{[}Z1,Z2{]}},
-then \code{'\{basename{[}2{]}{[}0{]}\}'} is the \href{http://docs.python.org/2/library/os.path.html\#os.path.basename}{basename} for
-\begin{itemize}
-\item {} 
-the third set of inputs (\textbf{X,Y,Z}) and
-
-\item {} 
-the first file name string in each \textbf{Input} of that set (\textbf{X1, Y1, Z1})
-
-\end{itemize}
-\end{quote}
-
-
-\subsection{All vs all comparisons with \emph{@product}}
-\label{tutorials/new_tutorial/combinatorics:all-vs-all-comparisons-with-product}\label{tutorials/new_tutorial/combinatorics:new-manual-product}\begin{quote}
-
-{\hyperref[decorators/product:decorators-product]{\emph{@product}}} generates the Cartesian \textbf{product} between sets of input files,
-i.e. all vs all comparisons.
-
-The effect is analogous to a nested for loop.
-
-{\hyperref[decorators/product:decorators-product]{\emph{@product}}} can be useful, for example, in bioinformatics for finding
-the corresponding genes (orthologues) for a set of proteins in multiple species.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{product}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} product(\PYGZsq{}ABC\PYGZsq{}, \PYGZsq{}XYZ\PYGZsq{}) \PYGZhy{}\PYGZhy{}\PYGZgt{} AX AY AZ BX BY BZ CX CY CZ}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{p}{[} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a} \PYG{o+ow}{in} \PYG{n}{product}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{ABC}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{XYZ}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{]}
-\PYG{g+go}{[\PYGZsq{}AX\PYGZsq{}, \PYGZsq{}AY\PYGZsq{}, \PYGZsq{}AZ\PYGZsq{}, \PYGZsq{}BX\PYGZsq{}, \PYGZsq{}BY\PYGZsq{}, \PYGZsq{}BZ\PYGZsq{}, \PYGZsq{}CX\PYGZsq{}, \PYGZsq{}CY\PYGZsq{}, \PYGZsq{}CZ\PYGZsq{}]}
-\end{Verbatim}
-
-This example Calculates the \textbf{@product} of \textbf{A,B} and \textbf{P,Q} and \textbf{X,Y} files
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   Three sets of initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ab}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{p.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{q.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}pq}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{x.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{x.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{y.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{y.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]} \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}xy}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @product}
-\PYG{n+nd}{@product}\PYG{p}{(}   \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ab}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 1}
-
-            \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}pq}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 2}
-
-            \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}xy}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 3}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}                 \PYG{c}{\PYGZsh{} Output Replacement string}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}          \PYG{c}{\PYGZsh{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}          \PYG{c}{\PYGZsh{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}.product}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}     \PYG{c}{\PYGZsh{}}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                 \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{} Extra parameter: basename for 1st set of files, 1st file name}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{}                               2nd}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{}                               3rd}
-             \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{product\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{} basenames      = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}parameter  = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}file}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output\PYGZus{}parameter = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-This results in:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a p x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a p y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a q x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a q y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b p x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b p y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b q x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b q y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}y.product}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Permute all k-tuple orderings of inputs without repeats using \emph{@permutations}}
-\label{tutorials/new_tutorial/combinatorics:permute-all-k-tuple-orderings-of-inputs-without-repeats-using-permutations}\label{tutorials/new_tutorial/combinatorics:new-manual-permutations}\begin{quote}
-\begin{description}
-\item[{Generates the \textbf{permutations} for all the elements of a set of \textbf{Input} (e.g. \textbf{A B C D}),}] \leavevmode\begin{itemize}
-\item {} 
-r-length tuples of \emph{input} elements
-
-\item {} 
-excluding repeated elements (\textbf{A A})
-
-\item {} 
-and order of the tuples is significant (both \textbf{A B} and  \textbf{B A}).
-
-\end{itemize}
-
-\end{description}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{permutations}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} permutations(\PYGZsq{}ABCD\PYGZsq{}, 2) \PYGZhy{}\PYGZhy{}\PYGZgt{} AB AC AD BA BC BD CA CB CD DA DB DC}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{p}{[} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a} \PYG{o+ow}{in} \PYG{n}{permutations}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ABCD}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{)}\PYG{p}{]}
-\PYG{g+go}{[\PYGZsq{}AB\PYGZsq{}, \PYGZsq{}AC\PYGZsq{}, \PYGZsq{}AD\PYGZsq{}, \PYGZsq{}BA\PYGZsq{}, \PYGZsq{}BC\PYGZsq{}, \PYGZsq{}BD\PYGZsq{}, \PYGZsq{}CA\PYGZsq{}, \PYGZsq{}CB\PYGZsq{}, \PYGZsq{}CD\PYGZsq{}, \PYGZsq{}DA\PYGZsq{}, \PYGZsq{}DB\PYGZsq{}, \PYGZsq{}DC\PYGZsq{}]}
-\end{Verbatim}
-
-This following example calculates the \textbf{@permutations} of \textbf{A,B,C,D} files
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @permutations}
-\PYG{n+nd}{@permutations}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}      \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 2 at a time}
-              \PYG{l+m+mi}{2}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}.permutations}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}                                2nd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{permutations\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-This results in:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-
-\PYG{g+go}{A \PYGZhy{} B}
-\PYG{g+go}{A \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} A}
-\PYG{g+go}{B \PYGZhy{} C}
-\PYG{g+go}{B \PYGZhy{} D}
-\PYG{g+go}{C \PYGZhy{} A}
-\PYG{g+go}{C \PYGZhy{} B}
-\PYG{g+go}{C \PYGZhy{} D}
-\PYG{g+go}{D \PYGZhy{} A}
-\PYG{g+go}{D \PYGZhy{} B}
-\PYG{g+go}{D \PYGZhy{} C}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Select unordered k-tuples within inputs excluding repeated elements using \emph{@combinations}}
-\label{tutorials/new_tutorial/combinatorics:new-manual-combinations}\label{tutorials/new_tutorial/combinatorics:select-unordered-k-tuples-within-inputs-excluding-repeated-elements-using-combinations}\begin{quote}
-\begin{description}
-\item[{Generates the \textbf{combinations} for all the elements of a set of \textbf{Input} (e.g. \textbf{A B C D}),}] \leavevmode\begin{itemize}
-\item {} 
-r-length tuples of \emph{input} elements
-
-\item {} 
-without repeated elements (\textbf{A A})
-
-\item {} 
-where order of the tuples is irrelevant (either \textbf{A B} or  \textbf{B A}, not both).
-
-\end{itemize}
-
-\end{description}
-
-{\hyperref[decorators/combinations:decorators-combinations]{\emph{@combinations}}} can be useful, for example, in calculating a transition probability matrix
-for a set of states. The diagonals are meaningless ``self-self'' transitions which are excluded.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{combinations}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} combinations(\PYGZsq{}ABCD\PYGZsq{}, 3) \PYGZhy{}\PYGZhy{}\PYGZgt{} ABC ABD ACD BCD}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{p}{[} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a} \PYG{o+ow}{in} \PYG{n}{combinations}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ABCD}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{)}\PYG{p}{]}
-\PYG{g+go}{[\PYGZsq{}ABC\PYGZsq{}, \PYGZsq{}ABD\PYGZsq{}, \PYGZsq{}ACD\PYGZsq{}, \PYGZsq{}BCD\PYGZsq{}]}
-\end{Verbatim}
-
-This example calculates the \textbf{@combinations} of \textbf{A,B,C,D} files
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @combinations}
-\PYG{n+nd}{@combinations}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}      \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 3 at a time}
-              \PYG{l+m+mi}{3}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][1]\PYGZcb{}.combinations}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              2nd}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              3rd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{combinations\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-This results in:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{A \PYGZhy{} B \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} B \PYGZhy{} D}
-\PYG{g+go}{A \PYGZhy{} C \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} C \PYGZhy{} D}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Select unordered k-tuples within inputs \emph{including} repeated elements with \emph{@combinations\_with\_replacement}}
-\label{tutorials/new_tutorial/combinatorics:select-unordered-k-tuples-within-inputs-including-repeated-elements-with-combinations-with-replacement}\label{tutorials/new_tutorial/combinatorics:new-manual-combinations-with-replacement}\begin{quote}
-\begin{description}
-\item[{Generates the \textbf{combinations\_with\_replacement} for all the elements of a set of \textbf{Input} (e.g. \textbf{A B C D}),}] \leavevmode\begin{itemize}
-\item {} 
-r-length tuples of \emph{input} elements
-
-\item {} 
-including repeated elements (\textbf{A A})
-
-\item {} 
-where order of the tuples is irrelevant (either \textbf{A B} or  \textbf{B A}, not both).
-
-\end{itemize}
-
-\end{description}
-
-{\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}} can be useful,
-for example, in bioinformatics for finding evolutionary relationships between genetic elements such as proteins
-and genes. Self-self comparisons can be used a baseline for scaling similarity scores.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{combinations\PYGZus{}with\PYGZus{}replacement}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} combinations\PYGZus{}with\PYGZus{}replacement(\PYGZsq{}ABCD\PYGZsq{}, 2) \PYGZhy{}\PYGZhy{}\PYGZgt{} AA AB AC AD BB BC BD CC CD DD}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{p}{[} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a} \PYG{o+ow}{in} \PYG{n}{combinations\PYGZus{}with\PYGZus{}replacement}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{ABCD}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{)}\PYG{p}{]}
-\PYG{g+go}{[\PYGZsq{}AA\PYGZsq{}, \PYGZsq{}AB\PYGZsq{}, \PYGZsq{}AC\PYGZsq{}, \PYGZsq{}AD\PYGZsq{}, \PYGZsq{}BB\PYGZsq{}, \PYGZsq{}BC\PYGZsq{}, \PYGZsq{}BD\PYGZsq{}, \PYGZsq{}CC\PYGZsq{}, \PYGZsq{}CD\PYGZsq{}, \PYGZsq{}DD\PYGZsq{}]}
-\end{Verbatim}
-
-This example calculates the \textbf{@combinations\_with\_replacement} of \textbf{A,B,C,D} files
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @combinations\PYGZus{}with\PYGZus{}replacement}
-\PYG{n+nd}{@combinations\PYGZus{}with\PYGZus{}replacement}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}   \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                                  \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 2 at a time}
-              \PYG{l+m+mi}{2}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}.combinations\PYGZus{}with\PYGZus{}replacement}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              2rd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{combinations\PYGZus{}with\PYGZus{}replacement\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-This results in:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{A \PYGZhy{} A}
-\PYG{g+go}{A \PYGZhy{} B}
-\PYG{g+go}{A \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} B}
-\PYG{g+go}{B \PYGZhy{} C}
-\PYG{g+go}{B \PYGZhy{} D}
-\PYG{g+go}{C \PYGZhy{} C}
-\PYG{g+go}{C \PYGZhy{} D}
-\PYG{g+go}{D \PYGZhy{} D}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{@active\_if!Tutorial}\index{Tutorial!@active\_if}
-
-\section{\textbf{Chapter 18}: Turning parts of the pipeline on and off at runtime with \emph{@active\_if}}
-\label{tutorials/new_tutorial/active_if:new-manual-active-if}\label{tutorials/new_tutorial/active_if:index-0}\label{tutorials/new_tutorial/active_if::doc}\label{tutorials/new_tutorial/active_if:new-manual-active-if-chapter-num-turning-parts-of-the-pipeline-on-and-off-at-runtime-with-active-if}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/active_if:decorators-active-if]{\emph{@active\_if syntax in detail}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/active_if:overview}\begin{quote}
-
-It is sometimes useful to be able to switch on and off parts of a pipeline. For example, a pipeline
-might have two difference code paths depending on the type of data it is being asked to analyse.
-
-One surprisingly easy way to do this is to use a python \code{if} statement around particular task functions:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
- \PYG{n}{run\PYGZus{}task1} \PYG{o}{=} \PYG{n+nb+bp}{True}
-
- \PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.foo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.foo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{create\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-     \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
- \PYG{k}{if} \PYG{n}{run\PYGZus{}task1}\PYG{p}{:}
-     \PYG{c}{\PYGZsh{} might not run}
-     \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.foo}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bar}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-     \PYG{k}{def} \PYG{n+nf}{foobar}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-         \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{foobar}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bar}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.result}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{wrap\PYGZus{}up}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-         \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
- \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\begin{description}
-\item[{This simple solution has a number of drawbacks:}] \leavevmode\begin{enumerate}
-\item {} 
-The on/off decision is a one off event that happens when the script is loaded. Ideally, we
-would like some flexibility, and postpone the decision until \code{pipeline\_run()} is invoked.
-
-\item {} 
-When \code{if} is false, the entire task function becomes invisible, and if there are any
-downstream tasks, as in the above example, \emph{Ruffus} will complain loudly about
-missing dependencies.
-
-\end{enumerate}
-
-\end{description}
-\end{quote}
-
-
-\subsection{\emph{@active\_if}  controls the state of tasks}
-\label{tutorials/new_tutorial/active_if:active-if-controls-the-state-of-tasks}\begin{quote}
-\begin{itemize}
-\item {} 
-Switches tasks on and off at run time depending on its parameters
-
-\item {} 
-Evaluated each time \code{pipeline\_run}, \code{pipeline\_printout} or \code{pipeline\_printout\_graph} is called.
-
-\item {} 
-Dormant tasks behave as if they are up to date and have no output.
-
-\end{itemize}
-
-The Design and initial implementation were contributed by Jacob Biesinger
-
-The following example shows its flexibility and syntax:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}1} \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2} \PYG{o}{=} \PYG{n+nb+bp}{False}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}3} \PYG{o}{=} \PYG{n+nb+bp}{True}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}    task1}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.foo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.foo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}files}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    create\PYGZus{}files}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{outfile} \PYG{o}{+} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Only runs if all three run\PYGZus{}if\PYGZus{}true conditions are met}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   @active\PYGZus{}if determines if task is active}
-\PYG{n+nd}{@active\PYGZus{}if}\PYG{p}{(}\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}1}\PYG{p}{,} \PYG{k}{lambda}\PYG{p}{:} \PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2}\PYG{p}{)}
-\PYG{n+nd}{@active\PYGZus{}if}\PYG{p}{(}\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}3}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.foo}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bar}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{} @active\PYGZus{}if switches off task because run\PYGZus{}if\PYGZus{}true\PYGZus{}2 == False}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} @active\PYGZus{}if switches on task because all run\PYGZus{}if\PYGZus{}true conditions are met}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2} \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-The task starts off inactive:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} @active\PYGZus{}if switches off task \PYGZdq{}this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive\PYGZdq{} because run\PYGZus{}if\PYGZus{}true\PYGZus{}2 == False}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-
-\PYG{g+go}{Task enters queue = create\PYGZus{}files}
-\PYG{g+go}{create\PYGZus{}files}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} a.foo] Missing file [a.foo]}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} b.foo] Missing file [b.foo]}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} a.foo] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} b.foo] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}files}
-\PYG{g+go}{Inactive Task = this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}
-\end{Verbatim}
-\end{quote}
-
-Now turn on the task:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} @active\PYGZus{}if switches on task \PYGZdq{}this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive\PYGZdq{} because all run\PYGZus{}if\PYGZus{}true conditions are met}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2} \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-
-\PYG{g+go}{Task enters queue = this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}
-
-\PYG{g+go}{    Job  = [a.foo \PYGZhy{}\PYGZgt{} a.bar] Missing file [a.bar]}
-\PYG{g+go}{    Job  = [b.foo \PYGZhy{}\PYGZgt{} b.bar] Missing file [b.bar]}
-\PYG{g+go}{    Job  = [a.foo \PYGZhy{}\PYGZgt{} a.bar] completed}
-\PYG{g+go}{    Job  = [b.foo \PYGZhy{}\PYGZgt{} b.bar] completed}
-\PYG{g+go}{Completed Task = this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{posttask!Tutorial}\index{Tutorial!posttask}
-
-\section{\textbf{Chapter 19}: Signal the completion of each stage of our pipeline with \emph{@posttask}}
-\label{tutorials/new_tutorial/posttask:new-manual-posttask}\label{tutorials/new_tutorial/posttask:index-0}\label{tutorials/new_tutorial/posttask::doc}\label{tutorials/new_tutorial/posttask:new-manual-posttask-chapter-num-signal-the-completion-of-each-stage-of-our-pipeline-with-posttask}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} syntax
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/posttask:overview}\begin{quote}
-
-It is often useful to signal the completion of each task by specifying a specific
-action to be taken or function to be called. This can range from
-printing out some message, or  \href{http://en.wikipedia.org/wiki/Touch\_(Unix)}{touching} some sentinel file,
-to emailing the author. This is particular useful if the {\hyperref[glossary:term-task]{\emph{task}}} is a recipe apply to an unspecified number
-of parameters in parallel in different {\hyperref[glossary:term-job]{\emph{job}}}s. If the task is never run, or if it
-fails, needless-to-say no task completion action will happen.
-
-\emph{Ruffus} uses the {\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} decorator for this purpose.
-\end{quote}
-
-
-\subsubsection{\textbf{@posttask}}
-\label{tutorials/new_tutorial/posttask:posttask}\begin{quote}
-
-We can signal the completion of each task by specifying
-one or more function(s) using {\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{k}{def} \PYG{n+nf}{task\PYGZus{}finished}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hooray}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{n}{task\PYGZus{}finished}\PYG{p}{)}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-This is such a short function, we might as well write it in-line:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{k}{lambda}\PYG{p}{:} \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hooray}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\begin{notice}{note}{Note:}
-The function(s) provided to {\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} will be called if the pipeline passes
-through a task, even if none of its jobs are run because they are up-to-date.
-This happens when a upstream task is out-of-date, and the execution passes through
-this point in the pipeline. See the example in {\hyperref[tutorials/new_tutorial/dependencies:new-manual-dependencies]{\emph{Appendix 2: How dependency is checked}}}
-of this manual.
-\end{notice}
-
-\index{@posttask!touchfile (Manual)}\index{touchfile !@posttask (Manual)}
-
-\subsubsection{\emph{touch\_file}}
-\label{tutorials/new_tutorial/posttask:touch-file}\label{tutorials/new_tutorial/posttask:index-1}\label{tutorials/new_tutorial/posttask:new-manual-posttask-touch-file}\begin{quote}
-
-One way to note the completion of a task is to create some sort of
-``flag'' file. Each stage in a traditional \code{make} pipeline would contain a
-\code{touch completed.flag}.
-
-This is such a useful idiom that \emph{Ruffus} provides the shorthand {\hyperref[decorators/indicator_objects:decorators-touch-file]{\emph{touch\_file}}}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{n}{touch\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{task\PYGZus{}completed.flag}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Adding several post task actions}
-\label{tutorials/new_tutorial/posttask:adding-several-post-task-actions}\begin{quote}
-
-You can, of course, add more than one different action to be taken on completion of the
-task, either by stacking up as many {\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} decorators
-as necessary, or by including several functions in the same {\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{n}{print\PYGZus{}hooray}\PYG{p}{,} \PYG{n}{print\PYGZus{}whoppee}\PYG{p}{)}
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{n}{print\PYGZus{}hip\PYGZus{}hip}\PYG{p}{,} \PYG{n}{touch\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{sentinel\PYGZus{}flag}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{inputs!Tutorial}\index{Tutorial!inputs}\index{add\_inputs!Tutorial}\index{Tutorial!add\_inputs}\index{string substiution for inputs!Tutorial}\index{Tutorial!string substiution for inputs}
-
-\section{\textbf{Chapter 20}: Manipulating task inputs via string substitution using \emph{inputs()} and  \emph{add\_inputs()}}
-\label{tutorials/new_tutorial/inputs:new-manual-inputs}\label{tutorials/new_tutorial/inputs:index-0}\label{tutorials/new_tutorial/inputs:new-manual-inputs-chapter-num-manipulating-task-inputs-via-string-substitution-using-inputs-and-add-inputs}\label{tutorials/new_tutorial/inputs::doc}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs()}}} syntax
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs()}}} syntax
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/inputs_code:new-manual-inputs-code]{\emph{Chapter 20: Python Code for Manipulating task inputs via string substitution using inputs()  and  add\_inputs()}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/inputs:overview}\begin{quote}
-
-The previous chapters have been described how \emph{Ruffus} allows the \textbf{Output} names for each job
-to be generated from the \emph{Input} names via string substitution. This is how \emph{Ruffus} can
-automatically chain multiple tasks in a pipeline together seamlessly.
-
-Sometimes it is useful to be able to modify the \textbf{Input}  by string substitution
-as well. There are two situations where this additional flexibility is needed:
-\begin{enumerate}
-\item {} 
-You need to add additional prequisites or filenames to the \textbf{Input} of every single job
-
-\item {} 
-You need to add additional \textbf{Input} file names which are some variant of the existing ones.
-
-\end{enumerate}
-
-Both will be much more obvious with some examples
-\end{quote}
-
-
-\subsection{Adding additional \emph{input} prerequisites per job with \emph{add\_inputs()}}
-\label{tutorials/new_tutorial/inputs:adding-additional-input-prerequisites-per-job-with-add-inputs}
-
-\subsubsection{1. Example: compiling c++ code}
-\label{tutorials/new_tutorial/inputs:example-compiling-c-code}\begin{quote}
-
-Let us first compile some c++ (\code{"*.cpp"}) files using plain {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} syntax:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} source files exist before our pipeline}
-\PYG{n}{source\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{k}{for} \PYG{n}{source\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{source\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{source\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}filename}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{2. Example: Adding a common header file with \emph{add\_inputs()}}
-\label{tutorials/new_tutorial/inputs:example-adding-a-common-header-file-with-add-inputs}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} source files exist before our pipeline}
-\PYG{n}{source\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{k}{for} \PYG{n}{source\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{source\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{source\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} common (universal) header exists before our pipeline}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{} make header files}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}matching\PYGZus{}headers}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{c}{\PYGZsh{} add header to the input of every job}
-            \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                        \PYG{c}{\PYGZsh{} add result of task create\PYGZus{}matching\PYGZus{}headers to the input of every job}
-                       \PYG{n}{create\PYGZus{}matching\PYGZus{}headers}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}filename}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-
-    \PYG{o}{\PYGZgt{}\PYGZgt{}}\PYG{o}{\PYGZgt{}} \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-        \PYG{n}{Job}  \PYG{o}{=} \PYG{p}{[}\PYG{n}{hasty}\PYG{o}{.}\PYG{n}{cpp} \PYG{o}{\PYGZhy{}}\PYG{o}{\PYGZgt{}} \PYG{n}{hasty}\PYG{o}{.}\PYG{n}{h}\PYG{p}{]} \PYG{n}{completed}
-        \PYG{n}{Job}  \PYG{o}{=} \PYG{p}{[}\PYG{n}{messy}\PYG{o}{.}\PYG{n}{cpp} \PYG{o}{\PYGZhy{}}\PYG{o}{\PYGZgt{}} \PYG{n}{messy}\PYG{o}{.}\PYG{n}{h}\PYG{p}{]} \PYG{n}{completed}
-        \PYG{n}{Job}  \PYG{o}{=} \PYG{p}{[}\PYG{n}{tasty}\PYG{o}{.}\PYG{n}{cpp} \PYG{o}{\PYGZhy{}}\PYG{o}{\PYGZgt{}} \PYG{n}{tasty}\PYG{o}{.}\PYG{n}{h}\PYG{p}{]} \PYG{n}{completed}
-    \PYG{n}{Completed} \PYG{n}{Task} \PYG{o}{=} \PYG{n}{create\PYGZus{}matching\PYGZus{}headers}
-        \PYG{n}{Job}  \PYG{o}{=} \PYG{p}{[}\PYG{p}{[}\PYG{n}{hasty}\PYG{o}{.}\PYG{n}{cpp}\PYG{p}{,} \PYG{n}{universal}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{hasty}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{messy}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{tasty}\PYG{o}{.}\PYG{n}{h}\PYG{p}{]} \PYG{o}{\PYGZhy{}}\PYG{o}{\PYGZgt{}} \PYG{n}{hasty}\PYG{o}{.}\PYG{n}{o}\PYG{p}{]} \PYG{n}{completed}
-        \PYG{n}{Job}  \PYG{o}{=} \PYG{p}{[}\PYG{p}{[}\PYG{n}{messy}\PYG{o}{.}\PYG{n}{cpp}\PYG{p}{,} \PYG{n}{universal}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{hasty}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{messy}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{tasty}\PYG{o}{.}\PYG{n}{h}\PYG{p}{]} \PYG{o}{\PYGZhy{}}\PYG{o}{\PYGZgt{}} \PYG{n}{messy}\PYG{o}{.}\PYG{n}{o}\PYG{p}{]} \PYG{n}{completed}
-        \PYG{n}{Job}  \PYG{o}{=} \PYG{p}{[}\PYG{p}{[}\PYG{n}{tasty}\PYG{o}{.}\PYG{n}{cpp}\PYG{p}{,} \PYG{n}{universal}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{hasty}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{messy}\PYG{o}{.}\PYG{n}{h}\PYG{p}{,} \PYG{n}{tasty}\PYG{o}{.}\PYG{n}{h}\PYG{p}{]} \PYG{o}{\PYGZhy{}}\PYG{o}{\PYGZgt{}} \PYG{n}{tasty}\PYG{o}{.}\PYG{n}{o}\PYG{p}{]} \PYG{n}{completed}
-    \PYG{n}{Completed} \PYG{n}{Task} \PYG{o}{=} \PYG{n+nb}{compile}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{3. Example: Additional \emph{Input} can be tasks}
-\label{tutorials/new_tutorial/inputs:example-additional-input-can-be-tasks}\begin{quote}
-
-We can also add a task name to {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs()}}}.
-This chains the \textbf{Output}, i.e. run time results, of any previous task as
-an additional \textbf{Input} to every single job in the task.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} make header files}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}matching\PYGZus{}headers}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{c}{\PYGZsh{} add header to the input of every job}
-            \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                        \PYG{c}{\PYGZsh{} add result of task create\PYGZus{}matching\PYGZus{}headers to the input of every job}
-                       \PYG{n}{create\PYGZus{}matching\PYGZus{}headers}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}filenames}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[hasty.cpp, universal.h, hasty.h, messy.h, tasty.h] \PYGZhy{}\PYGZgt{} hasty.o] completed}
-\PYG{g+go}{    Job  = [[messy.cpp, universal.h, hasty.h, messy.h, tasty.h] \PYGZhy{}\PYGZgt{} messy.o] completed}
-\PYG{g+go}{    Job  = [[tasty.cpp, universal.h, hasty.h, messy.h, tasty.h] \PYGZhy{}\PYGZgt{} tasty.o] completed}
-\PYG{g+go}{Completed Task = compile}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{4. Example: Add corresponding files using \emph{add\_inputs()} with \emph{formatter} or \emph{regex}}
-\label{tutorials/new_tutorial/inputs:example-add-corresponding-files-using-add-inputs-with-formatter-or-regex}\begin{quote}
-
-The previous example created headers corresponding to our source files and added them
-as the \textbf{Input} to the compilation. That is generally not what you want. Instead,
-what is generally need is a way to
-\begin{enumerate}
-\item {} 
-Look up the exact corresponding header for the \emph{specific} job, and not add all
-possible files to all jobs in a task. When compiling \code{hasty.cpp}, we just need
-to add \code{hasty.h} (and \code{universal.h}).
-
-\item {} 
-Add a pre-existing file name (\code{hasty.h} already exists. Don't create it via
-another task.)
-
-\end{enumerate}
-
-This is a surprisingly common requirement: In bioinformatics sometimes DNA or RNA
-sequence files come singly in  \href{http://en.wikipedia.org/wiki/FASTQ\_format}{*.fastq}
-and sometimes in \href{http://en.wikipedia.org/wiki/DNA\_sequencing\_theory\#Pairwise\_end-sequencing}{matching pairs}:
-\code{*1.fastq, *2.fastq} etc. In the latter case, we often need to make sure that both
-sequence files are being processed in tandem. One way is to take one file name (\code{*1.fastq})
-and look up the other.
-\begin{quote}
-
-{\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs()}}} uses standard \emph{Ruffus} string substitution
-via {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} and {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} to lookup (generate) \textbf{Input} file names.
-(As a rule {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} only substitutes \textbf{Output} file names.)
-\end{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{source\PYGZus{}files}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{c}{\PYGZsh{} corresponding header for each source file}
-            \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                       \PYG{c}{\PYGZsh{} add header to the input of every job}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}filenames}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-This script gives the following output
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[hasty.cpp, hasty.h, universal.h] \PYGZhy{}\PYGZgt{} hasty.o] completed}
-\PYG{g+go}{    Job  = [[messy.cpp, messy.h, universal.h] \PYGZhy{}\PYGZgt{} messy.o] completed}
-\PYG{g+go}{    Job  = [[tasty.cpp, tasty.h, universal.h] \PYGZhy{}\PYGZgt{} tasty.o] completed}
-\PYG{g+go}{Completed Task = compile}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Replacing all input parameters with \emph{inputs()}}
-\label{tutorials/new_tutorial/inputs:replacing-all-input-parameters-with-inputs}\begin{quote}
-
-The previous examples all \emph{added} to the set of \textbf{Input} file names.
-Sometimes it is necessary to replace all the \textbf{Input} parameters altogether.
-\end{quote}
-
-
-\subsubsection{5. Example: Running matching python scripts using \emph{inputs()}}
-\label{tutorials/new_tutorial/inputs:example-running-matching-python-scripts-using-inputs}\begin{quote}
-
-Here is a contrived example: we wish to find all cython/python files which have been
-compiled into corresponding c++ source files.
-Instead of compiling the c++, we shall invoke the corresponding python scripts.
-
-Given three c++ files and their corresponding python scripts:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{source\PYGZus{}files}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-
-            \PYG{c}{\PYGZsh{} corresponding python file for each source file}
-            \PYG{n}{inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{run\PYGZus{}corresponding\PYGZus{}python}\PYG{p}{(}\PYG{n}{input\PYGZus{}filenames}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-The \emph{Ruffus} code will call each python script corresponding to their c++ counterpart:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [hasty.py \PYGZhy{}\PYGZgt{} hasty.results] completed}
-\PYG{g+go}{    Job  = [messy.py \PYGZhy{}\PYGZgt{} messy.results] completed}
-\PYG{g+go}{    Job  = [tasty.py \PYGZhy{}\PYGZgt{} tasty.results] completed}
-\PYG{g+go}{Completed Task = run\PYGZus{}corresponding\PYGZus{}python}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{on\_the\_fly!Tutorial}\index{Tutorial!on\_the\_fly}
-
-\section{\textbf{Chapter 21}: Esoteric: Generating parameters on the fly with \emph{@files}}
-\label{tutorials/new_tutorial/onthefly:index-0}\label{tutorials/new_tutorial/onthefly::doc}\label{tutorials/new_tutorial/onthefly:new-manual-on-the-fly-chapter-num-esoteric-generating-parameters-on-the-fly-with-files}\label{tutorials/new_tutorial/onthefly:new-manual-on-the-fly}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/files_ex:decorators-files-on-the-fly]{\emph{@files on-the-fly syntax in detail}}}
-
-\end{itemize}
-
-
-
-\begin{notice}{note}{Note:}
-Remember to look at the example code:
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/onthefly_code:new-manual-on-the-fly-code]{\emph{Chapter 21: Esoteric: Python Code for Generating parameters on the fly with @files}}}
-
-\end{itemize}
-\end{notice}
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/onthefly:overview}\begin{quote}
-
-The different \emph{Ruffus} {\hyperref[decorators/decorators:decorators]{\emph{decorators}}} connect up different tasks and
-generate \emph{Output} (file names) from your \emph{Input} in all sorts of different ways.
-
-However, sometimes, none of them \emph{quite} do exactly what you need. And it becomes
-necessary to generate your own \emph{Input} and \emph{Output} parameters on the fly.
-
-Although this additional flexibility comes at the cost of a lot of extra inconvenient
-code, you can continue to leverage the rest of \emph{Ruffus} functionality such as
-checking whether files are up to date or not.
-\end{quote}
-
-\index{@files!Tutorial on-the-fly parameter generation}\index{Tutorial on-the-fly parameter generation!@files}
-
-\subsection{\emph{@files} syntax}
-\label{tutorials/new_tutorial/onthefly:index-1}\label{tutorials/new_tutorial/onthefly:files-syntax}\begin{quote}
-
-To generate parameters on the fly, use the {\hyperref[decorators/files_ex:decorators-files-on-the-fly]{\emph{@files}}}
-with a {\hyperref[glossary:term-generator]{\emph{generator}}} function which yields one list / tuple of parameters per job.
-
-For example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{} generator function}
-\PYG{k}{def} \PYG{n+nf}{generate\PYGZus{}parameters\PYGZus{}on\PYGZus{}the\PYGZus{}fly}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    returns one list of parameters per job}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{parameters} \PYG{o}{=} \PYG{p}{[}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.input}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.output}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{(}\PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{)}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 1st job}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.input}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.output}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{(}\PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{4}\PYG{p}{)}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 2nd job}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.input}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.output}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{(}\PYG{l+m+mi}{5}\PYG{p}{,} \PYG{l+m+mi}{6}\PYG{p}{)}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 3rd job}
-                    \PYG{p}{]}
-    \PYG{k}{for} \PYG{n}{job\PYGZus{}parameters} \PYG{o+ow}{in} \PYG{n}{parameters}\PYG{p}{:}
-        \PYG{k}{yield} \PYG{n}{job\PYGZus{}parameters}
-
-\PYG{c}{\PYGZsh{} tell ruffus that parameters should be generated on the fly}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n}{generate\PYGZus{}parameters\PYGZus{}on\PYGZus{}the\PYGZus{}fly}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{pipeline\PYGZus{}task}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{,} \PYG{n}{output}\PYG{p}{,} \PYG{n}{extra}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-    \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{ + }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{ =\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{extra}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{p}{,} \PYG{n}{extra}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{,} \PYG{n}{extra}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{+} \PYG{n}{extra}\PYG{p}{[}\PYG{l+m [...]
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-Produces:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\end{Verbatim}
-\begin{description}
-\item[{Task = parallel\_task}] \leavevmode
-1 + 2 = 3
-Job = {[}''A'', 1, 2{]} completed
-3 + 4 = 7
-Job = {[}''B'', 3, 4{]} completed
-5 + 6 = 11
-Job = {[}''C'', 5, 6{]} completed
-
-\end{description}
-\end{quote}
-
-\begin{notice}{note}{Note:}
-Be aware that the parameter generating function may be invoked
-{\hyperref[tutorials/new_tutorial/dependencies:new-manual-dependencies-checking-multiple-times]{\emph{more than once}}}:
-* The first time to check if this part of the pipeline is up-to-date.
-* The second time when the pipeline task function is run.
-\end{notice}
-
-The resulting custom \emph{inputs}, \emph{outputs} parameters per job are
-treated normally for the purposes of checking to see if jobs are up-to-date and
-need to be re-run.
-\end{quote}
-
-
-\subsection{A Cartesian Product, all vs all example}
-\label{tutorials/new_tutorial/onthefly:a-cartesian-product-all-vs-all-example}\begin{quote}
-
-The {\hyperref[tutorials/new_tutorial/onthefly_code:new-manual-on-the-fly-code]{\emph{accompanying example}}} provides a more realistic reason why
-you would want to generate parameters on the fly. It is a fun piece of code, which generates
-N x M combinations from two sets of files as the \emph{inputs} of a pipeline stage.
-
-The \emph{inputs} / \emph{outputs} filenames are generated as a pair of nested for-loops to produce
-the N (outside loop) x M (inside loop) combinations, with the appropriate parameters
-for each job \code{yield}ed per iteration of the inner loop. The gist of this is:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Generator function}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}        N x M jobs}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{k}{def} \PYG{n+nf}{generate\PYGZus{}simulation\PYGZus{}params} \PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Custom function to generate}
-\PYG{l+s+sd}{    file names for gene/gwas simulation study}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{k}{for} \PYG{n}{sim\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{get\PYGZus{}simulation\PYGZus{}files}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{for} \PYG{p}{(}\PYG{n}{gene}\PYG{p}{,} \PYG{n}{gwas}\PYG{p}{)} \PYG{o+ow}{in} \PYG{n}{get\PYGZus{}gene\PYGZus{}gwas\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-            \PYG{n}{result\PYGZus{}file} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{.}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{.results}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{gene}\PYG{p}{,} \PYG{n}{sim\PYGZus{}file}\PYG{p}{)}
-            \PYG{k}{yield} \PYG{p}{(}\PYG{n}{gene}\PYG{p}{,} \PYG{n}{gwas}\PYG{p}{,} \PYG{n}{sim\PYGZus{}file}\PYG{p}{)}\PYG{p}{,} \PYG{n}{result\PYGZus{}file}
-
-
-
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n}{generate\PYGZus{}simulation\PYGZus{}params}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{...}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\begin{description}
-\item[{If \code{get\_gene\_gwas\_file\_pairs()} produces:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{c.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}
-\end{Verbatim}
-
-\item[{and \code{get\_gene\_gwas\_file\_pairs()} produces:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{p}{[}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.gene}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.gwas}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,} \PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.gene}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.gwas}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{]}
-\end{Verbatim}
-
-\end{description}
-
-then we would end up with \code{3} x \code{2} = \code{6} jobs and the following equivalent function calls:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.gene}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.gwas}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.gene.a.sim.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.gene}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.gwas}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.gene.a.sim.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.gene}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.gwas}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.gene.b.sim.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.gene}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.gwas}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.gene.b.sim.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.gene}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.gwas}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{c.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.gene.c.sim.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.gene}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.gwas}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{c.sim}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.gene.c.sim.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-The {\hyperref[tutorials/new_tutorial/onthefly_code:new-manual-on-the-fly-code]{\emph{accompanying code}}} looks slightly more complicated because
-of some extra bookkeeping.
-
-You can compare this approach with the alternative of using {\hyperref[decorators/product:decorators-product]{\emph{@product}}}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}        N x M jobs}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{n+nd}{@product}\PYG{p}{(}   \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{simulation\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.simulation}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-
-            \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.gene}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-
-            \PYG{c}{\PYGZsh{} add gwas as an input: looks like *.gene but with a differnt extension}
-            \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[1][0]/\PYGZob{}basename[1][0]\PYGZcb{}.gwas}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}.\PYGZob{}basename[1][0]\PYGZcb{}.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}    \PYG{c}{\PYGZsh{} output file}
-\PYG{k}{def} \PYG{n+nf}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{...}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{@parallel!Tutorial}\index{Tutorial!@parallel}
-
-\section{\textbf{Chapter 22}: Esoteric: Running jobs in parallel without files using \emph{@parallel}}
-\label{tutorials/new_tutorial/parallel:new-manual-parallel-chapter-num-esoteric-running-jobs-in-parallel-without-files-using-parallel}\label{tutorials/new_tutorial/parallel:index-0}\label{tutorials/new_tutorial/parallel::doc}\label{tutorials/new_tutorial/parallel:new-manual-deprecated-parallel}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/parallel:decorators-parallel]{\emph{@parallel}}} syntax in detail
-
-\end{itemize}
-
-
-
-
-\subsection{\textbf{@parallel}}
-\label{tutorials/new_tutorial/parallel:parallel}\begin{quote}
-
-\textbf{@parallel} supplies parameters for multiple \textbf{jobs} exactly like {\hyperref[tutorials/new_tutorial/deprecated_files:new-manual-deprecated-files]{\emph{@files}}} except that:
-\begin{enumerate}
-\item {} 
-The first two parameters are not treated like \emph{inputs} and \emph{ouputs} parameters,
-and strings are not assumed to be file names
-
-\item {} 
-Thus no checking of whether each job is up-to-date is made using \emph{inputs} and \emph{outputs} files
-
-\item {} 
-No expansions of \href{http://docs.python.org/library/glob.html}{\emph{glob}} patterns or \emph{output} from previous tasks is carried out.
-
-\end{enumerate}
-
-This syntax is most useful when a pipeline stage does not involve creating or consuming any files, and
-you wish to forego the conveniences of {\hyperref[tutorials/new_tutorial/deprecated_files:new-manual-deprecated-files]{\emph{@files}}}, {\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{@transform}}} etc.
-
-The following code performs some arithmetic in parallel:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{parameters} \PYG{o}{=} \PYG{p}{[}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 1st job}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{4}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 2nd job}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{l+m+mi}{6}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 3rd job}
-             \PYG{p}{]}
-\PYG{n+nd}{@parallel}\PYG{p}{(}\PYG{n}{parameters}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{parallel\PYGZus{}task}\PYG{p}{(}\PYG{n}{name}\PYG{p}{,} \PYG{n}{param1}\PYG{p}{,} \PYG{n}{param2}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{    Parallel task }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{: }\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{name}\PYG{p}{)}
-    \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{ + }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{ = }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{param1}\PYG{p}{,} \PYG{n}{param2}\PYG{p}{,} \PYG{n}{param1} \PYG{o}{+} \PYG{n}{param2}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{parallel\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-produces the following:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-Task = parallel\_task
-    Parallel task A: 1 + 2 = 3
-    Job = ["A", 1, 2] completed
-    Parallel task B: 3 + 4 = 7
-    Job = ["B", 3, 4] completed
-    Parallel task C: 5 + 6 = 11
-    Job = ["C", 5, 6] completed
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{check\_if\_uptodate!Tutorial}\index{Tutorial!check\_if\_uptodate}
-
-\section{\textbf{Chapter 23}: Esoteric: Writing custom functions to decide which jobs are up to date with \emph{@check\_if\_uptodate}}
-\label{tutorials/new_tutorial/check_if_uptodate:index-0}\label{tutorials/new_tutorial/check_if_uptodate:new-manual-check-if-uptodate}\label{tutorials/new_tutorial/check_if_uptodate::doc}\label{tutorials/new_tutorial/check_if_uptodate:new-manual-check-if-uptodate-chapter-num-esoteric-writing-custom-functions-to-decide-which-jobs-are-up-to-date-with-check-if-uptodate}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate  syntax in detail}}}
-
-\end{itemize}
-
-
-
-
-\subsection{\textbf{@check\_if\_uptodate} : Manual dependency checking}
-\label{tutorials/new_tutorial/check_if_uptodate:check-if-uptodate-manual-dependency-checking}\begin{quote}
-\begin{description}
-\item[{tasks specified with most decorators such as}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}
-
-\item {} 
-{\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}}
-
-\item {} 
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}}
-
-\item {} 
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@collate}}}
-
-\end{itemize}
-
-\end{description}
-
-have automatic dependency checking based on file modification times.
-
-Sometimes, you might want to decide have more control over whether to run jobs, especially
-if a task does not rely on or produce files (i.e. with {\hyperref[decorators/parallel:decorators-parallel]{\emph{@parallel}}})
-
-You can write your own custom function to decide whether to run a job.
-This takes as many parameters as your task function, and needs to return a
-tuple for whether an update is required, and why (i.e. \code{tuple(bool, str)})
-
-This simple example which creates the file \code{"a.1"} if it does not exist:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-could be rewritten more laboriously as:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{os}
-\PYG{k}{def} \PYG{n+nf}{check\PYGZus{}file\PYGZus{}exists}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{if} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{exists}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{return} \PYG{n+nb+bp}{False}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{File already exists}\PYG{l+s}{\PYGZdq{}}
-    \PYG{k}{return} \PYG{n+nb+bp}{True}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ is missing}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{output\PYGZus{}file}
-
-\PYG{n+nd}{@parallel}\PYG{p}{(}\PYG{p}{[}\PYG{p}{[}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate}\PYG{p}{(}\PYG{n}{check\PYGZus{}file\PYGZus{}exists}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\begin{description}
-\item[{Both produce the same output:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-Task = create\_if\_necessary
-    Job = [null, "a.1"] completed
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\begin{notice}{note}{Note:}
-The function specified by {\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate}}} can be called
-more than once for each job.
-
-See the {\hyperref[tutorials/new_tutorial/dependencies:new-manual-dependencies]{\emph{description here}}} of how \emph{Ruffus} decides which tasks to run.
-\end{notice}
-
-\index{flowchart colours!Tutorial}\index{Tutorial!flowchart colours}
-
-\section{\textbf{Appendix 1}: Flow Chart Colours with \emph{pipeline\_printout\_graph(...)}}
-\label{tutorials/new_tutorial/flowchart_colours:index-0}\label{tutorials/new_tutorial/flowchart_colours:new-manual-flowchart-colours-chapter-num-flow-chart-colours-with-pipeline-printout-graph}\label{tutorials/new_tutorial/flowchart_colours::doc}\label{tutorials/new_tutorial/flowchart_colours:new-manual-flowchart-colours}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph]{\emph{pipeline\_printout\_graph(...)}}}
-
-\item {} 
-\code{Download code}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/flowchart_colours_code:new-manual-flowchart-colours-code]{\emph{Code}}} for experimenting with colours
-
-\end{itemize}
-
-
-
-
-\subsection{Flowchart colours}
-\label{tutorials/new_tutorial/flowchart_colours:flowchart-colours}
-The appearance of \emph{Ruffus} flowcharts produced by {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph]{\emph{pipeline\_printout\_graph}}}
-can be extensively customised.
-
-This is mainly controlled by the {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph-user-colour-scheme]{\emph{user\_colour\_scheme}}}  (note UK spelling of ``colour'') parameter
-
-Example:
-\begin{quote}
-
-Use colour scheme index  = 1
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{flowchart.svg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{svg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{n}{final\PYGZus{}task}\PYG{p}{]}\PYG{p}{,}
-                         \PYG{n}{user\PYGZus{}colour\PYGZus{}scheme} \PYG{o}{=} \PYG{p}{\PYGZob{}}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{colour\PYGZus{}scheme\PYGZus{}index}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:}\PYG{l+m+mi}{1}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Pipeline}\PYG{l+s}{\PYGZdq{}}      \PYG{p}{:}\PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF3232}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}} \PYG{p}{\PYGZcb{}}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Key}\PYG{l+s}{\PYGZdq{}}           \PYG{p}{:}\PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Red}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                                                                  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fillcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}F6F4F4}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}} \PYG{p}{\PYGZcb{}}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Task to run}\PYG{l+s}{\PYGZdq{}}   \PYG{p}{:}\PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{linecolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}0044A0}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}} \PYG{p}{\PYGZcb{}}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Final target}\PYG{l+s}{\PYGZdq{}}  \PYG{p}{:}\PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fillcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}EFA03B}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                                                                  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{black}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                                                                  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dashed}\PYG{l+s}{\PYGZdq{}}    \PYG{p}{:} \PYG{l+m+mi}{0}           \PYG{p}{\PYGZcb{}}
-                                               \PYG{p}{\PYGZcb{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\begin{description}
-\item[{There are 8 colour schemes by setting \code{"colour\_scheme\_index"}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{flowchart.svg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{svg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{n}{final\PYGZus{}task}\PYG{p}{]}\PYG{p}{,}
-                          \PYG{n}{user\PYGZus{}colour\PYGZus{}scheme} \PYG{o}{=} \PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{colour\PYGZus{}scheme\PYGZus{}index}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:}\PYG{l+m+mi}{6}\PYG{p}{\PYGZcb{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-These colours were chosen after much fierce arguments between the authors and friends, and much
-inspiration from  \href{http://kuler.adobe.com/\#create/fromacolor}{http://kuler.adobe.com/\#create/fromacolor}. Please
-feel free to submit any additional sets of colours for our consideration.
-
-(Click here for image in \code{svg}.)
-
-\includegraphics{flowchart_colour_schemes.png}
-
-\index{Checking dependencies!Tutorial}\index{Tutorial!Checking dependencies}
-
-\section{\textbf{Appendix 2}: How dependency is checked}
-\label{tutorials/new_tutorial/dependencies:new-manual-dependencies-chapter-num-how-dependency-is-checked}\label{tutorials/new_tutorial/dependencies:index-0}\label{tutorials/new_tutorial/dependencies::doc}\label{tutorials/new_tutorial/dependencies:new-manual-dependencies}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/dependencies:overview}\begin{quote}
-
-How does \emph{Ruffus} decide how to run your pipeline?
-\begin{itemize}
-\item {} 
-In which order should pipelined functions be called?
-
-\item {} 
-Which parts of the pipeline are up-to-date and do not need to be rerun?
-
-\end{itemize}
-\end{quote}
-
-
-\subsubsection{Running all out-of-date tasks and dependents}
-\label{tutorials/new_tutorial/dependencies:running-all-out-of-date-tasks-and-dependents}\begin{quote}
-
-\scalebox{0.500000}{\includegraphics{manual_dependencies_flowchart_intro.png}}
-
-By default, \emph{Ruffus} will
-\begin{itemize}
-\item {} 
-build a flow chart (dependency tree) of pipelined tasks (functions)
-
-\item {} 
-start from the most ancestral tasks with the fewest dependencies (\code{task1} and \code{task4} in the flowchart above).
-
-\item {} 
-walk up the tree to find the first incomplete / out-of-date tasks (i.e. \code{task3} and \code{task5}.
-
-\item {} 
-start running from there
-
-\end{itemize}
-\begin{description}
-\item[{All down-stream (dependent) tasks will be re-run anyway, so we don't have to test}] \leavevmode
-whether they are up-to-date or not.
-
-\end{description}
-\phantomsection\label{tutorials/new_tutorial/dependencies:new-manual-dependencies-checking-multiple-times}
-\begin{notice}{note}{Note:}
-This means that \emph{Ruffus} \emph{may} ask any task if their jobs are out of date more than once:
-\begin{itemize}
-\item {} 
-once when deciding which parts of the pipeline have to be run
-
-\item {} 
-once just before executing the task.
-
-\end{itemize}
-\end{notice}
-
-\emph{Ruffus} tries to be clever / efficient, and does the minimal amount of querying.
-\end{quote}
-
-
-\subsubsection{Forced Reruns}
-\label{tutorials/new_tutorial/dependencies:forced-reruns}\label{tutorials/new_tutorial/dependencies:new-manual-dependencies-forced-reruns}\begin{quote}
-
-Even if a pipeline stage appears to be up to date,
-you can always force the pipeline to include from one or more task functions.
-
-This is particularly useful, for example, if the pipeline data hasn't changed but
-the analysis or computional code has.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{forcedtorun\PYGZus{}tasks} \PYG{o}{=} \PYG{p}{[}\PYG{n}{up\PYGZus{}to\PYGZus{}date\PYGZus{}task1}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-will run all tasks from \code{up\_to\_date\_task1} to \code{final\_task}
-\end{quote}
-
-Both the ``target'' and the ``forced'' lists can include as many tasks as you wish. All dependencies
-are still carried out and out-of-date jobs rerun.
-\end{quote}
-
-
-\subsubsection{Esoteric option: Minimal Reruns}
-\label{tutorials/new_tutorial/dependencies:new-manual-dependencies-minimal-reruns}\label{tutorials/new_tutorial/dependencies:esoteric-option-minimal-reruns}\begin{quote}
-
-In the above example, if we were to delete the results of \code{up\_to\_date\_task1}, \emph{Ruffus}
-would rerun \code{up\_to\_date\_task1}, \code{up\_to\_date\_task2} and \code{task3}.
-
-However, you might argue that so long as \code{up\_to\_date\_task2} is up-to-date, and it
-is the only necessary prerequisite for \code{task3}, we should not be concerned about
-\code{up\_to\_date\_task1}.
-
-This is enabled with:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{task6}\PYG{p}{]}\PYG{p}{,} \PYG{n}{gnu\PYGZus{}make\PYGZus{}maximal\PYGZus{}rebuild\PYGZus{}mode} \PYG{o}{=} \PYG{n+nb+bp}{False}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-This option walks down the dependency tree and proceeds no further when it encounters
-an up-to-date task (\code{up\_to\_date\_task2}) whatever the state of what lies beyond it.
-
-This rather dangerous option is useful if you don't want to keep all the intermediate
-files/results from upstream tasks. The pipeline will only not involve any incomplete
-tasks which precede an up-to-date result.
-
-This is seldom what you intend, and you should always check that the appropriate stages
-of the pipeline are executed in the flowchart output.
-\end{quote}
-
-\index{exceptions!Tutorial}\index{Tutorial!exceptions}
-
-\section{\textbf{Appendix 3}: Exceptions thrown inside pipelines}
-\label{tutorials/new_tutorial/exceptions:new-manual-exceptions-chapter-num-exceptions-thrown-inside-pipelines}\label{tutorials/new_tutorial/exceptions:new-manual-exceptions}\label{tutorials/new_tutorial/exceptions:index-0}\label{tutorials/new_tutorial/exceptions::doc}
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/exceptions:overview}\begin{quote}
-
-The goal for \emph{Ruffus} is that exceptions should just work \emph{out-of-the-box} without any fuss.
-This is especially important for exceptions that come from your code which may be raised
-in a different process. Often multiple parallel operations (jobs or tasks) fail at the
-same time. \emph{Ruffus} will forward each of these exceptions with the tracebacks so you
-can jump straight to the offending line.
-
-This example shows separate exceptions from two jobs running in parallel:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{d.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{e.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{throw\PYGZus{}exceptions\PYGZus{}here}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{OOPS}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+go}{    \PYGZgt{}\PYGZgt{}\PYGZgt{} pipeline\PYGZus{}run(multiprocess = 2)}
-
-\PYG{g+go}{    ruffus.ruffus\PYGZus{}exceptions.RethrownJobError:}
-
-\PYG{g+go}{    Original exceptions:}
-
-\PYG{g+go}{        Exception \PYGZsh{}1}
-\PYG{g+go}{          \PYGZsq{}exceptions.Exception(OOPS)\PYGZsq{} raised in ...}
-\PYG{g+go}{           Task = def throw\PYGZus{}exceptions\PYGZus{}here(...):}
-\PYG{g+go}{           Job  = [None \PYGZhy{}\PYGZgt{} b.start]}
-
-\PYG{g+go}{        Traceback (most recent call last):}
-\PYG{g+go}{          File \PYGZdq{}/usr/local/lib/python2.7/dist\PYGZhy{}packages/ruffus/task.py\PYGZdq{}, line 685, in run\PYGZus{}pooled\PYGZus{}job\PYGZus{}without\PYGZus{}exceptions}
-\PYG{g+go}{            return\PYGZus{}value =  job\PYGZus{}wrapper(param, user\PYGZus{}defined\PYGZus{}work\PYGZus{}func, register\PYGZus{}cleanup, touch\PYGZus{}files\PYGZus{}only)}
-\PYG{g+go}{          File \PYGZdq{}/usr/local/lib/python2.7/dist\PYGZhy{}packages/ruffus/task.py\PYGZdq{}, line 549, in job\PYGZus{}wrapper\PYGZus{}output\PYGZus{}files}
-\PYG{g+go}{            job\PYGZus{}wrapper\PYGZus{}io\PYGZus{}files(param, user\PYGZus{}defined\PYGZus{}work\PYGZus{}func, register\PYGZus{}cleanup, touch\PYGZus{}files\PYGZus{}only, output\PYGZus{}files\PYGZus{}only = True)}
-\PYG{g+go}{          File \PYGZdq{}/usr/local/lib/python2.7/dist\PYGZhy{}packages/ruffus/task.py\PYGZdq{}, line 504, in job\PYGZus{}wrapper\PYGZus{}io\PYGZus{}files}
-\PYG{g+go}{            ret\PYGZus{}val = user\PYGZus{}defined\PYGZus{}work\PYGZus{}func(*(param[1:]))}
-\PYG{g+go}{          File \PYGZdq{}\PYGZlt{}stdin\PYGZgt{}\PYGZdq{}, line 3, in throw\PYGZus{}exceptions\PYGZus{}here}
-\PYG{g+go}{        Exception: OOPS}
-
-
-\PYG{g+go}{        Exception \PYGZsh{}2}
-\PYG{g+go}{          \PYGZsq{}exceptions.Exception(OOPS)\PYGZsq{} raised in ...}
-\PYG{g+go}{           Task = def throw\PYGZus{}exceptions\PYGZus{}here(...):}
-\PYG{g+go}{           Job  = [None \PYGZhy{}\PYGZgt{} a.start]}
-
-\PYG{g+go}{        Traceback (most recent call last):}
-\PYG{g+go}{          File \PYGZdq{}/usr/local/lib/python2.7/dist\PYGZhy{}packages/ruffus/task.py\PYGZdq{}, line 685, in run\PYGZus{}pooled\PYGZus{}job\PYGZus{}without\PYGZus{}exceptions}
-\PYG{g+go}{            return\PYGZus{}value =  job\PYGZus{}wrapper(param, user\PYGZus{}defined\PYGZus{}work\PYGZus{}func, register\PYGZus{}cleanup, touch\PYGZus{}files\PYGZus{}only)}
-\PYG{g+go}{          File \PYGZdq{}/usr/local/lib/python2.7/dist\PYGZhy{}packages/ruffus/task.py\PYGZdq{}, line 549, in job\PYGZus{}wrapper\PYGZus{}output\PYGZus{}files}
-\PYG{g+go}{            job\PYGZus{}wrapper\PYGZus{}io\PYGZus{}files(param, user\PYGZus{}defined\PYGZus{}work\PYGZus{}func, register\PYGZus{}cleanup, touch\PYGZus{}files\PYGZus{}only, output\PYGZus{}files\PYGZus{}only = True)}
-\PYG{g+go}{          File \PYGZdq{}/usr/local/lib/python2.7/dist\PYGZhy{}packages/ruffus/task.py\PYGZdq{}, line 504, in job\PYGZus{}wrapper\PYGZus{}io\PYGZus{}files}
-\PYG{g+go}{            ret\PYGZus{}val = user\PYGZus{}defined\PYGZus{}work\PYGZus{}func(*(param[1:]))}
-\PYG{g+go}{          File \PYGZdq{}\PYGZlt{}stdin\PYGZgt{}\PYGZdq{}, line 3, in throw\PYGZus{}exceptions\PYGZus{}here}
-\PYG{g+go}{        Exception: OOPS}
-
-
-\PYG{g+go}{.. image:: ../../images/manual\PYGZus{}exceptions.png}
-\end{Verbatim}
-\end{quote}
-\phantomsection\label{tutorials/new_tutorial/exceptions:new-manual-exceptions-multiple-errors}
-\index{signalling}\index{interrupts}\index{break}\index{errors}\index{exceptions}\index{multiple errors}
-
-\subsection{Pipelines running in parallel accumulate Exceptions}
-\label{tutorials/new_tutorial/exceptions:index-1}\label{tutorials/new_tutorial/exceptions:pipelines-running-in-parallel-accumulate-exceptions}\begin{quote}
-
-As show above, by default \emph{Ruffus} accumulates \code{NN} exceptions before interrupting the pipeline prematurely where
-\code{NN} is the specified parallelism for {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(multiprocess = NN)}}}
-
-This seems a fair tradeoff between being able to gather detailed error information for
-running jobs, and not wasting too much time for a task that is going to fail anyway.
-\end{quote}
-
-
-\subsection{Terminate pipeline immediately upon Exceptions}
-\label{tutorials/new_tutorial/exceptions:terminate-pipeline-immediately-upon-exceptions}
-
-\subsubsection{Set \emph{pipeline\_run(exceptions\_terminate\_immediately = True)}}
-\label{tutorials/new_tutorial/exceptions:set-pipeline-run-exceptions-terminate-immediately-true}\begin{quote}
-
-To have all exceptions interrupt the pipeline immediately, invoke:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{exceptions\PYGZus{}terminate\PYGZus{}immediately} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-For example, with this change, only a single exception will be thrown before the pipeline is interrupted:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{d.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{e.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{throw\PYGZus{}exceptions\PYGZus{}here}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{OOPS}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{,} \PYG{n}{exceptions\PYGZus{}terminate\PYGZus{}immediately} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+go}{    \PYGZgt{}\PYGZgt{}\PYGZgt{} pipeline\PYGZus{}run(multiprocess = 2)}
-
-\PYG{g+go}{    ruffus.ruffus\PYGZus{}exceptions.RethrownJobError:}
-
-\PYG{g+go}{    Original exception:}
-
-\PYG{g+go}{        Exception \PYGZsh{}1}
-\PYG{g+go}{          \PYGZsq{}exceptions.Exception(OOPS)\PYGZsq{} raised in ...}
-\PYG{g+go}{           Task = def throw\PYGZus{}exceptions\PYGZus{}here(...):}
-\PYG{g+go}{           Job  = [None \PYGZhy{}\PYGZgt{} a.start]}
-
-\PYG{g+go}{        Traceback (most recent call last):}
-\PYG{g+go}{          [Tedious traceback snipped out!!!....]}
-\PYG{g+go}{        Exception: OOPS}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{raise \texttt{Ruffus.JobSignalledBreak}}
-\label{tutorials/new_tutorial/exceptions:raise-ruffus-jobsignalledbreak}\begin{quote}
-
-The same can be accomplished on a finer scale by throwing the \code{Ruffus.JobSignalledBreak} Exception. Unlike
-other exceptions, this causes an immediate halt in pipeline execution. If there are other exceptions in play at that
-point, they will be rethrown in the main process but no new exceptions will be added.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{d.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{e.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{throw\PYGZus{}exceptions\PYGZus{}here}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{raise} \PYG{n}{JobSignalledBreak}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{OOPS}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Display exceptions as they occur}
-\label{tutorials/new_tutorial/exceptions:display-exceptions-as-they-occur}\begin{quote}
-
-In the following example, the jobs throw exceptions
-at two second staggered intervals into the job. With \code{log\_exceptions = True}, the
-exceptions are displayed as they occur even though the pipeline continues running.
-
-logger.error(...) will be invoked with the string representation of the each exception, and associated stack trace.
-
-The default logger prints to sys.stderr, but as usual can be changed to any class from the logging module or compatible object via
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(logger = XXX)}}}
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{time}\PYG{o}{,} \PYG{n+nn}{os}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{3.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{4.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{5.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{throw\PYGZus{}exceptions\PYGZus{}here}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{delay} \PYG{o}{=} \PYG{n+nb}{int}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{splitext}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{)}
-    \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{n}{delay} \PYG{o}{*} \PYG{l+m+mi}{2}\PYG{p}{)}
-    \PYG{k}{raise} \PYG{n}{JobSignalledBreak}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{OOPS}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{log\PYGZus{}exceptions} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{Ruffus names list!Tutorial}\index{Tutorial!Ruffus names list}
-
-\section{\textbf{Appendix 4}: Names exported from Ruffus}
-\label{tutorials/new_tutorial/list_of_ruffus_names:new-manual-ruffus-names-chapter-num-names-exported-from-ruffus}\label{tutorials/new_tutorial/list_of_ruffus_names:index-0}\label{tutorials/new_tutorial/list_of_ruffus_names::doc}\label{tutorials/new_tutorial/list_of_ruffus_names:new-manual-ruffus-names}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Ruffus Names}
-\label{tutorials/new_tutorial/list_of_ruffus_names:ruffus-names}\begin{quote}
-
-This is a list of all the names \emph{Ruffus} makes available:
-
-\begin{tabular}{|p{0.475\linewidth}|p{0.475\linewidth}|}
-\hline
-\textbf{\relax 
-Category
-} & \textbf{\relax 
-Manual
-}\\\hline
-
-\textbf{Pipeline functions}
- & 
-\begin{DUlineblock}{0em}
-\item[] {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout()}}} ({\hyperref[tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout]{\emph{Manual}}})
-\item[] {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph]{\emph{pipeline\_printout()}}} ({\hyperref[tutorials/new_tutorial/pipeline_printout_graph:new-manual-pipeline-printout-graph]{\emph{Manual}}})
-\item[] {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_printout()}}} ({\hyperref[tutorials/new_tutorial/introduction:new-manual-pipeline-run]{\emph{Manual}}})
-\end{DUlineblock}
-\\\hline
-
-\textbf{Decorators}
- & 
-\begin{DUlineblock}{0em}
-\item[] {\hyperref[decorators/active_if:decorators-active-if]{\emph{@active\_if}}} ({\hyperref[tutorials/new_tutorial/active_if:new-manual-active-if]{\emph{Manual}}})
-\item[] {\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate}}} ({\hyperref[tutorials/new_tutorial/check_if_uptodate:new-manual-check-if-uptodate]{\emph{Manual}}})
-\item[] {\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} ({\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-collate]{\emph{Manual}}})
-\item[] {\hyperref[decorators/files:decorators-files]{\emph{@files}}} ({\hyperref[tutorials/new_tutorial/deprecated_files:new-manual-deprecated-files]{\emph{Manual}}})
-\item[] {\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}} ({\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-follows]{\emph{Manual}}})
-\item[] {\hyperref[decorators/jobs_limit:decorators-jobs-limit]{\emph{@jobs\_limit}}} ({\hyperref[tutorials/new_tutorial/multiprocessing:new-manual-jobs-limit]{\emph{Manual}}})
-\item[] {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} ({\hyperref[tutorials/new_tutorial/merge:new-manual-merge]{\emph{Manual}}})
-\item[] {\hyperref[decorators/mkdir:decorators-mkdir]{\emph{@mkdir}}} ({\hyperref[tutorials/new_tutorial/mkdir:new-manual-mkdir]{\emph{Manual}}})
-\item[] {\hyperref[decorators/originate:decorators-originate]{\emph{@originate}}} ({\hyperref[tutorials/new_tutorial/originate:new-manual-originate]{\emph{Manual}}})
-\item[] {\hyperref[decorators/parallel:decorators-parallel]{\emph{@parallel}}} ({\hyperref[tutorials/new_tutorial/parallel:new-manual-deprecated-parallel]{\emph{Manual}}})
-\item[] {\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} ({\hyperref[tutorials/new_tutorial/posttask:new-manual-posttask]{\emph{Manual}}})
-\item[] {\hyperref[decorators/split:decorators-split]{\emph{@split}}} ({\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{Manual}}})
-\item[] {\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}} ({\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-subdivide]{\emph{Manual}}})
-\item[] {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} ({\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{Manual}}})
-\item[] {\hyperref[decorators/files_re:decorators-files-re]{\emph{@files\_re}}} ({\hyperref[tutorials/new_tutorial/deprecated_files_re:new-manual-deprecated-files-re]{\emph{Manual}}})
-\end{DUlineblock}
-\\\hline
-
-\textbf{Loggers}
- & 
-\begin{DUlineblock}{0em}
-\item[] stderr\_logger
-\item[] black\_hole\_logger
-\end{DUlineblock}
-\\\hline
-
-\textbf{Parameter disambiguating Indicators}
- & 
-\begin{DUlineblock}{0em}
-\item[] {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} ({\hyperref[tutorials/new_tutorial/output_file_names:new-manual-suffix]{\emph{Manual}}})
-\item[] {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} ({\hyperref[tutorials/new_tutorial/output_file_names:new-manual-regex]{\emph{Manual}}})
-\item[] {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} ({\hyperref[tutorials/new_tutorial/output_file_names:new-manual-formatter]{\emph{Manual}}})
-\item[] {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} ({\hyperref[tutorials/new_tutorial/inputs:new-manual-inputs]{\emph{Manual}}})
-\item[] {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{inputs}}} ({\hyperref[tutorials/new_tutorial/inputs:new-manual-inputs]{\emph{Manual}}})
-\item[] {\hyperref[decorators/indicator_objects:decorators-touch-file]{\emph{touch\_file}}} ({\hyperref[tutorials/new_tutorial/posttask:new-manual-posttask-touch-file]{\emph{Manual}}})
-\item[] {\hyperref[decorators/indicator_objects:decorators-combine]{\emph{combine}}}
-\item[] {\hyperref[decorators/follows:decorators-follows-mkdir]{\emph{mkdir}}} ({\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-follows-mkdir]{\emph{Manual}}})
-\item[] {\hyperref[decorators/indicator_objects:decorators-output-from]{\emph{output\_from}}} ({\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-output-from]{\emph{Manual}}})
-\end{DUlineblock}
-\\\hline
-
-\textbf{Decorators in ruffus.combinatorics}
- & 
-\begin{DUlineblock}{0em}
-\item[] {\hyperref[decorators/combinations:decorators-combinations]{\emph{@combinations}}} ({\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinations]{\emph{Manual}}})
-\item[] {\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}} ({\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinations-with-replacement]{\emph{Manual}}})
-\item[] {\hyperref[decorators/permutations:decorators-permutations]{\emph{@permutations}}} ({\hyperref[tutorials/new_tutorial/combinatorics:new-manual-permutations]{\emph{Manual}}})
-\item[] {\hyperref[decorators/product:decorators-product]{\emph{@product}}} ({\hyperref[tutorials/new_tutorial/combinatorics:new-manual-product]{\emph{Manual}}})
-\end{DUlineblock}
-\\\hline
-
-\textbf{Decorators in ruffus.cmdline}
- & 
-\begin{DUlineblock}{0em}
-\item[] {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline-get-argparse]{\emph{get\_argparse}}}
-\item[] {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline-setup-logging]{\emph{setup\_logging}}}
-\item[] {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline-run]{\emph{run}}}
-\item[] {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline-message]{\emph{MESSAGE}}}
-\end{DUlineblock}
-\\\hline
-\end{tabular}
-
-\end{quote}
-
-\index{deprecated @files!Tutorial}\index{Tutorial!deprecated @files}
-
-\section{\textbf{Appendix 5}: \textbf{@files}: Deprecated syntax}
-\label{tutorials/new_tutorial/deprecated_files:new-manual-deprecated-files}\label{tutorials/new_tutorial/deprecated_files:index-0}\label{tutorials/new_tutorial/deprecated_files::doc}\label{tutorials/new_tutorial/deprecated_files:new-manual-deprecated-files-chapter-num-files-deprecated-syntax}
-\begin{notice}{warning}{Warning:}\begin{itemize}
-\item {} 
-\textbf{This is deprecated syntax}
-
-\textbf{which is no longer supported and}
-
-\textbf{should NOT be used in new code.}
-
-\end{itemize}
-\end{notice}
-
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{decorators}}}
-
-\item {} 
-{\hyperref[decorators/files:decorators-files]{\emph{@files}}} syntax in detail
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/deprecated_files:overview}\begin{quote}
-
-\begin{DUlineblock}{0em}
-\item[] The python functions which do the actual work of each stage  or
-{\hyperref[glossary:term-task]{\emph{task}}} of a \emph{Ruffus} pipeline are written by you.
-\item[] The role of \emph{Ruffus} is to make sure these functions are called in the right order,
-with the right parameters, running in parallel using multiprocessing if desired.
-\end{DUlineblock}
-
-The easiest way to specify parameters to \emph{Ruffus} {\hyperref[glossary:term-task]{\emph{task}}} functions is to use
-the {\hyperref[decorators/files:decorators-files]{\emph{@files}}} decorator.
-
-\index{@files!Manual}\index{Manual!@files}\end{quote}
-
-
-\subsection{\textbf{@files}}
-\label{tutorials/new_tutorial/deprecated_files:files}\label{tutorials/new_tutorial/deprecated_files:index-1}\begin{quote}
-
-Running this code:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{single\PYGZus{}job\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfiles}\PYG{p}{,} \PYG{n}{text}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{o} \PYG{o+ow}{in} \PYG{n}{outfiles}\PYG{p}{:} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{o}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} prepare input file}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\begin{description}
-\item[{Is equivalent to calling:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{single\PYGZus{}job\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\item[{And produces:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job = [a.1 \PYGZhy{}\PYGZgt{} [a.2, b.2], A file] completed}
-\PYG{g+go}{Completed Task = single\PYGZus{}job\PYGZus{}io\PYGZus{}task}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\emph{Ruffus} will automatically check if your task is up to date. The second time {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run()}}}
-is called, nothing will happen. But if you update \code{a.1}, the task will rerun:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job = [a.1 \PYGZhy{}\PYGZgt{} [a.2, b.2], A file] completed}
-\PYG{g+go}{Completed Task = single\PYGZus{}job\PYGZus{}io\PYGZus{}task}
-\end{Verbatim}
-\end{quote}
-
-See {\hyperref[tutorials/new_tutorial/checkpointing:new-manual-skip-up-to-date-rules]{\emph{chapter 2}}} for a more in-depth discussion of how \emph{Ruffus}
-decides which parts of the pipeline are complete and up-to-date.
-\end{quote}
-
-\index{@files!in parallel}\index{in parallel!@files}
-
-\subsection{Running the same code on different parameters in parallel}
-\label{tutorials/new_tutorial/deprecated_files:new-manual-files-parallel}\label{tutorials/new_tutorial/deprecated_files:index-2}\label{tutorials/new_tutorial/deprecated_files:running-the-same-code-on-different-parameters-in-parallel}\begin{quote}
-
-Your pipeline may require the same function to be called multiple times on independent parameters.
-In which case, you can supply all the parameters to @files, each will be sent to separate jobs that
-may run in parallel if necessary. \emph{Ruffus} will check if each separate {\hyperref[glossary:term-job]{\emph{job}}} is up-to-date using
-the \emph{inputs} and \emph{outputs} (first two) parameters (See the {\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-only-rerun-out-of-date]{\emph{Up-to-date jobs are not re-run unnecessarily}}} ).
-
-For example, if a sequence
-(e.g. a list or tuple) of 5 parameters are passed to \textbf{@files}, that indicates
-there will also be 5 separate jobs:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{parameters} \PYG{o}{=} \PYG{p}{[}
-                    \PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.file}\PYG{l+s}{\PYGZsq{}}           \PYG{p}{]}\PYG{p}{,}             \PYG{c}{\PYGZsh{} 1st job}
-                    \PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{4}        \PYG{p}{]}\PYG{p}{,}             \PYG{c}{\PYGZsh{} 2st job}
-                    \PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}   \PYG{p}{]}\PYG{p}{,}             \PYG{c}{\PYGZsh{} 3st job}
-                    \PYG{p}{[} \PYG{l+m+mi}{67}\PYG{p}{,} \PYG{p}{[}\PYG{l+m+mi}{13}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job4.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]} \PYG{p}{]}\PYG{p}{,}             \PYG{c}{\PYGZsh{} 4st job}
-                    \PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job5.file}\PYG{l+s}{\PYGZsq{}}           \PYG{p}{]}\PYG{p}{,}             \PYG{c}{\PYGZsh{} 5st job}
-              \PYG{p}{]}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n}{parameters}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task\PYGZus{}file}\PYG{p}{(}\PYG{o}{*}\PYG{n}{params}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-\begin{DUlineblock}{0em}
-\item[] \emph{Ruffus} creates as many jobs as there are elements in \code{parameters}.
-\item[] In turn, each of these elements consist of series of parameters which will be
-passed to each separate job.
-\end{DUlineblock}
-
-Thus the above code is equivalent to calling:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{task\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{n}{task\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{4}\PYG{p}{)}
-\PYG{n}{task\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}\PYG{p}{)}
-\PYG{n}{task\PYGZus{}file}\PYG{p}{(}\PYG{l+m+mi}{67}\PYG{p}{,} \PYG{p}{[}\PYG{l+m+mi}{13}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job4.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{n}{task\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job5.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-What \code{task\_file()} does with these parameters is up to you!
-
-The only constraint on the parameters is that \emph{Ruffus} will treat any first
-parameter of each job as the \emph{inputs} and any second as the \emph{output}. Any
-strings in the \emph{inputs} or \emph{output} parameters (including those nested in sequences)
-will be treated as file names.
-
-Thus, to pick the parameters out of one of the above jobs:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{task\PYGZus{}file}\PYG{p}{(}\PYG{l+m+mi}{67}\PYG{p}{,} \PYG{p}{[}\PYG{l+m+mi}{13}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job4.file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{DUlineblock}{0em}
-\item[] \emph{inputs}  == \code{67}
-\item[] \emph{outputs} == \code{{[}13, 'job4.file'{]}}
-\item[] 
-\item[]
-\begin{DUlineblock}{\DUlineblockindent}
-\item[] The solitary output filename is \code{job4.file}
-\end{DUlineblock}
-\end{DUlineblock}
-\end{quote}
-\end{quote}
-
-\index{@files!check if up to date}\index{check if up to date!@files}\phantomsection\label{tutorials/new_tutorial/deprecated_files:new-manual-files-is-uptodate}
-
-\subsubsection{Checking if jobs are up to date}
-\label{tutorials/new_tutorial/deprecated_files:new-manual-files-is-uptodate}\label{tutorials/new_tutorial/deprecated_files:checking-if-jobs-are-up-to-date}\label{tutorials/new_tutorial/deprecated_files:new-manual-files-example}\label{tutorials/new_tutorial/deprecated_files:index-3}\begin{quote}
-
-\begin{DUlineblock}{0em}
-\item[] Usually we do not want to run all the stages in a pipeline but only where
-the input data has changed or is no longer up to date.
-\item[] One easy way to do this is to check the modification times for files produced
-at each stage of the pipeline.
-\end{DUlineblock}
-
-\begin{DUlineblock}{0em}
-\item[] Let us first create our starting files \code{a.1} and \code{b.1}
-\item[] We can then run the following pipeline function to create
-\end{DUlineblock}
-\begin{quote}
-\begin{itemize}
-\item {} 
-\code{a.2} from \code{a.1} and
-
-\item {} 
-\code{b.2} from \code{b.1}
-
-\end{itemize}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} create starting files}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{parameters} \PYG{o}{=} \PYG{p}{[}
-                    \PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 1st job}
-                    \PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 2nd job}
-              \PYG{p}{]}
-
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n}{parameters}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{,} \PYG{n}{text}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} copy infile contents to outfile}
-    \PYG{n}{infile\PYGZus{}text} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)}
-    \PYG{n}{f} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{infile\PYGZus{}text} \PYG{o}{+} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{+} \PYG{n}{text}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\begin{description}
-\item[{This produces the following output:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job = [a.1 \PYGZhy{}\PYGZgt{} a.2, A file] completed}
-\PYG{g+go}{    Job = [b.1 \PYGZhy{}\PYGZgt{} b.2, B file] completed}
-\PYG{g+go}{Completed Task = parallel\PYGZus{}io\PYGZus{}task}
-\end{Verbatim}
-
-\end{description}
-
-\begin{DUlineblock}{0em}
-\item[] If you called {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run()}}} again, nothing would happen because the files are up to date:
-\item[] \code{a.2} is more recent than \code{a.1} and
-\item[] \code{b.2} is more recent than \code{b.1}
-\end{DUlineblock}
-\begin{description}
-\item[{However, if you subsequently modified \code{a.1} again:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{1}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-you would see the following:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\PYG{g+go}{Task = parallel\PYGZus{}io\PYGZus{}task}
-\PYG{g+go}{    Job = [\PYGZdq{}a.1\PYGZdq{} \PYGZhy{}\PYGZgt{} \PYGZdq{}a.2\PYGZdq{}, \PYGZdq{}A file\PYGZdq{}] completed}
-\PYG{g+go}{    Job = [\PYGZdq{}b.1\PYGZdq{} \PYGZhy{}\PYGZgt{} \PYGZdq{}b.2\PYGZdq{}, \PYGZdq{}B file\PYGZdq{}] unnecessary: already up to date}
-\PYG{g+go}{Completed Task = parallel\PYGZus{}io\PYGZus{}task}
-\end{Verbatim}
-
-The 2nd job is up to date and will be skipped.
-\end{quote}
-
-\index{deprecated @files\_re!Tutorial}\index{Tutorial!deprecated @files\_re}
-
-\section{\textbf{Appendix 6}: \textbf{@files\_re}: Deprecated \emph{syntax using regular expressions}}
-\label{tutorials/new_tutorial/deprecated_files_re:new-manual-deprecated-files-re}\label{tutorials/new_tutorial/deprecated_files_re:index-0}\label{tutorials/new_tutorial/deprecated_files_re::doc}\label{tutorials/new_tutorial/deprecated_files_re:new-manual-deprecated-files-re-chapter-num-files-re-deprecated-syntax-using-regular-expressions}
-\begin{notice}{warning}{Warning:}\begin{itemize}
-\item {} 
-\textbf{This is deprecated syntax}
-
-\textbf{which is no longer supported and}
-
-\textbf{should NOT be used in new code.}
-
-\end{itemize}
-\end{notice}
-
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{decorators}}}
-
-\item {} 
-{\hyperref[decorators/files_re:decorators-files-re]{\emph{@files\_re}}} syntax in detail
-
-\end{itemize}
-
-
-
-
-\subsection{Overview}
-\label{tutorials/new_tutorial/deprecated_files_re:overview}\begin{quote}
-
-\textbf{@files\_re} combines the functionality of @transform, @collate and @merge in
-one overloaded decorator.
-
-This is the reason why its use is discouraged. \textbf{@files\_re} syntax is far too overloaded
-and context-dependent to support its myriad of different functions.
-
-The following documentation is provided to help maintain historical \emph{Ruffus} usage.
-\end{quote}
-
-
-\subsubsection{Transforming input and output filenames}
-\label{tutorials/new_tutorial/deprecated_files_re:transforming-input-and-output-filenames}\begin{quote}
-
-For example, the following code takes files from
-the previous pipeline task, and makes new output parameters with the \code{.sums} suffix
-in place of the \code{.chunks} suffix:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{step\PYGZus{}4\PYGZus{}split\PYGZus{}numbers\PYGZus{}into\PYGZus{}chunks}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{step\PYGZus{}5\PYGZus{}calculate\PYGZus{}sum\PYGZus{}of\PYGZus{}squares} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   calculate sums and sums of squares for all values in the input\PYGZus{}file\PYGZus{}name}
-    \PYG{c}{\PYGZsh{}       writing to output\PYGZus{}file\PYGZus{}name}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-This can be written using @files\_re equivalently:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- at files\_re(step\_4\_split\_numbers\_into\_chunks, r".chunks", r".sums")
-def step\_5\_calculate\_sum\_of\_squares (input\_file\_name, output\_file\_name):
-""
-\end{Verbatim}
-\end{quote}
-\end{quote}
-\phantomsection\label{tutorials/new_tutorial/deprecated_files_re:new-manual-files-re-combine}
-\index{combine!Manual}\index{Manual!combine}
-
-\subsubsection{Collating many \emph{inputs} into a single \emph{output}}
-\label{tutorials/new_tutorial/deprecated_files_re:collating-many-inputs-into-a-single-output}\label{tutorials/new_tutorial/deprecated_files_re:index-1}\begin{quote}
-
-Similarly, the following code collects \textbf{inputs}
-from the same species in the same directory:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@collate}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{*.animals}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} inputs = all *.animal files}
-            \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{mammals.([\PYGZca{}.]+)}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,}    \PYG{c}{\PYGZsh{} regular expression}
-            \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/animals.in\PYGZus{}my\PYGZus{}zoo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}      \PYG{c}{\PYGZsh{} single output file per species}
-            \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZsq{}} \PYG{p}{)}                       \PYG{c}{\PYGZsh{} species name}
-\PYG{k}{def} \PYG{n+nf}{capture\PYGZus{}mammals}\PYG{p}{(}\PYG{n}{infiles}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{,} \PYG{n}{species}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} summarise all animals of this species}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-This can be written using @files\_re equivalently using the {\hyperref[decorators/indicator_objects:decorators-combine]{\emph{combine}}} indicator:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@files\PYGZus{}re}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{*.animals}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}                           \PYG{c}{\PYGZsh{} inputs = all *.animal files}
-            \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{mammals.([\PYGZca{}.]+)}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}                  \PYG{c}{\PYGZsh{} regular expression}
-            \PYG{n}{combine}\PYG{p}{(}\PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/animals.in\PYGZus{}my\PYGZus{}zoo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,}    \PYG{c}{\PYGZsh{} single output file per species}
-            \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZsq{}} \PYG{p}{)}                              \PYG{c}{\PYGZsh{} species name}
-\PYG{k}{def} \PYG{n+nf}{capture\PYGZus{}mammals}\PYG{p}{(}\PYG{n}{infiles}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{,} \PYG{n}{species}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} summarise all animals of this species}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Generating \emph{input} and \emph{output} parameter using regular expresssions}
-\label{tutorials/new_tutorial/deprecated_files_re:generating-input-and-output-parameter-using-regular-expresssions}\begin{quote}
-
-The following code generates additional
-\emph{input} prerequisite file names which match the original \emph{input} files.
-
-We want each job of our \code{analyse()} function to get corresponding pairs
-of \code{xx.chunks} and \code{xx.red\_indian} files when
-\begin{quote}
-
-\code{*.chunks} are generated by the task function \code{split\_up\_problem()} and
-\code{*.red\_indian} are generated by the task function \code{make\_red\_indians()}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{make\PYGZus{}red\PYGZus{}indians}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{split\PYGZus{}up\PYGZus{}problem}\PYG{p}{,}                \PYG{c}{\PYGZsh{} starting set of *inputs*}
-            \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*).chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}          \PYG{c}{\PYGZsh{} regular expression}
-            \PYG{n}{inputs}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}0\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}               \PYG{c}{\PYGZsh{} xx.chunks}
-                    \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.red\PYGZus{}indian}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}\PYG{p}{,}     \PYG{c}{\PYGZsh{} important.file}
-             \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.results}\PYG{l+s}{\PYGZdq{}}                  \PYG{c}{\PYGZsh{} xx.results}
-              \PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{analyse}\PYG{p}{(}\PYG{n}{input\PYGZus{}filenames}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Do analysis here}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-The equivalent code using @files\_re looks very similar:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- at follows(make\_red\_indians)
- at files\_re( split\_up\_problem,        \# starting set of *inputs*
-           r"(.*).chunks",          \# regular expression
-           [r"\PYGZbs{}g\textless{}0\textgreater{}",               \# xx.chunks
-            r"\PYGZbs{}1.red\_indian"]),     \# important.file
-             r"\PYGZbs{}1.results")         \# xx.results
-def analyse(input\_filenames, output\_file\_name):
-    "Do analysis here"
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-Example code for:
-
-
-\section{\textbf{Chapter 1}: Python Code for An introduction to basic Ruffus syntax}
-\label{tutorials/new_tutorial/introduction_code:new-manual-introduction-code}\label{tutorials/new_tutorial/introduction_code:new-manual-introduction-chapter-num-python-code-for-an-introduction-to-basic-ruffus-syntax}\label{tutorials/new_tutorial/introduction_code::doc}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform syntax in detail}}}
-
-\item {} 
-Back to \textbf{Chapter 1}: {\hyperref[tutorials/new_tutorial/introduction:new-manual-introduction]{\emph{An introduction to basic Ruffus syntax}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Your first Ruffus script}
-\label{tutorials/new_tutorial/introduction_code:your-first-ruffus-script}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{p}{:}\PYG{p}{:}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   The starting data files would normally exist beforehand!}
-\PYG{c}{\PYGZsh{}       We create some empty files for this example}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{starting\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-
-\PYG{k}{for} \PYG{n}{ff} \PYG{o+ow}{in} \PYG{n}{starting\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{ff}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 1 fasta\PYGZhy{}\PYGZgt{}sam}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{starting\PYGZus{}files}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} Input = starting files}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.fasta}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                  \PYG{c}{\PYGZsh{}         suffix = .fasta}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                            \PYG{c}{\PYGZsh{} Output  suffix = .sam}
-\PYG{k}{def} \PYG{n+nf}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                    \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 2 sam\PYGZhy{}\PYGZgt{}bam}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{,}                   \PYG{c}{\PYGZsh{} Input = previous stage}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{}         suffix = .sam}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                            \PYG{c}{\PYGZsh{} Output  suffix = .bam}
-\PYG{k}{def} \PYG{n+nf}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                      \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 3 bam\PYGZhy{}\PYGZgt{}statistics}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{,}                  \PYG{c}{\PYGZsh{} Input = previous stage}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{}         suffix = .bam}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.statistics}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} Output  suffix = .statistics}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{use\PYGZus{}linear\PYGZus{}model}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                \PYG{c}{\PYGZsh{} Extra statistics parameter}
-\PYG{k}{def} \PYG{n+nf}{summarise\PYGZus{}bam\PYGZus{}file}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                       \PYG{n}{output\PYGZus{}file}\PYG{p}{,}
-                       \PYG{n}{extra\PYGZus{}stats\PYGZus{}parameter}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Sketch of real analysis function}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Resulting Output}
-\label{tutorials/new_tutorial/introduction_code:resulting-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [a.fasta \PYGZhy{}\PYGZgt{} a.sam] completed}
-\PYG{g+go}{    Job  = [b.fasta \PYGZhy{}\PYGZgt{} b.sam] completed}
-\PYG{g+go}{    Job  = [c.fasta \PYGZhy{}\PYGZgt{} c.sam] completed}
-\PYG{g+go}{Completed Task = map\PYGZus{}dna\PYGZus{}sequence}
-\PYG{g+go}{    Job  = [a.sam \PYGZhy{}\PYGZgt{} a.bam] completed}
-\PYG{g+go}{    Job  = [b.sam \PYGZhy{}\PYGZgt{} b.bam] completed}
-\PYG{g+go}{    Job  = [c.sam \PYGZhy{}\PYGZgt{} c.bam] completed}
-\PYG{g+go}{Completed Task = compress\PYGZus{}sam\PYGZus{}file}
-\PYG{g+go}{    Job  = [a.bam \PYGZhy{}\PYGZgt{} a.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{    Job  = [b.bam \PYGZhy{}\PYGZgt{} b.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{    Job  = [c.bam \PYGZhy{}\PYGZgt{} c.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{Completed Task = summarise\PYGZus{}bam\PYGZus{}file}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 1}: Python Code for Transforming data in a pipeline with \texttt{@transform}}
-\label{tutorials/new_tutorial/transform_code:new-manual-transform-code}\label{tutorials/new_tutorial/transform_code::doc}\label{tutorials/new_tutorial/transform_code:new-manual-introduction-chapter-num-python-code-for-transforming-data-in-a-pipeline-with-transform}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform syntax in detail}}}
-
-\item {} 
-Back to \textbf{Chapter 2}: {\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{Transforming data in a pipeline with @transform}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Your first Ruffus script}
-\label{tutorials/new_tutorial/transform_code:your-first-ruffus-script}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   The starting data files would normally exist beforehand!}
-\PYG{c}{\PYGZsh{}       We create some empty files for this example}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{starting\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.2.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                  \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.2.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                  \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.2.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{]}
-
-
-\PYG{k}{for} \PYG{n}{ff\PYGZus{}pair} \PYG{o+ow}{in} \PYG{n}{starting\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{ff\PYGZus{}pair}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{ff\PYGZus{}pair}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 1 fasta\PYGZhy{}\PYGZgt{}sam}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{starting\PYGZus{}files}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} Input = starting files}
-           \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.1.fastq}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                 \PYG{c}{\PYGZsh{}         suffix = .1.fastq}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                             \PYG{c}{\PYGZsh{} Output  suffix = .sam}
-\PYG{k}{def} \PYG{n+nf}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,}
-                    \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} remember there are two input files now}
-    \PYG{n}{ii1} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{)}
-    \PYG{n}{ii2} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 2 sam\PYGZhy{}\PYGZgt{}bam}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{map\PYGZus{}dna\PYGZus{}sequence}\PYG{p}{,}                   \PYG{c}{\PYGZsh{} Input = previous stage}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{}         suffix = .sam}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                            \PYG{c}{\PYGZsh{} Output  suffix = .bam}
-\PYG{k}{def} \PYG{n+nf}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                      \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   STAGE 3 bam\PYGZhy{}\PYGZgt{}statistics}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{compress\PYGZus{}sam\PYGZus{}file}\PYG{p}{,}                  \PYG{c}{\PYGZsh{} Input = previous stage}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{}         suffix = .bam}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.statistics}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} Output  suffix = .statistics}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{use\PYGZus{}linear\PYGZus{}model}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                \PYG{c}{\PYGZsh{} Extra statistics parameter}
-\PYG{k}{def} \PYG{n+nf}{summarise\PYGZus{}bam\PYGZus{}file}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                       \PYG{n}{output\PYGZus{}file}\PYG{p}{,}
-                       \PYG{n}{extra\PYGZus{}stats\PYGZus{}parameter}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Sketch of real analysis function}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{ii} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}
-    \PYG{n}{oo} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Resulting Output}
-\label{tutorials/new_tutorial/transform_code:resulting-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[a.1.fastq, a.2.fastq] \PYGZhy{}\PYGZgt{} a.sam] completed}
-\PYG{g+go}{    Job  = [[b.1.fastq, b.2.fastq] \PYGZhy{}\PYGZgt{} b.sam] completed}
-\PYG{g+go}{    Job  = [[c.1.fastq, c.2.fastq] \PYGZhy{}\PYGZgt{} c.sam] completed}
-\PYG{g+go}{Completed Task = map\PYGZus{}dna\PYGZus{}sequence}
-\PYG{g+go}{    Job  = [a.sam \PYGZhy{}\PYGZgt{} a.bam] completed}
-\PYG{g+go}{    Job  = [b.sam \PYGZhy{}\PYGZgt{} b.bam] completed}
-\PYG{g+go}{    Job  = [c.sam \PYGZhy{}\PYGZgt{} c.bam] completed}
-\PYG{g+go}{Completed Task = compress\PYGZus{}sam\PYGZus{}file}
-\PYG{g+go}{    Job  = [a.bam \PYGZhy{}\PYGZgt{} a.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{    Job  = [b.bam \PYGZhy{}\PYGZgt{} b.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{    Job  = [c.bam \PYGZhy{}\PYGZgt{} c.statistics, use\PYGZus{}linear\PYGZus{}model] completed}
-\PYG{g+go}{Completed Task = summarise\PYGZus{}bam\PYGZus{}file}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 3}: Python Code for More on \texttt{@transform}-ing data}
-\label{tutorials/new_tutorial/transform_in_parallel_code:new-manual-transform-in-parallel-code}\label{tutorials/new_tutorial/transform_in_parallel_code::doc}\label{tutorials/new_tutorial/transform_in_parallel_code:new-manual-transform-in-parallel-chapter-num-python-code-for-more-on-transform-ing-data}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform syntax in detail}}}
-
-\item {} 
-Back to \textbf{Chapter 3}: {\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-transform-in-parallel]{\emph{More on @transform-ing data and @originate}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Producing several items / files per job}
-\label{tutorials/new_tutorial/transform_in_parallel_code:producing-several-items-files-per-job}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   Create pairs of input files}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{first\PYGZus{}task\PYGZus{}params} \PYG{o}{=} \PYG{p}{[}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                    \PYG{p}{]}
-
-\PYG{k}{for} \PYG{n}{input\PYGZus{}file\PYGZus{}pairs} \PYG{o+ow}{in} \PYG{n}{first\PYGZus{}task\PYGZus{}params}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{input\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}pairs}\PYG{p}{:}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-            \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   second task}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Resulting Output}
-\label{tutorials/new_tutorial/transform_in_parallel_code:resulting-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[job1.a.start, job1.b.start] \PYGZhy{}\PYGZgt{} [job1.a.output.1, job1.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job2.a.start, job2.b.start] \PYGZhy{}\PYGZgt{} [job2.a.output.1, job2.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job3.a.start, job3.b.start] \PYGZhy{}\PYGZgt{} [job3.a.output.1, job3.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = first\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job1.a.output.1, job1.a.output.extra.1] \PYGZhy{}\PYGZgt{} job1.a.output2] completed}
-\PYG{g+go}{    Job  = [[job2.a.output.1, job2.a.output.extra.1] \PYGZhy{}\PYGZgt{} job2.a.output2] completed}
-\PYG{g+go}{    Job  = [[job3.a.output.1, job3.a.output.extra.1] \PYGZhy{}\PYGZgt{} job3.a.output2] completed}
-\PYG{g+go}{Completed Task = second\PYGZus{}task}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Defining tasks function out of order}
-\label{tutorials/new_tutorial/transform_in_parallel_code:defining-tasks-function-out-of-order}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}   Create pairs of input files}
- \PYG{c}{\PYGZsh{}}
- \PYG{n}{first\PYGZus{}task\PYGZus{}params} \PYG{o}{=} \PYG{p}{[}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{]}
-
- \PYG{k}{for} \PYG{n}{input\PYGZus{}file\PYGZus{}pairs} \PYG{o+ow}{in} \PYG{n}{first\PYGZus{}task\PYGZus{}params}\PYG{p}{:}
-     \PYG{k}{for} \PYG{n}{input\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}pairs}\PYG{p}{:}
-         \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   second task defined first}
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   task name string wrapped in output\PYGZus{}from(...)}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{output\PYGZus{}from}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{first\PYGZus{}task}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   first task}
- \PYG{c}{\PYGZsh{}}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                         \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                          \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                        \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                 \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{:}
-         \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-             \PYG{k}{pass}
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}       Run}
- \PYG{c}{\PYGZsh{}}
- \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Resulting Output}
-\label{tutorials/new_tutorial/transform_in_parallel_code:id1}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[job1.a.start, job1.b.start] \PYGZhy{}\PYGZgt{} [job1.a.output.1, job1.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job2.a.start, job2.b.start] \PYGZhy{}\PYGZgt{} [job2.a.output.1, job2.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job3.a.start, job3.b.start] \PYGZhy{}\PYGZgt{} [job3.a.output.1, job3.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = first\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job1.a.output.1, job1.a.output.extra.1] \PYGZhy{}\PYGZgt{} job1.a.output2] completed}
-\PYG{g+go}{    Job  = [[job2.a.output.1, job2.a.output.extra.1] \PYGZhy{}\PYGZgt{} job2.a.output2] completed}
-\PYG{g+go}{    Job  = [[job3.a.output.1, job3.a.output.extra.1] \PYGZhy{}\PYGZgt{} job3.a.output2] completed}
-\PYG{g+go}{Completed Task = second\PYGZus{}task}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Multiple dependencies}
-\label{tutorials/new_tutorial/transform_in_parallel_code:new-manual-transform-multiple-dependencies-code}\label{tutorials/new_tutorial/transform_in_parallel_code:multiple-dependencies}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
- \PYG{k+kn}{import} \PYG{n+nn}{time}
- \PYG{k+kn}{import} \PYG{n+nn}{random}
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}   Create pairs of input files}
- \PYG{c}{\PYGZsh{}}
- \PYG{n}{first\PYGZus{}task\PYGZus{}params} \PYG{o}{=} \PYG{p}{[}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{]}
- \PYG{n}{second\PYGZus{}task\PYGZus{}params} \PYG{o}{=} \PYG{p}{[}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job4.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job4.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job5.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job5.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                      \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job6.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job6.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{]}
-
- \PYG{k}{for} \PYG{n}{input\PYGZus{}file\PYGZus{}pairs} \PYG{o+ow}{in} \PYG{n}{first\PYGZus{}task\PYGZus{}params} \PYG{o}{+} \PYG{n}{second\PYGZus{}task\PYGZus{}params}\PYG{p}{:}
-     \PYG{k}{for} \PYG{n}{input\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}pairs}\PYG{p}{:}
-         \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   first task}
- \PYG{c}{\PYGZsh{}}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                         \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                          \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                        \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                 \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{:}
-         \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-             \PYG{k}{pass}
-     \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{n}{random}\PYG{o}{.}\PYG{n}{random}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   second task}
- \PYG{c}{\PYGZsh{}}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{second\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                         \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                          \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                        \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                 \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{:}
-         \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-             \PYG{k}{pass}
-     \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{n}{random}\PYG{o}{.}\PYG{n}{random}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}   third task}
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}       depends on both first\PYGZus{}task() and second\PYGZus{}task()}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{n}{first\PYGZus{}task}\PYG{p}{,} \PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{third\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
- \PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZh [...]
- \PYG{c}{\PYGZsh{}}
- \PYG{c}{\PYGZsh{}       Run}
- \PYG{c}{\PYGZsh{}}
- \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{third\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{6}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Resulting Output}
-\label{tutorials/new_tutorial/transform_in_parallel_code:id2}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{third\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{6}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[job3.a.start, job3.b.start] \PYGZhy{}\PYGZgt{} [job3.a.output.1, job3.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job6.a.start, job6.b.start] \PYGZhy{}\PYGZgt{} [job6.a.output.1, job6.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job1.a.start, job1.b.start] \PYGZhy{}\PYGZgt{} [job1.a.output.1, job1.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job4.a.start, job4.b.start] \PYGZhy{}\PYGZgt{} [job4.a.output.1, job4.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job5.a.start, job5.b.start] \PYGZhy{}\PYGZgt{} [job5.a.output.1, job5.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = second\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job2.a.start, job2.b.start] \PYGZhy{}\PYGZgt{} [job2.a.output.1, job2.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = first\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job1.a.output.1, job1.a.output.extra.1] \PYGZhy{}\PYGZgt{} job1.a.output2] completed}
-\PYG{g+go}{    Job  = [[job2.a.output.1, job2.a.output.extra.1] \PYGZhy{}\PYGZgt{} job2.a.output2] completed}
-\PYG{g+go}{    Job  = [[job3.a.output.1, job3.a.output.extra.1] \PYGZhy{}\PYGZgt{} job3.a.output2] completed}
-\PYG{g+go}{    Job  = [[job4.a.output.1, job4.a.output.extra.1] \PYGZhy{}\PYGZgt{} job4.a.output2] completed}
-\PYG{g+go}{    Job  = [[job5.a.output.1, job5.a.output.extra.1] \PYGZhy{}\PYGZgt{} job5.a.output2] completed}
-\PYG{g+go}{    Job  = [[job6.a.output.1, job6.a.output.extra.1] \PYGZhy{}\PYGZgt{} job6.a.output2] completed}
-\PYG{g+go}{Completed Task = third\PYGZus{}task}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Multiple dependencies after @follows}
-\label{tutorials/new_tutorial/transform_in_parallel_code:multiple-dependencies-after-follows}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{time}
-\PYG{k+kn}{import} \PYG{n+nn}{random}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   Create pairs of input files}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{first\PYGZus{}task\PYGZus{}params} \PYG{o}{=} \PYG{p}{[}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                    \PYG{p}{]}
-\PYG{n}{second\PYGZus{}task\PYGZus{}params} \PYG{o}{=} \PYG{p}{[}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job4.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job4.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job5.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job5.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                     \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job6.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job6.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-                    \PYG{p}{]}
-
-\PYG{k}{for} \PYG{n}{input\PYGZus{}file\PYGZus{}pairs} \PYG{o+ow}{in} \PYG{n}{first\PYGZus{}task\PYGZus{}params} \PYG{o}{+} \PYG{n}{second\PYGZus{}task\PYGZus{}params}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{input\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}pairs}\PYG{p}{:}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-            \PYG{k}{pass}
-    \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{n}{random}\PYG{o}{.}\PYG{n}{random}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   second task}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{first\PYGZus{}task}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{second\PYGZus{}task\PYGZus{}params}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.extra.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{some\PYGZus{}extra.string.for\PYGZus{}example}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{,}
-                \PYG{n}{extra\PYGZus{}parameter\PYGZus{}str}\PYG{p}{,} \PYG{n}{extra\PYGZus{}parameter\PYGZus{}num}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}file\PYGZus{}pair}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-            \PYG{k}{pass}
-    \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{n}{random}\PYG{o}{.}\PYG{n}{random}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   third task}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       depends on both first\PYGZus{}task() and second\PYGZus{}task()}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{n}{first\PYGZus{}task}\PYG{p}{,} \PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{third\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{third\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{6}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Resulting Output: \texttt{first\_task} completes before \texttt{second\_task}}
-\label{tutorials/new_tutorial/transform_in_parallel_code:resulting-output-first-task-completes-before-second-task}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{third\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{6}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[job2.a.start, job2.b.start] \PYGZhy{}\PYGZgt{} [job2.a.output.1, job2.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job3.a.start, job3.b.start] \PYGZhy{}\PYGZgt{} [job3.a.output.1, job3.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job1.a.start, job1.b.start] \PYGZhy{}\PYGZgt{} [job1.a.output.1, job1.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = first\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job4.a.start, job4.b.start] \PYGZhy{}\PYGZgt{} [job4.a.output.1, job4.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job6.a.start, job6.b.start] \PYGZhy{}\PYGZgt{} [job6.a.output.1, job6.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{    Job  = [[job5.a.start, job5.b.start] \PYGZhy{}\PYGZgt{} [job5.a.output.1, job5.a.output.extra.1], some\PYGZus{}extra.string.for\PYGZus{}example, 14] completed}
-\PYG{g+go}{Completed Task = second\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job1.a.output.1, job1.a.output.extra.1] \PYGZhy{}\PYGZgt{} job1.a.output2] completed}
-\PYG{g+go}{    Job  = [[job2.a.output.1, job2.a.output.extra.1] \PYGZhy{}\PYGZgt{} job2.a.output2] completed}
-\PYG{g+go}{    Job  = [[job3.a.output.1, job3.a.output.extra.1] \PYGZhy{}\PYGZgt{} job3.a.output2] completed}
-\PYG{g+go}{    Job  = [[job4.a.output.1, job4.a.output.extra.1] \PYGZhy{}\PYGZgt{} job4.a.output2] completed}
-\PYG{g+go}{    Job  = [[job5.a.output.1, job5.a.output.extra.1] \PYGZhy{}\PYGZgt{} job5.a.output2] completed}
-\PYG{g+go}{    Job  = [[job6.a.output.1, job6.a.output.extra.1] \PYGZhy{}\PYGZgt{} job6.a.output2] completed}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 4}: Python Code for Creating files with \texttt{@originate}}
-\label{tutorials/new_tutorial/originate_code:new-manual-originate-code}\label{tutorials/new_tutorial/originate_code::doc}\label{tutorials/new_tutorial/originate_code:new-manual-originate-chapter-num-python-code-for-creating-files-with-originate}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform syntax in detail}}}
-
-\item {} 
-Back to \textbf{Chapter 4}: {\hyperref[tutorials/new_tutorial/originate:new-manual-originate]{\emph{@originate}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Using \texttt{@originate}}
-\label{tutorials/new_tutorial/originate_code:using-originate}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} create both files as necessary}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   second task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Resulting Output}
-\label{tutorials/new_tutorial/originate_code:resulting-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-    Job  = [None -\textgreater{} [job1.a.start, job1.b.start]] completed
-    Job  = [None -\textgreater{} [job2.a.start, job2.b.start]] completed
-    Job  = [None -\textgreater{} [job3.a.start, job3.b.start]] completed
-Completed Task = create\_initial\_file\_pairs
-    Job  = [[job1.a.start, job1.b.start] -\textgreater{} job1.a.output.1] completed
-    Job  = [[job2.a.start, job2.b.start] -\textgreater{} job2.a.output.1] completed
-    Job  = [[job3.a.start, job3.b.start] -\textgreater{} job3.a.output.1] completed
-Completed Task = first\_task
-    Job  = [job1.a.output.1 -\textgreater{} job1.a.output.2] completed
-    Job  = [job2.a.output.1 -\textgreater{} job2.a.output.2] completed
-    Job  = [job3.a.output.1 -\textgreater{} job3.a.output.2] completed
-Completed Task = second\_task
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 5}: Python Code for Understanding how your pipeline works with \emph{pipeline\_printout(...)}}
-\label{tutorials/new_tutorial/pipeline_printout_code::doc}\label{tutorials/new_tutorial/pipeline_printout_code:new-manual-pipeline-printout-code}\label{tutorials/new_tutorial/pipeline_printout_code:new-manual-pipeline-printout-chapter-num-python-code-for-understanding-how-your-pipeline-works-with-pipeline-printout}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}} syntax
-
-\item {} 
-Back to \textbf{Chapter 5}: {\hyperref[tutorials/new_tutorial/pipeline_printout:new-manual-pipeline-printout]{\emph{Understanding how your pipeline works}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Display the initial state of the pipeline}
-\label{tutorials/new_tutorial/pipeline_printout_code:display-the-initial-state-of-the-pipeline}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} create both files as necessary}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   second task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{1}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Normal Output}
-\label{tutorials/new_tutorial/pipeline_printout_code:normal-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{1}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which will be run:}
-
-\PYG{g+go}{Task = create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}
-\PYG{g+go}{Task = first\PYGZus{}task}
-\PYG{g+go}{Task = second\PYGZus{}task}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{High Verbosity Output}
-\label{tutorials/new_tutorial/pipeline_printout_code:high-verbosity-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which will be run:}
-
-\PYG{g+go}{Task = create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}
-\PYG{g+go}{       Job  = [None}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.a.start}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.b.start]}
-\PYG{g+go}{         Job needs update: Missing files [job1.a.start, job1.b.start]}
-\PYG{g+go}{       Job  = [None}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.a.start}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.b.start]}
-\PYG{g+go}{         Job needs update: Missing files [job2.a.start, job2.b.start]}
-\PYG{g+go}{       Job  = [None}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.a.start}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.b.start]}
-\PYG{g+go}{         Job needs update: Missing files [job3.a.start, job3.b.start]}
-
-\PYG{g+go}{Task = first\PYGZus{}task}
-\PYG{g+go}{       Job  = [[job1.a.start, job1.b.start]}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.a.output.1]}
-\PYG{g+go}{         Job needs update: Missing files [job1.a.start, job1.b.start, job1.a.output.1]}
-\PYG{g+go}{       Job  = [[job2.a.start, job2.b.start]}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.a.output.1]}
-\PYG{g+go}{         Job needs update: Missing files [job2.a.start, job2.b.start, job2.a.output.1]}
-\PYG{g+go}{       Job  = [[job3.a.start, job3.b.start]}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.a.output.1]}
-\PYG{g+go}{         Job needs update: Missing files [job3.a.start, job3.b.start, job3.a.output.1]}
-
-\PYG{g+go}{Task = second\PYGZus{}task}
-\PYG{g+go}{       Job  = [job1.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.a.output.2]}
-\PYG{g+go}{         Job needs update: Missing files [job1.a.output.1, job1.a.output.2]}
-\PYG{g+go}{       Job  = [job2.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.a.output.2]}
-\PYG{g+go}{         Job needs update: Missing files [job2.a.output.1, job2.a.output.2]}
-\PYG{g+go}{       Job  = [job3.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.a.output.2]}
-\PYG{g+go}{         Job needs update: Missing files [job3.a.output.1, job3.a.output.2]}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Display the partially up-to-date pipeline}
-\label{tutorials/new_tutorial/pipeline_printout_code:display-the-partially-up-to-date-pipeline}\begin{quote}
-
-Run the pipeline, modify \code{job1.stage} so that the second task is no longer up-to-date
-and printout the pipeline stage again:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{3}\PYG{p}{)}
-\PYG{g+go}{Task enters queue = create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} [job1.a.start, job1.b.start]]}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} [job2.a.start, job2.b.start]]}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} [job3.a.start, job3.b.start]]}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} [job1.a.start, job1.b.start]] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} [job2.a.start, job2.b.start]] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} [job3.a.start, job3.b.start]] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}
-\PYG{g+go}{Task enters queue = first\PYGZus{}task}
-\PYG{g+go}{    Job  = [[job1.a.start, job1.b.start] \PYGZhy{}\PYGZgt{} job1.a.output.1]}
-\PYG{g+go}{    Job  = [[job2.a.start, job2.b.start] \PYGZhy{}\PYGZgt{} job2.a.output.1]}
-\PYG{g+go}{    Job  = [[job3.a.start, job3.b.start] \PYGZhy{}\PYGZgt{} job3.a.output.1]}
-\PYG{g+go}{    Job  = [[job1.a.start, job1.b.start] \PYGZhy{}\PYGZgt{} job1.a.output.1] completed}
-\PYG{g+go}{    Job  = [[job2.a.start, job2.b.start] \PYGZhy{}\PYGZgt{} job2.a.output.1] completed}
-\PYG{g+go}{    Job  = [[job3.a.start, job3.b.start] \PYGZhy{}\PYGZgt{} job3.a.output.1] completed}
-\PYG{g+go}{Completed Task = first\PYGZus{}task}
-\PYG{g+go}{Task enters queue = second\PYGZus{}task}
-\PYG{g+go}{    Job  = [job1.a.output.1 \PYGZhy{}\PYGZgt{} job1.a.output.2]}
-\PYG{g+go}{    Job  = [job2.a.output.1 \PYGZhy{}\PYGZgt{} job2.a.output.2]}
-\PYG{g+go}{    Job  = [job3.a.output.1 \PYGZhy{}\PYGZgt{} job3.a.output.2]}
-\PYG{g+go}{    Job  = [job1.a.output.1 \PYGZhy{}\PYGZgt{} job1.a.output.2] completed}
-\PYG{g+go}{    Job  = [job2.a.output.1 \PYGZhy{}\PYGZgt{} job2.a.output.2] completed}
-\PYG{g+go}{    Job  = [job3.a.output.1 \PYGZhy{}\PYGZgt{} job3.a.output.2] completed}
-\PYG{g+go}{Completed Task = second\PYGZus{}task}
-
-
-\PYG{g+go}{\PYGZsh{} modify job1.stage1}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{job1.a.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{close}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-At a verbosity of 6, even jobs which are up-to-date will be displayed:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{6}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which are up\PYGZhy{}to\PYGZhy{}date:}
-
-\PYG{g+go}{Task = create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}
-\PYG{g+go}{       Job  = [None}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.a.start}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.b.start]}
-\PYG{g+go}{       Job  = [None}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.a.start}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.b.start]}
-\PYG{g+go}{       Job  = [None}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.a.start}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.b.start]}
-
-\PYG{g+go}{Task = first\PYGZus{}task}
-\PYG{g+go}{       Job  = [[job1.a.start, job1.b.start]}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.a.output.1]}
-\PYG{g+go}{       Job  = [[job2.a.start, job2.b.start]}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.a.output.1]}
-\PYG{g+go}{       Job  = [[job3.a.start, job3.b.start]}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.a.output.1]}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-
-
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which will be run:}
-
-\PYG{g+go}{Task = second\PYGZus{}task}
-\PYG{g+go}{       Job  = [job1.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job1.a.output.2]}
-\PYG{g+go}{         Job needs update:}
-\PYG{g+go}{         Input files:}
-\PYG{g+go}{          * 22 Jul 2014 15:29:19.33: job1.a.output.1}
-\PYG{g+go}{         Output files:}
-\PYG{g+go}{          * 22 Jul 2014 15:29:07.53: job1.a.output.2}
-
-\PYG{g+go}{       Job  = [job2.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job2.a.output.2]}
-\PYG{g+go}{       Job  = [job3.a.output.1}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{} job3.a.output.2]}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\end{Verbatim}
-
-We can now see that the there is only one job in ``second\_task'' which needs to be re-run
-because `job1.stage1' has been modified after `job1.stage2'
-\end{quote}
-
-
-\section{\textbf{Chapter 7}: Python Code for Displaying the pipeline visually with \emph{pipeline\_printout\_graph(...)}}
-\label{tutorials/new_tutorial/pipeline_printout_graph_code:new-manual-pipeline-printout-graph-chapter-num-python-code-for-displaying-the-pipeline-visually-with-pipeline-printout-graph}\label{tutorials/new_tutorial/pipeline_printout_graph_code::doc}\label{tutorials/new_tutorial/pipeline_printout_graph_code:new-manual-pipeline-printout-graph-code}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph]{\emph{pipeline\_printout\_graph(...)}}} syntax
-
-\item {} 
-Back to \textbf{Chapter 7}: {\hyperref[tutorials/new_tutorial/pipeline_printout_graph:new-manual-pipeline-printout-graph]{\emph{Displaying the pipeline visually}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Code}
-\label{tutorials/new_tutorial/pipeline_printout_graph_code:code}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\},numbers=left,firstnumber=1,stepnumber=1]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} create both files as necessary}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   second task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{first\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}  Print graph before running pipeline}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Show flow chart and tasks before running the pipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Show flow chart and tasks before running the pipeline}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{simple\PYGZus{}tutorial\PYGZus{}stage5\PYGZus{}before.png}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{png}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                         \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,}
-                         \PYG{n}{minimal\PYGZus{}key\PYGZus{}legend}\PYG{o}{=}\PYG{n+nb+bp}{True}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{} modify job1.stage1}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{job1.a.output.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{close}\PYG{p}{(}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}  Print graph after everything apart from {}`{}`job1.a.output.1{}`{}` is update}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Show flow chart and tasks after running the pipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Show flow chart and tasks after running the pipeline}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{simple\PYGZus{}tutorial\PYGZus{}stage5\PYGZus{}after.png}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{png}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                         \PYG{p}{[}\PYG{n}{second\PYGZus{}task}\PYG{p}{]}\PYG{p}{,}
-                         \PYG{n}{no\PYGZus{}key\PYGZus{}legend}\PYG{o}{=}\PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Resulting Flowcharts}
-\label{tutorials/new_tutorial/pipeline_printout_graph_code:resulting-flowcharts}\begin{quote}
-
-\begin{tabular}{|p{0.475\linewidth}|p{0.475\linewidth}|}
-\hline
-
-{\hfill\scalebox{0.950000}{\includegraphics{simple_tutorial_stage5_before.png}}\hfill}
-
-\begin{center}Before
-\end{center} & 
-{\hfill\scalebox{0.950000}{\includegraphics{simple_tutorial_stage5_after.png}}\hfill}
-
-\begin{center}After
-\end{center}\\\hline
-\end{tabular}
-
-
-\begin{tabular}{|p{0.950\linewidth}|}
-\hline
-
-{\hfill\scalebox{0.500000}{\includegraphics{tutorial_key.png}}\hfill}
-
-\begin{center}Legend
-\end{center}\\\hline
-\end{tabular}
-
-\end{quote}
-
-
-\section{\textbf{Chapter 8}: Python Code for Specifying output file names with \emph{formatter()} and \emph{regex()}}
-\label{tutorials/new_tutorial/output_file_names_code::doc}\label{tutorials/new_tutorial/output_file_names_code:new-manual-output-file-names-chapter-num-python-code-for-specifying-output-file-names-with-formatter-and-regex}\label{tutorials/new_tutorial/output_file_names_code:new-manual-output-file-names-code}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}} syntax
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} syntax
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} syntax
-
-\item {} 
-Back to \textbf{Chapter 8}: {\hyperref[tutorials/new_tutorial/output_file_names:new-manual-output-file-names]{\emph{Specifying output file names}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Example Code for \emph{suffix()}}
-\label{tutorials/new_tutorial/output_file_names_code:example-code-for-suffix}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} create both files as necessary}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   suffix}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,}             \PYG{c}{\PYGZsh{} name of previous task(s) (or list of files, or a glob)}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                     \PYG{c}{\PYGZsh{} matching suffix of the \PYGZdq{}input file\PYGZdq{}}
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{45}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output.b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}   \PYG{c}{\PYGZsh{} resulting suffix}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{  input\PYGZus{}parameters  = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}files}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{  output\PYGZus{}parameters = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{first\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Example Code for \emph{formatter()}}
-\label{tutorials/new_tutorial/output_file_names_code:example-code-for-formatter}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.c.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} create both files as necessary}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   formatter}
-\PYG{c}{\PYGZsh{}}
-
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} Input}
-
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job(?P\PYGZlt{}JOBNUMBER\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+).a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}           \PYG{c}{\PYGZsh{} Extract job number}
-                      \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job[123].b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                       \PYG{c}{\PYGZsh{} Match only \PYGZdq{}b\PYGZdq{} files}
-
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}             \PYG{c}{\PYGZsh{} Replacement list}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[1]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{45}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}parameters = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}files}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output\PYGZus{}parameters = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Example Code for \emph{formatter()} with replacements in \emph{extra} arguments}
-\label{tutorials/new_tutorial/output_file_names_code:example-code-for-formatter-with-replacements-in-extra-arguments}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.c.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   print job number as an extra argument}
-\PYG{c}{\PYGZsh{}}
-
-\PYG{c}{\PYGZsh{}   first task}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} Input}
-
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job(?P\PYGZlt{}JOBNUMBER\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+).a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}           \PYG{c}{\PYGZsh{} Extract job number}
-                      \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job[123].b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                       \PYG{c}{\PYGZsh{} Match only \PYGZdq{}b\PYGZdq{} files}
-
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}             \PYG{c}{\PYGZsh{} Replacement list}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[1]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}JOBNUMBER[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}\PYG{p}{,} \PYG{n}{job\PYGZus{}number}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{n}{job\PYGZus{}number}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{:}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}files}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Example Code for \emph{formatter()} in Zoos}
-\label{tutorials/new_tutorial/output_file_names_code:example-code-for-formatter-in-zoos}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   Make directories}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}
-            \PYG{c}{\PYGZsh{}   List of animals and plants}
-            \PYG{p}{[}    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.handreared.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.tame.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile/reptiles.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose/flowering.handreared.plants}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}   Put different animals in different directories depending on their clade}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}/\PYGZob{}tame[0]\PYGZcb{}.\PYGZob{}subdir[0][0]\PYGZcb{}.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subdir[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}tame[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Food for the \PYGZob{}tameness:11s\PYGZcb{} \PYGZob{}animal\PYGZus{}name:9s\PYGZcb{} = \PYGZob{}output\PYGZus{}file:90s\PYGZcb{} will be placed in \PYGZob{}new\PYGZus{}directory\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-
-
-\PYG{n}{Results} \PYG{o+ow}{in}\PYG{p}{:}
-
-\PYG{p}{:}\PYG{p}{:}
-
-    \PYG{o}{\PYGZgt{}\PYGZgt{}}\PYG{o}{\PYGZgt{}} \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{wild}        \PYG{n}{crocodile} \PYG{o}{=} \PYG{o}{.}\PYG{o}{/}\PYG{n}{reptiles}\PYG{o}{/}\PYG{n}{wild}\PYG{o}{.}\PYG{n}{crocodile}\PYG{o}{.}\PYG{n}{food} \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{o}{.}\PYG{o}{/}\PYG{n}{reptiles}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{tame}        \PYG{n}{dog}       \PYG{o}{=} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}\PYG{o}{/}\PYG{n}{tame}\PYG{o}{.}\PYG{n}{dog}\PYG{o}{.}\PYG{n}{food}        \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{wild}        \PYG{n}{dog}       \PYG{o}{=} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}\PYG{o}{/}\PYG{n}{wild}\PYG{o}{.}\PYG{n}{dog}\PYG{o}{.}\PYG{n}{food}        \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{handreared}  \PYG{n}{lion}      \PYG{o}{=} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}\PYG{o}{/}\PYG{n}{handreared}\PYG{o}{.}\PYG{n}{lion}\PYG{o}{.}\PYG{n}{food} \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{wild}        \PYG{n}{lion}      \PYG{o}{=} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}\PYG{o}{/}\PYG{n}{wild}\PYG{o}{.}\PYG{n}{lion}\PYG{o}{.}\PYG{n}{food}       \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{wild}        \PYG{n}{tiger}     \PYG{o}{=} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}\PYG{o}{/}\PYG{n}{wild}\PYG{o}{.}\PYG{n}{tiger}\PYG{o}{.}\PYG{n}{food}      \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{o}{.}\PYG{o}{/}\PYG{n}{mammals}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Example Code for \emph{regex()} in zoos}
-\label{tutorials/new_tutorial/output_file_names_code:example-code-for-regex-in-zoos}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   Make directories}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}
-            \PYG{c}{\PYGZsh{}   List of animals and plants}
-            \PYG{p}{[}    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.handreared.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.tame.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile/reptiles.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose/flowering.handreared.plants}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-
-\PYG{c}{\PYGZsh{}   Put different animals in different directories depending on their clade}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                        \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*?/?)(}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+)/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}clade\PYGZgt{}/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}tame\PYGZgt{}.}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                            \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                             \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                                       \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                  \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Food for the \PYGZob{}tameness:11s\PYGZcb{} \PYGZob{}animal\PYGZus{}name:9s\PYGZcb{} = \PYGZob{}output\PYGZus{}file:90s\PYGZcb{} will be placed in \PYGZob{}new\PYGZus{}directory\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-
-
-\PYG{n}{Results} \PYG{o+ow}{in}\PYG{p}{:}
-
-\PYG{p}{:}\PYG{p}{:}
-
-    \PYG{o}{\PYGZgt{}\PYGZgt{}}\PYG{o}{\PYGZgt{}} \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{wild}        \PYG{n}{crocodile} \PYG{o}{=} \PYG{n}{reptiles}\PYG{o}{/}\PYG{n}{wild}\PYG{o}{.}\PYG{n}{crocodile}\PYG{o}{.}\PYG{n}{food} \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{n}{reptiles}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{tame}        \PYG{n}{dog}       \PYG{o}{=} \PYG{n}{mammals}\PYG{o}{/}\PYG{n}{tame}\PYG{o}{.}\PYG{n}{dog}\PYG{o}{.}\PYG{n}{food}        \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{n}{mammals}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{wild}        \PYG{n}{dog}       \PYG{o}{=} \PYG{n}{mammals}\PYG{o}{/}\PYG{n}{wild}\PYG{o}{.}\PYG{n}{dog}\PYG{o}{.}\PYG{n}{food}        \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{n}{mammals}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{handreared}  \PYG{n}{lion}      \PYG{o}{=} \PYG{n}{mammals}\PYG{o}{/}\PYG{n}{handreared}\PYG{o}{.}\PYG{n}{lion}\PYG{o}{.}\PYG{n}{food} \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{n}{mammals}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{wild}        \PYG{n}{lion}      \PYG{o}{=} \PYG{n}{mammals}\PYG{o}{/}\PYG{n}{wild}\PYG{o}{.}\PYG{n}{lion}\PYG{o}{.}\PYG{n}{food}       \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{n}{mammals}
-    \PYG{n}{Food} \PYG{k}{for} \PYG{n}{the} \PYG{n}{wild}        \PYG{n}{tiger}     \PYG{o}{=} \PYG{n}{mammals}\PYG{o}{/}\PYG{n}{wild}\PYG{o}{.}\PYG{n}{tiger}\PYG{o}{.}\PYG{n}{food}      \PYG{n}{will} \PYG{n}{be} \PYG{n}{placed} \PYG{o+ow}{in} \PYG{n}{mammals}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 9}: Python Code for Preparing directories for output with \emph{@mkdir()}}
-\label{tutorials/new_tutorial/mkdir_code:new-manual-mkdir-code}\label{tutorials/new_tutorial/mkdir_code::doc}\label{tutorials/new_tutorial/mkdir_code:new-manual-mkdir-chapter-num-python-code-for-preparing-directories-for-output-with-mkdir}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/mkdir:decorators-mkdir]{\emph{mkdir()}}} syntax
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}} syntax
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} syntax
-
-\item {} 
-Back to \textbf{Chapter 9}: {\hyperref[tutorials/new_tutorial/mkdir:new-manual-mkdir]{\emph{Preparing directories for output with @mkdir()}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Code for \emph{formatter()} Zoo example}
-\label{tutorials/new_tutorial/mkdir_code:code-for-formatter-zoo-example}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   Make directories}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{n+nd}{@originate}\PYG{p}{(}
-            \PYG{c}{\PYGZsh{}   List of animals and plants}
-            \PYG{p}{[}    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.handreared.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.tame.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile/reptiles.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose/flowering.handreared.plants}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{} create directories for each clade}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}    \PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                               \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-\PYG{c}{\PYGZsh{}   Put different animals in different directories depending on their clade}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}       \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}/\PYGZob{}tame[0]\PYGZcb{}.\PYGZob{}subdir[0][0]\PYGZcb{}.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subpath[0][1]\PYGZcb{}/\PYGZob{}clade[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}subdir[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}tame[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}40s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}90s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-        \PYG{c}{\PYGZsh{} this works now}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Code for \emph{regex()} Zoo example}
-\label{tutorials/new_tutorial/mkdir_code:code-for-regex-zoo-example}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   Make directories}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{n+nd}{@originate}\PYG{p}{(}
-            \PYG{c}{\PYGZsh{}   List of animals and plants}
-            \PYG{p}{[}    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tiger/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lion/mammals.handreared.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.tame.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog/mammals.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile/reptiles.wild.animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rose/flowering.handreared.plants}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{} create directories for each clade}
-\PYG{n+nd}{@mkdir}\PYG{p}{(}    \PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                       \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*?/?)(}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+)/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                             \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-\PYG{c}{\PYGZsh{}   Put different animals in different directories depending on their clade}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                        \PYG{c}{\PYGZsh{} Input}
-
-           \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*?/?)(}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+)/(?P\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).(?P\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{w+).animals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{c}{\PYGZsh{} Only animals: ignore plants!}
-
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}clade\PYGZgt{}/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}tame\PYGZgt{}.}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2.food}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                            \PYG{c}{\PYGZsh{} Replacement}
-
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}clade\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                             \PYG{c}{\PYGZsh{} new\PYGZus{}directory}
-           \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                                       \PYG{c}{\PYGZsh{} animal\PYGZus{}name}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{g\PYGZlt{}tame\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                                  \PYG{c}{\PYGZsh{} tameness}
-\PYG{k}{def} \PYG{n+nf}{feed}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{new\PYGZus{}directory}\PYG{p}{,} \PYG{n}{animal\PYGZus{}name}\PYG{p}{,} \PYG{n}{tameness}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}40s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}90s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{} this works now}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 10}: Python Code for Checkpointing: Interrupted Pipelines and Exceptions}
-\label{tutorials/new_tutorial/checkpointing_code:new-manual-checkpointing-chapter-num-python-code-for-checkpointing-interrupted-pipelines-and-exceptions}\label{tutorials/new_tutorial/checkpointing_code::doc}\label{tutorials/new_tutorial/checkpointing_code:new-manual-checkpointing-code}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/checkpointing:new-manual-checkpointing]{\emph{Back to \textbar{}new\_manual.checkpointing.chapter\_num\textbar{}: Interrupted Pipelines and Exceptions}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Code for .:ref:\emph{suffix() \textless{}decorators.suffix\textgreater{}} example}
-\label{tutorials/new_tutorial/checkpointing_code:code-for-ref-suffix-decorators-suffix-example}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 12}: Python Code for Splitting up large tasks / files with \textbf{@split}}
-\label{tutorials/new_tutorial/split_code:new-manual-split-chapter-num-python-code-for-splitting-up-large-tasks-files-with-split}\label{tutorials/new_tutorial/split_code::doc}\label{tutorials/new_tutorial/split_code:new-manual-split-code}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/split:decorators-split]{\emph{@split syntax in detail}}}
-
-\item {} 
-Back to \textbf{Chapter 12}: {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{Splitting up large tasks / files with @split}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Splitting large jobs}
-\label{tutorials/new_tutorial/split_code:splitting-large-jobs}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n}{NUMBER\PYGZus{}OF\PYGZus{}RANDOMS} \PYG{o}{=} \PYG{l+m+mi}{10000}
-\PYG{n}{CHUNK\PYGZus{}SIZE} \PYG{o}{=} \PYG{l+m+mi}{1000}
-
-
-\PYG{k+kn}{import} \PYG{n+nn}{random}\PYG{o}{,} \PYG{n+nn}{os}\PYG{o}{,} \PYG{n+nn}{glob}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Create random numbers}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{random\PYGZus{}numbers.list}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}random\PYGZus{}numbers}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{f} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{NUMBER\PYGZus{}OF\PYGZus{}RANDOMS}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{f}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}g}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{random}\PYG{o}{.}\PYG{n}{random}\PYG{p}{(}\PYG{p}{)} \PYG{o}{*} \PYG{l+m+mf}{100.0}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   split initial file}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n}{create\PYGZus{}random\PYGZus{}numbers}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}problem} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{        splits random numbers file into xxx files of chunk\PYGZus{}size each}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   clean up any files from previous runs}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}for ff in glob.glob(\PYGZdq{}*.chunks\PYGZdq{}):}
-    \PYG{k}{for} \PYG{n}{ff} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{ff}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   create new file every chunk\PYGZus{}size lines and}
-    \PYG{c}{\PYGZsh{}       copy each line into current file}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb+bp}{None}
-    \PYG{n}{cnt\PYGZus{}files} \PYG{o}{=} \PYG{l+m+mi}{0}
-    \PYG{k}{for} \PYG{n}{input\PYGZus{}file\PYGZus{}name} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-        \PYG{k}{for} \PYG{n}{i}\PYG{p}{,} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{enumerate}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-            \PYG{k}{if} \PYG{n}{i} \PYG{o}{\PYGZpc{}} \PYG{n}{CHUNK\PYGZus{}SIZE} \PYG{o}{==} \PYG{l+m+mi}{0}\PYG{p}{:}
-                \PYG{n}{cnt\PYGZus{}files} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-                \PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.chunks}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{cnt\PYGZus{}files}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-            \PYG{n}{output\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Calculate sum and sum of squares for each chunk file}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{split\PYGZus{}problem}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{sum\PYGZus{}of\PYGZus{}squares} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{output} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n}{sum\PYGZus{}squared}\PYG{p}{,} \PYG{n+nb}{sum} \PYG{o}{=} \PYG{p}{[}\PYG{l+m+mf}{0.0}\PYG{p}{,} \PYG{l+m+mf}{0.0}\PYG{p}{]}
-    \PYG{n}{cnt\PYGZus{}values} \PYG{o}{=} \PYG{l+m+mi}{0}
-    \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{cnt\PYGZus{}values} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-        \PYG{n}{val} \PYG{o}{=} \PYG{n+nb}{float}\PYG{p}{(}\PYG{n}{line}\PYG{o}{.}\PYG{n}{rstrip}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-        \PYG{n}{sum\PYGZus{}squared} \PYG{o}{+}\PYG{o}{=} \PYG{n}{val} \PYG{o}{*} \PYG{n}{val}
-        \PYG{n+nb}{sum} \PYG{o}{+}\PYG{o}{=} \PYG{n}{val}
-    \PYG{n}{output}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n+nb}{repr}\PYG{p}{(}\PYG{n}{sum\PYGZus{}squared}\PYG{p}{)}\PYG{p}{,} \PYG{n+nb}{repr}\PYG{p}{(}\PYG{n+nb}{sum}\PYG{p}{)}\PYG{p}{,} \PYG{n}{cnt\PYGZus{}values}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Resulting Output}
-\label{tutorials/new_tutorial/split_code:resulting-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} random\PYGZus{}numbers.list] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}random\PYGZus{}numbers}
-\PYG{g+go}{    Job  = [[random\PYGZus{}numbers.list] \PYGZhy{}\PYGZgt{} *.chunks] completed}
-\PYG{g+go}{Completed Task = split\PYGZus{}problem}
-\PYG{g+go}{    Job  = [1.chunks \PYGZhy{}\PYGZgt{} 1.sums] completed}
-\PYG{g+go}{    Job  = [10.chunks \PYGZhy{}\PYGZgt{} 10.sums] completed}
-\PYG{g+go}{    Job  = [2.chunks \PYGZhy{}\PYGZgt{} 2.sums] completed}
-\PYG{g+go}{    Job  = [3.chunks \PYGZhy{}\PYGZgt{} 3.sums] completed}
-\PYG{g+go}{    Job  = [4.chunks \PYGZhy{}\PYGZgt{} 4.sums] completed}
-\PYG{g+go}{    Job  = [5.chunks \PYGZhy{}\PYGZgt{} 5.sums] completed}
-\PYG{g+go}{    Job  = [6.chunks \PYGZhy{}\PYGZgt{} 6.sums] completed}
-\PYG{g+go}{    Job  = [7.chunks \PYGZhy{}\PYGZgt{} 7.sums] completed}
-\PYG{g+go}{    Job  = [8.chunks \PYGZhy{}\PYGZgt{} 8.sums] completed}
-\PYG{g+go}{    Job  = [9.chunks \PYGZhy{}\PYGZgt{} 9.sums] completed}
-\PYG{g+go}{Completed Task = sum\PYGZus{}of\PYGZus{}squares}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 13}: Python Code for  \texttt{@merge} multiple input into a single result}
-\label{tutorials/new_tutorial/merge_code::doc}\label{tutorials/new_tutorial/merge_code:new-manual-merge-code}\label{tutorials/new_tutorial/merge_code:new-manual-merge-chapter-num-python-code-for-merge-multiple-input-into-a-single-result}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/merge:decorators-merge]{\emph{@merge syntax in detail}}}
-
-\item {} 
-Back to \textbf{Chapter 13}: {\hyperref[tutorials/new_tutorial/merge:new-manual-merge]{\emph{Splitting up large tasks / files with @merge}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Splitting large jobs}
-\label{tutorials/new_tutorial/merge_code:splitting-large-jobs}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n}{NUMBER\PYGZus{}OF\PYGZus{}RANDOMS} \PYG{o}{=} \PYG{l+m+mi}{10000}
-\PYG{n}{CHUNK\PYGZus{}SIZE} \PYG{o}{=} \PYG{l+m+mi}{1000}
-
-
-\PYG{k+kn}{import} \PYG{n+nn}{random}\PYG{o}{,} \PYG{n+nn}{os}\PYG{o}{,} \PYG{n+nn}{glob}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Create random numbers}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{random\PYGZus{}numbers.list}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}random\PYGZus{}numbers}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{f} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{NUMBER\PYGZus{}OF\PYGZus{}RANDOMS}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{f}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}g}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{random}\PYG{o}{.}\PYG{n}{random}\PYG{p}{(}\PYG{p}{)} \PYG{o}{*} \PYG{l+m+mf}{100.0}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   split initial file}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n}{create\PYGZus{}random\PYGZus{}numbers}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}problem} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{        splits random numbers file into xxx files of chunk\PYGZus{}size each}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   clean up any files from previous runs}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}for ff in glob.glob(\PYGZdq{}*.chunks\PYGZdq{}):}
-    \PYG{k}{for} \PYG{n}{ff} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{ff}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   create new file every chunk\PYGZus{}size lines and}
-    \PYG{c}{\PYGZsh{}       copy each line into current file}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb+bp}{None}
-    \PYG{n}{cnt\PYGZus{}files} \PYG{o}{=} \PYG{l+m+mi}{0}
-    \PYG{k}{for} \PYG{n}{input\PYGZus{}file\PYGZus{}name} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-        \PYG{k}{for} \PYG{n}{i}\PYG{p}{,} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{enumerate}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-            \PYG{k}{if} \PYG{n}{i} \PYG{o}{\PYGZpc{}} \PYG{n}{CHUNK\PYGZus{}SIZE} \PYG{o}{==} \PYG{l+m+mi}{0}\PYG{p}{:}
-                \PYG{n}{cnt\PYGZus{}files} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-                \PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.chunks}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{cnt\PYGZus{}files}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-            \PYG{n}{output\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Calculate sum and sum of squares for each chunk file}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{split\PYGZus{}problem}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.chunks}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.sums}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{sum\PYGZus{}of\PYGZus{}squares} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{output} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n}{sum\PYGZus{}squared}\PYG{p}{,} \PYG{n+nb}{sum} \PYG{o}{=} \PYG{p}{[}\PYG{l+m+mf}{0.0}\PYG{p}{,} \PYG{l+m+mf}{0.0}\PYG{p}{]}
-    \PYG{n}{cnt\PYGZus{}values} \PYG{o}{=} \PYG{l+m+mi}{0}
-    \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{cnt\PYGZus{}values} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-        \PYG{n}{val} \PYG{o}{=} \PYG{n+nb}{float}\PYG{p}{(}\PYG{n}{line}\PYG{o}{.}\PYG{n}{rstrip}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-        \PYG{n}{sum\PYGZus{}squared} \PYG{o}{+}\PYG{o}{=} \PYG{n}{val} \PYG{o}{*} \PYG{n}{val}
-        \PYG{n+nb}{sum} \PYG{o}{+}\PYG{o}{=} \PYG{n}{val}
-    \PYG{n}{output}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n+nb}{repr}\PYG{p}{(}\PYG{n}{sum\PYGZus{}squared}\PYG{p}{)}\PYG{p}{,} \PYG{n+nb}{repr}\PYG{p}{(}\PYG{n+nb}{sum}\PYG{p}{)}\PYG{p}{,} \PYG{n}{cnt\PYGZus{}values}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Calculate variance from sums}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@merge}\PYG{p}{(}\PYG{n}{sum\PYGZus{}of\PYGZus{}squares}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{variance.result}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{calculate\PYGZus{}variance} \PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Calculate variance naively}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   initialise variables}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{all\PYGZus{}sum\PYGZus{}squared} \PYG{o}{=} \PYG{l+m+mf}{0.0}
-    \PYG{n}{all\PYGZus{}sum}         \PYG{o}{=} \PYG{l+m+mf}{0.0}
-    \PYG{n}{all\PYGZus{}cnt\PYGZus{}values}  \PYG{o}{=} \PYG{l+m+mf}{0.0}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{} added up all the sum\PYGZus{}squared, and sum and cnt\PYGZus{}values from all the chunks}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{input\PYGZus{}file\PYGZus{}name} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-        \PYG{n}{sum\PYGZus{}squared}\PYG{p}{,} \PYG{n+nb}{sum}\PYG{p}{,} \PYG{n}{cnt\PYGZus{}values} \PYG{o}{=} \PYG{n+nb}{map}\PYG{p}{(}\PYG{n+nb}{float}\PYG{p}{,} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{o}{.}\PYG{n}{readlines}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-        \PYG{n}{all\PYGZus{}sum\PYGZus{}squared} \PYG{o}{+}\PYG{o}{=} \PYG{n}{sum\PYGZus{}squared}
-        \PYG{n}{all\PYGZus{}sum}         \PYG{o}{+}\PYG{o}{=} \PYG{n+nb}{sum}
-        \PYG{n}{all\PYGZus{}cnt\PYGZus{}values}  \PYG{o}{+}\PYG{o}{=} \PYG{n}{cnt\PYGZus{}values}
-    \PYG{n}{all\PYGZus{}mean} \PYG{o}{=} \PYG{n}{all\PYGZus{}sum} \PYG{o}{/} \PYG{n}{all\PYGZus{}cnt\PYGZus{}values}
-    \PYG{n}{variance} \PYG{o}{=} \PYG{p}{(}\PYG{n}{all\PYGZus{}sum\PYGZus{}squared} \PYG{o}{\PYGZhy{}} \PYG{n}{all\PYGZus{}sum} \PYG{o}{*} \PYG{n}{all\PYGZus{}mean}\PYG{p}{)}\PYG{o}{/}\PYG{p}{(}\PYG{n}{all\PYGZus{}cnt\PYGZus{}values}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   print output}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{variance}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Resulting Output}
-\label{tutorials/new_tutorial/merge_code:resulting-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} random\PYGZus{}numbers.list] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}random\PYGZus{}numbers}
-\PYG{g+go}{    Job  = [[random\PYGZus{}numbers.list] \PYGZhy{}\PYGZgt{} *.chunks] completed}
-\PYG{g+go}{Completed Task = split\PYGZus{}problem}
-\PYG{g+go}{    Job  = [1.chunks \PYGZhy{}\PYGZgt{} 1.sums] completed}
-\PYG{g+go}{    Job  = [10.chunks \PYGZhy{}\PYGZgt{} 10.sums] completed}
-\PYG{g+go}{    Job  = [2.chunks \PYGZhy{}\PYGZgt{} 2.sums] completed}
-\PYG{g+go}{    Job  = [3.chunks \PYGZhy{}\PYGZgt{} 3.sums] completed}
-\PYG{g+go}{    Job  = [4.chunks \PYGZhy{}\PYGZgt{} 4.sums] completed}
-\PYG{g+go}{    Job  = [5.chunks \PYGZhy{}\PYGZgt{} 5.sums] completed}
-\PYG{g+go}{    Job  = [6.chunks \PYGZhy{}\PYGZgt{} 6.sums] completed}
-\PYG{g+go}{    Job  = [7.chunks \PYGZhy{}\PYGZgt{} 7.sums] completed}
-\PYG{g+go}{    Job  = [8.chunks \PYGZhy{}\PYGZgt{} 8.sums] completed}
-\PYG{g+go}{    Job  = [9.chunks \PYGZhy{}\PYGZgt{} 9.sums] completed}
-\PYG{g+go}{Completed Task = sum\PYGZus{}of\PYGZus{}squares}
-\PYG{g+go}{    Job  = [[1.sums, 10.sums, 2.sums, 3.sums, 4.sums, 5.sums, 6.sums, 7.sums, 8.sums, 9.sums] \PYGZhy{}\PYGZgt{} variance.result] completed}
-\PYG{g+go}{Completed Task = calculate\PYGZus{}variance}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 14}: Python Code for Multiprocessing, \texttt{drmaa} and Computation Clusters}
-\label{tutorials/new_tutorial/multiprocessing_code:new-manual-multiprocessing-code}\label{tutorials/new_tutorial/multiprocessing_code:new-manual-multiprocessing-chapter-num-python-code-for-multiprocessing-drmaa-and-computation-clusters}\label{tutorials/new_tutorial/multiprocessing_code::doc}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/jobs_limit:decorators-jobs-limit]{\emph{@jobs\_limit}}} syntax
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run()}}} syntax
-
-\item {} 
-{\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job]{\emph{drmaa\_wrapper.run\_job()}}} syntax
-
-\item {} 
-Back to \textbf{Chapter 14}: {\hyperref[tutorials/new_tutorial/multiprocessing:new-manual-multiprocessing]{\emph{Multiprocessing, drmaa and Computation Clusters}}}
-
-\end{itemize}
-
-
-
-
-\subsection{\emph{@jobs\_limit}}
-\label{tutorials/new_tutorial/multiprocessing_code:jobs-limit}\begin{quote}
-\begin{itemize}
-\item {} 
-First 2 tasks are constrained to a parallelism of 3 shared jobs at a time
-
-\item {} 
-Final task is constrained to a parallelism of 5 jobs at a time
-
-\item {} 
-The entire pipeline is constrained to a (theoretical) parallelism of 10 jobs at a time
-
-\end{itemize}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{time}
-
-\PYG{c}{\PYGZsh{} make list of 10 files}
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*stage1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{make\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{l+m+mi}{10}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{if} \PYG{n}{i} \PYG{o}{\PYGZlt{}} \PYG{l+m+mi}{5}\PYG{p}{:}
-            \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.small\PYGZus{}stage1}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{i}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-        \PYG{k}{else}\PYG{p}{:}
-            \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.big\PYGZus{}stage1}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{i}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n+nd}{@jobs\PYGZus{}limit}\PYG{p}{(}\PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ftp\PYGZus{}download\PYGZus{}limit}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{make\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.small\PYGZus{}stage1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{stage1\PYGZus{}small}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FTP downloading }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{}Start}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{input\PYGZus{}file}
-    \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{)}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FTP downloading }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{}Finished}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{input\PYGZus{}file}
-
-\PYG{n+nd}{@jobs\PYGZus{}limit}\PYG{p}{(}\PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ftp\PYGZus{}download\PYGZus{}limit}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{make\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.big\PYGZus{}stage1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{stage1\PYGZus{}big}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FTP downloading }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{}Start}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{input\PYGZus{}file}
-    \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{)}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FTP downloading }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{}Finished}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{input\PYGZus{}file}
-
-\PYG{n+nd}{@jobs\PYGZus{}limit}\PYG{p}{(}\PYG{l+m+mi}{5}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{n}{stage1\PYGZus{}small}\PYG{p}{,} \PYG{n}{stage1\PYGZus{}big}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage3}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{stage2}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Processing stage2 }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{}Start}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{input\PYGZus{}file}
-    \PYG{n}{time}\PYG{o}{.}\PYG{n}{sleep}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{)}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Processing stage2 }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{}Finished}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{input\PYGZus{}file}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{10}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-Giving:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{10}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{0}\PYG{p}{)}
-
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} 3 jobs at a time, interleaved}
-\PYG{g+go}{FTP downloading 5.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 6.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 7.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 5.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 8.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 6.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 9.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 7.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 0.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 8.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 1.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 9.big\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 2.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 0.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 3.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 1.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 4.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{FTP downloading 2.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 3.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{FTP downloading 4.small\PYGZus{}stage1 \PYGZhy{}\PYGZgt{}Finished}
-
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} 5 jobs at a time, interleaved}
-\PYG{g+go}{Processing stage2 0.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 1.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 2.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 3.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 4.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 0.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 5.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 1.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 6.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 2.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 4.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 7.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 8.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 3.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 9.stage2 \PYGZhy{}\PYGZgt{}Start}
-\PYG{g+go}{Processing stage2 5.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 7.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 6.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 8.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\PYG{g+go}{Processing stage2 9.stage2 \PYGZhy{}\PYGZgt{}Finished}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Using  \texttt{ruffus.drmaa\_wrapper}}
-\label{tutorials/new_tutorial/multiprocessing_code:using-ruffus-drmaa-wrapper}\label{tutorials/new_tutorial/multiprocessing_code:id1}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}!/usr/bin/python}
-\PYG{n}{job\PYGZus{}queue\PYGZus{}name}    \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{YOUR\PYGZus{}QUEUE\PYGZus{}NAME\PYGZus{}GOES\PYGZus{}HERE}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{job\PYGZus{}other\PYGZus{}options} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}P YOUR\PYGZus{}PROJECT\PYGZus{}NAME\PYGZus{}GOES\PYGZus{}HERE}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.drmaa\PYGZus{}wrapper} \PYG{k+kn}{import} \PYG{n}{run\PYGZus{}job}\PYG{p}{,} \PYG{n}{error\PYGZus{}drmaa\PYGZus{}job}
-
-\PYG{n}{parser} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{get\PYGZus{}argparse}\PYG{p}{(}\PYG{n}{description}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{WHAT DOES THIS PIPELINE DO?}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-
-\PYG{n}{options} \PYG{o}{=} \PYG{n}{parser}\PYG{o}{.}\PYG{n}{parse\PYGZus{}args}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}  logger which can be passed to multiprocessing ruffus tasks}
-\PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{setup\PYGZus{}logging} \PYG{p}{(}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{log\PYGZus{}file}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   start shared drmaa session for all jobs / tasks in pipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{k+kn}{import} \PYG{n+nn}{drmaa}
-\PYG{n}{drmaa\PYGZus{}session} \PYG{o}{=} \PYG{n}{drmaa}\PYG{o}{.}\PYG{n}{Session}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{drmaa\PYGZus{}session}\PYG{o}{.}\PYG{n}{initialize}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.chromosome}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{X.chromosome}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-           \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}test\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{try}\PYG{p}{:}
-        \PYG{n}{stdout\PYGZus{}res}\PYG{p}{,} \PYG{n}{stderr\PYGZus{}res} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-        \PYG{n}{job\PYGZus{}queue\PYGZus{}name}\PYG{p}{,} \PYG{n}{job\PYGZus{}other\PYGZus{}options} \PYG{o}{=} \PYG{n}{get\PYGZus{}queue\PYGZus{}options}\PYG{p}{(}\PYG{p}{)}
-
-        \PYG{c}{\PYGZsh{}}
-        \PYG{c}{\PYGZsh{}   ruffus.drmaa\PYGZus{}wrapper.run\PYGZus{}job}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{n}{stdout\PYGZus{}res}\PYG{p}{,} \PYG{n}{stderr\PYGZus{}res}  \PYG{o}{=} \PYG{n}{run\PYGZus{}job}\PYG{p}{(}\PYG{n}{cmd\PYGZus{}str}           \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{touch }\PYG{l+s}{\PYGZdq{}} \PYG{o}{+} \PYG{n}{output\PYGZus{}file}\PYG{p}{,}
-                                          \PYG{n}{job\PYGZus{}name}          \PYG{o}{=} \PYG{n}{job\PYGZus{}name}\PYG{p}{,}
-                                          \PYG{n}{logger}            \PYG{o}{=} \PYG{n}{logger}\PYG{p}{,}
-                                          \PYG{n}{drmaa\PYGZus{}session}     \PYG{o}{=} \PYG{n}{drmaa\PYGZus{}session}\PYG{p}{,}
-                                          \PYG{n}{run\PYGZus{}locally}       \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{local\PYGZus{}run}\PYG{p}{,}
-                                          \PYG{n}{job\PYGZus{}queue\PYGZus{}name}    \PYG{o}{=} \PYG{n}{job\PYGZus{}queue\PYGZus{}name}\PYG{p}{,}
-                                          \PYG{n}{job\PYGZus{}other\PYGZus{}options} \PYG{o}{=} \PYG{n}{job\PYGZus{}other\PYGZus{}options}\PYG{p}{)}
-
-    \PYG{c}{\PYGZsh{} relay all the stdout, stderr, drmaa output to diagnose failures}
-    \PYG{k}{except} \PYG{n}{error\PYGZus{}drmaa\PYGZus{}job} \PYG{k}{as} \PYG{n}{err}\PYG{p}{:}
-        \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n+nb}{map}\PYG{p}{(}\PYG{n+nb}{str}\PYG{p}{,}
-                            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Failed to run:}\PYG{l+s}{\PYGZdq{}}
-                            \PYG{n}{cmd}\PYG{p}{,}
-                            \PYG{n}{err}\PYG{p}{,}
-                            \PYG{n}{stdout\PYGZus{}res}\PYG{p}{,}
-                            \PYG{n}{stderr\PYGZus{}res}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{k}{if} \PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}} \PYG{o}{==} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZus{}\PYGZus{}main\PYGZus{}\PYGZus{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}
-    \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{run} \PYG{p}{(}\PYG{n}{options}\PYG{p}{,} \PYG{n}{multithread} \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{jobs}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{} cleanup drmaa}
-    \PYG{n}{drmaa\PYGZus{}session}\PYG{o}{.}\PYG{n}{exit}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 15}: Python Code for Logging progress through a pipeline}
-\label{tutorials/new_tutorial/logging_code:new-manual-logging-chapter-num-python-code-for-logging-progress-through-a-pipeline}\label{tutorials/new_tutorial/logging_code::doc}\label{tutorials/new_tutorial/logging_code:new-manual-logging-code}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-Back to \textbf{Chapter 15}: {\hyperref[tutorials/new_tutorial/logging:new-manual-logging]{\emph{Logging progress through a pipeline}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Rotating set of file logs}
-\label{tutorials/new_tutorial/logging_code:rotating-set-of-file-logs}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{logging}
-\PYG{k+kn}{import} \PYG{n+nn}{logging.handlers}
-
-\PYG{n}{LOG\PYGZus{}FILENAME} \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/tmp/ruffus.log}\PYG{l+s}{\PYGZsq{}}
-
-\PYG{c}{\PYGZsh{} Set up a specific logger with our desired output level}
-\PYG{n}{logger} \PYG{o}{=} \PYG{n}{logging}\PYG{o}{.}\PYG{n}{getLogger}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{My\PYGZus{}Ruffus\PYGZus{}logger}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{n}{logger}\PYG{o}{.}\PYG{n}{setLevel}\PYG{p}{(}\PYG{n}{logging}\PYG{o}{.}\PYG{n}{DEBUG}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} Rotate a set of 5 log files every 2kb}
-\PYG{n}{handler} \PYG{o}{=} \PYG{n}{logging}\PYG{o}{.}\PYG{n}{handlers}\PYG{o}{.}\PYG{n}{RotatingFileHandler}\PYG{p}{(}
-              \PYG{n}{LOG\PYGZus{}FILENAME}\PYG{p}{,} \PYG{n}{maxBytes}\PYG{o}{=}\PYG{l+m+mi}{2000}\PYG{p}{,} \PYG{n}{backupCount}\PYG{o}{=}\PYG{l+m+mi}{5}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} Add the log message handler to the logger}
-\PYG{n}{logger}\PYG{o}{.}\PYG{n}{addHandler}\PYG{p}{(}\PYG{n}{handler}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} Ruffus pipeline}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{} Start with some initial data file of yours...}
-\PYG{n}{initial\PYGZus{}file} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{job1.input}\PYG{l+s}{\PYGZdq{}}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{initial\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{initial\PYGZus{}file}\PYG{p}{,}
-            \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.input}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.output1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Some detailed description}\PYG{l+s}{\PYGZdq{}}
-    \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   use our custom logging object}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{logger}\PYG{o}{=}\PYG{n}{logger}\PYG{p}{)}
-\PYG{k}{print} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/tmp/ruffus.log}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 16}: Python Code for \emph{@subdivide} tasks to run efficiently and regroup with \emph{@collate}}
-\label{tutorials/new_tutorial/subdivide_collate_code:new-manual-subdivide-collate-code}\label{tutorials/new_tutorial/subdivide_collate_code::doc}\label{tutorials/new_tutorial/subdivide_collate_code:new-manual-subdivide-collate-chapter-num-python-code-for-subdivide-tasks-to-run-efficiently-and-regroup-with-collate}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/jobs_limit:decorators-jobs-limit]{\emph{@jobs\_limit}}} syntax
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run()}}} syntax
-
-\item {} 
-{\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job]{\emph{drmaa\_wrapper.run\_job()}}} syntax
-
-\item {} 
-Back to \textbf{Chapter 16}: {\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-subdivide-collate]{\emph{:ref:{}`@subdivide tasks to run efficiently and regroup with @collate}}}
-
-\end{itemize}
-
-
-
-
-\subsection{\emph{@subdivide} and regroup with \emph{@collate} example}
-\label{tutorials/new_tutorial/subdivide_collate_code:subdivide-and-regroup-with-collate-example}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{os}\PYG{o}{,} \PYG{n+nn}{random}\PYG{o}{,} \PYG{n+nn}{sys}
-
-\PYG{c}{\PYGZsh{} Create files a random number of lines}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}test\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{cnt\PYGZus{}lines} \PYG{o}{=} \PYG{n}{random}\PYG{o}{.}\PYG{n}{randint}\PYG{p}{(}\PYG{l+m+mi}{1}\PYG{p}{,}\PYG{l+m+mi}{3}\PYG{p}{)} \PYG{o}{*} \PYG{l+m+mi}{2}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:}
-        \PYG{k}{for} \PYG{n}{ii} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{cnt\PYGZus{}lines}\PYG{p}{)}\PYG{p}{:}
-            \PYG{n}{oo}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{data item = }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{ii}\PYG{p}{)}
-        \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{        }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ has }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{ lines}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{cnt\PYGZus{}lines}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   subdivide the input files into NNN fragment files of 2 lines each}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@subdivide}\PYG{p}{(} \PYG{n}{create\PYGZus{}test\PYGZus{}files}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}.*.fragment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{subdivide\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name\PYGZus{}stem}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   cleanup any previous results}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{oo} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{oo}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   Output files contain two lines each}
-    \PYG{c}{\PYGZsh{}       (new output files every even line)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{cnt\PYGZus{}output\PYGZus{}files} \PYG{o}{=} \PYG{l+m+mi}{0}
-    \PYG{k}{for} \PYG{n}{ii}\PYG{p}{,} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{enumerate}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{if} \PYG{n}{ii} \PYG{o}{\PYGZpc{}} \PYG{l+m+mi}{2} \PYG{o}{==} \PYG{l+m+mi}{0}\PYG{p}{:}
-            \PYG{n}{cnt\PYGZus{}output\PYGZus{}files} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-            \PYG{n}{output\PYGZus{}file\PYGZus{}name} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{.}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.fragment}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name\PYGZus{}stem}\PYG{p}{,} \PYG{n}{cnt\PYGZus{}output\PYGZus{}files}\PYG{p}{)}
-            \PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-            \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{        Subdivide }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}
-        \PYG{n}{output\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Analyse each fragment independently}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{subdivide\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.fragment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.analysed}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{analyse\PYGZus{}fragments}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{        Analysing }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:}
-        \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-            \PYG{n}{oo}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{analysed }\PYG{l+s}{\PYGZdq{}} \PYG{o}{+} \PYG{n}{line}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Group results using original names}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@collate}\PYG{p}{(}   \PYG{n}{analyse\PYGZus{}fragments}\PYG{p}{,}
-
-            \PYG{c}{\PYGZsh{} split file name into [abc].NUMBER.analysed}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/(?P\PYGZlt{}NAME\PYGZgt{}[abc]+)}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.analysed\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}NAME[0]\PYGZcb{}.final\PYGZus{}result}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{recombine\PYGZus{}analyses}\PYG{p}{(}\PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:}
-        \PYG{k}{for} \PYG{n}{input\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{input\PYGZus{}file\PYGZus{}names}\PYG{p}{:}
-            \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{        Recombine }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}
-            \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-                \PYG{n}{oo}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-
-
-
-
-\PYG{c}{\PYGZsh{}pipeline\PYGZus{}printout(sys.stdout, verbose = 3)}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{1}\PYG{p}{)}
-\end{Verbatim}
-
-Results in
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{1}\PYG{p}{)}
-
-\PYG{g+go}{        a.start has 2 lines}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} a.start] completed}
-\PYG{g+go}{        b.start has 6 lines}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} b.start] completed}
-\PYG{g+go}{        c.start has 6 lines}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} c.start] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}test\PYGZus{}files}
-
-\PYG{g+go}{        Subdivide a.start \PYGZhy{}\PYGZgt{} /home/lg/temp/a.1.fragment}
-\PYG{g+go}{    Job  = [a.start \PYGZhy{}\PYGZgt{} a.*.fragment, a] completed}
-\PYG{g+go}{        Subdivide b.start \PYGZhy{}\PYGZgt{} /home/lg/temp/b.1.fragment}
-\PYG{g+go}{        Subdivide b.start \PYGZhy{}\PYGZgt{} /home/lg/temp/b.2.fragment}
-\PYG{g+go}{        Subdivide b.start \PYGZhy{}\PYGZgt{} /home/lg/temp/b.3.fragment}
-\PYG{g+go}{    Job  = [b.start \PYGZhy{}\PYGZgt{} b.*.fragment, b] completed}
-\PYG{g+go}{        Subdivide c.start \PYGZhy{}\PYGZgt{} /home/lg/temp/c.1.fragment}
-\PYG{g+go}{        Subdivide c.start \PYGZhy{}\PYGZgt{} /home/lg/temp/c.2.fragment}
-\PYG{g+go}{        Subdivide c.start \PYGZhy{}\PYGZgt{} /home/lg/temp/c.3.fragment}
-\PYG{g+go}{    Job  = [c.start \PYGZhy{}\PYGZgt{} c.*.fragment, c] completed}
-\PYG{g+go}{Completed Task = subdivide\PYGZus{}files}
-
-\PYG{g+go}{        Analysing /home/lg/temp/a.1.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/a.1.analysed}
-\PYG{g+go}{    Job  = [a.1.fragment \PYGZhy{}\PYGZgt{} a.1.analysed] completed}
-\PYG{g+go}{        Analysing /home/lg/temp/b.1.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/b.1.analysed}
-\PYG{g+go}{    Job  = [b.1.fragment \PYGZhy{}\PYGZgt{} b.1.analysed] completed}
-\PYG{g+go}{        Analysing /home/lg/temp/b.2.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/b.2.analysed}
-\PYG{g+go}{    Job  = [b.2.fragment \PYGZhy{}\PYGZgt{} b.2.analysed] completed}
-\PYG{g+go}{        Analysing /home/lg/temp/b.3.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/b.3.analysed}
-\PYG{g+go}{    Job  = [b.3.fragment \PYGZhy{}\PYGZgt{} b.3.analysed] completed}
-\PYG{g+go}{        Analysing /home/lg/temp/c.1.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/c.1.analysed}
-\PYG{g+go}{    Job  = [c.1.fragment \PYGZhy{}\PYGZgt{} c.1.analysed] completed}
-\PYG{g+go}{        Analysing /home/lg/temp/c.2.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/c.2.analysed}
-\PYG{g+go}{    Job  = [c.2.fragment \PYGZhy{}\PYGZgt{} c.2.analysed] completed}
-\PYG{g+go}{        Analysing /home/lg/temp/c.3.fragment \PYGZhy{}\PYGZgt{} /home/lg/temp/c.3.analysed}
-\PYG{g+go}{    Job  = [c.3.fragment \PYGZhy{}\PYGZgt{} c.3.analysed] completed}
-\PYG{g+go}{Completed Task = analyse\PYGZus{}fragments}
-
-\PYG{g+go}{        Recombine /home/lg/temp/a.1.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/a.final\PYGZus{}result}
-\PYG{g+go}{    Job  = [[a.1.analysed] \PYGZhy{}\PYGZgt{} a.final\PYGZus{}result] completed}
-\PYG{g+go}{        Recombine /home/lg/temp/b.1.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/b.final\PYGZus{}result}
-\PYG{g+go}{        Recombine /home/lg/temp/b.2.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/b.final\PYGZus{}result}
-\PYG{g+go}{        Recombine /home/lg/temp/b.3.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/b.final\PYGZus{}result}
-\PYG{g+go}{    Job  = [[b.1.analysed, b.2.analysed, b.3.analysed] \PYGZhy{}\PYGZgt{} b.final\PYGZus{}result] completed}
-\PYG{g+go}{        Recombine /home/lg/temp/c.1.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/c.final\PYGZus{}result}
-\PYG{g+go}{        Recombine /home/lg/temp/c.2.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/c.final\PYGZus{}result}
-\PYG{g+go}{        Recombine /home/lg/temp/c.3.analysed \PYGZhy{}\PYGZgt{} /home/lg/temp/c.final\PYGZus{}result}
-\PYG{g+go}{    Job  = [[c.1.analysed, c.2.analysed, c.3.analysed] \PYGZhy{}\PYGZgt{} c.final\PYGZus{}result] completed}
-\PYG{g+go}{Completed Task = recombine\PYGZus{}analyses}
-\end{Verbatim}
-\end{quote}
-
-
-\section{\textbf{Chapter 17}: Python Code for \emph{@combinations}, \emph{@permutations} and all versus all \emph{@product}}
-\label{tutorials/new_tutorial/combinatorics_code:new-manual-combinatorics-chapter-num-python-code-for-combinations-permutations-and-all-versus-all-product}\label{tutorials/new_tutorial/combinatorics_code::doc}\label{tutorials/new_tutorial/combinatorics_code:new-manual-combinatorics-code}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}}
-
-\item {} 
-{\hyperref[decorators/combinations:decorators-combinations]{\emph{@combinations}}}
-
-\item {} 
-{\hyperref[decorators/permutations:decorators-permutations]{\emph{@permutations}}}
-
-\item {} 
-{\hyperref[decorators/product:decorators-product]{\emph{@product}}}
-
-\item {} 
-Back to \textbf{Chapter 17}: {\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinatorics]{\emph{Preparing directories for output with @combinatorics()}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Example code for \emph{@product}}
-\label{tutorials/new_tutorial/combinatorics_code:example-code-for-product}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   Three sets of initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ab}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{p.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{q.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}pq}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{x.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{x.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{y.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{y.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]} \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}xy}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @product}
-\PYG{n+nd}{@product}\PYG{p}{(}   \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ab}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 1}
-
-            \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}pq}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 2}
-
-            \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}xy}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 3}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}                 \PYG{c}{\PYGZsh{} Output Replacement string}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}          \PYG{c}{\PYGZsh{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}          \PYG{c}{\PYGZsh{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}.product}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}     \PYG{c}{\PYGZsh{}}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                 \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{} Extra parameter: basename for 1st set of files, 1st file name}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{}                               2nd}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{}                               3rd}
-             \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{product\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{} basenames      = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}parameter  = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}file}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output\PYGZus{}parameter = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a p x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a p y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a q x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a q y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b p x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b p y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b q x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b q y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}y.product}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Example code for \emph{@permutations}}
-\label{tutorials/new_tutorial/combinatorics_code:example-code-for-permutations}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @permutations}
-\PYG{n+nd}{@permutations}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}      \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 2 at a time}
-              \PYG{l+m+mi}{2}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}.permutations}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}                                2nd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{permutations\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-
-\PYG{g+go}{A \PYGZhy{} B}
-\PYG{g+go}{A \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} A}
-\PYG{g+go}{B \PYGZhy{} C}
-\PYG{g+go}{B \PYGZhy{} D}
-\PYG{g+go}{C \PYGZhy{} A}
-\PYG{g+go}{C \PYGZhy{} B}
-\PYG{g+go}{C \PYGZhy{} D}
-\PYG{g+go}{D \PYGZhy{} A}
-\PYG{g+go}{D \PYGZhy{} B}
-\PYG{g+go}{D \PYGZhy{} C}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Example code for \emph{@combinations}}
-\label{tutorials/new_tutorial/combinatorics_code:example-code-for-combinations}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @combinations}
-\PYG{n+nd}{@combinations}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}      \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 3 at a time}
-              \PYG{l+m+mi}{3}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][1]\PYGZcb{}.combinations}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              2nd}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              3rd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{combinations\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{A \PYGZhy{} B \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} B \PYGZhy{} D}
-\PYG{g+go}{A \PYGZhy{} C \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} C \PYGZhy{} D}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Example code for \emph{@combinations\_with\_replacement}}
-\label{tutorials/new_tutorial/combinatorics_code:example-code-for-combinations-with-replacement}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @combinations\PYGZus{}with\PYGZus{}replacement}
-\PYG{n+nd}{@combinations\PYGZus{}with\PYGZus{}replacement}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}   \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                                  \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 2 at a time}
-              \PYG{l+m+mi}{2}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}.combinations\PYGZus{}with\PYGZus{}replacement}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              2rd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{combinations\PYGZus{}with\PYGZus{}replacement\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{A \PYGZhy{} A}
-\PYG{g+go}{A \PYGZhy{} B}
-\PYG{g+go}{A \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} B}
-\PYG{g+go}{B \PYGZhy{} C}
-\PYG{g+go}{B \PYGZhy{} D}
-\PYG{g+go}{C \PYGZhy{} C}
-\PYG{g+go}{C \PYGZhy{} D}
-\PYG{g+go}{D \PYGZhy{} D}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\section{\textbf{Chapter 20}: Python Code for Manipulating task inputs via string substitution using \emph{inputs()}  and  \emph{add\_inputs()}}
-\label{tutorials/new_tutorial/inputs_code:new-manual-inputs-code}\label{tutorials/new_tutorial/inputs_code::doc}\label{tutorials/new_tutorial/inputs_code:new-manual-inputs-chapter-num-python-code-for-manipulating-task-inputs-via-string-substitution-using-inputs-and-add-inputs}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs()}}} syntax
-
-\item {} 
-{\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs()}}} syntax
-
-\item {} 
-Back to \textbf{Chapter 20}: {\hyperref[tutorials/new_tutorial/inputs:new-manual-inputs]{\emph{Manipulating task inputs via string substitution}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Example code for adding additional \emph{input} prerequisites per job with \emph{add\_inputs()}}
-\label{tutorials/new_tutorial/inputs_code:example-code-for-adding-additional-input-prerequisites-per-job-with-add-inputs}
-
-\subsubsection{1. Example: compiling c++ code}
-\label{tutorials/new_tutorial/inputs_code:example-compiling-c-code}\label{tutorials/new_tutorial/inputs_code:new-manual-inputs-example1}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} source files exist before our pipeline}
-\PYG{n}{source\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{k}{for} \PYG{n}{source\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{source\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{source\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}filename}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-Giving:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [hasty.cpp \PYGZhy{}\PYGZgt{} hasty.o] completed}
-\PYG{g+go}{    Job  = [messy.cpp \PYGZhy{}\PYGZgt{} messy.o] completed}
-\PYG{g+go}{    Job  = [tasty.cpp \PYGZhy{}\PYGZgt{} tasty.o] completed}
-\PYG{g+go}{Completed Task = compile}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{2. Example: Adding a common header file with \emph{add\_inputs()}}
-\label{tutorials/new_tutorial/inputs_code:new-manual-inputs-example2}\label{tutorials/new_tutorial/inputs_code:example-adding-a-common-header-file-with-add-inputs}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} source files exist before our pipeline}
-\PYG{n}{source\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{k}{for} \PYG{n}{source\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{source\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{source\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} common (universal) header exists before our pipeline}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{c}{\PYGZsh{} add header to the input of every job}
-            \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}filename}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-Giving:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[hasty.cpp, universal.h] \PYGZhy{}\PYGZgt{} hasty.o] completed}
-\PYG{g+go}{    Job  = [[messy.cpp, universal.h] \PYGZhy{}\PYGZgt{} messy.o] completed}
-\PYG{g+go}{    Job  = [[tasty.cpp, universal.h] \PYGZhy{}\PYGZgt{} tasty.o] completed}
-\PYG{g+go}{Completed Task = compile}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{3. Example: Additional \emph{Input} can be tasks}
-\label{tutorials/new_tutorial/inputs_code:example-additional-input-can-be-tasks}\label{tutorials/new_tutorial/inputs_code:new-manual-inputs-example3}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} source files exist before our pipeline}
-\PYG{n}{source\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{k}{for} \PYG{n}{source\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{source\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{source\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} common (universal) header exists before our pipeline}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{} make header files}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}matching\PYGZus{}headers}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{c}{\PYGZsh{} add header to the input of every job}
-            \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                        \PYG{c}{\PYGZsh{} add result of task create\PYGZus{}matching\PYGZus{}headers to the input of every job}
-                       \PYG{n}{create\PYGZus{}matching\PYGZus{}headers}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}filename}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-Giving:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [hasty.cpp \PYGZhy{}\PYGZgt{} hasty.h] completed}
-\PYG{g+go}{    Job  = [messy.cpp \PYGZhy{}\PYGZgt{} messy.h] completed}
-\PYG{g+go}{    Job  = [tasty.cpp \PYGZhy{}\PYGZgt{} tasty.h] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}matching\PYGZus{}headers}
-\PYG{g+go}{    Job  = [[hasty.cpp, universal.h, hasty.h, messy.h, tasty.h] \PYGZhy{}\PYGZgt{} hasty.o] completed}
-\PYG{g+go}{    Job  = [[messy.cpp, universal.h, hasty.h, messy.h, tasty.h] \PYGZhy{}\PYGZgt{} messy.o] completed}
-\PYG{g+go}{    Job  = [[tasty.cpp, universal.h, hasty.h, messy.h, tasty.h] \PYGZhy{}\PYGZgt{} tasty.o] completed}
-\PYG{g+go}{Completed Task = compile}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{4. Example: Add corresponding files using \emph{add\_inputs()} with \emph{formatter} or \emph{regex}}
-\label{tutorials/new_tutorial/inputs_code:new-manual-inputs-example4}\label{tutorials/new_tutorial/inputs_code:example-add-corresponding-files-using-add-inputs-with-formatter-or-regex}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} source files exist before our pipeline}
-\PYG{n}{source\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{n}{header\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{k}{for} \PYG{n}{source\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{source\PYGZus{}files} \PYG{o}{+} \PYG{n}{header\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{source\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} common (universal) header exists before our pipeline}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{source\PYGZus{}files}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                        \PYG{c}{\PYGZsh{} corresponding header for each source file}
-            \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                       \PYG{c}{\PYGZsh{} add header to the input of every job}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}filename}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-Giving:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [[hasty.cpp, hasty.h, universal.h] \PYGZhy{}\PYGZgt{} hasty.o] completed}
-\PYG{g+go}{    Job  = [[messy.cpp, messy.h, universal.h] \PYGZhy{}\PYGZgt{} messy.o] completed}
-\PYG{g+go}{    Job  = [[tasty.cpp, tasty.h, universal.h] \PYGZhy{}\PYGZgt{} tasty.o] completed}
-\PYG{g+go}{Completed Task = compile}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Example code for replacing all input parameters with \emph{inputs()}}
-\label{tutorials/new_tutorial/inputs_code:example-code-for-replacing-all-input-parameters-with-inputs}
-
-\subsubsection{5. Example: Running matching python scripts using \emph{inputs()}}
-\label{tutorials/new_tutorial/inputs_code:example-running-matching-python-scripts-using-inputs}\label{tutorials/new_tutorial/inputs_code:new-manual-inputs-example5}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} source files exist before our pipeline}
-\PYG{n}{source\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.cpp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{n}{python\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hasty.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tasty.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{messy.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{k}{for} \PYG{n}{source\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{source\PYGZus{}files} \PYG{o}{+} \PYG{n}{python\PYGZus{}files}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{source\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} common (universal) header exists before our pipeline}
-\PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{source\PYGZus{}files}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.cpp\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{c}{\PYGZsh{} corresponding python file for each source file}
-            \PYG{n}{inputs}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{run\PYGZus{}corresponding\PYGZus{}python}\PYG{p}{(}\PYG{n}{input\PYGZus{}filenames}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-Giving:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [hasty.py \PYGZhy{}\PYGZgt{} hasty.results] completed}
-\PYG{g+go}{    Job  = [messy.py \PYGZhy{}\PYGZgt{} messy.results] completed}
-\PYG{g+go}{    Job  = [tasty.py \PYGZhy{}\PYGZgt{} tasty.results] completed}
-\PYG{g+go}{Completed Task = run\PYGZus{}corresponding\PYGZus{}python}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\section{\textbf{Chapter 21}: Esoteric: Python Code for Generating parameters on the fly with \emph{@files}}
-\label{tutorials/new_tutorial/onthefly_code:new-manual-on-the-fly-code}\label{tutorials/new_tutorial/onthefly_code::doc}\label{tutorials/new_tutorial/onthefly_code:new-manual-on-the-fly-chapter-num-esoteric-python-code-for-generating-parameters-on-the-fly-with-files}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[decorators/files_ex:decorators-files-on-the-fly]{\emph{@files on-the-fly syntax in detail}}}
-
-\item {} 
-Back to \textbf{Chapter 21}: {\hyperref[tutorials/new_tutorial/onthefly:new-manual-on-the-fly]{\emph{Generating parameters on the fly}}}
-
-\end{itemize}
-
-
-
-
-\subsection{Introduction}
-\label{tutorials/new_tutorial/onthefly_code:introduction}\begin{quote}
-
-\begin{DUlineblock}{0em}
-\item[] This script takes N pairs of input file pairs (with the suffices .gene and .gwas)
-\item[] and runs them against M sets of simulation data (with the suffix .simulation)
-\item[] A summary per input file pair is then produced
-\end{DUlineblock}
-
-In pseudo-code:
-\begin{quote}
-
-STEP\_1:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-for n\_file in NNN\_pairs\_of\_input\_files:
-    for m\_file in MMM\_simulation\_data:
-
-        [n\_file.gene,
-         n\_file.gwas,
-         m\_file.simulation] -\textgreater{} n\_file.m\_file.simulation\_res
-\end{Verbatim}
-
-STEP\_2:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-for n\_file in NNN\_pairs\_of\_input\_files:
-
-    n\_file.*.simulation\_res -\textgreater{} n\_file.mean
-\end{Verbatim}
-
-\begin{DUlineblock}{0em}
-\item[] n = CNT\_GENE\_GWAS\_FILES
-\item[] m = CNT\_SIMULATION\_FILES
-\end{DUlineblock}
-\end{quote}
-\end{quote}
-
-
-\subsection{Code}
-\label{tutorials/new_tutorial/onthefly_code:code}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{os}
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   constants}
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-\PYG{n}{working\PYGZus{}dir}             \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{temp\PYGZus{}NxM}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{simulation\PYGZus{}data\PYGZus{}dir}     \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{simulation}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}           \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{gene}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{CNT\PYGZus{}GENE\PYGZus{}GWAS\PYGZus{}FILES}     \PYG{o}{=} \PYG{l+m+mi}{2}
-\PYG{n}{CNT\PYGZus{}SIMULATION\PYGZus{}FILES}    \PYG{o}{=} \PYG{l+m+mi}{3}
-
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   imports}
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-\PYG{k+kn}{import} \PYG{n+nn}{os}\PYG{o}{,} \PYG{n+nn}{sys}
-\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{izip}
-\PYG{k+kn}{import} \PYG{n+nn}{glob}
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Functions}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   get gene gwas file pairs}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{k}{def} \PYG{n+nf}{get\PYGZus{}gene\PYGZus{}gwas\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}  \PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Helper function to get all *.gene, *.gwas from the direction specified}
-\PYG{l+s+sd}{        in \PYGZhy{}\PYGZhy{}gene\PYGZus{}data\PYGZus{}dir}
-
-\PYG{l+s+sd}{    Returns}
-\PYG{l+s+sd}{        file pairs with both .gene and .gwas extensions,}
-\PYG{l+s+sd}{        corresponding roots (no extension) of each file}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{gene\PYGZus{}files} \PYG{o}{=} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.gene}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-    \PYG{n}{gwas\PYGZus{}files} \PYG{o}{=} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.gwas}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{common\PYGZus{}roots} \PYG{o}{=} \PYG{n+nb}{set}\PYG{p}{(}\PYG{n+nb}{map}\PYG{p}{(}\PYG{k}{lambda} \PYG{n}{x}\PYG{p}{:} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{splitext}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{split}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{,} \PYG{n}{gene\PYGZus{}files}\PYG{p}{)}\PYG{p}{)}
-    \PYG{n}{common\PYGZus{}roots} \PYG{o}{\PYGZam{}}\PYG{o}{=}\PYG{n+nb}{set}\PYG{p}{(}\PYG{n+nb}{map}\PYG{p}{(}\PYG{k}{lambda} \PYG{n}{x}\PYG{p}{:} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{splitext}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{split}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{,} \PYG{n}{gwas\PYGZus{}files}\PYG{p}{)}\PYG{p}{)}
-    \PYG{n}{common\PYGZus{}roots} \PYG{o}{=} \PYG{n+nb}{list}\PYG{p}{(}\PYG{n}{common\PYGZus{}roots}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{p} \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{p}{;} \PYG{n}{g\PYGZus{}dir} \PYG{o}{=} \PYG{n}{gene\PYGZus{}data\PYGZus{}dir}
-    \PYG{n}{file\PYGZus{}pairs} \PYG{o}{=} \PYG{p}{[}\PYG{p}{[}\PYG{n}{p}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{g\PYGZus{}dir}\PYG{p}{,} \PYG{n}{x} \PYG{o}{+} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.gene}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{p}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{g\PYGZus{}dir}\PYG{p}{,} \PYG{n}{x} \PYG{o}{+} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.gwas}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{]} \PYG{k}{for} \PYG{n}{x} \PYG{o+ow}{in} \PYG{n}{common\PYGZus{}roots}\PYG{p}{]}
-    \PYG{k}{return} \PYG{n}{file\PYGZus{}pairs}\PYG{p}{,} \PYG{n}{common\PYGZus{}roots}
-
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   get simulation files}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{k}{def} \PYG{n+nf}{get\PYGZus{}simulation\PYGZus{}files}\PYG{p}{(}  \PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Helper function to get all *.simulation from the direction specified}
-\PYG{l+s+sd}{        in \PYGZhy{}\PYGZhy{}simulation\PYGZus{}data\PYGZus{}dir}
-\PYG{l+s+sd}{        Returns}
-\PYG{l+s+sd}{            file with .simulation extensions,}
-\PYG{l+s+sd}{            corresponding roots (no extension) of each file}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{simulation\PYGZus{}files} \PYG{o}{=} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{simulation\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.simulation}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-    \PYG{n}{simulation\PYGZus{}roots} \PYG{o}{=}\PYG{n+nb}{map}\PYG{p}{(}\PYG{k}{lambda} \PYG{n}{x}\PYG{p}{:} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{splitext}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{split}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{,} \PYG{n}{simulation\PYGZus{}files}\PYG{p}{)}
-    \PYG{k}{return} \PYG{n}{simulation\PYGZus{}files}\PYG{p}{,} \PYG{n}{simulation\PYGZus{}roots}
-
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Main logic}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-
-
-
-
-
-
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   setup\PYGZus{}simulation\PYGZus{}data}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} mkdir: makes sure output directories exist before task}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{mkdir}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{n}{simulation\PYGZus{}data\PYGZus{}dir}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{setup\PYGZus{}simulation\PYGZus{}data} \PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    create simulation files}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{CNT\PYGZus{}GENE\PYGZus{}GWAS\PYGZus{}FILES}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}03d}\PYG{l+s}{.gene}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{i}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}03d}\PYG{l+s}{.gwas}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{i}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{} gene files without corresponding gwas and vice versa}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{orphan1.gene}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{orphan2.gwas}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{orphan3.gwas}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{CNT\PYGZus{}SIMULATION\PYGZus{}FILES}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{simulation\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}03d}\PYG{l+s}{.simulation}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{i}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-
-
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   cleanup\PYGZus{}simulation\PYGZus{}data}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{k}{def} \PYG{n+nf}{try\PYGZus{}rmdir} \PYG{p}{(}\PYG{n}{d}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{if} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{exists}\PYG{p}{(}\PYG{n}{d}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{try}\PYG{p}{:}
-            \PYG{n}{os}\PYG{o}{.}\PYG{n}{rmdir}\PYG{p}{(}\PYG{n}{d}\PYG{p}{)}
-        \PYG{k}{except} \PYG{n+ne}{OSError}\PYG{p}{:}
-            \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Warning:}\PYG{l+s+se}{\PYGZbs{}t}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ is not empty and will not be removed.}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{d}\PYG{p}{)}
-
-
-
-\PYG{k}{def} \PYG{n+nf}{cleanup\PYGZus{}simulation\PYGZus{}data} \PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    cleanup files}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Cleanup working directory and simulation files.}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   cleanup gene and gwas files}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{f} \PYG{o+ow}{in} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.gene}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{f}\PYG{p}{)}
-    \PYG{k}{for} \PYG{n}{f} \PYG{o+ow}{in} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.gwas}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{f}\PYG{p}{)}
-    \PYG{n}{try\PYGZus{}rmdir}\PYG{p}{(}\PYG{n}{gene\PYGZus{}data\PYGZus{}dir}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   cleanup simulation}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{f} \PYG{o+ow}{in} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{simulation\PYGZus{}data\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.simulation}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{f}\PYG{p}{)}
-    \PYG{n}{try\PYGZus{}rmdir}\PYG{p}{(}\PYG{n}{simulation\PYGZus{}data\PYGZus{}dir}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   cleanup working\PYGZus{}dir}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{f} \PYG{o+ow}{in} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{simulation\PYGZus{}results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.simulation\PYGZus{}res}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{f}\PYG{p}{)}
-    \PYG{n}{try\PYGZus{}rmdir}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{simulation\PYGZus{}results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{f} \PYG{o+ow}{in} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.mean}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{f}\PYG{p}{)}
-    \PYG{n}{try\PYGZus{}rmdir}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Step 1:}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}        for n\PYGZus{}file in NNN\PYGZus{}pairs\PYGZus{}of\PYGZus{}input\PYGZus{}files:}
-\PYG{c}{\PYGZsh{}            for m\PYGZus{}file in MMM\PYGZus{}simulation\PYGZus{}data:}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}                [n\PYGZus{}file.gene,}
-\PYG{c}{\PYGZsh{}                 n\PYGZus{}file.gwas,}
-\PYG{c}{\PYGZsh{}                 m\PYGZus{}file.simulation] \PYGZhy{}\PYGZgt{} working\PYGZus{}dir/n\PYGZus{}file.m\PYGZus{}file.simulation\PYGZus{}res}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{k}{def} \PYG{n+nf}{generate\PYGZus{}simulation\PYGZus{}params} \PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Custom function to generate}
-\PYG{l+s+sd}{    file names for gene/gwas simulation study}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{simulation\PYGZus{}files}\PYG{p}{,} \PYG{n}{simulation\PYGZus{}file\PYGZus{}roots}    \PYG{o}{=} \PYG{n}{get\PYGZus{}simulation\PYGZus{}files}\PYG{p}{(}\PYG{p}{)}
-    \PYG{n}{gene\PYGZus{}gwas\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,} \PYG{n}{gene\PYGZus{}gwas\PYGZus{}file\PYGZus{}roots} \PYG{o}{=}  \PYG{n}{get\PYGZus{}gene\PYGZus{}gwas\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{sim\PYGZus{}file}\PYG{p}{,} \PYG{n}{sim\PYGZus{}file\PYGZus{}root} \PYG{o+ow}{in} \PYG{n}{izip}\PYG{p}{(}\PYG{n}{simulation\PYGZus{}files}\PYG{p}{,} \PYG{n}{simulation\PYGZus{}file\PYGZus{}roots}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{for} \PYG{p}{(}\PYG{n}{gene}\PYG{p}{,} \PYG{n}{gwas}\PYG{p}{)}\PYG{p}{,} \PYG{n}{gene\PYGZus{}file\PYGZus{}root} \PYG{o+ow}{in} \PYG{n}{izip}\PYG{p}{(}\PYG{n}{gene\PYGZus{}gwas\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,} \PYG{n}{gene\PYGZus{}gwas\PYGZus{}file\PYGZus{}roots}\PYG{p}{)}\PYG{p}{:}
-            \PYG{c}{\PYGZsh{}}
-            \PYG{n}{result\PYGZus{}file} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{.}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{.simulation\PYGZus{}res}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{gene\PYGZus{}file\PYGZus{}root}\PYG{p}{,} \PYG{n}{sim\PYGZus{}file\PYGZus{}root}\PYG{p}{)}
-            \PYG{n}{result\PYGZus{}file\PYGZus{}path} \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{simulation\PYGZus{}results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{result\PYGZus{}file}\PYG{p}{)}
-            \PYG{c}{\PYGZsh{}}
-            \PYG{k}{yield} \PYG{p}{[}\PYG{n}{gene}\PYG{p}{,} \PYG{n}{gwas}\PYG{p}{,} \PYG{n}{sim\PYGZus{}file}\PYG{p}{]}\PYG{p}{,} \PYG{n}{result\PYGZus{}file\PYGZus{}path}\PYG{p}{,} \PYG{n}{gene\PYGZus{}file\PYGZus{}root}\PYG{p}{,} \PYG{n}{sim\PYGZus{}file\PYGZus{}root}\PYG{p}{,} \PYG{n}{result\PYGZus{}file}
-
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} mkdir: makes sure output directories exist before task}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{mkdir}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{simulation\PYGZus{}results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n}{generate\PYGZus{}simulation\PYGZus{}params}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{gwas\PYGZus{}simulation}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{result\PYGZus{}file\PYGZus{}path}\PYG{p}{,} \PYG{n}{gene\PYGZus{}file\PYGZus{}root}\PYG{p}{,} \PYG{n}{sim\PYGZus{}file\PYGZus{}root}\PYG{p}{,} \PYG{n}{result\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Dummy calculation of gene gwas vs simulation data}
-\PYG{l+s+sd}{    Normally runs in parallel on a computational cluster}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{p}{(}\PYG{n}{gene\PYGZus{}file}\PYG{p}{,}
-    \PYG{n}{gwas\PYGZus{}file}\PYG{p}{,}
-    \PYG{n}{simulation\PYGZus{}data\PYGZus{}file}\PYG{p}{)} \PYG{o}{=} \PYG{n}{input\PYGZus{}files}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{simulation\PYGZus{}res\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{result\PYGZus{}file\PYGZus{}path}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n}{simulation\PYGZus{}res\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ + }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{gene\PYGZus{}file\PYGZus{}root}\PYG{p}{,} \PYG{n}{sim\PYGZus{}file\PYGZus{}root}\PYG{p}{,} \PYG{n}{result\PYGZus{}file}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Step 2:}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Statistical summary per gene/gwas file pair}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}        for n\PYGZus{}file in NNN\PYGZus{}pairs\PYGZus{}of\PYGZus{}input\PYGZus{}files:}
-\PYG{c}{\PYGZsh{}            working\PYGZus{}dir/simulation\PYGZus{}results/n.*.simulation\PYGZus{}res}
-\PYG{c}{\PYGZsh{}               \PYGZhy{}\PYGZgt{} working\PYGZus{}dir/n.mean}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-
-
-\PYG{n+nd}{@collate}\PYG{p}{(}\PYG{n}{gwas\PYGZus{}simulation}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{simulation\PYGZus{}results/(}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+).}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+.simulation\PYGZus{}res}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.mean}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{k}{lambda} \PYG{p}{:} \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{OK}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{statistical\PYGZus{}summary} \PYG{p}{(}\PYG{n}{result\PYGZus{}files}\PYG{p}{,} \PYG{n}{summary\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Simulate statistical summary}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{summary\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{summary\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{for} \PYG{n}{f} \PYG{o+ow}{in} \PYG{n}{result\PYGZus{}files}\PYG{p}{:}
-        \PYG{n}{summary\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{f}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{setup\PYGZus{}simulation\PYGZus{}data}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{statistical\PYGZus{}summary}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} uncomment to printout flowchar}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} pipeline\PYGZus{}printout(sys.stdout, [statistical\PYGZus{}summary], verbose=2)}
-\PYG{c}{\PYGZsh{} graph\PYGZus{}printout (\PYGZdq{}flowchart.jpg\PYGZdq{}, \PYGZdq{}jpg\PYGZdq{}, [statistical\PYGZus{}summary])}
-\PYG{c}{\PYGZsh{}}
-
-\PYG{n}{cleanup\PYGZus{}simulation\PYGZus{}data} \PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Resulting Output}
-\label{tutorials/new_tutorial/onthefly_code:resulting-output}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{setup\PYGZus{}simulation\PYGZus{}data}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{)}
-\PYG{g+go}{    Make directories [temp\PYGZus{}NxM/gene, temp\PYGZus{}NxM/simulation] completed}
-\PYG{g+go}{Completed Task = setup\PYGZus{}simulation\PYGZus{}data\PYGZus{}mkdir\PYGZus{}1}
-\PYG{g+go}{    Job completed}
-\PYG{g+go}{Completed Task = setup\PYGZus{}simulation\PYGZus{}data}
-
-
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{statistical\PYGZus{}summary}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{)}
-\PYG{g+go}{    Make directories [temp\PYGZus{}NxM, temp\PYGZus{}NxM/simulation\PYGZus{}results] completed}
-\PYG{g+go}{Completed Task = gwas\PYGZus{}simulation\PYGZus{}mkdir\PYGZus{}1}
-\PYG{g+go}{    Job = [[temp\PYGZus{}NxM/gene/001.gene, temp\PYGZus{}NxM/gene/001.gwas, temp\PYGZus{}NxM/simulation/000.simulation] \PYGZhy{}\PYGZgt{} temp\PYGZus{}NxM/simulation\PYGZus{}results/001.000.simulation\PYGZus{}res, 001, 000, 001.000.simulation\PYGZus{}res] completed}
-\PYG{g+go}{    Job = [[temp\PYGZus{}NxM/gene/000.gene, temp\PYGZus{}NxM/gene/000.gwas, temp\PYGZus{}NxM/simulation/000.simulation] \PYGZhy{}\PYGZgt{} temp\PYGZus{}NxM/simulation\PYGZus{}results/000.000.simulation\PYGZus{}res, 000, 000, 000.000.simulation\PYGZus{}res] completed}
-\PYG{g+go}{    Job = [[temp\PYGZus{}NxM/gene/001.gene, temp\PYGZus{}NxM/gene/001.gwas, temp\PYGZus{}NxM/simulation/001.simulation] \PYGZhy{}\PYGZgt{} temp\PYGZus{}NxM/simulation\PYGZus{}results/001.001.simulation\PYGZus{}res, 001, 001, 001.001.simulation\PYGZus{}res] completed}
-\PYG{g+go}{    Job = [[temp\PYGZus{}NxM/gene/000.gene, temp\PYGZus{}NxM/gene/000.gwas, temp\PYGZus{}NxM/simulation/001.simulation] \PYGZhy{}\PYGZgt{} temp\PYGZus{}NxM/simulation\PYGZus{}results/000.001.simulation\PYGZus{}res, 000, 001, 000.001.simulation\PYGZus{}res] completed}
-\PYG{g+go}{    Job = [[temp\PYGZus{}NxM/gene/000.gene, temp\PYGZus{}NxM/gene/000.gwas, temp\PYGZus{}NxM/simulation/002.simulation] \PYGZhy{}\PYGZgt{} temp\PYGZus{}NxM/simulation\PYGZus{}results/000.002.simulation\PYGZus{}res, 000, 002, 000.002.simulation\PYGZus{}res] completed}
-\PYG{g+go}{    Job = [[temp\PYGZus{}NxM/gene/001.gene, temp\PYGZus{}NxM/gene/001.gwas, temp\PYGZus{}NxM/simulation/002.simulation] \PYGZhy{}\PYGZgt{} temp\PYGZus{}NxM/simulation\PYGZus{}results/001.002.simulation\PYGZus{}res, 001, 002, 001.002.simulation\PYGZus{}res] completed}
-\PYG{g+go}{Completed Task = gwas\PYGZus{}simulation}
-\PYG{g+go}{    Job = [[temp\PYGZus{}NxM/simulation\PYGZus{}results/000.000.simulation\PYGZus{}res, temp\PYGZus{}NxM/simulation\PYGZus{}results/000.001.simulation\PYGZus{}res, temp\PYGZus{}NxM/simulation\PYGZus{}results/000.002.simulation\PYGZus{}res] \PYGZhy{}\PYGZgt{} temp\PYGZus{}NxM/000.mean] completed}
-\PYG{g+go}{    Job = [[temp\PYGZus{}NxM/simulation\PYGZus{}results/001.000.simulation\PYGZus{}res, temp\PYGZus{}NxM/simulation\PYGZus{}results/001.001.simulation\PYGZus{}res, temp\PYGZus{}NxM/simulation\PYGZus{}results/001.002.simulation\PYGZus{}res] \PYGZhy{}\PYGZgt{} temp\PYGZus{}NxM/001.mean] completed}
-\end{Verbatim}
-\end{quote}
-
-\index{flowchart colours!Tutorial}\index{Tutorial!flowchart colours}
-
-\section{\textbf{Appendix 1}: Python code for Flow Chart Colours with \emph{pipeline\_printout\_graph(...)}}
-\label{tutorials/new_tutorial/flowchart_colours_code:index-0}\label{tutorials/new_tutorial/flowchart_colours_code:new-manual-flowchart-colours-code}\label{tutorials/new_tutorial/flowchart_colours_code:new-manual-flowchart-colours-chapter-num-python-code-for-flow-chart-colours-with-pipeline-printout-graph}\label{tutorials/new_tutorial/flowchart_colours_code::doc}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/manual_contents:new-manual-table-of-contents]{\emph{Manual Table of Contents}}}
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph]{\emph{pipeline\_printout\_graph(...)}}}
-
-\item {} 
-\code{Download code}
-
-\item {} 
-Back to {\hyperref[tutorials/new_tutorial/flowchart_colours:new-manual-flowchart-colours]{\emph{Flowchart colours}}}
-
-\end{itemize}
-
-This example shows how flowchart colours can be customised.
-
-
-
-
-\subsection{Code}
-\label{tutorials/new_tutorial/flowchart_colours_code:code}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}!/usr/bin/env python}
-\PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-
-\PYG{l+s+sd}{    play\PYGZus{}with\PYGZus{}colours.py}
-\PYG{l+s+sd}{    [\PYGZhy{}\PYGZhy{}log\PYGZus{}file PATH]}
-\PYG{l+s+sd}{    [\PYGZhy{}\PYGZhy{}verbose]}
-
-\PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-
-\PYG{c}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   play\PYGZus{}with\PYGZus{}colours.py}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Copyright (c) 7/13/2010 Leo Goodstadt}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Permission is hereby granted, free of charge, to any person obtaining a copy}
-\PYG{c}{\PYGZsh{}   of this software and associated documentation files (the \PYGZdq{}Software\PYGZdq{}), to deal}
-\PYG{c}{\PYGZsh{}   in the Software without restriction, including without limitation the rights}
-\PYG{c}{\PYGZsh{}   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell}
-\PYG{c}{\PYGZsh{}   copies of the Software, and to permit persons to whom the Software is}
-\PYG{c}{\PYGZsh{}   furnished to do so, subject to the following conditions:}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   The above copyright notice and this permission notice shall be included in}
-\PYG{c}{\PYGZsh{}   all copies or substantial portions of the Software.}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   THE SOFTWARE IS PROVIDED \PYGZdq{}AS IS\PYGZdq{}, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR}
-\PYG{c}{\PYGZsh{}   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,}
-\PYG{c}{\PYGZsh{}   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE}
-\PYG{c}{\PYGZsh{}   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER}
-\PYG{c}{\PYGZsh{}   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,}
-\PYG{c}{\PYGZsh{}   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN}
-\PYG{c}{\PYGZsh{}   THE SOFTWARE.}
-\PYG{c}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh [...]
-
-\PYG{k+kn}{import} \PYG{n+nn}{sys}\PYG{o}{,} \PYG{n+nn}{os}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   options}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-
-\PYG{k+kn}{from} \PYG{n+nn}{optparse} \PYG{k+kn}{import} \PYG{n}{OptionParser}
-\PYG{k+kn}{import} \PYG{n+nn}{StringIO}
-
-\PYG{n}{parser} \PYG{o}{=} \PYG{n}{OptionParser}\PYG{p}{(}\PYG{n}{version}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZpc{}}\PYG{l+s}{play\PYGZus{}with\PYGZus{}colours 1.0}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                      \PYG{n}{usage} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{    play\PYGZus{}with\PYGZus{}colours }\PYG{l+s}{\PYGZdq{}}
-                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}flowchart FILE [options] }\PYG{l+s}{\PYGZdq{}}
-                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[\PYGZhy{}\PYGZhy{}colour\PYGZus{}scheme\PYGZus{}index INT ] }\PYG{l+s}{\PYGZdq{}}
-                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[\PYGZhy{}\PYGZhy{}key\PYGZus{}legend\PYGZus{}in\PYGZus{}graph]}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   pipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}flowchart}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{flowchart}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                    \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FILE}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                    \PYG{n+nb}{type}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{string}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                    \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Don}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{t actually run any commands; just print the pipeline }\PYG{l+s}{\PYGZdq{}}
-                         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{as a flowchart.}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}colour\PYGZus{}scheme\PYGZus{}index}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{colour\PYGZus{}scheme\PYGZus{}index}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                    \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{INTEGER}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                    \PYG{n+nb}{type}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{int}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                    \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Index of colour scheme for flow chart.}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}key\PYGZus{}legend\PYGZus{}in\PYGZus{}graph}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{key\PYGZus{}legend\PYGZus{}in\PYGZus{}graph}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                    \PYG{n}{action}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{store\PYGZus{}true}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{default}\PYG{o}{=}\PYG{n+nb+bp}{False}\PYG{p}{,}
-                    \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Print out legend and key for dependency graph.}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{p}{(}\PYG{n}{options}\PYG{p}{,} \PYG{n}{remaining\PYGZus{}args}\PYG{p}{)} \PYG{o}{=} \PYG{n}{parser}\PYG{o}{.}\PYG{n}{parse\PYGZus{}args}\PYG{p}{(}\PYG{p}{)}
-\PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{options}\PYG{o}{.}\PYG{n}{flowchart}\PYG{p}{:}
-    \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Missing mandatory parameter: \PYGZhy{}\PYGZhy{}flowchart.}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   imports}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.ruffus\PYGZus{}exceptions} \PYG{k+kn}{import} \PYG{n}{JobSignalledBreak}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Pipeline}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} up to date tasks}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate} \PYG{p}{(}\PYG{k}{lambda} \PYG{p}{:} \PYG{p}{(}\PYG{n+nb+bp}{False}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task1}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate} \PYG{p}{(}\PYG{k}{lambda} \PYG{p}{:} \PYG{p}{(}\PYG{n+nb+bp}{False}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task1}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task2}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate} \PYG{p}{(}\PYG{k}{lambda} \PYG{p}{:} \PYG{p}{(}\PYG{n+nb+bp}{False}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task2}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task3}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-
-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate} \PYG{p}{(}\PYG{k}{lambda} \PYG{p}{:} \PYG{p}{(}\PYG{n+nb+bp}{False}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task3}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}final\PYGZus{}target}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} Explicitly specified}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate} \PYG{p}{(}\PYG{k}{lambda} \PYG{p}{:} \PYG{p}{(}\PYG{n+nb+bp}{False}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task1}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Explicitly\PYGZus{}specified\PYGZus{}task}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-
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-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} Tasks to run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Explicitly\PYGZus{}specified\PYGZus{}task}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Task\PYGZus{}to\PYGZus{}run1}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Task\PYGZus{}to\PYGZus{}run1}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Task\PYGZus{}to\PYGZus{}run2}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
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-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Task\PYGZus{}to\PYGZus{}run2}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Task\PYGZus{}to\PYGZus{}run3}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
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-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate} \PYG{p}{(}\PYG{k}{lambda} \PYG{p}{:} \PYG{p}{(}\PYG{n+nb+bp}{False}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Task\PYGZus{}to\PYGZus{}run2}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task\PYGZus{}forced\PYGZus{}to\PYGZus{}rerun}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} Final target}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task\PYGZus{}forced\PYGZus{}to\PYGZus{}rerun}\PYG{p}{,} \PYG{n}{Task\PYGZus{}to\PYGZus{}run3}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Final\PYGZus{}target}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} Ignored downstream}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Final\PYGZus{}target}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Downstream\PYGZus{}task1\PYGZus{}ignored}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{Final\PYGZus{}target}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Downstream\PYGZus{}task2\PYGZus{}ignored}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
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-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Main logic}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-\PYG{k+kn}{from} \PYG{n+nn}{collections} \PYG{k+kn}{import} \PYG{n}{defaultdict}
-\PYG{n}{custom\PYGZus{}flow\PYGZus{}chart\PYGZus{}colour\PYGZus{}scheme} \PYG{o}{=} \PYG{n}{defaultdict}\PYG{p}{(}\PYG{n+nb}{dict}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Base chart on this overall colour scheme index}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{custom\PYGZus{}flow\PYGZus{}chart\PYGZus{}colour\PYGZus{}scheme}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{colour\PYGZus{}scheme\PYGZus{}index}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{colour\PYGZus{}scheme\PYGZus{}index}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Overriding colours}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{if} \PYG{n}{options}\PYG{o}{.}\PYG{n}{colour\PYGZus{}scheme\PYGZus{}index} \PYG{o}{==} \PYG{n+nb+bp}{None}\PYG{p}{:}
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-    \PYG{n}{custom\PYGZus{}flow\PYGZus{}chart\PYGZus{}colour\PYGZus{}scheme}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Final target}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fillcolor}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}                         \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}EFA03B}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}
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-    \PYG{n}{custom\PYGZus{}flow\PYGZus{}chart\PYGZus{}colour\PYGZus{}scheme}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Down stream}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}                          \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{gray}\PYG{l+s}{\PYGZdq{}}
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-
-\PYG{k}{if} \PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}} \PYG{o}{==} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZus{}\PYGZus{}main\PYGZus{}\PYGZus{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}
-    \PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(}
-
-                                    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{options}\PYG{o}{.}\PYG{n}{flowchart}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                                    \PYG{c}{\PYGZsh{} use flowchart file name extension to decide flowchart format}
-                                    \PYG{c}{\PYGZsh{}   e.g. svg, jpg etc.}
-                                    \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{splitext}\PYG{p}{(}\PYG{n}{options}\PYG{o}{.}\PYG{n}{flowchart}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{:}\PYG{p}{]}\PYG{p}{,}
-
-                                    \PYG{c}{\PYGZsh{} final targets}
-                                    \PYG{p}{[}\PYG{n}{Final\PYGZus{}target}\PYG{p}{,} \PYG{n}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}final\PYGZus{}target}\PYG{p}{]}\PYG{p}{,}
-
-                                    \PYG{c}{\PYGZsh{} Explicitly specified tasks}
-                                    \PYG{p}{[}\PYG{n}{Explicitly\PYGZus{}specified\PYGZus{}task}\PYG{p}{]}\PYG{p}{,}
-
-                                    \PYG{c}{\PYGZsh{} Do we want key legend}
-                                    \PYG{n}{no\PYGZus{}key\PYGZus{}legend}   \PYG{o}{=} \PYG{o+ow}{not} \PYG{n}{options}\PYG{o}{.}\PYG{n}{key\PYGZus{}legend\PYGZus{}in\PYGZus{}graph}\PYG{p}{,}
-
-                                    \PYG{c}{\PYGZsh{} Print all the task types whether used or not}
-                                    \PYG{n}{minimal\PYGZus{}key\PYGZus{}legend}             \PYG{o}{=} \PYG{n+nb+bp}{False}\PYG{p}{,}
-
-                                    \PYG{n}{user\PYGZus{}colour\PYGZus{}scheme} \PYG{o}{=} \PYG{n}{custom\PYGZus{}flow\PYGZus{}chart\PYGZus{}colour\PYGZus{}scheme}\PYG{p}{,}
-                                    \PYG{n}{pipeline\PYGZus{}name} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Colour schemes}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\chapter{Overview:}
-\label{contents:overview}
-
-\section{Cheat Sheet}
-\label{cheatsheet:cheat-sheet}\label{cheatsheet::doc}\label{cheatsheet:id1}
-The \code{ruffus} module is a lightweight way to add support
-for running computational pipelines.
-
-\begin{DUlineblock}{0em}
-\item[] Each stage or \textbf{task} in a computational pipeline is represented by a python function
-\item[] Each python function can be called in parallel to run multiple \textbf{jobs}.
-\end{DUlineblock}
-
-
-\subsection{1. Annotate functions with \textbf{Ruffus} decorators}
-\label{cheatsheet:annotate-functions-with-ruffus-decorators}
-
-\subsubsection{Core}
-\label{cheatsheet:core}
-\begin{tabular}{|p{0.317\linewidth}|p{0.317\linewidth}|p{0.317\linewidth}|}
-\hline
-\textbf{\relax 
-Decorator
-} & \textbf{\relax 
-Syntax
-} & \textbf{\relax }\\\hline
-
- at originate ({\hyperref[tutorials/new_tutorial/originate:new-manual-originate]{\emph{Manual}}})
- & 
-{\hyperref[decorators/originate:decorators-originate]{\emph{@originate}}} ( \code{output\_files}, {[}\code{extra\_parameters},...{]} )
- & \\\hline
-
- at split ({\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{Manual}}})
- & 
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}} ( \code{tasks\_or\_file\_names}, \code{output\_files}, {[}\code{extra\_parameters},...{]} )
- & \\\hline
-
- at transform ({\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{Manual}}})
- & 
-\begin{DUlineblock}{0em}
-\item[] {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/transform_ex:decorators-transform-suffix-string]{\emph{suffix}}}\emph{(}\code{suffix\_string}\emph{)}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )
-\item[] {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/transform_ex:decorators-transform-matching-regex]{\emph{regex}}}\emph{(}\code{regex\_pattern}\emph{)}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )
-\end{DUlineblock}
- & \\\hline
-
- at merge ({\hyperref[tutorials/new_tutorial/merge:new-manual-merge]{\emph{Manual}}})
- & 
-{\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} (\code{tasks\_or\_file\_names}, \code{output}, {[}\code{extra\_parameters},...{]} )
- & \\\hline
-
- at posttask ({\hyperref[tutorials/new_tutorial/posttask:new-manual-posttask]{\emph{Manual}}})
- & 
-\begin{DUlineblock}{0em}
-\item[] {\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} ( \code{signal\_task\_completion\_function} )
-\item[] {\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} ({\hyperref[decorators/indicator_objects:decorators-touch-file]{\emph{touch\_file}}}( \code{'task1.completed'} ))
-\end{DUlineblock}
- & \\\hline
-\end{tabular}
-
-
-
-\subsubsection{See \emph{Decorators} for a complete list of decorators}
-\label{cheatsheet:see-decorators-for-a-complete-list-of-decorators}
-
-\subsection{2. Print dependency graph if necessary}
-\label{cheatsheet:print-dependency-graph-if-necessary}\begin{itemize}
-\item {} 
-For a graphical flowchart in \code{jpg}, \code{svg}, \code{dot}, \code{png}, \code{ps}, \code{gif} formats:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{flowchart.svg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{itemize}
-\begin{itemize}
-\item {} 
-For a text printout of all jobs
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-\end{itemize}
-
-
-\subsection{3. Run the pipeline}
-\label{cheatsheet:run-the-pipeline}
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{multiprocess} \PYG{o}{=} \PYG{n}{N\PYGZus{}PARALLEL\PYGZus{}JOBS}\PYG{p}{)}
-\end{Verbatim}
-\phantomsection\label{pipeline_functions:pipeline-functions}
-See {\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run}\phantomsection\label{pipeline_functions:pipeline-run}\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout}\phantomsection\label{pipeline_functions:pipeline-printout}\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph}\phantomsection\label{pipeline_functions:pipeline-printout-graph}\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-get-task-n [...]
-
-\section{Pipeline functions}
-\label{pipeline_functions:ppg-history-file}\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-history-file}\label{pipeline_functions::doc}\label{pipeline_functions:id1}\begin{quote}
-
-There are only four functions for \textbf{Ruffus} pipelines:
-\begin{itemize}
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}} executes a pipeline
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout}}} prints a list of tasks and jobs which will be run in a pipeline
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph]{\emph{pipeline\_printout\_graph}}} prints a schematic flowchart of pipeline tasks in various graphical formats
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-get-task-names]{\emph{pipeline\_get\_task\_names}}} returns a list of all task names in the pipeline
-
-\end{itemize}
-\end{quote}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run}
-\index{pipeline functions!pipeline\_run}\index{pipeline\_run!Run pipeline}\index{Run pipeline!pipeline\_run}
-
-\subsection{\emph{pipeline\_run}}
-\label{pipeline_functions:id2}\label{pipeline_functions:index-0}
-\textbf{pipeline\_run} ( {\hyperref[pipeline_functions:pipeline-functions-pipeline-run-target-tasks]{\emph{target\_tasks}}} = {[}{]},  {\hyperref[pipeline_functions:pipeline-functions-pipeline-run-forcedtorun-tasks]{\emph{forcedtorun\_tasks}}} = {[}{]}, {\hyperref[pipeline_functions:pipeline-functions-pipeline-run-multiprocess]{\emph{multiprocess}}} = 1, {\hyperref[pipeline_functions:pipeline-functions-pipeline-run-logger]{\emph{logger}}} = stderr\_logger, {\hyperref[pipeline_functions:p [...]
-\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Runs all specified pipelined functions if they or any antecedent tasks are
-incomplete or out-of-date.
-\end{quote}
-
-\textbf{Example}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Run task2 whatever its state, and also task1 and antecedents if they are incomplete}
-\PYG{c}{\PYGZsh{}   Do not log pipeline progress messages to stderr}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{task1}\PYG{p}{,} \PYG{n}{task2}\PYG{p}{]}\PYG{p}{,} \PYG{n}{forcedtorun\PYGZus{}tasks} \PYG{o}{=} \PYG{p}{[}\PYG{n}{task2}\PYG{p}{]}\PYG{p}{,} \PYG{n}{logger} \PYG{o}{=} \PYG{n}{blackhole\PYGZus{}logger}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-target-tasks}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{target\_tasks}}] \leavevmode
-Pipeline functions and any necessary antecedents (specified implicitly or with {\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}})
-which should be invoked with the appropriate parameters if they are incomplete or out-of-date.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-forcedtorun-tasks}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{forcedtorun\_tasks}}] \leavevmode
-Optional. These pipeline functions will be invoked regardless of their state.
-Any antecedents tasks will also be executed if they are out-of-date or incomplete.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-multiprocess}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{multiprocess}}] \leavevmode
-Optional. The number of processes which should be dedicated to running in parallel independent
-tasks and jobs within each task. If \code{multiprocess} is set to 1, the pipeline will
-execute in the main process.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-multithread}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{multithread}}] \leavevmode
-Optional. The number of threads which should be dedicated to running in parallel independent
-tasks and jobs within each task. Should be used only with drmaa. Otherwise the CPython \href{https://wiki.python.org/moin/GlobalInterpreterLock}{global interpreter lock (GIL)}
-will slow down your pipeline
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-logger}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{logger}}] \leavevmode
-For logging messages indicating the progress of the pipeline in terms of tasks and jobs.
-Defaults to outputting to sys.stderr.
-Setting \code{logger=blackhole\_logger} will prevent any logging output.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-gnu-make}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{gnu\_make\_maximal\_rebuild\_mode}}] \leavevmode
-\begin{notice}{warning}{Warning:}
-This is a dangerous option. Use rarely and with caution
-\end{notice}
-
-Optional parameter governing how \textbf{Ruffus} determines which part of the pipeline is
-out of date and needs to be re-run. If set to \code{False}, \textbf{ruffus} will work back
-from the \code{target\_tasks} and only execute the pipeline after the first up-to-date
-tasks that it encounters. For example, if there are four tasks:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   task1 \PYGZhy{}\PYGZgt{} task2 \PYGZhy{}\PYGZgt{} task3 \PYGZhy{}\PYGZgt{} task4 \PYGZhy{}\PYGZgt{} task5}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{target\PYGZus{}tasks} \PYG{o}{=} \PYG{p}{[}\PYG{n}{task5}\PYG{p}{]}
-\end{Verbatim}
-\end{quote}
-
-If \code{task3()} is up-to-date, then only \code{task4()} and \code{task5()} will be run.
-This will be the case even if \code{task2()} and \code{task1()} are incomplete.
-
-This allows you to remove all intermediate results produced by \code{task1 -\textgreater{} task3}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-verbose}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{verbose}}] \leavevmode
-Optional parameter indicating the verbosity of the messages sent to \code{logger}:
-(Defaults to level 1 if unspecified)
-\begin{itemize}
-\item {} 
-level \textbf{0} : \emph{nothing}
-
-\item {} 
-level \textbf{1} : \emph{Out-of-date Task names}
-
-\item {} 
-level \textbf{2} : \emph{All Tasks (including any task function docstrings)}
-
-\item {} 
-level \textbf{3} : \emph{Out-of-date Jobs in Out-of-date Tasks, no explanation}
-
-\item {} 
-level \textbf{4} : \emph{Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings}
-
-\item {} 
-level \textbf{5} : \emph{All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)}
-
-\item {} 
-level \textbf{6} : \emph{All jobs in All Tasks whether out of date or not}
-
-\item {} 
-level \textbf{10}: \emph{logs messages useful only for debugging ruffus pipeline code}
-
-\end{itemize}
-
-\code{verbose \textgreater{}= 10} are intended for debugging \textbf{Ruffus} by the developers and the details
-are liable to change from release to release
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-runtime-data}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{runtime\_data}}] \leavevmode
-Experimental feature for passing data to tasks at run time
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-one-second-per-job}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{one\_second\_per\_job}}] \leavevmode
-To work around poor file timepstamp resolution for some file systems.
-Defaults to True if checksum\_level is 0 forcing Tasks to take a minimum of 1 second to complete.
-If your file system has coarse grained time stamps, you can turn on this delay
-by setting \emph{one\_second\_per\_job} to \code{True}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-touch-files-only}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{touch\_files\_only}}] \leavevmode
-Create or update output files only to simulate the running of the pipeline.
-Does not invoke real task functions to run jobs. This is most useful to force a
-pipeline to acknowledge that a particular part is now up-to-date.
-
-This will not work properly if the identities of some files are not known before hand,
-and depend on run time. In other words, not recommended if \code{@split} or custom parameter generators are being used.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-exceptions-terminate-immediately}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{exceptions\_terminate\_immediately}}] \leavevmode
-Exceptions cause immediate termination of the pipeline.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-log-exceptions}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{log\_exceptions}}] \leavevmode
-Print exceptions to the logger as soon as they occur.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-history-file}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{history\_file}}] \leavevmode
-The database file which stores checksums and file timestamps for input/output files.
-Defaults to \code{.ruffus\_history.sqlite} if unspecified
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-checksum-level}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{checksum\_level}}] \leavevmode
-Several options for checking up-to-dateness are available: Default is level 1.
-\begin{itemize}
-\item {} 
-level 0 : Use only file timestamps
-
-\item {} 
-level 1 : above, plus timestamp of successful job completion
-
-\item {} 
-level 2 : above, plus a checksum of the pipeline function body
-
-\item {} 
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-\end{itemize}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-run-verbose-abbreviated-path}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{verbose\_abbreviated\_path}}] \leavevmode
-Whether input and output paths are abbreviated. Defaults to 2 if unspecified
-\begin{itemize}
-\item {} 
-level 0: The full (expanded, abspath) input or output path
-
-\item {} 
-level \textgreater{} 1: The number of subdirectories to include. Abbreviated paths are prefixed with \code{{[},,,{]}/}
-
-\item {} 
-level \textless{} 0: Input / Output parameters are truncated to \code{MMM} letters where \code{verbose\_abbreviated\_path ==-MMM}. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by \code{\textless{}???\textgreater{}}
-
-\end{itemize}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout}
-\index{pipeline functions!pipeline\_run}\index{pipeline\_printout!Printout simulated run of the pipeline}\index{Printout simulated run of the pipeline!pipeline\_printout}
-
-\subsection{\emph{pipeline\_printout}}
-\label{pipeline_functions:index-1}\label{pipeline_functions:id3}
-\textbf{pipeline\_printout} ({\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-output-stream]{\emph{output\_stream}}} = sys.stdout, {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-target-tasks]{\emph{target\_tasks}}} = {[}{]}, {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-forcedtorun-tasks]{\emph{forcedtorun\_tasks}}} = {[}{]}, {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-verbose]{\emph{verbose}}} = 1, {\hyper [...]
-\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Prints out all the pipelined functions which will be invoked given specified \code{target\_tasks}
-without actually running the pipeline. Because this is a simulation, some of the job
-parameters may be incorrect. For example, the results of a {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{@split}}}
-operation is not predetermined and will only be known after the pipelined function
-splits up the original data. Parameters of all downstream pipelined functions will
-be changed depending on this initial operation.
-\end{quote}
-\begin{description}
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Simulate running task2 whatever its state, and also task1 and antecedents}
-\PYG{c}{\PYGZsh{}     if they are incomplete}
-\PYG{c}{\PYGZsh{}   Print out results to STDOUT}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{task1}\PYG{p}{,} \PYG{n}{task2}\PYG{p}{]}\PYG{p}{,} \PYG{n}{forcedtorun\PYGZus{}tasks} \PYG{o}{=} \PYG{p}{[}\PYG{n}{task2}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{1}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-output-stream}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_stream}}] \leavevmode
-Where to printout the results of simulating the running of the pipeline.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-target-tasks}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{target\_tasks}}] \leavevmode
-As in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}}: Pipeline functions and any necessary antecedents (specified implicitly or with {\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}})
-which should be invoked with the appropriate parameters if they are incomplete or out-of-date.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-forcedtorun-tasks}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{forcedtorun\_tasks}}] \leavevmode
-As in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}}:These pipeline functions will be invoked regardless of their state.
-Any antecedents tasks will also be executed if they are out-of-date or incomplete.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-verbose}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{verbose}}] \leavevmode
-Optional parameter indicating the verbosity of the messages sent to \code{logger}:
-(Defaults to level 4 if unspecified)
-\begin{itemize}
-\item {} 
-level \textbf{0} : \emph{nothing}
-
-\item {} 
-level \textbf{1} : \emph{Out-of-date Task names}
-
-\item {} 
-level \textbf{2} : \emph{All Tasks (including any task function docstrings)}
-
-\item {} 
-level \textbf{3} : \emph{Out-of-date Jobs in Out-of-date Tasks, no explanation}
-
-\item {} 
-level \textbf{4} : \emph{Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings}
-
-\item {} 
-level \textbf{5} : \emph{All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)}
-
-\item {} 
-level \textbf{6} : \emph{All jobs in All Tasks whether out of date or not}
-
-\item {} 
-level \textbf{10}: \emph{logs messages useful only for debugging ruffus pipeline code}
-
-\end{itemize}
-
-\code{verbose \textgreater{}= 10} are intended for debugging \textbf{Ruffus} by the developers and the details
-are liable to change from release to release
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-indent}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{indent}}] \leavevmode
-Optional parameter governing the indentation when printing out the component job
-parameters of each task function.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-gnu-make}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{gnu\_make\_maximal\_rebuild\_mode}}] \leavevmode
-\begin{notice}{warning}{Warning:}
-This is a dangerous option. Use rarely and with caution
-\end{notice}
-
-See explanation in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run-gnu-make]{\emph{pipeline\_run}}}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-wrap-width}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{wrap\_width}}] \leavevmode
-Optional parameter governing the length of each line before it starts wrapping
-around.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-runtime-data}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{runtime\_data}}] \leavevmode
-Experimental feature for passing data to tasks at run time
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-history-file}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{history\_file}}] \leavevmode
-The database file which stores checksums and file timestamps for input/output files.
-Defaults to \code{.ruffus\_history.sqlite} if unspecified
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-checksum-level}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{checksum\_level}}] \leavevmode
-Several options for checking up-to-dateness are available: Default is level 1.
-\begin{itemize}
-\item {} 
-level 0 : Use only file timestamps
-
-\item {} 
-level 1 : above, plus timestamp of successful job completion
-
-\item {} 
-level 2 : above, plus a checksum of the pipeline function body
-
-\item {} 
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-\end{itemize}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-verbose-abbreviated-path}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{verbose\_abbreviated\_path}}] \leavevmode
-Whether input and output paths are abbreviated. Defaults to 2 if unspecified
-\begin{itemize}
-\item {} 
-level 0: The full (expanded, abspath) input or output path
-
-\item {} 
-level \textgreater{} 1: The number of subdirectories to include. Abbreviated paths are prefixed with \code{{[},,,{]}/}
-
-\item {} 
-level \textless{} 0: Input / Output parameters are truncated to \code{MMM} letters where \code{verbose\_abbreviated\_path ==-MMM}. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by \code{\textless{}???\textgreater{}}
-
-\end{itemize}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph}
-\index{pipeline functions!pipeline\_printout\_graph}\index{pipeline\_printout\_graph!print flowchart representation of pipeline functions}\index{print flowchart representation of pipeline functions!pipeline\_printout\_graph}
-
-\subsection{\emph{pipeline\_printout\_graph}}
-\label{pipeline_functions:id4}\label{pipeline_functions:index-2}
-\textbf{pipeline\_printout\_graph} ({\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph-stream]{\emph{stream}}}, {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph-output-format]{\emph{output\_format}}} = None, {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph-target-tasks]{\emph{target\_tasks}}} = {[}{]}, {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph-forcedtorun-tasks]{\emph{forcedtorun\_tasks}} [...]
-\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Prints out flowchart of all the pipelined functions which will be invoked given specified \code{target\_tasks}
-without actually running the pipeline.
-
-See {\hyperref[tutorials/new_tutorial/flowchart_colours:new-manual-flowchart-colours]{\emph{Flowchart colours}}}
-\end{quote}
-\begin{description}
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{flowchart.jpg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{jpg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{n}{task1}\PYG{p}{,} \PYG{n}{task16}\PYG{p}{]}\PYG{p}{,}
-                            \PYG{n}{forcedtorun\PYGZus{}tasks} \PYG{o}{=} \PYG{p}{[}\PYG{n}{task2}\PYG{p}{]}\PYG{p}{,}
-                            \PYG{n}{no\PYGZus{}key\PYGZus{}legend} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\textbf{Customising appearance:}
-\begin{quote}
-
-The {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph-user-colour-scheme]{\emph{user\_colour\_scheme}}} parameter can be used to change
-flowchart colours. This allows the default {\hyperref[tutorials/new_tutorial/flowchart_colours:new-manual-flowchart-colours]{\emph{Colour Schemes}}}
-to be set. An example of customising flowchart appearance is available {\hyperref[tutorials/new_tutorial/flowchart_colours_code:new-manual-flowchart-colours-code]{\emph{(see code)}}} .
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-stream}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{stream}}] \leavevmode
-The file or file-like object to which the flowchart should be printed.
-If a string is provided, it is assumed that this is the name of the output file
-which will be opened automatically.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-output-format}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_format}}] \leavevmode
-If missing, defaults to the extension of the \emph{stream} file name (i.e. \code{jpg} for \code{a.jpg})
-
-\begin{DUlineblock}{0em}
-\item[] If the programme \code{dot} can be found on the executio path, this
-can be any number of \href{http://www.graphviz.org/doc/info/output.html}{formats}
-supported by \href{http://www.graphviz.org/}{Graphviz}, including, for example,
-\code{jpg}, \code{png}, \code{pdf}, \code{svg} etc.
-\item[] Otherwise, \textbf{ruffus} will only output without error in the \href{http://en.wikipedia.org/wiki/DOT\_language}{dot} format, which
-is a plain-text graph description language.
-\end{DUlineblock}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-target-tasks}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{target\_tasks}}] \leavevmode
-As in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}}: Pipeline functions and any necessary antecedents (specified implicitly or with {\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}})
-which should be invoked with the appropriate parameters if they are incomplete or out-of-date.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-forcedtorun-tasks}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{forcedtorun\_tasks}}] \leavevmode
-As in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}}:These pipeline functions will be invoked regardless of their state.
-Any antecedents tasks will also be executed if they are out-of-date or incomplete.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-draw-vertically}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{draw\_vertically}}] \leavevmode
-Draw flowchart in vertical orientation
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-ignore-upstream-of-target}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{ignore\_upstream\_of\_target}}] \leavevmode
-Start drawing flowchart from specified target tasks. Do not draw tasks which are
-downstream (subsequent) to the targets.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-skip-uptodate-tasks}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{ignore\_upstream\_of\_target}}] \leavevmode
-Do not draw up-to-date / completed tasks in the flowchart unless they are
-lie on the execution path of the pipeline.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-gnu-make}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{gnu\_make\_maximal\_rebuild\_mode}}] \leavevmode
-\begin{notice}{warning}{Warning:}
-This is a dangerous option. Use rarely and with caution
-\end{notice}
-
-See explanation in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run-gnu-make]{\emph{pipeline\_run}}}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-test-all-task-for-update}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{test\_all\_task\_for\_update}}] \leavevmode
-\begin{DUlineblock}{0em}
-\item[] Indicates whether intermediate tasks are out of date or not. Normally \textbf{Ruffus} will
-stop checking dependent tasks for completion or whether they are out-of-date once it has
-discovered the maximal extent of the pipeline which has to be run.
-\item[] For displaying the flow of the pipeline, this is hardly very informative.
-\end{DUlineblock}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-no-key-legend}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{no\_key\_legend}}] \leavevmode
-Do not include key legend explaining the colour scheme of the flowchart.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-minimal-key-legend}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{minimal\_key\_legend}}] \leavevmode
-Do not include unused task types in key legend.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-user-colour-scheme}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{user\_colour\_scheme}}] \leavevmode
-Dictionary specifying colour scheme for flowchart
-
-See complete {\hyperref[tutorials/new_tutorial/flowchart_colours:new-manual-flowchart-colours]{\emph{list of Colour Schemes}}}.
-
-\begin{DUlineblock}{0em}
-\item[] Colours can be names e.g. \code{"black"} or quoted hex e.g. \code{'"\#F6F4F4"'} (note extra quotes)
-\item[] Default values will be used unless specified
-\end{DUlineblock}
-
-\begin{tabular}{|p{0.317\linewidth}|p{0.317\linewidth}|p{0.317\linewidth}|}
-\hline
-\textbf{\relax 
-key
-} & \textbf{\relax 
-Subkey
-} & \textbf{\relax }\\\hline
-\begin{itemize}
-\item {} 
-\code{'colour\_scheme\_index'}
-
-\end{itemize}
- & 
-\begin{DUlineblock}{0em}
-\item[] index of default colour scheme,
-\item[] 0-7, defaults to 0 unless specified
-\end{DUlineblock}
- & \\\hline
-\begin{itemize}
-\item {} 
-\code{'Final target'}
-
-\item {} 
-\code{'Explicitly specified task'}
-
-\item {} 
-\code{'Task to run'}
-
-\item {} 
-\code{'Down stream'}
-
-\item {} 
-\code{'Up-to-date Final target'}
-
-\item {} 
-\code{'Up-to-date task forced to rerun'}
-
-\item {} 
-\code{'Up-to-date task'}
-
-\item {} 
-\code{'Vicious cycle'}
-
-\end{itemize}
- & \begin{itemize}
-\item {} 
-\code{'fillcolor'}
-
-\item {} 
-\code{'fontcolor'}
-
-\item {} 
-\code{'color'}
-
-\item {} 
-\code{'dashed'}   = \code{0/1}
-
-\end{itemize}
- & 
-Colours / attributes for each task type
-\\\hline
-\begin{itemize}
-\item {} 
-\code{'Vicious cycle'}
-
-\item {} 
-\code{'Task to run'}
-
-\item {} 
-\code{'Up-to-date'}
-
-\end{itemize}
- & \begin{itemize}
-\item {} 
-\code{'linecolor'}
-
-\end{itemize}
- & 
-Colours for arrows between tasks
-\\\hline
-\begin{itemize}
-\item {} 
-\code{'Pipeline'}
-
-\end{itemize}
- & \begin{itemize}
-\item {} 
-\code{'fontcolor'}
-
-\end{itemize}
- & 
-Flowchart title colour
-\\\hline
-\begin{itemize}
-\item {} 
-\code{'Key'}
-
-\end{itemize}
- & \begin{itemize}
-\item {} 
-\code{'fontcolor'}
-
-\item {} 
-\code{'fillcolor'}
-
-\end{itemize}
- & 
-Legend colours
-\\\hline
-\end{tabular}
-
-
-Example:
-\begin{quote}
-
-Use colour scheme index  = 1
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{flowchart.svg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{svg}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{n}{final\PYGZus{}task}\PYG{p}{]}\PYG{p}{,}
-                         \PYG{n}{user\PYGZus{}colour\PYGZus{}scheme} \PYG{o}{=} \PYG{p}{\PYGZob{}}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{colour\PYGZus{}scheme\PYGZus{}index}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:}\PYG{l+m+mi}{1}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Pipeline}\PYG{l+s}{\PYGZdq{}}      \PYG{p}{:}\PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF3232}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}} \PYG{p}{\PYGZcb{}}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Key}\PYG{l+s}{\PYGZdq{}}           \PYG{p}{:}\PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Red}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                                                                  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fillcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}F6F4F4}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}} \PYG{p}{\PYGZcb{}}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Task to run}\PYG{l+s}{\PYGZdq{}}   \PYG{p}{:}\PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{linecolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}0044A0}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}} \PYG{p}{\PYGZcb{}}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Final target}\PYG{l+s}{\PYGZdq{}}  \PYG{p}{:}\PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fillcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}EFA03B}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                                                                  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}} \PYG{p}{:} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{black}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                                                                  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dashed}\PYG{l+s}{\PYGZdq{}}    \PYG{p}{:} \PYG{l+m+mi}{0}           \PYG{p}{\PYGZcb{}}
-                                               \PYG{p}{\PYGZcb{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-pipeline-name}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{pipeline\_name}}] \leavevmode
-Specify title for flowchart
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-size}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{size}}] \leavevmode
-Size in inches for flowchart
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-dpi}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{dpi}}] \leavevmode
-Resolution in dots per inch. Ignored for svg output
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-runtime-data}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{runtime\_data}}] \leavevmode
-Experimental feature for passing data to tasks at run time
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-history-file}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{history\_file}}] \leavevmode
-The database file which stores checksums and file timestamps for input/output files.
-Defaults to \code{.ruffus\_history.sqlite} if unspecified
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-printout-graph-checksum-level}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{checksum\_level}}] \leavevmode
-Several options for checking up-to-dateness are available: Default is level 1.
-\begin{itemize}
-\item {} 
-level 0 : Use only file timestamps
-
-\item {} 
-level 1 : above, plus timestamp of successful job completion
-
-\item {} 
-level 2 : above, plus a checksum of the pipeline function body
-
-\item {} 
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-\end{itemize}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{pipeline_functions:pipeline-functions-pipeline-get-task-names}
-\index{pipeline functions!pipeline\_get\_task\_names}\index{pipeline\_get\_task\_names!print list of task names without running the pipeline}\index{print list of task names without running the pipeline!pipeline\_get\_task\_names}
-
-\subsection{\emph{pipeline\_get\_task\_names}}
-\label{pipeline_functions:id5}\label{pipeline_functions:index-3}
-\textbf{pipeline\_get\_task\_names} ()
-\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Returns a list of all task names in the pipeline without running the pipeline or checking to see if the tasks are connected correctly
-\end{quote}
-
-\textbf{Example}:
-\begin{quote}
-
-Given:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}data}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}data}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.task1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task1}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{task1}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.task1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.task2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task2}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-Produces a list of three task names:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}get\PYGZus{}task\PYGZus{}names} \PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{[\PYGZsq{}create\PYGZus{}data\PYGZsq{}, \PYGZsq{}task1\PYGZsq{}, \PYGZsq{}task2\PYGZsq{}]}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-functions}\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job}\phantomsection\label{drmaa_wrapper_functions:run-job}\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-cmd-str}\phantomsection\label{drmaa_wrapper_functions:dw-cmd-str}\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-job-script-directory}\phantomsection\label{drmaa_wrapper_functions:dw-job-script-directory}\phantomsection\ [...]
-
-\section{drmaa functions}
-\label{drmaa_wrapper_functions:dw-touch-only}\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-touch-only}\label{drmaa_wrapper_functions::doc}\label{drmaa_wrapper_functions:id1}\begin{quote}
-
-\code{drmaa\_wrapper} is not exported automatically by ruffus and must be specified explicitly:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} imported ruffus.drmaa\PYGZus{}wrapper explicitly}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.drmaa\PYGZus{}wrapper} \PYG{k+kn}{import} \PYG{n}{run\PYGZus{}job}\PYG{p}{,} \PYG{n}{error\PYGZus{}drmaa\PYGZus{}job}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job}
-\index{drmaa !run\_job}\index{run\_job!Run drmaa}\index{Run drmaa!run\_job}
-
-\subsection{\emph{run\_job}}
-\label{drmaa_wrapper_functions:id2}\label{drmaa_wrapper_functions:index-0}
-\textbf{run\_job} ({\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job-cmd-str]{\emph{cmd\_str}}}, {\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job-job-name]{\emph{job\_name}}} = None, {\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job-job-other-options]{\emph{job\_other\_options}}} = None, {\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job-job-script-directory]{\emph{job\_script\_directory}}} = None, {\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job-job-e [...]
-\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-\code{ruffus.drmaa\_wrapper.run\_job} dispatches a command with arguments to a cluster or Grid Engine node and waits for the command to complete.
-
-It is the semantic equivalent of calling \href{http://docs.python.org/2/library/os.html\#os.system}{os.system}  or
-\href{http://docs.python.org/2/library/subprocess.html\#subprocess.check\_call}{subprocess.check\_output}.
-\end{quote}
-
-\textbf{Example}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.drmaa\PYGZus{}wrapper} \PYG{k+kn}{import} \PYG{n}{run\PYGZus{}job}\PYG{p}{,} \PYG{n}{error\PYGZus{}drmaa\PYGZus{}job}
-\PYG{k+kn}{import} \PYG{n+nn}{drmaa}
-\PYG{n}{my\PYGZus{}drmaa\PYGZus{}session} \PYG{o}{=} \PYG{n}{drmaa}\PYG{o}{.}\PYG{n}{Session}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{my\PYGZus{}drmaa\PYGZus{}session}\PYG{o}{.}\PYG{n}{initialize}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{n}{run\PYGZus{}job}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ls}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-        \PYG{n}{job\PYGZus{}name} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{test}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-        \PYG{n}{job\PYGZus{}other\PYGZus{}options}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}P mott\PYGZhy{}flint.prja \PYGZhy{}q short.qa}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-        \PYG{n}{job\PYGZus{}script\PYGZus{}directory} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{test\PYGZus{}dir}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-        \PYG{n}{job\PYGZus{}environment}\PYG{o}{=}\PYG{p}{\PYGZob{}} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{BASH\PYGZus{}ENV}\PYG{l+s}{\PYGZsq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZti{}/.bashrc}\PYG{l+s}{\PYGZsq{}} \PYG{p}{\PYGZcb{}}\PYG{p}{,}
-        \PYG{n}{retain\PYGZus{}job\PYGZus{}scripts} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{,} \PYG{n}{drmaa\PYGZus{}session}\PYG{o}{=}\PYG{n}{my\PYGZus{}drmaa\PYGZus{}session}\PYG{p}{)}
-\PYG{n}{run\PYGZus{}job}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ls}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-        \PYG{n}{job\PYGZus{}name} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{test}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-        \PYG{n}{job\PYGZus{}other\PYGZus{}options}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}P mott\PYGZhy{}flint.prja \PYGZhy{}q short.qa}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-        \PYG{n}{job\PYGZus{}script\PYGZus{}directory} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{test\PYGZus{}dir}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-        \PYG{n}{job\PYGZus{}environment}\PYG{o}{=}\PYG{p}{\PYGZob{}} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{BASH\PYGZus{}ENV}\PYG{l+s}{\PYGZsq{}} \PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZti{}/.bashrc}\PYG{l+s}{\PYGZsq{}} \PYG{p}{\PYGZcb{}}\PYG{p}{,}
-        \PYG{n}{retain\PYGZus{}job\PYGZus{}scripts} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{,}
-        \PYG{n}{drmaa\PYGZus{}session}\PYG{o}{=}\PYG{n}{my\PYGZus{}drmaa\PYGZus{}session}\PYG{p}{,}
-        \PYG{n}{working\PYGZus{}directory} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/gpfs1/well/mott\PYGZhy{}flint/lg/src/oss/ruffus/doc}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   catch exceptions}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{try}\PYG{p}{:}
-    \PYG{n}{stdout\PYGZus{}res}\PYG{p}{,} \PYG{n}{stderr\PYGZus{}res}  \PYG{o}{=} \PYG{n}{run\PYGZus{}job}\PYG{p}{(}\PYG{n}{cmd}\PYG{p}{,}
-                                      \PYG{n}{job\PYGZus{}name}          \PYG{o}{=} \PYG{n}{job\PYGZus{}name}\PYG{p}{,}
-                                      \PYG{n}{logger}            \PYG{o}{=} \PYG{n}{logger}\PYG{p}{,}
-                                      \PYG{n}{drmaa\PYGZus{}session}     \PYG{o}{=} \PYG{n}{drmaa\PYGZus{}session}\PYG{p}{,}
-                                      \PYG{n}{run\PYGZus{}locally}       \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{local\PYGZus{}run}\PYG{p}{,}
-                                      \PYG{n}{job\PYGZus{}other\PYGZus{}options} \PYG{o}{=} \PYG{n}{get\PYGZus{}queue\PYGZus{}name}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} relay all the stdout, stderr, drmaa output to diagnose failures}
-\PYG{k}{except} \PYG{n}{error\PYGZus{}drmaa\PYGZus{}job} \PYG{k}{as} \PYG{n}{err}\PYG{p}{:}
-    \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n+nb}{map}\PYG{p}{(}\PYG{n+nb}{str}\PYG{p}{,}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Failed to run:}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                         \PYG{n}{cmd}\PYG{p}{,}
-                         \PYG{n}{err}\PYG{p}{,}
-                         \PYG{n}{stdout\PYGZus{}res}\PYG{p}{,}
-                         \PYG{n}{stderr\PYGZus{}res}\PYG{p}{]}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{n}{my\PYGZus{}drmaa\PYGZus{}session}\PYG{o}{.}\PYG{n}{exit}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-cmd-str}\begin{itemize}
-\item {} 
-\emph{cmd\_str}
-\begin{quote}
-
-The command which will be run remotely including all parameters
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-job-name}\begin{itemize}
-\item {} 
-\emph{job\_name}
-\begin{quote}
-
-A descriptive name for the command. This will be displayed by \href{http://gridscheduler.sourceforge.net/htmlman/htmlman1/qstat.html}{SGE qstat}, for example.
-Defaults to ``ruffus\_job''
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-job-other-options}\begin{itemize}
-\item {} 
-\emph{job\_other\_options}
-\begin{quote}
-
-Other drmaa parameters can be passed verbatim as a string.
-
-Examples for SGE include project name (\code{-P project\_name}), parallel environment (\code{-pe parallel\_environ}), account (\code{-A account\_string}), resource (\code{-l resource=expression}),
-queue name (\code{-q a\_queue\_name}), queue priority (\code{-p 15}).
-
-These are parameters which you normally need to include when submitting jobs interactively, for example via
-\href{http://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html}{SGE qsub}
-or \href{http://apps.man.poznan.pl/trac/slurm-drmaa/wiki/WikiStart\#Nativespecification}{SLURM} (\href{https://computing.llnl.gov/linux/slurm/srun.html}{srun})
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-job-script-directory}\begin{itemize}
-\item {} 
-\emph{job\_script\_directory}
-\begin{quote}
-
-The directory where drmaa temporary script files will be found. Defaults to the current working directory.
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-job-environment}\begin{itemize}
-\item {} 
-\emph{job\_environment}
-\begin{quote}
-
-A dictionary of key / values with environment variables. E.g. \code{"\{'BASH\_ENV': '\textasciitilde{}/.bashrc'\}"}
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-working-directory}\begin{itemize}
-\item {} 
-\emph{working\_directory}
-\begin{itemize}
-\item {} 
-Sets the working directory.
-
-\item {} 
-Should be a fully qualified path.
-
-\item {} 
-Defaults to the current working directory.
-
-\end{itemize}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-retain-job-scripts}\begin{itemize}
-\item {} 
-\emph{retain\_job\_scripts}
-\begin{quote}
-
-Do not delete temporary script files containg drmaa commands. Useful for
-debugging, running on the command line directly, and can provide a useful record of the commands.
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-logger}\begin{itemize}
-\item {} 
-\emph{logger}
-\begin{quote}
-
-For logging messages indicating the progress of the pipeline in terms of tasks and jobs. Takes objects with the standard python
-\href{https://docs.python.org/2/library/logging.html}{logging} module interface.
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-drmaa-session}\begin{itemize}
-\item {} 
-\emph{drmaa\_session}
-\begin{quote}
-
-A shared drmaa session created and managed separately.
-
-In the main part of your \textbf{Ruffus} pipeline script somewhere there should be code looking like this:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   start shared drmaa session for all jobs / tasks in pipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{k+kn}{import} \PYG{n+nn}{drmaa}
-\PYG{n}{drmaa\PYGZus{}session} \PYG{o}{=} \PYG{n}{drmaa}\PYG{o}{.}\PYG{n}{Session}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{drmaa\PYGZus{}session}\PYG{o}{.}\PYG{n}{initialize}\PYG{p}{(}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   pipeline functions}
-\PYG{c}{\PYGZsh{}}
-
-\PYG{k}{if} \PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}} \PYG{o}{==} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZus{}\PYGZus{}main\PYGZus{}\PYGZus{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}
-    \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{run} \PYG{p}{(}\PYG{n}{options}\PYG{p}{,} \PYG{n}{multithread} \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{jobs}\PYG{p}{)}
-    \PYG{n}{drmaa\PYGZus{}session}\PYG{o}{.}\PYG{n}{exit}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-run-locally}\begin{itemize}
-\item {} 
-\emph{run\_locally}
-\begin{quote}
-
-Runs commands locally using the standard python \href{https://docs.python.org/2/library/subprocess.html}{subprocess} module
-rather than dispatching remotely. This allows scripts to be debugged easily
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-touch-only}\begin{itemize}
-\item {} 
-\emph{touch\_only}
-\begin{quote}
-
-Create or update {\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job-output-files]{\emph{Output files}}}
-only to simulate the running of the pipeline.
-Does not dispatch commands remotely or locally. This is most useful to force a
-pipeline to acknowledge that a particular part is now up-to-date.
-
-See also: {\hyperref[pipeline_functions:pipeline-functions-pipeline-run-touch-files-only]{\emph{pipeline\_run(touch\_files\_only=True)}}}
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{drmaa_wrapper_functions:drmaa-wrapper-run-job-output-files}\begin{itemize}
-\item {} 
-\emph{output\_files}
-\begin{quote}
-
-Output files which will be created or updated if  {\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job-touch-only]{\emph{touch\_only}}} \code{=True}
-\end{quote}
-
-\end{itemize}
-
-
-\section{Installation}
-\label{installation:installation}\label{installation::doc}\label{installation:id1}
-\code{Ruffus} is a lightweight python module for building computational pipelines.
-
-
-\subsection{The easy way}
-\label{installation:the-easy-way}\begin{quote}
-
-\emph{Ruffus} is available as an
-\href{http://peak.telecommunity.com/DevCenter/EasyInstall}{easy-install} -able package
-on the \href{http://pypi.python.org/pypi/Sphinx}{Python Package Index}.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-sudo pip install ruffus --upgrade
-\end{Verbatim}
-
-This may also work for older installations
-\begin{enumerate}
-\item {} 
-Install setuptools:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-wget peak.telecommunity.com/dist/ez\_setup.py
-sudo python ez\_setup.py
-\end{Verbatim}
-
-\item {} 
-Install \emph{Ruffus} automatically:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-easy\_install -U ruffus
-\end{Verbatim}
-
-\end{enumerate}
-\end{quote}
-
-
-\subsection{The most up-to-date code:}
-\label{installation:the-most-up-to-date-code}\begin{itemize}
-\item {} 
-\href{https://pypi.python.org/pypi/ruffus}{Download the latest sources} or
-
-\item {} 
-Check out the latest code from Google using git:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-git clone https://bunbun68@code.google.com/p/ruffus/ .
-\end{Verbatim}
-
-\item {} 
-Bleeding edge Ruffus development takes place on github:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-git clone git at github.com:bunbun/ruffus.git .
-\end{Verbatim}
-
-\item {} 
-To install after downloading, change to the , type:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-python ./setup.py install
-\end{Verbatim}
-
-\end{itemize}
-
-
-\subsubsection{Graphical flowcharts}
-\label{installation:graphical-flowcharts}\begin{quote}
-
-\textbf{Ruffus} relies on the \code{dot} programme from \href{http://www.graphviz.org/}{Graphviz}
-(``Graph visualisation'') to make pretty flowchart representations of your pipelines in multiple
-graphical formats (e.g. \code{png}, \code{jpg}). The crossplatform Graphviz package can be
-\href{http://www.graphviz.org/Download.php}{downloaded here} for Windows,
-Linux, Macs and Solaris. Some Linux
-distributions may include prebuilt packages.
-\begin{description}
-\item[{For Fedora, try}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-yum list 'graphviz*'
-\end{Verbatim}
-
-\item[{For ubuntu / Debian, try}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-sudo apt-get install graphviz
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\index{Design!Ruffus}\index{Ruffus!Design}
-
-\section{Design \& Architecture}
-\label{design:index-0}\label{design::doc}\label{design:design-architecture}\begin{quote}
-
-The \emph{ruffus} module has the following design goals:
-\begin{itemize}
-\item {} 
-Simplicity.
-
-\item {} 
-Intuitive
-
-\item {} 
-Lightweight
-
-\item {} 
-Unintrusive
-
-\item {} 
-Flexible/Powerful
-
-\end{itemize}
-
-Computational pipelines, especially in science, are best thought of in terms of data
-flowing through successive, dependent stages (\textbf{ruffus} calls these {\hyperref[glossary:term-task]{\emph{task}}}s).
-Traditionally, files have been used to
-link pipelined stages together. This means that computational pipelines can be managed
-using traditional software construction (\emph{build}) systems.
-\end{quote}
-
-
-\subsection{\emph{GNU Make}}
-\label{design:gnu-make}\begin{quote}
-
-The grand-daddy of these is UNIX \href{http://en.wikipedia.org/wiki/Make\_(software)}{make}.
-\href{http://www.gnu.org/software/make/}{GNU make} is ubiquitous in the linux world for
-installing and compiling software.
-It has been widely used to build computational pipelines because it supports:
-\begin{itemize}
-\item {} 
-Stopping and restarting computational processes
-
-\item {} 
-Running multiple, even thousands of jobs in parallel
-
-\end{itemize}
-\end{quote}
-
-
-\subsubsection{Deficiencies of \emph{make} / \emph{gmake}}
-\label{design:design-make-syntax-ugly}\label{design:deficiencies-of-make-gmake}\begin{quote}
-
-However, make and \href{http://www.gnu.org/software/make/}{GNU make} use a specialised (domain-specific)
-language, which has is been much criticised because of poor support for modern
-programming languages features, such as variable scope, pattern matching, debugging.
-Make scripts require large amounts of often obscure shell scripting
-and makefiles can quickly become unmaintainable.
-\end{quote}
-
-
-\subsection{\emph{Scons}, \emph{Rake} and other \emph{Make} alternatives}
-\label{design:design-scons-and-rake}\label{design:scons-rake-and-other-make-alternatives}\begin{quote}
-
-Many attempts have been made to produce a more modern version of make, with less of its
-historical baggage. These include the Java-based \href{http://ant.apache.org/}{Apache ant} which is specified in xml.
-
-More interesting are a new breed of build systems whose scripts are written in modern programming
-languages, rather than a specially-invented ``build'' specificiation syntax.
-These include the Python \href{http://www.scons.org/}{scons}, Ruby \href{http://rake.rubyforge.org/}{rake} and
-its python port \href{http://packages.python.org/Smithy/}{Smithy}.
-
-The great advantages are that computation pipelines do not need to be artificially parcelled out
-between (the often second-class) workflow management code, and the logic which does the real computation
-in the pipeline. It also means that workflow management can use all the standard language and library
-features, for example, to read in directories, match file names using regular expressions and so on.
-
-\textbf{Ruffus} is much like scons in that the modern dynamic programming language python is used seamlessly
-throughout its pipeline scripts.
-\end{quote}
-
-
-\subsubsection{Implicit dependencies: disadvantages of \emph{make} / \emph{scons} / \emph{rake}}
-\label{design:design-implicit-dependencies}\label{design:implicit-dependencies-disadvantages-of-make-scons-rake}\begin{quote}
-
-Although Python \href{http://www.scons.org/}{scons} and Ruby \href{http://rake.rubyforge.org/}{rake}
-are in many ways more powerful and easier to use for building software, they are still an
-imperfect fit to the world of computational pipelines.
-
-This is a result of the way dependencies are specified, an essential part of their design inherited
-from \href{http://www.gnu.org/software/make/}{GNU make}.
-
-The order of operations in all of these tools is specified in a \emph{declarative} rather than
-\emph{imperative} manner. This means that the sequence of steps that a build should take are
-not spelled out explicity and directly. Instead recipes are provided for turning input files
-of each type to another.
-
-So, for example, knowing that \code{a-\textgreater{}b}, \code{b-\textgreater{}c}, \code{c-\textgreater{}d}, the build
-system can infer how to get from \code{a} to \code{d} by performing the necessary operations in the correct order.
-\begin{description}
-\item[{This is immensely powerful for three reasons:}] \leavevmode\begin{enumerate}
-\item {} 
-The plumbing, such as dependency checking, passing output
-from one stage to another, are handled automatically by the build system. (This is the whole point!)
-
-\item {} 
-The same \emph{recipe} can be re-used at different points in the build.
-
-\item {} 
-\begin{DUlineblock}{0em}
-\item[] Intermediate files do not need to be retained.
-\item[] Given the automatic inference that \code{a-\textgreater{}b-\textgreater{}c-\textgreater{}d},
-we don't need to keep \code{b} and \code{c} files around once \code{d} has been produced.
-\item[] 
-\end{DUlineblock}
-
-\end{enumerate}
-
-\end{description}
-
-The disadvantage is that because stages are specified only indirectly, in terms of
-file name matches, the flow through a complex build or a pipeline can be difficult to trace, and nigh
-impossible to debug when there are problems.
-\end{quote}
-
-
-\subsubsection{Explicit dependencies in \emph{Ruffus}}
-\label{design:explicit-dependencies-in-ruffus}\label{design:design-explicit-dependencies-in-ruffus}\begin{quote}
-
-\textbf{Ruffus} takes a different approach. The order of operations is specified explicitly rather than inferred
-indirectly from the input and output types. So, for example, we would explicitly specify three successive and
-linked operations \code{a-\textgreater{}b}, \code{b-\textgreater{}c}, \code{c-\textgreater{}d}. The build system knows that the operations always proceed in
-this order.
-
-Looking at a \textbf{Ruffus} script, it is always clear immediately what is the succession of computational steps
-which will be taken.
-
-\textbf{Ruffus} values clarity over syntactic cleverness.
-\end{quote}
-
-
-\subsubsection{Static dependencies: What \emph{make} / \emph{scons} / \emph{rake} can't do (easily)}
-\label{design:static-dependencies-what-make-scons-rake-can-t-do-easily}\label{design:design-static-dependencies}\begin{quote}
-
-\href{http://www.gnu.org/software/make/}{GNU make}, \href{http://www.scons.org/}{scons} and \href{http://rake.rubyforge.org/}{rake}
-work by infer a static dependency (diacyclic) graph between all the files which
-are used by a computational pipeline. These tools locate the target that they are supposed
-to build and work backward through the dependency graph from that target,
-rebuilding anything that is out of date.This is perfect for building software,
-where the list of files data files can be computed \textbf{statically} at the beginning of the build.
-
-This is not ideal matches for scientific computational pipelines because:
-\begin{itemize}
-\item {} 
-\begin{DUlineblock}{0em}
-\item[] Though the \emph{stages} of a pipeline (i.e. \emph{compile} or \emph{DNA alignment}) are
-invariably well-specified in advance, the number of
-operations (\emph{job}s) involved at each stage may not be.
-\item[] 
-\end{DUlineblock}
-
-\item {} 
-\begin{DUlineblock}{0em}
-\item[] A common approach is to break up large data sets into manageable chunks which
-can be operated on in parallel in computational clusters or farms
-(See \href{http://en.wikipedia.org/wiki/Embarrassingly\_parallel}{embarassingly parallel problems}).
-\item[] This means that the number of parallel operations or jobs varies with the data (the number of manageable chunks),
-and dependency trees cannot be calculated statically beforehand.
-\item[] 
-\end{DUlineblock}
-
-\end{itemize}
-
-Computational pipelines require \textbf{dynamic} dependencies which are not calculated up-front, but
-at each stage of the pipeline
-
-This is a \emph{known} issue with traditional build systems each of which has partial strategies to work around
-this problem:
-\begin{itemize}
-\item {} 
-gmake always builds the dependencies when first invoked, so dynamic dependencies require (complex!) recursive calls to gmake
-
-\item {} 
-\href{http://objectmix.com/ruby/759716-rake-dependencies-unknown-prior-running-tasks-2.html}{Rake dependencies unknown prior to running tasks}.
-
-\item {} 
-\href{http://www.scons.org/wiki/DynamicSourceGenerator}{Scons: Using a Source Generator to Add Targets Dynamically}
-
-\end{itemize}
-
-\textbf{Ruffus} explicitly and straightforwardly handles tasks which produce an indeterminate (i.e. runtime dependent)
-number of output, using its \textbf{@split}, \textbf{@transform}, \textbf{merge} function annotations.
-\end{quote}
-
-
-\subsection{Managing pipelines stage-by-stage using \textbf{Ruffus}}
-\label{design:managing-pipelines-stage-by-stage-using-ruffus}\begin{quote}
-
-\textbf{Ruffus} manages pipeline stages directly.
-\begin{enumerate}
-\item {} 
-\begin{DUlineblock}{0em}
-\item[] The computational operations for each stage of the pipeline are written by you, in
-separate python functions.
-\item[] (These correspond to \href{http://www.gnu.org/software/make/manual/make.html\#Pattern-Rules}{gmake pattern rules})
-\item[] 
-\end{DUlineblock}
-
-\item {} 
-\begin{DUlineblock}{0em}
-\item[] The dependencies between pipeline stages (python functions) are specified up-front.
-\item[] These can be displayed as a flow chart.
-\end{DUlineblock}
-
-\includegraphics{front_page_flowchart.png}
-
-\item {} 
-\textbf{Ruffus} makes sure pipeline stage functions are called in the right order,
-with the right parameters, running in parallel using multiprocessing if necessary.
-
-\item {} 
-Data file timestamps can be used to automatically determine if all or any parts
-of the pipeline are out-of-date and need to be rerun.
-
-\item {} 
-Separate pipeline stages, and operations within each pipeline stage,
-can be run in parallel provided they are not inter-dependent.
-
-\end{enumerate}
-
-Another way of looking at this is that \textbf{ruffus} re-constructs datafile dependencies dynamically
-on-the-fly when it gets to each stage of the pipeline, giving much more flexibility.
-\end{quote}
-
-
-\subsubsection{Disadvantages of the Ruffus design}
-\label{design:disadvantages-of-the-ruffus-design}\begin{quote}
-
-Are there any disadvantages to this trade-off for additional clarity?
-\begin{enumerate}
-\item {} 
-Each pipeline stage needs to take the right input and output. For example if we specified the
-steps in the wrong order: \code{a-\textgreater{}b}, \code{c-\textgreater{}d}, \code{b-\textgreater{}c}, then no useful output would be produced.
-
-\item {} 
-We cannot re-use the same recipes in different parts of the pipeline
-
-\item {} 
-Intermediate files need to be retained.
-
-\end{enumerate}
-
-In our experience, it is always obvious when pipeline operations are in the wrong order, precisely because the
-order of computation is the very essense of the design of each pipeline. Ruffus produces extra diagnostics when
-no output is created in a pipeline stage (usually happens for incorrectly specified regular expressions.)
-
-Re-use of recipes is as simple as an extra call to common function code.
-
-Finally, some users have proposed future enhancements to \textbf{Ruffus} to handle unnecessary temporary / intermediate files.
-\end{quote}
-
-\index{Design!Comparison of Ruffus with alternatives}\index{Comparison of Ruffus with alternatives!Design}
-
-\subsection{Alternatives to \textbf{Ruffus}}
-\label{design:index-1}\label{design:alternatives-to-ruffus}\begin{quote}
-
-A comparison of more make-like tools is available from \href{http://biowiki.org/MakeComparison}{Ian Holmes' group}.
-
-Build systems include:
-\begin{itemize}
-\item {} 
-\href{http://www.gnu.org/software/make/}{GNU make}
-
-\item {} 
-\href{http://www.scons.org/}{scons}
-
-\item {} 
-\href{http://ant.apache.org/}{ant}
-
-\item {} 
-\href{http://rake.rubyforge.org/}{rake}
-
-\end{itemize}
-
-There are also complete workload managements systems such as Condor.
-Various bioinformatics pipelines are also available, including that used by the
-leading genome annotation website Ensembl, Pegasys, GPIPE, Taverna, Wildfire, MOWserv,
-Triana, Cyrille2 etc. These all are either hardwired to specific databases, and tasks,
-or have steep learning curves for both the scientist/developer and the IT system
-administrators.
-
-\textbf{Ruffus} is designed to be lightweight and unintrusive enough to use for writing pipelines
-with just 10 lines of code.
-\end{quote}
-
-
-\strong{See also:}
-
-
-\textbf{Bioinformatics workload managements systems}
-\begin{quote}
-\begin{description}
-\item[{Condor:}] \leavevmode
-\href{http://www.cs.wisc.edu/condor/description.html}{http://www.cs.wisc.edu/condor/description.html}
-
-\item[{Ensembl Analysis pipeline:}] \leavevmode
-\href{http://www.ncbi.nlm.nih.gov/pubmed/15123589}{http://www.ncbi.nlm.nih.gov/pubmed/15123589}
-
-\item[{Pegasys:}] \leavevmode
-\href{http://www.ncbi.nlm.nih.gov/pubmed/15096276}{http://www.ncbi.nlm.nih.gov/pubmed/15096276}
-
-\item[{GPIPE:}] \leavevmode
-\href{http://www.biomedcentral.com/pubmed/15096276}{http://www.biomedcentral.com/pubmed/15096276}
-
-\item[{Taverna:}] \leavevmode
-\href{http://www.ncbi.nlm.nih.gov/pubmed/15201187}{http://www.ncbi.nlm.nih.gov/pubmed/15201187}
-
-\item[{Wildfire:}] \leavevmode
-\href{http://www.biomedcentral.com/pubmed/15788106}{http://www.biomedcentral.com/pubmed/15788106}
-
-\item[{MOWserv:}] \leavevmode
-\href{http://www.biomedcentral.com/pubmed/16257987}{http://www.biomedcentral.com/pubmed/16257987}
-
-\item[{Triana:}] \leavevmode
-\href{http://dx.doi.org/10.1007/s10723-005-9007-3}{http://dx.doi.org/10.1007/s10723-005-9007-3}
-
-\item[{Cyrille2:}] \leavevmode
-\href{http://www.biomedcentral.com/1471-2105/9/96}{http://www.biomedcentral.com/1471-2105/9/96}
-
-\end{description}
-\end{quote}
-
-
-
-\index{Acknowledgements}
-
-\subsubsection{Acknowledgements}
-\label{design:acknowledgements}\label{design:index-2}\begin{itemize}
-\item {} 
-Bruce Eckel's insightful article on
-\href{http://www.artima.com/weblogs/viewpost.jsp?thread=241209}{A Decorator Based Build System}
-was the obvious inspiration for the use of decorators in \emph{Ruffus}.
-\begin{description}
-\item[{The rest of the \emph{Ruffus} takes uses a different approach. In particular:}] \leavevmode\begin{enumerate}
-\item {} 
-\emph{Ruffus} uses task-based not file-based dependencies
-
-\item {} 
-\emph{Ruffus} tries to have minimal impact on the functions it decorates.
-
-Bruce Eckel's design wraps functions in ``rule'' objects.
-
-\emph{Ruffus} tasks are added as attributes of the functions which can be still be
-called normally. This is how \emph{Ruffus} decorators can be layered in any order
-onto the same task.
-
-\end{enumerate}
-
-\end{description}
-
-\item {} 
-Languages like c++ and Java would probably use a ``mixin'' approach.
-Python's easy support for reflection and function references,
-as well as the necessity of marshalling over process boundaries, dictated the
-internal architecture of \emph{Ruffus}.
-
-\item {} 
-The \href{http://www.boost.org}{Boost Graph library} for text book implementations of directed
-graph traversals.
-
-\item {} 
-\href{http://www.graphviz.org/}{Graphviz}. Just works. Wonderful.
-
-\item {} 
-Andreas Heger, Christoffer Nellåker and Grant Belgard for driving Ruffus towards
-ever simpler syntax.
-
-\end{itemize}
-
-
-\section{Major Features added to Ruffus}
-\label{history:glob}\label{history::doc}\label{history:major-features-added-to-ruffus}
-\begin{notice}{note}{Note:}
-See {\hyperref[todo:todo]{\emph{To do list}}} for future enhancements to Ruffus
-\end{notice}
-
-
-\subsection{version 2.5RC}
-\label{history:version-2-5rc}\begin{quote}
-
-31st July 2014: Release Candidate
-
-5th August 2014: Release
-\end{quote}
-
-
-\subsubsection{1) Python3 compatability (but at least python 2.6 is now required)}
-\label{history:python3-compatability-but-at-least-python-2-6-is-now-required}\begin{quote}
-
-Ruffus v2.5 is now python3 compatible. This has required surprisingly many changes to the codebase. Please report any bugs to me.
-
-\begin{notice}{note}{Note:}
-\textbf{Ruffus now requires at least python 2.6}
-
-It proved to be impossible to support python 2.5 and python 3.x at the same time.
-\end{notice}
-\end{quote}
-
-
-\subsubsection{2) Ctrl-C interrupts}
-\label{history:ctrl-c-interrupts}\begin{quote}
-
-Ruffus now mostly(!) terminates gracefully when interrupted by Ctrl-C .
-
-Please send me bug reports for when this doesn't work with a minimally reproducible case.
-
-This means that, in general, if an \code{Exception} is thrown during your pipeline but you don't want to wait for the rest of the jobs to complete, you can still press Ctrl-C at any point.
-Note that you may still need to clean up spawned processes, for example, using \code{qdel} if you are using \code{Ruffus.drmaa\_wrapper}
-\end{quote}
-
-
-\subsubsection{3) Customising flowcharts in pipeline\_printout\_graph() with \texttt{@graphviz}}
-\label{history:customising-flowcharts-in-pipeline-printout-graph-with-graphviz}\begin{quote}
-
-\emph{Contributed by Sean Davis, with improved syntax via Jake Biesinger}
-
-The graphics for each task can have its own attributes (URL, shape, colour) etc. by adding
-\href{http://www.graphviz.org/doc/info/attrs.html}{graphviz attributes}
-using the \code{@graphviz} decorator.
-\begin{itemize}
-\item {} 
-This allows HTML formatting in the task names (using the \code{label} parameter as in the following example).
-HTML labels \textbf{must} be enclosed in \code{\textless{}} and \code{\textgreater{}}. E.g.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{label} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZlt{}Line \PYGZlt{}BR/\PYGZgt{} wrapped task\PYGZus{}name()\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-\item {} 
-You can also opt to keep the task name and wrap it with a prefix and suffix:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{label\PYGZus{}suffix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{??? }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{label\PYGZus{}prefix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{: What is this?}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-\item {} 
-The \code{URL} attribute allows the generation of clickable svg, and also client / server
-side image maps usable in web pages.
-See \href{http://www.graphviz.org/content/output-formats\#dimap}{Graphviz documentation}
-
-\end{itemize}
-
-Example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@graphviz}\PYG{p}{(}\PYG{n}{URL}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{http://cnn.com}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{fillcolor} \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FFCCCC}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                \PYG{n}{color} \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF0000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{pencolor}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF0000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{fontcolor}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}4B6000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                \PYG{n}{label\PYGZus{}suffix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{???}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{label\PYGZus{}prefix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{What is this?\PYGZlt{}BR/\PYGZgt{} }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{n}{label} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZlt{}What \PYGZlt{}FONT COLOR=}\PYG{l+s+se}{\PYGZbs{}\PYGZdq{}}\PYG{l+s}{red}\PYG{l+s+se}{\PYGZbs{}\PYGZdq{}}\PYG{l+s}{\PYGZgt{}is\PYGZlt{}/FONT\PYGZgt{}this\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{n}{shape}\PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{component}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{height} \PYG{o}{=} \PYG{l+m+mf}{1.5}\PYG{p}{,} \PYG{n}{peripheries} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,}
-                \PYG{n}{style}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dashed}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task2}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   Can use dictionary if you wish...}
-\PYG{n}{graphviz\PYGZus{}params} \PYG{o}{=} \PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{URL}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{http://cnn.com}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF00FF}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{\PYGZcb{}}
-\PYG{n+nd}{@graphviz}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n}{graphviz\PYGZus{}params}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{myTask}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{,}\PYG{n}{output}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\scalebox{0.300000}{\includegraphics{history_html_flowchart.png}}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{4. Consistent verbosity levels}
-\label{history:consistent-verbosity-levels}\begin{quote}
-
-The verbosity levels are now more fine-grained and consistent between pipeline\_printout and pipeline\_run.
-Note that At verbosity \textgreater{} 2, \code{pipeline\_run}  outputs lists of up-to-date tasks before running the pipeline.
-Many users who defaulted to using a verbosity of 3 may want to move up to \code{verbose = 4}.
-\begin{itemize}
-\item {} 
-\textbf{level 0} : \emph{Nothing}
-
-\item {} 
-\textbf{level 1} : \emph{Out-of-date Task names}
-
-\item {} 
-\textbf{level 2} : \emph{All Tasks (including any task function docstrings)}
-
-\item {} 
-\textbf{level 3} : \emph{Out-of-date Jobs in Out-of-date Tasks, no explanation}
-
-\item {} 
-\textbf{level 4} : \emph{Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings}
-
-\item {} 
-\textbf{level 5} : \emph{All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)}
-
-\item {} 
-\textbf{level 6} : \emph{All jobs in All Tasks whether out of date or not}
-
-\item {} 
-\textbf{level 10}: \emph{Logs messages useful only for debugging ruffus pipeline code}
-
-\end{itemize}
-\begin{itemize}
-\item {} 
-Defaults to \textbf{level 4} for pipeline\_printout: \emph{Out of date jobs, with explanations and warnings}
-
-\item {} 
-Defaults to \textbf{level 1} for pipeline\_run: \emph{Out-of-date Task names}
-
-\end{itemize}
-\end{quote}
-
-
-\subsubsection{5. Allow abbreviated paths from \texttt{pipeline\_run} or \texttt{pipeline\_printout}}
-\label{history:allow-abbreviated-paths-from-pipeline-run-or-pipeline-printout}\begin{quote}
-
-\begin{notice}{note}{Note:}
-Please contact me with suggestions if you find the abbreviations useful but ``aesthetically challenged''!
-\end{notice}
-
-Some pipelines produce interminable lists of long filenames. It would be nice to be able to abbreviate this
-to just enough information to follow the progress.
-\begin{description}
-\item[{Ruffus now allows either}] \leavevmode\begin{enumerate}
-\item {} 
-Only the nth top level sub-directories to be included
-
-\item {} 
-The message to be truncated to a specified number of characters (to fit on a line, for example)
-
-Note that the number of characters specified is the separate length of the input and output parameters,
-not the entire message. You many need to specify a smaller limit that you expect (e.g. \code{60} rather than \emph{80})
-
-\end{enumerate}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{n}{NNN}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{n}{MMM}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-The \code{verbose\_abbreviated\_path} parameter restricts the length of input / output file paths to either
-\begin{quote}
-\begin{itemize}
-\item {} 
-NNN levels of nested paths
-
-\item {} 
-A total of MMM characters, MMM is specified by setting \code{verbose\_abbreviated\_path} to -MMM (i.e. negative values)
-
-\end{itemize}
-
-\code{verbose\_abbreviated\_path} defaults to \code{2}
-\end{quote}
-
-For example:
-\begin{quote}
-
-Given \code{{[}"aa/bb/cc/dddd.txt", "aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt"{]}}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{c}{\PYGZsh{} Original relative paths}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[aa/bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
- \PYG{c}{\PYGZsh{} Full abspath}
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{l+m+mi}{0}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[/test/ruffus/src/aa/bb/cc/dddd.txt, /test/ruffus/src/aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
- \PYG{c}{\PYGZsh{} Specifed level of nested directories}
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{l+m+mi}{1}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[.../dddd.txt, .../gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{l+m+mi}{2}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[.../cc/dddd.txt, .../ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{l+m+mi}{3}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[.../bb/cc/dddd.txt, .../eeee/ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-
-
- \PYG{c}{\PYGZsh{} Truncated to MMM characters}
- \PYG{n}{verbose\PYGZus{}abbreviated\PYGZus{}path} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{60}
- \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZlt{}???\PYGZgt{} /bb/cc/dddd.txt, aaa/bbbb/cccc/eeed/eeee/ffff/gggg.txt]}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-If you are using \code{ruffus.cmdline}, the abbreviated path lengths can be specified on
-the command line as an extension to the verbosity:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{c}{\PYGZsh{} verbosity of 4}
- yourscript.py \PYGZhy{}\PYGZhy{}verbose 4
-
- \PYG{c}{\PYGZsh{} display three levels of nested directories}
- yourscript.py \PYGZhy{}\PYGZhy{}verbose 4:3
-
- \PYG{c}{\PYGZsh{} restrict input and output parameters to 60 letters}
- yourscript.py \PYGZhy{}\PYGZhy{}verbose 4:\PYGZhy{}60
-\end{Verbatim}
-
-The number after the colon is the abbreviated path length
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Other changes}
-\label{history:other-changes}\begin{itemize}
-\item {} 
-BUG FIX: Output producing wild cards was not saved in the checksum files!!!
-
-\item {} 
-BUG FIX: @mkdir bug under Windows. Thanks to Sean Turley. (Aargh! Different exceptions are thrown in Windows vs. Linux for the same condition!)
-
-\item {} 
-Added {\hyperref[pipeline_functions:pipeline-functions-pipeline-get-task-names]{\emph{pipeline\_get\_task\_names(...)}}} which returns all task name as a list of strings. Thanks to Clare Sloggett
-
-\end{itemize}
-
-
-\subsection{version 2.4.1}
-\label{history:version-2-4-1}\begin{quote}
-
-26th April 2014
-\begin{itemize}
-\item {} 
-Breaking changes to drmaa API suggested by Bernie Pope to ensure portability across different drmaa implementations (SGE, SLURM etc.)
-
-\end{itemize}
-\end{quote}
-
-
-\subsection{version 2.4}
-\label{history:version-2-4}\begin{quote}
-
-4th April 2014
-\end{quote}
-
-
-\subsubsection{Additions to \texttt{ruffus} namespace}
-\label{history:additions-to-ruffus-namespace}\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/output_file_names:new-manual-formatter]{\emph{formatter()}}} ({\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{syntax}}})
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/originate:new-manual-originate]{\emph{originate()}}} ({\hyperref[decorators/originate:decorators-originate]{\emph{syntax}}})
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-subdivide]{\emph{subdivide()}}} ({\hyperref[decorators/subdivide:decorators-subdivide]{\emph{syntax}}})
-
-\end{itemize}
-
-
-\subsubsection{Installation: use pip}
-\label{history:installation-use-pip}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-sudo pip install ruffus --upgrade
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{1) Command Line support}
-\label{history:command-line-support}\begin{quote}
-
-The optional \code{Ruffus.cmdline} module provides support for a set of common command
-line arguments which make writing \emph{Ruffus} pipelines much more pleasant.
-See {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline]{\emph{manual}}}
-\end{quote}
-
-
-\subsubsection{2) Check pointing}
-\label{history:check-pointing}\begin{itemize}
-\item {} 
-Contributed by \textbf{Jake Biesinger}
-
-\item {} 
-See {\hyperref[tutorials/new_tutorial/checkpointing:new-manual-checkpointing]{\emph{Manual}}}
-
-\item {} 
-Uses a fault resistant sqlite database file to log i/o files, and additional checksums
-
-\item {} 
-defaults to checking file timestamps stored in the current directory (\code{ruffus\_utilility.RUFFUS\_HISTORY\_FILE = '.ruffus\_history.sqlite'})
-
-\item {} 
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(..., checksum\_level = N, ...)}}}
-\begin{itemize}
-\item {} 
-level 0 = CHECKSUM\_FILE\_TIMESTAMPS      : Classic mode. Use only file timestamps (no checksum file will be created)
-
-\item {} 
-level 1 = CHECKSUM\_HISTORY\_TIMESTAMPS   : Also store timestamps in a database after successful job completion
-
-\item {} 
-level 2 = CHECKSUM\_FUNCTIONS            : As above, plus a checksum of the pipeline function body
-
-\item {} 
-level 3 = CHECKSUM\_FUNCTIONS\_AND\_PARAMS : As above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-\item {} 
-defaults to level 1
-
-\end{itemize}
-
-\item {} 
-Can speed up trivial tasks: Previously Ruffus always added an extra 1 second pause between tasks
-to guard against file systems (Ext3, FAT, some NFS) with low timestamp granularity.
-
-\end{itemize}
-
-
-\subsubsection{3) \emph{subdivide()} (\emph{syntax})}
-\label{history:subdivide-syntax}\begin{itemize}
-\item {} 
-Take a list of input jobs (like {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}) but further splits each into multiple jobs, i.e. it is a \textbf{many-\textgreater{}even more} relationship
-
-\item {} 
-synonym for the deprecated \code{@split(..., regex(), ...)}
-
-\end{itemize}
-
-
-\subsubsection{4) \emph{mkdir()} (\emph{syntax}) with \emph{formatter()}, \emph{suffix()}  and \emph{regex()}}
-\label{history:mkdir-syntax-with-formatter-suffix-and-regex}\begin{itemize}
-\item {} 
-allows directories to be created depending on runtime parameters or the output of previous tasks
-
-\item {} 
-behaves just like {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} but with its own (internal) function which does the actual work of making a directory
-
-\item {} 
-Previous behavior is retained:\code{mkdir} continues to work seamlessly inside {\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}}
-
-\end{itemize}
-
-
-\subsubsection{5) \emph{originate()} (\emph{syntax})}
-\label{history:originate-syntax}\begin{itemize}
-\item {} 
-Generates output files without dependencies from scratch  (\emph{ex nihilo}!)
-
-\item {} 
-For first step in a pipeline
-
-\item {} 
-Task function obviously only takes output and not input parameters. (There \emph{are} no inputs!)
-
-\item {} 
-synonym for {\hyperref[decorators/split:decorators-split]{\emph{@split(None,...)}}}
-
-\item {} 
-See {\hyperref[decorators/originate:decorators-originate]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/originate:new-manual-originate]{\emph{Manual}}}
-
-\end{itemize}
-
-
-\subsubsection{6) New flexible \emph{formatter()} (\emph{syntax}) alternative to \emph{regex()}  \& \emph{suffix()}}
-\label{history:new-flexible-formatter-syntax-alternative-to-regex-suffix}\begin{itemize}
-\item {} 
-Easy manipulation of path subcomponents in the style of \href{http://docs.python.org/2/library/os.path.html\#os.path.split}{os.path.split()}
-
-\item {} 
-Regular expressions are no longer necessary for path manipulation
-
-\item {} 
-Familiar python syntax
-
-\item {} 
-Optional regular expression matches
-
-\item {} 
-Can refer to any in the list of N input files (not only the first file as for \code{regex(...)})
-
-\item {} 
-Can even refer to individual letters within a match
-
-\end{itemize}
-
-
-\subsubsection{7) Combinatorics (all vs. all decorators)}
-\label{history:combinatorics-all-vs-all-decorators}\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/combinatorics:new-manual-product]{\emph{@product}}}  (See \href{http://docs.python.org/2/library/itertools.html\#itertools.product}{itertools.product})
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/combinatorics:new-manual-permutations]{\emph{@permutations}}}  (See \href{http://docs.python.org/2/library/itertools.html\#itertools.permutations}{itertools.permutations})
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinations]{\emph{@combinations}}} (See \href{http://docs.python.org/2/library/itertools.html\#itertools.combinations}{itertools.combinations})
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}} (See \href{http://docs.python.org/2/library/itertools.html\#itertools.combinations\_with\_replacement}{itertools.combinations\_with\_replacement})
-
-\item {} 
-in optional {\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinatorics]{\emph{combinatorics}}} module
-
-\item {} 
-Only {\hyperref[tutorials/new_tutorial/output_file_names:new-manual-formatter]{\emph{formatter()}}} provides the necessary flexibility to construct the output. ({\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}} and {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}} are not supported.)
-
-\item {} 
-See {\hyperref[decorators/decorators:decorators-combinatorics]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinatorics]{\emph{Manual}}}
-
-\end{itemize}
-
-
-\subsubsection{8) drmaa support and multithreading:}
-\label{history:drmaa-support-and-multithreading}\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/multiprocessing:new-manual-ruffus-drmaa-wrapper-run-job]{\emph{ruffus.drmaa\_wrapper.run\_job()}}} ({\hyperref[drmaa_wrapper_functions:drmaa-wrapper-run-job]{\emph{syntax}}})
-
-\item {} 
-Optional helper module allows jobs to dispatch work to a computational cluster and wait until it completes.
-
-\item {} 
-Requires \code{multithread} rather than \code{multiprocess}
-
-\end{itemize}
-
-
-\subsubsection{9) \texttt{pipeline\_run(...)} and exceptions}
-\label{history:pipeline-run-and-exceptions}\begin{quote}
-
-See {\hyperref[tutorials/new_tutorial/exceptions:new-manual-exceptions]{\emph{Manual}}}
-\begin{itemize}
-\item {} 
-Optionally terminate pipeline after first exception
-
-\item {} 
-Display exceptions without delay
-
-\end{itemize}
-\end{quote}
-
-
-\subsubsection{10) Miscellaneous}
-\label{history:miscellaneous}\begin{quote}
-\begin{description}
-\item[{Better error messages for \code{formatter()}, \code{suffix()} and \code{regex()} for \code{pipeline\_printout(..., verbose \textgreater{}= 3, ...)}}] \leavevmode\begin{itemize}
-\item {} 
-Error messages for showing mismatching regular expression and offending file name
-
-\item {} 
-Wrong capture group names or out of range indices will raise informative Exception
-
-\end{itemize}
-
-\end{description}
-\end{quote}
-
-
-\subsection{version 2.3}
-\label{history:version-2-3}\begin{quote}
-
-1st September, 2013
-\begin{itemize}
-\item {} \begin{description}
-\item[{\code{@active\_if} turns off tasks at runtime}] \leavevmode
-The Design and initial implementation were contributed by Jacob Biesinger
-
-Takes one or more parameters which can be either booleans or functions or callable objects which return True / False:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}1} \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2} \PYG{o}{=} \PYG{n+nb+bp}{False}
-
-\PYG{n+nd}{@active\PYGZus{}if}\PYG{p}{(}\PYG{n}{run\PYGZus{}if\PYGZus{}true}\PYG{p}{,} \PYG{k}{lambda}\PYG{p}{:} \PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-The expressions inside @active\_if are evaluated each time
-\code{pipeline\_run}, \code{pipeline\_printout} or \code{pipeline\_printout\_graph} is called.
-
-Dormant tasks behave as if they are up to date and have no output.
-
-\end{description}
-
-\item {} \begin{description}
-\item[{Command line parsing}] \leavevmode\begin{itemize}
-\item {} 
-Supports both argparse (python 2.7) and optparse (python 2.6):
-
-\item {} 
-\code{Ruffus.cmdline} module is optional.
-
-\item {} 
-See {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline]{\emph{manual}}}
-
-\end{itemize}
-
-\end{description}
-
-\item {} \begin{description}
-\item[{Optionally terminate pipeline after first exception}] \leavevmode
-To have all exceptions interrupt immediately:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{o}{.}\PYG{o}{.}\PYG{o}{.}\PYG{p}{,} \PYG{n}{exceptions\PYGZus{}terminate\PYGZus{}immediately} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-
-By default ruffus accumulates \code{NN} errors before interrupting the pipeline prematurely. \code{NN} is the specified parallelism for \code{pipeline\_run(..., multiprocess = NN)}.
-
-Otherwise, a pipeline will only be interrupted immediately if exceptions of type \code{ruffus.JobSignalledBreak} are thrown.
-
-\end{description}
-
-\item {} 
-Display exceptions without delay
-\begin{quote}
-
-By default, Ruffus re-throws exceptions in ensemble after pipeline termination.
-
-To see exceptions as they occur:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{o}{.}\PYG{o}{.}\PYG{o}{.}\PYG{p}{,} \PYG{n}{log\PYGZus{}exceptions} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-
-\code{logger.error(...)} will be invoked with the string representation of the each exception, and associated stack trace.
-
-The default logger prints to sys.stderr, but this can be changed to any class from the logging module or compatible object via \code{pipeline\_run(..., logger = ???)}
-\end{quote}
-
-\item {} 
-Improved \code{pipeline\_printout()}
-\begin{itemize}
-\item {} 
-\emph{@split} operations now show the 1-\textgreater{}many output in pipeline\_printout
-\begin{quote}
-
-This make it clearer that \code{@split} is creating multiple output parameters (rather than a single output parameter consisting of a list):
-
-\begin{Verbatim}[commandchars=\\\{\}]
-Task = split\_animals
-     Job = [None
-           -\textgreater{} cows
-           -\textgreater{} horses
-           -\textgreater{} pigs
-            , any\_extra\_parameters]
-\end{Verbatim}
-\end{quote}
-
-\item {} 
-File date and time are displayed in human readable form and out of date files are flagged with asterisks.
-
-\end{itemize}
-
-\end{itemize}
-\end{quote}
-
-
-\subsection{version 2.2}
-\label{history:version-2-2}\begin{quote}
-
-22nd July, 2010
-\begin{itemize}
-\item {} 
-Simplifying \textbf{@transform} syntax with \textbf{suffix(...)}
-\begin{quote}
-
-Regular expressions within ruffus are very powerful, and can allow files to be moved
-from one directory to another and renamed at will.
-
-However, using consistent file extensions and
-\code{@transform(..., suffix(...))} makes the code much simpler and easier to read.
-
-Previously, \code{suffix(...)} did not cooperate well with \code{inputs(...)}.
-For example, finding the corresponding header file (''.h'') for the matching input
-required a complicated \code{regex(...)} regular expression and \code{input(...)}. This simple case,
-e.g. matching ``something.c'' with ``something.h'', is now much easier in Ruffus.
-\begin{description}
-\item[{For example:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{source\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{something.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{more\PYGZus{}code.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{source\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{common.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{p}{(} \PYG{n}{source\PYGZus{}file}\PYG{p}{,}
-      \PYG{n}{header\PYGZus{}file}\PYG{p}{,}
-      \PYG{n}{common\PYGZus{}header}\PYG{p}{)} \PYG{o}{=} \PYG{n}{input\PYGZus{}files}
-    \PYG{c}{\PYGZsh{} call compiler to make object file}
-\end{Verbatim}
-
-This is equivalent to calling:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{something.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{something.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{common.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{something.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{more\PYGZus{}code.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{more\PYGZus{}code.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{common.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{more\PYGZus{}code.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\end{description}
-
-The \code{\textbackslash{}1} matches everything \emph{but} the suffix and will be applied to both \code{glob}s and file names.
-\end{quote}
-
-\end{itemize}
-
-For simplicity and compatibility with previous versions, there is always an implied r''1'' before
-the output parameters. I.e. output parameters strings are \emph{always} substituted.
-\begin{itemize}
-\item {} 
-Tasks and glob in \textbf{inputs(...)} and \textbf{add\_inputs(...)}
-\begin{quote}
-
-\code{glob}s and tasks can be added as the prerequisites / input files using
-\code{inputs(...)} and \code{add\_inputs(...)}. \code{glob} expansions will take place when the task
-is run.
-\end{quote}
-
-\item {} 
-Advanced form of \textbf{@split} with \textbf{regex}:
-\begin{quote}
-
-The standard \code{@split} divided one set of inputs into multiple outputs (the number of which
-can be determined at runtime).
-
-This is a \code{one-\textgreater{}many} operation.
-
-An advanced form of \code{@split} has been added which can split each of several files further.
-
-In other words, this is a \code{many-\textgreater{}"many more"} operation.
-\begin{description}
-\item[{For example, given three starting files:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{original\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{original\PYGZus{}0.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{original\PYGZus{}1.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{original\PYGZus{}2.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\end{Verbatim}
-
-\item[{We can split each into its own set of sub-sections:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n}{original\PYGZus{}files}\PYG{p}{,}
-   \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{starting\PYGZus{}(}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+).fa}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                         \PYG{c}{\PYGZsh{} match starting files}
-         \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{files.split.}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.*.fa}\PYG{l+s}{\PYGZdq{}}                         \PYG{c}{\PYGZsh{} glob pattern}
-         \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}                                         \PYG{c}{\PYGZsh{} index of original file}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{,} \PYG{n}{original\PYGZus{}index}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{        Code to split each input\PYGZus{}file}
-\PYG{l+s+sd}{            \PYGZdq{}original\PYGZus{}0.file\PYGZdq{} \PYGZhy{}\PYGZgt{} \PYGZdq{}files.split.0.*.fa\PYGZdq{}}
-\PYG{l+s+sd}{            \PYGZdq{}original\PYGZus{}1.file\PYGZdq{} \PYGZhy{}\PYGZgt{} \PYGZdq{}files.split.1.*.fa\PYGZdq{}}
-\PYG{l+s+sd}{            \PYGZdq{}original\PYGZus{}2.file\PYGZdq{} \PYGZhy{}\PYGZgt{} \PYGZdq{}files.split.2.*.fa\PYGZdq{}}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\end{Verbatim}
-
-\end{description}
-
-This is, conceptually, the reverse of the @collate(...) decorator
-\end{quote}
-
-\item {} 
-Ruffus will complain about unescaped regular expression special characters:
-\begin{quote}
-
-Ruffus uses ``\textbackslash{}1'' and ``\textbackslash{}2'' in regular expression substitutions. Even seasoned python
-users may not remember that these have to be `escaped' in strings. The best option is
-to use `raw' python strings e.g.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1\PYGZus{}substitutes}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2correctly}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{3four}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{4times}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-Ruffus will throw an exception if it sees an unescaped ``\textbackslash{}1'' or ``\textbackslash{}2'' in a file name,
-which should catch most of these bugs.
-\end{quote}
-
-\item {} 
-Prettier output from \emph{pipeline\_printout\_graph}
-\begin{quote}
-
-Changed to nicer colours, symbols etc. for a more professional look.
- at split and @merge tasks now look different from @transform.
-Colours, size and resolution are now fully customisable:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-pipeline\_printout\_graph( \#...
-                         user\_colour\_scheme = \PYGZob{}
-                                                "colour\_scheme\_index":1,
-                                                "Task to run"  : \PYGZob{}"fillcolor":"blue"\PYGZcb{},
-                                                 pipeline\_name : "My flowchart",
-                                                 size          : (11,8),
-                                                 dpi           : 120)\PYGZcb{})
-\end{Verbatim}
-
-An SVG bug in firefox has been worked around so that font size are displayed correctly.
-\end{quote}
-
-\end{itemize}
-\end{quote}
-
-
-\subsection{version 2.1.1}
-\label{history:version-2-1-1}\begin{itemize}
-\item {} \begin{description}
-\item[{\textbf{@transform(.., add\_inputs(...))}}] \leavevmode
-\code{add\_inputs(...)} allows the addition of extra input dependencies / parameters for each job.
-\begin{description}
-\item[{Unlike \code{inputs(...)}, the original input parameter is retained:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-from ruffus import *
- at transform(["a.input", "b.input"], suffix(".input"), add\_inputs("just.1.more","just.2.more"), ".output")
-def task(i, o):
-""
-\end{Verbatim}
-
-\item[{Produces:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-Job = [[a.input, just.1.more, just.2.more] -\textgreater{}a.output]
-Job = [[b.input, just.1.more, just.2.more] -\textgreater{}b.output]
-\end{Verbatim}
-
-\end{description}
-
-Like \code{inputs}, \code{add\_inputs} accepts strings, tasks and \code{glob} s
-This minor syntactic change promises add much clarity to Ruffus code.
-\code{add\_inputs()} is available for \code{@transform}, \code{@collate} and \code{@split}
-
-\end{description}
-
-\end{itemize}
-
-
-\subsection{version 2.1.0}
-\label{history:version-2-1-0}\begin{itemize}
-\item {} 
-\textbf{@jobs\_limit}
-Some tasks are resource intensive and too many jobs should not be run at the
-same time. Examples include disk intensive operations such as unzipping, or
-downloading from FTP sites.
-
-Adding:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@jobs\PYGZus{}limit}\PYG{p}{(}\PYG{l+m+mi}{4}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{new\PYGZus{}data\PYGZus{}list}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.big\PYGZus{}data.gz}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.big\PYGZus{}data}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{unzip}\PYG{p}{(}\PYG{n}{i}\PYG{p}{,} \PYG{n}{o}\PYG{p}{)}\PYG{p}{:}
-  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{unzip code goes here}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-would limit the unzip operation to 4 jobs at a time, even if the rest of the
-pipeline runs highly in parallel.
-
-(Thanks to Rob Young for suggesting this.)
-
-\end{itemize}
-
-
-\subsection{version 2.0.10}
-\label{history:version-2-0-10}\begin{itemize}
-\item {} 
-\textbf{touch\_files\_only} option for \textbf{pipeline\_run}
-
-When the pipeline runs, task functions will not be run. Instead, the output files for
-each job (in each task) will be \code{touch}-ed if necessary.
-This can be useful for simulating a pipeline run so that all files look as
-if they are up-to-date.
-
-Caveats:
-\begin{itemize}
-\item {} 
-This may not work correctly where output files are only determined at runtime, e.g. with \textbf{@split}
-
-\item {} 
-Only the output from pipelined jobs which are currently out-of-date will be \code{touch}-ed.
-In other words, the pipeline runs \emph{as normal}, the only difference is that the
-output files are \code{touch}-ed instead of being created by the python task functions
-which would otherwise have been called.
-
-\end{itemize}
-
-\item {} 
-Parameter substitution for \textbf{inputs(...)}
-
-The \textbf{inputs(...)} parameter in \textbf{@transform}, \textbf{@collate} can now take tasks and \code{glob} s,
-and these will be expanded appropriately (after regular expression replacement).
-
-For example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dir/a.input}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*)}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{/(.+).input}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-              \PYG{n}{inputs}\PYG{p}{(}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2.other}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/*.more}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{elsewhere/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2.output}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task1}\PYG{p}{(}\PYG{n}{i}\PYG{p}{,} \PYG{n}{o}\PYG{p}{)}\PYG{p}{:}
-  \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{  Some pipeline task}
-\PYG{l+s+sd}{  \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\end{Verbatim}
-
-Is equivalent to calling:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{task1}\PYG{p}{(}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dir/a.other}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dir/1.more}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dir/2.more}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{elsewhere/a.output}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-
-\begin{quote}
-
-Here:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/*.more}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-is first converted to:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{dir/*.more}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-which matches:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dir/1.more}\PYG{l+s}{\PYGZdq{}}
-\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dir/2.more}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-\end{itemize}
-
-
-\subsection{version 2.0.9}
-\label{history:version-2-0-9}\begin{itemize}
-\item {} 
-Better display of logging output
-
-\item {} 
-Advanced form of \textbf{@split}
-This is an experimental feature.
-
-Hitherto, \textbf{@split} only takes 1 set of input (tasks/files/\code{glob} s) and split these
-into an indeterminate number of output.
-\begin{quote}
-
-This is a one-\textgreater{}many operation.
-\end{quote}
-
-Sometimes it is desirable to take multiple input files, and split each of them further.
-\begin{quote}
-
-This is a many-\textgreater{}many (more) operation.
-\end{quote}
-
-It is possible to hack something together using \textbf{@transform} but downstream tasks would not
-aware that each job in \textbf{@transform} produces multiple outputs (rather than one input,
-one output per job).
-
-The syntax looks like:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n}{get\PYGZus{}files}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.+).original}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.*.split}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}files}\PYG{p}{(}\PYG{n}{i}\PYG{p}{,} \PYG{n}{o}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{pass}
-\end{Verbatim}
-
-If \code{get\_files()} returned \code{A.original}, \code{B.original} and \code{C.original},
-\code{split\_files()} might lead to the following operations:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-A.original
-        -\textgreater{} A.1.original
-        -\textgreater{} A.2.original
-        -\textgreater{} A.3.original
-B.original
-        -\textgreater{} B.1.original
-        -\textgreater{} B.2.original
-C.original
-        -\textgreater{} C.1.original
-        -\textgreater{} C.2.original
-        -\textgreater{} C.3.original
-        -\textgreater{} C.4.original
-        -\textgreater{} C.5.original
-\end{Verbatim}
-
-Note that each input (\code{A/B/C.original}) can produce a number of output, the exact
-number of which does not have to be pre-determined.
-This is similar to \textbf{@split}
-
-Tasks following \code{split\_files} will have ten inputs corresponding to each of the
-output from \code{split\_files}.
-
-If \textbf{@transform} was used instead of \textbf{@split}, then tasks following \code{split\_files}
-would only have 3 inputs.
-
-\end{itemize}
-
-
-\subsection{version 2.0.8}
-\label{history:version-2-0-8}\begin{itemize}
-\item {} 
-File names can be in unicode
-
-\item {} 
-File systems with 1 second timestamp granularity no longer cause problems.
-
-\end{itemize}
-
-
-\subsection{version 2.0.2}
-\label{history:version-2-0-2}\begin{itemize}
-\item {} 
-Much prettier /useful output from {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout}}}
-
-\item {} 
-New tutorial / manual
-
-\end{itemize}
-
-
-\subsection{version 2.0}
-\label{history:version-2-0}\begin{itemize}
-\item {} 
-Revamped documentation:
-\begin{itemize}
-\item {} 
-Rewritten tutorial
-
-\item {} 
-Comprehensive manual
-
-\item {} 
-New syntax help
-
-\end{itemize}
-
-\item {} 
-Major redesign. New decorators include
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{@split}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{@transform}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/merge:new-manual-merge]{\emph{@merge}}}
-
-\item {} 
-{\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-collate]{\emph{@collate}}}
-
-\end{itemize}
-
-\item {} 
-Major redesign. Decorator \emph{inputs} can mix
-\begin{itemize}
-\item {} 
-Output from previous tasks
-
-\item {} 
-\href{http://docs.python.org/library/glob.html}{\emph{glob}} patterns e.g. \code{*.txt}
-
-\item {} 
-Files names
-
-\item {} 
-Any other data type
-
-\end{itemize}
-
-\end{itemize}
-
-
-\subsection{version 1.1.4}
-\label{history:version-1-1-4}\begin{quote}
-
-Tasks can get their input by automatically chaining to the output from one or more parent tasks using {\hyperref[decorators/files_re:decorators-files-re]{\emph{@files\_re}}}
-\end{quote}
-
-
-\subsection{version 1.0.7}
-\label{history:version-1-0-7}\begin{quote}
-
-Added \emph{proxy\_logger} module for accessing a shared log across multiple jobs in different processes.
-\end{quote}
-
-
-\subsection{version 1.0}
-\label{history:version-1-0}\begin{quote}
-
-Initial Release in Oxford
-\end{quote}
-
-
-\section{Fixed Bugs}
-\label{history:fixed-bugs}\begin{quote}
-
-Full list at \href{http://code.google.com/p/ruffus/wiki/LatestChanges}{``Latest Changes wiki entry''}
-\end{quote}
-
-
-\section{Future Changes to Ruffus}
-\label{todo:todo}\label{todo::doc}\label{todo:future-changes-to-ruffus}\begin{quote}
-
-I would appreciated feedback and help on all these issues and where next to take \emph{ruffus}.
-
-\textbf{Future Changes} are features where we more or less know where we are going and how to get there.
-
-\textbf{Planned Improvements} describes features we would like in Ruffus but where the implementation
-or syntax has not yet been (fully) worked out.
-
-If you have suggestions or contributions, please either write to me ( ruffus\_lib at llew.org.uk) or
-send a pull request via the \href{https://github.com/bunbun/ruffus}{git site}.
-\end{quote}
-
-
-\subsection{Todo: pipeline\_printout\_graph should print inactive tasks}
-\label{todo:todo-pipeline-printout-graph-should-print-inactive-tasks}\label{todo:todo-inactive-tasks-in-pipeline-printout-graph}
-
-\subsection{Todo: Mark input strings as non-file names, and add support for dynamically returned parameters}
-\label{todo:todo-dynamic-strings}\label{todo:todo-mark-input-strings-as-non-file-names-and-add-support-for-dynamically-returned-parameters}\begin{quote}
-\begin{enumerate}
-\item {} 
-Use indicator object.
-
-\item {} 
-What is a good name? \code{"output\_from()"}, \code{"NOT\_FILE\_NAME"} :-)
-
-\item {} 
-They will still participate in suffix, formatter and regex replacement
-
-\end{enumerate}
-
-Bernie Pope suggests that we should generalise this:
-
-If any object in the input parameters is a (non-list/tuple) class instance, check (getattr) whether it has a \code{ruffus\_params()} function.
-If it does, call it to obtain a list which is substituted in place.
-If there are string nested within, these will also take part in Ruffus string substitution.
-Objects with \code{ruffus\_params()} always ``decay'' to the results of the function call
-
-\code{output\_from} would be a simple wrapper which returns the internal string via \code{ruffus\_params()}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{class} \PYG{n+nc}{output\PYGZus{}from} \PYG{p}{(}\PYG{n+nb}{object}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{def} \PYG{n+nf}{\PYGZus{}\PYGZus{}init\PYGZus{}\PYGZus{}}\PYG{p}{(}\PYG{n+nb+bp}{self}\PYG{p}{,} \PYG{n+nb}{str}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{str} \PYG{o}{=} \PYG{n+nb}{str}
-    \PYG{k}{def} \PYG{n+nf}{ruffus\PYGZus{}params}\PYG{p}{(}\PYG{n+nb+bp}{self}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{return} \PYG{p}{[}\PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{str}\PYG{p}{]}
-\end{Verbatim}
-
-Returning a list should be like wildcards and should not introduce an unnecessary level of indirection for output parameters, i.e. suffix(''.txt'') or formatter() / ``\{basename{[}0{]}\}'' should work.
-
-Check!
-\end{quote}
-
-
-\subsection{Todo: Allow ``extra'' parameters to be used in output substitution}
-\label{todo:todo-allow-extra-parameters-to-be-used-in-output-substitution}\label{todo:todo-extra-parameters}\begin{quote}
-
-Formatter substitution can refer to the original elements in the input and extra parameters (without converting them to strings either). This refers to the original (nested) data structure.
-
-This will allow normal python datatypes to be handed down and slipstreamed into a pipeline more easily.
-
-The syntax would use Ruffus (\textgreater{} version 2.4) formatter:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{o}{.}\PYG{o}{.}\PYG{o}{.}\PYG{p}{,} \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,} \PYG{p}{[}
-                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}EXTRAS[0][1][3]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}    \PYG{c}{\PYGZsh{} EXTRAS}
-                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{[INPUTS[1][2]]}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}\PYG{o}{.}\PYG{o}{.}\PYG{o}{.}\PYG{p}{)}  \PYG{c}{\PYGZsh{} INPUTS}
-\PYG{k}{def} \PYG{n+nf}{taskfunc}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\code{EXTRA} and \code{INPUTS} indicate that we are referring to the input and extra parameters.
-
-These are the full (nested) parameters in all their original form. In the case of the input parameters, this obvious depends on the decorator, so
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.text}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.text}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{,} \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}INPUTS[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{taskfunc}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-would give
-
-\begin{Verbatim}[commandchars=\\\{\}]
-job \#1
-   input  == "a.text"
-   output == "a"
-
-job \#2
-   input  == [1, "b.text"]
-   output == 1
-\end{Verbatim}
-
-The entire string must consist of \code{INPUTS} or \code{EXTRAS} followed by optionally N levels of square brackets. i.e. They must match \code{"(INPUTS\textbar{}EXTRAS)(\textbackslash{}{[}\textbackslash{}d+\textbackslash{}{]})+"}
-
-No string conversion takes place.
-
-For \code{INPUTS} or \code{EXTRAS} which have objects with a \code{ruffus\_params()} function (see Todo item above),
-the original object rather than the result of \code{ruffus\_params()} is forwarded.
-\end{quote}
-
-
-\subsection{Todo: Extra signalling before and after each task and job}
-\label{todo:todo-extra-signalling-before-and-after-each-task-and-job}\label{todo:todo-pre-post-job}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@prejob}\PYG{p}{(}\PYG{n}{custom\PYGZus{}func}\PYG{p}{)}
-\PYG{n+nd}{@postjob}\PYG{p}{(}\PYG{n}{custom\PYGZus{}func}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\code{@prejob} / \code{@postjob} would be run in the child processes.
-\end{quote}
-
-
-\subsection{Todo: \texttt{@split} / \texttt{@subdivide} returns the actual output created}
-\label{todo:todo-new-decorators}\label{todo:todo-split-subdivide-returns-the-actual-output-created}\begin{itemize}
-\item {} 
-\textbf{overrides} (not replaces) wild cards.
-
-\item {} 
-Returns a list, each with output and extra paramters.
-
-\item {} 
-Won't include extraneous files which were not created in the pipeline but which just happened to match the wild card
-
-\item {} 
-We should have \code{ruffus\_output\_params}, \code{ruffus\_extra\_params} wrappers for clarity:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}into\PYGZus{}txt\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{output\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file\PYGZus{}name} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:}
-            \PYG{k}{pass}
-    \PYG{k}{return} \PYG{p}{[}
-            \PYG{n}{ruffus\PYGZus{}output}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{p}{[}\PYG{n}{ruffus\PYGZus{}output}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}\PYG{p}{,} \PYG{n}{ruffus\PYGZus{}extras}\PYG{p}{(}\PYG{l+m+mi}{13}\PYG{p}{,} \PYG{l+m+mi}{14}\PYG{p}{)}\PYG{p}{]}\PYG{p}{,}
-            \PYG{p}{]}
-\end{Verbatim}
-
-\item {} 
-Consider yielding?
-
-\end{itemize}
-
-
-\subsubsection{Checkpointing}
-\label{todo:checkpointing}\begin{itemize}
-\item {} 
-If checkpoint file is used, the actual files are saved and checked the next time
-
-\item {} 
-If no files are generated, no files are checked the next time...
-
-\item {} 
-The output files do not have to match the wildcard though we can output a warning message if that happens...
-This is obviously dangerous because the behavior will change if the pipeline is rerun without using the checkpoint file
-
-\item {} 
-What happens if the task function changes?
-
-\end{itemize}
-
-
-\subsection{Todo: New decorators}
-\label{todo:id1}
-
-\subsubsection{Todo: \texttt{@originate}}
-\label{todo:todo-originate}\begin{quote}
-
-Each (serial) invocation returns lists of output parameters until returns
-None. (Empty list = \code{continue}, None = \code{break}).
-\end{quote}
-
-
-\subsubsection{Todo: \texttt{@recombine}}
-\label{todo:todo-recombine}\begin{quote}
-
-Like \code{@collate} but automatically regroups jobs which were a result of a previous \code{@subdivide} / \code{@split} (even after intervening \code{@transform} )
-
-This is the only way job trickling can work without stalling the pipeline: We would know
-how many jobs were pending for each \code{@recombine} job and which jobs go together.
-\end{quote}
-
-
-\subsection{Todo: Named parameters in decorators for clarity}
-\label{todo:todo-named-parameters-in-decorators-for-clarity}
-
-\subsection{Todo: Bioinformatics example to end all examples}
-\label{todo:todo-bioinformatics-example-to-end-all-examples}\label{todo:todo-bioinformatics-example}\begin{quote}
-\begin{description}
-\item[{Uses}] \leavevmode\begin{itemize}
-\item {} 
-\code{@product}
-
-\item {} 
-\code{@subdivide}
-
-\item {} 
-\code{@transform}
-
-\item {} 
-\code{@collate}
-
-\item {} 
-\code{@merge}
-
-\end{itemize}
-
-\end{description}
-\end{quote}
-
-
-\subsection{Todo: Allow the next task to start before all jobs in the previous task have finished}
-\label{todo:todo-allow-the-next-task-to-start-before-all-jobs-in-the-previous-task-have-finished}\begin{quote}
-
-Jake (Biesinger) calls this \textbf{Job Trickling}!
-\begin{itemize}
-\item {} 
-A single long running job no longer will hold up the entire pipeline
-
-\item {} 
-Calculates dependencies dynamically at the job level.
-
-\item {} 
-Goal is to have a long running (months) pipeline to which we can keep adding input...
-
-\item {} 
-We can choose between prioritising completion of the entire pipeline for some jobs
-(depth first) or trying to complete as many tasks as possible (breadth first)
-
-\end{itemize}
-\end{quote}
-
-
-\subsubsection{Converting to per-job rather than per task dependencies}
-\label{todo:converting-to-per-job-rather-than-per-task-dependencies}\begin{quote}
-
-Some decorators prevent per job (rather than per task) dependency calculations, and
-will call a pipeline stall until the dependent tasks are completed (the current situation):
-\begin{itemize}
-\item {} \begin{description}
-\item[{Some types of jobs unavoidably depend on an entire previous task completing:}] \leavevmode\begin{itemize}
-\item {} 
-\code{add\_inputs()}, \code{inputs()}
-
-\item {} 
-\code{@merge}
-
-\item {} 
-\code{@split} (implicit \code{@merge})
-
-\end{itemize}
-
-\end{description}
-
-\item {} \begin{description}
-\item[{\code{@split}, \code{@originate} produce variable amount of output at runtime and must be completed before the next task can be run.}] \leavevmode\begin{itemize}
-\item {} 
-Should \code{yield} instead of return?
-
-\end{itemize}
-
-\end{description}
-
-\item {} \begin{description}
-\item[{\code{@collate} needs to pattern match all the inputs of a previous task}] \leavevmode\begin{itemize}
-\item {} 
-Replace \code{@collate} with \code{@recombine} which ``remembers'' and reverses the results of a previous
-\code{@subdivide} or \code{@split}
-
-\item {} 
-Jobs need unique job\_id tag
-
-\item {} 
-Jobs are assigned (nested) grouping id which accompany them down the
-pipeline after \code{@subdivide} / \code{@split} and are removed after \code{@recombine}
-
-\item {} 
-Should have a count of jobs so we always know \emph{when} an ``input slot'' is full
-
-\end{itemize}
-
-\end{description}
-
-\item {} 
-Funny ``single file'' mode for \code{@transform,} \code{@files} needs to be
-regularised so it is a syntactic (front end) convenience (oddity!)
-and not plague the inards of ruffus
-
-\end{itemize}
-
-Breaking change: to force the entirety of the previous task to complete before the next one, use \code{@follows}
-\end{quote}
-
-
-\subsubsection{Implementation}
-\label{todo:implementation}\begin{itemize}
-\item {} 
-``Push'' model. Completing jobs ``check in'' their outputs to ``input slots'' for all the sucessor jobs.
-
-\item {} 
-When ``input slots'' are full for any job, it is put on the dispatch queue to be run.
-
-\item {} 
-The priority (depth first or breadth first) can be set here.
-
-\item {} 
-\code{pipeline\_run} / \code{Pipeline\_printout} create a task dependency tree structure (from decorator dependencies) (a runtime pipeline object)
-
-\item {} 
-Each task in the pipeline object knows which other tasks wait on it.
-
-\item {} 
-When output is created by a job, it sends messages to (i.e. function calls) all dependent tasks in the pipeline object with the new output
-
-\item {} 
-Sets of output such as from \code{@split} and \code{@subdivide} and \code{@originate} have a
-terminating condition and/or a associated count (\# of output)
-
-\item {} 
-Tasks in the pipeline object forward incoming inputs to task input slots (for slots common to all jobs in a
-task: \code{@inputs}, \code{@add\_inputs}) or to slots in new jobs in the pipeline object
-
-\item {} 
-When all slots are full in each job, this triggers putting the job parameters onto the job submission queue
-
-\item {} 
-The pipeline object should allow Ruffus to be reentrant?
-
-\end{itemize}
-
-
-\section{Planned Improvements to Ruffus}
-\label{todo:planned-improvements-to-ruffus}\phantomsection\label{todo:todo-run-on-cluster}\begin{itemize}
-\item {} 
-\code{@split} needs to be able to specify at run time the number of
-resulting jobs without using wild cards
-
-\item {} 
-legacy support for wild cards and file names.
-
-\end{itemize}
-
-
-\subsection{Planned: Running python code (task functions) transparently on remote cluster nodes}
-\label{todo:planned-running-python-code-task-functions-transparently-on-remote-cluster-nodes}\begin{quote}
-
-Wait until next release.
-
-Will bump Ruffus to v.3.0 if can run python jobs transparently on a cluster!
-
-abstract out \code{task.run\_pooled\_job\_without\_exceptions()} as a function which can be supplied to \code{pipeline\_run}
-
-Common ``job'' interface:
-\begin{itemize}
-\item {} 
-marshalled arguments
-
-\item {} 
-marshalled function
-
-\item {} 
-submission timestamp
-
-\end{itemize}
-\begin{description}
-\item[{Returns}] \leavevmode\begin{itemize}
-\item {} 
-completion timestamp
-
-\item {} 
-returned values
-
-\item {} 
-exception
-
-\end{itemize}
-
-\end{description}
-\begin{enumerate}
-\item {} 
-Full version use libpythongrid?
-* Christian Widmer \textless{}\href{mailto:ckwidmer at gmail.com}{ckwidmer at gmail.com}\textgreater{}
-* Cheng Soon Ong \textless{}\href{mailto:chengsoon.ong at unimelb.edu.au}{chengsoon.ong at unimelb.edu.au}\textgreater{}
-* \href{https://code.google.com/p/pythongrid/source/browse/\#git\%2Fpythongrid}{https://code.google.com/p/pythongrid/source/browse/\#git\%2Fpythongrid}
-* Probably not good to base Ruffus entirely on libpythongrid to minimise dependencies, the use of sophisticated configuration policies etc.
-
-\item {} 
-Start with light-weight file-based protocol
-* specify where the scripts should live
-* use drmaa to start jobs
-* have executable ruffus module which knows how to load deserialise (unmarshall) function / parameters from disk. This would be what drmaa starts up, given the marshalled data as an argument
-* time stamp
-* ``heart beat'' to check that the job is still running
-
-\item {} 
-Next step: socket-based protocol
-* use specified master port in ruffus script
-* start remote processes using drmaa
-* child receives marshalled data and the address::port in the ruffus script (head node) to initiate hand shake or die
-* process recycling: run successive jobs on the same remote process for reduced overhead, until exceeds max number of jobs on the same process, min/max time on the same process
-* resubmit if die (Don't do sophisticated stuff like libpythongrid).
-
-\end{enumerate}
-\end{quote}
-\phantomsection\label{todo:todo-job-trickling}
-
-\subsection{Planned: Custom parameter generator}
-\label{todo:todo-job-trickling}\label{todo:planned-custom-parameter-generator}\label{todo:todo-custom-parameters}\begin{quote}
-
-Request on mailing list
-\begin{quote}
-\begin{quote}
-
-I've often wished that I could use an arbitrary function to process the input filepath instead of just a regex.
-\end{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{def} \PYG{n+nf}{f}\PYG{p}{(}\PYG{n}{inputs}\PYG{p}{,} \PYG{n}{outputs}\PYG{p}{,} \PYG{n}{extra\PYGZus{}param1}\PYG{p}{,} \PYG{n}{extra\PYGZus{}param2}\PYG{p}{)}\PYG{p}{:}
-     \PYG{c}{\PYGZsh{} do something to generate parameters}
-     \PYG{k}{return} \PYG{n}{new\PYGZus{}output\PYGZus{}param}\PYG{p}{,} \PYG{n}{new\PYGZus{}extra\PYGZus{}param1}\PYG{p}{,} \PYG{n}{new\PYGZus{}extra\PYGZus{}param2}
-\end{Verbatim}
-
-now f() can be used inside a Ruffus decorator to generate the outputs from inputs, instead of being forced to use a regex for the job.
-
-Cheers,
-Bernie.
-\end{quote}
-
-Leverages built-in Ruffus functionality.
-Don't have to write entire parameter generation from scratch.
-\begin{itemize}
-\item {} 
-Gets passed an iterator where you can do a for loop to get input parameters / a flattened list of files
-
-\item {} 
-Other parameters are forwarded as is
-
-\item {} 
-The duty of the function is to \code{yield} input, output, extra parameters
-
-\end{itemize}
-
-Simple to do but how do we prevent this from being a job-trickling barrier?
-
-Postpone until we have an initial design for job-trickling: Ruffus v.4 ;-(
-\end{quote}
-
-
-\subsection{Planned: Ruffus GUI interface.}
-\label{todo:planned-ruffus-gui-interface}\label{todo:todo-gui}\begin{quote}
-
-Desktop (PyQT or web-based solution?)  I'd love to see an svg pipeline picture that I could actually interact with
-\end{quote}
-
-
-\subsection{Planned: Non-decorator / Function interface to Ruffus}
-\label{todo:planned-non-decorator-function-interface-to-ruffus}
-
-\subsection{Planned: Remove intermediate files}
-\label{todo:planned-remove-intermediate-files}\label{todo:todo-intermediate-files}\begin{quote}
-
-Often large intermediate files are produced in the middle of a pipeline which could be
-removed. However, their absence would cause the pipeline to appear out of date. What is
-the best way to solve this?
-
-In gmake, all intermediate files which are not marked \code{.PRECIOUS} are deleted.
-\begin{description}
-\item[{We do not want to manually mark intermediate files for several reasons:}] \leavevmode\begin{itemize}
-\item {} 
-The syntax would be horrible and clunky
-
-\item {} 
-The gmake distinction between \code{implicit} and \code{explicit} rules is not one we
-would like to impose on Ruffus
-
-\item {} 
-Gmake uses statically determined (DAG) dependency trees so it is quite natural and
-easy to prune intermediate paths
-
-\end{itemize}
-
-\end{description}
-
-Our preferred solution should impose little to no semantic load on Ruffus, i.e. it should
-not make it more complex / difficult to use. There are several alternatives we are
-considering:
-\begin{enumerate}
-\item {} 
-Have an \textbf{update} mode in which pipeline\_run would ignore missing files and only run tasks with existing, out-of-date files.
-
-\item {} 
-Optionally ignore all out-of-date dependencies beyond a specified point in the pipeline
-
-\item {} 
-Add a decorator to flag sections of the pipeline where intermediate files can be removed
-
-\end{enumerate}
-
-Option (1) is rather unnerving because it makes inadvertent errors difficult to detect.
-
-Option (2) involves relying on the user of a script to remember the corect chain of dependencies in
-often complicated pipelines. It would be advised to keep a flowchart to hand. Again,
-the chances of error are much greater.
-
-Option (3) springs from the observation by Andreas Heger that parts of a pipeline with
-disposable intermediate files can usually be encapsulated as an autonomous section.
-Within this subpipeline, all is well provided that the outputs of the last task are complete
-and up-to-date with reference to the inputs of the first task. Intermediate files
-could be removed with impunity.
-
-The suggestion is that these autonomous subpipelines could be marked out using the Ruffus
-decorator syntax:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   First task in autonomous subpipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{who.isit}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{its.me}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Several intermediate tasks}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{subpipeline\PYGZus{}task1}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.me}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.her}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task2\PYGZus{}etc}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{)}\PYG{p}{:}
-   \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Final task}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@sub\PYGZus{}pipeline}\PYG{p}{(}\PYG{n}{subpipeline\PYGZus{}task1}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{subpipeline\PYGZus{}task1}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.her}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.you}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{final\PYGZus{}task}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{)}\PYG{p}{:}
-   \PYG{k}{pass}
-\end{Verbatim}
-
-\textbf{@sub\_pipeline} marks out all tasks between \code{first\_task} and \code{final\_task} and
-intermediate files such as \code{"its.me"}, \code{"its.her} can be deleted. The pipeline will
-only run if \code{"its.you"} is missing or out-of-date compared with \code{"who.isit"}.
-
-Over the next few Ruffus releases we will see if this is a good design, and whether
-better keyword can be found than \textbf{@sub\_pipeline} (candidates include \textbf{@shortcut}
-and \textbf{@intermediate})
-\end{quote}
-
-
-\subsection{Planned: @retry\_on\_error(NUM\_OF\_RETRIES)}
-\label{todo:planned-retry-on-error-num-of-retries}\label{todo:todo-retry}
-
-\subsection{Planned: Clean up}
-\label{todo:planned-clean-up}\label{todo:todo-cleanup}\begin{quote}
-
-The plan is to store the files and directories created via
-a standard interface.
-
-The placeholders for this are a function call \code{register\_cleanup}.
-
-Jobs can specify the files they created and which need to be
-deleted by returning a list of file names from the job function.
-
-So:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-raise Exception = Error
-
-return False = halt pipeline now
-
-return string / list of strings = cleanup files/directories later
-
-return anything else = ignored
-\end{Verbatim}
-
-The cleanup file/directory store interface can be connected to
-a text file or a database.
-
-The cleanup function would look like this:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-pipeline\_cleanup(cleanup\_log("../cleanup.log"), [instance ="october19th" ])
-pipeline\_cleanup(cleanup\_msql\_db("user", "password", "hash\_record\_table"))
-\end{Verbatim}
-
-The parameters for where and how to store the list of created files could be
-similarly passed to pipeline\_run as an extra parameter:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-pipeline\_run(cleanup\_log("../cleanup.log"), [instance ="october19th" ])
-pipeline\_run(cleanup\_msql\_db("user", "password", "hash\_record\_table"))
-\end{Verbatim}
-
-where \emph{cleanup\_log} and \emph{cleanup\_msql\_db} are classes which have functions for
-\begin{enumerate}
-\item {} 
-storing file
-
-\item {} 
-retrieving file
-
-\item {} 
-clearing entries
-
-\end{enumerate}
-\begin{itemize}
-\item {} 
-Files would be deleted in reverse order, and directories after files.
-
-\item {} 
-By default, only empty directories would be removed.
-
-But this could be changed with a \code{-{-}forced\_remove\_dir} option
-
-\item {} 
-An \code{-{-}remove\_empty\_parent\_directories} option would be
-supported by \href{http://docs.python.org/library/os.html\#os.removedirs}{os.removedirs(path)}.
-
-\end{itemize}
-\end{quote}
-
-
-\section{Implementation Tips}
-\label{implementation_notes:implementation-tips}\label{implementation_notes::doc}
-
-\subsection{Release}
-\label{implementation_notes:release}\begin{itemize}
-\item {} 
-Change \code{ruffus\_version.py}
-
-\item {} 
-Rebuild pdf and copy it to \code{doc/static\_data}
-\begin{quote}
-
-cd doc
-make latexpdf
-cp \_build/latex/ruffus.pdf static\_data
-\end{quote}
-
-\item {} 
-Rebuild documentation:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-make htmlsync
-\end{Verbatim}
-
-\item {} 
-tag git with, for example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-git tag -a v2.5RC -m "Version 2.5 Release Candidate"
-\end{Verbatim}
-
-\item {} 
-Upload to pypi:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-python setup.py sdist --format=gztar upload
-\end{Verbatim}
-
-\end{itemize}
-
-
-\subsection{dbdict.py}
-\label{implementation_notes:dbdict-py}\begin{quote}
-
-This is an sqlite backed dictionary originally written by Jacob Sondergaard and
-contributed by Jake Biesinger who added automatic pickling of python objects.
-
-The pickling code was refactored out by Leo Goodstadt into separate functions as
-part of the preparation to make Ruffus python3 ready.
-
-Python original saved (pickled) objects as 7 bit ASCII strings. Later formats
-(protocol = -1 is the latest format) uses 8 bit strings and are rather more efficient.
-
-These then need to be saved as BLOBs to sqlite3 rather than normal strings. We
-can signal this by wrapping the pickled string in a object providing a ``buffer interface''.
-This is \code{buffer} in python2.6/2.7 and \code{memoryview} in python3.
-
-\href{http://bugs.python.org/issue7723}{http://bugs.python.org/issue7723} suggests there is no portable python2/3 way to write
-blobs to Sqlite without these two incompatible wrappers.
-This would require conditional compilation:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{if} \PYG{n}{sys}\PYG{o}{.}\PYG{n}{hexversion} \PYG{o}{\PYGZgt{}}\PYG{o}{=} \PYG{l+m+mh}{0x03000000}\PYG{p}{:}
-    \PYG{n}{value} \PYG{o}{=} \PYG{n}{memoryview}\PYG{p}{(}\PYG{n}{pickle}\PYG{o}{.}\PYG{n}{dumps}\PYG{p}{(}\PYG{n}{value}\PYG{p}{,} \PYG{n}{protocol} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{1}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{else}\PYG{p}{:}
-    \PYG{n}{value} \PYG{o}{=} \PYG{n+nb}{buffer}\PYG{p}{(}\PYG{n}{pickle}\PYG{o}{.}\PYG{n}{dumps}\PYG{p}{(}\PYG{n}{value}\PYG{p}{,} \PYG{n}{protocol} \PYG{o}{=} \PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{1}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-
-Despite the discussion on the bug report, sqlite3.Binary seems to work.
-We shall see if this is portable to python3.
-\end{quote}
-
-
-\subsection{how to write new decorators}
-\label{implementation_notes:how-to-write-new-decorators}\begin{quote}
-
-New placeholder class. E.g. for \code{@new\_deco}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{class} \PYG{n+nc}{new\PYGZus{}deco}\PYG{p}{(}\PYG{n}{task\PYGZus{}decorator}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-Add to list of action names and ids:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{action\PYGZus{}names} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{unspecified}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{o}{.}\PYG{o}{.}\PYG{o}{.}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{task\PYGZus{}new\PYGZus{}deco}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-\PYG{n}{action\PYGZus{}task\PYGZus{}new\PYGZus{}deco}     \PYG{o}{=}  \PYG{l+m+mi}{15}
-\end{Verbatim}
-
-Add function:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{def} \PYG{n+nf}{task\PYGZus{}transform} \PYG{p}{(}\PYG{n+nb+bp}{self}\PYG{p}{,} \PYG{n}{orig\PYGZus{}args}\PYG{p}{)}\PYG{p}{:}
-\end{Verbatim}
-
-Add documentation to:
-\begin{itemize}
-\item {} 
-decorators/NEW\_DECORATOR.rst
-
-\item {} 
-decorators/decorators.rst
-
-\item {} 
-\_templates/layout.html
-
-\item {} 
-manual
-
-\end{itemize}
-\end{quote}
-
-
-\section{Implementation notes}
-\label{implementation_notes:implementation-notes}
-N.B. Remember to cite Jake Biesinger and see if he is interested to be a co-author if we ever resubmit the drastically changed version...
-He contributed checkpointing, travis and tox etc.
-
-
-\subsection{\texttt{Ctrl-C} handling}
-\label{implementation_notes:ctrl-c-handling}\label{implementation_notes:todo-misfeatures}\begin{quote}
-
-Pressing \code{Ctrl-C} left dangling process in Ruffus 2.4 because \code{KeyboardInterrupt} does not play nice with python \code{multiprocessing.Pool}
-See \href{http://stackoverflow.com/questions/1408356/keyboard-interrupts-with-pythons-multiprocessing-pool/1408476\#1408476}{http://stackoverflow.com/questions/1408356/keyboard-interrupts-with-pythons-multiprocessing-pool/1408476\#1408476}
-
-\href{http://bryceboe.com/2012/02/14/python-multiprocessing-pool-and-keyboardinterrupt-revisited/}{http://bryceboe.com/2012/02/14/python-multiprocessing-pool-and-keyboardinterrupt-revisited/} provides a reimplementation of Pool which
-however only works when you have a fixed number of jobs which should then run in parallel to completion. Ruffus is considerably more
-complicated because we have a variable number of jobs completing and being submitted into the job queue at any one time. Think
-of tasks stalling waiting for the dependent tasks to complete and then all the jobs of the task being released onto the queue
-
-The solution is
-\begin{enumerate}
-\item {} 
-Use a \code{timeout} parameter when using \code{IMapIterator.next(timeout=None)} to iterate through \code{pool.imap\_unordered} because only timed \code{condition} s can be interruptible by signals...!!
-
-\item {} 
-This involves rewriting the \code{for} loop manually as a \code{while} loop
-
-\item {} 
-We use a timeout of \code{99999999}, i.e. 3 years, which should be enough for any job to complete...
-
-\item {} 
-Googling after the fact, it looks like the galaxy guys (cool dudes or what) have written similar \href{https://galaxy-dist.readthedocs.org/en/latest/\_modules/galaxy/objectstore/s3\_multipart\_upload.html}{code}
-
-\item {} 
-\code{next()} for normal iterators do not take \code{timeout} as an extra parameter so we have to wrap next in a conditional :-(. The galaxy guys do a \href{http://en.wikipedia.org/wiki/Shim\_(computing)}{shim} around \code{next()} but that is as much obsfucation as a simple if...
-
-\item {} 
-After jobs are interrupted by a signal, we rethrow with our own exception because we want something that inherits from \code{Exception} unlike \code{KeyboardInterrupt}
-
-\item {} 
-When a signal happens, we need to immediately stop \code{feed\_job\_params\_to\_process\_pool()} from sending more parameters into the job queue (\code{parameter\_q})
-We use a proxy to a \code{multiprocessing.Event} (via \code{syncmanager.Event()}). When \code{death\_event} is set, all further processing stops...
-
-\item {} 
-We also signal that all jobs should finish by putting \code{all\_tasks\_complete()} into \code{parameter\_q} but only \code{death\_event} prevents jobs already in the queue from going through
-
-\item {} 
-Ater signalling, some of the child processes appear to be dead by the time we start cleaning up. \code{pool.terminate()} sometimes tries and fails to
-re-connect to the the \code{death\_event} proxy via sockets and throws an exception. We should really figure out a better solution but in the meantime
-wrapping it in a \code{try / except} allows a clean exit.
-
-\item {} 
-If a vanilla exception is raised without multiprocessing running, we still need to first save the exception in \code{job\_errors} (even if it is just one) before
-cleaning up, because the cleaning up process may lead to further (ignored) exceptions which would overwrite the current exception when we need to rethrow it
-
-\end{enumerate}
-
-Exceptions thrown in the middle of a multiprocessing / multithreading job appear to be handled gracefully.
-
-For drmaa jobs, \code{qdel} may still be necessary.
-\end{quote}
-
-
-\subsection{Python3 compatability}
-\label{implementation_notes:python3-compatability}\begin{quote}
-
-Required extensive changes especially in unit test code.
-
-Changes:
-\begin{enumerate}
-\item {} 
-\code{sort} in python3 does not order mixed types, i.e. \code{int()}, \code{list()} and \code{str()} are incommensurate
-\begin{itemize}
-\item {} 
-In \code{task.get\_output\_files (...)}, sort after conversion to string
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{sorted}\PYG{p}{(}\PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{output\PYGZus{}filenames}\PYG{p}{,} \PYG{n}{key} \PYG{o}{=} \PYG{k}{lambda} \PYG{n}{x}\PYG{p}{:} \PYG{n+nb}{str}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-
-\item {} 
-In \code{file\_name\_parameters.py}: \code{collate\_param\_factory (...)}, \code{sort} after conversion to string, then \code{groupby} without string conversion. This is
-because we can't guarantee that two different objects do not have the same string representation. But \code{groupby} requires that similar things are adjacent...
-
-In other words, \code{groupby} is a refinement of \code{sorted}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{for} \PYG{n}{output\PYGZus{}extra\PYGZus{}params}\PYG{p}{,} \PYG{n}{grouped\PYGZus{}params} \PYG{o+ow}{in} \PYG{n}{groupby}\PYG{p}{(}\PYG{n+nb}{sorted}\PYG{p}{(}\PYG{n}{io\PYGZus{}params\PYGZus{}iter}\PYG{p}{,} \PYG{n}{key} \PYG{o}{=} \PYG{n}{get\PYGZus{}output\PYGZus{}extras\PYGZus{}str}\PYG{p}{)}\PYG{p}{,} \PYG{n}{key} \PYG{o}{=} \PYG{n}{get\PYGZus{}output\PYGZus{}extras}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{itemize}
-
-\item {} 
-\code{print()} is a function
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{\PYGZus{}\PYGZus{}future\PYGZus{}\PYGZus{}} \PYG{k+kn}{import} \PYG{n}{print\PYGZus{}function}
-\end{Verbatim}
-
-\item {} 
-\code{items()} only returns a list in python2. Rewrite \code{dict.iteritems()} whenever this might cause a performance bottleneck
-
-\item {} 
-\code{zip} and \code{map} return iterators. Conditionally import in python2
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-\PYG{k}{if} \PYG{n}{sys}\PYG{o}{.}\PYG{n}{hexversion} \PYG{o}{\PYGZlt{}} \PYG{l+m+mh}{0x03000000}\PYG{p}{:}
-    \PYG{k+kn}{from} \PYG{n+nn}{future\PYGZus{}builtins} \PYG{k+kn}{import} \PYG{n+nb}{zip}\PYG{p}{,} \PYG{n+nb}{map}
-\end{Verbatim}
-
-\item {} 
-\code{cPickle-\textgreater{}pickle} \code{CStringIO-\textgreater{}io} need to be conditionally imported
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{try}\PYG{p}{:}
-    \PYG{k+kn}{import} \PYG{n+nn}{StringIO} \PYG{k+kn}{as} \PYG{n+nn}{io}
-\PYG{k}{except}\PYG{p}{:}
-    \PYG{k+kn}{import} \PYG{n+nn}{io} \PYG{k+kn}{as} \PYG{n+nn}{io}
-\end{Verbatim}
-
-\item {} 
-\code{map} code can be changed to list comprehensions. Use \code{2to3} to do heavy lifting
-
-\item {} 
-All normal strings are unicode in python3. Have to use \code{bytes} to support 8-bit char arrays.
-Normally, this means that \code{str} ``just works''. However, to provide special handling of
-both 8-bit and unicode strings in python2, we often need to check for \code{isinstance(xxx, basestring)}.
-
-We need to conditionally define:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{if} \PYG{n}{sys}\PYG{o}{.}\PYG{n}{hexversion} \PYG{o}{\PYGZgt{}}\PYG{o}{=} \PYG{l+m+mh}{0x03000000}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} everything is unicode in python3}
-    \PYG{n}{path\PYGZus{}str\PYGZus{}type} \PYG{o}{=} \PYG{n+nb}{str}
-\PYG{k}{else}\PYG{p}{:}
-    \PYG{n}{path\PYGZus{}str\PYGZus{}type} \PYG{o}{=} \PYG{n+nb}{basestring}
-
-\PYG{c}{\PYGZsh{} further down...}
-\PYG{k}{if} \PYG{n+nb}{isinstance}\PYG{p}{(}\PYG{n}{compiled\PYGZus{}regex}\PYG{p}{,} \PYG{n}{path\PYGZus{}str\PYGZus{}type}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{enumerate}
-\end{quote}
-
-
-\subsection{Refactoring: parameter handling}
-\label{implementation_notes:refactoring-parameter-handling}\begin{quote}
-\begin{description}
-\item[{Though the code is still split in a not very sensible way between \code{ruffus\_utility.py}, \code{file\_name\_parameters.py} and \code{task.py},}] \leavevmode
-some rationalisation has taken place, and comments added so further refactoring can be made more easily.
-
-\end{description}
-
-Common code for:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{file\PYGZus{}name\PYGZus{}parameters}\PYG{o}{.}\PYG{n}{split\PYGZus{}ex\PYGZus{}param\PYGZus{}factory}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{file\PYGZus{}name\PYGZus{}parameters}\PYG{o}{.}\PYG{n}{transform\PYGZus{}param\PYGZus{}factory}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{file\PYGZus{}name\PYGZus{}parameters}\PYG{o}{.}\PYG{n}{collate\PYGZus{}param\PYGZus{}factory}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-has been moved to \code{file\_name\_parameters.py.yield\_io\_params\_per\_job()}
-
-unit tests added to \code{test\_file\_name\_parameters.py} and \code{test\_ruffus\_utility.py}
-\end{quote}
-
-
-\subsection{\texttt{formatter}}
-\label{implementation_notes:formatter}\begin{quote}
-
-\code{get\_all\_paths\_components(paths, regex\_str)} in \code{ruffus\_utility.py}
-
-Input files names are first squished into a flat list of files.
-\code{get\_all\_paths\_components()} returns both the regular expression matches and the break down of the path.
-
-In case of name clashes, the classes with higher priority override:
-\begin{quote}
-\begin{enumerate}
-\item {} 
-Captures by name
-
-\item {} 
-Captures by index
-
-\item {} \begin{description}
-\item[{Path components:}] \leavevmode
-`ext' = extension with dot
-`basename' = file name without extension
-`path' = path before basename, not ending with slash
-`subdir' = list of directories starting with the most nested and ending with the root (if normalised)
-`subpath' = list of `path' with successive directories removed starting with the most nested and ending with the root (if normalised)
-
-\end{description}
-
-\end{enumerate}
-
-E.g.  \code{name = '/a/b/c/sample1.bam'}, \code{formatter=r"(.*)(?P\textless{}id\textgreater{}\textbackslash{}d+)\textbackslash{}.(.+)")} returns:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{l+m+mi}{0}\PYG{p}{:}          \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/a/b/c/sample1.bam}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}           \PYG{o}{/}\PYG{o}{/} \PYG{n}{Entire} \PYG{n}{match} \PYG{n}{captured} \PYG{n}{by} \PYG{n}{index}
-\PYG{l+m+mi}{1}\PYG{p}{:}          \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/a/b/c/sample}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}                \PYG{o}{/}\PYG{o}{/} \PYG{n}{captured} \PYG{n}{by} \PYG{n}{index}
-\PYG{l+m+mi}{2}\PYG{p}{:}          \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{bam}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}                          \PYG{o}{/}\PYG{o}{/} \PYG{n}{captured} \PYG{n}{by} \PYG{n}{index}
-\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{id}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}       \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZsq{}}                             \PYG{o}{/}\PYG{o}{/} \PYG{n}{captured} \PYG{n}{by} \PYG{n}{name}
-\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{ext}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}      \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{.bam}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{subdir}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{c}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{subpath}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}  \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/a/b/c}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/a/b}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/a}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{path}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}     \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{/a/b/c}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{basename}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{sample1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-\end{Verbatim}
-\end{quote}
-
-The code is in \code{ruffus\_utility.py}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{results} \PYG{o}{=} \PYG{n}{get\PYGZus{}all\PYGZus{}paths\PYGZus{}components}\PYG{p}{(}\PYG{n}{paths}\PYG{p}{,} \PYG{n}{regex\PYGZus{}str}\PYG{p}{)}
-\PYG{n}{string}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{n}{results}\PYG{p}{[}\PYG{l+m+mi}{2}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-All the magic is hidden inside black boxes \code{filename\_transform} classes:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{class} \PYG{n+nc}{t\PYGZus{}suffix\PYGZus{}filename\PYGZus{}transform}\PYG{p}{(}\PYG{n}{t\PYGZus{}filename\PYGZus{}transform}\PYG{p}{)}\PYG{p}{:}
-\PYG{k}{class} \PYG{n+nc}{t\PYGZus{}regex\PYGZus{}filename\PYGZus{}transform}\PYG{p}{(}\PYG{n}{t\PYGZus{}filename\PYGZus{}transform}\PYG{p}{)}\PYG{p}{:}
-\PYG{k}{class} \PYG{n+nc}{t\PYGZus{}format\PYGZus{}filename\PYGZus{}transform}\PYG{p}{(}\PYG{n}{t\PYGZus{}filename\PYGZus{}transform}\PYG{p}{)}\PYG{p}{:}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{\texttt{formatter()}: \texttt{regex()} and \texttt{suffix()}}
-\label{implementation_notes:formatter-regex-and-suffix}\begin{quote}
-
-The previous behaviour with regex() where mismatches fail even if no substitution is made is retained by the use of \code{re.subn()}.
-This is a corner case but I didn't want user code to break
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} filter on \PYGZdq{}.txt\PYGZdq{}}
-\PYG{n}{input\PYGZus{}filenames} \PYG{o}{=} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.wrong}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-\PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.txt)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} fails, no substitution possible}
-\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{c}{\PYGZsh{} fails anyway even through regular expression matches not referenced...}
-\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{output.filename}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{@product()}
-\label{implementation_notes:product}\begin{quote}
-\begin{itemize}
-\item {} 
-Use combinatoric generators from itertools and keep that naming scheme
-
-\item {} 
-Put all new generators in an \code{combinatorics} submodule namespace to avoid breaking user code. (They can imported if necessary.)
-
-\item {} 
-test code in test/test\_combinatorics.py
-
-\item {} 
-The \code{itertools.product(repeat)} parameter doesn't make sense for Ruffus and will not be used
-
-\item {} 
-Flexible number of pairs of \code{task} / \code{glob} / file names + \code{formatter()}
-
-\item {} 
-Only \code{formatter({[}OPTIONAl\_REGEX{]})} provides the necessary flexibility to construct the output so we won't bother with suffix and regex
-
-\item {} 
-Similar to \code{@transform} but with extra level of nested-ness
-
-\end{itemize}
-\begin{description}
-\item[{Retain same code for \code{@product} and \code{@transform} by adding an additional level of indirection:}] \leavevmode\begin{itemize}
-\item {} 
-generator wrap around \code{get\_strings\_in\_nested\_sequence} to convert nested input parameters either to a single flat list of file names or to nested lists of file names
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{file\PYGZus{}name\PYGZus{}parameters}\PYG{o}{.}\PYG{n}{input\PYGZus{}param\PYGZus{}to\PYGZus{}file\PYGZus{}name\PYGZus{}list} \PYG{p}{(}\PYG{n}{input\PYGZus{}params}\PYG{p}{)}
-\PYG{n}{file\PYGZus{}name\PYGZus{}parameters}\PYG{o}{.}\PYG{n}{list\PYGZus{}input\PYGZus{}param\PYGZus{}to\PYGZus{}file\PYGZus{}name\PYGZus{}list} \PYG{p}{(}\PYG{n}{input\PYGZus{}params}\PYG{p}{)}
-\end{Verbatim}
-
-\item {} 
-\code{t\_file\_names\_transform} class which stores a list of regular expressions, one for each \code{formatter()} object corresponding to a single set of input parameters
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{t\PYGZus{}formatter\PYGZus{}file\PYGZus{}names\PYGZus{}transform}
-\PYG{n}{t\PYGZus{}nested\PYGZus{}formatter\PYGZus{}file\PYGZus{}names\PYGZus{}transform}
-\end{Verbatim}
-
-\item {} 
-string substitution functions which will apply a list of \code{formatter} changes
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{ruffus}\PYG{o}{.}\PYG{n}{utility}\PYG{o}{.}\PYG{n}{t\PYGZus{}formatter\PYGZus{}replace}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{ruffus}\PYG{o}{.}\PYG{n}{utility}\PYG{o}{.}\PYG{n}{t\PYGZus{}nested\PYGZus{}formatter\PYGZus{}replace}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-\item {} 
-\code{ruffus\_uilility.swap\_doubly\_nested\_order()} makes the syntax / implementation very orthogonal
-
-\end{itemize}
-
-\end{description}
-\end{quote}
-
-
-\subsection{\texttt{@permutations(...),} \texttt{@combinations(...),} \texttt{@combinations\_with\_replacement(...)}}
-\label{implementation_notes:permutations-combinations-combinations-with-replacement}\begin{quote}
-
-Similar to \code{@product} extra level of nested-ness is self versus self
-\begin{description}
-\item[{Retain same code for \code{@product}}] \leavevmode\begin{itemize}
-\item {} 
-forward to a sinble \code{file\_name\_parameters.combinatorics\_param\_factory()}
-
-\item {} 
-use \code{combinatorics\_type} to dispatch to \code{combinatorics.permutations}, \code{combinatorics.combinations} and \code{combinatorics.combinations\_with\_replacement}
-
-\item {} 
-use \code{list\_input\_param\_to\_file\_name\_list} from \code{file\_name\_parameters.product\_param\_factory()}
-
-\end{itemize}
-
-\end{description}
-\end{quote}
-
-
-\subsection{drmaa alternatives}
-\label{implementation_notes:drmaa-alternatives}\begin{quote}
-
-Alternative, non-drmaa polling code at
-
-\href{https://github.com/bjpop/rubra/blob/master/rubra/cluster\_job.py}{https://github.com/bjpop/rubra/blob/master/rubra/cluster\_job.py}
-\end{quote}
-
-
-\subsection{Task completion monitoring}
-\label{implementation_notes:task-completion-monitoring}
-
-\subsubsection{How easy is it to abstract out the database?}
-\label{implementation_notes:how-easy-is-it-to-abstract-out-the-database}\begin{quote}
-\begin{itemize}
-\item {} \begin{description}
-\item[{The database is Jacob Sondergaard's \code{dbdict} which is a nosql / key-value store wrapper around sqlite}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{job\PYGZus{}history} \PYG{o}{=} \PYG{n}{dbdict}\PYG{o}{.}\PYG{n}{open}\PYG{p}{(}\PYG{n}{RUFFUS\PYGZus{}HISTORY\PYGZus{}FILE}\PYG{p}{,} \PYG{n}{picklevalues}\PYG{o}{=}\PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\item {} 
-The key is the output file name, so it is important not to confuse Ruffus by having different tasks generate the same output file!
-
-\item {} 
-Is it possible to abstract this so that \textbf{jobs} get timestamped as well?
-
-\item {} 
-If we should ever want to abstract out \code{dbdict}, we need to have a similar key-value store class,
-and make sure that a single instance of \code{dbdict} is used through \code{pipeline\_run} which is passed up
-and down the function call chain. \code{dbdict} would then be drop-in replaceable by our custom (e.g. flat-file-based) dbdict alternative.
-
-\end{itemize}
-
-To peek into the database:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nv}{\PYGZdl{} }sqlite3 .ruffus\PYGZus{}history.sqlite
-sqlite\PYGZgt{} .tables
-data
-sqlite\PYGZgt{} .schema data
-CREATE TABLE data \PYG{o}{(}key PRIMARY KEY,value\PYG{o}{)};
-sqlite\PYGZgt{} \PYG{k}{select }key from data order by key;
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Can we query the database, get Job history / stats?}
-\label{implementation_notes:can-we-query-the-database-get-job-history-stats}\begin{quote}
-
-Yes, if we write a function to read and dump the entire database but this is only useful with timestamps and task names. See below
-\end{quote}
-
-
-\subsubsection{What are the run time performance implications?}
-\label{implementation_notes:what-are-the-run-time-performance-implications}\begin{quote}
-
-Should be fast: a single db connection is created and used inside \code{pipeline\_run},  \code{pipeline\_printout},  \code{pipeline\_printout\_graph}
-\end{quote}
-
-
-\subsubsection{Avoid pauses between tasks}
-\label{implementation_notes:avoid-pauses-between-tasks}\begin{quote}
-
-Allows Ruffus to avoid adding an extra 1 second pause between tasks to guard against file systems with low timestamp granularity.
-\begin{itemize}
-\item {} 
-If the local file time looks to be in sync with the underlying file system, saved system time is used instead of file timestamps
-
-\end{itemize}
-\end{quote}
-
-
-\subsection{\texttt{@mkdir(...),}}
-\label{implementation_notes:mkdir}\begin{itemize}
-\item {} 
-\code{mkdir} continues to work seamlessly inside \code{@follows}) but also as its own decorator \code{@mkdir} due to the original happy orthogonal design
-
-\item {} 
-fixed bug in checking so that Ruffus does't blow up if non strings are in the output (number...)
-
-\item {} 
-note: adding the decorator to a previously undecorated function might have unintended consequences. The undecorated function turns into a zombie.
-
-\item {} 
-fixed ugly bug in \code{pipeline\_printout} for printing single line output
-
-\item {} 
-fixed description and printout indent
-
-\end{itemize}
-
-
-\section{FAQ}
-\label{faq:glob}\label{faq:faq}\label{faq::doc}
-
-\subsection{Citations}
-\label{faq:citations}
-
-\subsubsection{Q. How should \emph{Ruffus} be cited in academic publications?}
-\label{faq:q-how-should-ruffus-be-cited-in-academic-publications}\begin{quote}
-
-The official publication describing the original version of \emph{Ruffus} is:
-\begin{quote}
-
-\href{http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524}{Leo Goodstadt (2010)} : \textbf{Ruffus: a lightweight Python library for computational pipelines.} \emph{Bioinformatics} 26(21): 2778-2779
-\end{quote}
-\end{quote}
-
-
-\subsection{Good practices}
-\label{faq:good-practices}
-
-\subsubsection{Q. What is the best way of keeping my data and workings separate?}
-\label{faq:q-what-is-the-best-way-of-keeping-my-data-and-workings-separate}\begin{quote}
-
-It is good practice to run your pipeline in a temporary, ``working'' directory away from your original data.
-
-The first step of your pipeline might be to make softlinks to your original data in your working directory.
-This is example (relatively paranoid) code to do just this:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-    \PYG{k}{def} \PYG{n+nf}{re\PYGZus{}symlink} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{,} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)}\PYG{p}{:}
-        \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{        Helper function: relinks soft symbolic link if necessary}
-\PYG{l+s+sd}{        \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-        \PYG{c}{\PYGZsh{} Guard agains soft linking to oneself: Disastrous consequences of deleting the original files!!}
-        \PYG{k}{if} \PYG{n}{input\PYGZus{}file} \PYG{o}{==} \PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{:}
-            \PYG{n}{logger}\PYG{o}{.}\PYG{n}{debug}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Warning: No symbolic link made. You are using the original data directory as the working directory.}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-            \PYG{k}{return}
-        \PYG{c}{\PYGZsh{} Soft link already exists: delete for relink?}
-        \PYG{k}{if} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{lexists}\PYG{p}{(}\PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-            \PYG{c}{\PYGZsh{} do not delete or overwrite real (non\PYGZhy{}soft link) file}
-            \PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{islink}\PYG{p}{(}\PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-                \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ exists and is not a link}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{)}
-            \PYG{k}{try}\PYG{p}{:}
-                \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{)}
-            \PYG{k}{except}\PYG{p}{:}
-                \PYG{k}{with} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{:}
-                    \PYG{n}{logger}\PYG{o}{.}\PYG{n}{debug}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Can}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{t unlink }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{)}\PYG{p}{)}
-        \PYG{k}{with} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{:}
-            \PYG{n}{logger}\PYG{o}{.}\PYG{n}{debug}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{os.symlink(}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{, }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{)}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{)}\PYG{p}{)}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{c}{\PYGZsh{}   symbolic link relative to original directory so that the entire path}
-        \PYG{c}{\PYGZsh{}       can be moved around with breaking everything}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{symlink}\PYG{p}{(} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{relpath}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{abspath}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{)}\PYG{p}{,}
-                    \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{abspath}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{dirname}\PYG{p}{(}\PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}\PYG{p}{,} \PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{)}
-
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   First task should soft link data to working directory}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n+nd}{@jobs\PYGZus{}limit}\PYG{p}{(}\PYG{l+m+mi}{1}\PYG{p}{)}
-    \PYG{n+nd}{@mkdir}\PYG{p}{(}\PYG{n}{options}\PYG{o}{.}\PYG{n}{working\PYGZus{}dir}\PYG{p}{)}
-    \PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{input\PYGZus{}files}\PYG{p}{,}
-                \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-                \PYG{c}{\PYGZsh{} move to working directory}
-                \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{options}\PYG{o}{.}\PYG{n}{working\PYGZus{}dir}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0]\PYGZcb{}\PYGZob{}ext[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logging\PYGZus{}mutex}
-               \PYG{p}{)}
-    \PYG{k}{def} \PYG{n+nf}{soft\PYGZus{}link\PYGZus{}inputs\PYGZus{}to\PYGZus{}working\PYGZus{}directory} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{,} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)}\PYG{p}{:}
-        \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{        Make soft link in working directory}
-\PYG{l+s+sd}{        \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-        \PYG{k}{with} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{:}
-            \PYG{n}{logger}\PYG{o}{.}\PYG{n}{info}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Linking files }\PYG{l+s+si}{\PYGZpc{}(input\PYGZus{}file)s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}(soft\PYGZus{}link\PYGZus{}name)s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-        \PYG{n}{re\PYGZus{}symlink}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{soft\PYGZus{}link\PYGZus{}name}\PYG{p}{,} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Q. What is the best way of handling data in file pairs (or triplets etc.)}
-\label{faq:q-what-is-the-best-way-of-handling-data-in-file-pairs-or-triplets-etc}\label{faq:faq-paired-files}\begin{quote}
-
-In Bioinformatics, DNA data often consists of only the nucleotide sequence at the two ends of larger fragments.
-The \href{http://www.illumina.com/technology/next-generation-sequencing/paired-end-sequencing\_assay.ilmn}{paired\_end} or
-\href{http://en.wikipedia.org/wiki/Shotgun\_sequencing\#Whole\_genome\_shotgun\_sequencing}{mate pair} data frequently
-consists of of file pairs with conveniently related names such as ``\emph{.R1.fastq'' and ``}.R2.fastq''.
-
-At some point in data pipeline, these file pairs or triplets must find each other and be analysed in the same job.
-
-Provided these file pairs or triplets are named consistently, an easiest way to regroup them is to use the
-Ruffus {\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-collate]{\emph{@collate}}} decorator. For example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@collate}\PYG{p}{(}\PYG{n}{original\PYGZus{}data\PYGZus{}files}\PYG{p}{,}
-
-            \PYG{c}{\PYGZsh{} match file name up to the \PYGZdq{}R1.fastq.gz\PYGZdq{}}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{([\PYGZca{}/]+)R[12].fastq.gz\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-
-            \PYG{c}{\PYGZsh{} Create output parameter supplied to next task}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}1[0]\PYGZcb{}.sam}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{handle\PYGZus{}paired\PYGZus{}end}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}paired\PYGZus{}files}\PYG{p}{,} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} check that we really have a pair of two files not an orphaned singleton}
-    \PYG{k}{if} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{)} \PYG{o}{!=} \PYG{l+m+mi}{2}\PYG{p}{:}
-        \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{One of read pairs }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ missing}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,}\PYG{p}{)}\PYG{p}{)}
-
-    \PYG{c}{\PYGZsh{} do stuff here}
-\end{Verbatim}
-
-This (incomplete, untested) {\hyperref[examples/paired_end_data.py:faq-paired-files-code]{\emph{example code}}} shows what this would look like \emph{in vivo}.
-\end{quote}
-
-
-\subsection{General}
-\label{faq:general}
-
-\subsubsection{Q. \emph{Ruffus} won't create dependency graphs}
-\label{faq:q-ruffus-won-t-create-dependency-graphs}\begin{quote}
-
-A. You need to have installed \code{dot} from \href{http://www.graphviz.org/}{Graphviz} to produce
-pretty flowcharts likes this:
-\begin{quote}
-
-\includegraphics{pretty_flowchart.png}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Q. \emph{Ruffus} seems to be hanging in the same place}
-\label{faq:q-ruffus-seems-to-be-hanging-in-the-same-place}\begin{quote}
-
-A. If \emph{ruffus} is interrupted, for example, by a Ctrl-C,
-you will often find the following lines of code highlighted:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-File "build/bdist.linux-x86\_64/egg/ruffus/task.py", line 1904, in pipeline\_run
-File "build/bdist.linux-x86\_64/egg/ruffus/task.py", line 1380, in run\_all\_jobs\_in\_task
-File "/xxxx/python2.6/multiprocessing/pool.py", line 507, in next
-  self.\_cond.wait(timeout)
-File "/xxxxx/python2.6/threading.py", line 237, in wait
-  waiter.acquire()
-\end{Verbatim}
-
-This is \emph{not} where \emph{ruffus} is hanging but the boundary between the main programme process
-and the sub-processes which run \emph{ruffus} jobs in parallel.
-
-This is naturally where broken execution threads get washed up onto.
-\end{quote}
-
-
-\subsubsection{Q. Regular expression substitutions don't work}
-\label{faq:q-regular-expression-substitutions-don-t-work}\begin{quote}
-
-A. If you are using the special regular expression forms \code{"\textbackslash{}1"}, \code{"\textbackslash{}2"} etc.
-to refer to matching groups, remember to `escape' the subsitution pattern string.
-The best option is to use \href{http://docs.python.org/library/re.html}{`raw' python strings}.
-For example:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1\PYGZus{}substitutes}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2correctly}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{3four}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{4times}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-\end{quote}
-
-Ruffus will throw an exception if it sees an unescaped \code{"\textbackslash{}1"} or \code{"\textbackslash{}2"} in a file name.
-\end{quote}
-
-
-\subsubsection{Q. How to force a pipeline to appear up to date?}
-\label{faq:q-how-to-force-a-pipeline-to-appear-up-to-date}\begin{quote}
-
-\emph{I have made a trivial modification to one of my data files and now Ruffus wants to rerun my month long pipeline. How can I convince Ruffus that everything is fine and to leave things as they are?}
-
-The standard way to do what you are trying to do is to touch all the files downstream...
-That way the modification times of your analysis files would postdate your existing files.
-You can do this manually but Ruffus also provides direct support:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run} \PYG{p}{(}\PYG{n}{touch\PYGZus{}files\PYGZus{}only} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\end{Verbatim}
-
-pipeline\_run will run your script normally stepping over up-to-date tasks and starting
-with jobs which look out of date. However, after that, none of your pipeline task functions
-will be called, instead, each non-up-to-date file is \href{https://en.wikipedia.org/wiki/Touch\_(Unix)}{touch}-ed in
-turn so that the file modification dates follow on successively.
-
-See the documentation for {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run()}}}
-
-It is even simpler if you are using the new Ruffus.cmdline support from version 2.4. You can just type
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-your script \PYGZhy{}\PYGZhy{}touch\PYGZus{}files\PYGZus{}only \PYG{o}{[}\PYGZhy{}\PYGZhy{}other\PYGZus{}options\PYGZus{}of\PYGZus{}your\PYGZus{}own\PYGZus{}etc\PYG{o}{]}
-\end{Verbatim}
-\end{quote}
-
-See {\hyperref[tutorials/new_tutorial/command_line:new-manual-cmdline]{\emph{command line}}} documentation.
-\end{quote}
-
-
-\subsubsection{Q. How can I use my own decorators with Ruffus?}
-\label{faq:q-how-can-i-use-my-own-decorators-with-ruffus}
-(Thanks to Radhouane Aniba for contributing to this answer.)
-\begin{enumerate}
-\item {} 
-With care! If the following two points are observed:
-
-\end{enumerate}
-
-
-\paragraph{1. Use @wraps  from \texttt{functools} or Michele Simionato's decorator module}
-\label{faq:use-wraps-from-functools-or-michele-simionato-s-decorator-module}\begin{quote}
-
-These will automatically forward attributes from the task function correctly:
-\begin{itemize}
-\item {} 
-\code{\_\_name\_\_} and \code{\_\_module\_\_} is used to identify functions uniquely in a Ruffus pipeline, and
-
-\item {} 
-\code{pipeline\_task} is used to hold per task data
-
-\end{itemize}
-\end{quote}
-
-
-\paragraph{2. Always call Ruffus decorators first before your own decorators.}
-\label{faq:always-call-ruffus-decorators-first-before-your-own-decorators}\begin{quote}
-
-Otherwise, your decorator will be ignored.
-
-So this works:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{prev\PYGZus{}task}\PYG{p}{)}
-\PYG{n+nd}{@custom\PYGZus{}decorator}\PYG{p}{(}\PYG{n}{something}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{test}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-This is a bit futile
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} ignore @custom\PYGZus{}decorator}
-\PYG{n+nd}{@custom\PYGZus{}decorator}\PYG{p}{(}\PYG{n}{something}\PYG{p}{)}
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{prev\PYGZus{}task}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{test}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-This order dependency is an unfortunate quirk of how python decorators work. The last (rather futile)
-piece of code is equivalent to:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{test} \PYG{o}{=} \PYG{n}{custom\PYGZus{}decorator}\PYG{p}{(}\PYG{n}{something}\PYG{p}{)}\PYG{p}{(}\PYG{n}{ruffus}\PYG{o}{.}\PYG{n}{follows}\PYG{p}{(}\PYG{n}{prev\PYGZus{}task}\PYG{p}{)}\PYG{p}{(}\PYG{n}{test}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-
-Unfortunately, Ruffus has no idea that someone else (\code{custom\_decorator}) is also modifying the \code{test()} function
-after it (\code{ruffus.follows}) has had its go.
-\end{quote}
-
-
-\paragraph{Example decorator:}
-\label{faq:example-decorator}\begin{quote}
-
-Let us look at a decorator to time jobs:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{sys}\PYG{o}{,} \PYG{n+nn}{time}
-\PYG{k}{def} \PYG{n+nf}{time\PYGZus{}func\PYGZus{}call}\PYG{p}{(}\PYG{n}{func}\PYG{p}{,} \PYG{n}{stream}\PYG{p}{,} \PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}prints elapsed time to standard out, or any other file\PYGZhy{}like object with a .write() method.}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-   \PYG{n}{start} \PYG{o}{=} \PYG{n}{time}\PYG{o}{.}\PYG{n}{time}\PYG{p}{(}\PYG{p}{)}
-   \PYG{c}{\PYGZsh{} Run the decorated function.}
-   \PYG{n}{ret} \PYG{o}{=} \PYG{n}{func}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}
-   \PYG{c}{\PYGZsh{} Stop the timer.}
-   \PYG{n}{end} \PYG{o}{=} \PYG{n}{time}\PYG{o}{.}\PYG{n}{time}\PYG{p}{(}\PYG{p}{)}
-   \PYG{n}{elapsed} \PYG{o}{=} \PYG{n}{end} \PYG{o}{\PYGZhy{}} \PYG{n}{start}
-   \PYG{n}{stream}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}\PYGZcb{} took \PYGZob{}\PYGZcb{} seconds}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{n}{func}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}\PYG{p}{,} \PYG{n}{elapsed}\PYG{p}{)}\PYG{p}{)}
-   \PYG{k}{return} \PYG{n}{ret}
-
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-\PYG{k+kn}{import} \PYG{n+nn}{time}
-
-\PYG{n+nd}{@time\PYGZus{}job}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{First task}\PYG{l+s}{\PYGZdq{}}
-
-
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{first\PYGZus{}task}\PYG{p}{)}
-\PYG{n+nd}{@time\PYGZus{}job}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{second\PYGZus{}task}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Second task}\PYG{l+s}{\PYGZdq{}}
-
-
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{second\PYGZus{}task}\PYG{p}{)}
-\PYG{n+nd}{@time\PYGZus{}job}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{final\PYGZus{}task}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Final task}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-What would \code{@time\_job} look like?
-\end{quote}
-
-
-\paragraph{1. Using functools @wraps}
-\label{faq:using-functools-wraps}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{functools}
-\PYG{k}{def} \PYG{n+nf}{time\PYGZus{}job}\PYG{p}{(}\PYG{n}{stream}\PYG{o}{=}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{def} \PYG{n+nf}{actual\PYGZus{}time\PYGZus{}job}\PYG{p}{(}\PYG{n}{func}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n+nd}{@functools.wraps}\PYG{p}{(}\PYG{n}{func}\PYG{p}{)}
-        \PYG{k}{def} \PYG{n+nf}{wrapper}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}\PYG{p}{:}
-            \PYG{k}{return} \PYG{n}{time\PYGZus{}func\PYGZus{}call}\PYG{p}{(}\PYG{n}{func}\PYG{p}{,} \PYG{n}{stream}\PYG{p}{,} \PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}
-        \PYG{k}{return} \PYG{n}{wrapper}
-    \PYG{k}{return} \PYG{n}{actual\PYGZus{}time\PYGZus{}job}
-\end{Verbatim}
-\end{quote}
-
-
-\paragraph{2. Using Michele Simionato's decorator module}
-\label{faq:using-michele-simionato-s-decorator-module}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{decorator}
-\PYG{k}{def} \PYG{n+nf}{time\PYGZus{}job}\PYG{p}{(}\PYG{n}{stream}\PYG{o}{=}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{def} \PYG{n+nf}{time\PYGZus{}job}\PYG{p}{(}\PYG{n}{func}\PYG{p}{,} \PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{return} \PYG{n}{time\PYGZus{}func\PYGZus{}call}\PYG{p}{(}\PYG{n}{func}\PYG{p}{,} \PYG{n}{stream}\PYG{p}{,} \PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}
-    \PYG{k}{return} \PYG{n}{decorator}\PYG{o}{.}\PYG{n}{decorator}\PYG{p}{(}\PYG{n}{time\PYGZus{}job}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\paragraph{2. By hand, using a callable object}
-\label{faq:by-hand-using-a-callable-object}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{class} \PYG{n+nc}{time\PYGZus{}job}\PYG{p}{(}\PYG{n+nb}{object}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{def} \PYG{n+nf}{\PYGZus{}\PYGZus{}init\PYGZus{}\PYGZus{}}\PYG{p}{(}\PYG{n+nb+bp}{self}\PYG{p}{,} \PYG{n}{stream}\PYG{o}{=}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{stream} \PYG{o}{=} \PYG{n}{stream}
-    \PYG{k}{def} \PYG{n+nf}{\PYGZus{}\PYGZus{}call\PYGZus{}\PYGZus{}}\PYG{p}{(}\PYG{n+nb+bp}{self}\PYG{p}{,} \PYG{n}{func}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{def} \PYG{n+nf}{inner}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}\PYG{p}{:}
-            \PYG{k}{return} \PYG{n}{time\PYGZus{}func\PYGZus{}call}\PYG{p}{(}\PYG{n}{func}\PYG{p}{,} \PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{stream}\PYG{p}{,} \PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}
-        \PYG{c}{\PYGZsh{} remember to forward \PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}
-        \PYG{n}{inner}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}} \PYG{o}{=} \PYG{n}{func}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}
-        \PYG{n}{inner}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}module\PYGZus{}\PYGZus{}} \PYG{o}{=} \PYG{n}{func}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}module\PYGZus{}\PYGZus{}}
-        \PYG{n}{inner}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}doc\PYGZus{}\PYGZus{}} \PYG{o}{=} \PYG{n}{func}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}doc\PYGZus{}\PYGZus{}}
-        \PYG{k}{if} \PYG{n+nb}{hasattr}\PYG{p}{(}\PYG{n}{func}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{pipeline\PYGZus{}task}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-            \PYG{n}{inner}\PYG{o}{.}\PYG{n}{pipeline\PYGZus{}task} \PYG{o}{=} \PYG{n}{func}\PYG{o}{.}\PYG{n}{pipeline\PYGZus{}task}
-        \PYG{k}{return} \PYG{n}{inner}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Q. Can a task function in a \emph{Ruffus} pipeline be called normally outside of Ruffus?}
-\label{faq:q-can-a-task-function-in-a-ruffus-pipeline-be-called-normally-outside-of-ruffus}\begin{quote}
-
-A. Yes. Most python decorators wrap themselves around a function. However, \emph{Ruffus} leaves the
-original function untouched and unwrapped. Instead, \emph{Ruffus} adds a \code{pipeline\_task} attribute
-to the task function to signal that this is a pipelined function.
-
-This means the original task function can be called just like any other python function.
-\end{quote}
-
-
-\subsubsection{Q. My  \emph{Ruffus} tasks create two files at a time. Why is the second one ignored in successive stages of my pipeline?}
-\label{faq:q-my-ruffus-tasks-create-two-files-at-a-time-why-is-the-second-one-ignored-in-successive-stages-of-my-pipeline}\begin{quote}
-
-\emph{This is my code:}
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{start.input}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{first\PYGZus{}output.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{second\PYGZus{}output.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task1}\PYG{p}{(}\PYG{n}{i}\PYG{p}{,}\PYG{n}{o}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{task1}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.result}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task2}\PYG{p}{(}\PYG{n}{i}\PYG{p}{,} \PYG{n}{o}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{task2}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{3}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
-Tasks which will be run:
-
-Task = task1
-       Job = [start.input
-             -\textgreater{}[first\_output.txt, second\_output.txt]]
-
-Task = task2
-       Job = [[first\_output.txt, second\_output.txt]
-             -\textgreater{}first\_output.result]
-
-\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
-\end{Verbatim}
-\end{quote}
-
-A: This code produces a single output of a tuple of 2 files. In fact, you want two
-outputs, each consisting of 1 file.
-
-You want a single job (single input) to be produce multiple outputs (multiple jobs
-in downstream tasks). This is a one-to-many operation which calls for
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{start.input}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{first\PYGZus{}output.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{second\PYGZus{}output.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task1}\PYG{p}{(}\PYG{n}{i}\PYG{p}{,}\PYG{n}{o}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{task1}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.result}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task2}\PYG{p}{(}\PYG{n}{i}\PYG{p}{,} \PYG{n}{o}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{task2}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{3}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
-Tasks which will be run:
-
-Task = task1
-       Job = [start.input
-             -\textgreater{}[first\_output.txt, second\_output.txt]]
-
-Task = task2
-       Job = [first\_output.txt
-             -\textgreater{}first\_output.result]
-       Job = [second\_output.txt
-             -\textgreater{}second\_output.result]
-
-\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Q. How can a \emph{Ruffus} task produce output which goes off in different directions?}
-\label{faq:q-how-can-a-ruffus-task-produce-output-which-goes-off-in-different-directions}\begin{quote}
-
-A. As above, anytime there is a situation which requires a one-to-many operation, you should reach
-for {\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}. The advanced form takes a regular expression, making
-it easier to produce multiple derivatives of the input file. The following example subdivides
-\emph{2} jobs each into \emph{3}, so that the subsequence task will run \emph{2} x \emph{3} = \emph{6} jobs.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-\PYG{n+nd}{@subdivide}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.input\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.input\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-            \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.+).input\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}      \PYG{c}{\PYGZsh{} match file prefix}
-           \PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.file\PYGZus{}type1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.file\PYGZus{}type2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-            \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.file\PYGZus{}type3}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}task}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{,} \PYG{n}{output}\PYG{p}{)}\PYG{p}{:}
-   \PYG{k}{pass}
-
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{split\PYGZus{}task}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.+)}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.test}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{test\PYGZus{}split\PYGZus{}output}\PYG{p}{(}\PYG{n}{i}\PYG{p}{,} \PYG{n}{o}\PYG{p}{)}\PYG{p}{:}
-   \PYG{k}{pass}
-
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{test\PYGZus{}split\PYGZus{}output}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-\end{Verbatim}
-
-Each of the original 2 files have been split in three so that test\_split\_output will run
-6 jobs simultaneously.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
-Tasks which will be run:
-
-Task = split\_task
-       Job = [1.input\_file -\textgreater{}[1.file\_type1, 1.file\_type2, 1.file\_type3]]
-       Job = [2.input\_file -\textgreater{}[2.file\_type1, 2.file\_type2, 2.file\_type3]]
-
-Task = test\_split\_output
-       Job = [1.file\_type1 -\textgreater{}1.file\_type1.test]
-       Job = [1.file\_type2 -\textgreater{}1.file\_type2.test]
-       Job = [1.file\_type3 -\textgreater{}1.file\_type3.test]
-       Job = [2.file\_type1 -\textgreater{}2.file\_type1.test]
-       Job = [2.file\_type2 -\textgreater{}2.file\_type2.test]
-       Job = [2.file\_type3 -\textgreater{}2.file\_type3.test]
-\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
-\end{Verbatim}
-\end{quote}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Q. Can I call extra code before each job?}
-\label{faq:q-can-i-call-extra-code-before-each-job}\begin{quote}
-
-A. This is easily accomplished by hijacking the process
-for checking if jobs are up to date or not ({\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate}}}):
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}
-
-\PYG{k}{def} \PYG{n+nf}{run\PYGZus{}this\PYGZus{}before\PYGZus{}each\PYGZus{}job} \PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Calling function before each job using these args}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{args}
-    \PYG{c}{\PYGZsh{} Remember to delegate to the default *Ruffus* code for checking if}
-    \PYG{c}{\PYGZsh{}   jobs need to run.}
-    \PYG{k}{return} \PYG{n}{needs\PYGZus{}update\PYGZus{}check\PYGZus{}modify\PYGZus{}time}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{)}
-
-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate}\PYG{p}{(}\PYG{n}{run\PYGZus{}this\PYGZus{}before\PYGZus{}each\PYGZus{}job}\PYG{p}{)}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{p}{[}\PYG{p}{[}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{p}{[}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task\PYGZus{}func}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{,} \PYG{n}{output}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{task\PYGZus{}func}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
-\textgreater{}\textgreater{}\textgreater{} pipeline\_run([task\_func])
-Calling function before each job using these args (None, 'a.1')
-Calling function before each job using these args (None, 'a.1')
-Calling function before each job using these args (None, 'b.1')
-    Job = [None -\textgreater{} a.1] completed
-    Job = [None -\textgreater{} b.1] completed
-Completed Task = task\_func
-\end{Verbatim}
-
-\begin{notice}{note}{Note:}
-Because \code{run\_this\_before\_each\_job(...)} is called whenever \emph{Ruffus} checks to see if
-a job is up to date or not, the function may be called twice for some jobs
-(e.g. \code{(None, 'a.1')} above).
-\end{notice}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Q. Does \emph{Ruffus} allow checkpointing: to distinguish interrupted and completed results?}
-\label{faq:q-does-ruffus-allow-checkpointing-to-distinguish-interrupted-and-completed-results}
-
-\paragraph{A. Use the builtin sqlite checkpointing}
-\label{faq:a-use-the-builtin-sqlite-checkpointing}\begin{quote}
-
-By default, \code{pipeline\_run(...)} will save the timestamps for output files from successfully run jobs to an sqlite database file (\code{.ruffus\_history.sqlite}) in the current directory .
-\begin{itemize}
-\item {} 
-If you are using \code{Ruffus.cmdline}, you can change the checksum / timestamp database file name on the command line using  \code{-{-}checksum\_file\_name NNNN}
-
-\item {} 
-\end{itemize}
-
-The level of timestamping / checksumming can be set via the \code{checksum\_level} parameter:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{o}{.}\PYG{o}{.}\PYG{o}{.}\PYG{p}{,} \PYG{n}{checksum\PYGZus{}level} \PYG{o}{=} \PYG{n}{N}\PYG{p}{,} \PYG{o}{.}\PYG{o}{.}\PYG{o}{.}\PYG{p}{)}
-\end{Verbatim}
-
-where the default is 1:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-level 0 : Use only file timestamps
-level 1 : above, plus timestamp of successful job completion
-level 2 : above, plus a checksum of the pipeline function body
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-\end{Verbatim}
-\end{quote}
-
-
-\paragraph{A. Use a flag file}
-\label{faq:a-use-a-flag-file}\begin{quote}
-
-When gmake is interrupted, it will delete the target file it is updating so that the target is
-remade from scratch when make is next run. Ruffus, by design, does not do this because, more often than
-not, the partial / incomplete file may be usefully if only to reveal, for example, what might have caused an interrupting error
-or exception. It also seems a bit too clever and underhand to go around the programmer's back to delete files...
-
-A common \emph{Ruffus} convention is create an empty checkpoint or ``flag'' file whose sole purpose
-is to record a modification-time and the successful completion of a job.
-
-This would be task with a completion flag:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Assuming a pipelined task function named \PYGZdq{}stage1\PYGZdq{}}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{stage1}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage2\PYGZus{}finished}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{stage2} \PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{task\PYGZus{}output\PYGZus{}file}\PYG{p}{,} \PYG{n}{flag\PYGZus{}file} \PYG{o}{=} \PYG{n}{output\PYGZus{}files}
-    \PYG{n}{cmd} \PYG{o}{=} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{do\PYGZus{}something2 }\PYG{l+s+si}{\PYGZpc{}(input\PYGZus{}file)s}\PYG{l+s}{ \PYGZgt{}\textbar{} }\PYG{l+s+si}{\PYGZpc{}(task\PYGZus{}output\PYGZus{}file)s}\PYG{l+s}{ }\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n}{cmd} \PYG{o}{=} \PYG{n}{cmd} \PYG{o}{\PYGZpc{}} \PYG{p}{\PYGZob{}}
-                    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:}               \PYG{n}{input\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{,}
-                    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{task\PYGZus{}output\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:}         \PYG{n}{task\PYGZus{}output\PYGZus{}file}
-                \PYG{p}{\PYGZcb{}}
-    \PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{os}\PYG{o}{.}\PYG{n}{system}\PYG{p}{(} \PYG{n}{cmd} \PYG{p}{)}\PYG{p}{:}
-        \PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{c}{\PYGZsh{}   It worked: Create completion flag\PYGZus{}file}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{flag\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888}
-\end{Verbatim}
-
-The flag\_files \code{xxx.stage2\_finished} indicate that each job is finished. If this is missing,
-\code{xxx.stage2} is only a partial, interrupted result.
-
-The only thing to be aware of is that the flag file will appear in the list of inputs of the
-downstream task, which should accordingly look like this:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{stage2}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage3}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage3\PYGZus{}finished}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{stage3} \PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-
-    \PYG{c}{\PYGZsh{}888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   Note that the first parameter is a LIST of input files, the last of which}
-    \PYG{c}{\PYGZsh{}       is the flag file from the previous task which we can ignore}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{previous\PYGZus{}flag\PYGZus{}file}  \PYG{o}{=} \PYG{n}{input\PYGZus{}files}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-    \PYG{n}{task\PYGZus{}output\PYGZus{}file}\PYG{p}{,} \PYG{n}{flag\PYGZus{}file}     \PYG{o}{=} \PYG{n}{output\PYGZus{}files}
-    \PYG{n}{cmd} \PYG{o}{=} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{do\PYGZus{}something3 }\PYG{l+s+si}{\PYGZpc{}(input\PYGZus{}file)s}\PYG{l+s}{ \PYGZgt{}\textbar{} }\PYG{l+s+si}{\PYGZpc{}(task\PYGZus{}output\PYGZus{}file)s}\PYG{l+s}{ }\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n}{cmd} \PYG{o}{=} \PYG{n}{cmd} \PYG{o}{\PYGZpc{}} \PYG{p}{\PYGZob{}}
-                    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:}               \PYG{n}{input\PYGZus{}file}\PYG{p}{,}
-                    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{task\PYGZus{}output\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:}         \PYG{n}{task\PYGZus{}output\PYGZus{}file}
-                \PYG{p}{\PYGZcb{}}
-    \PYG{c}{\PYGZsh{} completion flag file for this task}
-    \PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{os}\PYG{o}{.}\PYG{n}{system}\PYG{p}{(} \PYG{n}{cmd} \PYG{p}{)}\PYG{p}{:}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{flag\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-The {\hyperref[examples/bioinformatics/part2:examples-bioinformatics-part2-step2]{\emph{Bioinformatics example}}} contains {\hyperref[examples/bioinformatics/part2_code:examples-bioinformatics-part2-code]{\emph{code}}} for checkpointing.
-\end{quote}
-
-
-\paragraph{A. Use a temp file}
-\label{faq:a-use-a-temp-file}\begin{quote}
-
-Thanks to Martin Goodson for suggesting this and providing an example. In his words:
-
-``I normally use a decorator to create a temporary file which is only renamed after the task has completed without any problems. This seems a more elegant solution to the problem:''
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{def} \PYG{n+nf}{usetemp}\PYG{p}{(}\PYG{n}{task\PYGZus{}func}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{} Decorate a function to write to a tmp file and then rename it. So half finished tasks cannot create up to date targets.}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n+nd}{@wraps}\PYG{p}{(}\PYG{n}{task\PYGZus{}func}\PYG{p}{)}
-    \PYG{k}{def} \PYG{n+nf}{wrapper\PYGZus{}function}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{args}\PYG{o}{=}\PYG{n+nb}{list}\PYG{p}{(}\PYG{n}{args}\PYG{p}{)}
-        \PYG{n}{outnames}\PYG{o}{=}\PYG{n}{args}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}
-        \PYG{k}{if} \PYG{o+ow}{not} \PYG{n+nb}{isinstance}\PYG{p}{(}\PYG{n}{outnames}\PYG{p}{,} \PYG{n+nb}{basestring}\PYG{p}{)} \PYG{o+ow}{and}  \PYG{n+nb}{hasattr}\PYG{p}{(}\PYG{n}{outnames}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZus{}\PYGZus{}getitem\PYGZus{}\PYGZus{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{:}
-            \PYG{n}{tmpnames}\PYG{o}{=}\PYG{p}{[}\PYG{n+nb}{str}\PYG{p}{(}\PYG{n}{x}\PYG{p}{)}\PYG{o}{+}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.tmp}\PYG{l+s}{\PYGZdq{}} \PYG{k}{for} \PYG{n}{x} \PYG{o+ow}{in} \PYG{n}{outnames}\PYG{p}{]}
-            \PYG{n}{args}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{o}{=}\PYG{n}{tmpnames}
-            \PYG{n}{task\PYGZus{}func}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}
-            \PYG{k}{try}\PYG{p}{:}
-                \PYG{k}{for} \PYG{n}{tmp}\PYG{p}{,} \PYG{n}{name} \PYG{o+ow}{in} \PYG{n+nb}{zip}\PYG{p}{(}\PYG{n}{tmpnames}\PYG{p}{,} \PYG{n}{outnames}\PYG{p}{)}\PYG{p}{:}
-                    \PYG{k}{if} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{exists}\PYG{p}{(}\PYG{n}{tmp}\PYG{p}{)}\PYG{p}{:}
-                        \PYG{n}{os}\PYG{o}{.}\PYG{n}{rename}\PYG{p}{(}\PYG{n}{tmp}\PYG{p}{,} \PYG{n+nb}{str}\PYG{p}{(}\PYG{n}{name}\PYG{p}{)}\PYG{p}{)}
-            \PYG{k}{except} \PYG{n+ne}{BaseException} \PYG{k}{as} \PYG{n}{e}\PYG{p}{:}
-                \PYG{k}{for} \PYG{n}{name} \PYG{o+ow}{in} \PYG{n}{outnames}\PYG{p}{:}
-                    \PYG{k}{if} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{exists}\PYG{p}{(}\PYG{n}{name}\PYG{p}{)}\PYG{p}{:}
-                        \PYG{n}{os}\PYG{o}{.}\PYG{n}{remove}\PYG{p}{(}\PYG{n}{name}\PYG{p}{)}
-                \PYG{k}{raise} \PYG{p}{(}\PYG{n}{e}\PYG{p}{)}
-        \PYG{k}{else}\PYG{p}{:}
-            \PYG{n}{tmp}\PYG{o}{=}\PYG{n+nb}{str}\PYG{p}{(}\PYG{n}{outnames}\PYG{p}{)}\PYG{o}{+}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{.tmp}\PYG{l+s}{\PYGZsq{}}
-            \PYG{n}{args}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{o}{=}\PYG{n}{tmp}
-            \PYG{n}{task\PYGZus{}func}\PYG{p}{(}\PYG{o}{*}\PYG{n}{args}\PYG{p}{,} \PYG{o}{*}\PYG{o}{*}\PYG{n}{kwargs}\PYG{p}{)}
-            \PYG{n}{os}\PYG{o}{.}\PYG{n}{rename}\PYG{p}{(}\PYG{n}{tmp}\PYG{p}{,} \PYG{n+nb}{str}\PYG{p}{(}\PYG{n}{outnames}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{return} \PYG{n}{wrapper\PYGZus{}function}
-\end{Verbatim}
-\end{quote}
-
-Use like this:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{client1.price}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{n+nd}{@usetemp}
-\PYG{k}{def} \PYG{n+nf}{getusers}\PYG{p}{(}\PYG{n}{inputfile}\PYG{p}{,} \PYG{n}{outputname}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{}**************************************************}
-    \PYG{c}{\PYGZsh{} code goes here}
-    \PYG{c}{\PYGZsh{} outputname now refers to temporary file}
-    \PYG{k}{pass}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Windows}
-\label{faq:windows}
-
-\subsubsection{Q. Windows seems to spawn \emph{ruffus} processes recursively}
-\label{faq:q-windows-seems-to-spawn-ruffus-processes-recursively}\begin{quote}
-
-A. It is necessary to protect the ``entry point'' of the program under windows.
-Otherwise, a new process will be started each time the main module is imported
-by a new Python interpreter as an unintended side effects. Causing a cascade
-of new processes.
-
-See: \href{http://docs.python.org/library/multiprocessing.html\#multiprocessing-programming}{http://docs.python.org/library/multiprocessing.html\#multiprocessing-programming}
-
-This code works:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-if \_\_name\_\_ == '\_\_main\_\_':
-    try:
-        pipeline\_run([parallel\_task], multiprocess = 5)
-except Exception, e:
-    print e.args
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Sun Grid Engine / PBS / SLURM etc}
-\label{faq:sun-grid-engine-pbs-slurm-etc}
-
-\subsubsection{Q. Can Ruffus be used to manage a cluster or grid based pipeline?}
-\label{faq:q-can-ruffus-be-used-to-manage-a-cluster-or-grid-based-pipeline}\begin{quote}
-\begin{enumerate}
-\item {} 
-Some minimum modifications have to be made to your \emph{Ruffus} script to allow it to submit jobs to a cluster
-
-\end{enumerate}
-
-See {\hyperref[tutorials/new_tutorial/multiprocessing:new-manual-ruffus-drmaa-wrapper-run-job]{\emph{ruffus.drmaa\_wrapper}}}
-
-Thanks to Andreas Heger and others at CGAT and Bernie Pope for contributing ideas and code.
-\end{quote}
-
-
-\subsubsection{Q. When I submit lots of jobs via Sun Grid Engine (SGE), the head node occassionally freezes and dies}
-\label{faq:q-when-i-submit-lots-of-jobs-via-sun-grid-engine-sge-the-head-node-occassionally-freezes-and-dies}\begin{enumerate}
-\item {} 
-You need to use multithreading rather than multiprocessing. See {\hyperref[tutorials/new_tutorial/multiprocessing:new-manual-ruffus-drmaa-wrapper-run-job]{\emph{ruffus.drmaa\_wrapper}}}
-
-\end{enumerate}
-
-
-\subsubsection{Q. Keeping Large intermediate files}
-\label{faq:q-keeping-large-intermediate-files}\begin{quote}
-
-Sometimes pipelines create a large number of intermediate files which might not be needed later.
-
-Unfortunately, the current design of \emph{Ruffus} requires these files to hang around otherwise the pipeline
-will not know that it ran successfully.
-
-We have some tentative plans to get around this but in the meantime, Bernie Pope suggests
-truncating intermediate files in place, preserving timestamps:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} truncate a file to zero bytes, and preserve its original modification time}
-\PYG{k}{def} \PYG{n+nf}{zeroFile}\PYG{p}{(}\PYG{n+nb}{file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{if} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{exists}\PYG{p}{(}\PYG{n+nb}{file}\PYG{p}{)}\PYG{p}{:}
-        \PYG{c}{\PYGZsh{} save the current time of the file}
-        \PYG{n}{timeInfo} \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{stat}\PYG{p}{(}\PYG{n+nb}{file}\PYG{p}{)}
-        \PYG{k}{try}\PYG{p}{:}
-            \PYG{n}{f} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n+nb}{file}\PYG{p}{,}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-        \PYG{k}{except} \PYG{n+ne}{IOError}\PYG{p}{:}
-            \PYG{k}{pass}
-        \PYG{k}{else}\PYG{p}{:}
-            \PYG{n}{f}\PYG{o}{.}\PYG{n}{truncate}\PYG{p}{(}\PYG{l+m+mi}{0}\PYG{p}{)}
-            \PYG{n}{f}\PYG{o}{.}\PYG{n}{close}\PYG{p}{(}\PYG{p}{)}
-            \PYG{c}{\PYGZsh{} change the time of the file back to what it was}
-            \PYG{n}{os}\PYG{o}{.}\PYG{n}{utime}\PYG{p}{(}\PYG{n+nb}{file}\PYG{p}{,}\PYG{p}{(}\PYG{n}{timeInfo}\PYG{o}{.}\PYG{n}{st\PYGZus{}atime}\PYG{p}{,} \PYG{n}{timeInfo}\PYG{o}{.}\PYG{n}{st\PYGZus{}mtime}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsection{Sharing python objects between Ruffus processes running concurrently}
-\label{faq:sharing-python-objects-between-ruffus-processes-running-concurrently}\begin{quote}
-
-The design of Ruffus envisages that much of the data flow in pipelines occurs in files but it is also possible to pass python objects in memory.
-
-Ruffus uses the \href{http://docs.python.org/2/library/multiprocessing.html}{multiprocessing} module and much of the following is a summary of what is covered
-in depth in the Python Standard Library \href{http://docs.python.org/2/library/multiprocessing.html\#sharing-state-between-processes}{Documentation}.
-
-Running Ruffus using \code{pipeline\_run(..., multiprocess = NNN)} where \code{NNN} \textgreater{} 1 runs each job concurrently on up to \code{NNN} separate local processes.
-Each task function runs independently in a different python intepreter, possibly on a different CPU, in the most efficient way.
-However, this does mean we have to pay some attention to how data is sent across process boundaries (unlike the situation with \code{pipeline\_run(..., multithread = NNN)} ).
-
-The python code and data which comprises your multitasking Ruffus job is sent to a separate process in three ways:
-\begin{enumerate}
-\item {} 
-The python function code and data objects are \href{http://docs.python.org/2/library/pickle.html}{pickled}, i.e. converting into a byte stream, by the master process, sent to the remote process
-before being converted back into normal python (unpickling).
-
-\item {} 
-The parameters for your jobs, i.e. what Ruffus calls your task functions with, are separately \href{http://docs.python.org/2/library/pickle.html}{pickled} and sent to the remote process via
-\href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Queue}{multiprocessing.Queue}
-
-\item {} 
-You can share and synchronise other data yourselves. The canonical example is the logger provided by \code{Ruffus.cmdline.setup\_logging}
-
-\end{enumerate}
-
-\begin{notice}{note}{Note:}
-Check that your function code and data can be \href{http://docs.python.org/2/library/pickle.html\#what-can-be-pickled-and-unpickled}{pickled}.
-
-Only functions, built-in functions and classes defined at the top level of a module are picklable.
-\end{notice}
-
-The following answers are a short ``how-to'' for sharing and synchronising data yourselves.
-\end{quote}
-
-
-\subsubsection{Can ordinary python objects be shared between processes?}
-\label{faq:can-ordinary-python-objects-be-shared-between-processes}\begin{enumerate}
-\item {} 
-Objects which can be \href{http://docs.python.org/2/library/pickle.html}{pickled} can be shared as is. These include
-\begin{itemize}
-\item {} 
-numbers
-
-\item {} 
-strings
-
-\item {} 
-tuples, lists, sets, and dictionaries containing only objects which can be \href{http://docs.python.org/2/library/pickle.html}{pickled}.
-
-\end{itemize}
-
-\item {} 
-If these do not change during your pipeline, you can just use them without any further effort in your task.
-
-\item {} 
-If you need to use the value at the point when the task function is \emph{called}, then you need to pass the python object as parameters to your task.
-For example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
- \PYG{c}{\PYGZsh{} changing\PYGZus{}list changes...}
- \PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{previous\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.foo}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bar}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{changing\PYGZus{}list}\PYG{p}{)}
- \PYG{k}{def} \PYG{n+nf}{next\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{changing\PYGZus{}list}\PYG{p}{)}\PYG{p}{:}
-     \PYG{k}{pass}
-\end{Verbatim}
-
-\item {} 
-If you need to use the value when the task function is \emph{run} then see {\hyperref[faq:how-about-synchronising-python-objects-in-real-time]{\emph{the following answer.}}}.
-
-\end{enumerate}
-
-
-\subsubsection{Why am I getting \texttt{PicklingError}?}
-\label{faq:why-am-i-getting-picklingerror}\begin{quote}
-
-What is happening? Didn't \href{https://en.wikipedia.org/wiki/Battle\_of\_the\_Herrings}{Joan of Arc} solve this once and for all?
-\begin{enumerate}
-\item {} 
-Some of the data or code in your function cannot be \href{http://docs.python.org/2/library/pickle.html}{pickled} and is being asked to be sent by python \code{mulitprocessing} across process boundaries.
-\begin{quote}
-
-When you run your pipeline using multiprocess:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{n}{logger} \PYG{o}{=} \PYG{n}{ruffusLoggerProxy}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-You will get the following errors:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+ne}{Exception} \PYG{o+ow}{in} \PYG{n}{thread} \PYG{n}{Thread}\PYG{o}{\PYGZhy{}}\PYG{l+m+mi}{2}\PYG{p}{:}
-\PYG{n}{Traceback} \PYG{p}{(}\PYG{n}{most} \PYG{n}{recent} \PYG{n}{call} \PYG{n}{last}\PYG{p}{)}\PYG{p}{:}
-  \PYG{n}{File} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/path/to/python/python2.7/threading.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{line} \PYG{l+m+mi}{808}\PYG{p}{,} \PYG{o+ow}{in} \PYG{n}{\PYGZus{}\PYGZus{}bootstrap\PYGZus{}inner}
-    \PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{run}\PYG{p}{(}\PYG{p}{)}
-  \PYG{n}{File} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/path/to/python/python2.7/threading.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{line} \PYG{l+m+mi}{761}\PYG{p}{,} \PYG{o+ow}{in} \PYG{n}{run}
-    \PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}target}\PYG{p}{(}\PYG{o}{*}\PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}args}\PYG{p}{,} \PYG{o}{*} \PYG{o}{*}\PYG{n+nb+bp}{self}\PYG{o}{.}\PYG{n}{\PYGZus{}\PYGZus{}kwargs}\PYG{p}{)}
-  \PYG{n}{File} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/path/to/python/python2.7/multiprocessing/pool.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{line} \PYG{l+m+mi}{342}\PYG{p}{,} \PYG{o+ow}{in} \PYG{n}{\PYGZus{}handle\PYGZus{}tasks}
-    \PYG{n}{put}\PYG{p}{(}\PYG{n}{task}\PYG{p}{)}
-\PYG{n}{PicklingError}\PYG{p}{:} \PYG{n}{Can}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{t pickle \PYGZlt{}type }\PYG{l+s}{\PYGZsq{}}\PYG{n}{function}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZgt{}: attribute lookup \PYGZus{}\PYGZus{}builtin\PYGZus{}\PYGZus{}.function failed}
-\end{Verbatim}
-\end{quote}
-
-which go away when you set \code{pipeline\_run({[}{]}, multiprocess = 1, ...)}
-\end{quote}
-
-\end{enumerate}
-
-Unfortunately, pickling errors are particularly ill-served by standard python error messages. The only really good advice is to take the offending
-code and try and \href{http://docs.python.org/2/library/pickle.html}{pickle} it yourself and narrow down the errors. Check your objects against the list
-in the \href{http://docs.python.org/2/library/pickle.html\#what-can-be-pickled-and-unpickled}{pickle} module.
-Watch out especially for nested functions. These will have to be moved to file scope.
-Other objects may have to be passed in proxy (see below).
-\end{quote}
-
-
-\subsubsection{How about synchronising python objects in real time?}
-\label{faq:id1}\label{faq:how-about-synchronising-python-objects-in-real-time}\begin{quote}
-\begin{enumerate}
-\item {} 
-You can use managers and proxy objects from the \href{http://docs.python.org/library/multiprocessing.html}{multiprocessing} module.
-
-\end{enumerate}
-
-The underlying python object would be owned and managed by a (hidden) server process. Other processes can access the shared objects transparently by using proxies. This is how the logger provided by
-\code{Ruffus.cmdline.setup\_logging} works:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}  optional logger which can be passed to ruffus tasks}
-\PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{setup\PYGZus{}logging} \PYG{p}{(}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{log\PYGZus{}file}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-\end{Verbatim}
-
-\code{logger} is a proxy for the underlying python \href{http://docs.python.org/2/library/logging.html}{logger} object, and it can be shared freely between processes.
-
-The best course is to pass \code{logger} as a parameter to a \emph{Ruffus} task.
-
-The only caveat is that we should make sure multiple jobs are not writting to the log at the same time. To synchronise logging, we use proxy to a non-reentrant \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Lock}{multiprocessing.lock}.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{setup\PYGZus{}logging} \PYG{p}{(}\PYG{n}{\PYGZus{}\PYGZus{}name\PYGZus{}\PYGZus{}}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{log\PYGZus{}file}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{previous\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.foo}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bar}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{next\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{:}
-        \PYG{n}{logger}\PYG{o}{.}\PYG{n}{info}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{We are in the middle of next\PYGZus{}task: }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\subsubsection{Can I  share and synchronise my own python classes via proxies?}
-\label{faq:can-i-share-and-synchronise-my-own-python-classes-via-proxies}\begin{quote}
-\begin{enumerate}
-\item {} 
-\href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.managers.SyncManager}{multiprocessing.managers.SyncManager} provides out of the box support for lists, arrays and dicts etc.
-\begin{quote}
-
-Most of the time, we can use a ``vanilla'' manager provided by \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.sharedctypes.multiprocessing.Manager}{multiprocessing.Manager()}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{multiprocessing}
-\PYG{n}{manager} \PYG{o}{=} \PYG{n}{multiprocessing}\PYG{o}{.}\PYG{n}{Manager}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{n}{list\PYGZus{}proxy} \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{list}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{dict\PYGZus{}proxy} \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{dict}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{lock\PYGZus{}proxy}          \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{Lock}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{namespace\PYGZus{}proxy}     \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{Namespace}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{queue\PYGZus{}proxy}         \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{Queue}\PYG{p}{(}\PYG{p}{[}\PYG{n}{maxsize}\PYG{p}{]}\PYG{p}{)}
-\PYG{n}{rentrant\PYGZus{}lock\PYGZus{}proxy} \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{RLock}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{semaphore\PYGZus{}proxy}     \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{Semaphore}\PYG{p}{(}\PYG{p}{[}\PYG{n}{value}\PYG{p}{]}\PYG{p}{)}
-\PYG{n}{char\PYGZus{}array\PYGZus{}proxy}    \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{Array}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{c}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{n}{integer\PYGZus{}proxy}       \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{Value}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{i}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{6}\PYG{p}{)}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{previous\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.foo}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bar}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{lock\PYGZus{}proxy}\PYG{p}{,} \PYG{n}{dict\PYGZus{}proxy}\PYG{p}{,} \PYG{n}{list\PYGZus{}proxy}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{next\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{lock\PYGZus{}proxy}\PYG{p}{,} \PYG{n}{dict\PYGZus{}proxy}\PYG{p}{,} \PYG{n}{list\PYGZus{}proxy}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n}{lock\PYGZus{}proxy}\PYG{p}{:}
-        \PYG{n}{list\PYGZus{}proxy}\PYG{o}{.}\PYG{n}{append}\PYG{p}{(}\PYG{l+m+mi}{3}\PYG{p}{)}
-        \PYG{n}{dict\PYGZus{}proxy}\PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]} \PYG{o}{=} \PYG{l+m+mi}{5}
-\end{Verbatim}
-\end{quote}
-
-\end{enumerate}
-
-However, you can also create proxy custom classes for your own objects.
-
-In this case you may need to derive from  \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.managers.SyncManager}{multiprocessing.managers.SyncManager}
-and register proxy functions. See \code{Ruffus.proxy\_logger} for an example of how to do this.
-\end{quote}
-
-
-\subsubsection{How do I send python objects back and forth without tangling myself in horrible synchronisation code?}
-\label{faq:how-do-i-send-python-objects-back-and-forth-without-tangling-myself-in-horrible-synchronisation-code}\begin{quote}
-\begin{enumerate}
-\item {} 
-Sharing python objects by passing messages is a much more modern and safer way to coordinate multitasking than using synchronization primitives like locks.
-
-\end{enumerate}
-
-The python \href{http://docs.python.org/2/library/multiprocessing.html\#pipes-and-queues}{multiprocessing} module provides support for passing python objects as messages between processes.
-You can either use \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Pipe}{pipes}
-or \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Queue}{queues}.
-The idea is that one process pushes and object onto a \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Pipe}{pipe} or \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Queue}{queue}
-and the other processes pops it out at the other end. \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Pipe}{Pipes} are
-only two ended so \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Queue}{queues} are usually a better fit for sending data to multiple Ruffus jobs.
-
-Proxies for \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.managers.SyncManager.Queue}{queues} can be passed between processes as in the previous section
-\end{quote}
-
-
-\subsubsection{How do I share large amounts of data efficiently across processes?}
-\label{faq:how-do-i-share-large-amounts-of-data-efficiently-across-processes}\begin{quote}
-\begin{enumerate}
-\item {} 
-If it is really impractical to use data files on disk, you can put the data in shared memory.
-
-\end{enumerate}
-
-It is possible to create shared objects using shared memory which can be inherited by child processes or passed as Ruffus parameters.
-This is probably most efficently done via the \href{http://docs.python.org/2/library/multiprocessing.html\#multiprocessing.Array}{array}
-interface. Again, it is easy to create locks and proxies for synchronised access:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{multiprocessing} \PYG{k+kn}{import} \PYG{n}{Process}\PYG{p}{,} \PYG{n}{Lock}
-\PYG{k+kn}{from} \PYG{n+nn}{multiprocessing.sharedctypes} \PYG{k+kn}{import} \PYG{n}{Value}\PYG{p}{,} \PYG{n}{Array}
-\PYG{k+kn}{from} \PYG{n+nn}{ctypes} \PYG{k+kn}{import} \PYG{n}{Structure}\PYG{p}{,} \PYG{n}{c\PYGZus{}double}
-
-\PYG{n}{manager} \PYG{o}{=} \PYG{n}{multiprocessing}\PYG{o}{.}\PYG{n}{Manager}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{n}{lock\PYGZus{}proxy}          \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{Lock}\PYG{p}{(}\PYG{p}{)}
-\PYG{n}{int\PYGZus{}array\PYGZus{}proxy}     \PYG{o}{=} \PYG{n}{manager}\PYG{o}{.}\PYG{n}{Array}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{i}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+m+mi}{123}\PYG{p}{]} \PYG{o}{*} \PYG{l+m+mi}{100}\PYG{p}{)}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{previous\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.foo}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bar}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{lock\PYGZus{}proxy}\PYG{p}{,} \PYG{n}{int\PYGZus{}array\PYGZus{}proxy}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{next\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{lock\PYGZus{}proxy}\PYG{p}{,} \PYG{n}{int\PYGZus{}array\PYGZus{}proxy}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n}{lock\PYGZus{}proxy}\PYG{p}{:}
-        \PYG{n}{int\PYGZus{}array\PYGZus{}proxy}\PYG{p}{[}\PYG{l+m+mi}{23}\PYG{p}{]} \PYG{o}{=} \PYG{l+m+mi}{71}
-\end{Verbatim}
-\end{quote}
-
-
-\section{Glossary}
-\label{glossary:glossary}\label{glossary:glob}\label{glossary::doc}\phantomsection\label{glossary:id1}\phantomsection\label{glossary:glossary-task}\begin{description}
-\item[{\index{task|textbf}task}] \leavevmode\phantomsection\label{glossary:term-task}
-A stage in a computational pipeline.
-
-Each \textbf{task} in \emph{ruffus} is represented by a python function.
-
-For example, a task might be to find the products of a sets of two numbers:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-4 x 5 = 20
-5 x 6 = 30
-2 x 7 = 14
-\end{Verbatim}
-
-\item[{\index{job|textbf}job}] \leavevmode\phantomsection\label{glossary:term-job}
-Any number of operations which can be run in parallel and make up
-the work in a stage of a computional pipeline.
-
-Each \textbf{task} in \emph{ruffus} is a separate call to the \textbf{task} function.
-
-For example, if a task is to find products of numbers, each of these will be a separate job.
-\begin{quote}
-
-Job1:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-4 x 5 = 20
-\end{Verbatim}
-
-Job2:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-5 x 6 = 30
-\end{Verbatim}
-
-Job3:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-2 x 7 = 14
-\end{Verbatim}
-\end{quote}
-
-Jobs need not complete in order.
-
-\item[{\index{decorator|textbf}decorator}] \leavevmode\phantomsection\label{glossary:term-decorator}
-Ruffus decorators allow functions to be incorporated into a computational
-pipeline, with automatic generation of parameters, dependency checking etc.,
-without modifying any code within the function.
-Quoting from the \href{http://wiki.python.org/moin/PythonDecorators}{python wiki}:
-\begin{quote}
-
-A Python decorator is a specific change to the Python syntax that
-allows us to more conveniently alter functions and methods.
-
-Decorators dynamically alter the functionality of a function, method, or
-class without having to directly use subclasses or change the source code
-of the function being decorated.
-\end{quote}
-
-\item[{\index{generator|textbf}generator}] \leavevmode\phantomsection\label{glossary:term-generator}
-python generators are new to python 2.2
-(see \href{http://www.ibm.com/developerworks/library/l-pycon.html}{Charming Python: Iterators and simple generators}).
-They allow iterable data to be generated on the fly.
-
-Ruffus asks for generators when you want to generate \textbf{job} parameters dynamically.
-
-Each set of job parameters is returned by the \code{yield} keyword for
-greater clarity. For example,:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{def} \PYG{n+nf}{generate\PYGZus{}job\PYGZus{}parameters}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-
-    \PYG{k}{for} \PYG{n}{file\PYGZus{}index}\PYG{p}{,} \PYG{n}{file\PYGZus{}name} \PYG{o+ow}{in} \PYG{n}{iterate}\PYG{p}{(}\PYG{n}{all\PYGZus{}file\PYGZus{}names}\PYG{p}{)}\PYG{p}{:}
-
-        \PYG{c}{\PYGZsh{} parameter for each job}
-        \PYG{k}{yield} \PYG{n}{file\PYGZus{}index}\PYG{p}{,} \PYG{n}{file\PYGZus{}name}
-\end{Verbatim}
-
-Each job takes the parameters \code{file\_index} and \code{file\_name}
-
-\end{description}
-
-\includegraphics{logo.jpg}
-
-
-\section{Hall of Fame: User contributed flowcharts}
-\label{gallery:hall-of-fame-user-contributed-flowcharts}\label{gallery::doc}
-Please contribute your own work flows in your favourite colours with (an optional) short description
-to email: ruffus\_lib at llew.org.uk
-
-
-\subsection{RNASeq pipeline}
-\label{gallery:rnaseq-pipeline}\begin{quote}
-
-\href{http://en.wikipedia.org/wiki/RNA-Seq}{http://en.wikipedia.org/wiki/RNA-Seq}
-
-Mapping transcripts onto genomes using high-throughput sequencing technologies (\code{svg}).
-\includegraphics{gallery_rna_seq.png}\end{quote}
-
-
-\subsection{non-coding evolutionary constraints}
-\label{gallery:non-coding-evolutionary-constraints}\begin{quote}
-
-\href{http://en.wikipedia.org/wiki/Noncoding\_DNA}{http://en.wikipedia.org/wiki/Noncoding\_DNA}
-
-Non-protein coding evolutionary constraints in different species (\code{svg}).
-\includegraphics{gallery_dless.png}\end{quote}
-
-
-\subsection{SNP annotation}
-\label{gallery:snp-annotation}
-Predicting impact of different Single Nucleotide Polymorphisms
-
-\href{http://en.wikipedia.org/wiki/Single-nucleotide\_polymorphism}{http://en.wikipedia.org/wiki/Single-nucleotide\_polymorphism}
-
-Population variation across genomes (\code{svg}).
-\includegraphics{gallery_snp_annotation.png}
-Using ``pseudo'' targets to run only part of the pipeline (\code{svg}).
-\includegraphics{gallery_snp_annotation_consequences.png}
-
-\subsection{Chip-Seq analysis}
-\label{gallery:chip-seq-analysis}
-Analysing DNA binding sites with Chip-Seq
-\href{http://en.wikipedia.org/wiki/Chip-Sequencing}{http://en.wikipedia.org/wiki/Chip-Sequencing}
-\begin{quote}
-
-(\code{svg})
-\includegraphics{gallery_big_pipeline.png}\end{quote}
-
-\index{Ruffus!Etymology}\index{Etymology!Ruffus}\index{Ruffus!Name origins}\index{Name origins!Ruffus}
-
-\section{Why \emph{Ruffus}?}
-\label{why_ruffus:index-0}\label{why_ruffus:why-ruffus}\label{why_ruffus::doc}\label{why_ruffus:design-why-ruffus}
-\textbf{Cylindrophis ruffus} is the name of the
-\href{http://en.wikipedia.org/wiki/Cylindrophis\_ruffus}{red-tailed pipe snake} (bad python-y pun)
-which can be found in \href{http://www.discoverhongkong.com/eng/index.html}{Hong Kong} where the original author comes from.
-
-\emph{Ruffus} is a shy creature, and pretends to be a cobra or a \href{http://en.wikipedia.org/wiki/File:Bandedkrait.jpg}{banded krait} by putting up its red tail and ducking its
-head in its coils when startled.
-
-\begin{tabular}{|p{0.475\linewidth}|p{0.475\linewidth}|}
-\hline
-
-\includegraphics{wikimedia_cyl_ruffus.jpg}
- & 
-\scalebox{0.770000}{\includegraphics{wikimedia_bandedkrait.jpg}}
-\\\hline
-\begin{itemize}
-\item {} 
-Not venomous
-
-\item {} 
-\href{http://en.wikipedia.org/wiki/Mostly\_Harmless}{Mostly Harmless}
-
-\end{itemize}
- & \begin{itemize}
-\item {} 
-Deadly poisonous
-
-\item {} 
-\href{http://en.wikipedia.org/wiki/List\_of\_races\_and\_species\_in\_The\_Hitchhiker's\_Guide\_to\_the\_Galaxy\#Ravenous\_Bugblatter\_Beast\_of\_Traal}{Seriously unfriendly}
-
-\end{itemize}
-\\\hline
-\end{tabular}
-
-
-Be careful not to step on one when running down country park lanes at full speed
-in Hong Kong: this snake is a \href{http://www.hkras.org/eng/info/hkspp.htm}{rare breed}!
-
-\emph{Ruffus} does most of its work at night and sleeps during the day: typical of many (but alas not all) python programmers!
-
-The original \href{http://upload.wikimedia.org/wikipedia/commons/a/a1/Cyl\_ruffus\_061212\_2025\_tdp.jpg}{red-tail pipe} and \href{http://en.wikipedia.org/wiki/File:AB\_054\_Banded\_Krait.JPG}{banded krait} images are from wikimedia.
-
-
-\chapter{Examples}
-\label{contents:examples}
-
-\section{Construction of a simple pipeline to run BLAST jobs}
-\label{examples/bioinformatics/index:construction-of-a-simple-pipeline-to-run-blast-jobs}\label{examples/bioinformatics/index::doc}\label{examples/bioinformatics/index:examples-bioinformatics-part1}
-
-\subsection{Overview}
-\label{examples/bioinformatics/index:overview}\begin{quote}
-
-This is a simple example to illustrate the convenience \textbf{Ruffus}
-brings to simple tasks in bioinformatics.
-\begin{enumerate}
-\item {} 
-\textbf{Split} a problem into multiple fragments that can be
-
-\item {} 
-\textbf{Run in parallel} giving partial solutions that can be
-
-\item {} 
-\textbf{Recombined} into the complete solution.
-
-\end{enumerate}
-
-The example code runs a \href{http://blast.ncbi.nlm.nih.gov/}{ncbi}
-\href{http://en.wikipedia.org/wiki/BLAST}{blast} search for four sequences
-against the human \href{http://en.wikipedia.org/wiki/RefSeq}{refseq} protein sequence database.
-\begin{enumerate}
-\item {} 
-\textbf{Split} each of the four sequences into a separate file.
-
-\item {} 
-\textbf{Run in parallel} Blastall on each sequence file
-
-\item {} 
-\textbf{Recombine} the BLAST results by simple concatenation.
-
-\end{enumerate}
-
-In real life,
-\begin{itemize}
-\item {} 
-\href{http://blast.ncbi.nlm.nih.gov/}{BLAST} already provides support for multiprocessing
-
-\item {} 
-Sequence files would be split in much larger chunks, with many sequences
-
-\item {} 
-The jobs would be submitted to large computational farms (in our case, using the SunGrid Engine).
-
-\item {} 
-The High Scoring Pairs (HSPs) would be parsed / filtered / stored in your own formats.
-
-\end{itemize}
-
-\begin{notice}{note}{Note:}
-This bioinformatics example is intended to showcase \emph{some} of the features of Ruffus.
-\begin{enumerate}
-\item {} 
-See the {\hyperref[tutorials/new_tutorial/introduction:new-manual-introduction]{\emph{manual}}} to learn about the various features in Ruffus.
-
-\end{enumerate}
-\end{notice}
-\end{quote}
-
-
-\subsection{Prerequisites}
-\label{examples/bioinformatics/index:prerequisites}
-
-\subsubsection{1. Ruffus}
-\label{examples/bioinformatics/index:ruffus}\begin{quote}
-
-To install Ruffus on most systems with python installed:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-easy\_install -U ruffus
-\end{Verbatim}
-\end{quote}
-
-Otherwise, \href{http://code.google.com/p/ruffus/downloads/list}{download} Ruffus and run:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-tar -xvzf ruffus-xxx.tar.gz
-cd ruffus-xxx
-./setup install
-\end{Verbatim}
-\end{quote}
-
-where xxx is the latest Ruffus version.
-\end{quote}
-
-
-\subsubsection{2. BLAST}
-\label{examples/bioinformatics/index:blast}\begin{quote}
-
-This example assumes that the \href{http://blast.ncbi.nlm.nih.gov/}{BLAST} \code{blastall} and \code{formatdb} executables are
-installed and on the search path. Otherwise download from \href{http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web\&PAGE\_TYPE=BlastDocs\&DOC\_TYPE=Download}{here}.
-\end{quote}
-
-
-\subsubsection{3. human refseq sequence database}
-\label{examples/bioinformatics/index:human-refseq-sequence-database}\begin{quote}
-
-We also need to download the human refseq sequence file and format the ncbi database:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-wget ftp://ftp.ncbi.nih.gov/refseq/H\_sapiens/mRNA\_Prot/human.protein.faa.gz
-gunzip human.protein.faa.gz
-
-formatdb -i human.protein.faa
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{4. test sequences}
-\label{examples/bioinformatics/index:test-sequences}\begin{quote}
-
-Query sequences in FASTA format can be found in original.fa
-\end{quote}
-
-
-\subsection{Code}
-\label{examples/bioinformatics/index:code}\begin{quote}
-
-The code for this example can be found {\hyperref[examples/bioinformatics/part1_code:examples-bioinformatics-part1-code]{\emph{here}}}  and
-pasted into the python command shell.
-\end{quote}
-
-
-\subsection{Step 1. Splitting up the query sequences}
-\label{examples/bioinformatics/index:step-1-splitting-up-the-query-sequences}\begin{quote}
-
-We want each of our sequences in the query file original.fa to be placed
-in a separate files named \code{XXX.segment} where \code{XXX} = 1 -\textgreater{} the number of sequences.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{current\PYGZus{}file\PYGZus{}index} \PYG{o}{=} \PYG{l+m+mi}{0}
-\PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{original.fa}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} start a new file for each accession line}
-    \PYG{k}{if} \PYG{n}{line}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{==} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZgt{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}
-        \PYG{n}{current\PYGZus{}file\PYGZus{}index} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-        \PYG{n}{current\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.segment}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{current\PYGZus{}file\PYGZus{}index}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n}{current\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-To use this in a pipeline, we only need to wrap this in a function, ``decorated'' with the Ruffus
-keyword {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{@split}}}:
-\begin{quote}
-
-\includegraphics{examples_bioinformatics_split.jpg}
-\end{quote}
-
-\begin{DUlineblock}{0em}
-\item[] This indicates that we are splitting up the input file original.fa into however many
-\code{*.segment} files as it takes.
-\item[] The pipelined function itself takes two arguments, for the input and output.
-\end{DUlineblock}
-
-We shall see later this simple {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{@split}}} decorator already gives all the benefits of:
-\begin{itemize}
-\item {} 
-Dependency checking
-
-\item {} 
-Flowchart printing
-
-\end{itemize}
-\end{quote}
-
-
-\subsection{Step 2. Run BLAST jobs in parallel}
-\label{examples/bioinformatics/index:step-2-run-blast-jobs-in-parallel}\begin{quote}
-
-Assuming that blast is already installed, sequence matches can be found with this python
-code:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{os}\PYG{o}{.}\PYG{n}{system}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{blastall \PYGZhy{}p blastp \PYGZhy{}d human.protein.faa \PYGZhy{}i 1.segment \PYGZgt{} 1.blastResult}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-To pipeline this, we need to simply wrap in a function, decorated with the \textbf{Ruffus}
-keyword {\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{@transform}}}.
-\begin{quote}
-
-\includegraphics{examples_bioinformatics_transform.jpg}
-\end{quote}
-
-This indicates that we are taking all the output files from the previous \code{splitFasta}
-operation (\code{*.segment}) and {\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{@transform}}}-ing each to a new file with the \code{.blastResult}
-suffix. Each of these transformation operations can run in parallel if specified.
-\end{quote}
-
-
-\subsection{Step 3. Combining BLAST results}
-\label{examples/bioinformatics/index:step-3-combining-blast-results}\begin{quote}
-\begin{description}
-\item[{The following python code will concatenate the results together}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{final.blast\PYGZus{}results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n}{glob}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.blastResults}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{output\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{i}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-To pipeline this, we need again to decorate with the \textbf{Ruffus} keyword {\hyperref[tutorials/new_tutorial/merge:new-manual-merge]{\emph{@merge}}}.
-\begin{quote}
-
-\includegraphics{examples_bioinformatics_merge.jpg}
-\end{quote}
-
-This indicates that we are taking all the output files from the previous \code{runBlast}
-operation (\code{*.blastResults}) and {\hyperref[tutorials/new_tutorial/merge:new-manual-merge]{\emph{@merge}}}-ing them to the new file \code{final.blast\_results}.
-\end{quote}
-
-
-\subsection{Step 4. Running the pipeline}
-\label{examples/bioinformatics/index:step-4-running-the-pipeline}\begin{quote}
-
-We can run the completed pipeline using a maximum of 4 parallel processes by calling
-{\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}} :
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Though we have only asked Ruffus to run \code{combineBlastResults}, it traces all the dependencies
-of this task and runs all the necessary parts of the pipeline.
-
-\begin{notice}{note}{Note:}
-The full code for this example can be found  {\hyperref[examples/bioinformatics/part1_code:examples-bioinformatics-part1-code]{\emph{here}}}
-suitable for pasting into the python command shell.
-\end{notice}
-
-The \code{verbose} parameter causes the following output to be printed to stderr as the pipeline
-runs:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-\PYG{g+go}{    Job = [original.fa \PYGZhy{}\PYGZgt{} *.segment] completed}
-\PYG{g+go}{Completed Task = splitFasta}
-\PYG{g+go}{    Job = [1.segment \PYGZhy{}\PYGZgt{} 1.blastResult] completed}
-\PYG{g+go}{    Job = [3.segment \PYGZhy{}\PYGZgt{} 3.blastResult] completed}
-\PYG{g+go}{    Job = [2.segment \PYGZhy{}\PYGZgt{} 2.blastResult] completed}
-\PYG{g+go}{    Job = [4.segment \PYGZhy{}\PYGZgt{} 4.blastResult] completed}
-\PYG{g+go}{Completed Task = runBlast}
-\PYG{g+go}{    Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult] \PYGZhy{}\PYGZgt{} final.blast\PYGZus{}results] completed}
-\PYG{g+go}{Completed Task = combineBlastResults}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Step 5. Testing dependencies}
-\label{examples/bioinformatics/index:step-5-testing-dependencies}\begin{quote}
-
-If we invoked {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}} again, nothing
-further would happen because the
-pipeline is now up-to-date. But what if the pipeline had not run to completion?
-
-We can simulate the failure of one of the \code{blastall} jobs by deleting its results:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{4.blastResult}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Let us use the {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout}}}
-function to print out the dependencies of the pipeline at a high \code{verbose} level which
-will show both complete and incomplete jobs:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{import} \PYG{n+nn}{sys}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which are up\PYGZhy{}to\PYGZhy{}date:}
-
-\PYG{g+go}{Task = splitFasta}
-\PYG{g+go}{    \PYGZdq{}Split sequence file into as many fragments as appropriate depending on the size of}
-\PYG{g+go}{               original\PYGZus{}fasta\PYGZdq{}}
-
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\PYG{g+go}{Tasks which will be run:}
-
-\PYG{g+go}{Task = runBlast}
-\PYG{g+go}{    \PYGZdq{}Run blast\PYGZdq{}}
-\PYG{g+go}{       Job = [4.segment}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{}4.blastResult]}
-\PYG{g+go}{         Job needs update: Missing file 4.blastResult}
-
-\PYG{g+go}{Task = combineBlastResults}
-\PYG{g+go}{    \PYGZdq{}Combine blast results\PYGZdq{}}
-\PYG{g+go}{       Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult]}
-\PYG{g+go}{             \PYGZhy{}\PYGZgt{}final.blast\PYGZus{}results]}
-\PYG{g+go}{         Job needs update: Missing file 4.blastResult}
-
-\PYG{g+go}{\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}}
-\end{Verbatim}
-\end{quote}
-
-Only the parts of the pipeline which involve the missing BLAST result will be rerun.
-We can confirm this by invoking the pipeline.
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-
-\PYG{g+go}{    Job = [1.segment \PYGZhy{}\PYGZgt{} 1.blastResult] unnecessary: already up to date}
-\PYG{g+go}{    Job = [2.segment \PYGZhy{}\PYGZgt{} 2.blastResult] unnecessary: already up to date}
-\PYG{g+go}{    Job = [3.segment \PYGZhy{}\PYGZgt{} 3.blastResult] unnecessary: already up to date}
-\PYG{g+go}{    Job = [4.segment \PYGZhy{}\PYGZgt{} 4.blastResult] completed}
-\PYG{g+go}{Completed Task = runBlast}
-\PYG{g+go}{    Job = [[1.blastResult, 2.blastResult, 3.blastResult, 4.blastResult] \PYGZhy{}\PYGZgt{} final.blast\PYGZus{}results] completed}
-\PYG{g+go}{Completed Task = combineBlastResults}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{What is next?}
-\label{examples/bioinformatics/index:what-is-next}\begin{quote}
-
-In the {\hyperref[examples/bioinformatics/part2:examples-bioinformatics-part2]{\emph{next (short) part}}},
-we shall add some standard (boilerplate) code to
-turn this BLAST pipeline into a (slightly more) useful python program.
-\end{quote}
-
-
-\section{Part 2: A slightly more practical pipeline to run blasts jobs}
-\label{examples/bioinformatics/part2:part-2-a-slightly-more-practical-pipeline-to-run-blasts-jobs}\label{examples/bioinformatics/part2::doc}\label{examples/bioinformatics/part2:examples-bioinformatics-part2}
-
-\subsection{Overview}
-\label{examples/bioinformatics/part2:overview}\begin{quote}
-
-{\hyperref[examples/bioinformatics/index:examples-bioinformatics-part1]{\emph{Previously}}}, we had built
-a simple pipeline to split up a FASTA file of query sequences so
-that these can be matched against a sequence database in parallel.
-
-We shall wrap this code so that
-\begin{itemize}
-\item {} 
-It is more robust to interruptions
-
-\item {} 
-We can specify the file names on the command line
-
-\end{itemize}
-\end{quote}
-
-
-\subsection{Step 1. Cleaning up any leftover junk from previous pipeline runs}
-\label{examples/bioinformatics/part2:step-1-cleaning-up-any-leftover-junk-from-previous-pipeline-runs}\begin{quote}
-
-\begin{DUlineblock}{0em}
-\item[] We split up each of our sequences in the query file original.fa
-into a separate files named \code{XXX.segment} where \code{XXX} is the number of sequences in
-the FASTA file.
-\end{DUlineblock}
-
-\begin{DUlineblock}{0em}
-\item[] However, if we start with 6 sequences (giving \code{1.segment} ... \code{6.segment}), and we
-then edited original.fa
-so that only 5 were left, the file \code{6.segment} would still be left
-hanging around as an unwanted, extraneous and confusing orphan.
-\end{DUlineblock}
-
-As a general rule, it is a good idea to clean up the results of a previous run in
-a \emph{@split} operation:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{original.fa}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.segment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{splitFasta} \PYG{p}{(}\PYG{n}{seqFile}\PYG{p}{,} \PYG{n}{segments}\PYG{p}{)}\PYG{p}{:}
-
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   Clean up any segment files from previous runs before creating new one}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n}{glob}\PYG{o}{.}\PYG{n}{glob}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.segment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{i}\PYG{p}{)}
-
-    \PYG{c}{\PYGZsh{} code as before...}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Step 2. Adding a ``flag'' file to mark successful completion}
-\label{examples/bioinformatics/part2:step-2-adding-a-flag-file-to-mark-successful-completion}\label{examples/bioinformatics/part2:examples-bioinformatics-part2-step2}\begin{quote}
-
-When pipelined tasks are interrupted half way through an operation, the output may
-only contain part of the results in an incomplete or inconsistent state.
-There are three general options to deal with this:
-\begin{enumerate}
-\item {} 
-Catch any interrupting conditions and delete the incomplete output
-
-\item {} 
-Tag successfully completed output with a special marker at the end of the file
-
-\item {} 
-Create an empty ``flag'' file whose only point is to signal success
-
-\end{enumerate}
-
-Option (3) is the most reliable way and involves the least amount of work in Ruffus.
-We add flag files with the suffix \code{.blastSuccess} for our parallel BLAST jobs:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{splitFasta}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.segment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.blastResult}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.blastSuccess}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{runBlast}\PYG{p}{(}\PYG{n}{seqFile}\PYG{p}{,}  \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-
-    \PYG{n}{blastResultFile}\PYG{p}{,} \PYG{n}{flag\PYGZus{}file} \PYG{o}{=} \PYG{n}{output\PYGZus{}files}
-
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   Existing code unchanged}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{os}\PYG{o}{.}\PYG{n}{system}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{blastall \PYGZhy{}p blastp \PYGZhy{}d human.protein.faa }\PYG{l+s}{\PYGZdq{}}\PYG{o}{+}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}i }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{seqFile}\PYG{p}{,} \PYG{n}{blastResultFile}\PYG{p}{)}\PYG{p}{)}
-
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   \PYGZdq{}touch\PYGZdq{} flag file to indicate success}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{flag\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Step 3. Allowing the script to be invoked on the command line}
-\label{examples/bioinformatics/part2:step-3-allowing-the-script-to-be-invoked-on-the-command-line}\begin{quote}
-
-We allow the query sequence file, as well as the sequence database and end results
-to be specified at runtime using the standard python \href{http://docs.python.org/library/optparse.html}{optparse} module.
-We find this approach to run time arguments generally useful for many Ruffus scripts.
-The full code can be {\hyperref[examples/bioinformatics/part2_code:examples-bioinformatics-part2-code]{\emph{viewed here}}} and
-downloaded from run\_parallel\_blast.py.
-
-The different options can be inspected by running the script with the \code{-{-}help} or \code{-h}
-argument.
-
-The following options are useful for developing Ruffus scripts:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
---verbose \textbar{} -v    :  Print more detailed messages for each additional verbose level.
-                     E.g. run\_parallel\_blast --verbose --verbose --verbose ... (or -vvv)
-
---jobs \textbar{} -j       :  Specifies the number of jobs (operations) to run in parallel.
-
---flowchart FILE  :  Print flowchart of the pipeline to FILE. Flowchart format
-                     depends on extension. Alternatives include (".dot", ".jpg",
-                     "*.svg", "*.png" etc). Formats other than ".dot" require
-                     the dot program to be installed (http://www.graphviz.org/).
-
---just\_print \textbar{} -n    Only print a trace (description) of the pipeline.
-                     The level of detail is set by --verbose.
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-
-\subsection{Step 4. Printing out a flowchart for the pipeline}
-\label{examples/bioinformatics/part2:step-4-printing-out-a-flowchart-for-the-pipeline}\begin{quote}
-
-The \code{-{-}flowchart} argument results in a call to \code{pipeline\_printout\_graph(...)}
-This prints out a flowchart of the pipeline. Valid formats include ''.dot'', ''.jpg'', ''.svg'', ''.png''
-but all except for the first require the \code{dot} program to be installed
-(\href{http://www.graphviz.org/}{http://www.graphviz.org/}).
-
-The state of the pipeline is reflected in the flowchart:
-
-\includegraphics{examples_bioinformatics_pipeline.jpg}
-\end{quote}
-
-
-\subsection{Step 5. Errors}
-\label{examples/bioinformatics/part2:step-5-errors}\begin{quote}
-
-Because Ruffus scripts are just normal python functions, you can debug them using
-your usual tools, or jump to the offending line(s) even when the pipeline is running in
-parallel.
-
-For example, these are the what the error messages would look like if we had mis-spelt \code{blastal}.
-In {\hyperref[examples/bioinformatics/part2_code:examples-bioinformatics-part2-code]{\emph{run\_parallel\_blast.py}}},
-python exceptions are raised if the \code{blastall} command fails.
-
-Each of the exceptions for the parallel operations are printed out with the
-offending lines (line 204), and problems (\code{blastal} not found)
-highlighted in red.
-\begin{quote}
-
-\includegraphics{examples_bioinformatics_error.png}
-\end{quote}
-\end{quote}
-
-
-\subsection{Step 6. Will it run?}
-\label{examples/bioinformatics/part2:step-6-will-it-run}\begin{quote}
-
-The full code can be {\hyperref[examples/bioinformatics/part2_code:examples-bioinformatics-part2-code]{\emph{viewed here}}} and
-downloaded from run\_parallel\_blast.py.
-\end{quote}
-
-
-\section{Ruffus code}
-\label{examples/bioinformatics/part1_code:examples-bioinformatics-part1-code}\label{examples/bioinformatics/part1_code:ruffus-code}\label{examples/bioinformatics/part1_code::doc}
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{import} \PYG{n+nn}{os}\PYG{o}{,} \PYG{n+nn}{sys}
-
-\PYG{n}{exe\PYGZus{}path} \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{split}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{abspath}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{argv}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{)}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}
-\PYG{n}{sys}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{insert}\PYG{p}{(}\PYG{l+m+mi}{0}\PYG{p}{,} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{abspath}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{exe\PYGZus{}path}\PYG{p}{,}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{..}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{..}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{..}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-
-\PYG{n}{original\PYGZus{}fasta} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{original.fa}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{database\PYGZus{}file}  \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{human.protein.faa}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n}{original\PYGZus{}fasta}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.segment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{splitFasta} \PYG{p}{(}\PYG{n}{seqFile}\PYG{p}{,} \PYG{n}{segments}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}Split sequence file into}
-\PYG{l+s+sd}{       as many fragments as appropriate}
-\PYG{l+s+sd}{       depending on the size of original\PYGZus{}fasta\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{current\PYGZus{}file\PYGZus{}index} \PYG{o}{=} \PYG{l+m+mi}{0}
-    \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{original\PYGZus{}fasta}\PYG{p}{)}\PYG{p}{:}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{c}{\PYGZsh{} start a new file for each accession line}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{k}{if} \PYG{n}{line}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{==} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZgt{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}
-            \PYG{n}{current\PYGZus{}file\PYGZus{}index} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-            \PYG{n}{current\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.segment}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{current\PYGZus{}file\PYGZus{}index}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-        \PYG{n}{current\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-
-
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{splitFasta}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.segment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.blastResult}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{runBlast}\PYG{p}{(}\PYG{n}{seqFile}\PYG{p}{,}  \PYG{n}{blastResultFile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}Run blast\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{os}\PYG{o}{.}\PYG{n}{system}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{blastall \PYGZhy{}p blastp \PYGZhy{}d }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}i }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}}
-                \PYG{p}{(}\PYG{n}{database\PYGZus{}file}\PYG{p}{,} \PYG{n}{seqFile}\PYG{p}{,} \PYG{n}{blastResultFile}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{n+nd}{@merge}\PYG{p}{(}\PYG{n}{runBlast}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{final.blast\PYGZus{}results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{combineBlastResults} \PYG{p}{(}\PYG{n}{blastResultFiles}\PYG{p}{,} \PYG{n}{combinedBlastResultFile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}Combine blast results\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{combinedBlastResultFile}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n}{blastResultFiles}\PYG{p}{:}
-        \PYG{n}{output\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{i}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Simulate interuption of the pipeline by}
-\PYG{c}{\PYGZsh{}        deleting the output of one of the BLAST jobs}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{4.blastResult}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Re\PYGZhy{}running the pipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{2}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{4}\PYG{p}{)}
-\end{Verbatim}
-
-
-\section{Ruffus code}
-\label{examples/bioinformatics/part2_code:ruffus-code}\label{examples/bioinformatics/part2_code:examples-bioinformatics-part2-code}\label{examples/bioinformatics/part2_code::doc}
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}!/usr/bin/env python}
-\PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-
-\PYG{l+s+sd}{    run\PYGZus{}parallel\PYGZus{}blast.py}
-\PYG{l+s+sd}{    [\PYGZhy{}\PYGZhy{}log\PYGZus{}file PATH]}
-\PYG{l+s+sd}{    [\PYGZhy{}\PYGZhy{}quiet]}
-
-\PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-
-\PYG{c}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   run\PYGZus{}parallel\PYGZus{}blast}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Copyright (c) 4/21/2010 Leo Goodstadt}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Permission is hereby granted, free of charge, to any person obtaining a copy}
-\PYG{c}{\PYGZsh{}   of this software and associated documentation files (the \PYGZdq{}Software\PYGZdq{}), to deal}
-\PYG{c}{\PYGZsh{}   in the Software without restriction, including without limitation the rights}
-\PYG{c}{\PYGZsh{}   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell}
-\PYG{c}{\PYGZsh{}   copies of the Software, and to permit persons to whom the Software is}
-\PYG{c}{\PYGZsh{}   furnished to do so, subject to the following conditions:}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   The above copyright notice and this permission notice shall be included in}
-\PYG{c}{\PYGZsh{}   all copies or substantial portions of the Software.}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   THE SOFTWARE IS PROVIDED \PYGZdq{}AS IS\PYGZdq{}, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR}
-\PYG{c}{\PYGZsh{}   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,}
-\PYG{c}{\PYGZsh{}   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE}
-\PYG{c}{\PYGZsh{}   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER}
-\PYG{c}{\PYGZsh{}   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,}
-\PYG{c}{\PYGZsh{}   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN}
-\PYG{c}{\PYGZsh{}   THE SOFTWARE.}
-\PYG{c}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh [...]
-\PYG{k+kn}{import} \PYG{n+nn}{os}\PYG{o}{,} \PYG{n+nn}{sys}
-\PYG{n}{exe\PYGZus{}path} \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{split}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{abspath}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{argv}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{)}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}
-\PYG{n}{sys}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{insert}\PYG{p}{(}\PYG{l+m+mi}{0}\PYG{p}{,}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{abspath}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{exe\PYGZus{}path}\PYG{p}{,}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{..}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{..}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   options}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{k+kn}{from} \PYG{n+nn}{optparse} \PYG{k+kn}{import} \PYG{n}{OptionParser}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}\PYG{o}{,} \PYG{n+nn}{os}
-
-\PYG{n}{exe\PYGZus{}path} \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{split}\PYG{p}{(}\PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{abspath}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{argv}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{)}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}
-
-
-\PYG{n}{parser} \PYG{o}{=} \PYG{n}{OptionParser}\PYG{p}{(}\PYG{n}{version}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZpc{}}\PYG{l+s}{prog 1.0}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{usage} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{    }\PYG{l+s}{\PYGZpc{}}\PYG{l+s}{prog \PYGZhy{}\PYGZhy{}input\PYGZus{}file QUERY\PYGZus{}FASTA \PYGZhy{}\PYGZhy{}database\PYGZus{}file FASTA\PYGZus{}DATABASE [more\PYGZus{}options]}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}i}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}input\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FILE}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n+nb}{type}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{string}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Name and path of query sequence file in FASTA format. }\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}d}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}database\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{database\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FILE}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n+nb}{type}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{string}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Name and path of FASTA database to search. }\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}result\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{result\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FILE}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n+nb}{type}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{string}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{default}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{final.blast\PYGZus{}results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Name and path of where the files should end up. }\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}t}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}temp\PYGZus{}directory}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{temp\PYGZus{}directory}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{PATH}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n+nb}{type}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{string}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{default}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tmp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Name and path of temporary directory where calculations }\PYG{l+s}{\PYGZdq{}}
-                            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{should take place. }\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   general options: verbosity / logging}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}v}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}verbose}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{verbose}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{action}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{count}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{default}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{,}
-                  \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Print more detailed messages for each additional verbose level.}\PYG{l+s}{\PYGZdq{}}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ E.g. run\PYGZus{}parallel\PYGZus{}blast \PYGZhy{}\PYGZhy{}verbose \PYGZhy{}\PYGZhy{}verbose \PYGZhy{}\PYGZhy{}verbose ... (or \PYGZhy{}vvv)}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   pipeline}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}j}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}jobs}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{jobs}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{default}\PYG{o}{=}\PYG{l+m+mi}{1}\PYG{p}{,}
-                  \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{jobs}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n+nb}{type}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{int}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Specifies the number of jobs (operations) to run in parallel.}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}flowchart}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{flowchart}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FILE}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n+nb}{type}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{string}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                  \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Print flowchart of the pipeline to FILE. Flowchart format }\PYG{l+s}{\PYGZdq{}}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{depends on extension. Alternatives include (}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{.dot}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{, }\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{.jpg}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{, }\PYG{l+s}{\PYGZdq{}}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{*.svg}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{, }\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{*.png}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{ etc). Formats other than }\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{.dot}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{ require }\PYG{l+s}{\PYGZdq{}}
-                       \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{the dot program to be installed (http://www.graphviz.org/).}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}option}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}just\PYGZus{}print}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{dest}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{just\PYGZus{}print}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                    \PYG{n}{action}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{store\PYGZus{}true}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{default}\PYG{o}{=}\PYG{n+nb+bp}{False}\PYG{p}{,}
-                    \PYG{n}{help}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Only print a trace (description) of the pipeline. }\PYG{l+s}{\PYGZdq{}}
-                         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ The level of detail is set by \PYGZhy{}\PYGZhy{}verbose.}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{p}{(}\PYG{n}{options}\PYG{p}{,} \PYG{n}{remaining\PYGZus{}args}\PYG{p}{)} \PYG{o}{=} \PYG{n}{parser}\PYG{o}{.}\PYG{n}{parse\PYGZus{}args}\PYG{p}{(}\PYG{p}{)}
-
-
-\PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{options}\PYG{o}{.}\PYG{n}{flowchart}\PYG{p}{:}
-    \PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{options}\PYG{o}{.}\PYG{n}{database\PYGZus{}file}\PYG{p}{:}
-        \PYG{n}{parser}\PYG{o}{.}\PYG{n}{error}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}t}\PYG{l+s}{Missing parameter \PYGZhy{}\PYGZhy{}database\PYGZus{}file FILE}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{options}\PYG{o}{.}\PYG{n}{input\PYGZus{}file}\PYG{p}{:}
-        \PYG{n}{parser}\PYG{o}{.}\PYG{n}{error}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}t}\PYG{l+s}{Missing parameter \PYGZhy{}\PYGZhy{}input\PYGZus{}file FILE}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   imports}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{subprocess}
-
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Functions}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-\PYG{k}{def} \PYG{n+nf}{run\PYGZus{}cmd}\PYG{p}{(}\PYG{n}{cmd\PYGZus{}str}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    Throw exception if run command fails}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n}{process} \PYG{o}{=} \PYG{n}{subprocess}\PYG{o}{.}\PYG{n}{Popen}\PYG{p}{(}\PYG{n}{cmd\PYGZus{}str}\PYG{p}{,} \PYG{n}{stdout} \PYG{o}{=} \PYG{n}{subprocess}\PYG{o}{.}\PYG{n}{PIPE}\PYG{p}{,}
-                                \PYG{n}{stderr} \PYG{o}{=} \PYG{n}{subprocess}\PYG{o}{.}\PYG{n}{PIPE}\PYG{p}{,} \PYG{n}{shell} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-    \PYG{n}{stdout\PYGZus{}str}\PYG{p}{,} \PYG{n}{stderr\PYGZus{}str} \PYG{o}{=} \PYG{n}{process}\PYG{o}{.}\PYG{n}{communicate}\PYG{p}{(}\PYG{p}{)}
-    \PYG{k}{if} \PYG{n}{process}\PYG{o}{.}\PYG{n}{returncode} \PYG{o}{!=} \PYG{l+m+mi}{0}\PYG{p}{:}
-        \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Failed to run }\PYG{l+s}{\PYGZsq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZsq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{Non\PYGZhy{}zero exit status }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}}
-                            \PYG{p}{(}\PYG{n}{cmd\PYGZus{}str}\PYG{p}{,} \PYG{n}{stdout\PYGZus{}str}\PYG{p}{,} \PYG{n}{stderr\PYGZus{}str}\PYG{p}{,} \PYG{n}{process}\PYG{o}{.}\PYG{n}{returncode}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Logger}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{k+kn}{import} \PYG{n+nn}{logging}
-\PYG{n}{logger} \PYG{o}{=} \PYG{n}{logging}\PYG{o}{.}\PYG{n}{getLogger}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{run\PYGZus{}parallel\PYGZus{}blast}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{} We are interesting in all messages}
-\PYG{c}{\PYGZsh{}}
-\PYG{k}{if} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{:}
-    \PYG{n}{logger}\PYG{o}{.}\PYG{n}{setLevel}\PYG{p}{(}\PYG{n}{logging}\PYG{o}{.}\PYG{n}{DEBUG}\PYG{p}{)}
-    \PYG{n}{stderrhandler} \PYG{o}{=} \PYG{n}{logging}\PYG{o}{.}\PYG{n}{StreamHandler}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{p}{)}
-    \PYG{n}{stderrhandler}\PYG{o}{.}\PYG{n}{setFormatter}\PYG{p}{(}\PYG{n}{logging}\PYG{o}{.}\PYG{n}{Formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{    }\PYG{l+s+si}{\PYGZpc{}(message)s}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-    \PYG{n}{stderrhandler}\PYG{o}{.}\PYG{n}{setLevel}\PYG{p}{(}\PYG{n}{logging}\PYG{o}{.}\PYG{n}{DEBUG}\PYG{p}{)}
-    \PYG{n}{logger}\PYG{o}{.}\PYG{n}{addHandler}\PYG{p}{(}\PYG{n}{stderrhandler}\PYG{p}{)}
-
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Pipeline tasks}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-\PYG{n}{original\PYGZus{}fasta} \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{input\PYGZus{}file}
-\PYG{n}{database\PYGZus{}file}  \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{database\PYGZus{}file}
-\PYG{n}{temp\PYGZus{}directory} \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{temp\PYGZus{}directory}
-\PYG{n}{result\PYGZus{}file}    \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{result\PYGZus{}file}
-
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{mkdir}\PYG{p}{(}\PYG{n}{temp\PYGZus{}directory}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n}{original\PYGZus{}fasta}\PYG{p}{,} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{temp\PYGZus{}directory}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.segment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{splitFasta} \PYG{p}{(}\PYG{n}{seqFile}\PYG{p}{,} \PYG{n}{segments}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}Split sequence file into}
-\PYG{l+s+sd}{       as many fragments as appropriate}
-\PYG{l+s+sd}{       depending on the size of original\PYGZus{}fasta\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   Clean up any segment files from previous runs before creating new one}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n}{segments}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{i}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{current\PYGZus{}file\PYGZus{}index} \PYG{o}{=} \PYG{l+m+mi}{0}
-    \PYG{k}{for} \PYG{n}{line} \PYG{o+ow}{in} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{original\PYGZus{}fasta}\PYG{p}{)}\PYG{p}{:}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{c}{\PYGZsh{} start a new file for each accession line}
-        \PYG{c}{\PYGZsh{}}
-        \PYG{k}{if} \PYG{n}{line}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]} \PYG{o}{==} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZgt{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{:}
-            \PYG{n}{current\PYGZus{}file\PYGZus{}index} \PYG{o}{+}\PYG{o}{=} \PYG{l+m+mi}{1}
-            \PYG{n}{file\PYGZus{}name} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.segment}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{current\PYGZus{}file\PYGZus{}index}
-            \PYG{n}{file\PYGZus{}path} \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{temp\PYGZus{}directory}\PYG{p}{,} \PYG{n}{file\PYGZus{}name}\PYG{p}{)}
-            \PYG{n}{current\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{file\PYGZus{}path}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-        \PYG{n}{current\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{line}\PYG{p}{)}
-
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{splitFasta}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.segment}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.blastResult}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.blastSuccess}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{runBlast}\PYG{p}{(}\PYG{n}{seqFile}\PYG{p}{,}  \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{blastResultFile}\PYG{p}{,} \PYG{n}{flag\PYGZus{}file} \PYG{o}{=} \PYG{n}{output\PYGZus{}files}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{run\PYGZus{}cmd}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{blastall \PYGZhy{}p blastp \PYGZhy{}d human.protein.faa \PYGZhy{}i }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{seqFile}\PYG{p}{,} \PYG{n}{blastResultFile}\PYG{p}{)}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   \PYGZdq{}touch\PYGZdq{} flag file to indicate success}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{flag\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{n+nd}{@merge}\PYG{p}{(}\PYG{n}{runBlast}\PYG{p}{,} \PYG{n}{result\PYGZus{}file}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{combineBlastResults} \PYG{p}{(}\PYG{n}{blastResult\PYGZus{}and\PYGZus{}flag\PYGZus{}Files}\PYG{p}{,} \PYG{n}{combinedBlastResultFile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}Combine blast results\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{n}{output\PYGZus{}file} \PYG{o}{=} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{combinedBlastResultFile}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{k}{for} \PYG{n}{blastResult\PYGZus{}file}\PYG{p}{,} \PYG{n}{flag\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{blastResult\PYGZus{}and\PYGZus{}flag\PYGZus{}Files}\PYG{p}{:}
-        \PYG{n}{output\PYGZus{}file}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{blastResult\PYGZus{}file}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-
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-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Print list of tasks}
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-\PYG{k}{if} \PYG{n}{options}\PYG{o}{.}\PYG{n}{just\PYGZus{}print}\PYG{p}{:}
-    \PYG{n}{pipeline\PYGZus{}printout}\PYG{p}{(}\PYG{n}{sys}\PYG{o}{.}\PYG{n}{stdout}\PYG{p}{,} \PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,} \PYG{n}{verbose}\PYG{o}{=}\PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Print flowchart}
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-\PYG{k}{elif} \PYG{n}{options}\PYG{o}{.}\PYG{n}{flowchart}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} use file extension for output format}
-    \PYG{n}{output\PYGZus{}format} \PYG{o}{=} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{splitext}\PYG{p}{(}\PYG{n}{options}\PYG{o}{.}\PYG{n}{flowchart}\PYG{p}{)}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{:}\PYG{p}{]}
-    \PYG{n}{pipeline\PYGZus{}printout\PYGZus{}graph} \PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{options}\PYG{o}{.}\PYG{n}{flowchart}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-                             \PYG{n}{output\PYGZus{}format}\PYG{p}{,}
-                             \PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,}
-                             \PYG{n}{no\PYGZus{}key\PYGZus{}legend} \PYG{o}{=} \PYG{n+nb+bp}{True}\PYG{p}{)}
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-
-\PYG{c}{\PYGZsh{}   Run Pipeline}
-
-\PYG{c}{\PYGZsh{}88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888}
-\PYG{k}{else}\PYG{p}{:}
-    \PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{combineBlastResults}\PYG{p}{]}\PYG{p}{,}  \PYG{n}{multiprocess} \PYG{o}{=} \PYG{n}{options}\PYG{o}{.}\PYG{n}{jobs}\PYG{p}{,}
-                        \PYG{n}{logger} \PYG{o}{=} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{verbose}\PYG{o}{=}\PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-\end{Verbatim}
-
-
-\section{Example code for \emph{FAQ Good practices: ``What is the best way of handling data in file pairs (or triplets etc.)?''}}
-\label{examples/paired_end_data.py:example-code-for-faq-good-practices-what-is-the-best-way-of-handling-data-in-file-pairs-or-triplets-etc}\label{examples/paired_end_data.py:faq-paired-files-code}\label{examples/paired_end_data.py::doc}\begin{quote}
-
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-collate]{\emph{@collate}}}
-
-\end{itemize}
-
-
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}!/usr/bin/env python}
-\PYG{k+kn}{import} \PYG{n+nn}{sys}\PYG{o}{,} \PYG{n+nn}{os}
-
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{ruffus.cmdline} \PYG{k+kn}{as} \PYG{n+nn}{cmdline}
-\PYG{k+kn}{from} \PYG{n+nn}{subprocess} \PYG{k+kn}{import} \PYG{n}{check\PYGZus{}call}
-
-\PYG{n}{parser} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{get\PYGZus{}argparse}\PYG{p}{(}\PYG{n}{description}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Parimala}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{s pipeline?}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}                                                                                 .}
-\PYG{c}{\PYGZsh{}   Very flexible handling of input files                                         .}
-\PYG{c}{\PYGZsh{}                                                                                 .}
-\PYG{c}{\PYGZsh{}      input files can be specified flexibly as:                                  .}
-\PYG{c}{\PYGZsh{}                 \PYGZhy{}\PYGZhy{}input a.fastq b.fastq                                         .}
-\PYG{c}{\PYGZsh{}                 \PYGZhy{}\PYGZhy{}input a.fastq \PYGZhy{}\PYGZhy{}input b.fastq                                 .}
-\PYG{c}{\PYGZsh{}                 \PYGZhy{}\PYGZhy{}input *.fastq \PYGZhy{}\PYGZhy{}input other/*.fastq                           .}
-\PYG{c}{\PYGZsh{}                 \PYGZhy{}\PYGZhy{}input \PYGZdq{}*.fastq\PYGZdq{}                                               .}
-\PYG{c}{\PYGZsh{}                                                                                 .}
-\PYG{c}{\PYGZsh{}       The last form is expanded in the script and avoids limitations on command .}
-\PYG{c}{\PYGZsh{}           line lengths                                                          .}
-\PYG{c}{\PYGZsh{}                                                                                 .}
-\PYG{n}{parser}\PYG{o}{.}\PYG{n}{add\PYGZus{}argument}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZhy{}i}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZhy{}\PYGZhy{}input}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{nargs}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{+}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{metavar}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{FILE}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{action}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{append}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} [...]
-
-\PYG{n}{options} \PYG{o}{=} \PYG{n}{parser}\PYG{o}{.}\PYG{n}{parse\PYGZus{}args}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}  standard python logger which can be synchronised across concurrent Ruffus tasks}
-\PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex} \PYG{o}{=} \PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{setup\PYGZus{}logging} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{PARIMALA}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{log\PYGZus{}file}\PYG{p}{,} \PYG{n}{options}\PYG{o}{.}\PYG{n}{verbose}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}                                                                                .}
-\PYG{c}{\PYGZsh{}   Useful code to turn input files into a flat list                             .}
-\PYG{c}{\PYGZsh{}                                                                                .}
-\PYG{k+kn}{from} \PYG{n+nn}{glob} \PYG{k+kn}{import} \PYG{n}{glob}
-\PYG{n}{original\PYGZus{}data\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{n}{fn} \PYG{k}{for} \PYG{n}{grouped} \PYG{o+ow}{in} \PYG{n}{options}\PYG{o}{.}\PYG{n}{input} \PYG{k}{for} \PYG{n}{glob\PYGZus{}spec} \PYG{o+ow}{in} \PYG{n}{grouped} \PYG{k}{for} \PYG{n}{fn} \PYG{o+ow}{in} \PYG{n}{glob}\PYG{p}{(}\PYG{n}{glob\PYGZus{}spec}\PYG{p}{)}\PYG{p}{]} \PYG{k}{if} \PYG{n}{options}\PYG{o}{.}\PYG{n}{input} \PYG{k}{else} \PYG{p}{[}\PYG{p}{]}
-\PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{original\PYGZus{}data\PYGZus{}files}\PYG{p}{:}
-    \PYG{n}{original\PYGZus{}data\PYGZus{}files} \PYG{o}{=} \PYG{p}{[}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{C1W1\PYGZus{}R1.fastq.gz}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{C1W1\PYGZus{}R2.fastq.gz}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{]}
-    \PYG{c}{\PYGZsh{}raise Exception (\PYGZdq{}No matching files specified with \PYGZhy{}\PYGZhy{}input.\PYGZdq{})}
-
-\PYG{c}{\PYGZsh{}   \PYGZlt{}\PYGZlt{}\PYGZlt{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}  pipelined functions go here}
-
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}                                                                                .}
-\PYG{c}{\PYGZsh{}   Group together file pairs                                                    .}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{n+nd}{@collate}\PYG{p}{(}\PYG{n}{original\PYGZus{}data\PYGZus{}files}\PYG{p}{,}
-            \PYG{c}{\PYGZsh{} match file name up to the \PYGZdq{}R1.fastq.gz\PYGZdq{}}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{([\PYGZca{}/]+)R[12].fastq.gz\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{c}{\PYGZsh{} Create output parameter supplied to next task}
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}1[0]\PYGZcb{}paired.R1.fastq.gz}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} paired file 1}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}1[0]\PYGZcb{}paired.R2.fastq.gz}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} paired file 2}
-            \PYG{c}{\PYGZsh{} Extra parameters for our own convenience and use}
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}1[0]\PYGZcb{}unpaired.R1.fastq.gz}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} unpaired file 1}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}1[0]\PYGZcb{}unpaired.R2.fastq.gz}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} unpaired file 2}
-            \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{trim\PYGZus{}fastq}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}paired\PYGZus{}files}\PYG{p}{,} \PYG{n}{discarded\PYGZus{}unpaired\PYGZus{}files}\PYG{p}{,} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{if} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{)} \PYG{o}{!=} \PYG{l+m+mi}{2}\PYG{p}{:}
-        \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{One of read pairs }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ missing}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,}\PYG{p}{)}\PYG{p}{)}
-    \PYG{n}{cmd} \PYG{o}{=} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{java \PYGZhy{}jar \PYGZti{}/SPRING\PYGZhy{}SUMMER\PYGZus{}2014/Softwares/Trimmomatic/Trimmomatic\PYGZhy{}0.32/trimmomatic\PYGZhy{}0.32.jar }\PYG{l+s}{\PYGZdq{}}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ PE \PYGZhy{}phred33  }\PYG{l+s}{\PYGZdq{}}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZob{}input\PYGZus{}files[0]\PYGZcb{} \PYGZob{}input\PYGZus{}files[1]\PYGZcb{} }\PYG{l+s}{\PYGZdq{}}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZob{}output\PYGZus{}paired\PYGZus{}files[0]\PYGZcb{} \PYGZob{}output\PYGZus{}paired\PYGZus{}files[1]\PYGZcb{} }\PYG{l+s}{\PYGZdq{}}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZob{}discarded\PYGZus{}unpaired\PYGZus{}files[0]\PYGZcb{} \PYGZob{}discarded\PYGZus{}unpaired\PYGZus{}files[1]\PYGZcb{} }\PYG{l+s}{\PYGZdq{}}
-           \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:50 }\PYG{l+s}{\PYGZdq{}}
-        \PYG{p}{)}
-
-    \PYG{n}{check\PYGZus{}call}\PYG{p}{(}\PYG{n}{cmd}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}
-
-    \PYG{k}{with} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{:}
-            \PYG{n}{logger}\PYG{o}{.}\PYG{n}{debug}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Hooray trim\PYGZus{}fastq worked}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{c}{\PYGZsh{}                                                                                .}
-\PYG{c}{\PYGZsh{}   Each file pair now makes its way down the rest of the pipeline as            .}
-\PYG{c}{\PYGZsh{}       a couple                                                                 .}
-\PYG{c}{\PYGZsh{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus{}\PYGZus [...]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{trim\PYGZus{}fastq}\PYG{p}{,}
-            \PYG{c}{\PYGZsh{} regular expression match on first of pe files}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{([\PYGZca{}/]+)paired.R1.fastq.gz\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}
-            \PYG{c}{\PYGZsh{} Output parameter supplied to next task}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}1[0]\PYGZcb{}.sam}\PYG{l+s}{\PYGZdq{}}
-
-           \PYG{c}{\PYGZsh{} Extra parameters for our own convenience and use}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}1[0]\PYGZcb{}.pe\PYGZus{}soap\PYGZus{}pe}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}        \PYG{c}{\PYGZsh{} soap intermediate file}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}1[0]\PYGZcb{}.pe\PYGZus{}soap\PYGZus{}se}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}        \PYG{c}{\PYGZsh{} soap intermediate file}
-            \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{align\PYGZus{}seq}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{soap\PYGZus{}pe\PYGZus{}output\PYGZus{}file}\PYG{p}{,} \PYG{n}{soap\PYGZus{}se\PYGZus{}output\PYGZus{}file}\PYG{p}{,} \PYG{n}{logger}\PYG{p}{,} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{if} \PYG{n+nb}{len}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{)} \PYG{o}{!=} \PYG{l+m+mi}{2}\PYG{p}{:}
-        \PYG{k}{raise} \PYG{n+ne}{Exception}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{One of read pairs }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ missing}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,}\PYG{p}{)}\PYG{p}{)}
-    \PYG{n}{cmd} \PYG{o}{=} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZti{}/SPRING\PYGZhy{}SUMMER\PYGZus{}2014/Softwares/soap2.21release/soap }\PYG{l+s}{\PYGZdq{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{}a \PYGZob{}input\PYGZus{}files[0]\PYGZcb{} }\PYG{l+s}{\PYGZdq{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{}b \PYGZob{}input\PYGZus{}files[1]\PYGZcb{} }\PYG{l+s}{\PYGZdq{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{}D Y55\PYGZus{}genome.fa.index* }\PYG{l+s}{\PYGZdq{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{}o \PYGZob{}soap\PYGZus{}pe\PYGZus{}output\PYGZus{}file\PYGZcb{} \PYGZhy{}2 \PYGZob{}soap\PYGZus{}se\PYGZus{}output\PYGZus{}file\PYGZcb{} \PYGZhy{}m 400 \PYGZhy{}x 600}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-    \PYG{n}{check\PYGZus{}call}\PYG{p}{(}\PYG{n}{cmd}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}
-
-
-    \PYG{c}{\PYGZsh{}Soap\PYGZus{}to\PYGZus{}sam}
-    \PYG{n}{cmd} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ perl \PYGZti{}/SPRING\PYGZhy{}SUMMER\PYGZus{}2014/Softwares/soap2sam.pl \PYGZhy{}p \PYGZob{}soap\PYGZus{}pe\PYGZus{}output\PYGZus{}file\PYGZcb{} \PYGZgt{} \PYGZob{}output\PYGZus{}file\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}
-
-    \PYG{n}{check\PYGZus{}call}\PYG{p}{(}\PYG{n}{cmd}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}\PYG{p}{)}
-
-
-    \PYG{k}{with} \PYG{n}{logger\PYGZus{}mutex}\PYG{p}{:}
-            \PYG{n}{logger}\PYG{o}{.}\PYG{n}{debug}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Hooray align\PYGZus{}seq worked}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{n}{cmdline}\PYG{o}{.}\PYG{n}{run} \PYG{p}{(}\PYG{n}{options}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\chapter{Reference:}
-\label{contents:reference}
-
-\section{Decorators}
-\label{contents:decorators}
-
-\subsection{Ruffus Decorators}
-\label{decorators/decorators:glob}\label{decorators/decorators::doc}\label{decorators/decorators:ruffus-decorators}
-
-\strong{See also:}
-
-
-{\hyperref[decorators/indicator_objects:decorators-indicator-objects]{\emph{Indicator objects}}}
-
-
-
-
-\subsubsection{\emph{Core}}
-\label{decorators/decorators:core}\label{decorators/decorators:decorators}
-\begin{tabular}{|p{0.317\linewidth}|p{0.317\linewidth}|p{0.317\linewidth}|}
-\hline
-\textbf{\relax 
-Decorator
-} & \textbf{\relax 
-Examples
-} & \textbf{\relax }\\\hline
-
-\textbf{@originate} ({\hyperref[decorators/originate:decorators-originate]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/originate:new-manual-originate]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Creates (originates) a set of starting file without dependencies from scratch  (\emph{ex nihilo}!)
-
-\item {} 
-Only called to create files which do not exist.
-
-\item {} 
-Invoked onces (a job created) per item in the \code{output\_files} list.
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/originate:decorators-originate]{\emph{@originate}}} ( \code{output\_files}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@split} ({\hyperref[decorators/split:decorators-split]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/split:new-manual-split]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Splits a single input into multiple output
-
-\item {} 
-Globs in \code{output} can specify an indeterminate number of files.
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/split:decorators-split]{\emph{@split}}} ( \code{tasks\_or\_file\_names}, \code{output\_files}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@transform} ({\hyperref[decorators/transform:decorators-transform]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/transform:new-manual-transform]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Applies the task function to transform input data to output.
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/transform_ex:decorators-transform-suffix-string]{\emph{suffix}}}\emph{(}\code{suffix\_string}\emph{)}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/transform_ex:decorators-transform-matching-regex]{\emph{regex}}}\emph{(}\code{regex\_pattern}\emph{)}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/transform_ex:decorators-transform-matching-formatter]{\emph{formatter}}}\emph{(}\code{regex\_pattern}\emph{)}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@merge} ({\hyperref[decorators/merge:decorators-merge]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/merge:new-manual-merge]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Merges multiple input files into a single output.
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} (\code{tasks\_or\_file\_names}, \code{output}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-\end{tabular}
-
-
-
-\subsubsection{\emph{Combinatorics}}
-\label{decorators/decorators:combinatorics}\label{decorators/decorators:decorators-combinatorics}
-\begin{tabular}{|p{0.317\linewidth}|p{0.317\linewidth}|p{0.317\linewidth}|}
-\hline
-\textbf{\relax 
-Decorator
-} & \textbf{\relax 
-Examples
-} & \textbf{\relax }\\\hline
-
-\textbf{@product} ({\hyperref[decorators/product:decorators-product]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/combinatorics:new-manual-product]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Generates the \textbf{product}, i.e. all vs all comparisons, between sets of input files.
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/product:decorators-product]{\emph{@product}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/product:decorators-product-matching-formatter]{\emph{formatter}}} \emph{({[}} \code{regex\_pattern} \emph{{]})} ,*{[}* \code{tasks\_or\_file\_names}, {\hyperref[decorators/product:decorators-product-matching-formatter]{\emph{formatter}}} \emph{({[}} \code{regex\_pattern} \emph{{]}), {]}}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@permutations} ({\hyperref[decorators/permutations:decorators-permutations]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/combinatorics:new-manual-permutations]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Generates the \textbf{permutations}, between all the elements of a set of \textbf{Input}
-
-\item {} 
-Analogous to the python \href{http://docs.python.org/2/library/itertools.html\#itertools.permutations}{itertools.permutations}
-
-\item {} 
-permutations(`ABCD', 2) --\textgreater{} AB AC AD BA BC BD CA CB CD DA DB DC
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/permutations:decorators-permutations]{\emph{@permutations}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/product:decorators-product-matching-formatter]{\emph{formatter}}} \emph{({[}} \code{regex\_pattern} \emph{{]})}, \code{tuple\_size}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@combinations} ({\hyperref[decorators/combinations:decorators-combinations]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinations]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Generates the \textbf{permutations}, between all the elements of a set of \textbf{Input}
-
-\item {} 
-Analogous to the python \href{http://docs.python.org/2/library/itertools.html\#itertools.permutations}{itertools.combinations}
-
-\item {} 
-combinations(`ABCD', 3) --\textgreater{} ABC ABD ACD BCD
-
-\item {} 
-Generates the \textbf{combinations}, between all the elements of a set of \textbf{Input}:
-i.e. r-length tuples of \emph{input} elements with no repeated elements (\textbf{A A})
-and where order of the tuples is irrelevant (either \textbf{A B} or  \textbf{B A}, not both).
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/permutations:decorators-permutations]{\emph{@combinations}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/product:decorators-product-matching-formatter]{\emph{formatter}}} \emph{({[}} \code{regex\_pattern} \emph{{]})}, \code{tuple\_size}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@combinations\_with\_replacement} ({\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/combinatorics:new-manual-combinations-with-replacement]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Generates the \textbf{permutations}, between all the elements of a set of \textbf{Input}
-
-\item {} 
-Analogous to the python \href{http://docs.python.org/2/library/itertools.html\#itertools.permutations}{itertools.permutations}
-
-\item {} 
-combinations(`ABCD', 3) --\textgreater{} ABC ABD ACD BCD
-
-\item {} 
-Generates the \textbf{combinations\_with\_replacement}, between all the elements of a set of \textbf{Input}:
-i.e. r-length tuples of \emph{input} elements with no repeated elements (\textbf{A A})
-and where order of the tuples is irrelevant (either \textbf{A B} or  \textbf{B A}, not both).
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/permutations:decorators-permutations]{\emph{@combinations\_with\_replacement}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/product:decorators-product-matching-formatter]{\emph{formatter}}} \emph{({[}} \code{regex\_pattern} \emph{{]})}, \code{tuple\_size}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-\end{tabular}
-
-
-
-\subsubsection{\emph{Advanced}}
-\label{decorators/decorators:advanced}\begin{quote}
-
-\begin{tabular}{|p{0.317\linewidth}|p{0.317\linewidth}|p{0.317\linewidth}|}
-\hline
-\textbf{\relax 
-Decorator
-} & \textbf{\relax 
-Examples
-} & \textbf{\relax }\\\hline
-
-\textbf{@subdivide} ({\hyperref[decorators/subdivide:decorators-subdivide]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-subdivide]{\emph{Manual}}})
-- Subdivides a set of \emph{Inputs} each further into multiple \emph{Outputs}.
-- The number of files in each \emph{Output} can be set at runtime by the use of globs.
-- \textbf{Many to Even More} operator.
-- The use of \textbf{split} is a synonym for subdivide is deprecated.
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/subdivide:decorators-subdivide-matching-regex]{\emph{regex}}}\emph{(}\code{regex\_pattern}\emph{)}, {[} {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} \textbar{} {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}}\emph{(}\code{input\_pattern}\emph{)}, {]} \code{output\_pattern}, {[}\code{extra\_ [...]
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/subdivide:decorators-subdivide-matching-formatter]{\emph{formatter}}}\emph{(}{[}\code{regex\_pattern}{]} \emph{)}, {[} {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} \textbar{} {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}}\emph{(}\code{input\_pattern}\emph{)}, {]} \code{output\_pattern}, { [...]
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@transform} ({\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/inputs:new-manual-inputs]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Infers input as well as output from regular expression substitutions
-
-\item {} 
-Useful for adding additional file dependencies
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{@transform}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/transform_ex:decorators-transform-matching-regex]{\emph{regex}}}\emph{(}\code{regex\_pattern}\emph{)}, {[} {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} \textbar{} {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}}\emph{(}\code{input\_pattern}\emph{)}, {]} \code{output\_pattern}, {[}\cod [...]
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{@transform}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/transform_ex:decorators-transform-matching-formatter]{\emph{formatter}}}\emph{(}\code{regex\_pattern}\emph{)}, {[} {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} \textbar{} {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}}\emph{(}\code{input\_pattern}\emph{)}, {]} \code{output\_pattern}, [...]
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@collate} ({\hyperref[decorators/collate:decorators-collate]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/subdivide_collate:new-manual-collate]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Groups multiple input files using regular expression matching
-
-\item {} 
-Input resulting in the same output after substitution will be collated together.
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} (\code{tasks\_or\_file\_names}, {\hyperref[decorators/collate:decorators-collate-matching-regex]{\emph{regex}}}\emph{(}\code{regex\_pattern}\emph{)}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/collate_ex:decorators-collate-ex]{\emph{@collate}}} (\code{tasks\_or\_file\_names}, {\hyperref[decorators/collate_ex:decorators-collate-ex-matching-regex]{\emph{regex}}}\emph{(}\code{regex\_pattern}\emph{)}, {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} \textbar{} {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}}\emph{(}\code{input\_pattern}\emph{)}, \code{output\_pattern}, {[}\code{extra\_paramet [...]
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} (\code{tasks\_or\_file\_names}, {\hyperref[decorators/collate:decorators-collate-matching-formatter]{\emph{formatter}}}\emph{(}\code{formatter\_pattern}\emph{)}, \code{output\_pattern}, {[}\code{extra\_parameters},...{]} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/collate_ex:decorators-collate-ex]{\emph{@collate}}} (\code{tasks\_or\_file\_names}, {\hyperref[decorators/collate_ex:decorators-collate-ex-matching-formatter]{\emph{formatter}}}\emph{(}\code{formatter\_pattern}\emph{)}, {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} \textbar{} {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}}\emph{(}\code{input\_pattern}\emph{)}, \code{output\_pattern}, {[}\code{ex [...]
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@follows} ({\hyperref[decorators/follows:decorators-follows]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-follows]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Indicates task dependency
-
-\item {} 
-optional {\hyperref[decorators/follows:decorators-follows-directory-name]{\emph{mkdir}}} prerequisite ({\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-follows-mkdir]{\emph{see Manual}}})
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}} ( \code{task1}, \code{'task2'} ))}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}} ( \code{task1},  {\hyperref[decorators/follows:decorators-follows-directory-name]{\emph{mkdir}}}( \code{'my/directory/'} ))}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@posttask} ({\hyperref[decorators/posttask:decorators-posttask]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/posttask:new-manual-posttask]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Calls function after task completes
-
-\item {} 
-Optional {\hyperref[decorators/posttask:decorators-posttask-file-name]{\emph{touch\_file}}} indicator ({\hyperref[tutorials/new_tutorial/posttask:new-manual-posttask-touch-file]{\emph{Manual}}})
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} ( \code{signal\_task\_completion\_function} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}} ({\hyperref[decorators/indicator_objects:decorators-touch-file]{\emph{touch\_file}}}( \code{'task1.completed'} ))}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@active\_if} ({\hyperref[decorators/active_if:decorators-active-if]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/active_if:new-manual-active-if]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Switches tasks on and off at run time depending on its parameters
-
-\item {} 
-Evaluated each time {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(...)}}}, {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout]{\emph{pipeline\_printout(...)}}} or {\hyperref[pipeline_functions:pipeline-functions-pipeline-printout-graph]{\emph{pipeline\_printout\_graph(...)}}} is called.
-
-\item {} 
-Dormant tasks behave as if they are up to date and have no output.
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/active_if:decorators-active-if]{\emph{@active\_if}}} ( \code{on\_or\_off1, {[}on\_or\_off2, ...{]}} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@jobs\_limit} ({\hyperref[decorators/jobs_limit:decorators-jobs-limit]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/multiprocessing:new-manual-jobs-limit]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Limits the amount of multiprocessing for the specified task
-
-\item {} 
-Ensures that fewer than N jobs for this task are run in parallel
-
-\item {} 
-Overrides \code{multiprocess} parameter in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run(...)}}}
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/jobs_limit:decorators-jobs-limit]{\emph{@jobs\_limit}}} ( \code{NUMBER\_OF\_JOBS\_RUNNING\_CONCURRENTLY} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@mkdir} ({\hyperref[decorators/mkdir:decorators-mkdir]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/mkdir:new-manual-mkdir]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Generates paths for \href{http://docs.python.org/2/library/os.html\#os.makedirs}{os.makedirs}
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/mkdir:decorators-mkdir]{\emph{@mkdir}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/mkdir:decorators-mkdir-suffix-string]{\emph{suffix}}}\emph{(}\code{suffix\_string}\emph{)}, \code{output\_pattern} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/mkdir:decorators-mkdir]{\emph{@mkdir}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/mkdir:decorators-mkdir-matching-regex]{\emph{regex}}}\emph{(}\code{regex\_pattern}\emph{)}, \code{output\_pattern} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/mkdir:decorators-mkdir]{\emph{@mkdir}}} ( \code{tasks\_or\_file\_names}, {\hyperref[decorators/mkdir:decorators-mkdir-matching-formatter]{\emph{formatter}}}\emph{(}\code{regex\_pattern}\emph{)}, \code{output\_pattern})}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@graphviz} ({\hyperref[decorators/graphviz:decorators-graphviz]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/pipeline_printout_graph:new-manual-pipeline-printout-graph]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Customise the graphic for each task in printed flowcharts
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/graphviz:decorators-graphviz]{\emph{@graphviz}}} ( \code{graphviz\_parameter = XXX}, \code{{[}graphviz\_parameter2 = YYY ...{]}})}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-\end{tabular}
-
-\end{quote}
-
-
-\subsubsection{\emph{Esoteric!}}
-\label{decorators/decorators:esoteric}\begin{quote}
-
-\begin{tabular}{|p{0.317\linewidth}|p{0.317\linewidth}|p{0.317\linewidth}|}
-\hline
-\textbf{\relax 
-Decorator
-} & \textbf{\relax 
-Examples
-} & \textbf{\relax }\\\hline
-
-\textbf{@files} ({\hyperref[decorators/files:decorators-files]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/deprecated_files:new-manual-deprecated-files]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-I/O parameters
-
-\item {} 
-skips up-to-date jobs
-
-\item {} 
-Should use {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}} etc instead
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/files:decorators-files]{\emph{@files}}}( \code{parameter\_list} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/files:decorators-files]{\emph{@files}}}( \code{parameter\_generating\_function} )}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/files:decorators-files]{\emph{@files}}} ( \code{input\_file}, \code{output\_file}, \code{other\_params}, ... )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@parallel} ({\hyperref[decorators/parallel:decorators-parallel]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/parallel:new-manual-deprecated-parallel]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-By default, does not check if jobs are up to date
-
-\item {} 
-Best used in conjuction with {\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate}}}
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/parallel:decorators-parallel]{\emph{@parallel}}} ( \code{parameter\_list} ) ({\hyperref[tutorials/new_tutorial/parallel:new-manual-deprecated-parallel]{\emph{see Manual}}})}] \leavevmode
-
-
-\end{description}
-
-\item {} \begin{description}
-\item[{{\hyperref[decorators/parallel:decorators-parallel]{\emph{@parallel}}} ( \code{parameter\_generating\_function} ) ({\hyperref[tutorials/new_tutorial/onthefly:new-manual-on-the-fly]{\emph{see Manual}}})}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\textbf{@check\_if\_uptodate} ({\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{Summary}}} / {\hyperref[tutorials/new_tutorial/check_if_uptodate:new-manual-check-if-uptodate]{\emph{Manual}}})
-\begin{itemize}
-\item {} 
-Custom function to determine if jobs need to be run
-
-\end{itemize}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate}}} ( \code{is\_task\_up\_to\_date\_function} )}] \leavevmode
-
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-
-\begin{notice}{tip}{Tip:}\begin{description}
-\item[{The use of this overly complicated function is discouraged.}] \leavevmode
-\textbf{@files\_re} ({\hyperref[decorators/files_re:decorators-files-re]{\emph{Summary}}})
-\begin{itemize}
-\item {} 
-I/O file names via regular
-expressions
-
-\item {} 
-start from lists of file names
-or \href{http://docs.python.org/library/glob.html}{\emph{glob}} results
-
-\item {} 
-skips up-to-date jobs
-
-\end{itemize}
-
-\end{description}
-\end{notice}
- & \begin{itemize}
-\item {} \begin{description}
-\item[{{\hyperref[decorators/files_re:decorators-files-re]{\emph{@files\_re}}} ( \code{tasks\_or\_file\_names}, \code{matching\_regex}, {[}\code{input\_pattern},{]} \code{output\_pattern}, \code{...} )}] \leavevmode
-\code{input\_pattern}/\code{output\_pattern} are regex patterns
-used to create input/output file names from the starting
-list of either glob\_str or file names
-
-\end{description}
-
-\end{itemize}
- & \\\hline
-\end{tabular}
-
-\end{quote}
-
-
-\strong{See also:}
-
-
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}}
-
-
-
-\index{Indicator Object (Disambiguating parameters)}
-
-\subsection{Indicator Objects}
-\label{decorators/indicator_objects:decorators-indicator-objects}\label{decorators/indicator_objects:index-0}\label{decorators/indicator_objects::doc}\label{decorators/indicator_objects:indicator-objects}\begin{quote}
-
-How \emph{ruffus} disambiguates certain parameters to decorators.
-
-They are like \href{http://docs.python.org/tutorial/controlflow.html\#keyword-arguments}{keyword arguments} in python, a little more verbose but they make the syntax much simpler.
-
-Indicator objects are also ``self-documenting'' so you can see
-exactly what is happening clearly.
-\end{quote}
-
-\index{formatter!Indicator Object (Disambiguating parameters)}\index{Indicator Object (Disambiguating parameters)!formatter}
-
-\subsubsection{\emph{formatter}}
-\label{decorators/indicator_objects:decorators-formatter}\label{decorators/indicator_objects:formatter}\label{decorators/indicator_objects:index-1}\begin{quote}
-
-\textbf{formatter({[}} \code{regex \textbar{} None} \textbf{, regex \textbar{} None...{]})}
-\begin{itemize}
-\item {} 
-The optional enclosed parameters are a python regular expression strings
-
-\item {} 
-Each regular expression matches a corresponding \emph{Input} file name string
-
-\item {} 
-\emph{formatter} parses each file name string into path and regular expression components
-
-\item {} 
-Parsing fails altogether if the regular expression is not matched
-
-\end{itemize}
-
-Path components include:
-\begin{itemize}
-\item {} 
-\code{basename}: The \href{http://docs.python.org/2/library/os.path.html\#os.path.basename}{base name} \emph{excluding} \href{http://docs.python.org/2/library/os.path.html\#os.path.splitext}{extension}, \code{"file.name"}
-
-\item {} 
-\code{ext}     : The \href{http://docs.python.org/2/library/os.path.html\#os.path.splitext}{extension}, \code{".ext"}
-
-\item {} 
-\code{path}    : The \href{http://docs.python.org/2/library/os.path.html\#os.path.dirname}{dirname}, \code{"/directory/to/a"}
-
-\item {} 
-\code{subdir}  : A list of sub-directories in the \code{path} in reverse order, \code{{[}"a", "to", "directory", "/"{]}}
-
-\item {} 
-\code{subpath} : A list of descending sub-paths in reverse order, \code{{[}"/directory/to/a", "/directory/to", "/directory", "/"{]}}
-
-\end{itemize}
-
-The replacement string refers to these components using python \href{http://docs.python.org/2/library/string.html\#string-formatting}{string.format} style curly braces. \code{\{NAME\}}
-
-We refer to an element from the Nth input string by index, for example:
-\begin{itemize}
-\item {} 
-\code{"\{ext{[}0{]}\}"}     is the extension of the first input string.
-
-\item {} 
-\code{"\{basename{[}1{]}\}"} is the basename of the second input string.
-
-\item {} 
-\code{"\{basename{[}1{]}{[}0:3{]}\}"} are the first three letters from the basename of the second input string.
-
-\end{itemize}
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}
-
-\item {} 
-{\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}}
-
-\item {} 
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}
-
-\item {} 
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}}
-
-\item {} 
-{\hyperref[decorators/product:decorators-product]{\emph{@product}}}
-
-\item {} 
-{\hyperref[decorators/permutations:decorators-permutations]{\emph{@permutations}}}
-
-\item {} 
-{\hyperref[decorators/combinations:decorators-combinations]{\emph{@combinations}}}
-
-\item {} 
-{\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}}
-
-\end{itemize}
-
-\end{description}
-
-\textbf{@transform example}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   create initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}   \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job1.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job2.b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-               \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{job3.c.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}    \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   formatter}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}file\PYGZus{}pairs}\PYG{p}{,}                               \PYG{c}{\PYGZsh{} Input}
-
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job(?P\PYGZlt{}JOBNUMBER\PYGZgt{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{d+).a.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}           \PYG{c}{\PYGZsh{} Extract job number}
-                      \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.+/job[123].b.start}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                       \PYG{c}{\PYGZsh{} Match only \PYGZdq{}b\PYGZdq{} files}
-
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}             \PYG{c}{\PYGZsh{} Replacement list}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[1]\PYGZcb{}/jobs\PYGZob{}JOBNUMBER[0]\PYGZcb{}.output.b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{first\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}parameters = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}files}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output\PYGZus{}parameters = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameters}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This produces:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+go}{input\PYGZus{}parameters  =  [\PYGZsq{}job1.a.start\PYGZsq{},}
-\PYG{g+go}{                      \PYGZsq{}job1.b.start\PYGZsq{}]}
-\PYG{g+go}{output\PYGZus{}parameters =  [\PYGZsq{}/home/lg/src/temp/jobs1.output.a.1\PYGZsq{},}
-\PYG{g+go}{                      \PYGZsq{}/home/lg/src/temp/jobs1.output.b.1\PYGZsq{}, 45]}
-
-\PYG{g+go}{input\PYGZus{}parameters  =  [\PYGZsq{}job2.a.start\PYGZsq{},}
-\PYG{g+go}{                      \PYGZsq{}job2.b.start\PYGZsq{}]}
-\PYG{g+go}{output\PYGZus{}parameters =  [\PYGZsq{}/home/lg/src/temp/jobs2.output.a.1\PYGZsq{},}
-\PYG{g+go}{                      \PYGZsq{}/home/lg/src/temp/jobs2.output.b.1\PYGZsq{}, 45]}
-\end{Verbatim}
-\end{quote}
-
-\textbf{@permutations example}:
-\begin{quote}
-
-Combinatoric decorators such as {\hyperref[decorators/product:decorators-product]{\emph{@product}}} or
-{\hyperref[decorators/permutations:decorators-permutations]{\emph{@product}}} behave much
-like nested for loops in enumerating, combining, and permutating the original sets
-of inputs.
-
-The replacement strings require an extra level of indirection to refer to
-parsed components:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   create initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{c.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy{}\PYGZhy [...]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   formatter}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@permutations}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} Input}
-
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}                                           \PYG{c}{\PYGZsh{} match input file in permutations}
-            \PYG{l+m+mi}{2}\PYG{p}{,}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/\PYGZob{}basename[0][0]\PYGZcb{}\PYGZus{}vs\PYGZus{}\PYGZob{}basename[1][0]\PYGZcb{}.product}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}    \PYG{c}{\PYGZsh{} Output Replacement string}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                                 \PYG{c}{\PYGZsh{} path for 1st set of files, 1st file name}
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                                            \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}                                           \PYG{c}{\PYGZsh{} basename for 2nd set of files, 1st file name}
-\PYG{k}{def} \PYG{n+nf}{product\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}parameter  = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}file}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output\PYGZus{}parameter = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{shared\PYGZus{}path      = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{basenames        = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{basenames}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This produces:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}b.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/src/oss/ruffus/a\PYGZus{}vs\PYGZus{}b.product}
-\PYG{g+go}{shared\PYGZus{}path      =  /home/lg/src/oss/ruffus}
-\PYG{g+go}{basenames        =  [\PYGZsq{}a\PYGZsq{}, \PYGZsq{}b\PYGZsq{}]}
-
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}c.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/src/oss/ruffus/a\PYGZus{}vs\PYGZus{}c.product}
-\PYG{g+go}{shared\PYGZus{}path      =  /home/lg/src/oss/ruffus}
-\PYG{g+go}{basenames        =  [\PYGZsq{}a\PYGZsq{}, \PYGZsq{}c\PYGZsq{}]}
-
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}a.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/src/oss/ruffus/b\PYGZus{}vs\PYGZus{}a.product}
-\PYG{g+go}{shared\PYGZus{}path      =  /home/lg/src/oss/ruffus}
-\PYG{g+go}{basenames        =  [\PYGZsq{}b\PYGZsq{}, \PYGZsq{}a\PYGZsq{}]}
-
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}c.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/src/oss/ruffus/b\PYGZus{}vs\PYGZus{}c.product}
-\PYG{g+go}{shared\PYGZus{}path      =  /home/lg/src/oss/ruffus}
-\PYG{g+go}{basenames        =  [\PYGZsq{}b\PYGZsq{}, \PYGZsq{}c\PYGZsq{}]}
-
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}c.start\PYGZsq{}, \PYGZsq{}a.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/src/oss/ruffus/c\PYGZus{}vs\PYGZus{}a.product}
-\PYG{g+go}{shared\PYGZus{}path      =  /home/lg/src/oss/ruffus}
-\PYG{g+go}{basenames        =  [\PYGZsq{}c\PYGZsq{}, \PYGZsq{}a\PYGZsq{}]}
-
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}c.start\PYGZsq{}, \PYGZsq{}b.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/src/oss/ruffus/c\PYGZus{}vs\PYGZus{}b.product}
-\PYG{g+go}{shared\PYGZus{}path      =  /home/lg/src/oss/ruffus}
-\PYG{g+go}{basenames        =  [\PYGZsq{}c\PYGZsq{}, \PYGZsq{}b\PYGZsq{}]}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\index{suffix!Indicator Object (Disambiguating parameters)}\index{Indicator Object (Disambiguating parameters)!suffix}
-
-\subsubsection{\emph{suffix}}
-\label{decorators/indicator_objects:decorators-suffix}\label{decorators/indicator_objects:index-2}\label{decorators/indicator_objects:suffix}\begin{quote}
-
-\textbf{suffix(} \code{string} \textbf{)}
-
-The enclosed parameter is a string which must match \emph{exactly} to the end
-of a file name.
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}
-
-\end{itemize}
-
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Transforms {}`{}`*.c{}`{}` to {}`{}`*.o{}`{}`::}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{previous\PYGZus{}task}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\index{regex!Indicator Object (Disambiguating parameters)}\index{Indicator Object (Disambiguating parameters)!regex}
-
-\subsubsection{\emph{regex}}
-\label{decorators/indicator_objects:decorators-regex}\label{decorators/indicator_objects:regex}\label{decorators/indicator_objects:index-3}\begin{quote}
-
-\textbf{regex(} \code{regular\_expression} \textbf{)}
-
-The enclosed parameter is a python regular expression string,
-which must be wrapped in a \code{regex} indicator object.
-
-See python \href{http://docs.python.org/library/re.html}{regular expression (re)}
-documentation for details of regular expression syntax
-
-\textbf{Used by:}
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}
-
-\item {} 
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}
-
-\item {} 
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}}
-
-\item {} 
-The deprecated {\hyperref[decorators/files_re:decorators-files-re]{\emph{@files\_re}}}
-
-\end{itemize}
-\begin{description}
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{previous\PYGZus{}task}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{.c\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\index{add\_inputs!Indicator Object (Adding additional input parameters)}\index{Indicator Object (Adding additional input parameters)!add\_inputs}
-
-\subsubsection{\emph{add\_inputs}}
-\label{decorators/indicator_objects:index-4}\label{decorators/indicator_objects:add-inputs}\label{decorators/indicator_objects:decorators-add-inputs}\begin{quote}
-
-\textbf{add\_inputs(} \code{input\_file\_pattern} \textbf{)}
-
-The enclosed parameter(s) are pattern strings or a nested structure which is added to the
-input for each job.
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{@transform}}}
-
-\item {} 
-{\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{@collate}}}
-
-\item {} 
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}
-
-\end{itemize}
-
-\end{description}
-
-\textbf{Example @transform with suffix(...)}
-\begin{quote}
-
-A common task in compiling C code is to include the corresponding header file for the source.
-To compile \code{*.c} to \code{*.o}, adding \code{*.h} and the common header \code{universal.h}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p [...]
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} do something here}
-    \PYG{k}{pass}
-\end{Verbatim}
-\end{quote}
-
-\begin{DUlineblock}{0em}
-\item[] The starting files names are \code{1.c} and \code{2.c}.
-\item[] \code{suffix(".c")} matches ''.c'' so \code{\textbackslash{}1} stands for the unmatched prefices  \code{"1"} and \code{"2"}
-\end{DUlineblock}
-\begin{description}
-\item[{This will result in the following functional calls:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-A string like \code{universal.h} in \code{add\_inputs} will added \emph{as is}.
-\code{r"\textbackslash{}1.h"}, however, performs suffix substitution, with the special form \code{r"\textbackslash{}1"} matching everything up to the suffix.
-Remember to `escape' \code{r"\textbackslash{}1"} otherwise Ruffus will complain and throw an \code{Exception} to remind you.
-The most convenient way is to use a python ``raw'' string.
-\end{quote}
-
-\textbf{Example of add\_inputs(...) with regex(...)}
-\begin{quote}
-\begin{description}
-\item[{The suffix match (\code{suffix(...)}) is exactly equivalent to the following code using regular expression (\code{regex(...)}):}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZca{}(.+)}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.c\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{ [...]
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} do something here}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{description}
-
-The \code{suffix(..)} code is much simpler but the regular expression allows more complex substitutions.
-\end{quote}
-
-\textbf{add\_inputs(...) preserves original inputs}
-\begin{quote}
-
-\code{add\_inputs} nests the the original input parameters in a list before adding additional dependencies.
-\begin{description}
-\item[{This can be seen in the following example:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}    \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{A.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}
-                \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{B.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{C.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{]}\PYG{p}{]}\PYG{p}{,}
-                \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} do something here}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\item[{This will result in the following functional calls:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{A.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}\PYG{p}{,}        \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{3.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{B.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{C.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-The original parameters are retained unchanged as the first item in a list
-\end{quote}
-\end{quote}
-
-\index{inputs!Indicator Object (Replacing input parameters)}\index{Indicator Object (Replacing input parameters)!inputs}
-
-\subsubsection{\emph{inputs}}
-\label{decorators/indicator_objects:decorators-inputs}\label{decorators/indicator_objects:index-5}\label{decorators/indicator_objects:inputs}\begin{quote}
-
-\textbf{inputs(} \code{input\_file\_pattern} \textbf{)}
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{@transform}}}
-
-\item {} 
-{\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{@collate}}}
-
-\item {} 
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}
-
-\end{itemize}
-
-\end{description}
-
-The enclosed single parameter is a pattern string or a nested structure which is
-used to construct the input for each job.
-
-If more than one argument is supplied to inputs, an exception will be raised.
-
-Use a tuple or list (as in the following example) to send multiple input arguments to each job.
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-The advanced form of {\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{@transform}}}
-
-\end{itemize}
-
-\end{description}
-
-\textbf{inputs(...) replaces original inputs}
-\begin{quote}
-
-\code{inputs(...)} allows the original input parameters to be replaced wholescale.
-\begin{description}
-\item[{This can be seen in the following example:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}    \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{A.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}
-                \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{B.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{C.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{]}\PYG{p}{]}\PYG{p}{,}
-                \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{inputs}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{docs.rst}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.pyc}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} do something here}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\item[{This will result in the following functional calls:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{docs.rst}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.pyc}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{docs.rst}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.pyc}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-In this example, the corresponding python files have been sneakily substituted
-without trace in the place of the C source files.
-\end{quote}
-\end{quote}
-
-\index{@follows!mkdir (Syntax)}\index{mkdir!@follows (Syntax)}\index{Indicator Object (Disambiguating parameters)!mkdir}
-
-\subsubsection{\emph{mkdir}}
-\label{decorators/indicator_objects:index-6}\label{decorators/indicator_objects:mkdir}\label{decorators/indicator_objects:decorators-indicator-objects-mkdir}\begin{quote}
-
-\textbf{mkdir(} \code{directory\_name1} \textbf{, {[}} \code{directory\_name2} \textbf{, ...{]} )}
-
-The enclosed parameter is a directory name or a sequence of directory names.
-These directories will be created as part of the prerequisites of running a task.
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[decorators/follows:decorators-follows]{\emph{@follows}}}
-
-\end{itemize}
-
-\item[{\textbf{Example:}}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{mkdir}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/output/directory}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\index{@posttask!touch\_file (Syntax)}\index{touch\_file!@posttask (Syntax)}\index{Indicator Object (Disambiguating parameters)!touch\_file}
-
-\subsubsection{\emph{touch\_file}}
-\label{decorators/indicator_objects:touch-file}\label{decorators/indicator_objects:index-7}\label{decorators/indicator_objects:decorators-touch-file}\begin{quote}
-
-\textbf{touch\_file(} \code{file\_name} \textbf{)}
-
-The enclosed parameter is a file name. This file will be \code{touch}-ed after a
-task is executed.
-
-This will change the date/time stamp of the \code{file\_name} to the current date/time.
-If the file does not exist, an empty file will be created.
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask}}}
-
-\end{itemize}
-
-\item[{\textbf{Example:}}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{n}{touch\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{task\PYGZus{}completed.flag}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{do\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\index{output\_from!Indicator Object (Disambiguating parameters)}\index{Indicator Object (Disambiguating parameters)!output\_from}
-
-\subsubsection{\emph{output\_from}}
-\label{decorators/indicator_objects:index-8}\label{decorators/indicator_objects:decorators-output-from}\label{decorators/indicator_objects:output-from}\begin{quote}
-
-\textbf{output\_from (} \code{file\_name\_string1} \textbf{{[},} \code{file\_name\_string1} \textbf{, ...{]} )}
-
-Indicates that any enclosed strings are not file names but refer to task functions.
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[decorators/split:decorators-split]{\emph{@split}}}
-
-\item {} 
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}
-
-\item {} 
-{\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}}
-
-\item {} 
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}}
-
-\item {} 
-{\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}
-
-\item {} 
-{\hyperref[decorators/product:decorators-product]{\emph{@product}}}
-
-\item {} 
-{\hyperref[decorators/permutations:decorators-permutations]{\emph{@permutations}}}
-
-\item {} 
-{\hyperref[decorators/combinations:decorators-combinations]{\emph{@combinations}}}
-
-\item {} 
-{\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement]{\emph{@combinations\_with\_replacement}}}
-
-\item {} 
-{\hyperref[decorators/files:decorators-files]{\emph{@files}}}
-
-\end{itemize}
-
-\item[{\textbf{Example:}}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}from}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{task1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{76}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{task2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.split}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task2}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{,} \PYG{n}{output}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-is equivalent to:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{(}\PYG{n}{task1}\PYG{p}{,} \PYG{l+m+mi}{76}\PYG{p}{,} \PYG{n}{task2}\PYG{p}{)}\PYG{p}{)}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.split}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task2}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{,} \PYG{n}{output}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\index{@files\_re!combine (Deprecated Syntax)}\index{combine!@follows (Deprecated Syntax)}\index{Indicator Object (Disambiguating parameters)!combine}
-
-\subsubsection{\emph{combine}}
-\label{decorators/indicator_objects:combine}\label{decorators/indicator_objects:decorators-combine}\label{decorators/indicator_objects:index-9}\begin{quote}
-
-\textbf{combine(} \code{arguments} \textbf{)}
-
-\begin{notice}{warning}{Warning:}
-This is deprecated syntax.
-
-Please do not use!
-
-{\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} and {\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} are more powerful
-and have straightforward syntax.
-\end{notice}
-
-Indicates that the \emph{inputs} of {\hyperref[decorators/files_re:decorators-files-re]{\emph{@files\_re}}} will be collated
-or summarised into \emph{outputs} by category. See the {\hyperref[tutorials/new_tutorial/deprecated_files_re:new-manual-files-re-combine]{\emph{Manual}}}  or
-:ref:{}` @collate \textless{}new\_manual.collate\textgreater{}{}` for examples.
-\begin{description}
-\item[{\textbf{Used by:}}] \leavevmode\begin{itemize}
-\item {} 
-{\hyperref[tutorials/new_tutorial/deprecated_files_re:new-manual-files-re-combine]{\emph{@files\_re}}}
-
-\end{itemize}
-
-\item[{\textbf{Example:}}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@files\PYGZus{}re}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{*.animals}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}                           \PYG{c}{\PYGZsh{} inputs = all *.animal files}
-            \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{mammals.([\PYGZca{}.]+)}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}                  \PYG{c}{\PYGZsh{} regular expression}
-            \PYG{n}{combine}\PYG{p}{(}\PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1/animals.in\PYGZus{}my\PYGZus{}zoo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{,}    \PYG{c}{\PYGZsh{} single output file per species}
-            \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZsq{}} \PYG{p}{)}                              \PYG{c}{\PYGZsh{} species name}
-\PYG{k}{def} \PYG{n+nf}{capture\PYGZus{}mammals}\PYG{p}{(}\PYG{n}{infiles}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{,} \PYG{n}{species}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} summarise all animals of this species}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-\setbox0\vbox{
-\begin{minipage}{0.95\linewidth}
-\textbf{Core}
-
-\medskip
-
-\phantomsection\label{decorators/originate:decorators-originate}
-\index{@originate!Syntax}\index{Syntax!@originate}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@originate}
-\label{decorators/originate:originate}\label{decorators/originate::doc}\phantomsection\label{decorators/originate:decorators-originate-output-files}\phantomsection\label{decorators/originate:output-files}
-
-\subsubsection{\emph{@originate} ( \emph{output\_files}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/originate:decorators-originate-extra-parameters}\label{decorators/originate:originate-output-files-extra-parameters}\label{decorators/originate:extra-parameters}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode\begin{itemize}
-\item {} 
-Creates (originates) a set of starting file without dependencies from scratch  (\emph{ex nihilo}!)
-
-\item {} 
-Only called to create files which do not exist.
-
-\item {} 
-Invoked onces (a job created) per item in the \code{output\_files} list.
-
-\end{itemize}
-
-\begin{notice}{note}{Note:}
-The first argument for the task function is the \emph{Output}. There is by definition no
-\emph{Input} for \code{@originate}
-\end{notice}
-
-\end{description}
-
-\textbf{Example}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{d}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{extra}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{test}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{extra}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} a, extra] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} b, extra] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} c, extra] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} d, extra] completed}
-\PYG{g+go}{Completed Task = test}
-
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} all files exist: nothing to do}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} delete \PYGZsq{}a\PYGZsq{} so that it is missing}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{import} \PYG{n+nn}{os}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} a, extra] completed}
-\PYG{g+go}{Completed Task = test}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/originate:decorators-originate-output-files}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_files}}] \leavevmode\begin{itemize}
-\item {} 
-Can be a single file name or a list of files
-
-\item {} 
-Each item in the list is treated as the \emph{Output} of a separate job
-
-\end{itemize}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/originate:decorators-originate-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-Any extra parameters are passed verbatim to the task function
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/split:decorators-split}
-\index{@split!Syntax}\index{Syntax!@split}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@split}
-\label{decorators/split::doc}\label{decorators/split:split}\phantomsection\label{decorators/split:decorators-split-tasks-or-file-names}\phantomsection\label{decorators/split:tasks-or-file-names}\phantomsection\label{decorators/split:decorators-split-extra-parameters}\phantomsection\label{decorators/split:extra-parameters}
-
-\subsubsection{\emph{@split} ( \emph{tasks\_or\_file\_names}, \emph{output\_files}, {[}\emph{extra\_parameters},...{]}  )}
-\label{decorators/split:output-files}\label{decorators/split:decorators-split-output-files}\label{decorators/split:split-tasks-or-file-names-output-files-extra-parameters}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-\begin{DUlineblock}{0em}
-\item[] Splits a single set of input files into multiple output file names, where the number of
-output files may not be known beforehand.
-\item[] Only out of date tasks (comparing input and output files) will be run
-\end{DUlineblock}
-
-\end{description}
-
-\textbf{Example}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{big\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{*.little\PYGZus{}files}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}big\PYGZus{}to\PYGZus{}small}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}file = }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{input\PYGZus{}file}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output\PYGZus{}file = }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{output\PYGZus{}file}
-\end{Verbatim}
-
-.
-\begin{quote}
-
-will produce:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-input\_file = big\_file
-output\_file = *.little\_files
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/split:decorators-split-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} 
-(Nested) list of file name strings (as in the example above).
-\begin{quote}
-
-\begin{DUlineblock}{0em}
-\item[] File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.
-\item[] E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-\end{DUlineblock}
-\end{quote}
-
-\item {} 
-Task / list of tasks.
-\begin{quote}
-
-File names are taken from the output of the specified task(s)
-\end{quote}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/split:decorators-split-output-files}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_files}}] \leavevmode
-Specifies the resulting output file name(s).
-
-\begin{DUlineblock}{0em}
-\item[] These are used \textbf{only} to check if the task is up to date.
-\item[] Normally you would use either a \href{http://docs.python.org/library/glob.html}{\emph{glob}} (e.g. \code{*.little\_files} as above) or  a ``sentinel file''
-to indicate that the task has completed successfully.
-\item[] You can of course do both:
-\end{DUlineblock}
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{big\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{sentinel.file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.little\PYGZus{}files}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{split\PYGZus{}big\PYGZus{}to\PYGZus{}small}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-\end{quote}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/split:decorators-split-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{{[}\emph{extra\_parameters, ...}{]}}] \leavevmode
-Any extra parameters are passed verbatim to the task function
-
-\end{description}
-
-\end{itemize}
-
-
-\subsection{@split with \texttt{regex(...)}, \texttt{add\_inputs} and \texttt{inputs}}
-\label{decorators/split:split-with-regex-add-inputs-and-inputs}\begin{quote}
-
-This deprecated syntax is a synonym for {\hyperref[decorators/subdivide:decorators-subdivide]{\emph{@subdivide}}}.
-\end{quote}
-\phantomsection\label{decorators/transform:decorators-transform}
-\index{@transform!Syntax}\index{Syntax!@transform}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@transform}
-\label{decorators/transform::doc}\label{decorators/transform:transform}\phantomsection\label{decorators/transform:decorators-transform-tasks-or-file-names}\phantomsection\label{decorators/transform:tasks-or-file-names}\phantomsection\label{decorators/transform:decorators-transform-extra-parameters}\phantomsection\label{decorators/transform:extra-parameters}\phantomsection\label{decorators/transform:decorators-transform-output-pattern}\phantomsection\label{decorators/transform:output-patt [...]
-
-\subsubsection{\emph{@transform} ( \emph{tasks\_or\_file\_names}, \emph{suffix}\emph{(}\emph{suffix\_string}\emph{)}\textbar{} \emph{regex}\emph{(}\emph{matching\_regex}\emph{)} \textbar{}  \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/transform:suffix-string}\label{decorators/transform:transform-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-output-pattern-extra-parameters}\label{decorators/transform:decorators-transform-suffix-string}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-Applies the task function to transform data from input to output files.
-
-Output file names are specified from {\hyperref[decorators/transform:decorators-transform-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of specified tasks, or a list of file names, or a \href{http://docs.python.org/library/glob.html}{\emph{glob}} matching pattern.
-
-String replacement occurs either through suffix matches via {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} or
-the {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} or {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicators.
-
-Only out of date tasks (comparing input and output files) will be run
-
-\end{description}
-
-\textbf{Simple Example}
-\begin{quote}
-
-Transforms \code{*.c} to \code{*.o}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-Same example with a regular expression:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{.c\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-Both result in the following function calls:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} 1.c \PYGZhy{}\PYGZgt{} 1.o}
-\PYG{c}{\PYGZsh{} 2.c \PYGZhy{}\PYGZgt{} 2.o}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\textbf{Escaping regular expression patterns}
-\begin{quote}
-
-A string like \code{universal.h} in \code{add\_inputs} will added \emph{as is}.
-\code{r"\textbackslash{}1.h"}, however, performs suffix substitution, with the special form \code{r"\textbackslash{}1"} matching everything up to the suffix.
-Remember to `escape' \code{r"\textbackslash{}1"} otherwise Ruffus will complain and throw an Exception to remind you.
-The most convenient way is to use a python ``raw'' string.
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/transform:decorators-transform-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform:decorators-transform-suffix-string}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{suffix\_string}}] \leavevmode
-must be wrapped in a {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} indicator object.
-The end of each input file name which matches \code{suffix\_string} will be replaced by \code{output\_pattern}.
-
-Input file names which do not match suffix\_string will be ignored
-
-The non-suffix part of the match can be referred to using the \code{"\textbackslash{}1"} pattern. This
-can be useful for putting the output in different directory, for example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{my\PYGZus{}path/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-This results in the following function calls:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} 1.c \PYGZhy{}\PYGZgt{} my\PYGZus{}path/1.o}
-\PYG{c}{\PYGZsh{} 2.c \PYGZhy{}\PYGZgt{} my\PYGZus{}path/2.o}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}path/1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}path/2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-For convenience and visual clarity, the  \code{"\textbackslash{}1"} can be omitted from the output parameter.
-However, the \code{"\textbackslash{}1"} is mandatory for string substitutions in additional parameters,
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Compiling } [...]
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-Results in the following function calls:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Compiling 1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{verbatim}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Compiling 2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{verbatim}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Since r''1'' is optional for the output parameter, \code{"\textbackslash{}1.o"} and \code{".o"} are equivalent.
-However, strings in other parameters which do not contain r''1'' will be included verbatim, much
-like the string \code{"verbatim"} in the above example.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform:decorators-transform-matching-regex}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_regex}}] \leavevmode
-is a python regular expression string, which must be wrapped in
-a {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicator object
-See python \href{http://docs.python.org/library/re.html}{regular expression (re)}
-documentation for details of regular expression syntax
-Each output file name is created using regular expression substitution with \code{output\_pattern}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform:decorators-transform-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform:decorators-transform-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s).
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform:decorators-transform-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{{[}\emph{extra\_parameters, ...}{]}}] \leavevmode
-Any extra parameters are passed to the task function.
-
-If \code{regex(matching\_regex)} or \code{formatter(...){}`} is used, then substitution
-is first applied to (even nested) string parameters. Other data types are passed
-verbatim.
-
-For example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*).c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-will result in the following function calls:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\end{itemize}
-
-See {\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{here}}} for more advanced uses of transform.
-\phantomsection\label{decorators/merge:decorators-merge}
-\index{@merge!Syntax}\index{Syntax!@merge}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-\phantomsection\label{decorators/merge:decorators-merge-tasks-or-file-names}\phantomsection\label{decorators/merge:tasks-or-file-names}\phantomsection\label{decorators/merge:decorators-merge-extra-parameters}\phantomsection\label{decorators/merge:extra-parameters}
-
-\subsection{@merge}
-\label{decorators/merge:decorators-merge-output-file}\label{decorators/merge:merge}\label{decorators/merge::doc}\label{decorators/merge:output-file}
-
-\subsubsection{\emph{@merge} ( \emph{tasks\_or\_file\_names}, \emph{output\_file}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/merge:merge-tasks-or-file-names-output-file-extra-parameters}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-Merges multiple input files into a single output.
-
-Only out of date tasks (comparing input and output files) will be run
-
-\end{description}
-
-\textbf{Example}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@merge}\PYG{p}{(}\PYG{n}{previous\PYGZus{}task}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{all.summary}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{summarize}\PYG{p}{(}\PYG{n}{infiles}\PYG{p}{,} \PYG{n}{summary\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/merge:decorators-merge-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/merge:decorators-merge-output-file}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_file}}] \leavevmode
-Specifies the resulting output file name(s).
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/merge:decorators-merge-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters, ...}}] \leavevmode
-Any optional extra parameters are passed verbatim to the task function
-
-\end{description}
-
-\end{itemize}
-
-See {\hyperref[decorators/collate:decorators-collate]{\emph{here}}} for more advanced uses of merging.
-\end{minipage}}
-\begin{center}\setlength{\fboxsep}{5pt}\shadowbox{\box0}\end{center}
-\setbox0\vbox{
-\begin{minipage}{0.95\linewidth}
-\textbf{For advanced users}
-
-\medskip
-
-\phantomsection\label{decorators/subdivide:decorators-subdivide}
-\index{@subdivide!Syntax}\index{Syntax!@subdivide}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@subdivide}
-\label{decorators/subdivide:subdivide}\label{decorators/subdivide::doc}\phantomsection\label{decorators/subdivide:decorators-subdivide-tasks-or-file-names}\phantomsection\label{decorators/subdivide:tasks-or-file-names}\phantomsection\label{decorators/subdivide:decorators-subdivide-extra-parameters}\phantomsection\label{decorators/subdivide:extra-parameters}\phantomsection\label{decorators/subdivide:decorators-subdivide-output-pattern}\phantomsection\label{decorators/subdivide:output-patt [...]
-
-\subsubsection{\emph{@subdivide} ( \emph{tasks\_or\_file\_names}, \emph{regex}\emph{(}\emph{matching\_regex}\emph{)} \textbar{}  \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, {[} \emph{inputs} \emph{(}\emph{input\_pattern\_or\_glob}\emph{)} \textbar{} \emph{add\_inputs} \emph{(}\emph{input\_pattern\_or\_glob}\emph{)} {]}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]}  )}
-\label{decorators/subdivide:input-pattern-or-glob}\label{decorators/subdivide:decorators-subdivide-input-pattern-or-glob}\label{decorators/subdivide:subdivide-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-inputs-input-pattern-or-glob-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-\begin{itemize}
-\item {} 
-Subdivides a set of \emph{Inputs} each further into multiple \emph{Outputs}.
-
-\item {} 
-\textbf{Many to Even More} operator
-
-\item {} 
-The number of files in each \emph{Output} can be set at runtime by the use of globs
-
-\item {} 
-Output file names are specified using the {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} or {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicators from {\hyperref[decorators/subdivide:decorators-subdivide-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of specified tasks, or a list of file names, or a \href{http://docs.python.org/library/glob.html}{\emph{glob}} matching pattern.
-
-\item {} \begin{description}
-\item[{Additional inputs or dependencies can be added dynamically to the task:}] \leavevmode
-{\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}} nests the the original input parameters in a list before adding additional dependencies.
-
-{\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} replaces the original input parameters wholescale.
-
-\end{description}
-
-\item {} 
-Only out of date tasks (comparing input and output files) will be run.
-
-\end{itemize}
-
-\begin{notice}{note}{Note:}
-The use of \textbf{split} is a synonym for subdivide is deprecated.
-\end{notice}
-\end{quote}
-
-\textbf{Example}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{random} \PYG{k+kn}{import} \PYG{n}{randint}
-\PYG{k+kn}{from} \PYG{n+nn}{random} \PYG{k+kn}{import} \PYG{n}{os}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{0.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{1.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{2.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Subdivide each of 3 start files further into [NNN1, NNN2, NNN3] number of files}
-\PYG{c}{\PYGZsh{}      where NNN1, NNN2, NNN3 are determined at run time}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@subdivide}\PYG{p}{(}\PYG{n}{create\PYGZus{}files}\PYG{p}{,} \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}.*.step1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} Output parameter: Glob matches any number of output file names}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}          \PYG{c}{\PYGZsh{} Extra parameter:  Append to this for output file names}
-\PYG{k}{def} \PYG{n+nf}{subdivide\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name\PYGZus{}root}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{c}{\PYGZsh{}   IMPORTANT: cleanup rubbish from previous run first}
-    \PYG{c}{\PYGZsh{}}
-    \PYG{k}{for} \PYG{n}{oo} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{n}{os}\PYG{o}{.}\PYG{n}{unlink}\PYG{p}{(}\PYG{n}{oo}\PYG{p}{)}
-    \PYG{c}{\PYGZsh{}   The number of output files is decided at run time}
-    \PYG{n}{number\PYGZus{}of\PYGZus{}output\PYGZus{}files} \PYG{o}{=} \PYG{n}{randint}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{,}\PYG{l+m+mi}{4}\PYG{p}{)}
-    \PYG{k}{for} \PYG{n}{ii} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{n}{number\PYGZus{}of\PYGZus{}output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n}{output\PYGZus{}file\PYGZus{}name} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}output\PYGZus{}file\PYGZus{}name\PYGZus{}root\PYGZcb{}.\PYGZob{}ii\PYGZcb{}.step1}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{format}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n+nb}{locals}\PYG{p}{(}\PYG{p}{)}\PYG{p}{)}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-            \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Each output of subdivide\PYGZus{}files results in a separate job for downstream tasks}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{subdivide\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.step1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.step2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{analyse\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file\PYGZus{}name}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{pass}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\end{Verbatim}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{)}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} 0.start] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} 1.start] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} 2.start] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}files}
-\PYG{g+go}{    Job  = [0.start \PYGZhy{}\PYGZgt{} 0.*.step1, 0] completed}
-\PYG{g+go}{    Job  = [1.start \PYGZhy{}\PYGZgt{} 1.*.step1, 1] completed}
-\PYG{g+go}{    Job  = [2.start \PYGZhy{}\PYGZgt{} 2.*.step1, 2] completed}
-\PYG{g+go}{Completed Task = subdivide\PYGZus{}files}
-\PYG{g+go}{    Job  = [0.0.step1 \PYGZhy{}\PYGZgt{} 0.0.step2] completed}
-\PYG{g+go}{    Job  = [0.1.step1 \PYGZhy{}\PYGZgt{} 0.1.step2] completed}
-\PYG{g+go}{    Job  = [0.2.step1 \PYGZhy{}\PYGZgt{} 0.2.step2] completed}
-\PYG{g+go}{    Job  = [1.0.step1 \PYGZhy{}\PYGZgt{} 1.0.step2] completed}
-\PYG{g+go}{    Job  = [1.1.step1 \PYGZhy{}\PYGZgt{} 1.1.step2] completed}
-\PYG{g+go}{    Job  = [1.2.step1 \PYGZhy{}\PYGZgt{} 1.2.step2] completed}
-\PYG{g+go}{    Job  = [1.3.step1 \PYGZhy{}\PYGZgt{} 1.3.step2] completed}
-\PYG{g+go}{    Job  = [2.0.step1 \PYGZhy{}\PYGZgt{} 2.0.step2] completed}
-\PYG{g+go}{    Job  = [2.1.step1 \PYGZhy{}\PYGZgt{} 2.1.step2] completed}
-\PYG{g+go}{    Job  = [2.2.step1 \PYGZhy{}\PYGZgt{} 2.2.step2] completed}
-\PYG{g+go}{    Job  = [2.3.step1 \PYGZhy{}\PYGZgt{} 2.3.step2] completed}
-\PYG{g+go}{Completed Task = analyse\PYGZus{}files}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/subdivide:decorators-subdivide-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/subdivide:decorators-subdivide-matching-regex}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_regex}}] \leavevmode
-is a python regular expression string, which must be wrapped in
-a {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicator object
-See python \href{http://docs.python.org/library/re.html}{regular expression (re)}
-documentation for details of regular expression syntax
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/subdivide:decorators-subdivide-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/subdivide:decorators-subdivide-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s). Can include glob patterns.
-Strings are subject to {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} or {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}}
-substitution.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/subdivide:decorators-subdivide-input-pattern-or-glob}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{input\_pattern}}] \leavevmode
-Specifies the resulting input(s) to each job.
-Must be wrapped in an {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} or an {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{inputs}}} indicator object.
-
-Can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} 
-(Nested) list of file name strings.
-
-\end{enumerate}
-
-Strings are subject to {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} or {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} substitution.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/subdivide:decorators-subdivide-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-Any extra parameters are consumed by the task function and not forwarded further down the pipeline.
-Strings are subject to {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} or {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}}
-substitution.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform_ex:decorators-transform-ex}
-\index{@transform, inputs(...)!Syntax}\index{Syntax!@transform, inputs(...)}\index{@transform, add\_inputs(...)!Syntax}\index{Syntax!@transform, add\_inputs(...)}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@transform  with \texttt{add\_inputs} and \texttt{inputs}}
-\label{decorators/transform_ex:transform-with-add-inputs-and-inputs}\label{decorators/transform_ex::doc}\phantomsection\label{decorators/transform_ex:decorators-transform-tasks-or-file-names}\phantomsection\label{decorators/transform_ex:tasks-or-file-names}\phantomsection\label{decorators/transform_ex:decorators-transform-extra-parameters}\phantomsection\label{decorators/transform_ex:extra-parameters}\phantomsection\label{decorators/transform_ex:decorators-transform-output-pattern}\phant [...]
-
-\subsubsection{\emph{@transform} ( \emph{tasks\_or\_file\_names}, \emph{suffix}\emph{(}\emph{suffix\_string}\emph{)}\textbar{} \emph{regex}\emph{(}\emph{matching\_regex}\emph{)} \textbar{}  \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, \emph{inputs} \textbar{} \emph{add\_inputs}\emph{(}\emph{input\_pattern\_or\_glob}\emph{)}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/transform_ex:suffix-string}\label{decorators/transform_ex:transform-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-inputs-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters}\label{decorators/transform_ex:decorators-transform-suffix-string}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-This variant of \code{@transform} allows additional inputs or dependencies to be added
-dynamically to the task.
-
-Output file names and strings in the extra parameters
-are determined from {\hyperref[decorators/transform_ex:decorators-transform-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of up stream tasks, or a list of file names.
-
-This variant of \code{@transform} allows input file names to be derived in the same way.
-
-String replacement occurs either through suffix matches via {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} or
-the {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} or {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicators.
-
-\code{@collate} groups together all \textbf{Input} which result in identical \textbf{Output} and \textbf{extra}
-parameters.
-
-It is a \textbf{many to fewer} operation.
-
-{\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}} nests the the original input parameters in a list before adding additional dependencies.
-
-{\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} replaces the original input parameters wholescale.
-
-Only out of date tasks (comparing input and output files) will be run
-
-\end{description}
-
-\textbf{Example of} {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}}
-\begin{quote}
-
-A common task in compiling C code is to include the corresponding header file for the source.
-\begin{description}
-\item[{To compile \code{*.c} to \code{*.o}, adding \code{*.h} and the common header \code{universal.h}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p [...]
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\item[{This will result in the following functional calls:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\textbf{Example of} {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}}
-\begin{quote}
-
-\code{inputs(...)} allows the original input parameters to be replaced wholescale.
-\begin{description}
-\item[{This can be seen in the following example:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}    \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{A.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}
-                \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{B.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{C.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{]}\PYG{p}{]}\PYG{p}{,}
-                \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{inputs}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{docs.rst}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.pyc}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\item[{This will result in the following functional calls:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{docs.rst}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.pyc}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.py}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{docs.rst}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.pyc}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/transform_ex:decorators-transform-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform_ex:decorators-transform-suffix-string}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{suffix\_string}}] \leavevmode
-must be wrapped in a {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} indicator object.
-The end of each file name which matches suffix\_string will be replaced by \emph{output\_pattern}.
-Thus:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-will result in the following function calls:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-File names which do not match suffix\_string will be ignored
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform_ex:decorators-transform-matching-regex}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_regex}}] \leavevmode
-is a python regular expression string, which must be wrapped in
-a {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicator object
-See python \href{http://docs.python.org/library/re.html}{regular expression (re)}
-documentation for details of regular expression syntax
-Each output file name is created using regular expression substitution with \code{output\_pattern}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform_ex:decorators-transform-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform_ex:decorators-transform-input-pattern-or-glob}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{input\_pattern}}] \leavevmode
-Specifies the resulting input(s) to each job.
-Must be wrapped in an {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} or an {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{inputs}}} indicator object.
-
-Can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode
-Strings will be subject to substitution.
-File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform_ex:decorators-transform-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s).
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/transform_ex:decorators-transform-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{{[}\emph{extra\_parameters, ...}{]}}] \leavevmode
-Any extra parameters are passed to the task function.
-
-If the \code{regex(...)} or \code{formatter(...)} parameter is used, then substitution
-is first applied to (even nested) string parameters. Other data types are passed
-verbatim.
-
-For example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.*).c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{n}{inputs}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{ [...]
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infiles}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{,} \PYG{n}{file\PYGZus{}name\PYGZus{}root}\PYG{p}{)}\PYG{p}{:}
-    \PYG{c}{\PYGZsh{} do something here}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-will result in the following function calls:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{universal.h}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\end{itemize}
-
-See {\hyperref[decorators/transform:decorators-transform]{\emph{here}}} for more straightforward ways to use transform.
-\phantomsection\label{decorators/collate:decorators-collate}
-\index{@collate!Syntax}\index{Syntax!@collate}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@collate}
-\label{decorators/collate::doc}\label{decorators/collate:collate}\phantomsection\label{decorators/collate:decorators-collate-tasks-or-file-names}\phantomsection\label{decorators/collate:tasks-or-file-names}\phantomsection\label{decorators/collate:decorators-collate-extra-parameters}\phantomsection\label{decorators/collate:extra-parameters}\phantomsection\label{decorators/collate:decorators-collate-output-pattern}\phantomsection\label{decorators/collate:output-pattern}\phantomsection\labe [...]
-
-\subsubsection{\emph{@collate} ( \emph{tasks\_or\_file\_names}, \emph{regex}\emph{(}\emph{matching\_regex}\emph{)} \textbar{}  \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/collate:collate-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-output-pattern-extra-parameters}\label{decorators/collate:matching-formatter}\label{decorators/collate:decorators-collate-matching-formatter}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-Groups / collates sets of input files, each into a separate summary.
-
-Only out of date tasks (comparing input and output files) will be run
-
-Output file names and strings in the extra parameters
-are determined from {\hyperref[decorators/collate:decorators-collate-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of up stream tasks, or a list of file names.
-
-String replacement occurs either through suffix matches via {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} or
-the {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} or {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicators.
-
-\code{@collate} groups together all \textbf{Input} which result in identical \textbf{Output} and \textbf{extra}
-parameters.
-
-It is a \textbf{many to fewer} operation.
-
-\item[{\textbf{Example}:}] \leavevmode
-\code{regex(r".*(\textbackslash{}..+)"), "\textbackslash{}1.summary"} creates a separate summary file for each suffix:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{animal\PYGZus{}files} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.fish}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.fish}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.mammals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{d.mammals}\PYG{l+s}{\PYGZdq{}}
-\PYG{c}{\PYGZsh{} summarise by file suffix:}
-\PYG{n+nd}{@collate}\PYG{p}{(}\PYG{n}{animal\PYGZus{}files}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.(.+)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}  \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.summary}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{summarize}\PYG{p}{(}\PYG{n}{infiles}\PYG{p}{,} \PYG{n}{summary\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\end{description}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/collate:decorators-collate-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate:decorators-collate-matching-regex}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_regex}}] \leavevmode
-is a python regular expression string, which must be wrapped in
-a {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicator object
-See python \href{http://docs.python.org/library/re.html}{regular expression (re)}
-documentation for details of regular expression syntax
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate:decorators-collate-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate:decorators-collate-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s).
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate:decorators-collate-extra-parameters}\begin{quote}
-\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-Any extra parameters are passed verbatim to the task function
-
-\end{description}
-
-\end{itemize}
-\begin{enumerate}
-\item {} 
-\emph{outputs} and optional extra parameters are passed to the functions after string
-substitution in any strings. Non-string values are passed through unchanged.
-
-\item {} 
-Each collate job consists of input files which are aggregated by string substitution
-to a single set of output / extra parameter matches
-
-\item {} 
-In the above cases, \code{a.fish} and \code{b.fish} both produce \code{fish.summary} after regular
-expression subsitution, and are collated into a single job:
-\code{{[}"a.fish", "b.fish" -\textgreater{} "fish.summary"{]}}
-while \code{c.mammals}, \code{d.mammals} both produce \code{mammals.summary}, are collated in a separate job:
-\code{{[}"c.mammals", "d.mammals" -\textgreater{} "mammals.summary"{]}}
-
-\end{enumerate}
-
-\textbf{Example2}:
-\begin{quote}
-
-Suppose we had the following files:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{cows}\PYG{o}{.}\PYG{n}{mammals}\PYG{o}{.}\PYG{n}{animal}
-\PYG{n}{horses}\PYG{o}{.}\PYG{n}{mammals}\PYG{o}{.}\PYG{n}{animal}
-\PYG{n}{sheep}\PYG{o}{.}\PYG{n}{mammals}\PYG{o}{.}\PYG{n}{animal}
-
-\PYG{n}{snake}\PYG{o}{.}\PYG{n}{reptile}\PYG{o}{.}\PYG{n}{animal}
-\PYG{n}{lizard}\PYG{o}{.}\PYG{n}{reptile}\PYG{o}{.}\PYG{n}{animal}
-\PYG{n}{crocodile}\PYG{o}{.}\PYG{n}{reptile}\PYG{o}{.}\PYG{n}{animal}
-
-\PYG{n}{pufferfish}\PYG{o}{.}\PYG{n}{fish}\PYG{o}{.}\PYG{n}{animal}
-\end{Verbatim}
-
-and we wanted to end up with three different resulting output:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-cow.mammals.animal
-horse.mammals.animal
-sheep.mammals.animal
-    -\textgreater{} mammals.results
-
-snake.reptile.animal
-lizard.reptile.animal
-crocodile.reptile.animal
-    -\textgreater{} reptile.results
-
-pufferfish.fish.animal
-    -\textgreater{} fish.results
-\end{Verbatim}
-
-This is the \code{@collate} code required:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{animals} \PYG{o}{=} \PYG{p}{[}     \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{cows.mammals.animal}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{horses.mammals.animal}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{sheep.mammals.animal}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{snake.reptile.animal}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{lizard.reptile.animal}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{crocodile.reptile.animal}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{pufferfish.fish.animal}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}
-
-\PYG{n+nd}{@collate}\PYG{p}{(}\PYG{n}{animals}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{(.+)}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.(.+)}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.animal}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}  \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{2.results}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{c}{\PYGZsh{} \PYGZbs{}1 = species [cow, horse]}
-\PYG{c}{\PYGZsh{} \PYGZbs{}2 = phylogenetics group [mammals, reptile, fish]}
-\PYG{k}{def} \PYG{n+nf}{summarize\PYGZus{}animals\PYGZus{}into\PYGZus{}groups}\PYG{p}{(}\PYG{n}{species\PYGZus{}file}\PYG{p}{,} \PYG{n}{result\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ ... more code here}\PYG{l+s}{\PYGZdq{}}
-    \PYG{k}{pass}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-See {\hyperref[decorators/merge:decorators-merge]{\emph{@merge}}} for an alternative way to summarise files.
-\phantomsection\label{decorators/collate_ex:decorators-collate-ex}
-\index{@collate (Advanced Usage)!Syntax}\index{Syntax!@collate (Advanced Usage)}\index{@collate, inputs(...)!Syntax}\index{Syntax!@collate, inputs(...)}\index{@collate, add\_inputs(...)!Syntax}\index{Syntax!@collate, add\_inputs(...)}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@collate  with \texttt{add\_inputs} and \texttt{inputs}}
-\label{decorators/collate_ex:collate-with-add-inputs-and-inputs}\label{decorators/collate_ex::doc}\phantomsection\label{decorators/collate_ex:decorators-collate-ex-tasks-or-file-names}\phantomsection\label{decorators/collate_ex:tasks-or-file-names}\phantomsection\label{decorators/collate_ex:decorators-collate-ex-extra-parameters}\phantomsection\label{decorators/collate_ex:extra-parameters}\phantomsection\label{decorators/collate_ex:decorators-collate-ex-output-pattern}\phantomsection\lab [...]
-
-\subsubsection{\emph{@collate} ( \emph{tasks\_or\_file\_names}, \emph{regex}\emph{(}\emph{matching\_regex}\emph{)} \textbar{}  \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, {[}\emph{inputs}\emph{(}\emph{input\_pattern\_or\_glob}\emph{)} \textbar{} \emph{add\_inputs}\emph{(}\emph{input\_pattern\_or\_glob}\emph{)}{]} , \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/collate_ex:decorators-collate-ex-matching-formatter}\label{decorators/collate_ex:matching-formatter}\label{decorators/collate_ex:collate-tasks-or-file-names-regex-matching-regex-formatter-matching-formatter-inputs-input-pattern-or-glob-add-inputs-input-pattern-or-glob-output-pattern-extra-parameters}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-Groups / collates sets of input files, each into a separate summary.
-
-This variant of \code{@collate} allows additional inputs or dependencies to be added
-dynamically to the task.
-
-Output file names are determined from {\hyperref[decorators/collate_ex:decorators-collate-ex-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of up stream tasks, or a list of file names.
-
-This variant of \code{@collate} allows input file names to be derived in the same way.
-
-{\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}} nests the the original input parameters in a list before adding additional dependencies.
-
-{\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} replaces the original input parameters wholescale.
-
-Only out of date tasks (comparing input and output files) will be run
-
-\end{description}
-
-\textbf{Example of} {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{add\_inputs}}}
-\begin{quote}
-
-\code{regex(r".*(\textbackslash{}..+)"), "\textbackslash{}1.summary"} creates a separate summary file for each suffix.
-But we also add date of birth data for each species:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{animal\PYGZus{}files} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tuna.fish}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{shark.fish}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog.mammals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{cat.mammals}\PYG{l+s}{\PYGZdq{}}
-\PYG{c}{\PYGZsh{} summarise by file suffix:}
-\PYG{n+nd}{@collate}\PYG{p}{(}\PYG{n}{animal\PYGZus{}files}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{.+}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.(.+)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}  \PYG{n}{add\PYGZus{}inputs}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.date\PYGZus{}of\PYGZus{}birth}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.summary}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{summarize}\PYG{p}{(}\PYG{n}{infiles}\PYG{p}{,} \PYG{n}{summary\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-This results in the following equivalent function calls:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{summarize}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{shark.fish}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fish.date\PYGZus{}of\PYGZus{}birth}\PYG{l+s}{\PYGZdq{}}   \PYG{p}{]}\PYG{p}{,}
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tuna.fish}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}   \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fish.date\PYGZus{}of\PYGZus{}birth}\PYG{l+s}{\PYGZdq{}}   \PYG{p}{]} \PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fish.summary}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{summarize}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{cat.mammals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{mammals.date\PYGZus{}of\PYGZus{}birth}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,}
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog.mammals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{mammals.date\PYGZus{}of\PYGZus{}birth}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{mammals.summary}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Example of} {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{add\_inputs}}}
-\begin{quote}
-
-using \code{inputs(...)} will summarise only the dates of births for each species group:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{animal\PYGZus{}files} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{tuna.fish}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{shark.fish}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dog.mammals}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{cat.mammals}\PYG{l+s}{\PYGZdq{}}
-\PYG{c}{\PYGZsh{} summarise by file suffix:}
-\PYG{n+nd}{@collate}\PYG{p}{(}\PYG{n}{animal\PYGZus{}files}\PYG{p}{,} \PYG{n}{regex}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{.+}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{.(.+)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}  \PYG{n}{inputs}\PYG{p}{(}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.date\PYGZus{}of\PYGZus{}birth}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.summary}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{summarize}\PYG{p}{(}\PYG{n}{infiles}\PYG{p}{,} \PYG{n}{summary\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-This results in the following equivalent function calls:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{summarize}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fish.date\PYGZus{}of\PYGZus{}birth}\PYG{l+s}{\PYGZdq{}}   \PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fish.summary}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{summarize}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{mammals.date\PYGZus{}of\PYGZus{}birth}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{mammals.summary}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/collate_ex:decorators-collate-ex-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate_ex:decorators-collate-ex-matching-regex}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_regex}}] \leavevmode
-is a python regular expression string, which must be wrapped in
-a {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicator object
-See python \href{http://docs.python.org/library/re.html}{regular expression (re)}
-documentation for details of regular expression syntax
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate_ex:decorators-collate-ex-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate_ex:decorators-collate-ex-input-pattern-or-glob}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{input\_pattern}}] \leavevmode
-Specifies the resulting input(s) to each job.
-Must be wrapped in an {\hyperref[decorators/indicator_objects:decorators-inputs]{\emph{inputs}}} or an {\hyperref[decorators/indicator_objects:decorators-add-inputs]{\emph{inputs}}} indicator object.
-
-Can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode
-Strings will be subject to substitution.
-File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate_ex:decorators-collate-ex-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s).
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/collate_ex:decorators-collate-ex-extra-parameters}\begin{quote}
-\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-Any extra parameters are passed verbatim to the task function
-
-\end{description}
-
-\end{itemize}
-\begin{enumerate}
-\item {} 
-\emph{outputs} and optional extra parameters are passed to the functions after string
-substitution in any strings. Non-string values are passed through unchanged.
-
-\item {} 
-Each collate job consists of input files which are aggregated by string substitution
-to a single set of output / extra parameter matches
-
-\end{enumerate}
-\end{quote}
-
-See {\hyperref[decorators/collate:decorators-collate]{\emph{@collate}}} for more straightforward ways to use collate.
-\phantomsection\label{decorators/graphviz:decorators-graphviz}
-\index{@graphviz!Syntax}\index{Syntax!@graphviz}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@graphviz}
-\label{decorators/graphviz::doc}\label{decorators/graphviz:graphviz}
-
-\subsubsection{\emph{@graphviz} ( \emph{graphviz\_parameters},...{]} )}
-\label{decorators/graphviz:graphviz-graphviz-parameters}\label{decorators/graphviz:decorators-graphviz-graphviz-parameters}\label{decorators/graphviz:graphviz-parameters}\begin{quote}
-
-\emph{Contributed by Sean Davis, with improved syntax via Jake Biesinger}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-Customise the graphic for each task in printed flowcharts by adding
-\href{http://www.graphviz.org/doc/info/attrs.html}{graphviz attributes},
-(URL, shape, colour) to that node.
-\begin{itemize}
-\item {} 
-This allows HTML formatting in the task names (using the \code{label} parameter as in the following example).
-HTML labels \textbf{must} be enclosed in \code{\textless{}} and \code{\textgreater{}}. E.g.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{label} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZlt{}Line \PYGZlt{}BR/\PYGZgt{} wrapped task\PYGZus{}name()\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-\item {} 
-You can also opt to keep the task name and wrap it with a prefix and suffix:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{label\PYGZus{}suffix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{??? }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{label\PYGZus{}prefix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{: What is this?}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-\item {} 
-The \code{URL} attribute allows the generation of clickable svg, and also client / server
-side image maps usable in web pages.
-See \href{http://www.graphviz.org/content/output-formats\#dimap}{Graphviz documentation}
-
-\end{itemize}
-
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@graphviz}\PYG{p}{(}\PYG{n}{URL}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{http://cnn.com}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{fillcolor} \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FFCCCC}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                \PYG{n}{color} \PYG{o}{=} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF0000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{pencolor}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF0000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{n}{fontcolor}\PYG{o}{=}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}4B6000}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-                \PYG{n}{label\PYGZus{}suffix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{???}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{label\PYGZus{}prefix} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{What is this?\PYGZlt{}BR/\PYGZgt{} }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{n}{label} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZlt{}What \PYGZlt{}FONT COLOR=}\PYG{l+s+se}{\PYGZbs{}\PYGZdq{}}\PYG{l+s}{red}\PYG{l+s+se}{\PYGZbs{}\PYGZdq{}}\PYG{l+s}{\PYGZgt{}is\PYGZlt{}/FONT\PYGZgt{}this\PYGZgt{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-                \PYG{n}{shape}\PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{component}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{height} \PYG{o}{=} \PYG{l+m+mf}{1.5}\PYG{p}{,} \PYG{n}{peripheries} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{,}
-                \PYG{n}{style}\PYG{o}{=}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{dashed}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{Up\PYGZus{}to\PYGZus{}date\PYGZus{}task2}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   Can use dictionary if you wish...}
-\PYG{n}{graphviz\PYGZus{}params} \PYG{o}{=} \PYG{p}{\PYGZob{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{URL}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{http://cnn.com}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{fontcolor}\PYG{l+s}{\PYGZdq{}}\PYG{p}{:} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{}FF00FF}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsq{}}\PYG{p}{\PYGZcb{}}
-\PYG{n+nd}{@graphviz}\PYG{p}{(}\PYG{o}{*}\PYG{o}{*}\PYG{n}{graphviz\PYGZus{}params}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{myTask}\PYG{p}{(}\PYG{n+nb}{input}\PYG{p}{,}\PYG{n}{output}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-\scalebox{0.300000}{\includegraphics{history_html_flowchart1.png}}
-
-\end{description}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/graphviz:decorators-graphviz-graphviz-parameters}\begin{itemize}
-\item {} 
-named \emph{graphviz\_parameters}
-\begin{quote}
-
-Including among others:
-\begin{itemize}
-\item {} 
-URL (e.g. \code{"www.ruffus.org.uk"})
-
-\item {} 
-fillcolor
-
-\item {} 
-color
-
-\item {} 
-pencolor
-
-\item {} 
-fontcolor
-
-\item {} 
-label\_suffix (appended to task name)
-
-\item {} 
-label\_prefix (precedes task name)
-
-\item {} 
-label (replaces task name)
-
-\item {} 
-shape (e.g. \code{"component", "box", "diamond", "doubleoctagon"} etc., see \href{http://www.graphviz.org/doc/info/shapes.html}{graphviz} )
-
-\item {} 
-height
-
-\item {} 
-peripheries (Number of borders)
-
-\item {} 
-style (e.g. \code{"solid", "wedged", "dashed"}  etc., see \href{http://www.graphviz.org/doc/info/attrs.html\#k:style}{graphviz} )
-
-\end{itemize}
-
-Colours may specified as \code{'"\#FFCCCC"', 'red', 'red:blue', '/bugn9/7'} etc. see  \href{http://www.graphviz.org/doc/info/attrs.html\#k:color}{color names} and \href{http://www.graphviz.org/doc/info/colors.html}{colour schemes}
-\end{quote}
-
-\end{itemize}
-\phantomsection\label{decorators/mkdir:decorators-mkdir}
-\index{@mkdir!Syntax}\index{Syntax!@mkdir}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\item {} 
-More on @mkdir in the \code{Ruffus} {\hyperref[tutorials/new_tutorial/mkdir:new-manual-mkdir]{\emph{Manual}}}
-
-\item {} 
-{\hyperref[decorators/follows:decorators-follows]{\emph{@follows(mkdir(``dir''))}}} specifies the creation of a \emph{single} directory as a task pre-requisite.
-
-\end{itemize}
-
-
-
-
-\subsection{@mkdir}
-\label{decorators/mkdir:mkdir}\label{decorators/mkdir::doc}\phantomsection\label{decorators/mkdir:decorators-mkdir-tasks-or-file-names}\phantomsection\label{decorators/mkdir:tasks-or-file-names}\phantomsection\label{decorators/mkdir:decorators-mkdir-output-pattern}\phantomsection\label{decorators/mkdir:output-pattern}\phantomsection\label{decorators/mkdir:decorators-mkdir-matching-regex}\phantomsection\label{decorators/mkdir:matching-regex}\phantomsection\label{decorators/mkdir:decorator [...]
-
-\subsubsection{\emph{@mkdir} ( \emph{tasks\_or\_file\_names}, \emph{suffix}\emph{(}\emph{suffix\_string}\emph{)}\textbar{} \emph{regex}\emph{(}\emph{matching\_regex}\emph{)} \textbar{}  \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, \emph{output\_pattern})}
-\label{decorators/mkdir:suffix-string}\label{decorators/mkdir:mkdir-tasks-or-file-names-suffix-suffix-string-regex-matching-regex-formatter-matching-formatter-output-pattern}\label{decorators/mkdir:decorators-mkdir-suffix-string}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-\begin{itemize}
-\item {} 
-Prepares directories to receive \emph{Output} files
-
-\item {} 
-Used when \emph{Output} path names are generated at runtime from \emph{Inputs}. \textbf{mkdir} can make sure these runtime specified paths exist.
-
-\item {} 
-Directory names are generated from \textbf{Input} using string substitution via {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter()}}},  {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix()}}} or  {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex()}}}.
-
-\item {} 
-Behaves essentially like \code{@transform} but with its own (internal) function which does the actual work of making a directory
-
-\item {} 
-Does \emph{not} invoke the host task function to which it is attached
-
-\item {} 
-Makes specified directories using \href{http://docs.python.org/2/library/os.html\#os.makedirs}{os.makedirs}
-
-\item {} 
-Multiple directories can be created in a list
-
-\end{itemize}
-
-\begin{notice}{note}{Note:}
-Only missing directories are created.
-
-In other words, the same directory can be specified multiple times safely without, for example, being recreated repeatedly.
-
-Sometimes, for pipelines with multiple entry points, this is the only way to make sure that certain working or output
-directories are always created or available \emph{before} the pipeline runs.
-\end{notice}
-\end{quote}
-
-\textbf{Simple Example}
-\begin{quote}
-
-Creates multiple directories per job to hold the results of {\hyperref[decorators/transform:decorators-transform]{\emph{@transform}}}
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,}
-             \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-
-\PYG{c}{\PYGZsh{} create files without making directories \PYGZhy{}\PYGZgt{} ERROR}
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}/processed.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}.tmp/tmp.processed.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}files\PYGZus{}without\PYGZus{}mkdir}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{} create files after making corresponding directories}
-\PYG{n+nd}{@mkdir}\PYG{p}{(} \PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}
-        \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-        \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}         \PYG{c}{\PYGZsh{} create directory}
-         \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}.tmp}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}    \PYG{c}{\PYGZsh{} create directory.tmp}
-\PYG{n+nd}{@transform}\PYG{p}{(} \PYG{n}{create\PYGZus{}initial\PYGZus{}files}\PYG{p}{,}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}/processed.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0]\PYGZcb{}/\PYGZob{}basename[0]\PYGZcb{}.tmp/tmp.processed.txt}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}files\PYGZus{}with\PYGZus{}mkdir}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{0}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{[}\PYG{l+m+mi}{1}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}files\PYGZus{}without\PYGZus{}mkdir}\PYG{p}{]}\PYG{p}{)}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}files\PYGZus{}with\PYGZus{}mkdir}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Running without making the directories first gives errors:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}files\PYGZus{}without\PYGZus{}mkdir}\PYG{p}{]}\PYG{p}{)}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} A.start] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} B.start] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}initial\PYGZus{}files}
-
-\PYG{g+go}{    Traceback (most recent call last):}
-\PYG{g+go}{      File \PYGZdq{}\PYGZlt{}stdin\PYGZgt{}\PYGZdq{}, line 1, in \PYGZlt{}module\PYGZgt{}}
-\PYG{g+go}{      File \PYGZdq{}/usr/local/lib/python2.7/dist\PYGZhy{}packages/ruffus/task.py\PYGZdq{}, line 3738, in pipeline\PYGZus{}run}
-\PYG{g+go}{        raise job\PYGZus{}errors}
-\PYG{g+go}{    ruffus.ruffus\PYGZus{}exceptions.RethrownJobError:}
-
-\PYG{g+go}{    Original exception:}
-
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{}    Exception \PYGZsh{}1}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{}      \PYGZsq{}exceptions.IOError([Errno 2] No such file or directory: \PYGZsq{}A/processed.txt\PYGZsq{})\PYGZsq{} raised in ...}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{}       Task = def create\PYGZus{}files\PYGZus{}without\PYGZus{}mkdir(...):}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{}       Job  = [A.start \PYGZhy{}\PYGZgt{} [processed.txt, tmp.processed.txt]]}
-\end{Verbatim}
-\end{quote}
-
-Running after making the directories first:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}files\PYGZus{}with\PYGZus{}mkdir}\PYG{p}{]}\PYG{p}{)}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} A.start] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} B.start] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}initial\PYGZus{}files}
-\PYG{g+go}{    Make directories [A, A.tmp] completed}
-\PYG{g+go}{    Make directories [B, B.tmp] completed}
-\PYG{g+go}{Completed Task = (mkdir 1) before create\PYGZus{}files\PYGZus{}with\PYGZus{}mkdir}
-\PYG{g+go}{    Job  = [A.start \PYGZhy{}\PYGZgt{} [processed.txt, tmp.processed.txt]] completed}
-\PYG{g+go}{    Job  = [B.start \PYGZhy{}\PYGZgt{} [processed.txt, tmp.processed.txt]] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}files\PYGZus{}with\PYGZus{}mkdir}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\textbf{Escaping regular expression patterns}
-\begin{quote}
-
-A string like \code{universal.h} in \code{add\_inputs} will added \emph{as is}.
-\code{r"\textbackslash{}1.h"}, however, performs suffix substitution, with the special form \code{r"\textbackslash{}1"} matching everything up to the suffix.
-Remember to `escape' \code{r"\textbackslash{}1"} otherwise Ruffus will complain and throw an Exception to remind you.
-The most convenient way is to use a python ``raw'' string.
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/mkdir:decorators-mkdir-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/mkdir:decorators-mkdir-suffix-string}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{suffix\_string}}] \leavevmode
-must be wrapped in a {\hyperref[decorators/indicator_objects:decorators-suffix]{\emph{suffix}}} indicator object.
-The end of each input file name which matches \code{suffix\_string} will be replaced by \code{output\_pattern}.
-
-Input file names which do not match suffix\_string will be ignored
-
-The non-suffix part of the match can be referred to using the \code{"\textbackslash{}1"} pattern. This
-can be useful for putting the output in different directory, for example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@mkdir}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{my\PYGZus{}path/}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-This results in the following function calls:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{c}{\PYGZsh{} 1.c \PYGZhy{}\PYGZgt{} my\PYGZus{}path/1.o}
-\PYG{c}{\PYGZsh{} 2.c \PYGZhy{}\PYGZgt{} my\PYGZus{}path/2.o}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}path/1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}path/2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-For convenience and visual clarity, the  \code{"\textbackslash{}1"} can be omitted from the output parameter.
-However, the \code{"\textbackslash{}1"} is mandatory for string substitutions in additional parameters,
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nd}{@mkdir}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{r\PYGZdq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Compiling }\PYG [...]
-\PYG{k}{def} \PYG{n+nf}{compile}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-Results in the following function calls:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{1.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Compiling 1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{verbatim}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n+nb}{compile}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{2.o}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Compiling 2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{verbatim}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-Since r''1'' is optional for the output parameter, \code{"\textbackslash{}1.o"} and \code{".o"} are equivalent.
-However, strings in other parameters which do not contain r''1'' will be included verbatim, much
-like the string \code{"verbatim"} in the above example.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/mkdir:decorators-mkdir-matching-regex}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_regex}}] \leavevmode
-is a python regular expression string, which must be wrapped in
-a {\hyperref[decorators/indicator_objects:decorators-regex]{\emph{regex}}} indicator object
-See python \href{http://docs.python.org/library/re.html}{regular expression (re)}
-documentation for details of regular expression syntax
-Each output file name is created using regular expression substitution with \code{output\_pattern}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/mkdir:decorators-mkdir-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/mkdir:decorators-mkdir-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s).
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/jobs_limit:decorators-jobs-limit}
-\index{@jobs\_limit!Syntax}\index{Syntax!@jobs\_limit}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@jobs\_limit}
-\label{decorators/jobs_limit:jobs-limit}\label{decorators/jobs_limit::doc}\phantomsection\label{decorators/jobs_limit:decorators-jobs-limit-maximum-num-of-jobs}\phantomsection\label{decorators/jobs_limit:maximum-num-of-jobs}
-
-\subsubsection{\emph{@jobs\_limit} ( \emph{maximum\_num\_of\_jobs}, {[} \emph{name} {]})}
-\label{decorators/jobs_limit:decorators-jobs-limit-name}\label{decorators/jobs_limit:name}\label{decorators/jobs_limit:jobs-limit-maximum-num-of-jobs-name}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-\begin{DUlineblock}{0em}
-\item[] Manages the resources available for a task.
-\item[] Limits the number of concurrent jobs which can be run in parallel for this task
-\item[] Overrides the value for \code{multiprocess} in {\hyperref[pipeline_functions:pipeline-functions-pipeline-run]{\emph{pipeline\_run}}}
-\item[] If an optional \code{name} is given, the same limit is shared across all tasks with the same @job\_limit name.
-\end{DUlineblock}
-
-\end{description}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/jobs_limit:decorators-jobs-limit-maximum-num-of-jobs}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{maximum\_num\_of\_jobs}}] \leavevmode
-The maximum number of concurrent jobs for this task. Must be an integer number
-greater than or equal to 1.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/jobs_limit:decorators-jobs-limit-name}\begin{quote}
-\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{name}}] \leavevmode
-Optional name for the limit. All tasks with the same name share the same limit if they
-are running concurrently.
-
-\end{description}
-
-\end{itemize}
-\begin{description}
-\item[{\textbf{Example}}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{} make list of 10 files}
-\PYG{n+nd}{@split}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{*.stage1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{make\PYGZus{}files}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{i} \PYG{o+ow}{in} \PYG{n+nb}{range}\PYG{p}{(}\PYG{l+m+mi}{10}\PYG{p}{)}\PYG{p}{:}
-        \PYG{n+nb}{open}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{.stage1}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{i}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n+nd}{@jobs\PYGZus{}limit}\PYG{p}{(}\PYG{l+m+mi}{2}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{make\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{stage1}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{stage1}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.stage3}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{stage2}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{stage2}\PYG{p}{]}\PYG{p}{,} \PYG{n}{multiprocess} \PYG{o}{=} \PYG{l+m+mi}{5}\PYG{p}{)}
-\end{Verbatim}
-
-will run the 10 jobs of \code{stage1} 2 at a time, while {}`{}` stage2{}`{}` will
-run 5 at a time (from \code{multiprocess = 5}):
-
-\includegraphics{jobs_limit.png}
-
-\end{description}
-\end{quote}
-\phantomsection\label{decorators/posttask:decorators-posttask}
-\index{@posttask!Syntax}\index{Syntax!@posttask}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-\phantomsection\label{decorators/posttask:decorators-posttask-function}\phantomsection\label{decorators/posttask:function}
-
-\subsection{@posttask}
-\label{decorators/posttask:decorators-posttask-file-name}\label{decorators/posttask::doc}\label{decorators/posttask:posttask}\label{decorators/posttask:file-name}
-
-\subsubsection{\emph{@posttask} (\emph{function} \textbar{} \emph{touch\_file}\emph{(}\emph{file\_name}\emph{)})}
-\label{decorators/posttask:posttask-function-touch-file-file-name}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-Calls functions to signal the completion of each task
-
-\end{description}
-
-\textbf{Example}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{k}{def} \PYG{n+nf}{task\PYGZus{}finished}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{hooray}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{n}{task\PYGZus{}finished}\PYG{p}{)}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/posttask:decorators-posttask-function}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{function}:}] \leavevmode
-\code{function()} will be called when the ruffus passes through a task.
-
-This may happen even if all of the jobs are up-to-date:
-when a upstream task is out-of-date, and the execution passes through
-this point in the pipeline
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/posttask:decorators-posttask-file-name}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{file\_name}}] \leavevmode
-Files to be \code{touch}-ed after the task is executed.
-
-This will change the date/time stamp of the \code{file\_name} to the current date/time.
-If the file does not exist, an empty file will be created.
-
-Requires to be wrapped in a {\hyperref[decorators/indicator_objects:decorators-touch-file]{\emph{touch\_file}}} indicator object:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{n+nd}{@posttask}\PYG{p}{(}\PYG{n}{touch\PYGZus{}file}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{task\PYGZus{}completed.flag}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{)}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/active_if:decorators-active-if}
-\index{@active\_if!Syntax}\index{Syntax!@active\_if}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\item {} 
-More on @active\_if in the \code{Ruffus} {\hyperref[tutorials/new_tutorial/active_if:new-manual-active-if]{\emph{Manual}}}
-
-\end{itemize}
-
-
-
-
-\subsection{@active\_if}
-\label{decorators/active_if:active-if}\label{decorators/active_if::doc}
-
-\subsubsection{\emph{@active\_if}(on\_or\_off1, {[}on\_or\_off2,...{]})}
-\label{decorators/active_if:active-if-on-or-off1-on-or-off2}\label{decorators/active_if:decorators-active-if-on-or-off}\label{decorators/active_if:on-or-off}\begin{quote}
-
-\textbf{Purpose:}
-\begin{itemize}
-\item {} 
-Switches tasks on and off at run time depending on its parameters
-
-\item {} 
-Evaluated each time \code{pipeline\_run}, \code{pipeline\_printout} or \code{pipeline\_printout\_graph} is called.
-
-\item {} 
-The Design and initial implementation were contributed by Jacob Biesinger
-
-\item {} 
-Dormant tasks behave as if they are up to date and have no output.
-
-\end{itemize}
-
-\textbf{Example}:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}1} \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2} \PYG{o}{=} \PYG{n+nb+bp}{False}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}3} \PYG{o}{=} \PYG{n+nb+bp}{True}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}    task1}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.foo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.foo}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}files}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{l+s+sd}{\PYGZdq{}\PYGZdq{}\PYGZdq{}}
-\PYG{l+s+sd}{    create\PYGZus{}files}
-\PYG{l+s+sd}{    \PYGZdq{}\PYGZdq{}\PYGZdq{}}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n}{outfile} \PYG{o}{+} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   Only runs if all three run\PYGZus{}if\PYGZus{}true conditions are met}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   @active\PYGZus{}if determines if task is active}
-\PYG{n+nd}{@active\PYGZus{}if}\PYG{p}{(}\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}1}\PYG{p}{,} \PYG{k}{lambda}\PYG{p}{:} \PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2}\PYG{p}{)}
-\PYG{n+nd}{@active\PYGZus{}if}\PYG{p}{(}\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}3}\PYG{p}{)}
-\PYG{n+nd}{@transform}\PYG{p}{(}\PYG{n}{create\PYGZus{}files}\PYG{p}{,} \PYG{n}{suffix}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.foo}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{.bar}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ \PYGZhy{}\PYGZgt{} }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{} @active\PYGZus{}if switches off task because run\PYGZus{}if\PYGZus{}true\PYGZus{}2 == False}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-
-\PYG{c}{\PYGZsh{} @active\PYGZus{}if switches on task because all run\PYGZus{}if\PYGZus{}true conditions are met}
-\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2} \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-\end{Verbatim}
-
-Produces the following output:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} @active\PYGZus{}if switches off task \PYGZdq{}this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive\PYGZdq{} because run\PYGZus{}if\PYGZus{}true\PYGZus{}2 == False}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-
-\PYG{g+go}{Task enters queue = create\PYGZus{}files}
-\PYG{g+go}{create\PYGZus{}files}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} a.foo] Missing file [a.foo]}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} b.foo] Missing file [b.foo]}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} a.foo] completed}
-\PYG{g+go}{    Job  = [None \PYGZhy{}\PYGZgt{} b.foo] completed}
-\PYG{g+go}{Completed Task = create\PYGZus{}files}
-\PYG{g+go}{Inactive Task = this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}
-
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} @active\PYGZus{}if switches on task \PYGZdq{}this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive\PYGZdq{} because all run\PYGZus{}if\PYGZus{}true conditions are met}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{run\PYGZus{}if\PYGZus{}true\PYGZus{}2} \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose} \PYG{o}{=} \PYG{l+m+mi}{3}\PYG{p}{)}
-
-\PYG{g+go}{Task enters queue = this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}
-
-\PYG{g+go}{    Job  = [a.foo \PYGZhy{}\PYGZgt{} a.bar] Missing file [a.bar]}
-\PYG{g+go}{    Job  = [b.foo \PYGZhy{}\PYGZgt{} b.bar] Missing file [b.bar]}
-\PYG{g+go}{    Job  = [a.foo \PYGZhy{}\PYGZgt{} a.bar] completed}
-\PYG{g+go}{    Job  = [b.foo \PYGZhy{}\PYGZgt{} b.bar] completed}
-\PYG{g+go}{Completed Task = this\PYGZus{}task\PYGZus{}might\PYGZus{}be\PYGZus{}inactive}
-\end{Verbatim}
-\end{quote}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/active_if:decorators-active-if-on-or-off}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{on\_or\_off}:}] \leavevmode
-A comma separated list of boolean conditions. These can be values, functions or callable objects which return True / False
-
-Multiple \code{@active\_if} decorators can be stacked for clarity as in the example
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/follows:decorators-follows}
-\index{@follows!Syntax}\index{Syntax!@follows}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\item {} 
-More on @follows in the \code{Ruffus} {\hyperref[tutorials/new_tutorial/transform_in_parallel:new-manual-follows]{\emph{Manual}}}
-
-\end{itemize}
-
-\begin{notice}{note}{Note:}
-Only missing directories are created.
-
-In other words, the same directory can be specified multiple times safely without, for example, being recreated repeatedly.
-Sometimes, for pipelines with multiple entry points, this is the only way to make sure that certain working or output
-directories are always created or available \emph{before} the pipeline runs.
-\end{notice}
-
-
-
-
-\subsection{@follows}
-\label{decorators/follows:follows}\label{decorators/follows::doc}\phantomsection\label{decorators/follows:decorators-follows-mkdir}\phantomsection\label{decorators/follows:decorators-follows-task}\phantomsection\label{decorators/follows:task}\phantomsection\label{decorators/follows:decorators-follows-task-name}\phantomsection\label{decorators/follows:task-name}
-
-\subsubsection{\emph{@follows}(\emph{task} \textbar{} \emph{``task\_name''} \textbar{} \emph{mkdir} (\emph{directory\_name}), {[}more\_tasks, ...{]})}
-\label{decorators/follows:directory-name}\label{decorators/follows:decorators-follows-directory-name}\label{decorators/follows:follows-task-task-name-mkdir-directory-name-more-tasks}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Indicates either
-\begin{itemize}
-\item {} 
-task dependencies
-
-\item {} 
-that the task requires a directory to be created first \emph{if necessary}. (Existing directories will not be overwritten)
-
-\end{itemize}
-\end{quote}
-
-\textbf{Example}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k}{def} \PYG{n+nf}{task1}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{doing task 1}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{n+nd}{@follows}\PYG{p}{(}\PYG{n}{task1}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{task2}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{doing task 2}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/follows:decorators-follows-task}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{task}:}] \leavevmode
-a list of tasks which have to be run \textbf{before} this function
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/follows:decorators-follows-task-name}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{``task\_name''}:}] \leavevmode
-Dependencies can be quoted function names.
-Quoted function names allow dependencies to be added before the function is defined.
-
-Functions in other modules need to be fully qualified.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/follows:decorators-follows-directory-name}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{directory\_name}:}] \leavevmode
-Directories which need to be created (\emph{only if they don't exist}) before
-the task is run can be specified via a \code{mkdir} indicator object:
-\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
- at follows(task\_x, mkdir("/output/directory") ...)
-def task():
-    pass
-\end{Verbatim}
-\end{quote}
-
-\end{description}
-
-\end{itemize}
-\end{minipage}}
-\begin{center}\setlength{\fboxsep}{5pt}\shadowbox{\box0}\end{center}
-\setbox0\vbox{
-\begin{minipage}{0.95\linewidth}
-\textbf{Combinatorics}
-
-\medskip
-
-\phantomsection\label{decorators/product:decorators-product}
-\index{@product!Syntax}\index{Syntax!@product}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@product}
-\label{decorators/product:product}\label{decorators/product::doc}\phantomsection\label{decorators/product:decorators-product-tasks-or-file-names}\phantomsection\label{decorators/product:tasks-or-file-names}\phantomsection\label{decorators/product:decorators-product-extra-parameters}\phantomsection\label{decorators/product:extra-parameters}\phantomsection\label{decorators/product:decorators-product-output-pattern}\phantomsection\label{decorators/product:output-pattern}
-
-\subsubsection{\emph{@product} ( \emph{tasks\_or\_file\_names}, \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, {[}\emph{tasks\_or\_file\_names}, \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, ... {]}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/product:decorators-product-matching-formatter}\label{decorators/product:product-tasks-or-file-names-formatter-matching-formatter-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters}\label{decorators/product:matching-formatter}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Generates the Cartesian \textbf{product}, i.e. all vs all comparisons, between sets of input files.
-
-The effect is analogous to the python \href{http://docs.python.org/2/library/itertools.html\#itertools.product}{itertools}
-function of the same name, i.e. a nested for loop.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{product}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} product(\PYGZsq{}ABC\PYGZsq{}, \PYGZsq{}XYZ\PYGZsq{}) \PYGZhy{}\PYGZhy{}\PYGZgt{} AX AY AZ BX BY BZ CX CY CZ}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{p}{[} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a} \PYG{o+ow}{in} \PYG{n}{product}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{ABC}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{XYZ}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}\PYG{p}{]}
-\PYG{g+go}{[\PYGZsq{}AX\PYGZsq{}, \PYGZsq{}AY\PYGZsq{}, \PYGZsq{}AZ\PYGZsq{}, \PYGZsq{}BX\PYGZsq{}, \PYGZsq{}BY\PYGZsq{}, \PYGZsq{}BZ\PYGZsq{}, \PYGZsq{}CX\PYGZsq{}, \PYGZsq{}CY\PYGZsq{}, \PYGZsq{}CZ\PYGZsq{}]}
-\end{Verbatim}
-
-Only out of date tasks (comparing input and output files) will be run
-
-Output file names and strings in the extra parameters
-are determined from {\hyperref[decorators/product:decorators-product-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of up stream tasks, or a list of file names, after string replacement via
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}}.
-
-The replacement strings require an extra level of indirection to refer to
-parsed components:
-\begin{enumerate}
-\item {} 
-The first level refers to which \emph{set} of inputs (e.g. \textbf{A,B} or \textbf{P,Q} or \textbf{X,Y}
-in the following example.)
-
-\item {} 
-The second level refers to which input file in any particular \emph{set} of inputs.
-
-\end{enumerate}
-\begin{description}
-\item[{For example, \code{'\{basename{[}2{]}{[}0{]}\}'} is the \href{http://docs.python.org/2/library/os.path.html\#os.path.basename}{basename} for}] \leavevmode\begin{itemize}
-\item {} 
-the third set of inputs (\textbf{X,Y}) and
-
-\item {} 
-the first file name string in each \textbf{Input} of that set (\code{"x.1\_start"} and \code{"y.1\_start"})
-
-\end{itemize}
-
-\end{description}
-\end{quote}
-
-\textbf{Example}:
-\begin{quote}
-
-Calculates the \textbf{@product} of \textbf{A,B} and \textbf{P,Q} and \textbf{X, Y} files
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   Three sets of initial files}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ab}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{p.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{q.start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}pq}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{x.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{x.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{y.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{y.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]} \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}xy}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @product}
-\PYG{n+nd}{@product}\PYG{p}{(}   \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ab}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 1}
-
-            \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}pq}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 2}
-
-            \PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}xy}\PYG{p}{,}        \PYG{c}{\PYGZsh{} Input}
-            \PYG{n}{formatter}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{(.start)\PYGZdl{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{p}{,}         \PYG{c}{\PYGZsh{} match input file set \PYGZsh{} 3}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}                 \PYG{c}{\PYGZsh{} Output Replacement string}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}          \PYG{c}{\PYGZsh{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}          \PYG{c}{\PYGZsh{}}
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}.product}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}     \PYG{c}{\PYGZsh{}}
-
-            \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}                 \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-
-            \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{} Extra parameter: basename for 1st set of files, 1st file name}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{}                               2nd}
-             \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}            \PYG{c}{\PYGZsh{}                               3rd}
-             \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{product\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZsh{} basenames      = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{input\PYGZus{}parameter  = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{input\PYGZus{}file}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{output\PYGZus{}parameter = }\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a p x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a p y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a q x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  a q y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}a.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/a\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b p x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b p y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}p.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}p\PYGZus{}vs\PYGZus{}y.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b q x}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}x.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}x.product}
-
-\PYG{g+go}{\PYGZsh{} basenames      =  b q y}
-\PYG{g+go}{input\PYGZus{}parameter  =  (\PYGZsq{}b.start\PYGZsq{}, \PYGZsq{}q.start\PYGZsq{}, \PYGZsq{}y.start\PYGZsq{})}
-\PYG{g+go}{output\PYGZus{}parameter =  /home/lg/temp/b\PYGZus{}vs\PYGZus{}q\PYGZus{}vs\PYGZus{}y.product}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/product:decorators-product-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/product:decorators-product-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/product:decorators-product-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s) after string
-substitution
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/product:decorators-product-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-Optional extra parameters are passed to the functions after string
-substitution
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/permutations:decorators-permutations}
-\index{@permutations!Syntax}\index{Syntax!@permutations}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@permutations}
-\label{decorators/permutations:permutations}\label{decorators/permutations::doc}\phantomsection\label{decorators/permutations:decorators-permutations-tasks-or-file-names}\phantomsection\label{decorators/permutations:tasks-or-file-names}\phantomsection\label{decorators/permutations:decorators-permutations-extra-parameters}\phantomsection\label{decorators/permutations:extra-parameters}\phantomsection\label{decorators/permutations:decorators-permutations-output-pattern}\phantomsection\label [...]
-
-\subsubsection{\emph{@permutations} ( \emph{tasks\_or\_file\_names}, \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/permutations:matching-formatter}\label{decorators/permutations:decorators-permutations-matching-formatter}\label{decorators/permutations:permutations-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Generates the \textbf{permutations}, between all the elements of a set of \textbf{Input}
-
-The effect is analogous to the python \href{http://docs.python.org/2/library/itertools.html\#itertools.permutations}{itertools}
-function of the same name:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{permutations}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} permutations(\PYGZsq{}ABCD\PYGZsq{}, 2) \PYGZhy{}\PYGZhy{}\PYGZgt{} AB AC AD BA BC BD CA CB CD DA DB DC}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{p}{[} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a} \PYG{o+ow}{in} \PYG{n}{permutations}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ABCD}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{)}\PYG{p}{]}
-\PYG{g+go}{[\PYGZsq{}AB\PYGZsq{}, \PYGZsq{}AC\PYGZsq{}, \PYGZsq{}AD\PYGZsq{}, \PYGZsq{}BA\PYGZsq{}, \PYGZsq{}BC\PYGZsq{}, \PYGZsq{}BD\PYGZsq{}, \PYGZsq{}CA\PYGZsq{}, \PYGZsq{}CB\PYGZsq{}, \PYGZsq{}CD\PYGZsq{}, \PYGZsq{}DA\PYGZsq{}, \PYGZsq{}DB\PYGZsq{}, \PYGZsq{}DC\PYGZsq{}]}
-\end{Verbatim}
-
-Only out of date tasks (comparing input and output files) will be run
-
-Output file names and strings in the extra parameters
-are determined from {\hyperref[decorators/permutations:decorators-permutations-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of up stream tasks, or a list of file names, after string replacement via
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}}.
-
-The replacement strings require an extra level of indirection to refer to
-parsed components:
-\begin{enumerate}
-\item {} 
-The first level refers to which \emph{set} in each tuple of inputs.
-
-\item {} 
-The second level refers to which input file in any particular \emph{set} of inputs.
-
-\end{enumerate}
-\end{quote}
-
-\textbf{Example}:
-\begin{quote}
-
-Calculates the \textbf{@permutations} of \textbf{A,B,C,D} files
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @permutations}
-\PYG{n+nd}{@permutations}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}      \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 2 at a time}
-              \PYG{l+m+mi}{2}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}.permutations}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}                                2nd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{permutations\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-
-\PYG{g+go}{A \PYGZhy{} B}
-\PYG{g+go}{A \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} A}
-\PYG{g+go}{B \PYGZhy{} C}
-\PYG{g+go}{B \PYGZhy{} D}
-\PYG{g+go}{C \PYGZhy{} A}
-\PYG{g+go}{C \PYGZhy{} B}
-\PYG{g+go}{C \PYGZhy{} D}
-\PYG{g+go}{D \PYGZhy{} A}
-\PYG{g+go}{D \PYGZhy{} B}
-\PYG{g+go}{D \PYGZhy{} C}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/permutations:decorators-permutations-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/permutations:decorators-permutations-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/permutations:decorators-permutations-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s) after string
-substitution
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/permutations:decorators-permutations-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-Optional extra parameters are passed to the functions after string
-substitution
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/combinations:decorators-combinations}
-\index{@combinations!Syntax}\index{Syntax!@combinations}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@combinations}
-\label{decorators/combinations:combinations}\label{decorators/combinations::doc}\phantomsection\label{decorators/combinations:decorators-combinations-tasks-or-file-names}\phantomsection\label{decorators/combinations:tasks-or-file-names}\phantomsection\label{decorators/combinations:decorators-combinations-extra-parameters}\phantomsection\label{decorators/combinations:extra-parameters}\phantomsection\label{decorators/combinations:decorators-combinations-output-pattern}\phantomsection\label [...]
-
-\subsubsection{\emph{@combinations} ( \emph{tasks\_or\_file\_names}, \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/combinations:combinations-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters}\label{decorators/combinations:matching-formatter}\label{decorators/combinations:decorators-combinations-matching-formatter}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Generates the \textbf{combinations}, between all the elements of a set of \textbf{Input} (e.g. \textbf{A B C D}),
-i.e. r-length tuples of \emph{input} elements with no repeated elements (\textbf{A A})
-and where order of the tuples is irrelevant (either \textbf{A B} or  \textbf{B A}, not both).
-
-The effect is analogous to the python \href{http://docs.python.org/2/library/itertools.html\#itertools.combinations}{itertools}
-function of the same name:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{combinations}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} combinations(\PYGZsq{}ABCD\PYGZsq{}, 3) \PYGZhy{}\PYGZhy{}\PYGZgt{} ABC ABD ACD BCD}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{p}{[} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a} \PYG{o+ow}{in} \PYG{n}{combinations}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ABCD}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{)}\PYG{p}{]}
-\PYG{g+go}{[\PYGZsq{}ABC\PYGZsq{}, \PYGZsq{}ABD\PYGZsq{}, \PYGZsq{}ACD\PYGZsq{}, \PYGZsq{}BCD\PYGZsq{}]}
-\end{Verbatim}
-
-Only out of date tasks (comparing input and output files) will be run
-
-Output file names and strings in the extra parameters
-are determined from {\hyperref[decorators/combinations:decorators-combinations-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of up stream tasks, or a list of file names, after string replacement via
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}}.
-
-The replacement strings require an extra level of indirection to refer to
-parsed components:
-\begin{enumerate}
-\item {} 
-The first level refers to which \emph{set} in each tuple of inputs.
-
-\item {} 
-The second level refers to which input file in any particular \emph{set} of inputs.
-
-\end{enumerate}
-\end{quote}
-
-\textbf{Example}:
-\begin{quote}
-
-Calculates the \textbf{@combinations} of \textbf{A,B,C,D} files
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @combinations}
-\PYG{n+nd}{@combinations}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}      \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                    \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 3 at a time}
-              \PYG{l+m+mi}{3}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][1]\PYGZcb{}.combinations}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              2nd}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[2][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              3rd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{combinations\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{A \PYGZhy{} B \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} B \PYGZhy{} D}
-\PYG{g+go}{A \PYGZhy{} C \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} C \PYGZhy{} D}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/combinations:decorators-combinations-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/combinations:decorators-combinations-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/combinations:decorators-combinations-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s) after string
-substitution
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/combinations:decorators-combinations-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-Optional extra parameters are passed to the functions after string
-substitution
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/combinations_with_replacement:decorators-combinations-with-replacement}
-\index{@combinations\_with\_replacement!Syntax}\index{Syntax!@combinations\_with\_replacement}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@combinations\_with\_replacement}
-\label{decorators/combinations_with_replacement::doc}\label{decorators/combinations_with_replacement:combinations-with-replacement}\phantomsection\label{decorators/combinations_with_replacement:decorators-combinations-with-replacement-tasks-or-file-names}\phantomsection\label{decorators/combinations_with_replacement:tasks-or-file-names}\phantomsection\label{decorators/combinations_with_replacement:decorators-combinations-with-replacement-extra-parameters}\phantomsection\label{decorators/ [...]
-
-\subsubsection{\emph{@combinations\_with\_replacement} ( \emph{tasks\_or\_file\_names}, \emph{formatter}\emph{(}\emph{matching\_formatter}\emph{)}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]} )}
-\label{decorators/combinations_with_replacement:combinations-with-replacement-tasks-or-file-names-formatter-matching-formatter-output-pattern-extra-parameters}\label{decorators/combinations_with_replacement:matching-formatter}\label{decorators/combinations_with_replacement:decorators-combinations-with-replacement-matching-formatter}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Generates the \textbf{combinations\_with\_replacement}, between all the elements of a set of \textbf{Input} (e.g. \textbf{A B C D}),
-i.e. r-length tuples of \emph{input} elements included repeated elements (\textbf{A A})
-and where order of the tuples is irrelevant (either \textbf{A B} or  \textbf{B A}, not both).
-
-The effect is analogous to the python \href{http://docs.python.org/2/library/itertools.html\#itertools.combinations\_with\_replacement}{itertools}
-function of the same name:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{k+kn}{from} \PYG{n+nn}{itertools} \PYG{k+kn}{import} \PYG{n}{combinations\PYGZus{}with\PYGZus{}replacement}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{c}{\PYGZsh{} combinations\PYGZus{}with\PYGZus{}replacement(\PYGZsq{}ABCD\PYGZsq{}, 2) \PYGZhy{}\PYGZhy{}\PYGZgt{} AA AB AC AD BB BC BD CC CD DD}
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{p}{[} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{a}\PYG{p}{)} \PYG{k}{for} \PYG{n}{a} \PYG{o+ow}{in} \PYG{n}{combinations\PYGZus{}with\PYGZus{}replacement}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{ABCD}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{)}\PYG{p}{]}
-\PYG{g+go}{[\PYGZsq{}AA\PYGZsq{}, \PYGZsq{}AB\PYGZsq{}, \PYGZsq{}AC\PYGZsq{}, \PYGZsq{}AD\PYGZsq{}, \PYGZsq{}BB\PYGZsq{}, \PYGZsq{}BC\PYGZsq{}, \PYGZsq{}BD\PYGZsq{}, \PYGZsq{}CC\PYGZsq{}, \PYGZsq{}CD\PYGZsq{}, \PYGZsq{}DD\PYGZsq{}]}
-\end{Verbatim}
-
-Only out of date tasks (comparing input and output files) will be run
-
-Output file names and strings in the extra parameters
-are determined from {\hyperref[decorators/combinations_with_replacement:decorators-combinations-with-replacement-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of up stream tasks, or a list of file names, after string replacement via
-{\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}}.
-
-The replacement strings require an extra level of indirection to refer to
-parsed components:
-\begin{enumerate}
-\item {} 
-The first level refers to which \emph{set} in each tuple of inputs.
-
-\item {} 
-The second level refers to which input file in any particular \emph{set} of inputs.
-
-\end{enumerate}
-\end{quote}
-
-\textbf{Example}:
-\begin{quote}
-
-Calculates the \textbf{@combinations\_with\_replacement} of \textbf{A,B,C,D} files
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus.combinatorics} \PYG{k+kn}{import} \PYG{o}{*}
-
-\PYG{c}{\PYGZsh{}   initial file pairs}
-\PYG{n+nd}{@originate}\PYG{p}{(}\PYG{p}{[} \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,}
-             \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.1\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{D.2\PYGZus{}start}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{(}\PYG{n}{output\PYGZus{}files}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{for} \PYG{n}{output\PYGZus{}file} \PYG{o+ow}{in} \PYG{n}{output\PYGZus{}files}\PYG{p}{:}
-        \PYG{k}{with} \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)} \PYG{k}{as} \PYG{n}{oo}\PYG{p}{:} \PYG{k}{pass}
-
-\PYG{c}{\PYGZsh{}   @combinations\PYGZus{}with\PYGZus{}replacement}
-\PYG{n+nd}{@combinations\PYGZus{}with\PYGZus{}replacement}\PYG{p}{(}\PYG{n}{create\PYGZus{}initial\PYGZus{}files\PYGZus{}ABCD}\PYG{p}{,}   \PYG{c}{\PYGZsh{} Input}
-              \PYG{n}{formatter}\PYG{p}{(}\PYG{p}{)}\PYG{p}{,}                                  \PYG{c}{\PYGZsh{} match input files}
-
-              \PYG{c}{\PYGZsh{} tuple of 2 at a time}
-              \PYG{l+m+mi}{2}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Output Replacement string}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}/}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][1]\PYGZcb{}\PYGZus{}vs\PYGZus{}}\PYG{l+s}{\PYGZdq{}}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][1]\PYGZcb{}.combinations\PYGZus{}with\PYGZus{}replacement}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter: path for 1st set of files, 1st file name}
-              \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}path[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}
-
-              \PYG{c}{\PYGZsh{} Extra parameter}
-              \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[0][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{} basename for 1st set of files, 1st file name}
-               \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{\PYGZob{}basename[1][0]\PYGZcb{}}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,}  \PYG{c}{\PYGZsh{}              2rd}
-               \PYG{p}{]}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{combinations\PYGZus{}with\PYGZus{}replacement\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}parameter}\PYG{p}{,} \PYG{n}{shared\PYGZus{}path}\PYG{p}{,} \PYG{n}{basenames}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{print} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s}{\PYGZdq{}}\PYG{o}{.}\PYG{n}{join}\PYG{p}{(}\PYG{n}{basenames}\PYG{p}{)}
-
-
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}       Run}
-\PYG{c}{\PYGZsh{}}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\end{Verbatim}
-
-This results in:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{n}{verbose}\PYG{o}{=}\PYG{l+m+mi}{0}\PYG{p}{)}
-\PYG{g+go}{A \PYGZhy{} A}
-\PYG{g+go}{A \PYGZhy{} B}
-\PYG{g+go}{A \PYGZhy{} C}
-\PYG{g+go}{A \PYGZhy{} D}
-\PYG{g+go}{B \PYGZhy{} B}
-\PYG{g+go}{B \PYGZhy{} C}
-\PYG{g+go}{B \PYGZhy{} D}
-\PYG{g+go}{C \PYGZhy{} C}
-\PYG{g+go}{C \PYGZhy{} D}
-\PYG{g+go}{D \PYGZhy{} D}
-\end{Verbatim}
-\end{quote}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/combinations_with_replacement:decorators-combinations-with-replacement-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}}.}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/combinations_with_replacement:decorators-combinations-with-replacement-matching-formatter}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_formatter}}] \leavevmode
-a {\hyperref[decorators/indicator_objects:decorators-formatter]{\emph{formatter}}} indicator object containing optionally
-a  python \href{http://docs.python.org/library/re.html}{regular expression (re)}.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/combinations_with_replacement:decorators-combinations-with-replacement-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s) after string
-substitution
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/combinations_with_replacement:decorators-combinations-with-replacement-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-Optional extra parameters are passed to the functions after string
-substitution
-
-\end{description}
-
-\end{itemize}
-\end{minipage}}
-\begin{center}\setlength{\fboxsep}{5pt}\shadowbox{\box0}\end{center}
-\setbox0\vbox{
-\begin{minipage}{0.95\linewidth}
-\textbf{Esoteric}
-
-\medskip
-
-\phantomsection\label{decorators/files_ex:decorators-files-on-the-fly}
-\index{@files (on-the-fly parameter generation)!Syntax}\index{Syntax!@files (on-the-fly parameter generation)}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{Generating parameters on the fly for @files}
-\label{decorators/files_ex:decorators-files-custom-function}\label{decorators/files_ex::doc}\label{decorators/files_ex:custom-function}\label{decorators/files_ex:generating-parameters-on-the-fly-for-files}
-
-\subsubsection{\emph{@files} (\emph{custom\_function})}
-\label{decorators/files_ex:files-custom-function}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Uses a custom function to generate sets of parameters to separate jobs which can run in parallel.
-
-The first two parameters in each set represent the input and output which are
-used to see if the job is out of date and needs to be (re-)run.
-
-By default, out of date checking uses input/output file timestamps.
-(On some file systems, timestamps have a resolution in seconds.)
-See {\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate()}}} for alternatives.
-\end{quote}
-\begin{description}
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k}{def} \PYG{n+nf}{generate\PYGZus{}parameters\PYGZus{}on\PYGZus{}the\PYGZus{}fly}\PYG{p}{(}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{parameters} \PYG{o}{=} \PYG{p}{[}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{input\PYGZus{}file1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{output\PYGZus{}file1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 1st job}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{input\PYGZus{}file2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{output\PYGZus{}file2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{4}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 2nd job}
-                        \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{input\PYGZus{}file3}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{output\PYGZus{}file3}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{l+m+mi}{6}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 3rd job}
-                 \PYG{p}{]}
-    \PYG{k}{for} \PYG{n}{job\PYGZus{}parameters} \PYG{o+ow}{in} \PYG{n}{parameters}\PYG{p}{:}
-        \PYG{k}{yield} \PYG{n}{job\PYGZus{}parameters}
-
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n}{generate\PYGZus{}parameters\PYGZus{}on\PYGZus{}the\PYGZus{}fly}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{n}{param1}\PYG{p}{,} \PYG{n}{param2}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{parallel\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\item[{is the equivalent of calling:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{input\PYGZus{}file1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{output\PYGZus{}file1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{)}
-\PYG{n}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{input\PYGZus{}file2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{output\PYGZus{}file2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{4}\PYG{p}{)}
-\PYG{n}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{input\PYGZus{}file3}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{output\PYGZus{}file3}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{l+m+mi}{6}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/files_ex:decorators-files-custom-function}\begin{quote}
-\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{custom\_function}:}] \leavevmode
-Generator function which yields each time a complete set of parameters for one job
-
-\end{description}
-
-\end{itemize}
-\begin{description}
-\item[{\textbf{Checking if jobs are up to date:}}] \leavevmode
-Strings in \code{input} and \code{output} (including in nested sequences) are interpreted as file names and
-used to check if jobs are up-to-date.
-
-See {\hyperref[decorators/files:decorators-files-check-up-to-date]{\emph{above}}} for more details
-
-\end{description}
-\end{quote}
-\phantomsection\label{decorators/check_if_uptodate:decorators-check-if-uptodate}
-\index{@check\_if\_uptodate!Syntax}\index{Syntax!@check\_if\_uptodate}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@check\_if\_uptodate}
-\label{decorators/check_if_uptodate:decorators-check-if-uptodate-dependency-checking-function}\label{decorators/check_if_uptodate:check-if-uptodate}\label{decorators/check_if_uptodate::doc}\label{decorators/check_if_uptodate:dependency-checking-function}
-
-\subsubsection{\emph{@check\_if\_uptodate} (\emph{dependency\_checking\_function})}
-\label{decorators/check_if_uptodate:check-if-uptodate-dependency-checking-function}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-Checks to see if a job is up to date, and needs to be run.
-
-Usually used in conjunction with {\hyperref[decorators/parallel:decorators-parallel]{\emph{@parallel()}}}
-
-\end{description}
-
-\textbf{Example}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{k+kn}{import} \PYG{n+nn}{os}
-\PYG{k}{def} \PYG{n+nf}{check\PYGZus{}file\PYGZus{}exists}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{if} \PYG{o+ow}{not} \PYG{n}{os}\PYG{o}{.}\PYG{n}{path}\PYG{o}{.}\PYG{n}{exists}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-        \PYG{k}{return} \PYG{n+nb+bp}{True}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{Missing file }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{output\PYGZus{}file}
-    \PYG{k}{else}\PYG{p}{:}
-        \PYG{k}{return} \PYG{n+nb+bp}{False}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{File }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{ exists}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{output\PYGZus{}file}
-
-\PYG{n+nd}{@parallel}\PYG{p}{(}\PYG{p}{[}\PYG{p}{[}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{p}{]}\PYG{p}{)}
-\PYG{n+nd}{@check\PYGZus{}if\PYGZus{}uptodate}\PYG{p}{(}\PYG{n}{check\PYGZus{}file\PYGZus{}exists}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-Is equivalent to:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n+nb+bp}{None}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{(}\PYG{n}{input\PYGZus{}file}\PYG{p}{,} \PYG{n}{output\PYGZus{}file}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{output\PYGZus{}file}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{create\PYGZus{}if\PYGZus{}necessary}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-Both produce the same output:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-Task = create\_if\_necessary
-    Job = [null, "a.1"] completed
-\end{Verbatim}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/check_if_uptodate:decorators-check-if-uptodate-dependency-checking-function}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{dependency\_checking\_function}:}] \leavevmode
-returns two parameters: if job needs to be run, and a message explaining why
-
-dependency\_checking\_func() needs to handle the same number of parameters as the
-task function e.g. \code{input\_file} and \code{output\_file} above.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/parallel:decorators-parallel}
-\index{@parallel!Syntax}\index{Syntax!@parallel}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@parallel}
-\label{decorators/parallel::doc}\label{decorators/parallel:parallel}\phantomsection\label{decorators/parallel:decorators-parallel-job-params}\phantomsection\label{decorators/parallel:job-params}
-
-\subsubsection{\emph{@parallel} ( {[} {[}\emph{job\_params}, ...{]}, {[}\emph{job\_params}, ...{]}...{]} \textbar{} \emph{parameter\_generating\_function})}
-\label{decorators/parallel:decorators-parallel-parameter-generating-function}\label{decorators/parallel:parallel-job-params-job-params-parameter-generating-function}\label{decorators/parallel:parameter-generating-function}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-To apply the (task) function to a set of parameters in parallel without file dependency checking.
-
-Most useful allied to {\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate()}}}
-
-\end{description}
-
-\textbf{Example}:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{parameters} \PYG{o}{=} \PYG{p}{[}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 1st job}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{4}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 2nd job}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{l+m+mi}{6}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 3rd job}
-             \PYG{p}{]}
-\PYG{n+nd}{@parallel}\PYG{p}{(}\PYG{n}{parameters}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{parallel\PYGZus{}task}\PYG{p}{(}\PYG{n}{name}\PYG{p}{,} \PYG{n}{param1}\PYG{p}{,} \PYG{n}{param2}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{    Parallel task }\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s}{: }\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{n}{name}\PYG{p}{)}
-    \PYG{n}{sys}\PYG{o}{.}\PYG{n}{stderr}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{ + }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s}{ = }\PYG{l+s+si}{\PYGZpc{}d}\PYG{l+s+se}{\PYGZbs{}\PYGZbs{}}\PYG{l+s}{n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{param1}\PYG{p}{,} \PYG{n}{param2}\PYG{p}{,} \PYG{n}{param1} \PYG{o}{+} \PYG{n}{param2}\PYG{p}{)}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{parallel\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/parallel:decorators-parallel-job-params}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{job\_params}:}] \leavevmode
-Requires a sequence of parameters, one set for each job.
-
-Each set of parameters can be one or more items in a sequence which will be passed to
-the decorated task function iteratively (or in parallel)
-
-For example:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{parameters} \PYG{o}{=} \PYG{p}{[}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 1st job}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{4}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 2nd job}
-                 \PYG{p}{[}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{l+m+mi}{6}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 3rd job}
-             \PYG{p}{]}
-\PYG{n+nd}{@parallel}\PYG{p}{(}\PYG{n}{parameters}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{parallel\PYGZus{}task}\PYG{p}{(}\PYG{n}{name}\PYG{p}{,} \PYG{n}{param1}\PYG{p}{,} \PYG{n}{param2}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\end{Verbatim}
-
-Will result in the following function calls:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{parallel\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{1}\PYG{p}{,} \PYG{l+m+mi}{2}\PYG{p}{)}
-\PYG{n}{parallel\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{3}\PYG{p}{,} \PYG{l+m+mi}{4}\PYG{p}{)}
-\PYG{n}{parallel\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{C}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{5}\PYG{p}{,} \PYG{l+m+mi}{6}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/parallel:decorators-parallel-parameter-generating-function}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{parameter\_generating\_function}}] \leavevmode\begin{enumerate}
-\item {} 
-A generator yielding  set of parameters (as above) in turn and on the fly
-
-\item {} 
-A function returning a sequence of parameter sets, as above
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\end{minipage}}
-\begin{center}\setlength{\fboxsep}{5pt}\shadowbox{\box0}\end{center}
-\setbox0\vbox{
-\begin{minipage}{0.95\linewidth}
-\textbf{Deprecated}
-
-\medskip
-
-\phantomsection\label{decorators/files:decorators-files}
-\index{@files!Syntax}\index{Syntax!@files}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-\phantomsection\label{decorators/files:decorators-files-input}\phantomsection\label{decorators/files:input}\phantomsection\label{decorators/files:decorators-files-input1}\phantomsection\label{decorators/files:input1}\phantomsection\label{decorators/files:decorators-files-output}\phantomsection\label{decorators/files:output}\phantomsection\label{decorators/files:decorators-files-output1}\phantomsection\label{decorators/files:output1}\phantomsection\label{decorators/files:decorators-files- [...]
-
-\subsection{@files}
-\label{decorators/files:files}\label{decorators/files:decorators-files-extra-parameters1}\label{decorators/files::doc}\label{decorators/files:extra-parameters1}
-
-\subsubsection{\emph{@files} (\emph{input1}, \emph{output1}, {[}\emph{extra\_parameters1}, ...{]})}
-\label{decorators/files:files-input1-output1-extra-parameters1}
-
-\paragraph{@files for single jobs}
-\label{decorators/files:files-for-single-jobs}\begin{quote}
-\begin{description}
-\item[{\textbf{Purpose:}}] \leavevmode
-Provides parameters to run a task.
-
-The first two parameters in each set represent the input and output which are
-used to see if the job is out of date and needs to be (re-)run.
-
-By default, out of date checking uses input/output file timestamps.
-(On some file systems, timestamps have a resolution in seconds.)
-See {\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate()}}} for alternatives.
-
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{transform\PYGZus{}files}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{,} \PYG{n}{text}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{transform\PYGZus{}files}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\item[{If \code{a.2} is missing or was created before \code{a.1}, then the following will be called:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{transform\PYGZus{}files}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/files:decorators-files-input1}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{input}}] \leavevmode
-Input file names
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files:decorators-files-output1}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output}}] \leavevmode
-Output file names
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files:decorators-files-extra-parameters1}\begin{quote}
-\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-optional \code{extra\_parameters} are passed verbatim to each job.
-
-\end{description}
-
-\end{itemize}
-\begin{description}
-\item[{\textbf{Checking if jobs are up to date:}}] \leavevmode
-Strings in \code{input} and \code{output} (including in nested sequences) are interpreted as file names and
-used to check if jobs are up-to-date.
-
-See {\hyperref[decorators/files:decorators-files-check-up-to-date]{\emph{above}}} for more details
-
-\end{description}
-\end{quote}
-
-
-\subsubsection{\emph{@files} ( \emph{((} \emph{input}, \emph{output}, {[}\emph{extra\_parameters},...{]} \emph{), (...), ...)} )}
-\label{decorators/files:files-input-output-extra-parameters}
-
-\paragraph{@files in parallel}
-\label{decorators/files:files-in-parallel}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-Passes each set of parameters to separate jobs which can run in parallel
-
-The first two parameters in each set represent the input and output which are
-used to see if the job is out of date and needs to be (re-)run.
-
-By default, out of date checking uses input/output file timestamps.
-(On some file systems, timestamps have a resolution in seconds.)
-See {\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate()}}} for alternatives.
-\end{quote}
-\begin{description}
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{parameters} \PYG{o}{=} \PYG{p}{[}
-                    \PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 1st job}
-                    \PYG{p}{[} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{]}\PYG{p}{,} \PYG{c}{\PYGZsh{} 2nd job}
-              \PYG{p}{]}
-
-\PYG{n+nd}{@files}\PYG{p}{(}\PYG{n}{parameters}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{,} \PYG{n}{text}\PYG{p}{)}\PYG{p}{:}
-    \PYG{k}{pass}
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\item[{is the equivalent of calling:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{A file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{n}{parallel\PYGZus{}io\PYGZus{}task}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{b.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{B file}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/files:decorators-files-input}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{input}}] \leavevmode
-Input file names
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files:decorators-files-output}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output}}] \leavevmode
-Output file names
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files:decorators-files-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{extra\_parameters}}] \leavevmode
-optional \code{extra\_parameters} are passed verbatim to each job.
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files:decorators-files-check-up-to-date}\begin{quote}
-\begin{description}
-\item[{\textbf{Checking if jobs are up to date:}}] \leavevmode\begin{enumerate}
-\item {} 
-Strings in \code{input} and \code{output} (including in nested sequences) are interpreted as file names and
-used to check if jobs are up-to-date.
-
-\item {} 
-In the absence of input files (e.g. \code{input == None}), the job will run if any output file is missing.
-
-\item {} 
-In the absence of output files (e.g. \code{output == None}), the job will always run.
-
-\item {} 
-If any of the output files is missing, the job will run.
-
-\item {} 
-If any of the input files is missing when the job is run, a
-\code{MissingInputFileError} exception will be raised.
-
-\end{enumerate}
-
-\end{description}
-\end{quote}
-\phantomsection\label{decorators/files_re:decorators-files-re}
-\index{@files\_re!Syntax}\index{Syntax!@files\_re}
-
-\strong{See also:}
-
-\begin{itemize}
-\item {} 
-{\hyperref[decorators/decorators:decorators]{\emph{Decorators}}} for more decorators
-
-\end{itemize}
-
-
-
-
-\subsection{@files\_re}
-\label{decorators/files_re:files-re}\label{decorators/files_re::doc}\phantomsection\label{decorators/files_re:decorators-files-re-tasks-or-file-names}\phantomsection\label{decorators/files_re:tasks-or-file-names}\phantomsection\label{decorators/files_re:decorators-files-re-extra-parameters}\phantomsection\label{decorators/files_re:extra-parameters}\phantomsection\label{decorators/files_re:decorators-files-re-output-pattern}\phantomsection\label{decorators/files_re:output-pattern}\phantom [...]
-
-\subsubsection{\emph{@files\_re} (\emph{tasks\_or\_file\_names}, \emph{matching\_regex}, {[}\emph{input\_pattern}{]}, \emph{output\_pattern}, {[}\emph{extra\_parameters},...{]})}
-\label{decorators/files_re:files-re-tasks-or-file-names-matching-regex-input-pattern-output-pattern-extra-parameters}\label{decorators/files_re:matching-regex}\label{decorators/files_re:decorators-files-re-matching-regex}
-
-\paragraph{Legacy design now deprecated. We suggest using \emph{@transform()} instead}
-\label{decorators/files_re:legacy-design-now-deprecated-we-suggest-using-transform-instead}\begin{quote}
-
-\textbf{Purpose:}
-\begin{quote}
-
-All singing, all dancing decorator which can do everything that {\hyperref[decorators/merge:decorators-merge]{\emph{@merge()}}} and
-{\hyperref[decorators/transform:decorators-transform]{\emph{@transform()}}} can do.
-
-Applies the task function to transform data from input to output files.
-
-Output file names are determined from {\hyperref[decorators/files_re:decorators-files-re-tasks-or-file-names]{\emph{tasks\_or\_file\_names}}}, i.e. from the output
-of specified tasks, or a list of file names, using regular expression pattern substitutions.
-
-Only out of date tasks (comparing input and output files) will be run.
-\end{quote}
-\begin{description}
-\item[{\textbf{Example}:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   convert all files ending in \PYGZdq{}.1\PYGZdq{} into files ending in \PYGZdq{}.2\PYGZdq{}}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@files\PYGZus{}re}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{*.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{(.*).1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{transform\PYGZus{}func}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)} \PYG{o}{+} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{converted}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{task\PYGZus{}re}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\item[{If the following files are present \code{a.1}, \code{b.1}, \code{c.1}, this will result in the following function calls:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{transform\PYGZus{}func}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{transform\PYGZus{}func}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\PYG{n}{transform\PYGZus{}func}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\textbf{Parameters:}
-\end{quote}
-\phantomsection\label{decorators/files_re:decorators-files-re-tasks-or-file-names}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{tasks\_or\_file\_names}}] \leavevmode
-can be a:
-\begin{enumerate}
-\item {} \begin{description}
-\item[{Task / list of tasks (as in the example above).}] \leavevmode
-File names are taken from the output of the specified task(s)
-
-\end{description}
-
-\item {} \begin{description}
-\item[{(Nested) list of file name strings.}] \leavevmode\begin{description}
-\item[{File names containing \code{*{[}{]}?} will be expanded as a \href{http://docs.python.org/library/glob.html}{\emph{glob}} .}] \leavevmode
-E.g.:\code{"a.*" =\textgreater{} "a.1", "a.2"}
-
-\end{description}
-
-\end{description}
-
-\end{enumerate}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files_re:decorators-files-re-matching-regex}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{matching\_regex}}] \leavevmode
-a python regular expression string.
-
-\begin{DUlineblock}{0em}
-\item[] See python \href{http://docs.python.org/library/re.html}{regular expression (re)} documentation for details of regular expression syntax
-\item[] Each output file name is created using regular expression substitution with {\hyperref[decorators/files_re:decorators-files-re-output-pattern]{\emph{output\_pattern}}}
-\end{DUlineblock}
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files_re:decorators-files-re-input-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{input\_pattern}}] \leavevmode
-Optionally specifies the resulting input file name(s).
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files_re:decorators-files-re-output-pattern}\begin{itemize}
-\item {} \begin{description}
-\item[{\emph{output\_pattern}}] \leavevmode
-Specifies the resulting output file name(s).
-
-\end{description}
-
-\end{itemize}
-\phantomsection\label{decorators/files_re:decorators-files-re-extra-parameters}\begin{itemize}
-\item {} \begin{description}
-\item[{{[}\emph{extra\_parameters, ...}{]}}] \leavevmode
-Any extra parameters are passed to the task function.
-
-\begin{DUlineblock}{0em}
-\item[] Regular expression substitution is first applied to (even nested) string parameters.
-\item[] Other data types are passed verbatim.
-\end{DUlineblock}
-\begin{description}
-\item[{For example:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{ruffus} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{c}{\PYGZsh{}}
-\PYG{c}{\PYGZsh{}   convert all files ending in \PYGZdq{}.1\PYGZdq{} into files ending in \PYGZdq{}.2\PYGZdq{}}
-\PYG{c}{\PYGZsh{}}
-\PYG{n+nd}{@files\PYGZus{}re}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{*.1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{(.*).1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1.2}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{r\PYGZsq{}}\PYG{l+s}{\PYGZbs{}}\PYG{l+s}{1}\PYG{l+s}{\PYGZsq{}}\PYG{p}{,} \PYG{l+m+mi}{55}\PYG{p}{]}\PYG{p}{,} \PYG{l+m+mi}{17}\PYG{p}{)}
-\PYG{k}{def} \PYG{n+nf}{transform\PYGZus{}func}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{,} \PYG{n}{outfile}\PYG{p}{,} \PYG{n}{extras}\PYG{p}{,} \PYG{n}{extra3}\PYG{p}{)}\PYG{p}{:}
-    \PYG{n}{extra1}\PYG{p}{,} \PYG{n}{extra2} \PYG{o}{=} \PYG{n}{extras}
-    \PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{outfile}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{w}\PYG{l+s}{\PYGZdq{}}\PYG{p}{)}\PYG{o}{.}\PYG{n}{write}\PYG{p}{(}\PYG{n+nb}{open}\PYG{p}{(}\PYG{n}{infile}\PYG{p}{)}\PYG{o}{.}\PYG{n}{read}\PYG{p}{(}\PYG{p}{)} \PYG{o}{+} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{converted}\PYG{l+s+si}{\PYGZpc{}s}\PYG{l+s+se}{\PYGZbs{}n}\PYG{l+s}{\PYGZdq{}} \PYG{o}{\PYGZpc{}} \PYG{p}{(}\PYG{n}{extra1}\PYG{p}{,} \PYG{n}{extra2}\PYG{p}{,} \PYG{n}{extra3}\PYG [...]
-
-\PYG{n}{pipeline\PYGZus{}run}\PYG{p}{(}\PYG{p}{[}\PYG{n}{transform\PYGZus{}func}\PYG{p}{]}\PYG{p}{)}
-\end{Verbatim}
-
-\item[{If the following files are present \code{a.1}, \code{b.1}, \code{c.1}, this will result in the following function calls:}] \leavevmode
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{n}{transform\PYGZus{}func}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{a}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{55}\PYG{p}{]}\PYG{p}{,} \PYG{l+m+mi}{17}\PYG{p}{)}
-\PYG{n}{transform\PYGZus{}func}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{b}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{55}\PYG{p}{]}\PYG{p}{,} \PYG{l+m+mi}{17}\PYG{p}{)}
-\PYG{n}{transform\PYGZus{}func}\PYG{p}{(}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.1}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c.2}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{c}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{l+m+mi}{55}\PYG{p}{]}\PYG{p}{,} \PYG{l+m+mi}{17}\PYG{p}{)}
-\end{Verbatim}
-
-\end{description}
-
-\end{description}
-
-\end{itemize}
-\end{minipage}}
-\begin{center}\setlength{\fboxsep}{5pt}\shadowbox{\box0}\end{center}
-
-
-\section{Modules:}
-\label{contents:modules}
-
-\subsection{ruffus.Task}
-\label{task:ruffus-task}\label{task:glob}\label{task::doc}
-
-\subsubsection{Decorators}
-\label{task:decorators}\begin{quote}
-
-Basic Task decorators are:
-\begin{quote}
-
-{\hyperref[decorators/follows:decorators-follows]{\emph{@follows()}}}
-
-and
-
-{\hyperref[decorators/files:decorators-files]{\emph{@files()}}}
-\end{quote}
-
-Task decorators include:
-\begin{quote}
-
-{\hyperref[decorators/files:decorators-files]{\emph{@split()}}}
-
-{\hyperref[decorators/files:decorators-files]{\emph{@transform()}}}
-
-{\hyperref[decorators/files:decorators-files]{\emph{@merge()}}}
-
-{\hyperref[decorators/posttask:decorators-posttask]{\emph{@posttask()}}}
-\end{quote}
-
-More advanced users may require:
-\begin{quote}
-
-{\hyperref[decorators/transform_ex:decorators-transform-ex]{\emph{@transform()}}}
-
-{\hyperref[decorators/collate:decorators-collate]{\emph{@collate()}}}
-
-{\hyperref[decorators/parallel:decorators-parallel]{\emph{@parallel()}}}
-
-{\hyperref[decorators/check_if_uptodate:decorators-check-if-uptodate]{\emph{@check\_if\_uptodate()}}}
-
-{\hyperref[decorators/files_re:decorators-files-re]{\emph{@files\_re()}}}
-\end{quote}
-\end{quote}
-
-
-\subsubsection{Pipeline functions}
-\label{task:pipeline-functions}
-
-\paragraph{pipeline\_run}
-\label{task:pipeline-run}\index{pipeline\_run() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.pipeline_run}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{pipeline\_run}}{\emph{target\_tasks}, \emph{forcedtorun\_tasks=}\optional{}, \emph{multiprocess=1}, \emph{logger=stderr\_logger}, \emph{gnu\_make\_maximal\_rebuild\_mode=True}}{}
-Run pipelines.
-\begin{quote}\begin{description}
-\item[{Parameters}] \leavevmode\begin{itemize}
-\item {} 
-\textbf{target\_tasks} -- targets task functions which will be run if they are out-of-date
-
-\item {} 
-\textbf{forcedtorun\_tasks} -- task functions which will be run whether or not they are out-of-date
-
-\item {} 
-\textbf{multiprocess} -- The number of concurrent jobs running on different processes.
-
-\item {} 
-\textbf{multithread} -- The number of concurrent jobs running as different threads. If \textgreater{} 1, ruffus will use multithreading \emph{instead of} multiprocessing (and ignore the multiprocess parameter). Using multi threading is particularly useful to manage high performance clusters which otherwise are prone to ``processor storms'' when large number of cores finish jobs at the same time. (Thanks Andreas Heger)
-
-\item {} 
-\textbf{logger} (\href{http://docs.python.org/library/logging.html}{logging} objects) -- Where progress will be logged. Defaults to stderr output.
-
-\item {} 
-\textbf{verbose} -- level 0 : nothing
-level 1 : Out-of-date Task names
-level 2 : All Tasks (including any task function docstrings)
-level 3 : Out-of-date Jobs in Out-of-date Tasks, no explanation
-level 4 : Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings
-level 5 : All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)
-level 6 : All jobs in All Tasks whether out of date or not
-level 10: logs messages useful only for debugging ruffus pipeline code
-
-\item {} 
-\textbf{touch\_files\_only} -- Create or update input/output files only to simulate running the pipeline. Do not run jobs. If set to CHECKSUM\_REGENERATE, will regenerate the checksum history file to reflect the existing i/o files on disk.
-
-\item {} 
-\textbf{exceptions\_terminate\_immediately} -- Exceptions cause immediate termination
-rather than waiting for N jobs to finish where N = multiprocess
-
-\item {} 
-\textbf{log\_exceptions} -- Print exceptions to the logger as soon as they occur.
-
-\item {} 
-\textbf{checksum\_level} -- Several options for checking up-to-dateness are available: Default is level 1.
-level 0 : Use only file timestamps
-level 1 : above, plus timestamp of successful job completion
-level 2 : above, plus a checksum of the pipeline function body
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-\item {} 
-\textbf{one\_second\_per\_job} -- To work around poor file timepstamp resolution for some file systems. Defaults to True if checksum\_level is 0 forcing Tasks to take a minimum of 1 second to complete.
-
-\item {} 
-\textbf{runtime\_data} -- Experimental feature for passing data to tasks at run time
-
-\item {} 
-\textbf{gnu\_make\_maximal\_rebuild\_mode} -- Defaults to re-running \emph{all} out-of-date tasks. Runs minimal
-set to build targets if set to \code{True}. Use with caution.
-
-\item {} 
-\textbf{history\_file} -- The database file which stores checksums and file timestamps for input/output files.
-
-\item {} 
-\textbf{verbose\_abbreviated\_path} -- whether input and output paths are abbreviated.
-level 0: The full (expanded, abspath) input or output path
-level \textgreater{} 1: The number of subdirectories to include. Abbreviated paths are prefixed with \code{{[},,,{]}/}
-level \textless{} 0: level \textless{} 0: Input / Output parameters are truncated to \code{MMM} letters where \code{verbose\_abbreviated\_path ==-MMM}. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by \code{\textless{}???\textgreater{}}
-
-\end{itemize}
-
-\end{description}\end{quote}
-
-\end{fulllineitems}
-
-
-
-\paragraph{pipeline\_printout}
-\label{task:pipeline-printout}\index{pipeline\_printout() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.pipeline_printout}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{pipeline\_printout}}{\emph{output\_stream=None}, \emph{target\_tasks=}\optional{}, \emph{forcedtorun\_tasks=}\optional{}, \emph{verbose=None}, \emph{indent=4}, \emph{gnu\_make\_maximal\_rebuild\_mode=True}, \emph{wrap\_width=100}, \emph{runtime\_data=None}, \emph{checksum\_level=None}, \emph{history\_file=None}, \emph{verbose\_abbreviated\_path=None}}{}
-Printouts the parts of the pipeline which will be run
-
-Because the parameters of some jobs depend on the results of previous tasks, this function
-produces only the current snap-shot of task jobs. In particular, tasks which generate
-variable number of inputs into following tasks will not produce the full range of jobs.
-\begin{description}
-\item[{::}] \leavevmode
-verbose = 0 : Nothing
-verbose = 1 : Out-of-date Task names
-verbose = 2 : All Tasks (including any task function docstrings)
-verbose = 3 : Out-of-date Jobs in Out-of-date Tasks, no explanation
-verbose = 4 : Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings
-verbose = 5 : All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)
-verbose = 6 : All jobs in All Tasks whether out of date or not
-
-\end{description}
-\begin{quote}\begin{description}
-\item[{Parameters}] \leavevmode\begin{itemize}
-\item {} 
-\textbf{output\_stream} (file-like object with \code{write()} function) -- where to print to
-
-\item {} 
-\textbf{target\_tasks} -- targets task functions which will be run if they are out-of-date
-
-\item {} 
-\textbf{forcedtorun\_tasks} -- task functions which will be run whether or not they are out-of-date
-
-\item {} 
-\textbf{verbose} -- level 0 : nothing
-level 1 : Out-of-date Task names
-level 2 : All Tasks (including any task function docstrings)
-level 3 : Out-of-date Jobs in Out-of-date Tasks, no explanation
-level 4 : Out-of-date Jobs in Out-of-date Tasks, with explanations and warnings
-level 5 : All Jobs in Out-of-date Tasks,  (include only list of up-to-date tasks)
-level 6 : All jobs in All Tasks whether out of date or not
-level 10: logs messages useful only for debugging ruffus pipeline code
-
-\item {} 
-\textbf{indent} -- How much indentation for pretty format.
-
-\item {} 
-\textbf{gnu\_make\_maximal\_rebuild\_mode} -- Defaults to re-running \emph{all} out-of-date tasks. Runs minimal
-set to build targets if set to \code{True}. Use with caution.
-
-\item {} 
-\textbf{wrap\_width} -- The maximum length of each line
-
-\item {} 
-\textbf{runtime\_data} -- Experimental feature for passing data to tasks at run time
-
-\item {} 
-\textbf{checksum\_level} -- Several options for checking up-to-dateness are available: Default is level 1.
-level 0 : Use only file timestamps
-level 1 : As above, plus timestamp of successful job completion
-level 2 : As above, plus a checksum of the pipeline function body
-level 3 : As above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-\item {} 
-\textbf{history\_file} -- The database file which stores checksums and file timestamps for input/output files.
-
-\item {} 
-\textbf{verbose\_abbreviated\_path} -- whether input and output paths are abbreviated.
-level 0: The full (expanded, abspath) input or output path
-level \textgreater{} 1: The number of subdirectories to include. Abbreviated paths are prefixed with \code{{[},,,{]}/}
-level \textless{} 0: level \textless{} 0: Input / Output parameters are truncated to \code{MMM} letters where \code{verbose\_abbreviated\_path ==-MMM}. Subdirectories are first removed to see if this allows the paths to fit in the specified limit. Otherwise abbreviated paths are prefixed by \code{\textless{}???\textgreater{}}
-
-\end{itemize}
-
-\end{description}\end{quote}
-
-\end{fulllineitems}
-
-
-
-\paragraph{pipeline\_printout\_graph}
-\label{task:pipeline-printout-graph}\index{pipeline\_printout\_graph() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.pipeline_printout_graph}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{pipeline\_printout\_graph}}{\emph{stream}, \emph{output\_format=None}, \emph{target\_tasks=}\optional{}, \emph{forcedtorun\_tasks=}\optional{}, \emph{draw\_vertically=True}, \emph{ignore\_upstream\_of\_target=False}, \emph{skip\_uptodate\_tasks=False}, \emph{gnu\_make\_maximal\_rebuild\_mode=True}, \emph{test\_all\_task\_for\_update=True}, \emph{no\_key\_legend=False}, \emph{mi [...]
-print out pipeline dependencies in various formats
-\begin{quote}\begin{description}
-\item[{Parameters}] \leavevmode\begin{itemize}
-\item {} 
-\textbf{stream} (file-like object with \code{write()} function) -- where to print to
-
-\item {} 
-\textbf{output\_format} -- {[}''dot'', ``jpg'', ``svg'', ``ps'', ``png''{]}. All but the first depends on the \href{http://www.graphviz.org}{dot} program.
-
-\item {} 
-\textbf{target\_tasks} -- targets task functions which will be run if they are out-of-date.
-
-\item {} 
-\textbf{forcedtorun\_tasks} -- task functions which will be run whether or not they are out-of-date.
-
-\item {} 
-\textbf{draw\_vertically} -- Top to bottom instead of left to right.
-
-\item {} 
-\textbf{ignore\_upstream\_of\_target} -- Don't draw upstream tasks of targets.
-
-\item {} 
-\textbf{skip\_uptodate\_tasks} -- Don't draw up-to-date tasks if possible.
-
-\item {} 
-\textbf{gnu\_make\_maximal\_rebuild\_mode} -- Defaults to re-running \emph{all} out-of-date tasks. Runs minimal
-set to build targets if set to \code{True}. Use with caution.
-
-\item {} 
-\textbf{test\_all\_task\_for\_update} -- Ask all task functions if they are up-to-date.
-
-\item {} 
-\textbf{no\_key\_legend} -- Don't draw key/legend for graph.
-
-\item {} 
-\textbf{minimal\_key\_legend} -- Only add entries to the legend for task types which appear
-
-\item {} 
-\textbf{user\_colour\_scheme} -- Dictionary specifying colour scheme for flowchart
-
-\item {} 
-\textbf{pipeline\_name} -- Pipeline Title
-
-\item {} 
-\textbf{size} -- tuple of x and y dimensions
-
-\item {} 
-\textbf{dpi} -- print resolution
-
-\item {} 
-\textbf{runtime\_data} -- Experimental feature for passing data to tasks at run time
-
-\item {} 
-\textbf{history\_file} -- The database file which stores checksums and file timestamps for input/output files.
-
-\item {} 
-\textbf{checksum\_level} -- Several options for checking up-to-dateness are available: Default is level 1.
-level 0 : Use only file timestamps
-level 1 : above, plus timestamp of successful job completion
-level 2 : above, plus a checksum of the pipeline function body
-level 3 : above, plus a checksum of the pipeline function default arguments and the additional arguments passed in by task decorators
-
-\end{itemize}
-
-\end{description}\end{quote}
-
-\end{fulllineitems}
-
-
-
-\subsubsection{Logging}
-\label{task:id1}\index{t\_black\_hole\_logger (class in ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.t_black_hole_logger}\pysigline{\strong{class }\code{ruffus.task.}\bfcode{t\_black\_hole\_logger}}
-Does nothing!
-
-\end{fulllineitems}
-
-\index{t\_stderr\_logger (class in ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.t_stderr_logger}\pysigline{\strong{class }\code{ruffus.task.}\bfcode{t\_stderr\_logger}}
-Everything to stderr
-
-\end{fulllineitems}
-
-
-
-\subsubsection{Implementation:}
-\label{task:implementation}
-
-\paragraph{Parameter factories:}
-\label{task:parameter-factories}\index{merge\_param\_factory() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.merge_param_factory}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{merge\_param\_factory}}{\emph{input\_files\_task\_globs}, \emph{output\_param}, \emph{*extra\_params}}{}
-Factory for task\_merge
-
-\end{fulllineitems}
-
-\index{collate\_param\_factory() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.collate_param_factory}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{collate\_param\_factory}}{\emph{input\_files\_task\_globs}, \emph{flatten\_input}, \emph{file\_names\_transform}, \emph{extra\_input\_files\_task\_globs}, \emph{replace\_inputs}, \emph{output\_pattern}, \emph{*extra\_specs}}{}
-Factory for task\_collate
-
-Looks exactly like @transform except that all {[}input{]} which lead to the same {[}output / extra{]} are combined together
-
-\end{fulllineitems}
-
-\index{transform\_param\_factory() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.transform_param_factory}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{transform\_param\_factory}}{\emph{input\_files\_task\_globs}, \emph{flatten\_input}, \emph{file\_names\_transform}, \emph{extra\_input\_files\_task\_globs}, \emph{replace\_inputs}, \emph{output\_pattern}, \emph{*extra\_specs}}{}
-Factory for task\_transform
-
-\end{fulllineitems}
-
-\index{files\_param\_factory() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.files_param_factory}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{files\_param\_factory}}{\emph{input\_files\_task\_globs}, \emph{flatten\_input}, \emph{do\_not\_expand\_single\_job\_tasks}, \emph{output\_extras}}{}~\begin{description}
-\item[{Factory for functions which}] \leavevmode
-yield tuples of inputs, outputs / extras
-
-\end{description}
-
-..Note:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-1. Each job requires input/output file names
-2. Input/output file names can be a string, an arbitrarily nested sequence
-3. Non-string types are ignored
-3. Either Input or output file name must contain at least one string
-\end{Verbatim}
-
-\end{fulllineitems}
-
-\index{args\_param\_factory() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.args_param_factory}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{args\_param\_factory}}{\emph{orig\_args}}{}~\begin{description}
-\item[{Factory for functions which}] \leavevmode
-yield tuples of inputs, outputs / extras
-
-\end{description}
-
-..Note:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-1. Each job requires input/output file names
-2. Input/output file names can be a string, an arbitrarily nested sequence
-3. Non-string types are ignored
-3. Either Input or output file name must contain at least one string
-\end{Verbatim}
-
-\end{fulllineitems}
-
-\index{split\_param\_factory() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.split_param_factory}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{split\_param\_factory}}{\emph{input\_files\_task\_globs}, \emph{output\_files\_task\_globs}, \emph{*extra\_params}}{}
-Factory for task\_split
-
-\end{fulllineitems}
-
-
-
-\paragraph{Wrappers around jobs:}
-\label{task:wrappers-around-jobs}\index{job\_wrapper\_generic() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.job_wrapper_generic}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{job\_wrapper\_generic}}{\emph{param}, \emph{user\_defined\_work\_func}, \emph{register\_cleanup}, \emph{touch\_files\_only}}{}
-run func
-
-\end{fulllineitems}
-
-\index{job\_wrapper\_io\_files() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.job_wrapper_io_files}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{job\_wrapper\_io\_files}}{\emph{param}, \emph{user\_defined\_work\_func}, \emph{register\_cleanup}, \emph{touch\_files\_only}, \emph{output\_files\_only=False}}{}
-run func on any i/o if not up to date
-
-\end{fulllineitems}
-
-\index{job\_wrapper\_mkdir() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.job_wrapper_mkdir}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{job\_wrapper\_mkdir}}{\emph{param}, \emph{user\_defined\_work\_func}, \emph{register\_cleanup}, \emph{touch\_files\_only}}{}
-make directories if not exists
-
-\end{fulllineitems}
-
-
-
-\paragraph{Checking if job is update:}
-\label{task:checking-if-job-is-update}\index{needs\_update\_check\_modify\_time() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.needs_update_check_modify_time}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{needs\_update\_check\_modify\_time}}{\emph{*params}, \emph{**kwargs}}{}
-Given input and output files, see if all exist and whether output files are later than input files
-Each can be
-\begin{enumerate}
-\item {} 
-string: assumed to be a filename ``file1''
-
-\item {} 
-any other type
-
-\item {} 
-arbitrary nested sequence of (1) and (2)
-
-\end{enumerate}
-
-\end{fulllineitems}
-
-\index{needs\_update\_check\_directory\_missing() (in module ruffus.task)}
-
-\begin{fulllineitems}
-\phantomsection\label{task:ruffus.task.needs_update_check_directory_missing}\pysiglinewithargsret{\code{ruffus.task.}\bfcode{needs\_update\_check\_directory\_missing}}{\emph{*params}, \emph{**kwargs}}{}~\begin{description}
-\item[{Called per directory:}] \leavevmode
-Does it exist?
-Is it an ordinary file not a directory? (throw exception
-
-\end{description}
-
-\end{fulllineitems}
-
-
-
-\subsubsection{Exceptions and Errors}
-\label{task:exceptions-and-errors}
-
-\subsection{ruffus.proxy\_logger}
-\label{proxy_logger:glob}\label{proxy_logger::doc}\label{proxy_logger:ruffus-proxy-logger}\phantomsection\label{proxy_logger:proxy-logger}\phantomsection\label{proxy_logger:module-ruffus.proxy_logger}\phantomsection\label{proxy_logger:proxy-logger}\index{ruffus.proxy\_logger (module)}
-
-\subsubsection{Create proxy for logging for use with multiprocessing}
-\label{proxy_logger:create-proxy-for-logging-for-use-with-multiprocessing}
-These can be safely sent (marshalled) across process boundaries
-
-
-\paragraph{Example 1}
-\label{proxy_logger:example-1}\begin{quote}
-
-Set up logger from config file:
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{proxy\PYGZus{}logger} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{args}\PYG{o}{=}\PYG{p}{\PYGZob{}}\PYG{p}{\PYGZcb{}}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{config\PYGZus{}file}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/my/config/file}\PYG{l+s}{\PYGZdq{}}
-
-\PYG{p}{(}\PYG{n}{logger\PYGZus{}proxy}\PYG{p}{,}
- \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)} \PYG{o}{=} \PYG{n}{make\PYGZus{}shared\PYGZus{}logger\PYGZus{}and\PYGZus{}proxy} \PYG{p}{(}\PYG{n}{setup\PYGZus{}std\PYGZus{}shared\PYGZus{}logger}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}logger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{args}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\paragraph{Example 2}
-\label{proxy_logger:example-2}\begin{quote}
-
-Log to file \code{"/my/lg.log"} in the specified format (Time / Log name / Event type / Message).
-
-Delay file creation until first log.
-
-Only log \code{Debug} messages
-\begin{quote}
-
-Other alternatives for the logging threshold (\code{args{[}"level"{]}}) include
-\begin{itemize}
-\item {} 
-\code{logging.DEBUG}
-
-\item {} 
-\code{logging.INFO}
-
-\item {} 
-\code{logging.WARNING}
-
-\item {} 
-\code{logging.ERROR}
-
-\item {} 
-\code{logging.CRITICAL}
-
-\end{itemize}
-\end{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{proxy\PYGZus{}logger} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{args}\PYG{o}{=}\PYG{p}{\PYGZob{}}\PYG{p}{\PYGZcb{}}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{file\PYGZus{}name}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/my/lg.log}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{formatter}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}(asctime)s}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s+si}{\PYGZpc{}(name)s}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s+si}{\PYGZpc{}(levelname)6s}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s+si}{\PYGZpc{}(message)s}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{delay}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}     \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{level}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}     \PYG{o}{=} \PYG{n}{logging}\PYG{o}{.}\PYG{n}{DEBUG}
-
-\PYG{p}{(}\PYG{n}{logger\PYGZus{}proxy}\PYG{p}{,}
- \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)} \PYG{o}{=} \PYG{n}{make\PYGZus{}shared\PYGZus{}logger\PYGZus{}and\PYGZus{}proxy} \PYG{p}{(}\PYG{n}{setup\PYGZus{}std\PYGZus{}shared\PYGZus{}logger}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}logger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{args}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\paragraph{Example 3}
-\label{proxy_logger:example-3}\begin{quote}
-
-Rotate log files every 20 Kb, with up to 10 backups.
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{k+kn}{from} \PYG{n+nn}{proxy\PYGZus{}logger} \PYG{k+kn}{import} \PYG{o}{*}
-\PYG{n}{args}\PYG{o}{=}\PYG{p}{\PYGZob{}}\PYG{p}{\PYGZcb{}}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{file\PYGZus{}name}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{o}{=} \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{/my/lg.log}\PYG{l+s}{\PYGZdq{}}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{rotating}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]} \PYG{o}{=} \PYG{n+nb+bp}{True}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{maxBytes}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{o}{=}\PYG{l+m+mi}{20000}
-\PYG{n}{args}\PYG{p}{[}\PYG{l+s}{\PYGZdq{}}\PYG{l+s}{backupCount}\PYG{l+s}{\PYGZdq{}}\PYG{p}{]}\PYG{o}{=}\PYG{l+m+mi}{10}
-\PYG{p}{(}\PYG{n}{logger\PYGZus{}proxy}\PYG{p}{,}
- \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)} \PYG{o}{=} \PYG{n}{make\PYGZus{}shared\PYGZus{}logger\PYGZus{}and\PYGZus{}proxy} \PYG{p}{(}\PYG{n}{setup\PYGZus{}std\PYGZus{}shared\PYGZus{}logger}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}logger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{args}\PYG{p}{)}
-\end{Verbatim}
-\end{quote}
-
-
-\paragraph{To use:}
-\label{proxy_logger:to-use}\begin{quote}
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{p}{(}\PYG{n}{logger\PYGZus{}proxy}\PYG{p}{,}
- \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{)} \PYG{o}{=} \PYG{n}{make\PYGZus{}shared\PYGZus{}logger\PYGZus{}and\PYGZus{}proxy} \PYG{p}{(}\PYG{n}{setup\PYGZus{}std\PYGZus{}shared\PYGZus{}logger}\PYG{p}{,}
-                                                \PYG{l+s}{\PYGZdq{}}\PYG{l+s}{my\PYGZus{}logger}\PYG{l+s}{\PYGZdq{}}\PYG{p}{,} \PYG{n}{args}\PYG{p}{)}
-
-\PYG{k}{with} \PYG{n}{logging\PYGZus{}mutex}\PYG{p}{:}
-    \PYG{n}{my\PYGZus{}log}\PYG{o}{.}\PYG{n}{debug}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{This is a debug message}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-    \PYG{n}{my\PYGZus{}log}\PYG{o}{.}\PYG{n}{info}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{This is an info message}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-    \PYG{n}{my\PYGZus{}log}\PYG{o}{.}\PYG{n}{warning}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{This is a warning message}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-    \PYG{n}{my\PYGZus{}log}\PYG{o}{.}\PYG{n}{error}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{This is an error message}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-    \PYG{n}{my\PYGZus{}log}\PYG{o}{.}\PYG{n}{critical}\PYG{p}{(}\PYG{l+s}{\PYGZsq{}}\PYG{l+s}{This is a critical error message}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-    \PYG{n}{my\PYGZus{}log}\PYG{o}{.}\PYG{n}{log}\PYG{p}{(}\PYG{n}{logging}\PYG{o}{.}\PYG{n}{DEBUG}\PYG{p}{,} \PYG{l+s}{\PYGZsq{}}\PYG{l+s}{This is a debug message}\PYG{l+s}{\PYGZsq{}}\PYG{p}{)}
-\end{Verbatim}
-
-Note that the logging function \code{exception()} is not included because python
-stack trace information is not well-marshalled
-(\href{http://docs.python.org/library/pickle.html}{pickle}d) across processes.
-\end{quote}
-
-
-\subsubsection{Proxies for a log:}
-\label{proxy_logger:proxies-for-a-log}\index{make\_shared\_logger\_and\_proxy() (in module ruffus.proxy\_logger)}
-
-\begin{fulllineitems}
-\phantomsection\label{proxy_logger:ruffus.proxy_logger.make_shared_logger_and_proxy}\pysiglinewithargsret{\code{ruffus.proxy\_logger.}\bfcode{make\_shared\_logger\_and\_proxy}}{\emph{logger\_factory}, \emph{logger\_name}, \emph{args}}{}
-Make a \href{http://docs.python.org/library/logging.html}{logging} object
-called ``\code{logger\_name}'' by calling \code{logger\_factory}(\code{args})
-
-This function will return a proxy to the shared logger which can be copied to jobs
-in other processes, as well as a mutex which can be used to prevent simultaneous logging
-from happening.
-\begin{quote}\begin{description}
-\item[{Parameters}] \leavevmode\begin{itemize}
-\item {} 
-\textbf{logger\_factory} -- 
-functions which creates and returns an object with the
-\href{http://docs.python.org/library/logging.html}{logging} interface.
-\code{setup\_std\_shared\_logger()} is one example of a logger factory.
-
-
-\item {} 
-\textbf{logger\_name} -- name of log
-
-\item {} 
-\textbf{args} -- parameters passed (as a single argument) to \code{logger\_factory}
-
-\end{itemize}
-
-\item[{Returns}] \leavevmode
-a proxy to the shared logger which can be copied to jobs in other processes
-
-\item[{Returns}] \leavevmode
-a mutex which can be used to prevent simultaneous logging from happening
-
-\end{description}\end{quote}
-
-\end{fulllineitems}
-
-
-
-\subsubsection{Create a logging object}
-\label{proxy_logger:create-a-logging-object}\index{setup\_std\_shared\_logger() (in module ruffus.proxy\_logger)}
-
-\begin{fulllineitems}
-\phantomsection\label{proxy_logger:ruffus.proxy_logger.setup_std_shared_logger}\pysiglinewithargsret{\code{ruffus.proxy\_logger.}\bfcode{setup\_std\_shared\_logger}}{\emph{logger\_name}, \emph{args}}{}
-This function is a simple around wrapper around the python
-\href{http://docs.python.org/library/logging.html}{logging} module.
-
-This \emph{logger\_factory} example creates logging objects which can
-then be managed by proxy via \code{ruffus.proxy\_logger.make\_shared\_logger\_and\_proxy()}
-
-This can be:
-\begin{itemize}
-\item {} 
-a \href{http://docs.python.org/library/logging.html\#filehandler}{disk log file}
-
-\item {} 
-a automatically backed-up \href{http://docs.python.org/library/logging.html\#rotatingfilehandler}{(rotating) log}.
-
-\item {} 
-any log specified in a \href{http://docs.python.org/library/logging.html\#configuration-file-format}{configuration file}
-
-\end{itemize}
-
-These are specified in the \code{args} dictionary forwarded by \code{make\_shared\_logger\_and\_proxy()}
-\begin{quote}\begin{description}
-\item[{Parameters}] \leavevmode\begin{itemize}
-\item {} 
-\textbf{logger\_name} -- name of log
-
-\item {} 
-\textbf{args} -- 
-a dictionary of parameters forwarded from \code{make\_shared\_logger\_and\_proxy()}
-
-Valid entries include:
-\begin{quote}
-
-
-\begin{fulllineitems}
-\pysigline{\bfcode{"level"}}
-Sets the \href{http://docs.python.org/library/logging.html\#logging.Handler.setLevel}{threshold} for the logger.
-
-\end{fulllineitems}
-
-
-
-\begin{fulllineitems}
-\pysigline{\bfcode{"config\_file"}}
-The logging object is configured from this \href{http://docs.python.org/library/logging.html\#configuration-file-format}{configuration file}.
-
-\end{fulllineitems}
-
-
-
-\begin{fulllineitems}
-\pysigline{\bfcode{"file\_name"}}
-Sets disk log file name.
-
-\end{fulllineitems}
-
-
-
-\begin{fulllineitems}
-\pysigline{\bfcode{"rotating"}}
-Chooses a \href{http://docs.python.org/library/logging.html\#rotatingfilehandler}{(rotating) log}.
-
-\end{fulllineitems}
-
-
-
-\begin{fulllineitems}
-\pysigline{\bfcode{"maxBytes"}}
-Allows the file to rollover at a predetermined size
-
-\end{fulllineitems}
-
-
-
-\begin{fulllineitems}
-\pysigline{\bfcode{"backupCount"}}
-If backupCount is non-zero, the system will save old log files by appending the extensions \code{.1}, \code{.2}, \code{.3} etc., to the filename.
-
-\end{fulllineitems}
-
-
-
-\begin{fulllineitems}
-\pysigline{\bfcode{"delay"}}
-Defer file creation until the log is written to.
-
-\end{fulllineitems}
-
-
-
-\begin{fulllineitems}
-\pysigline{\bfcode{"formatter"}}
-\href{http://docs.python.org/library/logging.html\#formatter-objects}{Converts} the message to a logged entry string.
-For example,
-
-\begin{Verbatim}[commandchars=\\\{\}]
-\PYG{l+s}{\PYGZdq{}}\PYG{l+s+si}{\PYGZpc{}(asctime)s}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s+si}{\PYGZpc{}(name)s}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s+si}{\PYGZpc{}(levelname)6s}\PYG{l+s}{ \PYGZhy{} }\PYG{l+s+si}{\PYGZpc{}(message)s}\PYG{l+s}{\PYGZdq{}}
-\end{Verbatim}
-
-\end{fulllineitems}
-
-\end{quote}
-
-
-\end{itemize}
-
-\end{description}\end{quote}
-
-\end{fulllineitems}
-
-
-
-\chapter{Indices and tables}
-\label{contents:indices-and-tables}\begin{itemize}
-\item {} 
-\emph{genindex}
-
-\item {} 
-\emph{modindex}
-
-\item {} 
-\emph{search}
-
-\end{itemize}
-
-
-\renewcommand{\indexname}{Python Module Index}
-\begin{theindex}
-\def\bigletter#1{{\Large\sffamily#1}\nopagebreak\vspace{1mm}}
-\bigletter{r}
-\item {\texttt{ruffus.proxy\_logger}}, \pageref{proxy_logger:module-ruffus.proxy_logger}
-\end{theindex}
-
-\renewcommand{\indexname}{Index}
-\printindex
-\end{document}
diff --git a/doc/_build/latex/ruffus.toc b/doc/_build/latex/ruffus.toc
deleted file mode 100644
index 50ebbe0..0000000
--- a/doc/_build/latex/ruffus.toc
+++ /dev/null
@@ -1,544 +0,0 @@
-\select at language {english}
-\contentsline {chapter}{\numberline {1}Start Here:}{1}{chapter.1}
-\contentsline {section}{\numberline {1.1}Installation}{1}{section.1.1}
-\contentsline {subsection}{\numberline {1.1.1}The easy way}{1}{subsection.1.1.1}
-\contentsline {subsection}{\numberline {1.1.2}The most up-to-date code:}{1}{subsection.1.1.2}
-\contentsline {subsubsection}{Graphical flowcharts}{1}{subsubsection*.3}
-\contentsline {section}{\numberline {1.2}\textbf {Ruffus} Manual: List of Chapters and Example code}{2}{section.1.2}
-\contentsline {section}{\numberline {1.3}\textbf {Chapter 1}: An introduction to basic \emph {Ruffus} syntax}{3}{section.1.3}
-\contentsline {subsection}{\numberline {1.3.1}Overview}{3}{subsection.1.3.1}
-\contentsline {subsection}{\numberline {1.3.2}Importing \emph {Ruffus}}{4}{subsection.1.3.2}
-\contentsline {subsection}{\numberline {1.3.3}\emph {Ruffus} decorators}{4}{subsection.1.3.3}
-\contentsline {subsection}{\numberline {1.3.4}Your first \emph {Ruffus} pipeline}{5}{subsection.1.3.4}
-\contentsline {subsubsection}{1. Write down the file names}{5}{subsubsection*.5}
-\contentsline {subsubsection}{2. Write the python functions for each stage}{5}{subsubsection*.6}
-\contentsline {subsubsection}{3. Link the python functions into a pipeline}{7}{subsubsection*.7}
-\contentsline {subsubsection}{4. @transform syntax}{7}{subsubsection*.8}
-\contentsline {subsubsection}{5. Run the pipeline!}{8}{subsubsection*.9}
-\contentsline {section}{\numberline {1.4}\textbf {Chapter 2}: Transforming data in a pipeline with \emph {@transform}}{9}{section.1.4}
-\contentsline {subsection}{\numberline {1.4.1}Review}{9}{subsection.1.4.1}
-\contentsline {subsection}{\numberline {1.4.2}Task functions as recipes}{9}{subsection.1.4.2}
-\contentsline {subsection}{\numberline {1.4.3}\emph {@transform} is a 1 to 1 operation}{9}{subsection.1.4.3}
-\contentsline {subsubsection}{A pair of files as the \textbf {Input}}{10}{subsubsection*.10}
-\contentsline {subsection}{\numberline {1.4.4}\textbf {Input} and \textbf {Output} parameters}{10}{subsection.1.4.4}
-\contentsline {section}{\numberline {1.5}\textbf {Chapter 3}: More on \texttt {@transform}-ing data}{11}{section.1.5}
-\contentsline {subsection}{\numberline {1.5.1}Review}{11}{subsection.1.5.1}
-\contentsline {subsection}{\numberline {1.5.2}Running pipelines in parallel}{12}{subsection.1.5.2}
-\contentsline {subsection}{\numberline {1.5.3}Up-to-date jobs are not re-run unnecessarily}{12}{subsection.1.5.3}
-\contentsline {subsection}{\numberline {1.5.4}Defining pipeline tasks out of order}{13}{subsection.1.5.4}
-\contentsline {subsection}{\numberline {1.5.5}Multiple dependencies}{14}{subsection.1.5.5}
-\contentsline {subsection}{\numberline {1.5.6}\emph {@follows}}{14}{subsection.1.5.6}
-\contentsline {subsection}{\numberline {1.5.7}Making directories automatically with \emph {@follows} and \emph {mkdir}}{15}{subsection.1.5.7}
-\contentsline {subsection}{\numberline {1.5.8}Globs in the \textbf {Input} parameter}{15}{subsection.1.5.8}
-\contentsline {subsection}{\numberline {1.5.9}Mixing Tasks and Globs in the \textbf {Input} parameter}{16}{subsection.1.5.9}
-\contentsline {section}{\numberline {1.6}\textbf {Chapter 4}: Creating files with \texttt {@originate}}{16}{section.1.6}
-\contentsline {subsection}{\numberline {1.6.1}Simplifying our example with \emph {@originate}}{16}{subsection.1.6.1}
-\contentsline {section}{\numberline {1.7}\textbf {Chapter 5}: Understanding how your pipeline works with \emph {pipeline\_printout(...)}}{17}{section.1.7}
-\contentsline {subsection}{\numberline {1.7.1}Printing out which jobs will be run}{18}{subsection.1.7.1}
-\contentsline {subsection}{\numberline {1.7.2}Determining which jobs are out-of-date or not}{18}{subsection.1.7.2}
-\contentsline {subsection}{\numberline {1.7.3}Verbosity levels}{19}{subsection.1.7.3}
-\contentsline {subsection}{\numberline {1.7.4}Abbreviating long file paths with \texttt {verbose\_abbreviated\_path}}{19}{subsection.1.7.4}
-\contentsline {subsection}{\numberline {1.7.5}Getting a list of all tasks in a pipeline}{20}{subsection.1.7.5}
-\contentsline {section}{\numberline {1.8}\textbf {Chapter 6}: Running \emph {Ruffus} from the command line with ruffus.cmdline}{20}{section.1.8}
-\contentsline {subsection}{\numberline {1.8.1}Template for argparse}{21}{subsection.1.8.1}
-\contentsline {subsection}{\numberline {1.8.2}Command Line Arguments}{21}{subsection.1.8.2}
-\contentsline {subsection}{\numberline {1.8.3}1) Logging}{21}{subsection.1.8.3}
-\contentsline {subsubsection}{A) Only to the log file:}{22}{subsubsection*.13}
-\contentsline {subsubsection}{B) Only to the display:}{22}{subsubsection*.14}
-\contentsline {subsubsection}{C) To both simultaneously:}{22}{subsubsection*.15}
-\contentsline {subsection}{\numberline {1.8.4}2) Tracing pipeline progress}{22}{subsection.1.8.4}
-\contentsline {subsection}{\numberline {1.8.5}3) Printing a flowchart}{23}{subsection.1.8.5}
-\contentsline {subsection}{\numberline {1.8.6}4) Running in parallel on multiple processors}{23}{subsection.1.8.6}
-\contentsline {subsection}{\numberline {1.8.7}5) Setup checkpointing so that \emph {Ruffus} knows which files are out of date}{23}{subsection.1.8.7}
-\contentsline {subsubsection}{Recreating checkpoints}{23}{subsubsection*.16}
-\contentsline {subsubsection}{Touch files}{23}{subsubsection*.17}
-\contentsline {subsection}{\numberline {1.8.8}6) Skipping specified options}{23}{subsection.1.8.8}
-\contentsline {subsection}{\numberline {1.8.9}7) Specifying verbosity and abbreviating long paths}{24}{subsection.1.8.9}
-\contentsline {subsection}{\numberline {1.8.10}8) Displaying the version}{24}{subsection.1.8.10}
-\contentsline {subsection}{\numberline {1.8.11}Template for optparse}{24}{subsection.1.8.11}
-\contentsline {section}{\numberline {1.9}\textbf {Chapter 7}: Displaying the pipeline visually with \emph {pipeline\_printout\_graph(...)}}{25}{section.1.9}
-\contentsline {subsection}{\numberline {1.9.1}Printing out a flowchart of our pipeline}{25}{subsection.1.9.1}
-\contentsline {subsection}{\numberline {1.9.2}Command line options made easier with \texttt {ruffus.cmdline}}{26}{subsection.1.9.2}
-\contentsline {subsection}{\numberline {1.9.3}Horribly complicated pipelines!}{26}{subsection.1.9.3}
-\contentsline {subsection}{\numberline {1.9.4}Circular dependency errors in pipelines!}{27}{subsection.1.9.4}
-\contentsline {subsection}{\numberline {1.9.5}\texttt {@graphviz}: Customising the appearance of each task}{28}{subsection.1.9.5}
-\contentsline {section}{\numberline {1.10}\textbf {Chapter 8}: Specifying output file names with \emph {formatter()} and \emph {regex()}}{29}{section.1.10}
-\contentsline {subsection}{\numberline {1.10.1}Review}{29}{subsection.1.10.1}
-\contentsline {subsection}{\numberline {1.10.2}A different file name \emph {suffix()} for each pipeline stage}{30}{subsection.1.10.2}
-\contentsline {subsection}{\numberline {1.10.3}\emph {formatter()} manipulates pathnames and regular expression}{31}{subsection.1.10.3}
-\contentsline {subsubsection}{Path name components}{32}{subsubsection*.18}
-\contentsline {subsubsection}{Filter and parse using regular expressions}{33}{subsubsection*.19}
-\contentsline {subsubsection}{Using \emph {@transform()} with \emph {formatter()}}{33}{subsubsection*.20}
-\contentsline {subsubsection}{string substitution for ``extra'' arguments}{34}{subsubsection*.21}
-\contentsline {subsubsection}{Changing directories using \emph {formatter()} in a zoo...}{35}{subsubsection*.22}
-\contentsline {subsection}{\numberline {1.10.4}\emph {regex()} manipulates via regular expressions}{36}{subsection.1.10.4}
-\contentsline {section}{\numberline {1.11}\textbf {Chapter 9}: Preparing directories for output with \emph {@mkdir()}}{37}{section.1.11}
-\contentsline {subsection}{\numberline {1.11.1}Overview}{37}{subsection.1.11.1}
-\contentsline {subsection}{\numberline {1.11.2}Creating directories after string substitution in a zoo...}{38}{subsection.1.11.2}
-\contentsline {subsubsection}{using \emph {formatter()}}{38}{subsubsection*.23}
-\contentsline {subsubsection}{using \emph {regex()}}{39}{subsubsection*.24}
-\contentsline {section}{\numberline {1.12}\textbf {Chapter 10}: Checkpointing: Interrupted Pipelines and Exceptions}{39}{section.1.12}
-\contentsline {subsection}{\numberline {1.12.1}Overview}{40}{subsection.1.12.1}
-\contentsline {subsection}{\numberline {1.12.2}Interrupting tasks}{40}{subsection.1.12.2}
-\contentsline {subsection}{\numberline {1.12.3}Checkpointing: only log completed jobs}{41}{subsection.1.12.3}
-\contentsline {subsection}{\numberline {1.12.4}Do not share the same checkpoint file across for multiple pipelines!}{41}{subsection.1.12.4}
-\contentsline {subsection}{\numberline {1.12.5}Setting checkpoint file names}{41}{subsection.1.12.5}
-\contentsline {subsubsection}{environment variable \texttt {DEFAULT\_RUFFUS\_HISTORY\_FILE}}{42}{subsubsection*.25}
-\contentsline {subsubsection}{Setting the checkpoint file name manually}{42}{subsubsection*.26}
-\contentsline {subsection}{\numberline {1.12.6}Useful checkpoint file name policies \texttt {DEFAULT\_RUFFUS\_HISTORY\_FILE}}{42}{subsection.1.12.6}
-\contentsline {subsubsection}{Example 1: same directory, different name}{42}{subsubsection*.27}
-\contentsline {subsubsection}{Example 2: Different directory, same name}{42}{subsubsection*.28}
-\contentsline {subsubsection}{Example 2: Different directory, same name but keep one level of subdirectory to disambiguate}{43}{subsubsection*.29}
-\contentsline {subsubsection}{Example 2: nested in common directory}{43}{subsubsection*.30}
-\contentsline {subsection}{\numberline {1.12.7}Regenerating the checkpoint file}{43}{subsection.1.12.7}
-\contentsline {subsection}{\numberline {1.12.8}Rules for determining if files are up to date}{43}{subsection.1.12.8}
-\contentsline {subsection}{\numberline {1.12.9}Missing files generate exceptions}{44}{subsection.1.12.9}
-\contentsline {subsection}{\numberline {1.12.10}Caveats: Coarse Timestamp resolution}{44}{subsection.1.12.10}
-\contentsline {subsection}{\numberline {1.12.11}Flag files: Checkpointing for the paranoid}{44}{subsection.1.12.11}
-\contentsline {section}{\numberline {1.13}\textbf {Chapter 11}: Pipeline topologies and a compendium of \emph {Ruffus} decorators}{44}{section.1.13}
-\contentsline {subsection}{\numberline {1.13.1}Overview}{44}{subsection.1.13.1}
-\contentsline {subsection}{\numberline {1.13.2}\emph {@transform}}{45}{subsection.1.13.2}
-\contentsline {subsection}{\numberline {1.13.3}A bestiary of \emph {Ruffus} decorators}{45}{subsection.1.13.3}
-\contentsline {subsection}{\numberline {1.13.4}\emph {@originate}}{45}{subsection.1.13.4}
-\contentsline {subsection}{\numberline {1.13.5}\emph {@merge}}{45}{subsection.1.13.5}
-\contentsline {subsection}{\numberline {1.13.6}\emph {@split}}{45}{subsection.1.13.6}
-\contentsline {subsection}{\numberline {1.13.7}\emph {@subdivide}}{46}{subsection.1.13.7}
-\contentsline {subsection}{\numberline {1.13.8}\emph {@collate}}{46}{subsection.1.13.8}
-\contentsline {subsection}{\numberline {1.13.9}Combinatorics}{46}{subsection.1.13.9}
-\contentsline {subsection}{\numberline {1.13.10}\emph {@product}}{47}{subsection.1.13.10}
-\contentsline {subsection}{\numberline {1.13.11}\emph {@combinations}}{47}{subsection.1.13.11}
-\contentsline {subsection}{\numberline {1.13.12}\emph {@combinations\_with\_replacement}}{47}{subsection.1.13.12}
-\contentsline {subsection}{\numberline {1.13.13}\emph {@permutations}}{47}{subsection.1.13.13}
-\contentsline {section}{\numberline {1.14}\textbf {Chapter 12}: Splitting up large tasks / files with \textbf {@split}}{47}{section.1.14}
-\contentsline {subsection}{\numberline {1.14.1}Overview}{48}{subsection.1.14.1}
-\contentsline {subsection}{\numberline {1.14.2}Example: Calculate variance for a large list of numbers in parallel}{48}{subsection.1.14.2}
-\contentsline {subsection}{\numberline {1.14.3}Output files for \emph {@split}}{48}{subsection.1.14.3}
-\contentsline {subsection}{\numberline {1.14.4}Be careful in specifying \textbf {Output} globs}{49}{subsection.1.14.4}
-\contentsline {subsection}{\numberline {1.14.5}Clean up previous pipeline runs}{49}{subsection.1.14.5}
-\contentsline {subsection}{\numberline {1.14.6}1 to many}{49}{subsection.1.14.6}
-\contentsline {subsection}{\numberline {1.14.7}Nothing to many}{50}{subsection.1.14.7}
-\contentsline {section}{\numberline {1.15}\textbf {Chapter 13}: \texttt {@merge} multiple input into a single result}{51}{section.1.15}
-\contentsline {subsection}{\numberline {1.15.1}Overview of \emph {@merge}}{51}{subsection.1.15.1}
-\contentsline {subsection}{\numberline {1.15.2}\emph {@merge} is a many to one operator}{51}{subsection.1.15.2}
-\contentsline {subsection}{\numberline {1.15.3}Example: Combining partial solutions: Calculating variances}{51}{subsection.1.15.3}
-\contentsline {section}{\numberline {1.16}\textbf {Chapter 14}: Multiprocessing, \texttt {drmaa} and Computation Clusters}{53}{section.1.16}
-\contentsline {subsection}{\numberline {1.16.1}Overview}{53}{subsection.1.16.1}
-\contentsline {subsubsection}{Multi Processing}{53}{subsubsection*.31}
-\contentsline {subsubsection}{Data sharing}{53}{subsubsection*.32}
-\contentsline {subsection}{\numberline {1.16.2}Restricting parallelism with \emph {@jobs\_limit}}{53}{subsection.1.16.2}
-\contentsline {subsection}{\numberline {1.16.3}Using \texttt {drmaa} to dispatch work to Computational Clusters or Grid engines from Ruffus jobs}{54}{subsection.1.16.3}
-\contentsline {subsubsection}{1) Use a shared drmaa session:}{54}{subsubsection*.33}
-\contentsline {subsubsection}{2) import \texttt {ruffus.drmaa\_wrapper}}{54}{subsubsection*.34}
-\contentsline {subsubsection}{3) call \emph {drmaa\_wrapper.run\_job()}}{54}{subsubsection*.35}
-\contentsline {subsubsection}{4) Use multithread: \emph {pipeline\_run(multithread = NNN)}}{55}{subsubsection*.36}
-\contentsline {subsubsection}{5) Develop locally}{55}{subsubsection*.37}
-\contentsline {subsection}{\numberline {1.16.4}Forcing a pipeline to appear up to date}{56}{subsection.1.16.4}
-\contentsline {section}{\numberline {1.17}\textbf {Chapter 15}: Logging progress through a pipeline}{56}{section.1.17}
-\contentsline {subsection}{\numberline {1.17.1}Overview}{56}{subsection.1.17.1}
-\contentsline {subsection}{\numberline {1.17.2}Logging task/job completion}{57}{subsection.1.17.2}
-\contentsline {subsubsection}{Controlling logging verbosity}{57}{subsubsection*.38}
-\contentsline {subsection}{\numberline {1.17.3}Use \emph {ruffus.cmdline}}{57}{subsection.1.17.3}
-\contentsline {subsection}{\numberline {1.17.4}Customising logging}{57}{subsection.1.17.4}
-\contentsline {subsection}{\numberline {1.17.5}Log your own messages}{58}{subsection.1.17.5}
-\contentsline {subsubsection}{1. Set up logging}{58}{subsubsection*.39}
-\contentsline {subsubsection}{2. Share the proxy}{58}{subsubsection*.40}
-\contentsline {section}{\numberline {1.18}\textbf {Chapter 16}: \emph {@subdivide} tasks to run efficiently and regroup with \emph {@collate}}{59}{section.1.18}
-\contentsline {subsection}{\numberline {1.18.1}Overview}{59}{subsection.1.18.1}
-\contentsline {subsection}{\numberline {1.18.2}\emph {@subdivide} in parallel}{59}{subsection.1.18.2}
-\contentsline {subsection}{\numberline {1.18.3}Grouping using \emph {@collate}}{61}{subsection.1.18.3}
-\contentsline {section}{\numberline {1.19}\textbf {Chapter 17}: \emph {@combinations}, \emph {@permutations} and all versus all \emph {@product}}{62}{section.1.19}
-\contentsline {subsection}{\numberline {1.19.1}Overview}{62}{subsection.1.19.1}
-\contentsline {subsection}{\numberline {1.19.2}Generating output with \emph {formatter()}}{63}{subsection.1.19.2}
-\contentsline {subsection}{\numberline {1.19.3}All vs all comparisons with \emph {@product}}{63}{subsection.1.19.3}
-\contentsline {subsection}{\numberline {1.19.4}Permute all k-tuple orderings of inputs without repeats using \emph {@permutations}}{65}{subsection.1.19.4}
-\contentsline {subsection}{\numberline {1.19.5}Select unordered k-tuples within inputs excluding repeated elements using \emph {@combinations}}{66}{subsection.1.19.5}
-\contentsline {subsection}{\numberline {1.19.6}Select unordered k-tuples within inputs \emph {including} repeated elements with \emph {@combinations\_with\_replacement}}{67}{subsection.1.19.6}
-\contentsline {section}{\numberline {1.20}\textbf {Chapter 18}: Turning parts of the pipeline on and off at runtime with \emph {@active\_if}}{69}{section.1.20}
-\contentsline {subsection}{\numberline {1.20.1}Overview}{69}{subsection.1.20.1}
-\contentsline {subsection}{\numberline {1.20.2}\emph {@active\_if} controls the state of tasks}{69}{subsection.1.20.2}
-\contentsline {section}{\numberline {1.21}\textbf {Chapter 19}: Signal the completion of each stage of our pipeline with \emph {@posttask}}{71}{section.1.21}
-\contentsline {subsection}{\numberline {1.21.1}Overview}{71}{subsection.1.21.1}
-\contentsline {subsubsection}{\textbf {@posttask}}{71}{subsubsection*.41}
-\contentsline {subsubsection}{\emph {touch\_file}}{72}{subsubsection*.42}
-\contentsline {subsubsection}{Adding several post task actions}{72}{subsubsection*.43}
-\contentsline {section}{\numberline {1.22}\textbf {Chapter 20}: Manipulating task inputs via string substitution using \emph {inputs()} and \emph {add\_inputs()}}{72}{section.1.22}
-\contentsline {subsection}{\numberline {1.22.1}Overview}{72}{subsection.1.22.1}
-\contentsline {subsection}{\numberline {1.22.2}Adding additional \emph {input} prerequisites per job with \emph {add\_inputs()}}{73}{subsection.1.22.2}
-\contentsline {subsubsection}{1. Example: compiling c++ code}{73}{subsubsection*.44}
-\contentsline {subsubsection}{2. Example: Adding a common header file with \emph {add\_inputs()}}{73}{subsubsection*.45}
-\contentsline {subsubsection}{3. Example: Additional \emph {Input} can be tasks}{74}{subsubsection*.46}
-\contentsline {subsubsection}{4. Example: Add corresponding files using \emph {add\_inputs()} with \emph {formatter} or \emph {regex}}{74}{subsubsection*.47}
-\contentsline {subsection}{\numberline {1.22.3}Replacing all input parameters with \emph {inputs()}}{75}{subsection.1.22.3}
-\contentsline {subsubsection}{5. Example: Running matching python scripts using \emph {inputs()}}{75}{subsubsection*.48}
-\contentsline {section}{\numberline {1.23}\textbf {Chapter 21}: Esoteric: Generating parameters on the fly with \emph {@files}}{75}{section.1.23}
-\contentsline {subsection}{\numberline {1.23.1}Overview}{76}{subsection.1.23.1}
-\contentsline {subsection}{\numberline {1.23.2}\emph {@files} syntax}{76}{subsection.1.23.2}
-\contentsline {subsection}{\numberline {1.23.3}A Cartesian Product, all vs all example}{77}{subsection.1.23.3}
-\contentsline {section}{\numberline {1.24}\textbf {Chapter 22}: Esoteric: Running jobs in parallel without files using \emph {@parallel}}{78}{section.1.24}
-\contentsline {subsection}{\numberline {1.24.1}\textbf {@parallel}}{78}{subsection.1.24.1}
-\contentsline {section}{\numberline {1.25}\textbf {Chapter 23}: Esoteric: Writing custom functions to decide which jobs are up to date with \emph {@check\_if\_uptodate}}{79}{section.1.25}
-\contentsline {subsection}{\numberline {1.25.1}\textbf {@check\_if\_uptodate} : Manual dependency checking}{79}{subsection.1.25.1}
-\contentsline {section}{\numberline {1.26}\textbf {Appendix 1}: Flow Chart Colours with \emph {pipeline\_printout\_graph(...)}}{80}{section.1.26}
-\contentsline {subsection}{\numberline {1.26.1}Flowchart colours}{80}{subsection.1.26.1}
-\contentsline {section}{\numberline {1.27}\textbf {Appendix 2}: How dependency is checked}{81}{section.1.27}
-\contentsline {subsection}{\numberline {1.27.1}Overview}{81}{subsection.1.27.1}
-\contentsline {subsubsection}{Running all out-of-date tasks and dependents}{81}{subsubsection*.49}
-\contentsline {subsubsection}{Forced Reruns}{82}{subsubsection*.51}
-\contentsline {subsubsection}{Esoteric option: Minimal Reruns}{82}{subsubsection*.52}
-\contentsline {section}{\numberline {1.28}\textbf {Appendix 3}: Exceptions thrown inside pipelines}{83}{section.1.28}
-\contentsline {subsection}{\numberline {1.28.1}Overview}{83}{subsection.1.28.1}
-\contentsline {subsection}{\numberline {1.28.2}Pipelines running in parallel accumulate Exceptions}{84}{subsection.1.28.2}
-\contentsline {subsection}{\numberline {1.28.3}Terminate pipeline immediately upon Exceptions}{84}{subsection.1.28.3}
-\contentsline {subsubsection}{Set \emph {pipeline\_run(exceptions\_terminate\_immediately = True)}}{84}{subsubsection*.54}
-\contentsline {subsubsection}{raise \texttt {Ruffus.JobSignalledBreak}}{84}{subsubsection*.55}
-\contentsline {subsection}{\numberline {1.28.4}Display exceptions as they occur}{85}{subsection.1.28.4}
-\contentsline {section}{\numberline {1.29}\textbf {Appendix 4}: Names exported from Ruffus}{85}{section.1.29}
-\contentsline {subsection}{\numberline {1.29.1}Ruffus Names}{85}{subsection.1.29.1}
-\contentsline {section}{\numberline {1.30}\textbf {Appendix 5}: \textbf {@files}: Deprecated syntax}{87}{section.1.30}
-\contentsline {subsection}{\numberline {1.30.1}Overview}{87}{subsection.1.30.1}
-\contentsline {subsection}{\numberline {1.30.2}\textbf {@files}}{87}{subsection.1.30.2}
-\contentsline {subsection}{\numberline {1.30.3}Running the same code on different parameters in parallel}{88}{subsection.1.30.3}
-\contentsline {subsubsection}{Checking if jobs are up to date}{89}{subsubsection*.57}
-\contentsline {section}{\numberline {1.31}\textbf {Appendix 6}: \textbf {@files\_re}: Deprecated \emph {syntax using regular expressions}}{90}{section.1.31}
-\contentsline {subsection}{\numberline {1.31.1}Overview}{90}{subsection.1.31.1}
-\contentsline {subsubsection}{Transforming input and output filenames}{90}{subsubsection*.58}
-\contentsline {subsubsection}{Collating many \emph {inputs} into a single \emph {output}}{91}{subsubsection*.60}
-\contentsline {subsubsection}{Generating \emph {input} and \emph {output} parameter using regular expresssions}{91}{subsubsection*.61}
-\contentsline {section}{\numberline {1.32}\textbf {Chapter 1}: Python Code for An introduction to basic Ruffus syntax}{92}{section.1.32}
-\contentsline {subsection}{\numberline {1.32.1}Your first Ruffus script}{92}{subsection.1.32.1}
-\contentsline {subsection}{\numberline {1.32.2}Resulting Output}{93}{subsection.1.32.2}
-\contentsline {section}{\numberline {1.33}\textbf {Chapter 1}: Python Code for Transforming data in a pipeline with \texttt {@transform}}{93}{section.1.33}
-\contentsline {subsection}{\numberline {1.33.1}Your first Ruffus script}{93}{subsection.1.33.1}
-\contentsline {subsection}{\numberline {1.33.2}Resulting Output}{94}{subsection.1.33.2}
-\contentsline {section}{\numberline {1.34}\textbf {Chapter 3}: Python Code for More on \texttt {@transform}-ing data}{95}{section.1.34}
-\contentsline {subsection}{\numberline {1.34.1}Producing several items / files per job}{95}{subsection.1.34.1}
-\contentsline {subsubsection}{Resulting Output}{96}{subsubsection*.62}
-\contentsline {subsection}{\numberline {1.34.2}Defining tasks function out of order}{96}{subsection.1.34.2}
-\contentsline {subsubsection}{Resulting Output}{97}{subsubsection*.63}
-\contentsline {subsection}{\numberline {1.34.3}Multiple dependencies}{97}{subsection.1.34.3}
-\contentsline {subsubsection}{Resulting Output}{98}{subsubsection*.64}
-\contentsline {subsection}{\numberline {1.34.4}Multiple dependencies after @follows}{99}{subsection.1.34.4}
-\contentsline {subsubsection}{Resulting Output: \texttt {first\_task} completes before \texttt {second\_task}}{100}{subsubsection*.65}
-\contentsline {section}{\numberline {1.35}\textbf {Chapter 4}: Python Code for Creating files with \texttt {@originate}}{100}{section.1.35}
-\contentsline {subsection}{\numberline {1.35.1}Using \texttt {@originate}}{101}{subsection.1.35.1}
-\contentsline {subsection}{\numberline {1.35.2}Resulting Output}{101}{subsection.1.35.2}
-\contentsline {section}{\numberline {1.36}\textbf {Chapter 5}: Python Code for Understanding how your pipeline works with \emph {pipeline\_printout(...)}}{101}{section.1.36}
-\contentsline {subsection}{\numberline {1.36.1}Display the initial state of the pipeline}{102}{subsection.1.36.1}
-\contentsline {subsection}{\numberline {1.36.2}Normal Output}{102}{subsection.1.36.2}
-\contentsline {subsection}{\numberline {1.36.3}High Verbosity Output}{102}{subsection.1.36.3}
-\contentsline {subsection}{\numberline {1.36.4}Display the partially up-to-date pipeline}{103}{subsection.1.36.4}
-\contentsline {section}{\numberline {1.37}\textbf {Chapter 7}: Python Code for Displaying the pipeline visually with \emph {pipeline\_printout\_graph(...)}}{105}{section.1.37}
-\contentsline {subsection}{\numberline {1.37.1}Code}{105}{subsection.1.37.1}
-\contentsline {subsection}{\numberline {1.37.2}Resulting Flowcharts}{106}{subsection.1.37.2}
-\contentsline {section}{\numberline {1.38}\textbf {Chapter 8}: Python Code for Specifying output file names with \emph {formatter()} and \emph {regex()}}{107}{section.1.38}
-\contentsline {subsection}{\numberline {1.38.1}Example Code for \emph {suffix()}}{107}{subsection.1.38.1}
-\contentsline {subsection}{\numberline {1.38.2}Example Code for \emph {formatter()}}{107}{subsection.1.38.2}
-\contentsline {subsection}{\numberline {1.38.3}Example Code for \emph {formatter()} with replacements in \emph {extra} arguments}{108}{subsection.1.38.3}
-\contentsline {subsection}{\numberline {1.38.4}Example Code for \emph {formatter()} in Zoos}{109}{subsection.1.38.4}
-\contentsline {subsection}{\numberline {1.38.5}Example Code for \emph {regex()} in zoos}{110}{subsection.1.38.5}
-\contentsline {section}{\numberline {1.39}\textbf {Chapter 9}: Python Code for Preparing directories for output with \emph {@mkdir()}}{110}{section.1.39}
-\contentsline {subsection}{\numberline {1.39.1}Code for \emph {formatter()} Zoo example}{111}{subsection.1.39.1}
-\contentsline {subsection}{\numberline {1.39.2}Code for \emph {regex()} Zoo example}{111}{subsection.1.39.2}
-\contentsline {section}{\numberline {1.40}\textbf {Chapter 10}: Python Code for Checkpointing: Interrupted Pipelines and Exceptions}{112}{section.1.40}
-\contentsline {subsection}{\numberline {1.40.1}Code for .:ref:\emph {suffix() \textless {}decorators.suffix\textgreater {}} example}{112}{subsection.1.40.1}
-\contentsline {section}{\numberline {1.41}\textbf {Chapter 12}: Python Code for Splitting up large tasks / files with \textbf {@split}}{113}{section.1.41}
-\contentsline {subsection}{\numberline {1.41.1}Splitting large jobs}{113}{subsection.1.41.1}
-\contentsline {subsection}{\numberline {1.41.2}Resulting Output}{114}{subsection.1.41.2}
-\contentsline {section}{\numberline {1.42}\textbf {Chapter 13}: Python Code for \texttt {@merge} multiple input into a single result}{114}{section.1.42}
-\contentsline {subsection}{\numberline {1.42.1}Splitting large jobs}{115}{subsection.1.42.1}
-\contentsline {subsection}{\numberline {1.42.2}Resulting Output}{116}{subsection.1.42.2}
-\contentsline {section}{\numberline {1.43}\textbf {Chapter 14}: Python Code for Multiprocessing, \texttt {drmaa} and Computation Clusters}{117}{section.1.43}
-\contentsline {subsection}{\numberline {1.43.1}\emph {@jobs\_limit}}{117}{subsection.1.43.1}
-\contentsline {subsection}{\numberline {1.43.2}Using \texttt {ruffus.drmaa\_wrapper}}{119}{subsection.1.43.2}
-\contentsline {section}{\numberline {1.44}\textbf {Chapter 15}: Python Code for Logging progress through a pipeline}{120}{section.1.44}
-\contentsline {subsection}{\numberline {1.44.1}Rotating set of file logs}{120}{subsection.1.44.1}
-\contentsline {section}{\numberline {1.45}\textbf {Chapter 16}: Python Code for \emph {@subdivide} tasks to run efficiently and regroup with \emph {@collate}}{121}{section.1.45}
-\contentsline {subsection}{\numberline {1.45.1}\emph {@subdivide} and regroup with \emph {@collate} example}{121}{subsection.1.45.1}
-\contentsline {section}{\numberline {1.46}\textbf {Chapter 17}: Python Code for \emph {@combinations}, \emph {@permutations} and all versus all \emph {@product}}{123}{section.1.46}
-\contentsline {subsection}{\numberline {1.46.1}Example code for \emph {@product}}{123}{subsection.1.46.1}
-\contentsline {subsection}{\numberline {1.46.2}Example code for \emph {@permutations}}{125}{subsection.1.46.2}
-\contentsline {subsection}{\numberline {1.46.3}Example code for \emph {@combinations}}{126}{subsection.1.46.3}
-\contentsline {subsection}{\numberline {1.46.4}Example code for \emph {@combinations\_with\_replacement}}{127}{subsection.1.46.4}
-\contentsline {section}{\numberline {1.47}\textbf {Chapter 20}: Python Code for Manipulating task inputs via string substitution using \emph {inputs()} and \emph {add\_inputs()}}{128}{section.1.47}
-\contentsline {subsection}{\numberline {1.47.1}Example code for adding additional \emph {input} prerequisites per job with \emph {add\_inputs()}}{128}{subsection.1.47.1}
-\contentsline {subsubsection}{1. Example: compiling c++ code}{128}{subsubsection*.66}
-\contentsline {subsubsection}{2. Example: Adding a common header file with \emph {add\_inputs()}}{129}{subsubsection*.67}
-\contentsline {subsubsection}{3. Example: Additional \emph {Input} can be tasks}{129}{subsubsection*.68}
-\contentsline {subsubsection}{4. Example: Add corresponding files using \emph {add\_inputs()} with \emph {formatter} or \emph {regex}}{130}{subsubsection*.69}
-\contentsline {subsection}{\numberline {1.47.2}Example code for replacing all input parameters with \emph {inputs()}}{130}{subsection.1.47.2}
-\contentsline {subsubsection}{5. Example: Running matching python scripts using \emph {inputs()}}{130}{subsubsection*.70}
-\contentsline {section}{\numberline {1.48}\textbf {Chapter 21}: Esoteric: Python Code for Generating parameters on the fly with \emph {@files}}{131}{section.1.48}
-\contentsline {subsection}{\numberline {1.48.1}Introduction}{131}{subsection.1.48.1}
-\contentsline {subsection}{\numberline {1.48.2}Code}{132}{subsection.1.48.2}
-\contentsline {subsection}{\numberline {1.48.3}Resulting Output}{136}{subsection.1.48.3}
-\contentsline {section}{\numberline {1.49}\textbf {Appendix 1}: Python code for Flow Chart Colours with \emph {pipeline\_printout\_graph(...)}}{136}{section.1.49}
-\contentsline {subsection}{\numberline {1.49.1}Code}{137}{subsection.1.49.1}
-\contentsline {chapter}{\numberline {2}Overview:}{143}{chapter.2}
-\contentsline {section}{\numberline {2.1}Cheat Sheet}{143}{section.2.1}
-\contentsline {subsection}{\numberline {2.1.1}1. Annotate functions with \textbf {Ruffus} decorators}{144}{subsection.2.1.1}
-\contentsline {subsubsection}{Core}{144}{subsubsection*.71}
-\contentsline {subsubsection}{See \emph {Decorators} for a complete list of decorators}{144}{subsubsection*.72}
-\contentsline {subsection}{\numberline {2.1.2}2. Print dependency graph if necessary}{144}{subsection.2.1.2}
-\contentsline {subsection}{\numberline {2.1.3}3. Run the pipeline}{145}{subsection.2.1.3}
-\contentsline {section}{\numberline {2.2}Pipeline functions}{145}{section.2.2}
-\contentsline {subsection}{\numberline {2.2.1}\emph {pipeline\_run}}{145}{subsection.2.2.1}
-\contentsline {subsection}{\numberline {2.2.2}\emph {pipeline\_printout}}{147}{subsection.2.2.2}
-\contentsline {subsection}{\numberline {2.2.3}\emph {pipeline\_printout\_graph}}{148}{subsection.2.2.3}
-\contentsline {subsection}{\numberline {2.2.4}\emph {pipeline\_get\_task\_names}}{151}{subsection.2.2.4}
-\contentsline {section}{\numberline {2.3}drmaa functions}{151}{section.2.3}
-\contentsline {subsection}{\numberline {2.3.1}\emph {run\_job}}{151}{subsection.2.3.1}
-\contentsline {section}{\numberline {2.4}Installation}{154}{section.2.4}
-\contentsline {subsection}{\numberline {2.4.1}The easy way}{154}{subsection.2.4.1}
-\contentsline {subsection}{\numberline {2.4.2}The most up-to-date code:}{154}{subsection.2.4.2}
-\contentsline {subsubsection}{Graphical flowcharts}{154}{subsubsection*.254}
-\contentsline {section}{\numberline {2.5}Design \& Architecture}{155}{section.2.5}
-\contentsline {subsection}{\numberline {2.5.1}\emph {GNU Make}}{155}{subsection.2.5.1}
-\contentsline {subsubsection}{Deficiencies of \emph {make} / \emph {gmake}}{155}{subsubsection*.255}
-\contentsline {subsection}{\numberline {2.5.2}\emph {Scons}, \emph {Rake} and other \emph {Make} alternatives}{155}{subsection.2.5.2}
-\contentsline {subsubsection}{Implicit dependencies: disadvantages of \emph {make} / \emph {scons} / \emph {rake}}{156}{subsubsection*.256}
-\contentsline {subsubsection}{Explicit dependencies in \emph {Ruffus}}{156}{subsubsection*.257}
-\contentsline {subsubsection}{Static dependencies: What \emph {make} / \emph {scons} / \emph {rake} can't do (easily)}{156}{subsubsection*.258}
-\contentsline {subsection}{\numberline {2.5.3}Managing pipelines stage-by-stage using \textbf {Ruffus}}{157}{subsection.2.5.3}
-\contentsline {subsubsection}{Disadvantages of the Ruffus design}{158}{subsubsection*.259}
-\contentsline {subsection}{\numberline {2.5.4}Alternatives to \textbf {Ruffus}}{159}{subsection.2.5.4}
-\contentsline {subsubsection}{Acknowledgements}{159}{subsubsection*.260}
-\contentsline {section}{\numberline {2.6}Major Features added to Ruffus}{160}{section.2.6}
-\contentsline {subsection}{\numberline {2.6.1}version 2.5RC}{160}{subsection.2.6.1}
-\contentsline {subsubsection}{1) Python3 compatability (but at least python 2.6 is now required)}{160}{subsubsection*.261}
-\contentsline {subsubsection}{2) Ctrl-C interrupts}{160}{subsubsection*.262}
-\contentsline {subsubsection}{3) Customising flowcharts in pipeline\_printout\_graph() with \texttt {@graphviz}}{160}{subsubsection*.263}
-\contentsline {subsubsection}{4. Consistent verbosity levels}{161}{subsubsection*.264}
-\contentsline {subsubsection}{5. Allow abbreviated paths from \texttt {pipeline\_run} or \texttt {pipeline\_printout}}{162}{subsubsection*.265}
-\contentsline {subsubsection}{Other changes}{163}{subsubsection*.266}
-\contentsline {subsection}{\numberline {2.6.2}version 2.4.1}{163}{subsection.2.6.2}
-\contentsline {subsection}{\numberline {2.6.3}version 2.4}{163}{subsection.2.6.3}
-\contentsline {subsubsection}{Additions to \texttt {ruffus} namespace}{163}{subsubsection*.267}
-\contentsline {subsubsection}{Installation: use pip}{163}{subsubsection*.268}
-\contentsline {subsubsection}{1) Command Line support}{163}{subsubsection*.269}
-\contentsline {subsubsection}{2) Check pointing}{164}{subsubsection*.270}
-\contentsline {subsubsection}{3) \emph {subdivide()} (\emph {syntax})}{164}{subsubsection*.271}
-\contentsline {subsubsection}{4) \emph {mkdir()} (\emph {syntax}) with \emph {formatter()}, \emph {suffix()} and \emph {regex()}}{164}{subsubsection*.272}
-\contentsline {subsubsection}{5) \emph {originate()} (\emph {syntax})}{164}{subsubsection*.273}
-\contentsline {subsubsection}{6) New flexible \emph {formatter()} (\emph {syntax}) alternative to \emph {regex()} \& \emph {suffix()}}{165}{subsubsection*.274}
-\contentsline {subsubsection}{7) Combinatorics (all vs. all decorators)}{165}{subsubsection*.275}
-\contentsline {subsubsection}{8) drmaa support and multithreading:}{165}{subsubsection*.276}
-\contentsline {subsubsection}{9) \texttt {pipeline\_run(...)} and exceptions}{165}{subsubsection*.277}
-\contentsline {subsubsection}{10) Miscellaneous}{165}{subsubsection*.278}
-\contentsline {subsection}{\numberline {2.6.4}version 2.3}{166}{subsection.2.6.4}
-\contentsline {subsection}{\numberline {2.6.5}version 2.2}{167}{subsection.2.6.5}
-\contentsline {subsection}{\numberline {2.6.6}version 2.1.1}{168}{subsection.2.6.6}
-\contentsline {subsection}{\numberline {2.6.7}version 2.1.0}{169}{subsection.2.6.7}
-\contentsline {subsection}{\numberline {2.6.8}version 2.0.10}{169}{subsection.2.6.8}
-\contentsline {subsection}{\numberline {2.6.9}version 2.0.9}{170}{subsection.2.6.9}
-\contentsline {subsection}{\numberline {2.6.10}version 2.0.8}{171}{subsection.2.6.10}
-\contentsline {subsection}{\numberline {2.6.11}version 2.0.2}{171}{subsection.2.6.11}
-\contentsline {subsection}{\numberline {2.6.12}version 2.0}{171}{subsection.2.6.12}
-\contentsline {subsection}{\numberline {2.6.13}version 1.1.4}{171}{subsection.2.6.13}
-\contentsline {subsection}{\numberline {2.6.14}version 1.0.7}{171}{subsection.2.6.14}
-\contentsline {subsection}{\numberline {2.6.15}version 1.0}{171}{subsection.2.6.15}
-\contentsline {section}{\numberline {2.7}Fixed Bugs}{172}{section.2.7}
-\contentsline {section}{\numberline {2.8}Future Changes to Ruffus}{172}{section.2.8}
-\contentsline {subsection}{\numberline {2.8.1}Todo: pipeline\_printout\_graph should print inactive tasks}{172}{subsection.2.8.1}
-\contentsline {subsection}{\numberline {2.8.2}Todo: Mark input strings as non-file names, and add support for dynamically returned parameters}{172}{subsection.2.8.2}
-\contentsline {subsection}{\numberline {2.8.3}Todo: Allow ``extra'' parameters to be used in output substitution}{172}{subsection.2.8.3}
-\contentsline {subsection}{\numberline {2.8.4}Todo: Extra signalling before and after each task and job}{173}{subsection.2.8.4}
-\contentsline {subsection}{\numberline {2.8.5}Todo: \texttt {@split} / \texttt {@subdivide} returns the actual output created}{173}{subsection.2.8.5}
-\contentsline {subsubsection}{Checkpointing}{174}{subsubsection*.279}
-\contentsline {subsection}{\numberline {2.8.6}Todo: New decorators}{174}{subsection.2.8.6}
-\contentsline {subsubsection}{Todo: \texttt {@originate}}{174}{subsubsection*.280}
-\contentsline {subsubsection}{Todo: \texttt {@recombine}}{174}{subsubsection*.281}
-\contentsline {subsection}{\numberline {2.8.7}Todo: Named parameters in decorators for clarity}{174}{subsection.2.8.7}
-\contentsline {subsection}{\numberline {2.8.8}Todo: Bioinformatics example to end all examples}{174}{subsection.2.8.8}
-\contentsline {subsection}{\numberline {2.8.9}Todo: Allow the next task to start before all jobs in the previous task have finished}{175}{subsection.2.8.9}
-\contentsline {subsubsection}{Converting to per-job rather than per task dependencies}{175}{subsubsection*.282}
-\contentsline {subsubsection}{Implementation}{175}{subsubsection*.283}
-\contentsline {section}{\numberline {2.9}Planned Improvements to Ruffus}{176}{section.2.9}
-\contentsline {subsection}{\numberline {2.9.1}Planned: Running python code (task functions) transparently on remote cluster nodes}{176}{subsection.2.9.1}
-\contentsline {subsection}{\numberline {2.9.2}Planned: Custom parameter generator}{177}{subsection.2.9.2}
-\contentsline {subsection}{\numberline {2.9.3}Planned: Ruffus GUI interface.}{177}{subsection.2.9.3}
-\contentsline {subsection}{\numberline {2.9.4}Planned: Non-decorator / Function interface to Ruffus}{177}{subsection.2.9.4}
-\contentsline {subsection}{\numberline {2.9.5}Planned: Remove intermediate files}{177}{subsection.2.9.5}
-\contentsline {subsection}{\numberline {2.9.6}Planned: @retry\_on\_error(NUM\_OF\_RETRIES)}{178}{subsection.2.9.6}
-\contentsline {subsection}{\numberline {2.9.7}Planned: Clean up}{178}{subsection.2.9.7}
-\contentsline {section}{\numberline {2.10}Implementation Tips}{179}{section.2.10}
-\contentsline {subsection}{\numberline {2.10.1}Release}{179}{subsection.2.10.1}
-\contentsline {subsection}{\numberline {2.10.2}dbdict.py}{180}{subsection.2.10.2}
-\contentsline {subsection}{\numberline {2.10.3}how to write new decorators}{180}{subsection.2.10.3}
-\contentsline {section}{\numberline {2.11}Implementation notes}{181}{section.2.11}
-\contentsline {subsection}{\numberline {2.11.1}\texttt {Ctrl-C} handling}{181}{subsection.2.11.1}
-\contentsline {subsection}{\numberline {2.11.2}Python3 compatability}{182}{subsection.2.11.2}
-\contentsline {subsection}{\numberline {2.11.3}Refactoring: parameter handling}{183}{subsection.2.11.3}
-\contentsline {subsection}{\numberline {2.11.4}\texttt {formatter}}{183}{subsection.2.11.4}
-\contentsline {subsubsection}{\texttt {formatter()}: \texttt {regex()} and \texttt {suffix()}}{184}{subsubsection*.286}
-\contentsline {subsection}{\numberline {2.11.5}@product()}{184}{subsection.2.11.5}
-\contentsline {subsection}{\numberline {2.11.6}\texttt {@permutations(...),} \texttt {@combinations(...),} \texttt {@combinations\_with\_replacement(...)}}{185}{subsection.2.11.6}
-\contentsline {subsection}{\numberline {2.11.7}drmaa alternatives}{185}{subsection.2.11.7}
-\contentsline {subsection}{\numberline {2.11.8}Task completion monitoring}{185}{subsection.2.11.8}
-\contentsline {subsubsection}{How easy is it to abstract out the database?}{185}{subsubsection*.287}
-\contentsline {subsubsection}{Can we query the database, get Job history / stats?}{185}{subsubsection*.288}
-\contentsline {subsubsection}{What are the run time performance implications?}{186}{subsubsection*.289}
-\contentsline {subsubsection}{Avoid pauses between tasks}{186}{subsubsection*.290}
-\contentsline {subsection}{\numberline {2.11.9}\texttt {@mkdir(...),}}{186}{subsection.2.11.9}
-\contentsline {section}{\numberline {2.12}FAQ}{186}{section.2.12}
-\contentsline {subsection}{\numberline {2.12.1}Citations}{186}{subsection.2.12.1}
-\contentsline {subsubsection}{Q. How should \emph {Ruffus} be cited in academic publications?}{186}{subsubsection*.291}
-\contentsline {subsection}{\numberline {2.12.2}Good practices}{186}{subsection.2.12.2}
-\contentsline {subsubsection}{Q. What is the best way of keeping my data and workings separate?}{186}{subsubsection*.292}
-\contentsline {subsubsection}{Q. What is the best way of handling data in file pairs (or triplets etc.)}{187}{subsubsection*.293}
-\contentsline {subsection}{\numberline {2.12.3}General}{188}{subsection.2.12.3}
-\contentsline {subsubsection}{Q. \emph {Ruffus} won't create dependency graphs}{188}{subsubsection*.294}
-\contentsline {subsubsection}{Q. \emph {Ruffus} seems to be hanging in the same place}{188}{subsubsection*.295}
-\contentsline {subsubsection}{Q. Regular expression substitutions don't work}{188}{subsubsection*.296}
-\contentsline {subsubsection}{Q. How to force a pipeline to appear up to date?}{189}{subsubsection*.297}
-\contentsline {subsubsection}{Q. How can I use my own decorators with Ruffus?}{189}{subsubsection*.298}
-\contentsline {paragraph}{1. Use @wraps from \texttt {functools} or Michele Simionato's decorator module}{189}{paragraph*.299}
-\contentsline {paragraph}{2. Always call Ruffus decorators first before your own decorators.}{189}{paragraph*.300}
-\contentsline {paragraph}{Example decorator:}{190}{paragraph*.301}
-\contentsline {paragraph}{1. Using functools @wraps}{190}{paragraph*.302}
-\contentsline {paragraph}{2. Using Michele Simionato's decorator module}{191}{paragraph*.303}
-\contentsline {paragraph}{2. By hand, using a callable object}{191}{paragraph*.304}
-\contentsline {subsubsection}{Q. Can a task function in a \emph {Ruffus} pipeline be called normally outside of Ruffus?}{191}{subsubsection*.305}
-\contentsline {subsubsection}{Q. My \emph {Ruffus} tasks create two files at a time. Why is the second one ignored in successive stages of my pipeline?}{191}{subsubsection*.306}
-\contentsline {subsubsection}{Q. How can a \emph {Ruffus} task produce output which goes off in different directions?}{192}{subsubsection*.307}
-\contentsline {subsubsection}{Q. Can I call extra code before each job?}{193}{subsubsection*.308}
-\contentsline {subsubsection}{Q. Does \emph {Ruffus} allow checkpointing: to distinguish interrupted and completed results?}{194}{subsubsection*.309}
-\contentsline {paragraph}{A. Use the builtin sqlite checkpointing}{194}{paragraph*.310}
-\contentsline {paragraph}{A. Use a flag file}{194}{paragraph*.311}
-\contentsline {paragraph}{A. Use a temp file}{195}{paragraph*.312}
-\contentsline {subsection}{\numberline {2.12.4}Windows}{196}{subsection.2.12.4}
-\contentsline {subsubsection}{Q. Windows seems to spawn \emph {ruffus} processes recursively}{196}{subsubsection*.313}
-\contentsline {subsection}{\numberline {2.12.5}Sun Grid Engine / PBS / SLURM etc}{196}{subsection.2.12.5}
-\contentsline {subsubsection}{Q. Can Ruffus be used to manage a cluster or grid based pipeline?}{196}{subsubsection*.314}
-\contentsline {subsubsection}{Q. When I submit lots of jobs via Sun Grid Engine (SGE), the head node occassionally freezes and dies}{197}{subsubsection*.315}
-\contentsline {subsubsection}{Q. Keeping Large intermediate files}{197}{subsubsection*.316}
-\contentsline {subsection}{\numberline {2.12.6}Sharing python objects between Ruffus processes running concurrently}{197}{subsection.2.12.6}
-\contentsline {subsubsection}{Can ordinary python objects be shared between processes?}{198}{subsubsection*.317}
-\contentsline {subsubsection}{Why am I getting \texttt {PicklingError}?}{198}{subsubsection*.318}
-\contentsline {subsubsection}{How about synchronising python objects in real time?}{199}{subsubsection*.319}
-\contentsline {subsubsection}{Can I share and synchronise my own python classes via proxies?}{199}{subsubsection*.320}
-\contentsline {subsubsection}{How do I send python objects back and forth without tangling myself in horrible synchronisation code?}{200}{subsubsection*.321}
-\contentsline {subsubsection}{How do I share large amounts of data efficiently across processes?}{200}{subsubsection*.322}
-\contentsline {section}{\numberline {2.13}Glossary}{200}{section.2.13}
-\contentsline {section}{\numberline {2.14}Hall of Fame: User contributed flowcharts}{201}{section.2.14}
-\contentsline {subsection}{\numberline {2.14.1}RNASeq pipeline}{201}{subsection.2.14.1}
-\contentsline {subsection}{\numberline {2.14.2}non-coding evolutionary constraints}{203}{subsection.2.14.2}
-\contentsline {subsection}{\numberline {2.14.3}SNP annotation}{203}{subsection.2.14.3}
-\contentsline {subsection}{\numberline {2.14.4}Chip-Seq analysis}{204}{subsection.2.14.4}
-\contentsline {section}{\numberline {2.15}Why \emph {Ruffus}?}{204}{section.2.15}
-\contentsline {chapter}{\numberline {3}Examples}{207}{chapter.3}
-\contentsline {section}{\numberline {3.1}Construction of a simple pipeline to run BLAST jobs}{207}{section.3.1}
-\contentsline {subsection}{\numberline {3.1.1}Overview}{207}{subsection.3.1.1}
-\contentsline {subsection}{\numberline {3.1.2}Prerequisites}{207}{subsection.3.1.2}
-\contentsline {subsubsection}{1. Ruffus}{207}{subsubsection*.329}
-\contentsline {subsubsection}{2. BLAST}{208}{subsubsection*.330}
-\contentsline {subsubsection}{3. human refseq sequence database}{208}{subsubsection*.331}
-\contentsline {subsubsection}{4. test sequences}{208}{subsubsection*.332}
-\contentsline {subsection}{\numberline {3.1.3}Code}{208}{subsection.3.1.3}
-\contentsline {subsection}{\numberline {3.1.4}Step 1. Splitting up the query sequences}{208}{subsection.3.1.4}
-\contentsline {subsection}{\numberline {3.1.5}Step 2. Run BLAST jobs in parallel}{209}{subsection.3.1.5}
-\contentsline {subsection}{\numberline {3.1.6}Step 3. Combining BLAST results}{209}{subsection.3.1.6}
-\contentsline {subsection}{\numberline {3.1.7}Step 4. Running the pipeline}{210}{subsection.3.1.7}
-\contentsline {subsection}{\numberline {3.1.8}Step 5. Testing dependencies}{210}{subsection.3.1.8}
-\contentsline {subsection}{\numberline {3.1.9}What is next?}{211}{subsection.3.1.9}
-\contentsline {section}{\numberline {3.2}Part 2: A slightly more practical pipeline to run blasts jobs}{211}{section.3.2}
-\contentsline {subsection}{\numberline {3.2.1}Overview}{211}{subsection.3.2.1}
-\contentsline {subsection}{\numberline {3.2.2}Step 1. Cleaning up any leftover junk from previous pipeline runs}{212}{subsection.3.2.2}
-\contentsline {subsection}{\numberline {3.2.3}Step 2. Adding a ``flag'' file to mark successful completion}{212}{subsection.3.2.3}
-\contentsline {subsection}{\numberline {3.2.4}Step 3. Allowing the script to be invoked on the command line}{213}{subsection.3.2.4}
-\contentsline {subsection}{\numberline {3.2.5}Step 4. Printing out a flowchart for the pipeline}{213}{subsection.3.2.5}
-\contentsline {subsection}{\numberline {3.2.6}Step 5. Errors}{213}{subsection.3.2.6}
-\contentsline {subsection}{\numberline {3.2.7}Step 6. Will it run?}{214}{subsection.3.2.7}
-\contentsline {section}{\numberline {3.3}Ruffus code}{215}{section.3.3}
-\contentsline {section}{\numberline {3.4}Ruffus code}{216}{section.3.4}
-\contentsline {section}{\numberline {3.5}Example code for \emph {FAQ Good practices: ``What is the best way of handling data in file pairs (or triplets etc.)?''}}{220}{section.3.5}
-\contentsline {chapter}{\numberline {4}Reference:}{223}{chapter.4}
-\contentsline {section}{\numberline {4.1}Decorators}{223}{section.4.1}
-\contentsline {subsection}{\numberline {4.1.1}Ruffus Decorators}{223}{subsection.4.1.1}
-\contentsline {subsubsection}{\emph {Core}}{223}{subsubsection*.333}
-\contentsline {subsubsection}{\emph {Combinatorics}}{225}{subsubsection*.334}
-\contentsline {subsubsection}{\emph {Advanced}}{227}{subsubsection*.335}
-\contentsline {subsubsection}{\emph {Esoteric!}}{228}{subsubsection*.336}
-\contentsline {subsection}{\numberline {4.1.2}Indicator Objects}{228}{subsection.4.1.2}
-\contentsline {subsubsection}{\emph {formatter}}{228}{subsubsection*.337}
-\contentsline {subsubsection}{\emph {suffix}}{231}{subsubsection*.338}
-\contentsline {subsubsection}{\emph {regex}}{232}{subsubsection*.339}
-\contentsline {subsubsection}{\emph {add\_inputs}}{232}{subsubsection*.340}
-\contentsline {subsubsection}{\emph {inputs}}{233}{subsubsection*.341}
-\contentsline {subsubsection}{\emph {mkdir}}{234}{subsubsection*.342}
-\contentsline {subsubsection}{\emph {touch\_file}}{234}{subsubsection*.343}
-\contentsline {subsubsection}{\emph {output\_from}}{235}{subsubsection*.344}
-\contentsline {subsubsection}{\emph {combine}}{235}{subsubsection*.345}
-\contentsline {subsection}{\numberline {4.1.3}@originate}{237}{subsection.4.1.3}
-\contentsline {subsubsection}{\emph {@originate} ( \emph {output\_files}, {[}\emph {extra\_parameters},...{]} )}{237}{subsubsection*.349}
-\contentsline {subsection}{\numberline {4.1.4}@split}{237}{subsection.4.1.4}
-\contentsline {subsubsection}{\emph {@split} ( \emph {tasks\_or\_file\_names}, \emph {output\_files}, {[}\emph {extra\_parameters},...{]} )}{237}{subsubsection*.357}
-\contentsline {subsection}{\numberline {4.1.5}@split with \texttt {regex(...)}, \texttt {add\_inputs} and \texttt {inputs}}{237}{subsection.4.1.5}
-\contentsline {subsection}{\numberline {4.1.6}@transform}{237}{subsection.4.1.6}
-\contentsline {subsubsection}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{237}{subsubsection*.372}
-\contentsline {subsection}{\numberline {4.1.7}@merge}{237}{subsection.4.1.7}
-\contentsline {subsubsection}{\emph {@merge} ( \emph {tasks\_or\_file\_names}, \emph {output\_file}, {[}\emph {extra\_parameters},...{]} )}{237}{subsubsection*.384}
-\contentsline {subsection}{\numberline {4.1.8}@subdivide}{239}{subsection.4.1.8}
-\contentsline {subsubsection}{\emph {@subdivide} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[} \emph {inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs} \emph {(}\emph {input\_pattern\_or\_glob}\emph {)} {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{239}{subsubsection*.399}
-\contentsline {subsection}{\numberline {4.1.9}@transform with \texttt {add\_inputs} and \texttt {inputs}}{239}{subsection.4.1.9}
-\contentsline {subsubsection}{\emph {@transform} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {inputs} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{239}{subsubsection*.419}
-\contentsline {subsection}{\numberline {4.1.10}@collate}{239}{subsection.4.1.10}
-\contentsline {subsubsection}{\emph {@collate} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{239}{subsubsection*.436}
-\contentsline {subsection}{\numberline {4.1.11}@collate with \texttt {add\_inputs} and \texttt {inputs}}{239}{subsection.4.1.11}
-\contentsline {subsubsection}{\emph {@collate} ( \emph {tasks\_or\_file\_names}, \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[}\emph {inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)} \textbar {} \emph {add\_inputs}\emph {(}\emph {input\_pattern\_or\_glob}\emph {)}{]} , \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{239}{subsubsection*.453}
-\contentsline {subsection}{\numberline {4.1.12}@graphviz}{239}{subsection.4.1.12}
-\contentsline {subsubsection}{\emph {@graphviz} ( \emph {graphviz\_parameters},...{]} )}{239}{subsubsection*.461}
-\contentsline {subsection}{\numberline {4.1.13}@mkdir}{239}{subsection.4.1.13}
-\contentsline {subsubsection}{\emph {@mkdir} ( \emph {tasks\_or\_file\_names}, \emph {suffix}\emph {(}\emph {suffix\_string}\emph {)}\textbar {} \emph {regex}\emph {(}\emph {matching\_regex}\emph {)} \textbar {} \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern})}{239}{subsubsection*.472}
-\contentsline {subsection}{\numberline {4.1.14}@jobs\_limit}{239}{subsection.4.1.14}
-\contentsline {subsubsection}{\emph {@jobs\_limit} ( \emph {maximum\_num\_of\_jobs}, {[} \emph {name} {]})}{239}{subsubsection*.481}
-\contentsline {subsection}{\numberline {4.1.15}@posttask}{239}{subsection.4.1.15}
-\contentsline {subsubsection}{\emph {@posttask} (\emph {function} \textbar {} \emph {touch\_file}\emph {(}\emph {file\_name}\emph {)})}{239}{subsubsection*.487}
-\contentsline {subsection}{\numberline {4.1.16}@active\_if}{239}{subsection.4.1.16}
-\contentsline {subsubsection}{\emph {@active\_if}(on\_or\_off1, {[}on\_or\_off2,...{]})}{239}{subsubsection*.491}
-\contentsline {subsection}{\numberline {4.1.17}@follows}{239}{subsection.4.1.17}
-\contentsline {subsubsection}{\emph {@follows}(\emph {task} \textbar {} \emph {``task\_name''} \textbar {} \emph {mkdir} (\emph {directory\_name}), {[}more\_tasks, ...{]})}{239}{subsubsection*.499}
-\contentsline {subsection}{\numberline {4.1.18}@product}{241}{subsection.4.1.18}
-\contentsline {subsubsection}{\emph {@product} ( \emph {tasks\_or\_file\_names}, \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, {[}\emph {tasks\_or\_file\_names}, \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, ... {]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{241}{subsubsection*.510}
-\contentsline {subsection}{\numberline {4.1.19}@permutations}{241}{subsection.4.1.19}
-\contentsline {subsubsection}{\emph {@permutations} ( \emph {tasks\_or\_file\_names}, \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{241}{subsubsection*.522}
-\contentsline {subsection}{\numberline {4.1.20}@combinations}{241}{subsection.4.1.20}
-\contentsline {subsubsection}{\emph {@combinations} ( \emph {tasks\_or\_file\_names}, \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{241}{subsubsection*.534}
-\contentsline {subsection}{\numberline {4.1.21}@combinations\_with\_replacement}{241}{subsection.4.1.21}
-\contentsline {subsubsection}{\emph {@combinations\_with\_replacement} ( \emph {tasks\_or\_file\_names}, \emph {formatter}\emph {(}\emph {matching\_formatter}\emph {)}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]} )}{241}{subsubsection*.546}
-\contentsline {subsection}{\numberline {4.1.22}Generating parameters on the fly for @files}{243}{subsection.4.1.22}
-\contentsline {subsubsection}{\emph {@files} (\emph {custom\_function})}{243}{subsubsection*.552}
-\contentsline {subsection}{\numberline {4.1.23}@check\_if\_uptodate}{243}{subsection.4.1.23}
-\contentsline {subsubsection}{\emph {@check\_if\_uptodate} (\emph {dependency\_checking\_function})}{243}{subsubsection*.555}
-\contentsline {subsection}{\numberline {4.1.24}@parallel}{243}{subsection.4.1.24}
-\contentsline {subsubsection}{\emph {@parallel} ( {[} {[}\emph {job\_params}, ...{]}, {[}\emph {job\_params}, ...{]}...{]} \textbar {} \emph {parameter\_generating\_function})}{243}{subsubsection*.560}
-\contentsline {subsection}{\numberline {4.1.25}@files}{245}{subsection.4.1.25}
-\contentsline {subsubsection}{\emph {@files} (\emph {input1}, \emph {output1}, {[}\emph {extra\_parameters1}, ...{]})}{245}{subsubsection*.574}
-\contentsline {paragraph}{@files for single jobs}{245}{paragraph*.575}
-\contentsline {subsubsection}{\emph {@files} ( \emph {((} \emph {input}, \emph {output}, {[}\emph {extra\_parameters},...{]} \emph {), (...), ...)} )}{245}{subsubsection*.579}
-\contentsline {paragraph}{@files in parallel}{245}{paragraph*.580}
-\contentsline {subsection}{\numberline {4.1.26}@files\_re}{245}{subsection.4.1.26}
-\contentsline {subsubsection}{\emph {@files\_re} (\emph {tasks\_or\_file\_names}, \emph {matching\_regex}, {[}\emph {input\_pattern}{]}, \emph {output\_pattern}, {[}\emph {extra\_parameters},...{]})}{245}{subsubsection*.594}
-\contentsline {paragraph}{Legacy design now deprecated. We suggest using \emph {@transform()} instead}{245}{paragraph*.595}
-\contentsline {section}{\numberline {4.2}Modules:}{246}{section.4.2}
-\contentsline {subsection}{\numberline {4.2.1}ruffus.Task}{246}{subsection.4.2.1}
-\contentsline {subsubsection}{Decorators}{246}{subsubsection*.601}
-\contentsline {subsubsection}{Pipeline functions}{246}{subsubsection*.602}
-\contentsline {paragraph}{pipeline\_run}{246}{paragraph*.603}
-\contentsline {paragraph}{pipeline\_printout}{247}{paragraph*.605}
-\contentsline {paragraph}{pipeline\_printout\_graph}{248}{paragraph*.607}
-\contentsline {subsubsection}{Logging}{249}{subsubsection*.609}
-\contentsline {subsubsection}{Implementation:}{249}{subsubsection*.612}
-\contentsline {paragraph}{Parameter factories:}{249}{paragraph*.613}
-\contentsline {paragraph}{Wrappers around jobs:}{250}{paragraph*.620}
-\contentsline {paragraph}{Checking if job is update:}{250}{paragraph*.624}
-\contentsline {subsubsection}{Exceptions and Errors}{251}{subsubsection*.627}
-\contentsline {subsection}{\numberline {4.2.2}ruffus.proxy\_logger}{251}{subsection.4.2.2}
-\contentsline {subsubsection}{Create proxy for logging for use with multiprocessing}{251}{subsubsection*.631}
-\contentsline {paragraph}{Example 1}{251}{paragraph*.632}
-\contentsline {paragraph}{Example 2}{251}{paragraph*.633}
-\contentsline {paragraph}{Example 3}{251}{paragraph*.634}
-\contentsline {paragraph}{To use:}{252}{paragraph*.635}
-\contentsline {subsubsection}{Proxies for a log:}{252}{subsubsection*.636}
-\contentsline {subsubsection}{Create a logging object}{252}{subsubsection*.638}
-\contentsline {chapter}{\numberline {5}Indices and tables}{255}{chapter.5}
-\contentsline {chapter}{Python Module Index}{257}{section*.640}
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-\newcommand{\py at lightbox}{{%
-  \setlength\parskip{0pt}\par
-  \noindent\rule[0ex]{\linewidth}{0.5pt}%
-  \par\noindent\vspace{-0.5ex}%
-  }}
-\newcommand{\py at endlightbox}{{%
-  \setlength{\parskip}{0pt}%
-  \par\noindent\rule[0.5ex]{\linewidth}{0.5pt}%
-  \par\vspace{-0.5ex}%
-  }}
-
-% Some are quite plain:
-\newcommand{\py at noticestart@note}{\py at lightbox}
-\newcommand{\py at noticeend@note}{\py at endlightbox}
-\newcommand{\py at noticestart@hint}{\py at lightbox}
-\newcommand{\py at noticeend@hint}{\py at endlightbox}
-\newcommand{\py at noticestart@important}{\py at lightbox}
-\newcommand{\py at noticeend@important}{\py at endlightbox}
-\newcommand{\py at noticestart@tip}{\py at lightbox}
-\newcommand{\py at noticeend@tip}{\py at endlightbox}
-
-% Others gets more visible distinction:
-\newcommand{\py at noticestart@warning}{\py at heavybox}
-\newcommand{\py at noticeend@warning}{\py at endheavybox}
-\newcommand{\py at noticestart@caution}{\py at heavybox}
-\newcommand{\py at noticeend@caution}{\py at endheavybox}
-\newcommand{\py at noticestart@attention}{\py at heavybox}
-\newcommand{\py at noticeend@attention}{\py at endheavybox}
-\newcommand{\py at noticestart@danger}{\py at heavybox}
-\newcommand{\py at noticeend@danger}{\py at endheavybox}
-\newcommand{\py at noticestart@error}{\py at heavybox}
-\newcommand{\py at noticeend@error}{\py at endheavybox}
-
-\newenvironment{notice}[2]{
-  \def\py at noticetype{#1}
-  \csname py at noticestart@#1\endcsname
-  \strong{#2}
-}{\csname py at noticeend@\py at noticetype\endcsname}
-
-% Allow the release number to be specified independently of the
-% \date{}.  This allows the date to reflect the document's date and
-% release to specify the release that is documented.
-%
-\newcommand{\py at release}{}
-\newcommand{\version}{}
-\newcommand{\shortversion}{}
-\newcommand{\releaseinfo}{}
-\newcommand{\releasename}{Release}
-\newcommand{\release}[1]{%
-  \renewcommand{\py at release}{\releasename\space\version}%
-  \renewcommand{\version}{#1}}
-\newcommand{\setshortversion}[1]{%
-  \renewcommand{\shortversion}{#1}}
-\newcommand{\setreleaseinfo}[1]{%
-  \renewcommand{\releaseinfo}{#1}}
-
-% Allow specification of the author's address separately from the
-% author's name.  This can be used to format them differently, which
-% is a good thing.
-%
-\newcommand{\py at authoraddress}{}
-\newcommand{\authoraddress}[1]{\renewcommand{\py at authoraddress}{#1}}
-
-% This sets up the fancy chapter headings that make the documents look
-% at least a little better than the usual LaTeX output.
-%
-\@ifundefined{ChTitleVar}{}{
-  \ChNameVar{\raggedleft\normalsize\py at HeaderFamily}
-  \ChNumVar{\raggedleft \bfseries\Large\py at HeaderFamily}
-  \ChTitleVar{\raggedleft \textrm{\Huge\py at HeaderFamily}}
-  % This creates chapter heads without the leading \vspace*{}:
-  \def\@makechapterhead#1{%
-    {\parindent \z@ \raggedright \normalfont
-      \ifnum \c at secnumdepth >\m at ne
-        \DOCH
-      \fi
-      \interlinepenalty\@M
-      \DOTI{#1}
-    }
-  }
-}
-
-% Redefine description environment so that it is usable inside fulllineitems.
-%
-\renewcommand{\description}{%
-  \list{}{\labelwidth\z@%
-          \itemindent-\leftmargin%
-	  \labelsep5pt%
-          \let\makelabel=\descriptionlabel}}
-
-% Definition lists; requested by AMK for HOWTO documents.  Probably useful
-% elsewhere as well, so keep in in the general style support.
-%
-\newenvironment{definitions}{%
-  \begin{description}%
-  \def\term##1{\item[##1]\mbox{}\\*[0mm]}
-}{%
-  \end{description}%
-}
-
-% Tell TeX about pathological hyphenation cases:
-\hyphenation{Base-HTTP-Re-quest-Hand-ler}
-
-
-% The following is stuff copied from docutils' latex writer.
-%
-\newcommand{\optionlistlabel}[1]{\bf #1 \hfill}
-\newenvironment{optionlist}[1]
-{\begin{list}{}
-  {\setlength{\labelwidth}{#1}
-   \setlength{\rightmargin}{1cm}
-   \setlength{\leftmargin}{\rightmargin}
-   \addtolength{\leftmargin}{\labelwidth}
-   \addtolength{\leftmargin}{\labelsep}
-   \renewcommand{\makelabel}{\optionlistlabel}}
-}{\end{list}}
-
-\newlength{\lineblockindentation}
-\setlength{\lineblockindentation}{2.5em}
-\newenvironment{lineblock}[1]
-{\begin{list}{}
-  {\setlength{\partopsep}{\parskip}
-   \addtolength{\partopsep}{\baselineskip}
-   \topsep0pt\itemsep0.15\baselineskip\parsep0pt
-   \leftmargin#1}
- \raggedright}
-{\end{list}}
-
-% Redefine includgraphics for avoiding images larger than the screen size
-% If the size is not specified.
-\let\py at Oldincludegraphics\includegraphics
-
-\newbox\image at box%
-\newdimen\image at width%
-\renewcommand\includegraphics[2][\@empty]{%
-  \ifx#1\@empty%
-    \setbox\image at box=\hbox{\py at Oldincludegraphics{#2}}%
-    \image at width\wd\image at box%
-    \ifdim \image at width>\linewidth%
-      \setbox\image at box=\hbox{\py at Oldincludegraphics[width=\linewidth]{#2}}%
-      \box\image at box%
-    \else%
-      \py at Oldincludegraphics{#2}%
-    \fi%
-  \else%
-    \py at Oldincludegraphics[#1]{#2}%
-  \fi%
-}
-
-% to make pdf with correct encoded bookmarks in Japanese
-% this should precede the hyperref package
-\ifx\kanjiskip\undefined\else
-  \usepackage{atbegshi}
-  \ifx\ucs\undefined
-    \ifnum 42146=\euc"A4A2
-      \AtBeginShipoutFirst{\special{pdf:tounicode EUC-UCS2}}
-    \else
-      \AtBeginShipoutFirst{\special{pdf:tounicode 90ms-RKSJ-UCS2}}
-    \fi
-  \else
-    \AtBeginShipoutFirst{\special{pdf:tounicode UTF8-UCS2}}
-  \fi
-\fi
-
-% Include hyperref last.
-\RequirePackage[colorlinks,breaklinks,
-                linkcolor=InnerLinkColor,filecolor=OuterLinkColor,
-                menucolor=OuterLinkColor,urlcolor=OuterLinkColor,
-                citecolor=InnerLinkColor]{hyperref}
-% Fix anchor placement for figures with captions.
-% (Note: we don't use a package option here; instead, we give an explicit
-% \capstart for figures that actually have a caption.)
-\RequirePackage{hypcap}
-
-% From docutils.writers.latex2e
-\providecommand{\DUspan}[2]{%
-  {% group ("span") to limit the scope of styling commands
-    \@for\node at class@name:=#1\do{%
-    \ifcsname docutilsrole\node at class@name\endcsname%
-      \csname docutilsrole\node at class@name\endcsname%
-    \fi%
-    }%
-    {#2}% node content
-  }% close "span"
-}
-
-\providecommand*{\DUprovidelength}[2]{
-  \ifthenelse{\isundefined{#1}}{\newlength{#1}\setlength{#1}{#2}}{}
-}
-
-\DUprovidelength{\DUlineblockindent}{2.5em}
-\ifthenelse{\isundefined{\DUlineblock}}{
-  \newenvironment{DUlineblock}[1]{%
-    \list{}{\setlength{\partopsep}{\parskip}
-            \addtolength{\partopsep}{\baselineskip}
-            \setlength{\topsep}{0pt}
-            \setlength{\itemsep}{0.15\baselineskip}
-            \setlength{\parsep}{0pt}
-            \setlength{\leftmargin}{#1}}
-    \raggedright
-  }
-  {\endlist}
-}{}
-
-
-% From footmisc.sty: allows footnotes in titles
-\let\FN at sf@@footnote\footnote
-\def\footnote{\ifx\protect\@typeset at protect
-    \expandafter\FN at sf@@footnote
-  \else
-    \expandafter\FN at sf@gobble at opt
-  \fi
-}
-\edef\FN at sf@gobble at opt{\noexpand\protect
-  \expandafter\noexpand\csname FN at sf@gobble at opt \endcsname}
-\expandafter\def\csname FN at sf@gobble at opt \endcsname{%
-  \@ifnextchar[%]
-    \FN at sf@gobble at twobracket
-    \@gobble
-}
-\def\FN at sf@gobble at twobracket[#1]#2{}
-
-% adjust the margins for footer,
-% this works with the jsclasses only (Japanese standard document classes)
-\ifx\@jsc at uplatextrue\undefined\else
-  \hypersetup{setpagesize=false}
-  \setlength\footskip{2\baselineskip}
-  \addtolength{\textheight}{-2\baselineskip}
-\fi
-
-% fix the double index and bibliography on the table of contents
-% in jsclasses (Japanese standard document classes)
-\ifx\@jsc at uplatextrue\undefined\else
-  \renewcommand{\theindex}{
-    \cleardoublepage
-    \phantomsection
-    \py at OldTheindex
-  }
-  \renewcommand{\thebibliography}[1]{
-    \cleardoublepage
-    \phantomsection
-    \py at OldThebibliography{1}
-  }
-\fi
-
-% do not use \@chappos in Appendix in pTeX
-\ifx\kanjiskip\undefined\else
-  \renewcommand{\appendix}{\par
-    \setcounter{chapter}{0}
-      \setcounter{section}{0}
-      \gdef\@chapapp{\appendixname}
-      \gdef\@chappos{}
-      \gdef\thechapter{\@Alph\c at chapter}
-  }
-\fi
diff --git a/doc/_build/latex/sphinxhowto.cls b/doc/_build/latex/sphinxhowto.cls
deleted file mode 100644
index 26e63a7..0000000
--- a/doc/_build/latex/sphinxhowto.cls
+++ /dev/null
@@ -1,104 +0,0 @@
-%
-% sphinxhowto.cls for Sphinx (http://sphinx-doc.org/)
-%
-
-\NeedsTeXFormat{LaTeX2e}[1995/12/01]
-\ProvidesClass{sphinxhowto}[2009/06/02 Document class (Sphinx HOWTO)]
-
-% 'oneside' option overriding the 'twoside' default
-\newif\if at oneside
-\DeclareOption{oneside}{\@onesidetrue}
-% Pass remaining document options to the parent class.
-\DeclareOption*{\PassOptionsToClass{\CurrentOption}{\sphinxdocclass}}
-\ProcessOptions\relax
-
-% Default to two-side document
-\if at oneside
-% nothing to do (oneside is the default)
-\else
-\PassOptionsToClass{twoside}{\sphinxdocclass}
-\fi
-
-\LoadClass{\sphinxdocclass}
-
-% Set some sane defaults for section numbering depth and TOC depth.  You can
-% reset these counters in your preamble.
-%
-\setcounter{secnumdepth}{2}
-
-% Change the title page to look a bit better, and fit in with the fncychap
-% ``Bjarne'' style a bit better.
-%
-\renewcommand{\maketitle}{
-  \rule{\textwidth}{1pt}
-  \ifsphinxpdfoutput
-    \begingroup
-    % These \defs are required to deal with multi-line authors; it
-    % changes \\ to ', ' (comma-space), making it pass muster for
-    % generating document info in the PDF file.
-    \def\\{, }
-    \def\and{and }
-    \pdfinfo{
-      /Author (\@author)
-      /Title (\@title)
-    }
-    \endgroup
-  \fi
-  \begin{flushright}
-    \sphinxlogo%
-    {\rm\Huge\py at HeaderFamily \@title} \par
-    {\em\large\py at HeaderFamily \py at release\releaseinfo} \par
-    \vspace{25pt}
-    {\Large\py at HeaderFamily
-      \begin{tabular}[t]{c}
-        \@author
-      \end{tabular}} \par
-    \vspace{25pt}
-    \@date \par
-    \py at authoraddress \par
-  \end{flushright}
-  \@thanks
-  \setcounter{footnote}{0}
-  \let\thanks\relax\let\maketitle\relax
-  %\gdef\@thanks{}\gdef\@author{}\gdef\@title{}
-}
-
-\let\py at OldTableofcontents=\tableofcontents
-\renewcommand{\tableofcontents}{
-  \begingroup
-    \parskip = 0mm
-    \py at OldTableofcontents
-  \endgroup
-  \rule{\textwidth}{1pt}
-  \vspace{12pt}
-}  
-
-\@ifundefined{fancyhf}{
-  \pagestyle{plain}}{
-  \pagestyle{normal}}		% start this way; change for
-\pagenumbering{arabic}		% ToC & chapters
-
-\thispagestyle{empty}
-
-% Fix the bibliography environment to add an entry to the Table of
-% Contents.
-% For an article document class this environment is a section,
-% so no page break before it.
-\let\py at OldThebibliography=\thebibliography
-\renewcommand{\thebibliography}[1]{
-  \phantomsection
-  \py at OldThebibliography{1}
-  \addcontentsline{toc}{section}{\bibname}
-}
-
-% Same for the indices.
-% The memoir class already does this, so we don't duplicate it in that case.
-%
-\@ifclassloaded{memoir}{}{
-  \let\py at OldTheindex=\theindex
-  \renewcommand{\theindex}{
-    \phantomsection
-    \py at OldTheindex
-    \addcontentsline{toc}{section}{\indexname}
-  }
-}
diff --git a/doc/_build/latex/sphinxmanual.cls b/doc/_build/latex/sphinxmanual.cls
deleted file mode 100644
index 26df488..0000000
--- a/doc/_build/latex/sphinxmanual.cls
+++ /dev/null
@@ -1,147 +0,0 @@
-%
-% sphinxmanual.cls for Sphinx (http://sphinx-doc.org/)
-%
-
-\NeedsTeXFormat{LaTeX2e}[1995/12/01]
-\ProvidesClass{sphinxmanual}[2009/06/02 Document class (Sphinx manual)]
-
-% chapters starting at odd pages (overridden by 'openany' document option)
-\PassOptionsToClass{openright}{\sphinxdocclass}
-
-% 'oneside' option overriding the 'twoside' default
-\newif\if at oneside
-\DeclareOption{oneside}{\@onesidetrue}
-% Pass remaining document options to the parent class.
-\DeclareOption*{\PassOptionsToClass{\CurrentOption}{\sphinxdocclass}}
-\ProcessOptions\relax
-
-% Defaults two-side document
-\if at oneside
-% nothing to do (oneside is the default)
-\else
-\PassOptionsToClass{twoside}{\sphinxdocclass}
-\fi
-
-\LoadClass{\sphinxdocclass}
-
-% Set some sane defaults for section numbering depth and TOC depth.  You can
-% reset these counters in your preamble.
-%
-\setcounter{secnumdepth}{2}
-\setcounter{tocdepth}{1}
-
-% Change the title page to look a bit better, and fit in with the fncychap
-% ``Bjarne'' style a bit better.
-%
-\renewcommand{\maketitle}{%
-  \begin{titlepage}%
-    \let\footnotesize\small
-    \let\footnoterule\relax
-    \rule{\textwidth}{1pt}%
-    \ifsphinxpdfoutput
-      \begingroup
-      % These \defs are required to deal with multi-line authors; it
-      % changes \\ to ', ' (comma-space), making it pass muster for
-      % generating document info in the PDF file.
-      \def\\{, }
-      \def\and{and }
-      \pdfinfo{
-        /Author (\@author)
-        /Title (\@title)
-      }
-      \endgroup
-    \fi
-    \begin{flushright}%
-      \sphinxlogo%
-      {\rm\Huge\py at HeaderFamily \@title \par}%
-      {\em\LARGE\py at HeaderFamily \py at release\releaseinfo \par}
-      \vfill
-      {\LARGE\py at HeaderFamily
-        \begin{tabular}[t]{c}
-          \@author
-        \end{tabular}
-        \par}
-      \vfill\vfill
-      {\large
-       \@date \par
-       \vfill
-       \py at authoraddress \par
-      }%
-    \end{flushright}%\par
-    \@thanks
-  \end{titlepage}%
-  \cleardoublepage%
-  \setcounter{footnote}{0}%
-  \let\thanks\relax\let\maketitle\relax
-  %\gdef\@thanks{}\gdef\@author{}\gdef\@title{}
-}
-
-
-% Catch the end of the {abstract} environment, but here make sure the abstract
-% is followed by a blank page if the 'openright' option is used.
-%
-\let\py at OldEndAbstract=\endabstract
-\renewcommand{\endabstract}{
-  \if at openright
-    \ifodd\value{page}
-      \typeout{Adding blank page after the abstract.}
-      \vfil\pagebreak
-    \fi
-  \fi
-  \py at OldEndAbstract
-}
-
-% This wraps the \tableofcontents macro with all the magic to get the spacing
-% right and have the right number of pages if the 'openright' option has been
-% used.  This eliminates a fair amount of crud in the individual document files.
-%
-\let\py at OldTableofcontents=\tableofcontents
-\renewcommand{\tableofcontents}{%
-  \setcounter{page}{1}%
-  \pagebreak%
-  \pagestyle{plain}%
-  {%
-    \parskip = 0mm%
-    \py at OldTableofcontents%
-    \if at openright%
-      \ifodd\value{page}%
-        \typeout{Adding blank page after the table of contents.}%
-        \pagebreak\hspace{0pt}%
-      \fi%
-    \fi%
-    \cleardoublepage%
-  }%
-  \pagenumbering{arabic}%
-  \@ifundefined{fancyhf}{}{\pagestyle{normal}}%
-}
-\pagenumbering{roman}
-
-% This is needed to get the width of the section # area wide enough in the
-% library reference.  Doing it here keeps it the same for all the manuals.
-%
-\renewcommand*\l at section{\@dottedtocline{1}{1.5em}{2.6em}}
-\renewcommand*\l at subsection{\@dottedtocline{2}{4.1em}{3.5em}}
-
-% Fix the bibliography environment to add an entry to the Table of
-% Contents.
-% For a report document class this environment is a chapter.
-\let\py at OldThebibliography=\thebibliography
-\renewcommand{\thebibliography}[1]{
-  \cleardoublepage
-  \phantomsection
-  \py at OldThebibliography{1}
-  \addcontentsline{toc}{chapter}{\bibname}
-}
-
-% Same for the indices.
-% The memoir class already does this, so we don't duplicate it in that case.
-%
-\@ifclassloaded{memoir}{}{
-  \let\py at OldTheindex=\theindex
-  \renewcommand{\theindex}{
-    \cleardoublepage
-    \phantomsection
-    \py at OldTheindex
-    \addcontentsline{toc}{chapter}{\indexname}
-  }
-}
diff --git a/doc/_build/latex/tabulary.sty b/doc/_build/latex/tabulary.sty
deleted file mode 100644
index ba83c0a..0000000
--- a/doc/_build/latex/tabulary.sty
+++ /dev/null
@@ -1,452 +0,0 @@
-%%
-%% This is file `tabulary.sty',
-%% generated with the docstrip utility.
-%%
-%% The original source files were:
-%%
-%% tabulary.dtx  (with options: `package')
-%% DRAFT VERSION
-%%
-%% File `tabulary.dtx'.
-%% Copyright (C) 1995 1996 2003 David Carlisle
-%% This file may be distributed under the terms of the LPPL.
-%% See 00readme.txt for details.
-%%
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{tabulary}
-          [2007/10/02 v0.9 tabulary package (DPC)]
-\RequirePackage{array}
-\catcode`\Z=14
-\DeclareOption{debugshow}{\catcode`\Z=9\relax}
-\ProcessOptions
-\def\arraybackslash{\let\\=\@arraycr}
-\def\@finalstrut#1{%
-  \unskip\ifhmode\nobreak\fi\vrule\@width\z@\@height\z@\@depth\dp#1}
-\newcount\TY at count
-\def\tabulary{%
-  \let\TY at final\tabular
-  \let\endTY at final\endtabular
-  \TY at tabular}
-\def\TY at tabular#1{%
-  \edef\TY@{\@currenvir}%
-  {\ifnum0=`}\fi
-  \@ovxx\TY at linewidth
-  \@ovyy\TY at tablewidth
-  \count@\z@
-  \@tempswatrue
-  \@whilesw\if at tempswa\fi{%
-  \advance\count@\@ne
-  \expandafter\ifx\csname TY at F\the\count@\endcsname\relax
-    \@tempswafalse
-  \else
-    \expandafter\let\csname TY at SF\the\count@\expandafter\endcsname
-                     \csname TY at F\the\count@\endcsname
-    \global\expandafter\let\csname TY at F\the\count@\endcsname\relax
-    \expandafter\let\csname TY at S\the\count@\expandafter\endcsname
-                     \csname TY@\the\count@\endcsname
-  \fi}%
-    \global\TY at count\@ne
-    \TY at width\xdef{0pt}%
-    \global\TY at tablewidth\z@
-    \global\TY at linewidth#1\relax
-Z\message{^^J^^JTable^^J%
-Z        Target Width: \the\TY at linewidth^^J%
-Z        \string\tabcolsep: \the\tabcolsep\space
-Z        \string\arrayrulewidth: \the\arrayrulewidth\space
-Z        \string\doublerulesep: \the\doublerulesep^^J%
-Z        \string\tymin: \the\tymin\space
-Z        \string\tymax: \the\tymax^^J}%
-    \let\@classz\TY at classz
-    \let\verb\TX at verb
-    \toks@{}\TY at get@body}
-\let\TY@@mkpream\@mkpream
-\def\TY at mkpream{%
-    \def\@addamp{%
-      \if at firstamp \@firstampfalse \else
-      \global\advance\TY at count\@ne
-      \edef\@preamble{\@preamble &}\fi
-      \TY at width\xdef{0pt}}%
-    \def\@acol{%
-      \TY at subwidth\col at sep
-      \@addtopreamble{\hskip\col at sep}}%
-    \let\@arrayrule\TY at arrayrule
-    \let\@classvi\TY at classvi
-    \def\@classv{\save at decl
-      \expandafter\NC at ecs\@nextchar\extracolsep{}\extracolsep\@@@
-      \sbox\z@{\d at llarbegin\@nextchar\d at llarend}%
-      \TY at subwidth{\wd\z@}%
-      \@addtopreamble{\d at llarbegin\the at toks\the\count@\relax\d at llarend}%
-      \prepnext at tok}%
-  \global\let\@mkpream\TY@@mkpream
-  \TY@@mkpream}
-\def\TY at arrayrule{%
-  \TY at subwidth\arrayrulewidth
-  \@addtopreamble \vline}
-\def\TY at classvi{\ifcase \@lastchclass
-  \@acol \or
-  \TY at subwidth\doublerulesep
-  \@addtopreamble{\hskip \doublerulesep}\or
-  \@acol \or
-  \@classvii
-  \fi}
-\def\TY at tab{%
-  \setbox\z@\hbox\bgroup
-  \let\[$\let\]$%
-  \let\equation$\let\endequation$%
-    \col at sep\tabcolsep
-    \let\d at llarbegin\begingroup\let\d at llarend\endgroup
-    \let\@mkpream\TY at mkpream
-      \def\multicolumn##1##2##3{\multispan##1\relax}%
-    \CT at start\TY at tabarray}
-\def\TY at tabarray{\@ifnextchar[{\TY at array}{\@array[t]}}
-\def\TY at array[#1]{\@array[t]}
-\def\TY at width#1{%
-  \expandafter#1\csname TY@\the\TY at count\endcsname}
-\def\TY at subwidth#1{%
-  \TY at width\dimen@
-  \advance\dimen at -#1\relax
-  \TY at width\xdef{\the\dimen@}%
-  \global\advance\TY at linewidth-#1\relax}
-\def\endtabulary{%
-  \gdef\@halignto{}%
-  \let\TY at footnote\footnote%
-  \def\footnote{}% prevent footnotes from doing anything
-  \expandafter\TY at tab\the\toks@
-  \crcr\omit
-  {\xdef\TY at save@row{}%
-     \loop
-    \advance\TY at count\m at ne
-    \ifnum\TY at count>\z@
-    \xdef\TY at save@row{\TY at save@row&\omit}%
-    \repeat}\TY at save@row
-  \endarray\global\setbox1=\lastbox\setbox0=\vbox{\unvbox1
-    \unskip\global\setbox1=\lastbox}\egroup
-  \dimen@\TY at linewidth
-  \divide\dimen@\TY at count
-  \ifdim\dimen@<\tymin
-    \TY at warn{tymin too large (\the\tymin), resetting to \the\dimen@}%
-    \tymin\dimen@
-  \fi
-  \setbox\tw@=\hbox{\unhbox\@ne
-    \loop
-\@tempdima=\lastskip
-\ifdim\@tempdima>\z@
-Z   \message{ecs=\the\@tempdima^^J}%
-   \global\advance\TY at linewidth-\@tempdima
-\fi
-    \unskip
-    \setbox\tw@=\lastbox
-    \ifhbox\tw@
-Z     \message{Col \the\TY at count: Initial=\the\wd\tw@\space}%
-      \ifdim\wd\tw@>\tymax
-        \wd\tw@\tymax
-Z       \message{> max\space}%
-Z     \else
-Z       \message{ \@spaces\space}%
-      \fi
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-         \expandafter\xdef\csname TY at F\the\TY at count\endcsname
-                                                        {\the\dimen@}%
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-      \expandafter\ifx\csname TY at F\the\TY at count\endcsname\z@
-Z        \message{***}%
-         \global\advance\TY at linewidth-\dimen@
-         \expandafter\xdef\csname TY at F\the\TY at count\endcsname
-                                                        {\the\dimen@}%
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-Z        \message{> tymin}%
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-         \global\expandafter\let\csname TY at F\the\TY at count\endcsname
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-       \fi\fi
-       \advance\TY at count\m at ne
-    \repeat}%
-    \TY at checkmin
-    \TY at checkmin
-    \TY at checkmin
-    \TY at checkmin
-    \TY at count\z@
-    \let\TY at box\TY at box@v
-    \let\footnote\TY at footnote % restore footnotes
-  {\expandafter\TY at final\the\toks@\endTY at final}%
-  \count@\z@
-  \@tempswatrue
-  \@whilesw\if at tempswa\fi{%
-  \advance\count@\@ne
-  \expandafter\ifx\csname TY at SF\the\count@\endcsname\relax
-    \@tempswafalse
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-    \global\expandafter\let\csname TY at F\the\count@\expandafter\endcsname
-                   \csname TY at SF\the\count@\endcsname
-    \global\expandafter\let\csname TY@\the\count@\expandafter\endcsname
-                   \csname TY at S\the\count@\endcsname
-  \fi}%
-  \TY at linewidth\@ovxx
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-    \ifnum0=`{\fi}}
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-  \let\TY at checkmin\relax
-\ifdim\TY at tablewidth>\z@
-  \Gscale at div\TY at ratio\TY at linewidth\TY at tablewidth
- \ifdim\TY at tablewidth <\linewidth
-   \def\TY at ratio{1}%
- \fi
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-  \TY at warn{No suitable columns!}%
-  \def\TY at ratio{1}%
-\fi
-\count@\z@
-Z \message{^^JLine Width: \the\TY at linewidth,
-Z             Natural Width: \the\TY at tablewidth,
-Z             Ratio: \TY at ratio^^J}%
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-\ifnum\count@<\TY at count
-\advance\count@\@ne
-  \ifdim\csname TY at F\the\count@\endcsname>\tymin
-    \dimen@\csname TY@\the\count@\endcsname
-    \dimen@\TY at ratio\dimen@
-    \ifdim\dimen@<\tymin
-Z     \message{Column \the\count@\space ->}%
-      \global\expandafter\let\csname TY at F\the\count@\endcsname\tymin
-      \global\advance\TY at linewidth-\tymin
-      \global\advance\TY at tablewidth-\csname TY@\the\count@\endcsname
-      \let\TY at checkmin\TY@@checkmin
-    \else
-      \expandafter\xdef\csname TY at F\the\count@\endcsname{\the\dimen@}%
-      \advance\@tempdima\csname TY at F\the\count@\endcsname
-    \fi
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-Z \dimen@\csname TY at F\the\count@\endcsname\message{\the\dimen@, }%
-\repeat
-Z \message{^^JTotal:\the\@tempdima^^J}%
-}
-\let\TY@@checkmin\TY at checkmin
-\newdimen\TY at linewidth
-\def\tyformat{\everypar{{\nobreak\hskip\z at skip}}}
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-\tymin=10pt
-\newdimen\tymax
-\tymax=2\textwidth
-\def\@testpach{\@chclass
- \ifnum \@lastchclass=6 \@ne \@chnum \@ne \else
-  \ifnum \@lastchclass=7 5 \else
-   \ifnum \@lastchclass=8 \tw@ \else
-    \ifnum \@lastchclass=9 \thr@@
-   \else \z@
-   \ifnum \@lastchclass = 10 \else
-   \edef\@nextchar{\expandafter\string\@nextchar}%
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-    \if \@nextchar l\@ne \else
-     \if \@nextchar r\tw@ \else
-   \if \@nextchar C7 \else
-    \if \@nextchar L8 \else
-     \if \@nextchar R9 \else
-     \if \@nextchar J10 \else
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-   \if\@nextchar |\@ne \else
-    \if \@nextchar !6 \else
-     \if \@nextchar @7 \else
-      \if \@nextchar <8 \else
-       \if \@nextchar >9 \else
-  10
-  \@chnum
-  \if \@nextchar m\thr@@\else
-   \if \@nextchar p4 \else
-    \if \@nextchar b5 \else
-   \z@ \@chclass \z@ \@preamerr \z@ \fi \fi \fi \fi\fi \fi \fi\fi \fi
-     \fi  \fi  \fi  \fi  \fi  \fi \fi \fi \fi \fi \fi}
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-  \@classx
-  \@tempcnta\count@
-  \ifx\TY at box\TY at box@v
-    \global\advance\TY at count\@ne
-  \fi
-  \let\centering c%
-  \let\raggedright\noindent
-  \let\raggedleft\indent
-  \let\arraybackslash\relax
-  \prepnext at tok
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-    \global\expandafter\let\csname TY at F\the\TY at count\endcsname\z@
-  \fi
-  \ifnum\@chnum=6
-    \global\expandafter\let\csname TY at F\the\TY at count\endcsname\z@
-  \fi
-  \@addtopreamble{%
-    \ifcase\@chnum
-      \hfil \d at llarbegin\insert at column\d at llarend \hfil \or
-      \kern\z@
-       \d at llarbegin \insert at column \d at llarend \hfil \or
-      \hfil\kern\z@ \d at llarbegin \insert at column \d at llarend \or
-      $\vcenter\@startpbox{\@nextchar}\insert at column \@endpbox $\or
-      \vtop \@startpbox{\@nextchar}\insert at column \@endpbox \or
-      \vbox \@startpbox{\@nextchar}\insert at column \@endpbox \or
-      \d at llarbegin \insert at column \d at llarend \or% dubious "s" case
-      \TY at box\centering\or
-      \TY at box\raggedright\or
-      \TY at box\raggedleft\or
-      \TY at box\relax
-    \fi}\prepnext at tok}
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-  \ifx\centering#1%
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-  \ifx\raggedright#1%
-        \kern\z@%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-      \d at llarbegin \insert at column \d at llarend \hfil \else
-  \ifx\raggedleft#1%
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-  \ifx\relax#1%
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-  \fi  \fi  \fi  \fi}
-\def\TY at box@v#1{%
-      \vtop \@startpbox{\csname TY at F\the\TY at count\endcsname}%
-              #1\arraybackslash\tyformat
-                              \insert at column\@endpbox}
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-\def\Gscale at div#1#2#3{%
-  \setlength\dimen@{#3}%
-  \ifdim\dimen@=\z@
-    \PackageError{graphics}{Division by 0}\@eha
-    \dimen@#2%
-  \fi
-  \edef\@tempd{\the\dimen@}%
-  \setlength\dimen@{#2}%
-  \count at 65536\relax
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-    \dimen at -\dimen@
-    \count at -\count@
-  \fi
-  \loop
-    \ifdim\dimen@<8192\p@
-      \dimen@\tw@\dimen@
-      \divide\count@\tw@
-  \repeat
-  \dimen at ii=\@tempd\relax
-  \divide\dimen at ii\count@
-  \divide\dimen@\dimen at ii
-  \edef#1{\strip at pt\dimen@}}
-\long\def\TY at get@body#1\end
-  {\toks@\expandafter{\the\toks@#1}\TY at find@end}
-\def\TY at find@end#1{%
-  \def\@tempa{#1}%
-  \ifx\@tempa\TY@\def\@tempa{\end{#1}}\expandafter\@tempa
-  \else\toks@\expandafter
-    {\the\toks@\end{#1}}\expandafter\TY at get@body\fi}
-\def\TY at warn{%
-  \PackageWarning{tabulary}}
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-\AtBeginDocument{
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-\expandafter\def\expandafter\@mkpream\expandafter#\expandafter1%
-  \expandafter{%
-    \expandafter\let\expandafter\CT at setup\expandafter\relax
-    \expandafter\let\expandafter\CT at color\expandafter\relax
-    \expandafter\let\expandafter\CT at do@color\expandafter\relax
-    \expandafter\let\expandafter\color\expandafter\relax
-    \expandafter\let\expandafter\CT at column@color\expandafter\relax
-    \expandafter\let\expandafter\CT at row@color\expandafter\relax
-    \@mkpream{#1}}
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-\def\TY at classz{%
-  \@classx
-  \@tempcnta\count@
-  \ifx\TY at box\TY at box@v
-    \global\advance\TY at count\@ne
-  \fi
-  \let\centering c%
-  \let\raggedright\noindent
-  \let\raggedleft\indent
-  \let\arraybackslash\relax
-  \prepnext at tok
-\expandafter\CT at extract\the\toks\@tempcnta\columncolor!\@nil
-  \ifnum\@chnum<4
-    \global\expandafter\let\csname TY at F\the\TY at count\endcsname\z@
-  \fi
-  \ifnum\@chnum=6
-    \global\expandafter\let\csname TY at F\the\TY at count\endcsname\z@
-  \fi
-  \@addtopreamble{%
-    \setbox\z@\hbox\bgroup\bgroup
-    \ifcase\@chnum
-      \hskip\stretch{.5}\kern\z@
-      \d at llarbegin\insert at column\d at llarend\hskip\stretch{.5}\or
-      \kern\z@%<<<<<<<<<<<<<<<<<<<<<<<<<<<
-       \d at llarbegin \insert at column \d at llarend \hfill \or
-      \hfill\kern\z@ \d at llarbegin \insert at column \d at llarend \or
-      $\vcenter\@startpbox{\@nextchar}\insert at column \@endpbox $\or
-      \vtop \@startpbox{\@nextchar}\insert at column \@endpbox \or
-      \vbox \@startpbox{\@nextchar}\insert at column \@endpbox \or
-      \d at llarbegin \insert at column \d at llarend \or% dubious s case
-      \TY at box\centering\or
-      \TY at box\raggedright\or
-      \TY at box\raggedleft\or
-      \TY at box\relax
-    \fi
- \egroup\egroup
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-  \CT at setup
-  \CT at column@color
-  \CT at row@color
-  \CT at do@color
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-        \@tempdima\ht\z@
-        \advance\@tempdima\minrowclearance
-        \vrule\@height\@tempdima\@width\z@
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-}\prepnext at tok}%
-    \def\TY at arrayrule{%
-      \TY at subwidth\arrayrulewidth
-      \@addtopreamble{{\CT at arc@\vline}}}%
-    \def\TY at classvi{\ifcase \@lastchclass
-      \@acol \or
-      \TY at subwidth\doublerulesep
-      \ifx\CT at drsc@\relax
-        \@addtopreamble{\hskip\doublerulesep}%
-      \else
-        \@addtopreamble{{\CT at drsc@\vrule\@width\doublerulesep}}%
-      \fi\or
-      \@acol \or
-      \@classvii
-      \fi}%
-}{%
-\let\CT at start\relax
-}
-}
-{\uccode`\*=`\ %
-\uppercase{\gdef\TX at verb{%
-  \leavevmode\null\TX at vwarn
-  {\ifnum0=`}\fi\ttfamily\let\\\ignorespaces
-  \@ifstar{\let~*\TX at vb}{\TX at vb}}}}
-\def\TX at vb#1{\def\@tempa##1#1{\toks@{##1}\edef\@tempa{\the\toks@}%
-    \expandafter\TX at v\meaning\@tempa\\ \\\ifnum0=`{\fi}}\@tempa!}
-\def\TX at v#1!{\afterassignment\TX at vfirst\let\@tempa= }
-\begingroup
-\catcode`\*=\catcode`\#
-\catcode`\#=12
-\gdef\TX at vfirst{%
-  \if\@tempa#%
-    \def\@tempb{\TX at v@#}%
-  \else
-    \let\@tempb\TX at v@
-    \if\@tempa\space~\else\@tempa\fi
-  \fi
-  \@tempb}
-\gdef\TX at v@*1 *2{%
-  \TX at v@hash*1##\relax\if*2\\\else~\expandafter\TX at v@\fi*2}
-\gdef\TX at v@hash*1##*2{*1\ifx*2\relax\else#\expandafter\TX at v@hash\fi*2}
-\endgroup
-\def\TX at vwarn{%
-  \@warning{\noexpand\verb may be unreliable inside tabularx/y}%
-  \global\let\TX at vwarn\@empty}
-\endinput
-%%
-%% End of file `tabulary.sty'.
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-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-ruffus.git