From eb1950c98e008f4e5bb195324077e7b9f53e1637 Mon Sep 17 00:00:00 2001
From: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch>
Date: Tue, 24 Aug 2021 14:55:19 +0000
Subject: [PATCH] Change alfa output folder names
---
images/rule_graph.svg | 956 +++++++++---------
.../expected_output.files | 40 +-
.../expected_output.md5 | 40 +-
.../expected_output.md5 | 40 +-
.../expected_output.files | 40 +-
.../expected_output.md5 | 40 +-
workflow/Snakefile | 96 +-
7 files changed, 608 insertions(+), 644 deletions(-)
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index e18e021..0234a26 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,649 +1,601 @@
<?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 2.42.3 (20191010.1750)
+<!-- Generated by graphviz version 2.40.1 (20161225.0304)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1163pt" height="836pt"
- viewBox="0.00 0.00 1163.00 836.00" 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(4 832)">
+<svg width="1157pt" height="692pt"
+ viewBox="0.00 0.00 1157.18 692.00" 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(4 688)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="transparent" points="-4,4 -4,-832 1159,-832 1159,4 -4,4"/>
+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-688 1153.1835,-688 1153.1835,4 -4,4"/>
<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M681,-36C681,-36 651,-36 651,-36 645,-36 639,-30 639,-24 639,-24 639,-12 639,-12 639,-6 645,0 651,0 651,0 681,0 681,0 687,0 693,-6 693,-12 693,-12 693,-24 693,-24 693,-30 687,-36 681,-36"/>
-<text text-anchor="middle" x="666" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M544,-36C544,-36 514,-36 514,-36 508,-36 502,-30 502,-24 502,-24 502,-12 502,-12 502,-6 508,0 514,0 514,0 544,0 544,0 550,0 556,-6 556,-12 556,-12 556,-24 556,-24 556,-30 550,-36 544,-36"/>
+<text text-anchor="middle" x="529" y="-15" font-family="sans" font-size="10.00" fill="#000000">finish</text>
</g>
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<g id="node2" class="node">
<title>1</title>
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-<text text-anchor="middle" x="443" y="-87.5" font-family="sans" font-size="10.00">multiqc_report</text>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M456.8602,-108C456.8602,-108 401.1398,-108 401.1398,-108 395.1398,-108 389.1398,-102 389.1398,-96 389.1398,-96 389.1398,-84 389.1398,-84 389.1398,-78 395.1398,-72 401.1398,-72 401.1398,-72 456.8602,-72 456.8602,-72 462.8602,-72 468.8602,-78 468.8602,-84 468.8602,-84 468.8602,-96 468.8602,-96 468.8602,-102 462.8602,-108 456.8602,-108"/>
+<text text-anchor="middle" x="429" y="-87" font-family="sans" font-size="10.00" fill="#000000">multiqc_report</text>
</g>
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-<g id="edge2" class="edge">
+<g id="edge5" class="edge">
<title>1->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M487.06,-75.17C528.54,-62.15 589.97,-42.87 628.98,-30.62"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="630.38,-33.85 638.87,-27.52 628.28,-27.17 630.38,-33.85"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M454.2342,-71.8314C466.788,-62.7927 482.1283,-51.7476 495.6391,-42.0198"/>
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<g id="node3" class="node">
<title>2</title>
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-<text text-anchor="middle" x="1054" y="-231.5" font-family="sans" font-size="10.00">prepare_bigWig</text>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M143,-612C143,-612 113,-612 113,-612 107,-612 101,-606 101,-600 101,-600 101,-588 101,-588 101,-582 107,-576 113,-576 113,-576 143,-576 143,-576 149,-576 155,-582 155,-588 155,-588 155,-600 155,-600 155,-606 149,-612 143,-612"/>
+<text text-anchor="middle" x="128" y="-591" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
</g>
-<!-- 2->0 -->
-<g id="edge6" class="edge">
-<title>2->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1045.74,-215.87C1028.64,-182.37 985.97,-108.29 927,-72 856.49,-28.61 756.92,-19.99 703.45,-18.73"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="703.44,-15.23 693.39,-18.56 703.33,-22.23 703.44,-15.23"/>
+<!-- 2->1 -->
+<g id="edge9" class="edge">
+<title>2->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M100.8545,-579.3806C63.2813,-556.9399 0,-510.208 0,-450 0,-450 0,-450 0,-234 0,-170.1421 53.7658,-170.2031 112,-144 158.8006,-122.9416 301.8796,-104.2786 378.8092,-95.4317"/>
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</g>
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<g id="node4" class="node">
<title>3</title>
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-<text text-anchor="middle" x="727" y="-231.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M385,-684C385,-684 355,-684 355,-684 349,-684 343,-678 343,-672 343,-672 343,-660 343,-660 343,-654 349,-648 355,-648 355,-648 385,-648 385,-648 391,-648 397,-654 397,-660 397,-660 397,-672 397,-672 397,-678 391,-684 385,-684"/>
+<text text-anchor="middle" x="370" y="-663" font-family="sans" font-size="10.00" fill="#000000">start</text>
</g>
-<!-- 3->0 -->
-<g id="edge5" class="edge">
-<title>3->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M803.42,-219.49C845.4,-210.34 891.45,-196.85 904,-180 932.66,-141.5 934.03,-109.45 904,-72 879.27,-41.16 763.93,-27.11 703.36,-21.76"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="703.34,-18.25 693.08,-20.89 702.75,-25.22 703.34,-18.25"/>
+<!-- 3->2 -->
+<g id="edge15" class="edge">
+<title>3->2</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M342.7099,-657.8806C299.203,-644.9364 214.0484,-619.6012 165.0657,-605.0278"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="165.7732,-601.5867 155.1903,-602.0897 163.777,-608.2961 165.7732,-601.5867"/>
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-<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M571.5,-180C571.5,-180 520.5,-180 520.5,-180 514.5,-180 508.5,-174 508.5,-168 508.5,-168 508.5,-156 508.5,-156 508.5,-150 514.5,-144 520.5,-144 520.5,-144 571.5,-144 571.5,-144 577.5,-144 583.5,-150 583.5,-156 583.5,-156 583.5,-168 583.5,-168 583.5,-174 577.5,-180 571.5,-180"/>
-<text text-anchor="middle" x="546" y="-159.5" font-family="sans" font-size="10.00">pca_salmon</text>
+<!-- 6 -->
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M600.4332,-612C600.4332,-612 469.5668,-612 469.5668,-612 463.5668,-612 457.5668,-606 457.5668,-600 457.5668,-600 457.5668,-588 457.5668,-588 457.5668,-582 463.5668,-576 469.5668,-576 469.5668,-576 600.4332,-576 600.4332,-576 606.4332,-576 612.4332,-582 612.4332,-588 612.4332,-588 612.4332,-600 612.4332,-600 612.4332,-606 606.4332,-612 600.4332,-612"/>
+<text text-anchor="middle" x="535" y="-591" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
</g>
-<!-- 3->12 -->
-<g id="edge33" class="edge">
-<title>3->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M682.72,-215.88C655.57,-205.38 620.84,-191.94 593.17,-181.24"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="594.29,-177.92 583.7,-177.58 591.77,-184.45 594.29,-177.92"/>
+<!-- 3->6 -->
+<g id="edge19" class="edge">
+<title>3->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M397.2464,-654.1107C420.766,-643.8476 455.3737,-628.746 484.0164,-616.2474"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="485.7111,-619.3266 493.4767,-612.1193 482.9115,-612.9109 485.7111,-619.3266"/>
+</g>
+<!-- 11 -->
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M426.7483,-612C426.7483,-612 313.2517,-612 313.2517,-612 307.2517,-612 301.2517,-606 301.2517,-600 301.2517,-600 301.2517,-588 301.2517,-588 301.2517,-582 307.2517,-576 313.2517,-576 313.2517,-576 426.7483,-576 426.7483,-576 432.7483,-576 438.7483,-582 438.7483,-588 438.7483,-588 438.7483,-600 438.7483,-600 438.7483,-606 432.7483,-612 426.7483,-612"/>
+<text text-anchor="middle" x="370" y="-591" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+</g>
+<!-- 3->11 -->
+<g id="edge24" class="edge">
+<title>3->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M370,-647.8314C370,-640.131 370,-630.9743 370,-622.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="373.5001,-622.4132 370,-612.4133 366.5001,-622.4133 373.5001,-622.4132"/>
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<g id="node5" class="node">
<title>4</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M621,-252C621,-252 471,-252 471,-252 465,-252 459,-246 459,-240 459,-240 459,-228 459,-228 459,-222 465,-216 471,-216 471,-216 621,-216 621,-216 627,-216 633,-222 633,-228 633,-228 633,-240 633,-240 633,-246 627,-252 621,-252"/>
-<text text-anchor="middle" x="546" y="-231.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M372.943,-324C372.943,-324 227.057,-324 227.057,-324 221.057,-324 215.057,-318 215.057,-312 215.057,-312 215.057,-300 215.057,-300 215.057,-294 221.057,-288 227.057,-288 227.057,-288 372.943,-288 372.943,-288 378.943,-288 384.943,-294 384.943,-300 384.943,-300 384.943,-312 384.943,-312 384.943,-318 378.943,-324 372.943,-324"/>
+<text text-anchor="middle" x="300" y="-303" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
</g>
-<!-- 4->0 -->
-<g id="edge4" class="edge">
-<title>4->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M633.11,-217.5C636.11,-216.99 639.08,-216.49 642,-216 692.81,-207.51 837.52,-219.15 871,-180 928.86,-112.33 776.7,-53.58 703.16,-30.01"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="703.93,-26.58 693.34,-26.92 701.83,-33.26 703.93,-26.58"/>
+<!-- 4->1 -->
+<g id="edge11" class="edge">
+<title>4->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M318.8799,-287.8736C328.3386,-277.9819 339.3705,-265.1037 347,-252 372.6036,-208.0262 360.1142,-188.3839 385,-144 390.468,-134.2479 397.7252,-124.4966 404.7662,-116.0175"/>
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-<!-- 4->12 -->
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-<title>4->12</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="549.5,-190.1 546,-180.1 542.5,-190.1 549.5,-190.1"/>
+<!-- 30 -->
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M325.7806,-252C325.7806,-252 236.2194,-252 236.2194,-252 230.2194,-252 224.2194,-246 224.2194,-240 224.2194,-240 224.2194,-228 224.2194,-228 224.2194,-222 230.2194,-216 236.2194,-216 236.2194,-216 325.7806,-216 325.7806,-216 331.7806,-216 337.7806,-222 337.7806,-228 337.7806,-228 337.7806,-240 337.7806,-240 337.7806,-246 331.7806,-252 325.7806,-252"/>
+<text text-anchor="middle" x="281" y="-231" font-family="sans" font-size="10.00" fill="#000000">kallisto_merge_genes</text>
+</g>
+<!-- 4->30 -->
+<g id="edge57" class="edge">
+<title>4->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M295.2055,-287.8314C293.1511,-280.0463 290.704,-270.7729 288.4244,-262.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="291.7948,-261.1892 285.8591,-252.4133 285.0265,-262.9753 291.7948,-261.1892"/>
+</g>
+<!-- 31 -->
+<g id="node32" class="node">
+<title>31</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M194.1573,-252C194.1573,-252 85.8427,-252 85.8427,-252 79.8427,-252 73.8427,-246 73.8427,-240 73.8427,-240 73.8427,-228 73.8427,-228 73.8427,-222 79.8427,-216 85.8427,-216 85.8427,-216 194.1573,-216 194.1573,-216 200.1573,-216 206.1573,-222 206.1573,-228 206.1573,-228 206.1573,-240 206.1573,-240 206.1573,-246 200.1573,-252 194.1573,-252"/>
+<text text-anchor="middle" x="140" y="-231" font-family="sans" font-size="10.00" fill="#000000">kallisto_merge_transcripts</text>
+</g>
+<!-- 4->31 -->
+<g id="edge59" class="edge">
+<title>4->31</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M259.6252,-287.8314C238.3213,-278.2446 212.0017,-266.4008 189.4789,-256.2655"/>
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<g id="node6" class="node">
<title>5</title>
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-<text text-anchor="middle" x="139" y="-231.5" font-family="sans" font-size="10.00">kallisto_merge_transcripts</text>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M594.9235,-540C594.9235,-540 479.0765,-540 479.0765,-540 473.0765,-540 467.0765,-534 467.0765,-528 467.0765,-528 467.0765,-516 467.0765,-516 467.0765,-510 473.0765,-504 479.0765,-504 479.0765,-504 594.9235,-504 594.9235,-504 600.9235,-504 606.9235,-510 606.9235,-516 606.9235,-516 606.9235,-528 606.9235,-528 606.9235,-534 600.9235,-540 594.9235,-540"/>
+<text text-anchor="middle" x="537" y="-519" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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-<!-- 5->0 -->
-<g id="edge3" class="edge">
-<title>5->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M148.74,-215.79C168.99,-181.8 219.2,-106.38 284,-72 343.42,-40.48 544.85,-25.79 628.79,-20.93"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="629.11,-24.42 638.9,-20.36 628.72,-17.43 629.11,-24.42"/>
+<!-- 5->4 -->
+<g id="edge16" class="edge">
+<title>5->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M514.6736,-503.9997C485.2468,-480.0493 432.1604,-436.0576 389,-396 366.3099,-374.941 341.641,-349.8052 324.0422,-331.4567"/>
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<title>13</title>
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+<text text-anchor="middle" x="922" y="-447" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
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-<g id="edge35" class="edge">
+<g id="edge29" class="edge">
<title>5->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M178.87,-215.88C201.92,-205.98 231.04,-193.47 255.17,-183.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="256.69,-186.27 264.5,-179.11 253.93,-179.84 256.69,-186.27"/>
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-<g id="node7" class="node">
-<title>6</title>
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-<text text-anchor="middle" x="292" y="-231.5" font-family="sans" font-size="10.00">kallisto_merge_genes</text>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M650.9137,-324C650.9137,-324 545.0863,-324 545.0863,-324 539.0863,-324 533.0863,-318 533.0863,-312 533.0863,-312 533.0863,-300 533.0863,-300 533.0863,-294 539.0863,-288 545.0863,-288 545.0863,-288 650.9137,-288 650.9137,-288 656.9137,-288 662.9137,-294 662.9137,-300 662.9137,-300 662.9137,-312 662.9137,-312 662.9137,-318 656.9137,-324 650.9137,-324"/>
+<text text-anchor="middle" x="598" y="-303" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
</g>
-<!-- 6->0 -->
-<g id="edge1" class="edge">
-<title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M275.63,-215.9C260.04,-197.44 240.88,-167.53 255,-144 289.99,-85.69 325.89,-94.67 390,-72 472.37,-42.88 574.54,-28.56 628.52,-22.59"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="629.08,-26.05 638.65,-21.51 628.33,-19.09 629.08,-26.05"/>
+<!-- 5->24 -->
+<g id="edge46" class="edge">
+<title>5->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M536.2262,-503.7367C535.5703,-472.9041 537.0431,-409.0916 557,-360 560.9896,-350.186 567.2415,-340.5983 573.6719,-332.2907"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="576.4635,-334.4058 580.0845,-324.4489 571.0447,-329.9745 576.4635,-334.4058"/>
</g>
-<!-- 6->13 -->
-<g id="edge34" class="edge">
-<title>6->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M294.47,-215.7C295.57,-207.98 296.9,-198.71 298.13,-190.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="301.61,-190.5 299.56,-180.1 294.68,-189.51 301.61,-190.5"/>
+<!-- 6->5 -->
+<g id="edge18" class="edge">
+<title>6->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M535.5047,-575.8314C535.7186,-568.131 535.9729,-558.9743 536.2106,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="539.7094,-550.5066 536.4885,-540.4133 532.7121,-550.3122 539.7094,-550.5066"/>
</g>
<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M52,-756C52,-756 22,-756 22,-756 16,-756 10,-750 10,-744 10,-744 10,-732 10,-732 10,-726 16,-720 22,-720 22,-720 52,-720 52,-720 58,-720 64,-726 64,-732 64,-732 64,-744 64,-744 64,-750 58,-756 52,-756"/>
-<text text-anchor="middle" x="37" y="-735.5" font-family="sans" font-size="10.00">fastqc</text>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M291.8894,-396C291.8894,-396 206.1106,-396 206.1106,-396 200.1106,-396 194.1106,-390 194.1106,-384 194.1106,-384 194.1106,-372 194.1106,-372 194.1106,-366 200.1106,-360 206.1106,-360 206.1106,-360 291.8894,-360 291.8894,-360 297.8894,-360 303.8894,-366 303.8894,-372 303.8894,-372 303.8894,-384 303.8894,-384 303.8894,-390 297.8894,-396 291.8894,-396"/>
+<text text-anchor="middle" x="249" y="-375" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
</g>
-<!-- 7->1 -->
-<g id="edge7" class="edge">
-<title>7->1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M29.51,-719.89C18.7,-693.58 0,-641.37 0,-595 0,-595 0,-595 0,-233 0,-170.8 51.29,-169.54 108,-144 200.56,-102.32 320.38,-92.74 388.77,-90.93"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="388.96,-94.43 398.89,-90.71 388.81,-87.43 388.96,-94.43"/>
+<!-- 7->4 -->
+<g id="edge17" class="edge">
+<title>7->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M261.8695,-359.8314C267.6835,-351.6232 274.6696,-341.7606 281.0646,-332.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="284.0331,-334.5966 286.9573,-324.4133 278.321,-330.5505 284.0331,-334.5966"/>
+</g>
+<!-- 9 -->
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M185.258,-324C185.258,-324 56.742,-324 56.742,-324 50.742,-324 44.742,-318 44.742,-312 44.742,-312 44.742,-300 44.742,-300 44.742,-294 50.742,-288 56.742,-288 56.742,-288 185.258,-288 185.258,-288 191.258,-288 197.258,-294 197.258,-300 197.258,-300 197.258,-312 197.258,-312 197.258,-318 191.258,-324 185.258,-324"/>
+<text text-anchor="middle" x="121" y="-303" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
+</g>
+<!-- 7->9 -->
+<g id="edge21" class="edge">
+<title>7->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M216.7002,-359.8314C200.1766,-350.5368 179.8814,-339.1208 162.2393,-329.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="163.7212,-326.015 153.2895,-324.1628 160.2893,-332.116 163.7212,-326.015"/>
</g>
<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M202.5,-324C202.5,-324 39.5,-324 39.5,-324 33.5,-324 27.5,-318 27.5,-312 27.5,-312 27.5,-300 27.5,-300 27.5,-294 33.5,-288 39.5,-288 39.5,-288 202.5,-288 202.5,-288 208.5,-288 214.5,-294 214.5,-300 214.5,-300 214.5,-312 214.5,-312 214.5,-318 208.5,-324 202.5,-324"/>
-<text text-anchor="middle" x="121" y="-303.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M169.1476,-540C169.1476,-540 80.8524,-540 80.8524,-540 74.8524,-540 68.8524,-534 68.8524,-528 68.8524,-528 68.8524,-516 68.8524,-516 68.8524,-510 74.8524,-504 80.8524,-504 80.8524,-504 169.1476,-504 169.1476,-504 175.1476,-504 181.1476,-510 181.1476,-516 181.1476,-516 181.1476,-528 181.1476,-528 181.1476,-534 175.1476,-540 169.1476,-540"/>
+<text text-anchor="middle" x="125" y="-519" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
</g>
-<!-- 8->1 -->
-<g id="edge9" class="edge">
-<title>8->1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M90.23,-287.91C77.46,-279.02 64,-266.88 57,-252 50.19,-237.52 47.82,-229.11 57,-216 95.64,-160.83 291.94,-118.33 388.8,-100.36"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="389.49,-103.79 398.7,-98.55 388.23,-96.91 389.49,-103.79"/>
-</g>
-<!-- 8->5 -->
-<g id="edge21" class="edge">
-<title>8->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M125.45,-287.7C127.45,-279.9 129.87,-270.51 132.1,-261.83"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="135.5,-262.66 134.6,-252.1 128.72,-260.92 135.5,-262.66"/>
+<!-- 8->7 -->
+<g id="edge20" class="edge">
+<title>8->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M90.911,-503.9135C77.7792,-495.0032 64.2103,-482.9331 57,-468 50.0431,-453.5916 47.3385,-444.7536 57,-432 72.5024,-411.5361 134.4643,-396.6613 183.8625,-387.7667"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="184.6275,-391.1861 193.8739,-386.0136 183.4201,-384.291 184.6275,-391.1861"/>
</g>
-<!-- 8->6 -->
-<g id="edge23" class="edge">
-<title>8->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M162.83,-287.88C186.42,-278.22 216.06,-266.09 241,-255.88"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="242.38,-259.1 250.3,-252.07 239.72,-252.62 242.38,-259.1"/>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M254.0708,-468C254.0708,-468 77.9292,-468 77.9292,-468 71.9292,-468 65.9292,-462 65.9292,-456 65.9292,-456 65.9292,-444 65.9292,-444 65.9292,-438 71.9292,-432 77.9292,-432 77.9292,-432 254.0708,-432 254.0708,-432 260.0708,-432 266.0708,-438 266.0708,-444 266.0708,-444 266.0708,-456 266.0708,-456 266.0708,-462 260.0708,-468 254.0708,-468"/>
+<text text-anchor="middle" x="166" y="-447" font-family="sans" font-size="10.00" fill="#000000">concatenate_transcriptome_and_genome</text>
</g>
-<!-- 9 -->
-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M391,-324C391,-324 245,-324 245,-324 239,-324 233,-318 233,-312 233,-312 233,-300 233,-300 233,-294 239,-288 245,-288 245,-288 391,-288 391,-288 397,-288 403,-294 403,-300 403,-300 403,-312 403,-312 403,-318 397,-324 391,-324"/>
-<text text-anchor="middle" x="318" y="-303.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<!-- 8->26 -->
+<g id="edge50" class="edge">
+<title>8->26</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M135.346,-503.8314C139.9237,-495.7925 145.4052,-486.1666 150.4588,-477.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="153.6077,-478.8351 155.5147,-468.4133 147.5248,-475.3712 153.6077,-478.8351"/>
</g>
<!-- 9->1 -->
-<g id="edge10" class="edge">
+<g id="edge8" class="edge">
<title>9->1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M336.24,-287.95C345.57,-278.26 356.34,-265.4 363,-252 384.89,-207.97 362.75,-186.77 387,-144 393.19,-133.08 402.36,-123.05 411.49,-114.73"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="413.82,-117.34 419.09,-108.15 409.24,-112.05 413.82,-117.34"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M94.2769,-287.9104C82.9915,-278.6439 71.074,-266.295 65,-252 58.743,-237.2742 56.1221,-229.311 65,-216 100.676,-162.5099 288.1289,-118.2864 379.219,-99.5881"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="379.9401,-103.0132 389.0439,-97.5937 378.5474,-96.1531 379.9401,-103.0132"/>
</g>
-<!-- 9->5 -->
-<g id="edge22" class="edge">
-<title>9->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M274.21,-287.88C249.42,-278.18 218.22,-265.98 192.04,-255.74"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="193.23,-252.45 182.65,-252.07 190.68,-258.97 193.23,-252.45"/>
+<!-- 9->30 -->
+<g id="edge58" class="edge">
+<title>9->30</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M161.3748,-287.8314C182.6787,-278.2446 208.9983,-266.4008 231.5211,-256.2655"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="233.2326,-259.3334 240.9156,-252.038 230.3601,-252.95 233.2326,-259.3334"/>
</g>
-<!-- 9->6 -->
-<g id="edge24" class="edge">
-<title>9->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M311.57,-287.7C308.64,-279.81 305.11,-270.3 301.86,-261.55"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="305.12,-260.26 298.35,-252.1 298.55,-262.7 305.12,-260.26"/>
+<!-- 9->31 -->
+<g id="edge60" class="edge">
+<title>9->31</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M125.7945,-287.8314C127.8489,-280.0463 130.296,-270.7729 132.5756,-262.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="135.9735,-262.9753 135.1409,-252.4133 129.2052,-261.1892 135.9735,-262.9753"/>
</g>
<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M478,-180C478,-180 408,-180 408,-180 402,-180 396,-174 396,-168 396,-168 396,-156 396,-156 396,-150 402,-144 408,-144 408,-144 478,-144 478,-144 484,-144 490,-150 490,-156 490,-156 490,-168 490,-168 490,-174 484,-180 478,-180"/>
-<text text-anchor="middle" x="443" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M419.2386,-540C419.2386,-540 320.7614,-540 320.7614,-540 314.7614,-540 308.7614,-534 308.7614,-528 308.7614,-528 308.7614,-516 308.7614,-516 308.7614,-510 314.7614,-504 320.7614,-504 320.7614,-504 419.2386,-504 419.2386,-504 425.2386,-504 431.2386,-510 431.2386,-516 431.2386,-516 431.2386,-528 431.2386,-528 431.2386,-534 425.2386,-540 419.2386,-540"/>
+<text text-anchor="middle" x="370" y="-519" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
-<!-- 10->1 -->
-<g id="edge14" class="edge">
-<title>10->1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M443,-143.7C443,-135.98 443,-126.71 443,-118.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="446.5,-118.1 443,-108.1 439.5,-118.1 446.5,-118.1"/>
+<!-- 10->9 -->
+<g id="edge22" class="edge">
+<title>10->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M354.8082,-503.9899C337.2779,-484.1397 306.7627,-452.3339 275,-432 238.7168,-408.7722 218.8594,-422.6372 185,-396 163.4058,-379.0118 145.9329,-352.8408 134.7339,-333.0912"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="137.7669,-331.3428 129.8937,-324.253 131.6273,-334.7051 137.7669,-331.3428"/>
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-<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M849.5,-180C849.5,-180 762.5,-180 762.5,-180 756.5,-180 750.5,-174 750.5,-168 750.5,-168 750.5,-156 750.5,-156 750.5,-150 756.5,-144 762.5,-144 762.5,-144 849.5,-144 849.5,-144 855.5,-144 861.5,-150 861.5,-156 861.5,-156 861.5,-168 861.5,-168 861.5,-174 855.5,-180 849.5,-180"/>
-<text text-anchor="middle" x="806" y="-159.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
+<!-- 17 -->
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M817.8845,-468C817.8845,-468 742.1155,-468 742.1155,-468 736.1155,-468 730.1155,-462 730.1155,-456 730.1155,-456 730.1155,-444 730.1155,-444 730.1155,-438 736.1155,-432 742.1155,-432 742.1155,-432 817.8845,-432 817.8845,-432 823.8845,-432 829.8845,-438 829.8845,-444 829.8845,-444 829.8845,-456 829.8845,-456 829.8845,-462 823.8845,-468 817.8845,-468"/>
+<text text-anchor="middle" x="780" y="-447" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
</g>
-<!-- 11->1 -->
-<g id="edge11" class="edge">
-<title>11->1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M750.22,-145.89C747.45,-145.23 744.69,-144.6 742,-144 656.96,-125.2 557.17,-108.6 497.07,-99.18"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="497.47,-95.7 487.05,-97.62 496.4,-102.62 497.47,-95.7"/>
+<!-- 10->17 -->
+<g id="edge34" class="edge">
+<title>10->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M431.4892,-509.1321C440.3744,-507.3573 449.4146,-505.5974 458,-504 549.2476,-487.0222 655.5,-469.6713 720.2333,-459.3702"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="720.93,-462.8035 730.2574,-457.7786 719.8322,-455.8901 720.93,-462.8035"/>
+</g>
+<!-- 27 -->
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M503.2288,-324C503.2288,-324 414.7712,-324 414.7712,-324 408.7712,-324 402.7712,-318 402.7712,-312 402.7712,-312 402.7712,-300 402.7712,-300 402.7712,-294 408.7712,-288 414.7712,-288 414.7712,-288 503.2288,-288 503.2288,-288 509.2288,-288 515.2288,-294 515.2288,-300 515.2288,-300 515.2288,-312 515.2288,-312 515.2288,-318 509.2288,-324 503.2288,-324"/>
+<text text-anchor="middle" x="459" y="-303" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+</g>
+<!-- 10->27 -->
+<g id="edge52" class="edge">
+<title>10->27</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M367.757,-503.5876C364.8173,-471.9783 362.7678,-406.3259 389,-360 395.6896,-348.1862 406.1133,-338.0894 416.8921,-329.9336"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="419.0155,-332.7185 425.1479,-324.0788 414.9662,-327.0086 419.0155,-332.7185"/>
+</g>
+<!-- 11->10 -->
+<g id="edge23" class="edge">
+<title>11->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M370,-575.8314C370,-568.131 370,-558.9743 370,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="373.5001,-550.4132 370,-540.4133 366.5001,-550.4133 373.5001,-550.4132"/>
+</g>
+<!-- 12 -->
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M786.1524,-324C786.1524,-324 697.8476,-324 697.8476,-324 691.8476,-324 685.8476,-318 685.8476,-312 685.8476,-312 685.8476,-300 685.8476,-300 685.8476,-294 691.8476,-288 697.8476,-288 697.8476,-288 786.1524,-288 786.1524,-288 792.1524,-288 798.1524,-294 798.1524,-300 798.1524,-300 798.1524,-312 798.1524,-312 798.1524,-318 792.1524,-324 786.1524,-324"/>
+<text text-anchor="middle" x="742" y="-303" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
</g>
<!-- 12->1 -->
<g id="edge13" class="edge">
<title>12->1</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="478.53,-110.92 468.29,-108.19 474.6,-116.71 478.53,-110.92"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M741.1486,-287.8448C739.4304,-268.4464 734.292,-237.5796 719,-216 662.7731,-136.6545 545.4894,-106.7861 478.5795,-95.9143"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="479.1056,-92.4542 468.6884,-94.3861 478.0367,-99.3721 479.1056,-92.4542"/>
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-<!-- 13->1 -->
-<g id="edge8" class="edge">
-<title>13->1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M336.49,-143.88C355.44,-134.47 379.13,-122.71 399.36,-112.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="400.97,-115.77 408.37,-108.19 397.86,-109.5 400.97,-115.77"/>
+<!-- 13->12 -->
+<g id="edge25" class="edge">
+<title>13->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M959.3002,-431.9669C973.1458,-423.189 987.3358,-411.2027 995,-396 1002.2027,-381.7129 1005.0639,-372.4386 995,-360 971.9249,-331.4801 875.2729,-317.3695 808.3453,-310.8919"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="808.569,-307.3977 798.2871,-309.9538 807.9188,-314.3674 808.569,-307.3977"/>
+</g>
+<!-- 15 -->
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M973.7629,-396C973.7629,-396 820.2371,-396 820.2371,-396 814.2371,-396 808.2371,-390 808.2371,-384 808.2371,-384 808.2371,-372 808.2371,-372 808.2371,-366 814.2371,-360 820.2371,-360 820.2371,-360 973.7629,-360 973.7629,-360 979.7629,-360 985.7629,-366 985.7629,-372 985.7629,-372 985.7629,-384 985.7629,-384 985.7629,-390 979.7629,-396 973.7629,-396"/>
+<text text-anchor="middle" x="897" y="-375" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+</g>
+<!-- 13->15 -->
+<g id="edge31" class="edge">
+<title>13->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M915.6914,-431.8314C912.9883,-424.0463 909.7684,-414.7729 906.769,-406.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="909.98,-404.7119 903.3935,-396.4133 903.3673,-407.0081 909.98,-404.7119"/>
+</g>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1001.955,-324C1001.955,-324 970.045,-324 970.045,-324 964.045,-324 958.045,-318 958.045,-312 958.045,-312 958.045,-300 958.045,-300 958.045,-294 964.045,-288 970.045,-288 970.045,-288 1001.955,-288 1001.955,-288 1007.955,-288 1013.955,-294 1013.955,-300 1013.955,-300 1013.955,-312 1013.955,-312 1013.955,-318 1007.955,-324 1001.955,-324"/>
+<text text-anchor="middle" x="986" y="-303" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+</g>
+<!-- 13->20 -->
+<g id="edge38" class="edge">
+<title>13->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M980.0909,-433.899C998.6731,-425.7011 1017.2081,-413.6093 1028,-396 1040.5792,-375.4742 1026.9451,-350.5676 1011.9485,-332.1638"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1014.2455,-329.47 1005.0516,-324.2047 1008.9553,-334.0541 1014.2455,-329.47"/>
</g>
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M720.5,-180C720.5,-180 613.5,-180 613.5,-180 607.5,-180 601.5,-174 601.5,-168 601.5,-168 601.5,-156 601.5,-156 601.5,-150 607.5,-144 613.5,-144 613.5,-144 720.5,-144 720.5,-144 726.5,-144 732.5,-150 732.5,-156 732.5,-156 732.5,-168 732.5,-168 732.5,-174 726.5,-180 720.5,-180"/>
-<text text-anchor="middle" x="667" y="-159.5" font-family="sans" font-size="10.00">prepare_multiqc_config</text>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M957.9935,-540C957.9935,-540 886.0065,-540 886.0065,-540 880.0065,-540 874.0065,-534 874.0065,-528 874.0065,-528 874.0065,-516 874.0065,-516 874.0065,-510 880.0065,-504 886.0065,-504 886.0065,-504 957.9935,-504 957.9935,-504 963.9935,-504 969.9935,-510 969.9935,-516 969.9935,-516 969.9935,-528 969.9935,-528 969.9935,-534 963.9935,-540 957.9935,-540"/>
+<text text-anchor="middle" x="922" y="-519" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
</g>
-<!-- 14->1 -->
-<g id="edge12" class="edge">
-<title>14->1</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M612.49,-143.97C577.33,-132.98 531.81,-118.75 496.79,-107.81"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="497.8,-104.46 487.21,-104.82 495.71,-111.14 497.8,-104.46"/>
+<!-- 14->13 -->
+<g id="edge30" class="edge">
+<title>14->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M922,-503.8314C922,-496.131 922,-486.9743 922,-478.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="925.5001,-478.4132 922,-468.4133 918.5001,-478.4133 925.5001,-478.4132"/>
</g>
-<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M1087,-324C1087,-324 1021,-324 1021,-324 1015,-324 1009,-318 1009,-312 1009,-312 1009,-300 1009,-300 1009,-294 1015,-288 1021,-288 1021,-288 1087,-288 1087,-288 1093,-288 1099,-294 1099,-300 1099,-300 1099,-312 1099,-312 1099,-318 1093,-324 1087,-324"/>
-<text text-anchor="middle" x="1054" y="-303.5" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<!-- 14->17 -->
+<g id="edge33" class="edge">
+<title>14->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M886.1674,-503.8314C867.5843,-494.4089 844.7011,-482.8062 824.9435,-472.7883"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="826.323,-469.5635 815.8211,-468.1628 823.1573,-475.8069 826.323,-469.5635"/>
</g>
-<!-- 15->2 -->
-<g id="edge16" class="edge">
-<title>15->2</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1054,-287.7C1054,-279.98 1054,-270.71 1054,-262.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1057.5,-262.1 1054,-252.1 1050.5,-262.1 1057.5,-262.1"/>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1101.1305,-468C1101.1305,-468 1018.8695,-468 1018.8695,-468 1012.8695,-468 1006.8695,-462 1006.8695,-456 1006.8695,-456 1006.8695,-444 1006.8695,-444 1006.8695,-438 1012.8695,-432 1018.8695,-432 1018.8695,-432 1101.1305,-432 1101.1305,-432 1107.1305,-432 1113.1305,-438 1113.1305,-444 1113.1305,-444 1113.1305,-456 1113.1305,-456 1113.1305,-462 1107.1305,-468 1101.1305,-468"/>
+<text text-anchor="middle" x="1060" y="-447" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
</g>
-<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M989,-684C989,-684 909,-684 909,-684 903,-684 897,-678 897,-672 897,-672 897,-660 897,-660 897,-654 903,-648 909,-648 909,-648 989,-648 989,-648 995,-648 1001,-654 1001,-660 1001,-660 1001,-672 1001,-672 1001,-678 995,-684 989,-684"/>
-<text text-anchor="middle" x="949" y="-663.5" font-family="sans" font-size="10.00">create_index_star</text>
+<!-- 14->21 -->
+<g id="edge41" class="edge">
+<title>14->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M956.8232,-503.8314C974.8011,-494.4516 996.9203,-482.9112 1016.0616,-472.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1017.9411,-475.8916 1025.1879,-468.1628 1014.7031,-469.6855 1017.9411,-475.8916"/>
</g>
-<!-- 16->2 -->
-<g id="edge15" class="edge">
-<title>16->2</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1001.3,-656.32C1033.15,-648.9 1073.12,-635.52 1102,-612 1137.69,-582.92 1155,-569.04 1155,-523 1155,-523 1155,-523 1155,-377 1155,-328.19 1114.89,-284.51 1085.22,-258.87"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1087.09,-255.87 1077.17,-252.13 1082.59,-261.23 1087.09,-255.87"/>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M497.5586,-396C497.5586,-396 410.4414,-396 410.4414,-396 404.4414,-396 398.4414,-390 398.4414,-384 398.4414,-384 398.4414,-372 398.4414,-372 398.4414,-366 404.4414,-360 410.4414,-360 410.4414,-360 497.5586,-360 497.5586,-360 503.5586,-360 509.5586,-366 509.5586,-372 509.5586,-372 509.5586,-384 509.5586,-384 509.5586,-390 503.5586,-396 497.5586,-396"/>
+<text text-anchor="middle" x="454" y="-375" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
</g>
-<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#568ad8" stroke-width="2" d="M591.5,-396C591.5,-396 494.5,-396 494.5,-396 488.5,-396 482.5,-390 482.5,-384 482.5,-384 482.5,-372 482.5,-372 482.5,-366 488.5,-360 494.5,-360 494.5,-360 591.5,-360 591.5,-360 597.5,-360 603.5,-366 603.5,-372 603.5,-372 603.5,-384 603.5,-384 603.5,-390 597.5,-396 591.5,-396"/>
-<text text-anchor="middle" x="543" y="-375.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+<!-- 14->25 -->
+<g id="edge49" class="edge">
+<title>14->25</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M874.2459,-510.0692C833.3697,-499.6426 773.0505,-483.7475 721,-468 649.3741,-446.3301 568.0078,-418.4205 514.1193,-399.4667"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="514.9803,-396.0592 504.3855,-396.0354 512.653,-402.661 514.9803,-396.0592"/>
</g>
-<!-- 16->26 -->
-<g id="edge48" class="edge">
-<title>16->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M951.45,-647.88C956.59,-604.61 963.37,-490.23 902,-432 861.69,-393.75 706.5,-383.05 613.87,-380.09"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="613.83,-376.59 603.73,-379.79 613.62,-383.59 613.83,-376.59"/>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1085.0966,-108C1085.0966,-108 1022.9034,-108 1022.9034,-108 1016.9034,-108 1010.9034,-102 1010.9034,-96 1010.9034,-96 1010.9034,-84 1010.9034,-84 1010.9034,-78 1016.9034,-72 1022.9034,-72 1022.9034,-72 1085.0966,-72 1085.0966,-72 1091.0966,-72 1097.0966,-78 1097.0966,-84 1097.0966,-84 1097.0966,-96 1097.0966,-96 1097.0966,-102 1091.0966,-108 1085.0966,-108"/>
+<text text-anchor="middle" x="1054" y="-87" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
</g>
-<!-- 34 -->
-<g id="node35" class="node">
-<title>34</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M759.5,-612C759.5,-612 658.5,-612 658.5,-612 652.5,-612 646.5,-606 646.5,-600 646.5,-600 646.5,-588 646.5,-588 646.5,-582 652.5,-576 658.5,-576 658.5,-576 759.5,-576 759.5,-576 765.5,-576 771.5,-582 771.5,-588 771.5,-588 771.5,-600 771.5,-600 771.5,-606 765.5,-612 759.5,-612"/>
-<text text-anchor="middle" x="709" y="-591.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 14->33 -->
+<g id="edge61" class="edge">
+<title>14->33</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M969.9053,-514.5502C1021.9209,-505.5388 1100.4722,-488.9387 1122,-468 1151.9364,-438.8828 1149,-419.7612 1149,-378 1149,-378 1149,-378 1149,-234 1149,-186.0912 1111.9087,-141.8312 1084.079,-115.3654"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1086.2364,-112.5938 1076.5137,-108.3843 1081.4892,-117.7382 1086.2364,-112.5938"/>
</g>
-<!-- 16->34 -->
-<g id="edge62" class="edge">
-<title>16->34</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M896.92,-649.81C861.87,-639.59 815.28,-626 777.26,-614.91"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="777.87,-611.44 767.29,-612 775.91,-618.16 777.87,-611.44"/>
-</g>
-<!-- 37 -->
-<g id="node38" class="node">
-<title>37</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M908.5,-612C908.5,-612 825.5,-612 825.5,-612 819.5,-612 813.5,-606 813.5,-600 813.5,-600 813.5,-588 813.5,-588 813.5,-582 819.5,-576 825.5,-576 825.5,-576 908.5,-576 908.5,-576 914.5,-576 920.5,-582 920.5,-588 920.5,-588 920.5,-600 920.5,-600 920.5,-606 914.5,-612 908.5,-612"/>
-<text text-anchor="middle" x="867" y="-591.5" font-family="sans" font-size="10.00">map_genome_star</text>
-</g>
-<!-- 16->37 -->
-<g id="edge66" class="edge">
-<title>16->37</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M928.73,-647.7C918.5,-638.97 905.94,-628.24 894.82,-618.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="896.91,-615.94 887.04,-612.1 892.37,-621.26 896.91,-615.94"/>
-</g>
-<!-- 38 -->
-<g id="node39" class="node">
-<title>38</title>
-<path fill="none" stroke="#d87d56" stroke-width="2" d="M1081,-612C1081,-612 989,-612 989,-612 983,-612 977,-606 977,-600 977,-600 977,-588 977,-588 977,-582 983,-576 989,-576 989,-576 1081,-576 1081,-576 1087,-576 1093,-582 1093,-588 1093,-588 1093,-600 1093,-600 1093,-606 1087,-612 1081,-612"/>
-<text text-anchor="middle" x="1035" y="-591.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
-</g>
-<!-- 16->38 -->
-<g id="edge67" class="edge">
-<title>16->38</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M970.26,-647.7C981.09,-638.88 994.42,-628.03 1006.16,-618.47"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1008.44,-621.13 1013.99,-612.1 1004.02,-615.7 1008.44,-621.13"/>
+<!-- 15->12 -->
+<g id="edge28" class="edge">
+<title>15->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M857.887,-359.8314C837.2488,-350.2446 811.7516,-338.4008 789.9327,-328.2655"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="791.3756,-325.0766 780.8318,-324.038 788.4266,-331.4251 791.3756,-325.0766"/>
</g>
-<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M590,-324C590,-324 472,-324 472,-324 466,-324 460,-318 460,-312 460,-312 460,-300 460,-300 460,-294 466,-288 472,-288 472,-288 590,-288 590,-288 596,-288 602,-294 602,-300 602,-300 602,-312 602,-312 602,-318 596,-324 590,-324"/>
-<text text-anchor="middle" x="531" y="-303.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<!-- 15->20 -->
+<g id="edge40" class="edge">
+<title>15->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M919.4585,-359.8314C930.4205,-350.9632 943.7699,-340.1637 955.6265,-330.5718"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="957.9755,-333.1734 963.5487,-324.1628 953.5729,-327.7313 957.9755,-333.1734"/>
</g>
-<!-- 17->3 -->
-<g id="edge17" class="edge">
-<title>17->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M578.7,-287.97C606.08,-278.19 640.66,-265.84 669.53,-255.52"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="670.85,-258.77 679.09,-252.11 668.5,-252.18 670.85,-258.77"/>
+<!-- 16 -->
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M701.6866,-396C701.6866,-396 578.3134,-396 578.3134,-396 572.3134,-396 566.3134,-390 566.3134,-384 566.3134,-384 566.3134,-372 566.3134,-372 566.3134,-366 572.3134,-360 578.3134,-360 578.3134,-360 701.6866,-360 701.6866,-360 707.6866,-360 713.6866,-366 713.6866,-372 713.6866,-372 713.6866,-384 713.6866,-384 713.6866,-390 707.6866,-396 701.6866,-396"/>
+<text text-anchor="middle" x="640" y="-375" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
</g>
-<!-- 17->4 -->
-<g id="edge19" class="edge">
-<title>17->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M534.71,-287.7C536.36,-279.98 538.35,-270.71 540.19,-262.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="543.66,-262.62 542.33,-252.1 536.82,-261.15 543.66,-262.62"/>
+<!-- 16->12 -->
+<g id="edge27" class="edge">
+<title>16->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M665.7389,-359.8314C678.5437,-350.7927 694.1909,-339.7476 707.9719,-330.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="710.118,-332.7891 716.2693,-324.1628 706.0812,-327.0703 710.118,-332.7891"/>
+</g>
+<!-- 17->12 -->
+<g id="edge26" class="edge">
+<title>17->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M775.1873,-431.7623C768.6773,-407.0928 757.0047,-362.8598 749.3818,-333.9731"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="752.7094,-332.8656 746.7736,-324.0896 745.9411,-334.6517 752.7094,-332.8656"/>
+</g>
+<!-- 17->15 -->
+<g id="edge32" class="edge">
+<title>17->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M809.524,-431.8314C824.4891,-422.6221 842.8386,-411.3301 858.8603,-401.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="860.8032,-404.3847 867.4854,-396.1628 857.1345,-398.423 860.8032,-404.3847"/>
+</g>
+<!-- 17->20 -->
+<g id="edge39" class="edge">
+<title>17->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M778.7019,-431.6499C778.3213,-411.495 780.9523,-379.417 799,-360 819.1471,-338.3243 899.2594,-321.0315 947.853,-312.2704"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="948.7638,-315.6639 958.0045,-310.4813 947.5488,-308.7702 948.7638,-315.6639"/>
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<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M733.5,-324C733.5,-324 632.5,-324 632.5,-324 626.5,-324 620.5,-318 620.5,-312 620.5,-312 620.5,-300 620.5,-300 620.5,-294 626.5,-288 632.5,-288 632.5,-288 733.5,-288 733.5,-288 739.5,-288 745.5,-294 745.5,-300 745.5,-300 745.5,-312 745.5,-312 745.5,-318 739.5,-324 733.5,-324"/>
-<text text-anchor="middle" x="683" y="-303.5" font-family="sans" font-size="10.00">quantification_salmon</text>
-</g>
-<!-- 18->3 -->
-<g id="edge18" class="edge">
-<title>18->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M693.88,-287.7C698.99,-279.56 705.2,-269.69 710.84,-260.7"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="713.89,-262.43 716.25,-252.1 707.96,-258.71 713.89,-262.43"/>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M974,-180C974,-180 944,-180 944,-180 938,-180 932,-174 932,-168 932,-168 932,-156 932,-156 932,-150 938,-144 944,-144 944,-144 974,-144 974,-144 980,-144 986,-150 986,-156 986,-156 986,-168 986,-168 986,-174 980,-180 974,-180"/>
+<text text-anchor="middle" x="959" y="-159" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
</g>
-<!-- 18->4 -->
-<g id="edge20" class="edge">
-<title>18->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M649.49,-287.88C631.16,-278.51 608.26,-266.81 588.67,-256.8"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="590.14,-253.62 579.64,-252.19 586.96,-259.86 590.14,-253.62"/>
+<!-- 18->1 -->
+<g id="edge12" class="edge">
+<title>18->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M931.9886,-158.3305C847.6931,-146.8791 588.5801,-111.6788 478.8847,-96.7768"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="479.1265,-93.2776 468.7463,-95.3995 478.1841,-100.2139 479.1265,-93.2776"/>
</g>
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M206,-828C206,-828 176,-828 176,-828 170,-828 164,-822 164,-816 164,-816 164,-804 164,-804 164,-798 170,-792 176,-792 176,-792 206,-792 206,-792 212,-792 218,-798 218,-804 218,-804 218,-816 218,-816 218,-822 212,-828 206,-828"/>
-<text text-anchor="middle" x="191" y="-807.5" font-family="sans" font-size="10.00">start</text>
-</g>
-<!-- 19->7 -->
-<g id="edge25" class="edge">
-<title>19->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M163.82,-796.65C138.72,-785.24 101.23,-768.2 73.52,-755.6"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="74.72,-752.3 64.16,-751.35 71.82,-758.67 74.72,-752.3"/>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1108.837,-252C1108.837,-252 999.163,-252 999.163,-252 993.163,-252 987.163,-246 987.163,-240 987.163,-240 987.163,-228 987.163,-228 987.163,-222 993.163,-216 999.163,-216 999.163,-216 1108.837,-216 1108.837,-216 1114.837,-216 1120.837,-222 1120.837,-228 1120.837,-228 1120.837,-240 1120.837,-240 1120.837,-246 1114.837,-252 1108.837,-252"/>
+<text text-anchor="middle" x="1054" y="-231" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
</g>
-<!-- 27 -->
-<g id="node28" class="node">
-<title>27</title>
-<path fill="none" stroke="#56d8a2" stroke-width="2" d="M262.5,-756C262.5,-756 119.5,-756 119.5,-756 113.5,-756 107.5,-750 107.5,-744 107.5,-744 107.5,-732 107.5,-732 107.5,-726 113.5,-720 119.5,-720 119.5,-720 262.5,-720 262.5,-720 268.5,-720 274.5,-726 274.5,-732 274.5,-732 274.5,-744 274.5,-744 274.5,-750 268.5,-756 262.5,-756"/>
-<text text-anchor="middle" x="191" y="-735.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-</g>
-<!-- 19->27 -->
-<g id="edge49" class="edge">
-<title>19->27</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M191,-791.7C191,-783.98 191,-774.71 191,-766.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="194.5,-766.1 191,-756.1 187.5,-766.1 194.5,-766.1"/>
-</g>
-<!-- 29 -->
-<g id="node30" class="node">
-<title>29</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M430,-756C430,-756 304,-756 304,-756 298,-756 292,-750 292,-744 292,-744 292,-732 292,-732 292,-726 298,-720 304,-720 304,-720 430,-720 430,-720 436,-720 442,-726 442,-732 442,-732 442,-744 442,-744 442,-750 436,-756 430,-756"/>
-<text text-anchor="middle" x="367" y="-735.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-</g>
-<!-- 19->29 -->
-<g id="edge50" class="edge">
-<title>19->29</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M218.11,-798.22C243.72,-788.03 282.81,-772.48 314.51,-759.88"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="316.09,-763.01 324.09,-756.07 313.51,-756.51 316.09,-763.01"/>
+<!-- 19->18 -->
+<g id="edge35" class="edge">
+<title>19->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1030.0275,-215.8314C1018.2139,-206.8779 1003.8028,-195.9558 991.0565,-186.2955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="993.0486,-183.4137 982.9648,-180.1628 988.8205,-188.9925 993.0486,-183.4137"/>
</g>
-<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M262,-684C262,-684 134,-684 134,-684 128,-684 122,-678 122,-672 122,-672 122,-660 122,-660 122,-654 128,-648 134,-648 134,-648 262,-648 262,-648 268,-648 274,-654 274,-660 274,-660 274,-672 274,-672 274,-678 268,-684 262,-684"/>
-<text text-anchor="middle" x="198" y="-663.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<!-- 34 -->
+<g id="node35" class="node">
+<title>34</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M1084.4453,-180C1084.4453,-180 1023.5547,-180 1023.5547,-180 1017.5547,-180 1011.5547,-174 1011.5547,-168 1011.5547,-168 1011.5547,-156 1011.5547,-156 1011.5547,-150 1017.5547,-144 1023.5547,-144 1023.5547,-144 1084.4453,-144 1084.4453,-144 1090.4453,-144 1096.4453,-150 1096.4453,-156 1096.4453,-156 1096.4453,-168 1096.4453,-168 1096.4453,-174 1090.4453,-180 1084.4453,-180"/>
+<text text-anchor="middle" x="1054" y="-159" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
</g>
-<!-- 20->8 -->
-<g id="edge26" class="edge">
-<title>20->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M178.25,-647.91C152.03,-623.21 109,-574.79 109,-523 109,-523 109,-523 109,-449 109,-408.85 113.82,-362.55 117.35,-334.02"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="120.84,-334.37 118.63,-324.01 113.89,-333.49 120.84,-334.37"/>
+<!-- 19->34 -->
+<g id="edge63" class="edge">
+<title>19->34</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1054,-215.8314C1054,-208.131 1054,-198.9743 1054,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1057.5001,-190.4132 1054,-180.4133 1050.5001,-190.4133 1057.5001,-190.4132"/>
</g>
-<!-- 20->17 -->
+<!-- 20->19 -->
<g id="edge37" class="edge">
-<title>20->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M219.1,-647.68C246.54,-623.08 291,-575.16 291,-523 291,-523 291,-523 291,-449 291,-373.44 380.21,-337.23 449.85,-320.48"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="451.01,-323.8 459.97,-318.15 449.44,-316.98 451.01,-323.8"/>
-</g>
-<!-- 20->34 -->
-<g id="edge61" class="edge">
-<title>20->34</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M274.07,-650.74C279.79,-649.78 285.49,-648.85 291,-648 411.58,-629.35 552.47,-612.5 636.03,-603.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="636.63,-606.48 646.18,-601.88 635.85,-599.53 636.63,-606.48"/>
-</g>
-<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M248.5,-396C248.5,-396 151.5,-396 151.5,-396 145.5,-396 139.5,-390 139.5,-384 139.5,-384 139.5,-372 139.5,-372 139.5,-366 145.5,-360 151.5,-360 151.5,-360 248.5,-360 248.5,-360 254.5,-360 260.5,-366 260.5,-372 260.5,-372 260.5,-384 260.5,-384 260.5,-390 254.5,-396 248.5,-396"/>
-<text text-anchor="middle" x="200" y="-375.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
-</g>
-<!-- 21->8 -->
-<g id="edge27" class="edge">
-<title>21->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M180.47,-359.7C170.62,-350.97 158.51,-340.24 147.8,-330.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="150.11,-328.12 140.3,-324.1 145.47,-333.36 150.11,-328.12"/>
+<title>20->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1003.1593,-287.8314C1011.1511,-279.3694 1020.8038,-269.1489 1029.5416,-259.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1032.288,-262.0866 1036.6097,-252.4133 1027.1989,-257.2802 1032.288,-262.0866"/>
</g>
-<!-- 21->9 -->
-<g id="edge29" class="edge">
-<title>21->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M228.87,-359.88C244.29,-350.72 263.48,-339.34 280.1,-329.48"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="282.21,-332.3 289.02,-324.19 278.64,-326.28 282.21,-332.3"/>
+<!-- 21->18 -->
+<g id="edge36" class="edge">
+<title>21->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1057.3783,-431.9539C1054.5891,-413.6993 1049.7855,-384.7241 1044,-360 1036.4051,-327.5434 1041.5433,-315.6994 1023,-288 1008.7518,-266.7165 991.4322,-273.8077 978,-252 966.5351,-233.3863 961.8987,-208.9441 960.0662,-190.2295"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="963.5536,-189.9297 959.2958,-180.2281 956.5743,-190.4674 963.5536,-189.9297"/>
</g>
<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
-<path fill="none" stroke="#567bd8" stroke-width="2" d="M422,-684C422,-684 312,-684 312,-684 306,-684 300,-678 300,-672 300,-672 300,-660 300,-660 300,-654 306,-648 312,-648 312,-648 422,-648 422,-648 428,-648 434,-654 434,-660 434,-660 434,-672 434,-672 434,-678 428,-684 422,-684"/>
-<text text-anchor="middle" x="367" y="-663.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
-</g>
-<!-- 22->9 -->
-<g id="edge28" class="edge">
-<title>22->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M359.31,-647.91C348.21,-621.62 329,-569.45 329,-523 329,-523 329,-523 329,-449 329,-408.88 324.58,-362.57 321.34,-334.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="324.81,-333.54 320.17,-324.02 317.86,-334.36 324.81,-333.54"/>
-</g>
-<!-- 22->18 -->
-<g id="edge39" class="edge">
-<title>22->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M363.18,-647.99C356.94,-615.36 348.71,-543.69 386,-504 447.24,-438.81 510.16,-518.48 584,-468 632.16,-435.08 661.17,-370.23 674.41,-333.68"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="677.74,-334.77 677.73,-324.17 671.13,-332.46 677.74,-334.77"/>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M451.9209,-180C451.9209,-180 406.0791,-180 406.0791,-180 400.0791,-180 394.0791,-174 394.0791,-168 394.0791,-168 394.0791,-156 394.0791,-156 394.0791,-150 400.0791,-144 406.0791,-144 406.0791,-144 451.9209,-144 451.9209,-144 457.9209,-144 463.9209,-150 463.9209,-156 463.9209,-156 463.9209,-168 463.9209,-168 463.9209,-174 457.9209,-180 451.9209,-180"/>
+<text text-anchor="middle" x="429" y="-159" font-family="sans" font-size="10.00" fill="#000000">pca_salmon</text>
</g>
-<!-- 22->37 -->
-<g id="edge65" class="edge">
-<title>22->37</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M434.25,-657.81C516.32,-648.71 659.23,-631.81 781,-612 788.31,-610.81 795.95,-609.46 803.53,-608.05"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="804.25,-611.48 813.43,-606.17 802.95,-604.6 804.25,-611.48"/>
+<!-- 22->1 -->
+<g id="edge14" class="edge">
+<title>22->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M429,-143.8314C429,-136.131 429,-126.9743 429,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="432.5001,-118.4132 429,-108.4133 425.5001,-118.4133 432.5001,-118.4132"/>
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<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M452.5,-396C452.5,-396 369.5,-396 369.5,-396 363.5,-396 357.5,-390 357.5,-384 357.5,-384 357.5,-372 357.5,-372 357.5,-366 363.5,-360 369.5,-360 369.5,-360 452.5,-360 452.5,-360 458.5,-360 464.5,-366 464.5,-372 464.5,-372 464.5,-384 464.5,-384 464.5,-390 458.5,-396 452.5,-396"/>
-<text text-anchor="middle" x="411" y="-375.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
-</g>
-<!-- 23->10 -->
-<g id="edge30" class="edge">
-<title>23->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M413.56,-359.85C419.1,-322.83 432.21,-235.18 438.9,-190.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="442.41,-190.64 440.42,-180.23 435.48,-189.6 442.41,-190.64"/>
-</g>
-<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#68d856" stroke-width="2" d="M974,-252C974,-252 882,-252 882,-252 876,-252 870,-246 870,-240 870,-240 870,-228 870,-228 870,-222 876,-216 882,-216 882,-216 974,-216 974,-216 980,-216 986,-222 986,-228 986,-228 986,-240 986,-240 986,-246 980,-252 974,-252"/>
-<text text-anchor="middle" x="928" y="-231.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M521.9746,-252C521.9746,-252 406.0254,-252 406.0254,-252 400.0254,-252 394.0254,-246 394.0254,-240 394.0254,-240 394.0254,-228 394.0254,-228 394.0254,-222 400.0254,-216 406.0254,-216 406.0254,-216 521.9746,-216 521.9746,-216 527.9746,-216 533.9746,-222 533.9746,-228 533.9746,-228 533.9746,-240 533.9746,-240 533.9746,-246 527.9746,-252 521.9746,-252"/>
+<text text-anchor="middle" x="464" y="-231" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
</g>
-<!-- 24->11 -->
-<g id="edge31" class="edge">
-<title>24->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M898.16,-215.88C882.06,-206.64 862,-195.13 844.71,-185.21"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="846.37,-182.13 835.96,-180.19 842.89,-188.2 846.37,-182.13"/>
-</g>
-<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1115,-396C1115,-396 993,-396 993,-396 987,-396 981,-390 981,-384 981,-384 981,-372 981,-372 981,-366 987,-360 993,-360 993,-360 1115,-360 1115,-360 1121,-360 1127,-366 1127,-372 1127,-372 1127,-384 1127,-384 1127,-390 1121,-396 1115,-396"/>
-<text text-anchor="middle" x="1054" y="-375.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-</g>
-<!-- 25->15 -->
-<g id="edge36" class="edge">
-<title>25->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1054,-359.7C1054,-351.98 1054,-342.71 1054,-334.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1057.5,-334.1 1054,-324.1 1050.5,-334.1 1057.5,-334.1"/>
-</g>
-<!-- 31 -->
-<g id="node32" class="node">
-<title>31</title>
-<path fill="none" stroke="#56a9d8" stroke-width="2" d="M968,-324C968,-324 938,-324 938,-324 932,-324 926,-318 926,-312 926,-312 926,-300 926,-300 926,-294 932,-288 938,-288 938,-288 968,-288 968,-288 974,-288 980,-294 980,-300 980,-300 980,-312 980,-312 980,-318 974,-324 968,-324"/>
-<text text-anchor="middle" x="953" y="-303.5" font-family="sans" font-size="10.00">alfa_qc</text>
-</g>
-<!-- 25->31 -->
-<g id="edge55" class="edge">
-<title>25->31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1029.29,-359.88C1016.33,-350.89 1000.27,-339.76 986.23,-330.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="988.02,-327.01 977.8,-324.19 984.03,-332.76 988.02,-327.01"/>
-</g>
-<!-- 26->17 -->
-<g id="edge38" class="edge">
-<title>26->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M540.03,-359.7C538.71,-351.98 537.12,-342.71 535.65,-334.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="539.07,-333.37 533.93,-324.1 532.17,-334.55 539.07,-333.37"/>
+<!-- 23->0 -->
+<g id="edge2" class="edge">
+<title>23->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M534.0551,-216.5212C567.1209,-206.7127 601.4297,-193.7111 611,-180 642.4505,-134.9413 593.0504,-76.1333 558.3236,-43.1921"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="560.4564,-40.3974 550.7375,-36.1791 555.7046,-45.5375 560.4564,-40.3974"/>
</g>
-<!-- 26->18 -->
-<g id="edge40" class="edge">
-<title>26->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M577.25,-359.88C596.06,-350.47 619.58,-338.71 639.67,-328.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="641.24,-331.79 648.62,-324.19 638.11,-325.53 641.24,-331.79"/>
+<!-- 23->22 -->
+<g id="edge43" class="edge">
+<title>23->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M455.168,-215.8314C451.3014,-207.8771 446.6794,-198.369 442.4032,-189.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="445.4707,-187.8768 437.9509,-180.4133 439.1751,-190.9371 445.4707,-187.8768"/>
</g>
-<!-- 27->20 -->
-<g id="edge41" class="edge">
-<title>27->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M192.73,-719.7C193.5,-711.98 194.43,-702.71 195.29,-694.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="198.78,-694.4 196.29,-684.1 191.81,-693.71 198.78,-694.4"/>
+<!-- 24->23 -->
+<g id="edge45" class="edge">
+<title>24->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M564.1861,-287.8314C546.7293,-278.4516 525.2513,-266.9112 506.6648,-256.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="508.2686,-253.8129 497.803,-252.1628 504.9554,-259.9792 508.2686,-253.8129"/>
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<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
-<path fill="none" stroke="#8fd856" stroke-width="2" d="M250.5,-540C250.5,-540 149.5,-540 149.5,-540 143.5,-540 137.5,-534 137.5,-528 137.5,-528 137.5,-516 137.5,-516 137.5,-510 143.5,-504 149.5,-504 149.5,-504 250.5,-504 250.5,-504 256.5,-504 262.5,-510 262.5,-516 262.5,-516 262.5,-528 262.5,-528 262.5,-534 256.5,-540 250.5,-540"/>
-<text text-anchor="middle" x="200" y="-519.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M698.3516,-252C698.3516,-252 563.6484,-252 563.6484,-252 557.6484,-252 551.6484,-246 551.6484,-240 551.6484,-240 551.6484,-228 551.6484,-228 551.6484,-222 557.6484,-216 563.6484,-216 563.6484,-216 698.3516,-216 698.3516,-216 704.3516,-216 710.3516,-222 710.3516,-228 710.3516,-228 710.3516,-240 710.3516,-240 710.3516,-246 704.3516,-252 698.3516,-252"/>
+<text text-anchor="middle" x="631" y="-231" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
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-<!-- 28->21 -->
-<g id="edge42" class="edge">
-<title>28->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M200,-503.87C200,-479.67 200,-435.21 200,-406.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="203.5,-406.19 200,-396.19 196.5,-406.19 203.5,-406.19"/>
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-<!-- 33 -->
-<g id="node34" class="node">
-<title>33</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M563,-468C563,-468 369,-468 369,-468 363,-468 357,-462 357,-456 357,-456 357,-444 357,-444 357,-438 363,-432 369,-432 369,-432 563,-432 563,-432 569,-432 575,-438 575,-444 575,-444 575,-456 575,-456 575,-462 569,-468 563,-468"/>
-<text text-anchor="middle" x="466" y="-447.5" font-family="sans" font-size="10.00">concatenate_transcriptome_and_genome</text>
+<!-- 24->28 -->
+<g id="edge54" class="edge">
+<title>24->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M606.3273,-287.8314C609.973,-279.8771 614.3309,-270.369 618.3627,-261.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="621.5757,-262.9622 622.5606,-252.4133 615.2123,-260.0456 621.5757,-262.9622"/>
</g>
-<!-- 28->33 -->
-<g id="edge60" class="edge">
-<title>28->33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M262.7,-504.5C301.16,-494.38 350.61,-481.37 391.12,-470.71"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="392.16,-474.05 400.94,-468.12 390.38,-467.28 392.16,-474.05"/>
+<!-- 25->24 -->
+<g id="edge47" class="edge">
+<title>25->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M490.3373,-359.8314C509.3396,-350.3302 532.7758,-338.6121 552.9252,-328.5374"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="554.545,-331.6407 561.924,-324.038 551.4145,-325.3797 554.545,-331.6407"/>
</g>
-<!-- 29->22 -->
-<g id="edge43" class="edge">
-<title>29->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M367,-719.7C367,-711.98 367,-702.71 367,-694.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="370.5,-694.1 367,-684.1 363.5,-694.1 370.5,-694.1"/>
+<!-- 25->27 -->
+<g id="edge51" class="edge">
+<title>25->27</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M455.2617,-359.8314C455.7965,-352.131 456.4323,-342.9743 457.0266,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="460.52,-334.6317 457.7213,-324.4133 453.5368,-334.1467 460.52,-334.6317"/>
</g>
-<!-- 30 -->
-<g id="node31" class="node">
-<title>30</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M738.5,-468C738.5,-468 643.5,-468 643.5,-468 637.5,-468 631.5,-462 631.5,-456 631.5,-456 631.5,-444 631.5,-444 631.5,-438 637.5,-432 643.5,-432 643.5,-432 738.5,-432 738.5,-432 744.5,-432 750.5,-438 750.5,-444 750.5,-444 750.5,-456 750.5,-456 750.5,-462 744.5,-468 738.5,-468"/>
-<text text-anchor="middle" x="691" y="-447.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<!-- 26->25 -->
+<g id="edge48" class="edge">
+<title>26->25</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M238.3028,-431.9243C284.3104,-420.4224 343.4273,-405.6432 388.1335,-394.4666"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="389.1652,-397.8165 398.0177,-391.9956 387.4674,-391.0255 389.1652,-397.8165"/>
</g>
-<!-- 30->23 -->
+<!-- 27->23 -->
<g id="edge44" class="edge">
-<title>30->23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M631.5,-434.87C590.14,-424.96 533.5,-411.2 474.47,-396.09"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="475.15,-392.65 464.59,-393.56 473.41,-399.43 475.15,-392.65"/>
-</g>
-<!-- 31->24 -->
-<g id="edge45" class="edge">
-<title>31->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M946.82,-287.7C944,-279.81 940.61,-270.3 937.48,-261.55"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="940.77,-260.34 934.11,-252.1 934.18,-262.7 940.77,-260.34"/>
-</g>
-<!-- 32 -->
-<g id="node33" class="node">
-<title>32</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M881,-468C881,-468 845,-468 845,-468 839,-468 833,-462 833,-456 833,-456 833,-444 833,-444 833,-438 839,-432 845,-432 845,-432 881,-432 881,-432 887,-432 893,-438 893,-444 893,-444 893,-456 893,-456 893,-462 887,-468 881,-468"/>
-<text text-anchor="middle" x="863" y="-447.5" font-family="sans" font-size="10.00">star_rpm</text>
+<title>27->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M460.2617,-287.8314C460.7965,-280.131 461.4323,-270.9743 462.0266,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="465.52,-262.6317 462.7213,-252.4133 458.5368,-262.1467 465.52,-262.6317"/>
</g>
-<!-- 32->25 -->
-<g id="edge46" class="edge">
-<title>32->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M893.26,-437.91C921.34,-427.62 963.82,-412.05 998.07,-399.5"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="999.3,-402.77 1007.49,-396.05 996.89,-396.2 999.3,-402.77"/>
-</g>
-<!-- 33->26 -->
-<g id="edge47" class="edge">
-<title>33->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M485.03,-431.7C494.54,-423.05 506.21,-412.45 516.57,-403.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="519.14,-405.42 524.19,-396.1 514.43,-400.24 519.14,-405.42"/>
+<!-- 27->28 -->
+<g id="edge53" class="edge">
+<title>27->28</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M502.4029,-287.8314C525.5091,-278.159 554.1038,-266.1891 578.4577,-255.9944"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="580.0363,-259.128 587.9092,-252.038 577.3333,-252.6709 580.0363,-259.128"/>
</g>
-<!-- 34->30 -->
-<g id="edge52" class="edge">
-<title>34->30</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M646.75,-575.95C629.25,-567.98 612.22,-556.47 602,-540 593.56,-526.41 594.09,-517.91 602,-504 609.36,-491.04 621.29,-480.92 634.05,-473.16"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="635.96,-476.1 642.97,-468.15 632.53,-469.99 635.96,-476.1"/>
+<!-- 28->0 -->
+<g id="edge3" class="edge">
+<title>28->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M634.2764,-215.9608C639.0734,-183.764 644.3372,-115.6899 613,-72 601.064,-55.359 582.2584,-42.5778 565.4641,-33.6375"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="566.9023,-30.4429 556.3973,-29.0657 563.7506,-36.6933 566.9023,-30.4429"/>
</g>
-<!-- 34->32 -->
-<g id="edge57" class="edge">
-<title>34->32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M759.13,-575.89C778.61,-567.39 800.04,-555.55 816,-540 833.9,-522.55 846.48,-496.81 854.08,-477.5"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="857.39,-478.65 857.61,-468.06 850.83,-476.2 857.39,-478.65"/>
+<!-- 28->22 -->
+<g id="edge42" class="edge">
+<title>28->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M575.5095,-215.9253C547.3434,-206.5444 512.4328,-194.6048 473.445,-180.0761"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="474.5833,-176.765 463.991,-176.5319 472.126,-183.3195 474.5833,-176.765"/>
</g>
-<!-- 35 -->
-<g id="node36" class="node">
-<title>35</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M795,-540C795,-540 623,-540 623,-540 617,-540 611,-534 611,-528 611,-528 611,-516 611,-516 611,-510 617,-504 623,-504 623,-504 795,-504 795,-504 801,-504 807,-510 807,-516 807,-516 807,-528 807,-528 807,-534 801,-540 795,-540"/>
-<text text-anchor="middle" x="709" y="-519.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<!-- 29 -->
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M303.2514,-180C303.2514,-180 258.7486,-180 258.7486,-180 252.7486,-180 246.7486,-174 246.7486,-168 246.7486,-168 246.7486,-156 246.7486,-156 246.7486,-150 252.7486,-144 258.7486,-144 258.7486,-144 303.2514,-144 303.2514,-144 309.2514,-144 315.2514,-150 315.2514,-156 315.2514,-156 315.2514,-168 315.2514,-168 315.2514,-174 309.2514,-180 303.2514,-180"/>
+<text text-anchor="middle" x="281" y="-159" font-family="sans" font-size="10.00" fill="#000000">pca_kallisto</text>
</g>
-<!-- 34->35 -->
-<g id="edge63" class="edge">
-<title>34->35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M709,-575.7C709,-567.98 709,-558.71 709,-550.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="712.5,-550.1 709,-540.1 705.5,-550.1 712.5,-550.1"/>
+<!-- 29->1 -->
+<g id="edge10" class="edge">
+<title>29->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M315.3262,-145.3008C335.3506,-135.5592 360.8778,-123.1405 382.6667,-112.5405"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="384.2877,-115.6442 391.7489,-108.1222 381.2254,-109.3495 384.2877,-115.6442"/>
</g>
-<!-- 35->30 -->
-<g id="edge54" class="edge">
-<title>35->30</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M704.55,-503.7C702.55,-495.9 700.13,-486.51 697.9,-477.83"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="701.28,-476.92 695.4,-468.1 694.5,-478.66 701.28,-476.92"/>
+<!-- 30->0 -->
+<g id="edge4" class="edge">
+<title>30->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M261.6024,-215.8317C244.1784,-197.2294 223.4093,-167.7572 238,-144 292.5845,-55.1232 425.752,-28.786 491.297,-21.0991"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="492.0262,-24.5406 501.5898,-19.9811 491.2703,-17.5815 492.0262,-24.5406"/>
</g>
-<!-- 35->32 -->
-<g id="edge59" class="edge">
-<title>35->32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M746.67,-503.88C770,-493.27 799.9,-479.68 823.54,-468.93"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="825.27,-471.99 832.93,-464.67 822.38,-465.62 825.27,-471.99"/>
+<!-- 30->29 -->
+<g id="edge55" class="edge">
+<title>30->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M281,-215.8314C281,-208.131 281,-198.9743 281,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="284.5001,-190.4132 281,-180.4133 277.5001,-190.4133 284.5001,-190.4132"/>
</g>
-<!-- 36 -->
-<g id="node37" class="node">
-<title>36</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M543,-540C543,-540 407,-540 407,-540 401,-540 395,-534 395,-528 395,-528 395,-516 395,-516 395,-510 401,-504 407,-504 407,-504 543,-504 543,-504 549,-504 555,-510 555,-516 555,-516 555,-528 555,-528 555,-534 549,-540 543,-540"/>
-<text text-anchor="middle" x="475" y="-519.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+<!-- 31->0 -->
+<g id="edge6" class="edge">
+<title>31->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M148.4155,-215.9881C165.321,-181.9355 206.8267,-108.2845 265,-72 302.5067,-48.6059 428.5028,-30.3241 491.9035,-22.3552"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="492.3891,-25.8219 501.884,-21.1211 491.53,-18.8748 492.3891,-25.8219"/>
</g>
-<!-- 36->30 -->
-<g id="edge51" class="edge">
-<title>36->30</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M527.56,-503.97C558.01,-494.1 596.51,-481.62 628.5,-471.25"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="629.77,-474.52 638.2,-468.11 627.61,-467.86 629.77,-474.52"/>
+<!-- 31->29 -->
+<g id="edge56" class="edge">
+<title>31->29</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M175.5803,-215.8314C194.3142,-206.2651 217.4493,-194.4514 237.2693,-184.3306"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="239.0916,-187.33 246.406,-179.665 235.9082,-181.0957 239.0916,-187.33"/>
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-<!-- 37->30 -->
-<g id="edge53" class="edge">
-<title>37->30</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M861,-575.72C853.35,-555.98 838.38,-523.86 816,-504 800.01,-489.82 779.67,-479.03 760.07,-471.02"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="761.11,-467.67 750.52,-467.3 758.57,-474.19 761.11,-467.67"/>
+<!-- 32 -->
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M589.9502,-180C589.9502,-180 494.0498,-180 494.0498,-180 488.0498,-180 482.0498,-174 482.0498,-168 482.0498,-168 482.0498,-156 482.0498,-156 482.0498,-150 488.0498,-144 494.0498,-144 494.0498,-144 589.9502,-144 589.9502,-144 595.9502,-144 601.9502,-150 601.9502,-156 601.9502,-156 601.9502,-168 601.9502,-168 601.9502,-174 595.9502,-180 589.9502,-180"/>
+<text text-anchor="middle" x="542" y="-159" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
</g>
-<!-- 37->32 -->
-<g id="edge58" class="edge">
-<title>37->32</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M875.31,-575.79C879.74,-565.63 884.74,-552.38 887,-540 889.87,-524.26 890.38,-519.64 887,-504 885.04,-494.92 881.39,-485.52 877.51,-477.2"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="880.54,-475.42 872.95,-468.02 874.27,-478.53 880.54,-475.42"/>
+<!-- 32->1 -->
+<g id="edge7" class="edge">
+<title>32->1</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M513.4853,-143.8314C499.1658,-134.7074 481.6376,-123.539 466.2662,-113.7449"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="467.8199,-110.5847 457.5055,-108.1628 464.0583,-116.4882 467.8199,-110.5847"/>
</g>
-<!-- 37->35 -->
-<g id="edge64" class="edge">
-<title>37->35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M828.35,-575.88C806.75,-566.31 779.65,-554.3 756.73,-544.15"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="758.09,-540.92 747.53,-540.07 755.25,-547.32 758.09,-540.92"/>
+<!-- 33->0 -->
+<g id="edge1" class="edge">
+<title>33->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1010.5904,-84.0467C909.5978,-70.1963 660.3176,-36.0093 565.9788,-23.0714"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="566.4213,-19.5994 556.0384,-21.7081 565.4701,-26.5345 566.4213,-19.5994"/>
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-<!-- 38->31 -->
-<g id="edge56" class="edge">
-<title>38->31</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1028.85,-575.78C1016.85,-541.74 989.9,-463.32 972,-396 966.55,-375.52 961.6,-352.06 958.11,-334.37"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="961.48,-333.34 956.14,-324.18 954.6,-334.66 961.48,-333.34"/>
+<!-- 34->33 -->
+<g id="edge62" class="edge">
+<title>34->33</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1054,-143.8314C1054,-136.131 1054,-126.9743 1054,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1057.5001,-118.4132 1054,-108.4133 1050.5001,-118.4133 1057.5001,-118.4132"/>
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diff --git a/tests/test_integration_workflow/expected_output.files b/tests/test_integration_workflow/expected_output.files
index a9026e6..e0b0859 100644
--- a/tests/test_integration_workflow/expected_output.files
+++ b/tests/test_integration_workflow/expected_output.files
@@ -81,26 +81,26 @@ results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10
results/transcriptome/homo_sapiens/transcriptome.fa
results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
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-results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg
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-results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
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-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_plus.bw
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.minus.bg
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.plus.bg
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+69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_minus.bw
+ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_plus.bw
+69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_minus.bw
+ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_plus.bw
d8118d944149eecc691d182448696e7f results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt
a127fabda5c3aad9d95414dc4fbc11c3 results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt
0c6363588cf6ff74d49f27c164185918 results/multiqc_summary/multiqc_data/multiqc_star.txt
diff --git a/tests/test_integration_workflow_with_conda/expected_output.files b/tests/test_integration_workflow_with_conda/expected_output.files
index a9026e6..e0b0859 100644
--- a/tests/test_integration_workflow_with_conda/expected_output.files
+++ b/tests/test_integration_workflow_with_conda/expected_output.files
@@ -81,26 +81,26 @@ results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10
results/transcriptome/homo_sapiens/transcriptome.fa
results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
-results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg
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-results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg
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-results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
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-results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_plus.bw
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.minus.bg
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.MultimappersIncluded.plus.bg
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.minus.bg
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMappers.plus.bg
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+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_minus.bw
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_plus.bw
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_minus.bw
+results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_plus.bw
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+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_plus.bw
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_minus.bw
+results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_plus.bw
results/multiqc_summary/multiqc_data/multiqc_fastqc.txt
results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt
results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt
diff --git a/tests/test_integration_workflow_with_conda/expected_output.md5 b/tests/test_integration_workflow_with_conda/expected_output.md5
index 266f992..67dbbec 100644
--- a/tests/test_integration_workflow_with_conda/expected_output.md5
+++ b/tests/test_integration_workflow_with_conda/expected_output.md5
@@ -63,26 +63,26 @@ d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synt
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
-bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.minus.bg
-ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.UniqueMultiple.plus.bg
-bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.minus.bg
-ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.Unique.plus.bg
-90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.UniqueMultiple.minus.bg
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-53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
-53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
-ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMultiple_minus.bw
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-ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Unique_minus.bw
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-69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMultiple_minus.bw
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-69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Unique_minus.bw
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+53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/MultimappersIncluded/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_MultimappersIncluded_minus.bw
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+ed3428feeb7257b0a69ead76a417e339 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_minus.bw
+2767ca6a648f3e37b7e3b05ce7845460 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/bigWig/UniqueMappers/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_UniqueMappers_plus.bw
+69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_minus.bw
+ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/MultimappersIncluded/synthetic_10_reads_paired_synthetic_10_reads_paired_MultimappersIncluded_plus.bw
+69e2bf688165e9fb7c9c49a8763f5632 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_minus.bw
+ec5aab1b79e7880dfa590e5bc7db5232 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/bigWig/UniqueMappers/synthetic_10_reads_paired_synthetic_10_reads_paired_UniqueMappers_plus.bw
ba090b1b4a2473891de97493d3244956 results/multiqc_summary/multiqc_data/multiqc_fastqc.txt
d8118d944149eecc691d182448696e7f results/multiqc_summary/multiqc_data/multiqc_cutadapt.txt
a127fabda5c3aad9d95414dc4fbc11c3 results/multiqc_summary/multiqc_data/multiqc_cutadapt_1.txt
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 198ae95..a0ec1ac 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -31,6 +31,12 @@ directionality_dict = {
"alfa_plus": "str2",
"alfa_minus": "str1"},
}
+# dict for alfa output"
+alfa_dict = {
+ "MultimappersIncluded":"UniqueMultiple" ,
+ "UniqueMappers":"Unique"
+}
+
# Validat config
validate(config, os.path.join("..", "resources", "config_schema.json"))
logger.info(f'Config file after validation: {config}')
@@ -147,11 +153,11 @@ rule finish:
"samples",
"{sample}",
"bigWig",
- "{unique_type}",
- "{sample}_{unique_type}_{strand}.bw"),
+ "{renamed_unique}",
+ "{sample}_{renamed_unique}_{strand}.bw"),
sample=pd.unique(samples_table.index.values),
strand=["plus", "minus"],
- unique_type=["Unique", "UniqueMultiple"]),
+ renamed_unique=alfa_dict.keys()),
salmon_merge_genes = expand(
os.path.join(
config["output_dir"],
@@ -1344,7 +1350,7 @@ rule rename_star_rpm_for_alfa:
"STAR_coverage",
"{sample}_Signal.{unique}.{plus}.out.bg"),
sample=wildcards.sample,
- unique=wildcards.unique,
+ unique=alfa_dict[wildcards.renamed_unique],
plus=get_directionality(get_sample(
'libtype',
search_id='index',
@@ -1358,7 +1364,7 @@ rule rename_star_rpm_for_alfa:
"STAR_coverage",
"{sample}_Signal.{unique}.{minus}.out.bg"),
sample=wildcards.sample,
- unique=wildcards.unique,
+ unique=alfa_dict[wildcards.renamed_unique],
minus=get_directionality(get_sample(
'libtype',
search_id='index',
@@ -1370,15 +1376,15 @@ rule rename_star_rpm_for_alfa:
"samples",
"{sample}",
"ALFA",
- "{unique}",
- "{sample}.{unique}.plus.bg")),
+ "{renamed_unique}",
+ "{sample}.{renamed_unique}.plus.bg")),
minus = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
- "{unique}",
- "{sample}.{unique}.minus.bg"))
+ "{renamed_unique}",
+ "{sample}.{renamed_unique}.minus.bg"))
params:
cluster_log_path = config["cluster_log_dir"]
@@ -1388,12 +1394,12 @@ rule rename_star_rpm_for_alfa:
config["log_dir"],
"samples",
"{sample}",
- current_rule + "_{unique}.stderr.log"),
+ current_rule + "_{renamed_unique}.stderr.log"),
stdout = os.path.join(
config["log_dir"],
"samples",
"{sample}",
- current_rule + "_{unique}.stdout.log")
+ current_rule + "_{renamed_unique}.stdout.log")
singularity:
"docker://ubuntu:focal-20210416"
@@ -1479,20 +1485,26 @@ rule alfa_qc:
Run ALFA from stranded bedgraph files
'''
input:
- plus = os.path.join(
- config["output_dir"],
- "samples",
- "{sample}",
- "ALFA",
- "{unique}",
- "{sample}.{unique}.plus.bg"),
- minus = os.path.join(
- config["output_dir"],
- "samples",
- "{sample}",
- "ALFA",
- "{unique}",
- "{sample}.{unique}.minus.bg"),
+ plus = lambda wildcards:
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ wildcards.sample,
+ "ALFA",
+ wildcards.renamed_unique,
+ wildcards.sample + "." + wildcards.renamed_unique + ".plus.bg"
+ ),
+
+ minus = lambda wildcards:
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ wildcards.sample,
+ "ALFA",
+ wildcards.renamed_unique,
+ wildcards.sample + "." + wildcards.renamed_unique + ".minus.bg"
+ ),
+
gtf = lambda wildcards:
os.path.join(
config["alfa_indexes"],
@@ -1513,21 +1525,21 @@ rule alfa_qc:
"samples",
"{sample}",
"ALFA",
- "{unique}",
+ "{renamed_unique}",
"ALFA_plots.Biotypes.pdf")),
categories = temp(os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
- "{unique}",
+ "{renamed_unique}",
"ALFA_plots.Categories.pdf")),
table = os.path.join(
config["output_dir"],
"samples",
"{sample}",
"ALFA",
- "{unique}",
+ "{renamed_unique}",
"{sample}.ALFA_feature_counts.tsv")
params:
@@ -1570,7 +1582,7 @@ rule alfa_qc:
config["log_dir"],
"samples",
"{sample}",
- current_rule + ".{unique}.log")
+ current_rule + ".{renamed_unique}.log")
shell:
"(cd {params.out_dir}; \
@@ -1690,10 +1702,10 @@ rule multiqc_report:
"samples",
"{sample}",
"ALFA",
- "{unique}",
+ "{renamed_unique}",
"{sample}.ALFA_feature_counts.tsv"),
sample=pd.unique(samples_table.index.values),
- unique=["Unique", "UniqueMultiple"]),
+ renamed_unique=alfa_dict.keys()),
zpca_salmon = expand(os.path.join(
config["output_dir"],
@@ -1766,8 +1778,8 @@ rule sort_bed_4_big:
"samples",
"{sample}",
"ALFA",
- "{unique}",
- "{sample}.{unique}.{strand}.bg")
+ "{renamed_unique}",
+ "{sample}.{renamed_unique}.{strand}.bg")
output:
sorted_bg = temp(os.path.join(
@@ -1775,8 +1787,8 @@ rule sort_bed_4_big:
"samples",
"{sample}",
"bigWig",
- "{unique}",
- "{sample}_{unique}_{strand}.sorted.bg"))
+ "{renamed_unique}",
+ "{sample}_{renamed_unique}_{strand}.sorted.bg"))
params:
cluster_log_path = config["cluster_log_dir"],
@@ -1799,7 +1811,7 @@ rule sort_bed_4_big:
config["log_dir"],
"samples",
"{sample}",
- current_rule + "_{unique}_{strand}.stderr.log")
+ current_rule + "_{renamed_unique}_{strand}.stderr.log")
shell:
"(sortBed \
@@ -1819,8 +1831,8 @@ rule prepare_bigWig:
"samples",
"{sample}",
"bigWig",
- "{unique}",
- "{sample}_{unique}_{strand}.sorted.bg"),
+ "{renamed_unique}",
+ "{sample}_{renamed_unique}_{strand}.sorted.bg"),
chr_sizes = lambda wildcards:
os.path.join(
config['star_indexes'],
@@ -1841,8 +1853,8 @@ rule prepare_bigWig:
"samples",
"{sample}",
"bigWig",
- "{unique}",
- "{sample}_{unique}_{strand}.bw")
+ "{renamed_unique}",
+ "{sample}_{renamed_unique}_{strand}.bw")
params:
cluster_log_path = config["cluster_log_dir"],
@@ -1863,13 +1875,13 @@ rule prepare_bigWig:
config["log_dir"],
"samples",
"{sample}",
- current_rule + "_{unique}_{strand}.stderr.log"),
+ current_rule + "_{renamed_unique}_{strand}.stderr.log"),
stdout = os.path.join(
config["log_dir"],
"samples",
"{sample}",
- current_rule + "_{unique}_{strand}.stdout.log")
+ current_rule + "_{renamed_unique}_{strand}.stdout.log")
shell:
"(bedGraphToBigWig \
--
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