From 0def7b72ce85115ecc83aa892beed0af57e1e320 Mon Sep 17 00:00:00 2001
From: BIOPZ-Iborra de Toledo Paula <paula.iborradetoledo@unibas.ch>
Date: Fri, 6 Mar 2020 14:30:36 +0100
Subject: [PATCH] Extract transcript sequences from genome (fasta file) and
gene annotations (gtf file). Fixes #62
---
Snakefile | 55 +-
images/dag_test_workflow.svg | 542 ++++++++++--------
images/rule_graph.svg | 434 ++++++++------
.../expected_output.files | 1 +
.../expected_output.md5 | 1 +
5 files changed, 612 insertions(+), 421 deletions(-)
diff --git a/Snakefile b/Snakefile
index 68ac174..f26b9e1 100644
--- a/Snakefile
+++ b/Snakefile
@@ -102,6 +102,7 @@ rule finish:
salmon_merge_on=["tpm", "numreads"])
+
rule create_index_star:
"""
Create index for STAR alignments
@@ -169,17 +170,50 @@ rule create_index_star:
--sjdbGTFfile {input.gtf}) \
1> {log.stdout} 2> {log.stderr}"
+rule extract_transcriptome:
+ """ Create transcriptome from genome and gene annotations """
+ input:
+ genome = lambda wildcards:
+ samples_table['genome'][
+ samples_table['organism'] == wildcards.organism
+ ][0],
+ gtf = lambda wildcards:
+ samples_table['gtf'][
+ samples_table['organism'] == wildcards.organism
+ ][0]
+ output:
+ transcriptome = os.path.join(
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "transcriptome.fa",
+ )
+ log:
+ stderr = os.path.join(
+ config['log_dir'],
+ "{organism}_extract_transcriptome.log"),
+ stdout = os.path.join(
+ config['log_dir'],
+ "{organism}_extract_transcriptome.log")
+ singularity:
+ "docker://zavolab/cufflinks:2.2.1"
+ shell:
+ "(gffread \
+ -w {output.transcriptome} \
+ -g {input.genome} {input.gtf}) \
+ 1> {log.stdout} 2> {log.stderr}"
rule create_index_salmon:
"""
Create index for Salmon quantification
"""
input:
- transcriptome = lambda wildcards:
- samples_table['tr_fasta_filtered']
- [samples_table['organism'] == wildcards.organism]
- [0]
-
+ transcriptome = os.path.join(
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "transcriptome.fa",
+ )
output:
index = directory(
os.path.join(
@@ -218,11 +252,12 @@ rule create_index_kallisto:
Create index for Kallisto quantification
"""
input:
- transcriptome = lambda wildcards:
- samples_table['tr_fasta_filtered']
- [samples_table['organism'] == wildcards.organism]
- [0]
-
+ transcriptome = os.path.join(
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "transcriptome.fa",
+ )
output:
index = os.path.join(
config['kallisto_indexes'],
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 3327b03..2b1194f 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,353 +1,435 @@
<?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">
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+<!-- Generated by graphviz version 2.40.1 (20161225.0304)
-->
<!-- Title: snakemake_dag Pages: 1 -->
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<title>snakemake_dag</title>
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+<title>4</title>
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+<text text-anchor="middle" x="1066" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
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<!-- 4->0 -->
-<g id="edge4" class="edge"><title>4->0</title>
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+<title>4->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1121.5883,-146.2651C1124.7656,-145.4722 1127.9194,-144.711 1131,-144 1173.7241,-134.1398 1296.9662,-141.7146 1325,-108 1362.7844,-62.559 1261.3527,-35.5901 1203.3308,-24.2747"/>
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<!-- 4->9 -->
-<g id="edge26" class="edge"><title>4->9</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1238.97,-115.265 1246.74,-108.068 1236.18,-108.846 1238.97,-115.265"/>
+<g id="edge26" class="edge">
+<title>4->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1111.9263,-143.8314C1136.5923,-134.0734 1167.1691,-121.977 1193.086,-111.7242"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1194.3927,-114.9713 1202.404,-108.038 1191.8176,-108.4621 1194.3927,-114.9713"/>
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<!-- 4->10 -->
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="864.341,-104.659 853.859,-106.202 863.015,-111.533 864.341,-104.659"/>
+<g id="edge28" class="edge">
+<title>4->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1010.3968,-146.3286C1007.2232,-145.5194 1004.0744,-144.7374 1001,-144 925.9861,-126.0079 904.2024,-124.7801 825.7056,-108.3356"/>
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<!-- 4->11 -->
-<g id="edge30" class="edge"><title>4->11</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1002.5,-108.512 991.915,-108.068 999.913,-115.016 1002.5,-108.512"/>
+<g id="edge30" class="edge">
+<title>4->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1026.887,-143.8314C1006.2488,-134.2446 980.7516,-122.4008 958.9327,-112.2655"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="960.3756,-109.0766 949.8318,-108.038 957.4266,-115.4251 960.3756,-109.0766"/>
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<!-- 4->12 -->
-<g id="edge32" class="edge"><title>4->12</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1126.66,-117.945 1122.73,-108.104 1119.66,-118.245 1126.66,-117.945"/>
+<g id="edge32" class="edge">
+<title>4->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1070.5422,-143.8314C1072.4884,-136.0463 1074.8068,-126.7729 1076.9663,-118.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1080.3668,-118.9636 1079.3967,-108.4133 1073.5758,-117.2658 1080.3668,-118.9636"/>
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<!-- 5 -->
-<g id="node6" class="node"><title>5</title>
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-<text text-anchor="middle" x="854" y="-234" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<g id="node6" class="node">
+<title>5</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1294,-180C1294,-180 1152,-180 1152,-180 1146,-180 1140,-174 1140,-168 1140,-168 1140,-156 1140,-156 1140,-150 1146,-144 1152,-144 1152,-144 1294,-144 1294,-144 1300,-144 1306,-150 1306,-156 1306,-156 1306,-168 1306,-168 1306,-174 1300,-180 1294,-180"/>
+<text text-anchor="middle" x="1223" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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<!-- 5->0 -->
-<g id="edge5" class="edge"><title>5->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M810.971,-218.422C745.148,-189.906 632.065,-129.992 682,-72 722.482,-24.9863 915.576,-19.0926 997.796,-18.7562"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="997.952,-22.2561 1007.95,-18.741 997.941,-15.2561 997.952,-22.2561"/>
+<g id="edge5" class="edge">
+<title>5->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1306.0774,-146.1087C1326.3767,-138.1084 1345.7586,-126.081 1358,-108 1366.9701,-94.7509 1367.6615,-84.7536 1358,-72 1339.4067,-47.4559 1253.9804,-30.9519 1203.5562,-23.1627"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1203.7729,-19.6561 1193.3641,-21.6331 1202.7339,-26.5786 1203.7729,-19.6561"/>
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<!-- 6 -->
-<g id="node7" class="node"><title>6</title>
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-<text text-anchor="middle" x="1320" y="-234" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M1462,-180C1462,-180 1336,-180 1336,-180 1330,-180 1324,-174 1324,-168 1324,-168 1324,-156 1324,-156 1324,-150 1330,-144 1336,-144 1336,-144 1462,-144 1462,-144 1468,-144 1474,-150 1474,-156 1474,-156 1474,-168 1474,-168 1474,-174 1468,-180 1462,-180"/>
+<text text-anchor="middle" x="1399" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
</g>
<!-- 6->0 -->
-<g id="edge6" class="edge"><title>6->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.15,-15.365 1062.13,-18.8191 1072.11,-22.3649 1072.15,-15.365"/>
+<g id="edge6" class="edge">
+<title>6->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1399.4933,-143.8404C1399.0194,-123.5511 1395.0299,-91.0582 1376,-72 1351.9364,-47.9006 1256.9834,-30.8919 1203.3694,-22.9895"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1203.6275,-19.4906 1193.231,-21.531 1202.6307,-26.4193 1203.6275,-19.4906"/>
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<!-- 7 -->
-<g id="node8" class="node"><title>7</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1548,-108C1548,-108 1460,-108 1460,-108 1454,-108 1448,-102 1448,-96 1448,-96 1448,-84 1448,-84 1448,-78 1454,-72 1460,-72 1460,-72 1548,-72 1548,-72 1554,-72 1560,-78 1560,-84 1560,-84 1560,-96 1560,-96 1560,-102 1554,-108 1548,-108"/>
-<text text-anchor="middle" x="1504" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
-<text text-anchor="middle" x="1504" y="-82" font-family="sans" font-size="10.00">seqmode: paired_end</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M1631,-108C1631,-108 1543,-108 1543,-108 1537,-108 1531,-102 1531,-96 1531,-96 1531,-84 1531,-84 1531,-78 1537,-72 1543,-72 1543,-72 1631,-72 1631,-72 1637,-72 1643,-78 1643,-84 1643,-84 1643,-96 1643,-96 1643,-102 1637,-108 1631,-108"/>
+<text text-anchor="middle" x="1587" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<text text-anchor="middle" x="1587" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: paired_end</text>
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<!-- 7->0 -->
-<g id="edge7" class="edge"><title>7->0</title>
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+<g id="edge7" class="edge">
+<title>7->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1530.6589,-80.3645C1443.3141,-65.4266 1277.5807,-37.0827 1203.4604,-24.4065"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1203.6565,-20.8893 1193.2096,-22.6534 1202.4764,-27.7891 1203.6565,-20.8893"/>
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<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1733,-108C1733,-108 1645,-108 1645,-108 1639,-108 1633,-102 1633,-96 1633,-96 1633,-84 1633,-84 1633,-78 1639,-72 1645,-72 1645,-72 1733,-72 1733,-72 1739,-72 1745,-78 1745,-84 1745,-84 1745,-96 1745,-96 1745,-102 1739,-108 1733,-108"/>
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-<text text-anchor="middle" x="1689" y="-82" font-family="sans" font-size="10.00">seqmode: single_end</text>
+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M1817,-108C1817,-108 1729,-108 1729,-108 1723,-108 1717,-102 1717,-96 1717,-96 1717,-84 1717,-84 1717,-78 1723,-72 1729,-72 1729,-72 1817,-72 1817,-72 1823,-72 1829,-78 1829,-84 1829,-84 1829,-96 1829,-96 1829,-102 1823,-108 1817,-108"/>
+<text text-anchor="middle" x="1773" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<text text-anchor="middle" x="1773" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: single_end</text>
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<!-- 8->0 -->
-<g id="edge8" class="edge"><title>8->0</title>
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+<g id="edge8" class="edge">
+<title>8->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1716.7318,-81.1874C1696.3622,-78.1141 1673.1665,-74.7493 1652,-72 1485.0195,-50.3108 1285.0455,-29.8148 1203.4405,-21.6829"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1203.4754,-18.1692 1193.1784,-20.6634 1202.7833,-25.1349 1203.4754,-18.1692"/>
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<!-- 9->0 -->
-<g id="edge9" class="edge"><title>9->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.68,-25.8757 1062.11,-26.5606 1070.8,-32.6184 1072.68,-25.8757"/>
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+<title>9->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1227.3079,-71.8314C1217.3052,-63.0485 1205.145,-52.3712 1194.3001,-42.8489"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1196.5092,-40.1308 1186.6854,-36.1628 1191.8906,-45.3909 1196.5092,-40.1308"/>
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<!-- 10->0 -->
-<g id="edge10" class="edge"><title>10->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M842.811,-71.9656C891.409,-58.5722 957.482,-40.3633 998.132,-29.1604"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="999.183,-32.5015 1007.89,-26.4704 997.323,-25.7531 999.183,-32.5015"/>
+<g id="edge10" class="edge">
+<title>10->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M815.8137,-73.5955C818.5749,-73.0445 821.311,-72.5106 824,-72 934.2562,-51.0658 1065.5934,-31.945 1128.6213,-23.1269"/>
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<!-- 11->0 -->
-<g id="edge11" class="edge"><title>11->0</title>
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+<title>11->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M975.0181,-71.9243C1023.708,-58.1766 1088.9805,-39.7467 1129.2269,-28.383"/>
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<!-- 12->0 -->
-<g id="edge12" class="edge"><title>12->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1066.24,-39.6462 1056.26,-36.1043 1061.86,-45.1001 1066.24,-39.6462"/>
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+<title>12->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1104.6921,-71.8314C1114.6948,-63.0485 1126.855,-52.3712 1137.6999,-42.8489"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1140.1094,-45.3909 1145.3146,-36.1628 1135.4908,-40.1308 1140.1094,-45.3909"/>
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<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
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-<text text-anchor="middle" x="1003" y="-311" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M1157,-326.5C1157,-326.5 1045,-326.5 1045,-326.5 1039,-326.5 1033,-320.5 1033,-314.5 1033,-314.5 1033,-302.5 1033,-302.5 1033,-296.5 1039,-290.5 1045,-290.5 1045,-290.5 1157,-290.5 1157,-290.5 1163,-290.5 1169,-296.5 1169,-302.5 1169,-302.5 1169,-314.5 1169,-314.5 1169,-320.5 1163,-326.5 1157,-326.5"/>
+<text text-anchor="middle" x="1101" y="-306" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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<!-- 13->3 -->
-<g id="edge13" class="edge"><title>13->3</title>
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+<title>13->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1061.2604,-290.4899C1041.9483,-280.6704 1019.0698,-267.3804 1001,-252 979.3295,-233.5548 959.5156,-207.8273 946.1836,-188.6015"/>
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+<title>13->5</title>
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+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M1569.5,-252C1569.5,-252 1480.5,-252 1480.5,-252 1474.5,-252 1468.5,-246 1468.5,-240 1468.5,-240 1468.5,-228 1468.5,-228 1468.5,-222 1474.5,-216 1480.5,-216 1480.5,-216 1569.5,-216 1569.5,-216 1575.5,-216 1581.5,-222 1581.5,-228 1581.5,-228 1581.5,-240 1581.5,-240 1581.5,-246 1575.5,-252 1569.5,-252"/>
+<text text-anchor="middle" x="1525" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
</g>
-<!-- 13->22 -->
-<g id="edge38" class="edge"><title>13->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1071.35,-304.548C1151.34,-294.891 1287.69,-277.348 1404,-257 1412.21,-255.564 1420.8,-253.926 1429.29,-252.223"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1430.1,-255.631 1439.19,-250.202 1428.7,-248.773 1430.1,-255.631"/>
+<!-- 13->23 -->
+<g id="edge40" class="edge">
+<title>13->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1169.2893,-291.1449C1174.2568,-290.0326 1179.1991,-288.9712 1184,-288 1278.5777,-268.8678 1389.0545,-252.4437 1458.033,-242.8876"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1458.8912,-246.3025 1468.3201,-241.4708 1457.9361,-239.368 1458.8912,-246.3025"/>
</g>
<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#ced856" stroke-width="2" d="M1153.5,-257C1153.5,-257 1052.5,-257 1052.5,-257 1046.5,-257 1040.5,-251 1040.5,-245 1040.5,-245 1040.5,-228 1040.5,-228 1040.5,-222 1046.5,-216 1052.5,-216 1052.5,-216 1153.5,-216 1153.5,-216 1159.5,-216 1165.5,-222 1165.5,-228 1165.5,-228 1165.5,-245 1165.5,-245 1165.5,-251 1159.5,-257 1153.5,-257"/>
-<text text-anchor="middle" x="1103" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
-<text text-anchor="middle" x="1103" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
-<text text-anchor="middle" x="1103" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1107.5,-252C1107.5,-252 1022.5,-252 1022.5,-252 1016.5,-252 1010.5,-246 1010.5,-240 1010.5,-240 1010.5,-228 1010.5,-228 1010.5,-222 1016.5,-216 1022.5,-216 1022.5,-216 1107.5,-216 1107.5,-216 1113.5,-216 1119.5,-222 1119.5,-228 1119.5,-228 1119.5,-240 1119.5,-240 1119.5,-246 1113.5,-252 1107.5,-252"/>
+<text text-anchor="middle" x="1065" y="-237" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+<text text-anchor="middle" x="1065" y="-226" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
</g>
<!-- 14->3 -->
-<g id="edge14" class="edge"><title>14->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1071.88,-215.88C1057.09,-206.556 1039.32,-195.356 1023.96,-185.669"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.56,-182.539 1015.23,-180.166 1021.82,-188.46 1025.56,-182.539"/>
+<g id="edge14" class="edge">
+<title>14->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1030.6815,-215.8314C1012.9641,-206.4516 991.1655,-194.9112 972.3016,-184.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="973.7831,-181.7485 963.3076,-180.1628 970.5078,-187.935 973.7831,-181.7485"/>
</g>
<!-- 14->4 -->
-<g id="edge16" class="edge"><title>14->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1109.01,-215.689C1111.4,-207.82 1114.19,-198.64 1116.76,-190.168"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1120.19,-190.905 1119.74,-180.319 1113.49,-188.872 1120.19,-190.905"/>
+<g id="edge16" class="edge">
+<title>14->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1065.2523,-215.8314C1065.3593,-208.131 1065.4865,-198.9743 1065.6053,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1069.1049,-190.4609 1065.7443,-180.4133 1062.1056,-190.3637 1069.1049,-190.4609"/>
</g>
<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M1368,-331.5C1368,-331.5 1272,-331.5 1272,-331.5 1266,-331.5 1260,-325.5 1260,-319.5 1260,-319.5 1260,-307.5 1260,-307.5 1260,-301.5 1266,-295.5 1272,-295.5 1272,-295.5 1368,-295.5 1368,-295.5 1374,-295.5 1380,-301.5 1380,-307.5 1380,-307.5 1380,-319.5 1380,-319.5 1380,-325.5 1374,-331.5 1368,-331.5"/>
-<text text-anchor="middle" x="1320" y="-311" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M1449,-326.5C1449,-326.5 1353,-326.5 1353,-326.5 1347,-326.5 1341,-320.5 1341,-314.5 1341,-314.5 1341,-302.5 1341,-302.5 1341,-296.5 1347,-290.5 1353,-290.5 1353,-290.5 1449,-290.5 1449,-290.5 1455,-290.5 1461,-296.5 1461,-302.5 1461,-302.5 1461,-314.5 1461,-314.5 1461,-320.5 1455,-326.5 1449,-326.5"/>
+<text text-anchor="middle" x="1401" y="-306" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
<!-- 15->4 -->
-<g id="edge15" class="edge"><title>15->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1292.2,-295.305C1275.56,-284.728 1254.18,-270.629 1236,-257 1205.95,-234.472 1173.35,-206.391 1151.3,-186.814"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1153.48,-184.061 1143.68,-180.012 1148.81,-189.283 1153.48,-184.061"/>
+<g id="edge15" class="edge">
+<title>15->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1340.9243,-291.6426C1285.695,-276.0737 1211.4147,-254.9235 1205,-252 1165.8152,-234.1413 1124.8978,-206.3691 1097.6905,-186.3986"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1099.4735,-183.3631 1089.3583,-180.2112 1095.3002,-188.9831 1099.4735,-183.3631"/>
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<!-- 15->6 -->
-<g id="edge19" class="edge"><title>15->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1320,-295.481C1320,-286.436 1320,-275.097 1320,-264.851"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1323.5,-264.711 1320,-254.711 1316.5,-264.711 1323.5,-264.711"/>
+<g id="edge19" class="edge">
+<title>15->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1400.7507,-290.2419C1400.4075,-265.1025 1399.7863,-219.5981 1399.3837,-190.1029"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1402.8824,-189.9793 1399.2461,-180.028 1395.883,-190.0749 1402.8824,-189.9793"/>
</g>
-<!-- 23 -->
-<g id="node24" class="node"><title>23</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M1655.5,-254.5C1655.5,-254.5 1582.5,-254.5 1582.5,-254.5 1576.5,-254.5 1570.5,-248.5 1570.5,-242.5 1570.5,-242.5 1570.5,-230.5 1570.5,-230.5 1570.5,-224.5 1576.5,-218.5 1582.5,-218.5 1582.5,-218.5 1655.5,-218.5 1655.5,-218.5 1661.5,-218.5 1667.5,-224.5 1667.5,-230.5 1667.5,-230.5 1667.5,-242.5 1667.5,-242.5 1667.5,-248.5 1661.5,-254.5 1655.5,-254.5"/>
-<text text-anchor="middle" x="1619" y="-234" font-family="sans" font-size="10.00">map_genome_star</text>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M1684.5,-252C1684.5,-252 1611.5,-252 1611.5,-252 1605.5,-252 1599.5,-246 1599.5,-240 1599.5,-240 1599.5,-228 1599.5,-228 1599.5,-222 1605.5,-216 1611.5,-216 1611.5,-216 1684.5,-216 1684.5,-216 1690.5,-216 1696.5,-222 1696.5,-228 1696.5,-228 1696.5,-240 1696.5,-240 1696.5,-246 1690.5,-252 1684.5,-252"/>
+<text text-anchor="middle" x="1648" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
</g>
-<!-- 15->23 -->
-<g id="edge40" class="edge"><title>15->23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1380.11,-300.533C1427.04,-290.777 1494.01,-275.949 1560.49,-257.315"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1561.62,-260.631 1570.29,-254.538 1559.71,-253.896 1561.62,-260.631"/>
+<!-- 15->24 -->
+<g id="edge42" class="edge">
+<title>15->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1461.4049,-290.8195C1496.4471,-280.4971 1541.6598,-267.068 1589.5811,-252.4162"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.6628,-255.7455 1599.1992,-249.4702 1588.6126,-249.0524 1590.6628,-255.7455"/>
</g>
<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M904.5,-331.5C904.5,-331.5 803.5,-331.5 803.5,-331.5 797.5,-331.5 791.5,-325.5 791.5,-319.5 791.5,-319.5 791.5,-307.5 791.5,-307.5 791.5,-301.5 797.5,-295.5 803.5,-295.5 803.5,-295.5 904.5,-295.5 904.5,-295.5 910.5,-295.5 916.5,-301.5 916.5,-307.5 916.5,-307.5 916.5,-319.5 916.5,-319.5 916.5,-325.5 910.5,-331.5 904.5,-331.5"/>
-<text text-anchor="middle" x="854" y="-316.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
-<text text-anchor="middle" x="854" y="-305.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M1310,-252C1310,-252 1226,-252 1226,-252 1220,-252 1214,-246 1214,-240 1214,-240 1214,-228 1214,-228 1214,-222 1220,-216 1226,-216 1226,-216 1310,-216 1310,-216 1316,-216 1322,-222 1322,-228 1322,-228 1322,-240 1322,-240 1322,-246 1316,-252 1310,-252"/>
+<text text-anchor="middle" x="1268" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
</g>
<!-- 16->5 -->
-<g id="edge18" class="edge"><title>16->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M854,-295.481C854,-286.436 854,-275.097 854,-264.851"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="857.5,-264.711 854,-254.711 850.5,-264.711 857.5,-264.711"/>
+<g id="edge18" class="edge">
+<title>16->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1256.6446,-215.8314C1251.5674,-207.7079 1245.4773,-197.9637 1239.8824,-189.0118"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1242.7763,-187.0383 1234.5083,-180.4133 1236.8403,-190.7483 1242.7763,-187.0383"/>
</g>
<!-- 16->6 -->
-<g id="edge20" class="edge"><title>16->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M914.759,-295.473C918.551,-294.588 922.321,-293.754 926,-293 955.541,-286.944 1128.09,-263.327 1234.82,-248.924"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1235.49,-252.365 1244.93,-247.56 1234.56,-245.428 1235.49,-252.365"/>
+<g id="edge20" class="edge">
+<title>16->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1301.0568,-215.8314C1317.9677,-206.5368 1338.7385,-195.1208 1356.7941,-185.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1358.876,-188.0468 1365.9537,-180.1628 1355.5043,-181.9122 1358.876,-188.0468"/>
</g>
<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M1586,-180C1586,-180 1420,-180 1420,-180 1414,-180 1408,-174 1408,-168 1408,-168 1408,-156 1408,-156 1408,-150 1414,-144 1420,-144 1420,-144 1586,-144 1586,-144 1592,-144 1598,-150 1598,-156 1598,-156 1598,-168 1598,-168 1598,-174 1592,-180 1586,-180"/>
-<text text-anchor="middle" x="1503" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1670,-180C1670,-180 1504,-180 1504,-180 1498,-180 1492,-174 1492,-168 1492,-168 1492,-156 1492,-156 1492,-150 1498,-144 1504,-144 1504,-144 1670,-144 1670,-144 1676,-144 1682,-150 1682,-156 1682,-156 1682,-168 1682,-168 1682,-174 1676,-180 1670,-180"/>
+<text text-anchor="middle" x="1587" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 17->7 -->
-<g id="edge21" class="edge"><title>17->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1503.25,-143.697C1503.36,-135.983 1503.49,-126.712 1503.61,-118.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1507.11,-118.153 1503.76,-108.104 1500.11,-118.053 1507.11,-118.153"/>
+<g id="edge21" class="edge">
+<title>17->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1587,-143.8314C1587,-136.131 1587,-126.9743 1587,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.5001,-118.4132 1587,-108.4133 1583.5001,-118.4133 1590.5001,-118.4132"/>
</g>
<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1749.5,-180C1749.5,-180 1628.5,-180 1628.5,-180 1622.5,-180 1616.5,-174 1616.5,-168 1616.5,-168 1616.5,-156 1616.5,-156 1616.5,-150 1622.5,-144 1628.5,-144 1628.5,-144 1749.5,-144 1749.5,-144 1755.5,-144 1761.5,-150 1761.5,-156 1761.5,-156 1761.5,-168 1761.5,-168 1761.5,-174 1755.5,-180 1749.5,-180"/>
-<text text-anchor="middle" x="1689" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1833.5,-180C1833.5,-180 1712.5,-180 1712.5,-180 1706.5,-180 1700.5,-174 1700.5,-168 1700.5,-168 1700.5,-156 1700.5,-156 1700.5,-150 1706.5,-144 1712.5,-144 1712.5,-144 1833.5,-144 1833.5,-144 1839.5,-144 1845.5,-150 1845.5,-156 1845.5,-156 1845.5,-168 1845.5,-168 1845.5,-174 1839.5,-180 1833.5,-180"/>
+<text text-anchor="middle" x="1773" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
</g>
<!-- 18->7 -->
-<g id="edge22" class="edge"><title>18->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1643.74,-143.876C1618,-134.137 1585.59,-121.872 1558.46,-111.608"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1559.7,-108.334 1549.11,-108.068 1557.22,-114.881 1559.7,-108.334"/>
+<g id="edge22" class="edge">
+<title>18->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1726.0643,-143.8314C1700.8563,-134.0734 1669.6074,-121.977 1643.1209,-111.7242"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1644.1873,-108.384 1633.5981,-108.038 1641.6603,-114.912 1644.1873,-108.384"/>
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<!-- 18->8 -->
-<g id="edge24" class="edge"><title>18->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1689,-143.697C1689,-135.983 1689,-126.712 1689,-118.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1692.5,-118.104 1689,-108.104 1685.5,-118.104 1692.5,-118.104"/>
+<g id="edge24" class="edge">
+<title>18->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1773,-143.8314C1773,-136.131 1773,-126.9743 1773,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1776.5001,-118.4132 1773,-108.4133 1769.5001,-118.4133 1776.5001,-118.4132"/>
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<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M1942,-180C1942,-180 1792,-180 1792,-180 1786,-180 1780,-174 1780,-168 1780,-168 1780,-156 1780,-156 1780,-150 1786,-144 1792,-144 1792,-144 1942,-144 1942,-144 1948,-144 1954,-150 1954,-156 1954,-156 1954,-168 1954,-168 1954,-174 1948,-180 1942,-180"/>
-<text text-anchor="middle" x="1867" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M2026,-180C2026,-180 1876,-180 1876,-180 1870,-180 1864,-174 1864,-168 1864,-168 1864,-156 1864,-156 1864,-150 1870,-144 1876,-144 1876,-144 2026,-144 2026,-144 2032,-144 2038,-150 2038,-156 2038,-156 2038,-168 2038,-168 2038,-174 2032,-180 2026,-180"/>
+<text text-anchor="middle" x="1951" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
</g>
<!-- 19->8 -->
-<g id="edge23" class="edge"><title>19->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1823.46,-143.876C1798.8,-134.179 1767.78,-121.98 1741.75,-111.743"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1742.99,-108.471 1732.4,-108.068 1740.43,-114.985 1742.99,-108.471"/>
+<g id="edge23" class="edge">
+<title>19->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1906.0831,-143.8314C1882.065,-134.1162 1852.3166,-122.0831 1827.0408,-111.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1828.1767,-108.5432 1817.5939,-108.038 1825.5518,-115.0325 1828.1767,-108.5432"/>
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<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M1137,-406C1137,-406 869,-406 869,-406 863,-406 857,-400 857,-394 857,-394 857,-382 857,-382 857,-376 863,-370 869,-370 869,-370 1137,-370 1137,-370 1143,-370 1149,-376 1149,-382 1149,-382 1149,-394 1149,-394 1149,-400 1143,-406 1137,-406"/>
-<text text-anchor="middle" x="1003" y="-391" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1003" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M1222,-401C1222,-401 954,-401 954,-401 948,-401 942,-395 942,-389 942,-389 942,-377 942,-377 942,-371 948,-365 954,-365 954,-365 1222,-365 1222,-365 1228,-365 1234,-371 1234,-377 1234,-377 1234,-389 1234,-389 1234,-395 1228,-401 1222,-401"/>
+<text text-anchor="middle" x="1088" y="-386" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1088" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 20->13 -->
-<g id="edge33" class="edge"><title>20->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1003,-369.819C1003,-361.422 1003,-351.116 1003,-341.686"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1006.5,-341.558 1003,-331.558 999.5,-341.558 1006.5,-341.558"/>
+<g id="edge33" class="edge">
+<title>20->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1091.1469,-364.9656C1092.6369,-356.427 1094.4506,-346.0333 1096.1138,-336.502"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1099.5658,-337.0793 1097.837,-326.6265 1092.67,-335.876 1099.5658,-337.0793"/>
</g>
<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1460,-406C1460,-406 1180,-406 1180,-406 1174,-406 1168,-400 1168,-394 1168,-394 1168,-382 1168,-382 1168,-376 1174,-370 1180,-370 1180,-370 1460,-370 1460,-370 1466,-370 1472,-376 1472,-382 1472,-382 1472,-394 1472,-394 1472,-400 1466,-406 1460,-406"/>
-<text text-anchor="middle" x="1320" y="-391" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1320" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
-</g>
-<!-- 21->15 -->
-<g id="edge34" class="edge"><title>21->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1320,-369.819C1320,-361.422 1320,-351.116 1320,-341.686"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1323.5,-341.558 1320,-331.558 1316.5,-341.558 1323.5,-341.558"/>
-</g>
-<!-- 22->17 -->
-<g id="edge35" class="edge"><title>22->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1497.66,-218.319C1498.47,-209.922 1499.46,-199.616 1500.38,-190.186"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.88,-190.348 1501.35,-180.058 1496.91,-189.675 1503.88,-190.348"/>
-</g>
-<!-- 23->19 -->
-<g id="edge36" class="edge"><title>23->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1667.7,-221.263C1705.18,-210.306 1757.43,-195.031 1799.03,-182.87"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1800.2,-186.174 1808.82,-180.009 1798.24,-179.456 1800.2,-186.174"/>
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1306.5,-326.5C1306.5,-326.5 1205.5,-326.5 1205.5,-326.5 1199.5,-326.5 1193.5,-320.5 1193.5,-314.5 1193.5,-314.5 1193.5,-302.5 1193.5,-302.5 1193.5,-296.5 1199.5,-290.5 1205.5,-290.5 1205.5,-290.5 1306.5,-290.5 1306.5,-290.5 1312.5,-290.5 1318.5,-296.5 1318.5,-302.5 1318.5,-302.5 1318.5,-314.5 1318.5,-314.5 1318.5,-320.5 1312.5,-326.5 1306.5,-326.5"/>
+<text text-anchor="middle" x="1256" y="-311.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<text text-anchor="middle" x="1256" y="-300.5" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+</g>
+<!-- 21->14 -->
+<g id="edge34" class="edge">
+<title>21->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1209.7642,-290.4656C1182.9826,-280.0194 1149.0828,-266.7967 1120.8216,-255.7734"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1122.0603,-252.4997 1111.472,-252.1265 1119.5165,-259.0212 1122.0603,-252.4997"/>
+</g>
+<!-- 21->16 -->
+<g id="edge36" class="edge">
+<title>21->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1258.9049,-290.4656C1260.2802,-281.927 1261.9544,-271.5333 1263.4896,-262.002"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1266.9454,-262.5559 1265.0803,-252.1265 1260.0345,-261.4426 1266.9454,-262.5559"/>
</g>
-<!-- 24 -->
-<g id="node25" class="node"><title>24</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M1607.5,-334C1607.5,-334 1506.5,-334 1506.5,-334 1500.5,-334 1494.5,-328 1494.5,-322 1494.5,-322 1494.5,-305 1494.5,-305 1494.5,-299 1500.5,-293 1506.5,-293 1506.5,-293 1607.5,-293 1607.5,-293 1613.5,-293 1619.5,-299 1619.5,-305 1619.5,-305 1619.5,-322 1619.5,-322 1619.5,-328 1613.5,-334 1607.5,-334"/>
-<text text-anchor="middle" x="1557" y="-322" font-family="sans" font-size="10.00">create_index_star</text>
-<text text-anchor="middle" x="1557" y="-311" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="1557" y="-300" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
-</g>
-<!-- 24->22 -->
-<g id="edge37" class="edge"><title>24->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1540.97,-292.795C1533.47,-283.572 1524.45,-272.48 1516.46,-262.659"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1519.08,-260.327 1510.05,-254.777 1513.65,-264.744 1519.08,-260.327"/>
-</g>
-<!-- 24->23 -->
-<g id="edge39" class="edge"><title>24->23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1573.29,-292.795C1580.91,-283.572 1590.08,-272.48 1598.2,-262.659"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1601.04,-264.715 1604.72,-254.777 1595.65,-260.255 1601.04,-264.715"/>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1544,-401C1544,-401 1264,-401 1264,-401 1258,-401 1252,-395 1252,-389 1252,-389 1252,-377 1252,-377 1252,-371 1258,-365 1264,-365 1264,-365 1544,-365 1544,-365 1550,-365 1556,-371 1556,-377 1556,-377 1556,-389 1556,-389 1556,-395 1550,-401 1544,-401"/>
+<text text-anchor="middle" x="1404" y="-386" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1404" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+</g>
+<!-- 22->15 -->
+<g id="edge35" class="edge">
+<title>22->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1403.2738,-364.9656C1402.9336,-356.5178 1402.5203,-346.2542 1402.1399,-336.8064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1405.6295,-336.4776 1401.7299,-326.6265 1398.6352,-336.7593 1405.6295,-336.4776"/>
+</g>
+<!-- 23->17 -->
+<g id="edge37" class="edge">
+<title>23->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1540.6452,-215.8314C1547.8591,-207.454 1556.557,-197.3531 1564.4605,-188.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1567.2711,-190.2748 1571.1441,-180.4133 1561.9667,-185.7071 1567.2711,-190.2748"/>
+</g>
+<!-- 24->19 -->
+<g id="edge38" class="edge">
+<title>24->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1696.6822,-222.432C1742.0379,-211.6543 1810.6724,-195.3452 1865.2132,-182.385"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1866.3044,-185.7232 1875.2243,-180.0061 1864.6861,-178.9129 1866.3044,-185.7232"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M1615.5,-329C1615.5,-329 1514.5,-329 1514.5,-329 1508.5,-329 1502.5,-323 1502.5,-317 1502.5,-317 1502.5,-300 1502.5,-300 1502.5,-294 1508.5,-288 1514.5,-288 1514.5,-288 1615.5,-288 1615.5,-288 1621.5,-288 1627.5,-294 1627.5,-300 1627.5,-300 1627.5,-317 1627.5,-317 1627.5,-323 1621.5,-329 1615.5,-329"/>
+<text text-anchor="middle" x="1565" y="-317" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<text text-anchor="middle" x="1565" y="-306" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
+<text text-anchor="middle" x="1565" y="-295" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+</g>
+<!-- 25->23 -->
+<g id="edge39" class="edge">
+<title>25->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1553.8578,-287.7476C1549.397,-279.4394 1544.1995,-269.7591 1539.4543,-260.9211"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1542.5369,-259.2634 1534.7228,-252.1087 1536.3696,-262.5747 1542.5369,-259.2634"/>
+</g>
+<!-- 25->24 -->
+<g id="edge41" class="edge">
+<title>25->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1588.1201,-287.7476C1598.0583,-278.8272 1609.7587,-268.3251 1620.1677,-258.982"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1622.7213,-261.3931 1627.8252,-252.1087 1618.0455,-256.1838 1622.7213,-261.3931"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 0bf578e..05617e7 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,283 +1,355 @@
<?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 2.38.0 (20140413.2041)
+<!-- Generated by graphviz version 2.40.1 (20161225.0304)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1107pt" height="404pt"
- viewBox="0.00 0.00 1106.50 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1180pt" height="404pt"
+ viewBox="0.00 0.00 1180.00 404.00" 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(4 400)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-400 1102.5,-400 1102.5,4 -4,4"/>
+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-400 1176,-400 1176,4 -4,4"/>
<!-- 0 -->
-<g id="node1" class="node"><title>0</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M250.5,-36C250.5,-36 220.5,-36 220.5,-36 214.5,-36 208.5,-30 208.5,-24 208.5,-24 208.5,-12 208.5,-12 208.5,-6 214.5,-0 220.5,-0 220.5,-0 250.5,-0 250.5,-0 256.5,-0 262.5,-6 262.5,-12 262.5,-12 262.5,-24 262.5,-24 262.5,-30 256.5,-36 250.5,-36"/>
-<text text-anchor="middle" x="235.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
+<title>0</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M312,-36C312,-36 282,-36 282,-36 276,-36 270,-30 270,-24 270,-24 270,-12 270,-12 270,-6 276,0 282,0 282,0 312,0 312,0 318,0 324,-6 324,-12 324,-12 324,-24 324,-24 324,-30 318,-36 312,-36"/>
+<text text-anchor="middle" x="297" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
</g>
<!-- 1 -->
-<g id="node2" class="node"><title>1</title>
-<path fill="none" stroke="#56d882" stroke-width="2" d="M47,-108C47,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 47,-72 47,-72 53,-72 59,-78 59,-84 59,-84 59,-96 59,-96 59,-102 53,-108 47,-108"/>
-<text text-anchor="middle" x="29.5" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
+<g id="node2" class="node">
+<title>1</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M108.5,-108C108.5,-108 73.5,-108 73.5,-108 67.5,-108 61.5,-102 61.5,-96 61.5,-96 61.5,-84 61.5,-84 61.5,-78 67.5,-72 73.5,-72 73.5,-72 108.5,-72 108.5,-72 114.5,-72 120.5,-78 120.5,-84 120.5,-84 120.5,-96 120.5,-96 120.5,-102 114.5,-108 108.5,-108"/>
+<text text-anchor="middle" x="91" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
</g>
<!-- 1->0 -->
-<g id="edge9" class="edge"><title>1->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M59.1802,-75.6843C62.3088,-74.3943 65.4575,-73.1424 68.5,-72 112.501,-55.4786 164.225,-39.5929 198.319,-29.5943"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="199.684,-32.8425 208.306,-26.6862 197.727,-26.1217 199.684,-32.8425"/>
+<g id="edge1" class="edge">
+<title>1->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M120.6523,-75.8697C123.7863,-74.51 126.9439,-73.1944 130,-72 173.8524,-54.8612 225.6071,-38.7391 259.7492,-28.6502"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="261.1396,-31.8899 269.7514,-25.7183 259.1706,-25.1726 261.1396,-31.8899"/>
</g>
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-<g id="node3" class="node"><title>2</title>
-<path fill="none" stroke="#ced856" stroke-width="2" d="M119.5,-108C119.5,-108 89.5,-108 89.5,-108 83.5,-108 77.5,-102 77.5,-96 77.5,-96 77.5,-84 77.5,-84 77.5,-78 83.5,-72 89.5,-72 89.5,-72 119.5,-72 119.5,-72 125.5,-72 131.5,-78 131.5,-84 131.5,-84 131.5,-96 131.5,-96 131.5,-102 125.5,-108 119.5,-108"/>
-<text text-anchor="middle" x="104.5" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
+<g id="node3" class="node">
+<title>2</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M181,-108C181,-108 151,-108 151,-108 145,-108 139,-102 139,-96 139,-96 139,-84 139,-84 139,-78 145,-72 151,-72 151,-72 181,-72 181,-72 187,-72 193,-78 193,-84 193,-84 193,-96 193,-96 193,-102 187,-108 181,-108"/>
+<text text-anchor="middle" x="166" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
</g>
<!-- 2->0 -->
-<g id="edge1" class="edge"><title>2->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M131.643,-74.496C151.316,-63.9839 178.116,-49.6634 199.564,-38.2027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="201.221,-41.2853 208.391,-33.4855 197.922,-35.1115 201.221,-41.2853"/>
+<g id="edge8" class="edge">
+<title>2->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M193.1433,-75.0816C212.8158,-64.2692 239.6157,-49.5395 261.0636,-37.7513"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="262.8137,-40.7833 269.8915,-32.8993 259.4421,-34.6488 262.8137,-40.7833"/>
</g>
<!-- 3 -->
-<g id="node4" class="node"><title>3</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M393,-180C393,-180 290,-180 290,-180 284,-180 278,-174 278,-168 278,-168 278,-156 278,-156 278,-150 284,-144 290,-144 290,-144 393,-144 393,-144 399,-144 405,-150 405,-156 405,-156 405,-168 405,-168 405,-174 399,-180 393,-180"/>
-<text text-anchor="middle" x="341.5" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<g id="node4" class="node">
+<title>3</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M467.5,-180C467.5,-180 364.5,-180 364.5,-180 358.5,-180 352.5,-174 352.5,-168 352.5,-168 352.5,-156 352.5,-156 352.5,-150 358.5,-144 364.5,-144 364.5,-144 467.5,-144 467.5,-144 473.5,-144 479.5,-150 479.5,-156 479.5,-156 479.5,-168 479.5,-168 479.5,-174 473.5,-180 467.5,-180"/>
+<text text-anchor="middle" x="416" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
</g>
<!-- 3->0 -->
-<g id="edge3" class="edge"><title>3->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M298.969,-143.961C282.762,-135.446 265.551,-123.579 254.5,-108 241.756,-90.0343 237.257,-65.2413 235.803,-46.3852"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="239.295,-46.1334 235.267,-36.334 232.305,-46.5062 239.295,-46.1334"/>
+<g id="edge3" class="edge">
+<title>3->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M363.0147,-143.8877C345.6552,-135.5008 327.8125,-123.8039 316,-108 302.7514,-90.2747 298.2787,-65.3679 296.9629,-46.2482"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="300.4498,-45.8685 296.5157,-36.0312 293.4565,-46.1747 300.4498,-45.8685"/>
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<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M561.5,-108C561.5,-108 449.5,-108 449.5,-108 443.5,-108 437.5,-102 437.5,-96 437.5,-96 437.5,-84 437.5,-84 437.5,-78 443.5,-72 449.5,-72 449.5,-72 561.5,-72 561.5,-72 567.5,-72 573.5,-78 573.5,-84 573.5,-84 573.5,-96 573.5,-96 573.5,-102 567.5,-108 561.5,-108"/>
-<text text-anchor="middle" x="505.5" y="-87.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M449,-108C449,-108 337,-108 337,-108 331,-108 325,-102 325,-96 325,-96 325,-84 325,-84 325,-78 331,-72 337,-72 337,-72 449,-72 449,-72 455,-72 461,-78 461,-84 461,-84 461,-96 461,-96 461,-102 455,-108 449,-108"/>
+<text text-anchor="middle" x="393" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
</g>
<!-- 3->8 -->
-<g id="edge22" class="edge"><title>3->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M381.619,-143.876C404.138,-134.264 432.418,-122.193 456.271,-112.013"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="457.688,-115.213 465.511,-108.068 454.94,-108.775 457.688,-115.213"/>
+<g id="edge21" class="edge">
+<title>3->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M410.1961,-143.8314C407.7092,-136.0463 404.7469,-126.7729 401.9875,-118.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="405.2591,-116.874 398.882,-108.4133 398.591,-119.0041 405.2591,-116.874"/>
</g>
<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M407,-108C407,-108 276,-108 276,-108 270,-108 264,-102 264,-96 264,-96 264,-84 264,-84 264,-78 270,-72 276,-72 276,-72 407,-72 407,-72 413,-72 419,-78 419,-84 419,-84 419,-96 419,-96 419,-102 413,-108 407,-108"/>
-<text text-anchor="middle" x="341.5" y="-87.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M622.5,-108C622.5,-108 491.5,-108 491.5,-108 485.5,-108 479.5,-102 479.5,-96 479.5,-96 479.5,-84 479.5,-84 479.5,-78 485.5,-72 491.5,-72 491.5,-72 622.5,-72 622.5,-72 628.5,-72 634.5,-78 634.5,-84 634.5,-84 634.5,-96 634.5,-96 634.5,-102 628.5,-108 622.5,-108"/>
+<text text-anchor="middle" x="557" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
</g>
<!-- 3->9 -->
-<g id="edge24" class="edge"><title>3->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M341.5,-143.697C341.5,-135.983 341.5,-126.712 341.5,-118.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="345,-118.104 341.5,-108.104 338,-118.104 345,-118.104"/>
+<g id="edge23" class="edge">
+<title>3->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M451.5803,-143.8314C470.0325,-134.4089 492.7545,-122.8062 512.373,-112.7883"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="514.1168,-115.8278 521.4311,-108.1628 510.9333,-109.5935 514.1168,-115.8278"/>
</g>
<!-- 4 -->
-<g id="node5" class="node"><title>4</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M522,-180C522,-180 435,-180 435,-180 429,-180 423,-174 423,-168 423,-168 423,-156 423,-156 423,-150 429,-144 435,-144 435,-144 522,-144 522,-144 528,-144 534,-150 534,-156 534,-156 534,-168 534,-168 534,-174 528,-180 522,-180"/>
-<text text-anchor="middle" x="478.5" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<g id="node5" class="node">
+<title>4</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M596.5,-180C596.5,-180 509.5,-180 509.5,-180 503.5,-180 497.5,-174 497.5,-168 497.5,-168 497.5,-156 497.5,-156 497.5,-150 503.5,-144 509.5,-144 509.5,-144 596.5,-144 596.5,-144 602.5,-144 608.5,-150 608.5,-156 608.5,-156 608.5,-168 608.5,-168 608.5,-174 602.5,-180 596.5,-180"/>
+<text text-anchor="middle" x="553" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
</g>
<!-- 4->0 -->
-<g id="edge8" class="edge"><title>4->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M534.128,-145.789C552.813,-137.736 571.648,-125.711 582.5,-108 590.859,-94.3575 592.925,-84.1378 582.5,-72 542.885,-25.8749 354.205,-19.4546 272.908,-18.8661"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="272.647,-15.365 262.631,-18.8191 272.615,-22.3649 272.647,-15.365"/>
+<g id="edge9" class="edge">
+<title>4->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M602.5287,-143.9463C618.3254,-135.5649 634.0222,-123.8565 643,-108 650.8832,-94.0768 653.4049,-84.1547 643,-72 623.0507,-48.6958 419.4899,-28.5724 334.2384,-21.0998"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="334.4751,-17.6073 324.2105,-20.2315 333.8712,-24.5812 334.4751,-17.6073"/>
</g>
<!-- 4->8 -->
-<g id="edge21" class="edge"><title>4->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M485.174,-143.697C488.215,-135.813 491.883,-126.304 495.261,-117.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="498.569,-118.694 498.903,-108.104 492.038,-116.175 498.569,-118.694"/>
+<g id="edge22" class="edge">
+<title>4->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M512.6252,-143.8314C491.3213,-134.2446 465.0017,-122.4008 442.4789,-112.2655"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="443.6399,-108.95 433.0844,-108.038 440.7674,-115.3334 443.6399,-108.95"/>
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<!-- 4->9 -->
-<g id="edge23" class="edge"><title>4->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M444.986,-143.876C426.659,-134.512 403.764,-122.814 384.172,-112.803"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="385.64,-109.623 375.143,-108.19 382.455,-115.857 385.64,-109.623"/>
+<g id="edge24" class="edge">
+<title>4->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M554.0094,-143.8314C554.4372,-136.131 554.9459,-126.9743 555.4213,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="558.9169,-118.592 555.977,-108.4133 551.9276,-118.2037 558.9169,-118.592"/>
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<!-- 5 -->
-<g id="node6" class="node"><title>5</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M160.5,-252C160.5,-252 18.5,-252 18.5,-252 12.5,-252 6.5,-246 6.5,-240 6.5,-240 6.5,-228 6.5,-228 6.5,-222 12.5,-216 18.5,-216 18.5,-216 160.5,-216 160.5,-216 166.5,-216 172.5,-222 172.5,-228 172.5,-228 172.5,-240 172.5,-240 172.5,-246 166.5,-252 160.5,-252"/>
-<text text-anchor="middle" x="89.5" y="-231.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<g id="node6" class="node">
+<title>5</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M154,-180C154,-180 12,-180 12,-180 6,-180 0,-174 0,-168 0,-168 0,-156 0,-156 0,-150 6,-144 12,-144 12,-144 154,-144 154,-144 160,-144 166,-150 166,-156 166,-156 166,-168 166,-168 166,-174 160,-180 154,-180"/>
+<text text-anchor="middle" x="83" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
</g>
<!-- 5->0 -->
-<g id="edge5" class="edge"><title>5->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M101.201,-215.849C126.776,-178.362 187.778,-88.9491 217.965,-44.7025"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="220.999,-46.4656 223.743,-36.2325 215.216,-42.5206 220.999,-46.4656"/>
+<g id="edge4" class="edge">
+<title>5->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M132.4149,-143.9133C154.5952,-134.7238 180.5404,-122.4364 202,-108 229.3371,-89.6096 256.1879,-63.1737 274.3309,-43.709"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="277.1307,-45.8345 281.3126,-36.0999 271.9729,-41.102 277.1307,-45.8345"/>
</g>
<!-- 6 -->
-<g id="node7" class="node"><title>6</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M328.5,-252C328.5,-252 202.5,-252 202.5,-252 196.5,-252 190.5,-246 190.5,-240 190.5,-240 190.5,-228 190.5,-228 190.5,-222 196.5,-216 202.5,-216 202.5,-216 328.5,-216 328.5,-216 334.5,-216 340.5,-222 340.5,-228 340.5,-228 340.5,-240 340.5,-240 340.5,-246 334.5,-252 328.5,-252"/>
-<text text-anchor="middle" x="265.5" y="-231.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M322,-180C322,-180 196,-180 196,-180 190,-180 184,-174 184,-168 184,-168 184,-156 184,-156 184,-150 190,-144 196,-144 196,-144 322,-144 322,-144 328,-144 334,-150 334,-156 334,-156 334,-168 334,-168 334,-174 328,-180 322,-180"/>
+<text text-anchor="middle" x="259" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
</g>
<!-- 6->0 -->
-<g id="edge6" class="edge"><title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M260.264,-215.82C253.267,-191.918 241.205,-147.15 236.5,-108 234.027,-87.4178 233.871,-63.966 234.283,-46.3046"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="237.787,-46.237 234.597,-36.1336 230.79,-46.0207 237.787,-46.237"/>
+<g id="edge7" class="edge">
+<title>6->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M263.8127,-143.7623C270.3227,-119.0928 281.9953,-74.8598 289.6182,-45.9731"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="293.0589,-46.6517 292.2264,-36.0896 286.2906,-44.8656 293.0589,-46.6517"/>
</g>
<!-- 7 -->
-<g id="node8" class="node"><title>7</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M803.5,-108C803.5,-108 715.5,-108 715.5,-108 709.5,-108 703.5,-102 703.5,-96 703.5,-96 703.5,-84 703.5,-84 703.5,-78 709.5,-72 715.5,-72 715.5,-72 803.5,-72 803.5,-72 809.5,-72 815.5,-78 815.5,-84 815.5,-84 815.5,-96 815.5,-96 815.5,-102 809.5,-108 803.5,-108"/>
-<text text-anchor="middle" x="759.5" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M860,-108C860,-108 772,-108 772,-108 766,-108 760,-102 760,-96 760,-96 760,-84 760,-84 760,-78 766,-72 772,-72 772,-72 860,-72 860,-72 866,-72 872,-78 872,-84 872,-84 872,-96 872,-96 872,-102 866,-108 860,-108"/>
+<text text-anchor="middle" x="816" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
</g>
<!-- 7->0 -->
-<g id="edge4" class="edge"><title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M703.423,-81.5088C595.869,-67.1409 363.245,-36.0652 272.661,-23.9643"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="272.962,-20.4734 262.586,-22.6184 272.035,-27.4118 272.962,-20.4734"/>
+<g id="edge2" class="edge">
+<title>7->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M759.9648,-82.2263C653.3136,-67.4308 423.786,-35.5888 334.0397,-23.1385"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="334.4393,-19.6605 324.0532,-21.753 333.4774,-26.5941 334.4393,-19.6605"/>
</g>
<!-- 8->0 -->
-<g id="edge7" class="edge"><title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M439.796,-71.9656C387.194,-58.3281 315.335,-39.698 272.355,-28.555"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="273.158,-25.1475 262.6,-26.0258 271.401,-31.9235 273.158,-25.1475"/>
+<g id="edge5" class="edge">
+<title>8->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M368.7751,-71.8314C356.8372,-62.8779 342.2744,-51.9558 329.394,-42.2955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="331.3171,-39.3629 321.2171,-36.1628 327.1171,-44.9629 331.3171,-39.3629"/>
</g>
<!-- 9->0 -->
-<g id="edge2" class="edge"><title>9->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M315.569,-71.8761C301.838,-62.8083 284.794,-51.5523 269.964,-41.7592"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="271.804,-38.7798 261.53,-36.1898 267.946,-44.621 271.804,-38.7798"/>
+<g id="edge6" class="edge">
+<title>9->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M491.7266,-71.9243C441.9434,-58.1382 375.1578,-39.6437 334.1509,-28.2879"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="334.8783,-24.8577 324.3068,-25.5619 333.01,-31.6038 334.8783,-24.8577"/>
</g>
<!-- 10 -->
-<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M424.5,-324C424.5,-324 312.5,-324 312.5,-324 306.5,-324 300.5,-318 300.5,-312 300.5,-312 300.5,-300 300.5,-300 300.5,-294 306.5,-288 312.5,-288 312.5,-288 424.5,-288 424.5,-288 430.5,-288 436.5,-294 436.5,-300 436.5,-300 436.5,-312 436.5,-312 436.5,-318 430.5,-324 424.5,-324"/>
-<text text-anchor="middle" x="368.5" y="-303.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M349,-324C349,-324 237,-324 237,-324 231,-324 225,-318 225,-312 225,-312 225,-300 225,-300 225,-294 231,-288 237,-288 237,-288 349,-288 349,-288 355,-288 361,-294 361,-300 361,-300 361,-312 361,-312 361,-318 355,-324 349,-324"/>
+<text text-anchor="middle" x="293" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
</g>
<!-- 10->3 -->
-<g id="edge11" class="edge"><title>10->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M365.243,-287.871C360.642,-263.67 352.188,-219.211 346.709,-190.393"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="350.075,-189.359 344.768,-180.189 343.198,-190.667 350.075,-189.359"/>
+<g id="edge10" class="edge">
+<title>10->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M308.578,-287.7623C330.2044,-262.4436 369.4324,-216.5182 394.0265,-187.7251"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="396.7149,-189.9666 400.5485,-180.0896 391.3922,-185.4202 396.7149,-189.9666"/>
</g>
<!-- 10->5 -->
-<g id="edge14" class="edge"><title>10->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M300.606,-287.966C260.437,-277.887 209.4,-265.082 167.571,-254.588"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="168.25,-251.15 157.699,-252.111 166.546,-257.939 168.25,-251.15"/>
+<g id="edge14" class="edge">
+<title>10->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M253.7114,-287.9038C234.0069,-278.211 210.1177,-265.5019 190,-252 160.8684,-232.4485 130.5241,-206.2856 109.6225,-187.209"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="111.8218,-184.4762 102.0963,-180.2732 107.0781,-189.6238 111.8218,-184.4762"/>
</g>
-<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M692,-252C692,-252 603,-252 603,-252 597,-252 591,-246 591,-240 591,-240 591,-228 591,-228 591,-222 597,-216 603,-216 603,-216 692,-216 692,-216 698,-216 704,-222 704,-228 704,-228 704,-240 704,-240 704,-246 698,-252 692,-252"/>
-<text text-anchor="middle" x="647.5" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M780.5,-252C780.5,-252 691.5,-252 691.5,-252 685.5,-252 679.5,-246 679.5,-240 679.5,-240 679.5,-228 679.5,-228 679.5,-222 685.5,-216 691.5,-216 691.5,-216 780.5,-216 780.5,-216 786.5,-216 792.5,-222 792.5,-228 792.5,-228 792.5,-240 792.5,-240 792.5,-246 786.5,-252 780.5,-252"/>
+<text text-anchor="middle" x="736" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
</g>
-<!-- 10->19 -->
-<g id="edge29" class="edge"><title>10->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M436.394,-287.966C480.239,-276.965 537.032,-262.716 580.666,-251.768"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="581.764,-255.102 590.611,-249.273 580.06,-248.312 581.764,-255.102"/>
+<!-- 10->20 -->
+<g id="edge31" class="edge">
+<title>10->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M361.3709,-289.7061C364.2822,-289.1107 367.1679,-288.539 370,-288 473.953,-268.2165 595.6917,-251.5316 669.2698,-242.1508"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="669.8451,-245.6059 679.3255,-240.876 668.9647,-238.6615 669.8451,-245.6059"/>
</g>
<!-- 11 -->
-<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M494,-252C494,-252 409,-252 409,-252 403,-252 397,-246 397,-240 397,-240 397,-228 397,-228 397,-222 403,-216 409,-216 409,-216 494,-216 494,-216 500,-216 506,-222 506,-228 506,-228 506,-240 506,-240 506,-246 500,-252 494,-252"/>
-<text text-anchor="middle" x="451.5" y="-231.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M498.5,-252C498.5,-252 413.5,-252 413.5,-252 407.5,-252 401.5,-246 401.5,-240 401.5,-240 401.5,-228 401.5,-228 401.5,-222 407.5,-216 413.5,-216 413.5,-216 498.5,-216 498.5,-216 504.5,-216 510.5,-222 510.5,-228 510.5,-228 510.5,-240 510.5,-240 510.5,-246 504.5,-252 498.5,-252"/>
+<text text-anchor="middle" x="456" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
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<!-- 11->3 -->
-<g id="edge10" class="edge"><title>11->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M424.591,-215.876C410.342,-206.808 392.654,-195.552 377.264,-185.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="378.828,-182.606 368.512,-180.19 375.07,-188.511 378.828,-182.606"/>
+<g id="edge11" class="edge">
+<title>11->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M445.9063,-215.8314C441.4403,-207.7925 436.0925,-198.1666 431.1621,-189.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="434.1456,-187.4551 426.2296,-180.4133 428.0265,-190.8546 434.1456,-187.4551"/>
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<!-- 11->4 -->
-<g id="edge12" class="edge"><title>11->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M458.174,-215.697C461.215,-207.813 464.883,-198.304 468.261,-189.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="471.569,-190.694 471.903,-180.104 465.038,-188.175 471.569,-190.694"/>
+<g id="edge12" class="edge">
+<title>11->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M480.4772,-215.8314C492.5395,-206.8779 507.254,-195.9558 520.2686,-186.2955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="522.587,-188.9335 528.5306,-180.1628 518.4148,-183.3127 522.587,-188.9335"/>
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<!-- 12 -->
-<g id="node13" class="node"><title>12</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M582.5,-324C582.5,-324 486.5,-324 486.5,-324 480.5,-324 474.5,-318 474.5,-312 474.5,-312 474.5,-300 474.5,-300 474.5,-294 480.5,-288 486.5,-288 486.5,-288 582.5,-288 582.5,-288 588.5,-288 594.5,-294 594.5,-300 594.5,-300 594.5,-312 594.5,-312 594.5,-318 588.5,-324 582.5,-324"/>
-<text text-anchor="middle" x="534.5" y="-303.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M617,-324C617,-324 521,-324 521,-324 515,-324 509,-318 509,-312 509,-312 509,-300 509,-300 509,-294 515,-288 521,-288 521,-288 617,-288 617,-288 623,-288 629,-294 629,-300 629,-300 629,-312 629,-312 629,-318 623,-324 617,-324"/>
+<text text-anchor="middle" x="569" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
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<!-- 12->4 -->
-<g id="edge13" class="edge"><title>12->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M532.903,-287.986C530.719,-269.607 525.826,-239.765 515.5,-216 511.318,-206.375 505.254,-196.71 499.241,-188.318"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="501.872,-185.992 493.074,-180.089 496.27,-190.19 501.872,-185.992"/>
+<g id="edge13" class="edge">
+<title>12->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M566.9736,-287.7623C564.2446,-263.201 559.3608,-219.2474 556.1505,-190.3541"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="559.593,-189.6419 555.01,-180.0896 552.6358,-190.415 559.593,-189.6419"/>
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<!-- 12->6 -->
-<g id="edge16" class="edge"><title>12->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M474.466,-289.378C434.961,-279.098 382.94,-265.561 340.686,-254.565"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="341.56,-251.176 331,-252.045 339.797,-257.95 341.56,-251.176"/>
+<g id="edge17" class="edge">
+<title>12->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M508.9935,-289.7599C466.2685,-277.8079 412.8739,-261.968 392,-252 354.315,-234.0041 315.1964,-206.2553 289.2236,-186.3277"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="291.3169,-183.5219 281.2713,-180.1548 287.0246,-189.0515 291.3169,-183.5219"/>
</g>
-<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M807,-252C807,-252 734,-252 734,-252 728,-252 722,-246 722,-240 722,-240 722,-228 722,-228 722,-222 728,-216 734,-216 734,-216 807,-216 807,-216 813,-216 819,-222 819,-228 819,-228 819,-240 819,-240 819,-246 813,-252 807,-252"/>
-<text text-anchor="middle" x="770.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M895.5,-252C895.5,-252 822.5,-252 822.5,-252 816.5,-252 810.5,-246 810.5,-240 810.5,-240 810.5,-228 810.5,-228 810.5,-222 816.5,-216 822.5,-216 822.5,-216 895.5,-216 895.5,-216 901.5,-216 907.5,-222 907.5,-228 907.5,-228 907.5,-240 907.5,-240 907.5,-246 901.5,-252 895.5,-252"/>
+<text text-anchor="middle" x="859" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
</g>
-<!-- 12->20 -->
-<g id="edge31" class="edge"><title>12->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M592.147,-287.963C624.904,-278.274 666.932,-265.832 712.269,-252.363"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="713.403,-255.678 721.992,-249.474 711.409,-248.968 713.403,-255.678"/>
+<!-- 12->21 -->
+<g id="edge34" class="edge">
+<title>12->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M629.1827,-293.4061C674.1156,-283.6937 737.1966,-269.4079 800.5071,-252.3215"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="801.5267,-255.6714 810.2566,-249.6682 799.6884,-248.917 801.5267,-255.6714"/>
</g>
<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M200.5,-324C200.5,-324 116.5,-324 116.5,-324 110.5,-324 104.5,-318 104.5,-312 104.5,-312 104.5,-300 104.5,-300 104.5,-294 110.5,-288 116.5,-288 116.5,-288 200.5,-288 200.5,-288 206.5,-288 212.5,-294 212.5,-300 212.5,-300 212.5,-312 212.5,-312 212.5,-318 206.5,-324 200.5,-324"/>
-<text text-anchor="middle" x="158.5" y="-303.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M295,-252C295,-252 211,-252 211,-252 205,-252 199,-246 199,-240 199,-240 199,-228 199,-228 199,-222 205,-216 211,-216 211,-216 295,-216 295,-216 301,-216 307,-222 307,-228 307,-228 307,-240 307,-240 307,-246 301,-252 295,-252"/>
+<text text-anchor="middle" x="253" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
</g>
<!-- 13->5 -->
-<g id="edge15" class="edge"><title>13->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M141.444,-287.697C133.005,-279.135 122.675,-268.656 113.457,-259.304"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="115.873,-256.769 106.36,-252.104 110.887,-261.683 115.873,-256.769"/>
+<g id="edge15" class="edge">
+<title>13->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M210.1018,-215.8314C187.2643,-206.159 159.002,-194.1891 134.9313,-183.9944"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="136.1629,-180.7151 125.5897,-180.038 133.4329,-187.1608 136.1629,-180.7151"/>
</g>
<!-- 13->6 -->
-<g id="edge17" class="edge"><title>13->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M184.675,-287.876C198.536,-278.808 215.741,-267.552 230.711,-257.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="232.772,-260.593 239.224,-252.19 228.94,-254.735 232.772,-260.593"/>
+<g id="edge16" class="edge">
+<title>13->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M254.5141,-215.8314C255.1558,-208.131 255.9188,-198.9743 256.6319,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="260.1229,-190.6694 257.4656,-180.4133 253.1471,-190.088 260.1229,-190.6694"/>
</g>
<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M730.5,-180C730.5,-180 564.5,-180 564.5,-180 558.5,-180 552.5,-174 552.5,-168 552.5,-168 552.5,-156 552.5,-156 552.5,-150 558.5,-144 564.5,-144 564.5,-144 730.5,-144 730.5,-144 736.5,-144 742.5,-150 742.5,-156 742.5,-156 742.5,-168 742.5,-168 742.5,-174 736.5,-180 730.5,-180"/>
-<text text-anchor="middle" x="647.5" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M968,-180C968,-180 802,-180 802,-180 796,-180 790,-174 790,-168 790,-168 790,-156 790,-156 790,-150 796,-144 802,-144 802,-144 968,-144 968,-144 974,-144 980,-150 980,-156 980,-156 980,-168 980,-168 980,-174 974,-180 968,-180"/>
+<text text-anchor="middle" x="885" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 14->7 -->
-<g id="edge20" class="edge"><title>14->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M674.898,-143.876C689.407,-134.808 707.416,-123.552 723.085,-113.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="725.371,-116.458 731.996,-108.19 721.661,-110.522 725.371,-116.458"/>
+<g id="edge19" class="edge">
+<title>14->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M867.5884,-143.8314C859.479,-135.3694 849.6844,-125.1489 840.818,-115.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="843.0921,-113.2115 833.646,-108.4133 838.0382,-118.0549 843.0921,-113.2115"/>
</g>
<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M894,-180C894,-180 773,-180 773,-180 767,-180 761,-174 761,-168 761,-168 761,-156 761,-156 761,-150 767,-144 773,-144 773,-144 894,-144 894,-144 900,-144 906,-150 906,-156 906,-156 906,-168 906,-168 906,-174 900,-180 894,-180"/>
-<text text-anchor="middle" x="833.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M759.5,-180C759.5,-180 638.5,-180 638.5,-180 632.5,-180 626.5,-174 626.5,-168 626.5,-168 626.5,-156 626.5,-156 626.5,-150 632.5,-144 638.5,-144 638.5,-144 759.5,-144 759.5,-144 765.5,-144 771.5,-150 771.5,-156 771.5,-156 771.5,-168 771.5,-168 771.5,-174 765.5,-180 759.5,-180"/>
+<text text-anchor="middle" x="699" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
</g>
<!-- 15->7 -->
-<g id="edge18" class="edge"><title>15->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M815.208,-143.697C806.067,-135.05 794.86,-124.449 784.9,-115.027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="787.252,-112.434 777.582,-108.104 782.441,-117.519 787.252,-112.434"/>
+<g id="edge20" class="edge">
+<title>15->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M728.524,-143.8314C743.4891,-134.6221 761.8386,-123.3301 777.8603,-113.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="779.8032,-116.3847 786.4854,-108.1628 776.1345,-110.423 779.8032,-116.3847"/>
</g>
<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M1086.5,-180C1086.5,-180 936.5,-180 936.5,-180 930.5,-180 924.5,-174 924.5,-168 924.5,-168 924.5,-156 924.5,-156 924.5,-150 930.5,-144 936.5,-144 936.5,-144 1086.5,-144 1086.5,-144 1092.5,-144 1098.5,-150 1098.5,-156 1098.5,-156 1098.5,-168 1098.5,-168 1098.5,-174 1092.5,-180 1086.5,-180"/>
-<text text-anchor="middle" x="1011.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1160,-180C1160,-180 1010,-180 1010,-180 1004,-180 998,-174 998,-168 998,-168 998,-156 998,-156 998,-150 1004,-144 1010,-144 1010,-144 1160,-144 1160,-144 1166,-144 1172,-150 1172,-156 1172,-156 1172,-168 1172,-168 1172,-174 1166,-180 1160,-180"/>
+<text text-anchor="middle" x="1085" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
</g>
<!-- 16->7 -->
-<g id="edge19" class="edge"><title>16->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M950.176,-143.966C912.596,-133.527 864.484,-120.162 825.992,-109.47"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="826.489,-105.976 815.917,-106.671 824.615,-112.72 826.489,-105.976"/>
+<g id="edge18" class="edge">
+<title>16->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1017.4672,-143.9243C975.9721,-132.8178 923.0599,-118.6554 881.8743,-107.6318"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="882.7719,-104.2489 872.207,-105.0442 880.9619,-111.0109 882.7719,-104.2489"/>
</g>
<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M431.5,-396C431.5,-396 305.5,-396 305.5,-396 299.5,-396 293.5,-390 293.5,-384 293.5,-384 293.5,-372 293.5,-372 293.5,-366 299.5,-360 305.5,-360 305.5,-360 431.5,-360 431.5,-360 437.5,-360 443.5,-366 443.5,-372 443.5,-372 443.5,-384 443.5,-384 443.5,-390 437.5,-396 431.5,-396"/>
-<text text-anchor="middle" x="368.5" y="-375.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M356,-396C356,-396 230,-396 230,-396 224,-396 218,-390 218,-384 218,-384 218,-372 218,-372 218,-366 224,-360 230,-360 230,-360 356,-360 356,-360 362,-360 368,-366 368,-372 368,-372 368,-384 368,-384 368,-390 362,-396 356,-396"/>
+<text text-anchor="middle" x="293" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
</g>
<!-- 17->10 -->
-<g id="edge25" class="edge"><title>17->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M368.5,-359.697C368.5,-351.983 368.5,-342.712 368.5,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="372,-334.104 368.5,-324.104 365,-334.104 372,-334.104"/>
+<g id="edge25" class="edge">
+<title>17->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M293,-359.8314C293,-352.131 293,-342.9743 293,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="296.5001,-334.4132 293,-324.4133 289.5001,-334.4133 296.5001,-334.4132"/>
</g>
<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M589.5,-396C589.5,-396 479.5,-396 479.5,-396 473.5,-396 467.5,-390 467.5,-384 467.5,-384 467.5,-372 467.5,-372 467.5,-366 473.5,-360 479.5,-360 479.5,-360 589.5,-360 589.5,-360 595.5,-360 601.5,-366 601.5,-372 601.5,-372 601.5,-384 601.5,-384 601.5,-390 595.5,-396 589.5,-396"/>
-<text text-anchor="middle" x="534.5" y="-375.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-</g>
-<!-- 18->12 -->
-<g id="edge26" class="edge"><title>18->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M534.5,-359.697C534.5,-351.983 534.5,-342.712 534.5,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="538,-334.104 534.5,-324.104 531,-334.104 538,-334.104"/>
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M478.5,-324C478.5,-324 391.5,-324 391.5,-324 385.5,-324 379.5,-318 379.5,-312 379.5,-312 379.5,-300 379.5,-300 379.5,-294 385.5,-288 391.5,-288 391.5,-288 478.5,-288 478.5,-288 484.5,-288 490.5,-294 490.5,-300 490.5,-300 490.5,-312 490.5,-312 490.5,-318 484.5,-324 478.5,-324"/>
+<text text-anchor="middle" x="435" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+</g>
+<!-- 18->11 -->
+<g id="edge26" class="edge">
+<title>18->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M440.2992,-287.8314C442.5698,-280.0463 445.2746,-270.7729 447.794,-262.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="451.1894,-262.9933 450.6295,-252.4133 444.4694,-261.0332 451.1894,-262.9933"/>
+</g>
+<!-- 18->13 -->
+<g id="edge28" class="edge">
+<title>18->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M389.0737,-287.8314C364.4077,-278.0734 333.8309,-265.977 307.914,-255.7242"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="309.1824,-252.4621 298.596,-252.038 306.6073,-258.9713 309.1824,-252.4621"/>
</g>
-<!-- 19->14 -->
-<g id="edge27" class="edge"><title>19->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M647.5,-215.697C647.5,-207.983 647.5,-198.712 647.5,-190.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="651,-190.104 647.5,-180.104 644,-190.104 651,-190.104"/>
-</g>
-<!-- 20->16 -->
-<g id="edge28" class="edge"><title>20->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M819.27,-218.834C854.773,-208.522 903.337,-194.417 942.769,-182.963"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="943.956,-186.263 952.583,-180.113 942.004,-179.541 943.956,-186.263"/>
-</g>
-<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M736.5,-324C736.5,-324 666.5,-324 666.5,-324 660.5,-324 654.5,-318 654.5,-312 654.5,-312 654.5,-300 654.5,-300 654.5,-294 660.5,-288 666.5,-288 666.5,-288 736.5,-288 736.5,-288 742.5,-288 748.5,-294 748.5,-300 748.5,-300 748.5,-312 748.5,-312 748.5,-318 742.5,-324 736.5,-324"/>
-<text text-anchor="middle" x="701.5" y="-303.5" font-family="sans" font-size="10.00">create_index_star</text>
-</g>
-<!-- 21->19 -->
-<g id="edge30" class="edge"><title>21->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M688.152,-287.697C681.743,-279.389 673.942,-269.277 666.894,-260.141"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="669.574,-257.884 660.695,-252.104 664.032,-262.16 669.574,-257.884"/>
-</g>
-<!-- 21->20 -->
-<g id="edge32" class="edge"><title>21->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M718.556,-287.697C726.995,-279.135 737.325,-268.656 746.543,-259.304"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="749.113,-261.683 753.64,-252.104 744.127,-256.769 749.113,-261.683"/>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M624,-396C624,-396 514,-396 514,-396 508,-396 502,-390 502,-384 502,-384 502,-372 502,-372 502,-366 508,-360 514,-360 514,-360 624,-360 624,-360 630,-360 636,-366 636,-372 636,-372 636,-384 636,-384 636,-390 630,-396 624,-396"/>
+<text text-anchor="middle" x="569" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+</g>
+<!-- 19->12 -->
+<g id="edge27" class="edge">
+<title>19->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M569,-359.8314C569,-352.131 569,-342.9743 569,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="572.5001,-334.4132 569,-324.4133 565.5001,-334.4133 572.5001,-334.4132"/>
+</g>
+<!-- 20->14 -->
+<g id="edge29" class="edge">
+<title>20->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M773.599,-215.8314C793.3497,-206.2874 817.7297,-194.5065 838.6417,-184.4013"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="840.1903,-187.5403 847.6714,-180.038 837.1447,-181.2376 840.1903,-187.5403"/>
+</g>
+<!-- 21->16 -->
+<g id="edge30" class="edge">
+<title>21->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M907.7604,-218.4657C940.1409,-208.1498 983.0597,-194.4766 1018.5527,-183.169"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1019.886,-186.4177 1028.3517,-180.0472 1017.7611,-179.748 1019.886,-186.4177"/>
+</g>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M832,-324C832,-324 762,-324 762,-324 756,-324 750,-318 750,-312 750,-312 750,-300 750,-300 750,-294 756,-288 762,-288 762,-288 832,-288 832,-288 838,-288 844,-294 844,-300 844,-300 844,-312 844,-312 844,-318 838,-324 832,-324"/>
+<text text-anchor="middle" x="797" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+</g>
+<!-- 22->20 -->
+<g id="edge32" class="edge">
+<title>22->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M781.6071,-287.8314C774.5096,-279.454 765.952,-269.3531 758.176,-260.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="760.7348,-257.7807 751.6001,-252.4133 755.3939,-262.3056 760.7348,-257.7807"/>
+</g>
+<!-- 22->21 -->
+<g id="edge33" class="edge">
+<title>22->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M812.6452,-287.8314C819.8591,-279.454 828.557,-269.3531 836.4605,-260.1749"/>
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diff --git a/tests/test_integration_workflow/expected_output.files b/tests/test_integration_workflow/expected_output.files
index 1e17510..490153d 100644
--- a/tests/test_integration_workflow/expected_output.files
+++ b/tests/test_integration_workflow/expected_output.files
@@ -78,3 +78,4 @@ results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_qu
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias_3p
results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/unmapped_names.txt
+results/transcriptome/homo_sapiens/transcriptome.fa
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index d5d5e83..9bf33eb 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -78,3 +78,4 @@ e72f5d798c99272f8c0166dc77247db1 results/single_end/synthetic_10_reads_mate_1_s
92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias
92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias_3p
d41d8cd98f00b204e9800998ecf8427e results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/unmapped_names.txt
+79fc3e46b3ac1a72b80cb7bebf6058cd results/transcriptome/homo_sapiens/transcriptome.fa
--
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