From 5667e68dfa638877fa20e3eb5108a50db2cf40fa Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Fri, 6 Mar 2020 12:27:07 +0100
Subject: [PATCH] added rules to generate normalised coverage track #45
---
Snakefile | 14 +-
images/dag_test_workflow.svg | 607 ++++++++++--------
images/rule_graph.svg | 490 ++++++++------
.../expected_output.md5 | 8 +
workflow/rules/paired_end.snakefile.smk | 56 ++
workflow/rules/single_end.snakefile.smk | 56 ++
6 files changed, 777 insertions(+), 454 deletions(-)
diff --git a/Snakefile b/Snakefile
index 695d72f..0364d20 100644
--- a/Snakefile
+++ b/Snakefile
@@ -103,7 +103,19 @@ rule finish:
]
),
salmon_merge_genes = expand(os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "genes_{salmon_merge_on}.tsv"), salmon_merge_on=["tpm", "numreads"]),
- salmon_merge_transcripts = expand(os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "transcripts_{salmon_merge_on}.tsv"), salmon_merge_on=["tpm", "numreads"])
+ salmon_merge_transcripts = expand(os.path.join(config["output_dir"], "summary_salmon", "quantmerge", "transcripts_{salmon_merge_on}.tsv"), salmon_merge_on=["tpm", "numreads"]),
+ star_rpm = expand(os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str1.out.bg"),
+ zip,
+ sample=[i for i in list(samples_table.index.values)],
+ seqmode=[
+ samples_table.loc[i, 'seqmode']
+ for i in list(samples_table.index.values)
+ ])
rule create_index_star:
"""Create index for STAR alignments"""
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 3327b03..14e0982 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,353 +1,454 @@
<?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 2.42.3 (20191010.1750)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1962pt" height="414pt"
- viewBox="0.00 0.00 1962.00 414.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="2177pt" height="414pt"
+ viewBox="0.00 0.00 2176.50 414.00" 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(4 410)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-410 1958,-410 1958,4 -4,4"/>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-410 2172.5,-410 2172.5,4 -4,4"/>
<!-- 0 -->
-<g id="node1" class="node"><title>0</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M1050,-36C1050,-36 1020,-36 1020,-36 1014,-36 1008,-30 1008,-24 1008,-24 1008,-12 1008,-12 1008,-6 1014,-0 1020,-0 1020,-0 1050,-0 1050,-0 1056,-0 1062,-6 1062,-12 1062,-12 1062,-24 1062,-24 1062,-30 1056,-36 1050,-36"/>
-<text text-anchor="middle" x="1035" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
+<title>0</title>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M1171.5,-36C1171.5,-36 1141.5,-36 1141.5,-36 1135.5,-36 1129.5,-30 1129.5,-24 1129.5,-24 1129.5,-12 1129.5,-12 1129.5,-6 1135.5,0 1141.5,0 1141.5,0 1171.5,0 1171.5,0 1177.5,0 1183.5,-6 1183.5,-12 1183.5,-12 1183.5,-24 1183.5,-24 1183.5,-30 1177.5,-36 1171.5,-36"/>
+<text text-anchor="middle" x="1156.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
-<g id="node2" class="node"><title>1</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M280,-108C280,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 280,-72 280,-72 286,-72 292,-78 292,-84 292,-84 292,-96 292,-96 292,-102 286,-108 280,-108"/>
-<text text-anchor="middle" x="146" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
-<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node2" class="node">
+<title>1</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M313,-108C313,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 313,-72 313,-72 319,-72 325,-78 325,-84 325,-84 325,-96 325,-96 325,-102 319,-108 313,-108"/>
+<text text-anchor="middle" x="162.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
+<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 1->0 -->
-<g id="edge1" class="edge"><title>1->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M292.017,-72.8323C295.037,-72.5474 298.034,-72.2696 301,-72 567.9,-47.736 890.22,-27.651 997.94,-21.1875"/>
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+<g id="edge1" class="edge">
+<title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M325.41,-72.67C328.12,-72.44 330.82,-72.22 333.5,-72 636.55,-47.19 1003.18,-27.07 1119.34,-20.93"/>
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<!-- 2 -->
-<g id="node3" class="node"><title>2</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M602,-108C602,-108 322,-108 322,-108 316,-108 310,-102 310,-96 310,-96 310,-84 310,-84 310,-78 316,-72 322,-72 322,-72 602,-72 602,-72 608,-72 614,-78 614,-84 614,-84 614,-96 614,-96 614,-102 608,-108 602,-108"/>
-<text text-anchor="middle" x="462" y="-93" font-family="sans" font-size="10.00">fastqc</text>
-<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<g id="node3" class="node">
+<title>2</title>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M668,-108C668,-108 355,-108 355,-108 349,-108 343,-102 343,-96 343,-96 343,-84 343,-84 343,-78 349,-72 355,-72 355,-72 668,-72 668,-72 674,-72 680,-78 680,-84 680,-84 680,-96 680,-96 680,-102 674,-108 668,-108"/>
+<text text-anchor="middle" x="511.5" y="-93" font-family="sans" font-size="10.00">fastqc</text>
+<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
<!-- 2->0 -->
-<g id="edge2" class="edge"><title>2->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M601.439,-71.9656C732.107,-56.0027 918.769,-33.1992 997.595,-23.5696"/>
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+<g id="edge2" class="edge">
+<title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M668.46,-71.97C818.27,-55.71 1033.46,-32.35 1119.19,-23.05"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1119.67,-26.52 1129.23,-21.96 1118.91,-19.56 1119.67,-26.52"/>
</g>
<!-- 3 -->
-<g id="node4" class="node"><title>3</title>
-<path fill="none" stroke="#56d882" stroke-width="2" d="M1039.5,-180C1039.5,-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 1039.5,-144 1039.5,-144 1045.5,-144 1051.5,-150 1051.5,-156 1051.5,-156 1051.5,-168 1051.5,-168 1051.5,-174 1045.5,-180 1039.5,-180"/>
-<text text-anchor="middle" x="988" 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="#56d8c1" stroke-width="2" d="M1116.5,-180C1116.5,-180 998.5,-180 998.5,-180 992.5,-180 986.5,-174 986.5,-168 986.5,-168 986.5,-156 986.5,-156 986.5,-150 992.5,-144 998.5,-144 998.5,-144 1116.5,-144 1116.5,-144 1122.5,-144 1128.5,-150 1128.5,-156 1128.5,-156 1128.5,-168 1128.5,-168 1128.5,-174 1122.5,-180 1116.5,-180"/>
+<text text-anchor="middle" x="1057.5" y="-159.5" font-family="sans" font-size="10.00">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="M924.308,-161.332C821.372,-159.74 636.097,-146.808 700,-72 737.975,-27.5452 918.617,-20.167 997.736,-19.0937"/>
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+<g id="edge3" class="edge">
+<title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M986.41,-158.82C893.63,-153.49 749.15,-135.12 803.5,-72 843.98,-24.99 1037.08,-19.09 1119.3,-18.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1119.45,-22.26 1129.45,-18.74 1119.44,-15.26 1119.45,-22.26"/>
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<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M1342,-108C1342,-108 1230,-108 1230,-108 1224,-108 1218,-102 1218,-96 1218,-96 1218,-84 1218,-84 1218,-78 1224,-72 1230,-72 1230,-72 1342,-72 1342,-72 1348,-72 1354,-78 1354,-84 1354,-84 1354,-96 1354,-96 1354,-102 1348,-108 1342,-108"/>
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-<text text-anchor="middle" x="1286" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M952.5,-108C952.5,-108 824.5,-108 824.5,-108 818.5,-108 812.5,-102 812.5,-96 812.5,-96 812.5,-84 812.5,-84 812.5,-78 818.5,-72 824.5,-72 824.5,-72 952.5,-72 952.5,-72 958.5,-72 964.5,-78 964.5,-84 964.5,-84 964.5,-96 964.5,-96 964.5,-102 958.5,-108 952.5,-108"/>
+<text text-anchor="middle" x="888.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="888.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
<!-- 3->9 -->
-<g id="edge25" class="edge"><title>3->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1051.56,-146.069C1097.3,-135.326 1159.26,-120.772 1207.99,-109.324"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1208.93,-112.698 1217.87,-107.004 1207.33,-105.884 1208.93,-112.698"/>
+<g id="edge27" class="edge">
+<title>3->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1016.16,-143.88C992.95,-134.26 963.81,-122.19 939.23,-112.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="940.29,-108.66 929.71,-108.07 937.61,-115.13 940.29,-108.66"/>
</g>
<!-- 10 -->
-<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M841.5,-108C841.5,-108 720.5,-108 720.5,-108 714.5,-108 708.5,-102 708.5,-96 708.5,-96 708.5,-84 708.5,-84 708.5,-78 714.5,-72 720.5,-72 720.5,-72 841.5,-72 841.5,-72 847.5,-72 853.5,-78 853.5,-84 853.5,-84 853.5,-96 853.5,-96 853.5,-102 847.5,-108 841.5,-108"/>
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-<text text-anchor="middle" x="781" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M1132,-108C1132,-108 995,-108 995,-108 989,-108 983,-102 983,-96 983,-96 983,-84 983,-84 983,-78 989,-72 995,-72 995,-72 1132,-72 1132,-72 1138,-72 1144,-78 1144,-84 1144,-84 1144,-96 1144,-96 1144,-102 1138,-108 1132,-108"/>
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+<text text-anchor="middle" x="1063.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
<!-- 3->10 -->
-<g id="edge27" class="edge"><title>3->10</title>
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+<g id="edge29" class="edge">
+<title>3->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1058.98,-143.7C1059.64,-135.98 1060.44,-126.71 1061.18,-118.11"/>
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-<text text-anchor="middle" x="949" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1324.5,-108C1324.5,-108 1174.5,-108 1174.5,-108 1168.5,-108 1162.5,-102 1162.5,-96 1162.5,-96 1162.5,-84 1162.5,-84 1162.5,-78 1168.5,-72 1174.5,-72 1174.5,-72 1324.5,-72 1324.5,-72 1330.5,-72 1336.5,-78 1336.5,-84 1336.5,-84 1336.5,-96 1336.5,-96 1336.5,-102 1330.5,-108 1324.5,-108"/>
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+<text text-anchor="middle" x="1249.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 3->11 -->
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+<title>3->11</title>
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+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1516.5,-108C1516.5,-108 1366.5,-108 1366.5,-108 1360.5,-108 1354.5,-102 1354.5,-96 1354.5,-96 1354.5,-84 1354.5,-84 1354.5,-78 1360.5,-72 1366.5,-72 1366.5,-72 1516.5,-72 1516.5,-72 1522.5,-72 1528.5,-78 1528.5,-84 1528.5,-84 1528.5,-96 1528.5,-96 1528.5,-102 1522.5,-108 1516.5,-108"/>
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+<text text-anchor="middle" x="1441.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<!-- 3->12 -->
-<g id="edge31" class="edge"><title>3->12</title>
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+<title>3->12</title>
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<!-- 4->0 -->
-<g id="edge4" class="edge"><title>4->0</title>
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+<title>4->0</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="edge28" class="edge">
+<title>4->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1146.69,-146.08C1143.58,-145.37 1140.51,-144.68 1137.5,-144 1083.45,-131.87 1022.64,-118.91 974.64,-108.85"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="975.11,-105.37 964.6,-106.74 973.67,-112.22 975.11,-105.37"/>
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<!-- 4->10 -->
-<g id="edge28" class="edge"><title>4->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1069.22,-145.902C1066.44,-145.24 1063.69,-144.601 1061,-144 976.777,-125.189 952.487,-125.064 863.814,-108.122"/>
-<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="edge30" class="edge">
+<title>4->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1173.78,-143.88C1154,-134.39 1129.23,-122.51 1108.17,-112.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1109.63,-109.24 1099.1,-108.07 1106.6,-115.55 1109.63,-109.24"/>
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<!-- 4->11 -->
-<g id="edge30" class="edge"><title>4->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1081.95,-143.876C1057.67,-134.222 1027.16,-122.087 1001.49,-111.878"/>
-<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="edge32" class="edge">
+<title>4->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1219.39,-143.7C1223.99,-135.64 1229.56,-125.89 1234.65,-116.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1237.8,-118.52 1239.73,-108.1 1231.73,-115.05 1237.8,-118.52"/>
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<!-- 4->12 -->
-<g id="edge32" class="edge"><title>4->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1124.26,-143.697C1123.93,-135.983 1123.53,-126.712 1123.16,-118.112"/>
-<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="edge34" class="edge">
+<title>4->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1265.96,-143.97C1298.8,-134.06 1340.37,-121.51 1374.81,-111.12"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1376.23,-114.35 1384.79,-108.11 1374.21,-107.65 1376.23,-114.35"/>
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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="#97d856" stroke-width="2" d="M812,-254.5C812,-254.5 649,-254.5 649,-254.5 643,-254.5 637,-248.5 637,-242.5 637,-242.5 637,-230.5 637,-230.5 637,-224.5 643,-218.5 649,-218.5 649,-218.5 812,-218.5 812,-218.5 818,-218.5 824,-224.5 824,-230.5 824,-230.5 824,-242.5 824,-242.5 824,-248.5 818,-254.5 812,-254.5"/>
+<text text-anchor="middle" x="730.5" y="-234" font-family="sans" font-size="10.00">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="grey" stroke-width="2" d="M729.36,-218.28C728.16,-184.58 730.79,-109.88 773.5,-72 824.18,-27.05 1033.01,-20.03 1119.12,-19.08"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1119.27,-22.58 1129.23,-18.99 1119.2,-15.58 1119.27,-22.58"/>
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<!-- 6 -->
-<g id="node7" class="node"><title>6</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M1383,-254.5C1383,-254.5 1257,-254.5 1257,-254.5 1251,-254.5 1245,-248.5 1245,-242.5 1245,-242.5 1245,-230.5 1245,-230.5 1245,-224.5 1251,-218.5 1257,-218.5 1257,-218.5 1383,-218.5 1383,-218.5 1389,-218.5 1395,-224.5 1395,-230.5 1395,-230.5 1395,-242.5 1395,-242.5 1395,-248.5 1389,-254.5 1383,-254.5"/>
-<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="#c6d856" stroke-width="2" d="M1000.5,-254.5C1000.5,-254.5 854.5,-254.5 854.5,-254.5 848.5,-254.5 842.5,-248.5 842.5,-242.5 842.5,-242.5 842.5,-230.5 842.5,-230.5 842.5,-224.5 848.5,-218.5 854.5,-218.5 854.5,-218.5 1000.5,-218.5 1000.5,-218.5 1006.5,-218.5 1012.5,-224.5 1012.5,-230.5 1012.5,-230.5 1012.5,-242.5 1012.5,-242.5 1012.5,-248.5 1006.5,-254.5 1000.5,-254.5"/>
+<text text-anchor="middle" x="927.5" y="-234" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 6->0 -->
-<g id="edge6" class="edge"><title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1336.81,-218.244C1366.11,-186.077 1419.98,-116.217 1382,-72 1342.39,-25.8749 1153.71,-19.4546 1072.41,-18.8661"/>
-<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="grey" stroke-width="2" d="M894.01,-218.46C839.61,-188.64 742.52,-125.08 788.5,-72 831.06,-22.87 1034.39,-18.24 1119.21,-18.5"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1119.4,-22 1129.42,-18.56 1119.44,-15 1119.4,-22"/>
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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="#56c1d8" stroke-width="2" d="M1732.5,-108C1732.5,-108 1634.5,-108 1634.5,-108 1628.5,-108 1622.5,-102 1622.5,-96 1622.5,-96 1622.5,-84 1622.5,-84 1622.5,-78 1628.5,-72 1634.5,-72 1634.5,-72 1732.5,-72 1732.5,-72 1738.5,-72 1744.5,-78 1744.5,-84 1744.5,-84 1744.5,-96 1744.5,-96 1744.5,-102 1738.5,-108 1732.5,-108"/>
+<text text-anchor="middle" x="1683.5" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<text text-anchor="middle" x="1683.5" y="-82" font-family="sans" font-size="10.00">seqmode: paired_end</text>
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<!-- 7->0 -->
-<g id="edge7" class="edge"><title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1447.95,-74.8329C1443.24,-73.8126 1438.55,-72.8519 1434,-72 1302.03,-47.2826 1143.4,-29.8127 1072.47,-22.6347"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.55,-19.1257 1062.25,-21.611 1071.85,-26.0908 1072.55,-19.1257"/>
+<g id="edge7" class="edge">
+<title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1622.21,-74.55C1617.58,-73.63 1612.97,-72.77 1608.5,-72 1455.66,-45.79 1271.5,-28.62 1193.88,-22.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.9,-18.52 1183.65,-21.17 1193.32,-25.49 1193.9,-18.52"/>
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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"/>
-<text text-anchor="middle" x="1689" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
-<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="#56c1d8" stroke-width="2" d="M1870.5,-108C1870.5,-108 1774.5,-108 1774.5,-108 1768.5,-108 1762.5,-102 1762.5,-96 1762.5,-96 1762.5,-84 1762.5,-84 1762.5,-78 1768.5,-72 1774.5,-72 1774.5,-72 1870.5,-72 1870.5,-72 1876.5,-72 1882.5,-78 1882.5,-84 1882.5,-84 1882.5,-96 1882.5,-96 1882.5,-102 1876.5,-108 1870.5,-108"/>
+<text text-anchor="middle" x="1822.5" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<text text-anchor="middle" x="1822.5" y="-82" font-family="sans" font-size="10.00">seqmode: single_end</text>
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<!-- 8->0 -->
-<g id="edge8" class="edge"><title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1632.9,-80.5575C1612.77,-77.6595 1589.89,-74.5153 1569,-72 1382.98,-49.6022 1159.67,-29.6862 1072.46,-22.1756"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.54,-18.6691 1062.27,-21.3013 1071.94,-25.6435 1072.54,-18.6691"/>
+<g id="edge8" class="edge">
+<title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1762.4,-73.62C1759.4,-73.03 1756.42,-72.49 1753.5,-72 1543.73,-37.06 1288.4,-24.13 1193.95,-20.33"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.89,-16.83 1183.76,-19.94 1193.62,-23.82 1193.89,-16.83"/>
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<!-- 9->0 -->
-<g id="edge9" class="edge"><title>9->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1224.92,-71.9656C1177.03,-58.6095 1111.97,-40.4647 1071.77,-29.2542"/>
-<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"/>
+<g id="edge9" class="edge">
+<title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M953.72,-71.97C1005.79,-58.37 1076.86,-39.8 1119.57,-28.65"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1120.47,-32.03 1129.26,-26.11 1118.7,-25.25 1120.47,-32.03"/>
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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="grey" stroke-width="2" d="M1086.49,-71.7C1098.31,-62.8 1112.89,-51.82 1125.68,-42.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1127.89,-44.91 1133.78,-36.1 1123.68,-39.32 1127.89,-44.91"/>
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<!-- 11->0 -->
-<g id="edge11" class="edge"><title>11->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M970.258,-71.6966C981.089,-62.8807 994.418,-52.0321 1006.16,-42.4742"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1008.44,-45.1316 1013.99,-36.1043 1004.02,-39.7026 1008.44,-45.1316"/>
+<g id="edge11" class="edge">
+<title>11->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1226.51,-71.7C1214.69,-62.8 1200.11,-51.82 1187.32,-42.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1189.32,-39.32 1179.22,-36.1 1185.11,-44.91 1189.32,-39.32"/>
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<!-- 12->0 -->
-<g id="edge12" class="edge"><title>12->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1100.49,-71.6966C1089.54,-62.8807 1076.05,-52.0321 1064.18,-42.4742"/>
-<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"/>
+<g id="edge12" class="edge">
+<title>12->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1372.15,-71.97C1315.89,-58.15 1238.78,-39.21 1193.63,-28.12"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1194.24,-24.66 1183.69,-25.68 1192.57,-31.46 1194.24,-24.66"/>
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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="#56d8d8" stroke-width="2" d="M1397,-180C1397,-180 1302,-180 1302,-180 1296,-180 1290,-174 1290,-168 1290,-168 1290,-156 1290,-156 1290,-150 1296,-144 1302,-144 1302,-144 1397,-144 1397,-144 1403,-144 1409,-150 1409,-156 1409,-156 1409,-168 1409,-168 1409,-174 1403,-180 1397,-180"/>
+<text text-anchor="middle" x="1349.5" y="-159.5" font-family="sans" font-size="10.00">star_rpm_paired_end</text>
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-<g id="edge13" class="edge"><title>13->3</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="898.44,-255.951 887.934,-254.581 895.293,-262.203 898.44,-255.951"/>
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-<g id="node23" class="node"><title>22</title>
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-<text text-anchor="middle" x="1496" y="-234" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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-<g id="edge38" class="edge"><title>13->22</title>
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+<g id="edge13" class="edge">
+<title>13->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1409.17,-146.17C1471.04,-130.76 1558.9,-108.77 1559.5,-108 1569.33,-95.38 1570.05,-84.03 1559.5,-72 1535.53,-44.67 1289.12,-27 1193.84,-21.15"/>
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-<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>
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-<g id="edge14" class="edge"><title>14->3</title>
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-<g id="edge16" class="edge"><title>14->4</title>
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-<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="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M2156.5,-180C2156.5,-180 2062.5,-180 2062.5,-180 2056.5,-180 2050.5,-174 2050.5,-168 2050.5,-168 2050.5,-156 2050.5,-156 2050.5,-150 2056.5,-144 2062.5,-144 2062.5,-144 2156.5,-144 2156.5,-144 2162.5,-144 2168.5,-150 2168.5,-156 2168.5,-156 2168.5,-168 2168.5,-168 2168.5,-174 2162.5,-180 2156.5,-180"/>
+<text text-anchor="middle" x="2109.5" y="-159.5" font-family="sans" font-size="10.00">star_rpm_single_end</text>
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-<!-- 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>
-<!-- 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"/>
+<!-- 14->0 -->
+<g id="edge14" class="edge">
+<title>14->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2076.97,-143.9C2035.27,-122.89 1960.16,-88.06 1891.5,-72 1756.7,-40.47 1324.54,-24.37 1194.12,-20.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.95,-16.64 1183.85,-19.82 1193.73,-23.64 1193.95,-16.64"/>
</g>
-<!-- 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"/>
+<!-- 15 -->
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M1073.5,-331.5C1073.5,-331.5 945.5,-331.5 945.5,-331.5 939.5,-331.5 933.5,-325.5 933.5,-319.5 933.5,-319.5 933.5,-307.5 933.5,-307.5 933.5,-301.5 939.5,-295.5 945.5,-295.5 945.5,-295.5 1073.5,-295.5 1073.5,-295.5 1079.5,-295.5 1085.5,-301.5 1085.5,-307.5 1085.5,-307.5 1085.5,-319.5 1085.5,-319.5 1085.5,-325.5 1079.5,-331.5 1073.5,-331.5"/>
+<text text-anchor="middle" x="1009.5" y="-311" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+</g>
+<!-- 15->3 -->
+<g id="edge15" class="edge">
+<title>15->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1015.01,-295.35C1023.28,-269.58 1039,-220.63 1048.82,-190.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1052.19,-191 1051.91,-180.41 1045.52,-188.86 1052.19,-191"/>
+</g>
+<!-- 15->5 -->
+<g id="edge19" class="edge">
+<title>15->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M946.19,-295.48C903.89,-284.11 848.11,-269.12 803.87,-257.22"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="804.61,-253.8 794.04,-254.58 802.79,-260.56 804.61,-253.8"/>
</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>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1501,-254.5C1501,-254.5 1400,-254.5 1400,-254.5 1394,-254.5 1388,-248.5 1388,-242.5 1388,-242.5 1388,-230.5 1388,-230.5 1388,-224.5 1394,-218.5 1400,-218.5 1400,-218.5 1501,-218.5 1501,-218.5 1507,-218.5 1513,-224.5 1513,-230.5 1513,-230.5 1513,-242.5 1513,-242.5 1513,-248.5 1507,-254.5 1501,-254.5"/>
+<text text-anchor="middle" x="1450.5" y="-234" font-family="sans" font-size="10.00">pe_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->22 -->
+<g id="edge42" class="edge">
+<title>15->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1085.56,-299.56C1167.55,-285.62 1297.12,-263.58 1377.79,-249.87"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1378.59,-253.28 1387.86,-248.15 1377.42,-246.38 1378.59,-253.28"/>
</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>
-<!-- 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>
-<!-- 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="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M1240,-257C1240,-257 1125,-257 1125,-257 1119,-257 1113,-251 1113,-245 1113,-245 1113,-228 1113,-228 1113,-222 1119,-216 1125,-216 1125,-216 1240,-216 1240,-216 1246,-216 1252,-222 1252,-228 1252,-228 1252,-245 1252,-245 1252,-251 1246,-257 1240,-257"/>
+<text text-anchor="middle" x="1182.5" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="1182.5" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
+<text text-anchor="middle" x="1182.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 16->3 -->
+<g id="edge16" class="edge">
+<title>16->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1148.67,-215.88C1132.45,-206.47 1112.93,-195.15 1096.12,-185.4"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1097.5,-182.16 1087.1,-180.17 1093.99,-188.21 1097.5,-182.16"/>
+</g>
+<!-- 16->4 -->
+<g id="edge18" class="edge">
+<title>16->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1189.88,-215.69C1192.84,-207.73 1196.3,-198.44 1199.49,-189.89"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1202.84,-190.91 1203.05,-180.32 1196.28,-188.47 1202.84,-190.91"/>
</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>
-<!-- 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="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#80d856" stroke-width="2" d="M1375.5,-331.5C1375.5,-331.5 1265.5,-331.5 1265.5,-331.5 1259.5,-331.5 1253.5,-325.5 1253.5,-319.5 1253.5,-319.5 1253.5,-307.5 1253.5,-307.5 1253.5,-301.5 1259.5,-295.5 1265.5,-295.5 1265.5,-295.5 1375.5,-295.5 1375.5,-295.5 1381.5,-295.5 1387.5,-301.5 1387.5,-307.5 1387.5,-307.5 1387.5,-319.5 1387.5,-319.5 1387.5,-325.5 1381.5,-331.5 1375.5,-331.5"/>
+<text text-anchor="middle" x="1320.5" y="-311" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+</g>
+<!-- 17->4 -->
+<g id="edge17" class="edge">
+<title>17->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1311.57,-295.35C1300.86,-275.44 1281.79,-242.01 1261.5,-216 1253.77,-206.09 1244.4,-196.05 1235.74,-187.41"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1237.98,-184.7 1228.38,-180.21 1233.09,-189.71 1237.98,-184.7"/>
+</g>
+<!-- 17->6 -->
+<g id="edge21" class="edge">
+<title>17->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1253.39,-299.69C1189.84,-287.56 1093.79,-269.24 1022.41,-255.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1022.99,-252.16 1012.51,-253.72 1021.68,-259.04 1022.99,-252.16"/>
</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>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1768,-254.5C1768,-254.5 1685,-254.5 1685,-254.5 1679,-254.5 1673,-248.5 1673,-242.5 1673,-242.5 1673,-230.5 1673,-230.5 1673,-224.5 1679,-218.5 1685,-218.5 1685,-218.5 1768,-218.5 1768,-218.5 1774,-218.5 1780,-224.5 1780,-230.5 1780,-230.5 1780,-242.5 1780,-242.5 1780,-248.5 1774,-254.5 1768,-254.5"/>
+<text text-anchor="middle" x="1726.5" y="-234" font-family="sans" font-size="10.00">map_genome_star</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"/>
+<!-- 17->23 -->
+<g id="edge44" class="edge">
+<title>17->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1387.54,-300.12C1463.91,-286.01 1587.77,-263.13 1662.74,-249.28"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1663.79,-252.64 1672.99,-247.39 1662.52,-245.76 1663.79,-252.64"/>
</g>
-<!-- 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"/>
+<!-- 18 -->
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M830,-331.5C830,-331.5 715,-331.5 715,-331.5 709,-331.5 703,-325.5 703,-319.5 703,-319.5 703,-307.5 703,-307.5 703,-301.5 709,-295.5 715,-295.5 715,-295.5 830,-295.5 830,-295.5 836,-295.5 842,-301.5 842,-307.5 842,-307.5 842,-319.5 842,-319.5 842,-325.5 836,-331.5 830,-331.5"/>
+<text text-anchor="middle" x="772.5" y="-316.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<text text-anchor="middle" x="772.5" y="-305.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 18->5 -->
+<g id="edge20" class="edge">
+<title>18->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M762.97,-295.48C757.69,-286.05 751.02,-274.14 745.09,-263.56"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="748.08,-261.73 740.14,-254.71 741.97,-265.15 748.08,-261.73"/>
+</g>
+<!-- 18->6 -->
+<g id="edge22" class="edge">
+<title>18->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M807.67,-295.48C829.99,-284.68 859.06,-270.62 882.97,-259.04"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="884.72,-262.09 892.2,-254.58 881.67,-255.79 884.72,-262.09"/>
</g>
<!-- 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="#d8c356" stroke-width="2" d="M1628,-180C1628,-180 1439,-180 1439,-180 1433,-180 1427,-174 1427,-168 1427,-168 1427,-156 1427,-156 1427,-150 1433,-144 1439,-144 1439,-144 1628,-144 1628,-144 1634,-144 1640,-150 1640,-156 1640,-156 1640,-168 1640,-168 1640,-174 1634,-180 1628,-180"/>
+<text text-anchor="middle" x="1533.5" y="-159.5" font-family="sans" font-size="10.00">pe_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"/>
+<!-- 19->7 -->
+<g id="edge23" class="edge">
+<title>19->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1570.19,-143.88C1590.52,-134.39 1615.97,-122.51 1637.6,-112.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1639.34,-115.47 1646.93,-108.07 1636.38,-109.13 1639.34,-115.47"/>
</g>
<!-- 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>
-<!-- 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="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M1806.5,-180C1806.5,-180 1670.5,-180 1670.5,-180 1664.5,-180 1658.5,-174 1658.5,-168 1658.5,-168 1658.5,-156 1658.5,-156 1658.5,-150 1664.5,-144 1670.5,-144 1670.5,-144 1806.5,-144 1806.5,-144 1812.5,-144 1818.5,-150 1818.5,-156 1818.5,-156 1818.5,-168 1818.5,-168 1818.5,-174 1812.5,-180 1806.5,-180"/>
+<text text-anchor="middle" x="1738.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 20->7 -->
+<g id="edge24" class="edge">
+<title>20->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1724.9,-143.7C1718.38,-135.39 1710.43,-125.28 1703.25,-116.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1705.87,-113.81 1696.94,-108.1 1700.37,-118.13 1705.87,-113.81"/>
+</g>
+<!-- 20->8 -->
+<g id="edge26" class="edge">
+<title>20->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1759.26,-143.7C1769.74,-134.97 1782.61,-124.24 1794,-114.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1796.53,-117.19 1801.97,-108.1 1792.05,-111.82 1796.53,-117.19"/>
</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="#d89556" stroke-width="2" d="M2020.5,-180C2020.5,-180 1848.5,-180 1848.5,-180 1842.5,-180 1836.5,-174 1836.5,-168 1836.5,-168 1836.5,-156 1836.5,-156 1836.5,-150 1842.5,-144 1848.5,-144 1848.5,-144 2020.5,-144 2020.5,-144 2026.5,-144 2032.5,-150 2032.5,-156 2032.5,-156 2032.5,-168 2032.5,-168 2032.5,-174 2026.5,-180 2020.5,-180"/>
+<text text-anchor="middle" x="1934.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+</g>
+<!-- 21->8 -->
+<g id="edge25" class="edge">
+<title>21->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1907.1,-143.88C1892.59,-134.81 1874.58,-123.55 1858.91,-113.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1860.34,-110.52 1850,-108.19 1856.63,-116.46 1860.34,-110.52"/>
+</g>
+<!-- 22->13 -->
+<g id="edge35" class="edge">
+<title>22->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1426.56,-218.32C1413.11,-208.66 1396.13,-196.47 1381.54,-186"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1383.43,-183.05 1373.26,-180.06 1379.35,-188.73 1383.43,-183.05"/>
+</g>
+<!-- 22->19 -->
+<g id="edge39" class="edge">
+<title>22->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1470.17,-218.32C1480.92,-208.93 1494.4,-197.15 1506.16,-186.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1508.74,-189.27 1513.97,-180.06 1504.14,-184 1508.74,-189.27"/>
+</g>
+<!-- 23->14 -->
+<g id="edge36" class="edge">
+<title>23->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1780.23,-227.22C1841.02,-217.58 1943.19,-200.59 2040.24,-180.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2041.16,-183.58 2050.22,-178.08 2039.71,-176.73 2041.16,-183.58"/>
+</g>
+<!-- 23->21 -->
+<g id="edge40" class="edge">
+<title>23->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1775.53,-218.41C1805.57,-207.94 1844.2,-194.47 1875.86,-183.44"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1877.15,-186.7 1885.44,-180.1 1874.84,-180.09 1877.15,-186.7"/>
</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"/>
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M1141,-406C1141,-406 840,-406 840,-406 834,-406 828,-400 828,-394 828,-394 828,-382 828,-382 828,-376 834,-370 840,-370 840,-370 1141,-370 1141,-370 1147,-370 1153,-376 1153,-382 1153,-382 1153,-394 1153,-394 1153,-400 1147,-406 1141,-406"/>
+<text text-anchor="middle" x="990.5" y="-391" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="990.5" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 24->15 -->
+<g id="edge37" class="edge">
+<title>24->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M995,-369.82C997.23,-361.33 999.96,-350.89 1002.46,-341.38"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1005.88,-342.12 1005.03,-331.56 999.11,-340.34 1005.88,-342.12"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M1496,-406C1496,-406 1183,-406 1183,-406 1177,-406 1171,-400 1171,-394 1171,-394 1171,-382 1171,-382 1171,-376 1177,-370 1183,-370 1183,-370 1496,-370 1496,-370 1502,-370 1508,-376 1508,-382 1508,-382 1508,-394 1508,-394 1508,-400 1502,-406 1496,-406"/>
+<text text-anchor="middle" x="1339.5" y="-391" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1339.5" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+</g>
+<!-- 25->17 -->
+<g id="edge38" class="edge">
+<title>25->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1335,-369.82C1332.77,-361.33 1330.04,-350.89 1327.54,-341.38"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1330.89,-340.34 1324.97,-331.56 1324.12,-342.12 1330.89,-340.34"/>
+</g>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1568,-334C1568,-334 1453,-334 1453,-334 1447,-334 1441,-328 1441,-322 1441,-322 1441,-305 1441,-305 1441,-299 1447,-293 1453,-293 1453,-293 1568,-293 1568,-293 1574,-293 1580,-299 1580,-305 1580,-305 1580,-322 1580,-322 1580,-328 1574,-334 1568,-334"/>
+<text text-anchor="middle" x="1510.5" y="-322" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1510.5" y="-311" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1510.5" y="-300" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 26->22 -->
+<g id="edge41" class="edge">
+<title>26->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1494.74,-292.79C1487.36,-283.57 1478.48,-272.48 1470.63,-262.66"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1473.3,-260.4 1464.32,-254.78 1467.84,-264.77 1473.3,-260.4"/>
+</g>
+<!-- 26->23 -->
+<g id="edge43" class="edge">
+<title>26->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1566.69,-292.99C1597.73,-282.21 1636.25,-268.84 1667.69,-257.92"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1668.91,-261.2 1677.21,-254.61 1666.61,-254.59 1668.91,-261.2"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 0bf578e..d598135 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,283 +1,373 @@
<?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 2.42.3 (20191010.1750)
-->
<!-- 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="1392pt" height="404pt"
+ viewBox="0.00 0.00 1391.50 404.00" 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="white" stroke="transparent" points="-4,4 -4,-400 1387.5,-400 1387.5,4 -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="#59d856" stroke-width="2" d="M386.5,-36C386.5,-36 356.5,-36 356.5,-36 350.5,-36 344.5,-30 344.5,-24 344.5,-24 344.5,-12 344.5,-12 344.5,-6 350.5,0 356.5,0 356.5,0 386.5,0 386.5,0 392.5,0 398.5,-6 398.5,-12 398.5,-12 398.5,-24 398.5,-24 398.5,-30 392.5,-36 386.5,-36"/>
+<text text-anchor="middle" x="371.5" y="-15.5" font-family="sans" font-size="10.00">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="#d89556" stroke-width="2" d="M68.5,-108C68.5,-108 28.5,-108 28.5,-108 22.5,-108 16.5,-102 16.5,-96 16.5,-96 16.5,-84 16.5,-84 16.5,-78 22.5,-72 28.5,-72 28.5,-72 68.5,-72 68.5,-72 74.5,-72 80.5,-78 80.5,-84 80.5,-84 80.5,-96 80.5,-96 80.5,-102 74.5,-108 68.5,-108"/>
+<text text-anchor="middle" x="48.5" y="-87.5" font-family="sans" font-size="10.00">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="edge5" class="edge">
+<title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M80.5,-74.99C83.51,-73.9 86.55,-72.88 89.5,-72 175.21,-46.48 279.4,-30.69 333.99,-23.53"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="334.76,-26.96 344.23,-22.21 333.86,-20.02 334.76,-26.96"/>
</g>
<!-- 2 -->
-<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="#d8c356" stroke-width="2" d="M140.5,-108C140.5,-108 110.5,-108 110.5,-108 104.5,-108 98.5,-102 98.5,-96 98.5,-96 98.5,-84 98.5,-84 98.5,-78 104.5,-72 110.5,-72 110.5,-72 140.5,-72 140.5,-72 146.5,-72 152.5,-78 152.5,-84 152.5,-84 152.5,-96 152.5,-96 152.5,-102 146.5,-108 140.5,-108"/>
+<text text-anchor="middle" x="125.5" y="-87.5" font-family="sans" font-size="10.00">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="grey" stroke-width="2" d="M152.65,-77.12C157.23,-75.3 161.97,-73.52 166.5,-72 224.18,-52.69 292.95,-36.2 334.37,-26.95"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="335.28,-30.33 344.29,-24.76 333.77,-23.5 335.28,-30.33"/>
</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="#56a9d8" stroke-width="2" d="M430.5,-180C430.5,-180 312.5,-180 312.5,-180 306.5,-180 300.5,-174 300.5,-168 300.5,-168 300.5,-156 300.5,-156 300.5,-150 306.5,-144 312.5,-144 312.5,-144 430.5,-144 430.5,-144 436.5,-144 442.5,-150 442.5,-156 442.5,-156 442.5,-168 442.5,-168 442.5,-174 436.5,-180 430.5,-180"/>
+<text text-anchor="middle" x="371.5" y="-159.5" font-family="sans" font-size="10.00">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="edge11" class="edge">
+<title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M318.28,-143.96C301.61,-135.84 285.08,-124.23 275.5,-108 267.37,-94.22 267.37,-85.78 275.5,-72 288.25,-50.39 313.33,-36.98 334.65,-29.06"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="335.81,-32.36 344.12,-25.8 333.53,-25.74 335.81,-32.36"/>
</g>
<!-- 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="#c6d856" stroke-width="2" d="M616.5,-108C616.5,-108 488.5,-108 488.5,-108 482.5,-108 476.5,-102 476.5,-96 476.5,-96 476.5,-84 476.5,-84 476.5,-78 482.5,-72 488.5,-72 488.5,-72 616.5,-72 616.5,-72 622.5,-72 628.5,-78 628.5,-84 628.5,-84 628.5,-96 628.5,-96 628.5,-102 622.5,-108 616.5,-108"/>
+<text text-anchor="middle" x="552.5" y="-87.5" font-family="sans" font-size="10.00">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="edge24" class="edge">
+<title>3->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M415.78,-143.88C440.85,-134.18 472.4,-121.98 498.87,-111.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="500.3,-114.94 508.37,-108.07 497.78,-108.41 500.3,-114.94"/>
</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="#56d8c1" stroke-width="2" d="M446.5,-108C446.5,-108 296.5,-108 296.5,-108 290.5,-108 284.5,-102 284.5,-96 284.5,-96 284.5,-84 284.5,-84 284.5,-78 290.5,-72 296.5,-72 296.5,-72 446.5,-72 446.5,-72 452.5,-72 458.5,-78 458.5,-84 458.5,-84 458.5,-96 458.5,-96 458.5,-102 452.5,-108 446.5,-108"/>
+<text text-anchor="middle" x="371.5" y="-87.5" font-family="sans" font-size="10.00">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="edge26" class="edge">
+<title>3->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M371.5,-143.7C371.5,-135.98 371.5,-126.71 371.5,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="375,-118.1 371.5,-108.1 368,-118.1 375,-118.1"/>
</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="#68d856" stroke-width="2" d="M574,-180C574,-180 473,-180 473,-180 467,-180 461,-174 461,-168 461,-168 461,-156 461,-156 461,-150 467,-144 473,-144 473,-144 574,-144 574,-144 580,-144 586,-150 586,-156 586,-156 586,-168 586,-168 586,-174 580,-180 574,-180"/>
+<text text-anchor="middle" x="523.5" y="-159.5" font-family="sans" font-size="10.00">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="edge3" class="edge">
+<title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M586.13,-146.32C606,-138.39 625.82,-126.31 637.5,-108 646.1,-94.51 647.65,-84.37 637.5,-72 609.01,-37.27 475.24,-24.87 408.94,-20.8"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="409.09,-17.31 398.9,-20.22 408.68,-24.3 409.09,-17.31"/>
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<!-- 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="edge23" class="edge">
+<title>4->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M530.67,-143.7C533.93,-135.81 537.87,-126.3 541.5,-117.55"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="544.82,-118.68 545.41,-108.1 538.35,-116 544.82,-118.68"/>
</g>
<!-- 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="edge25" class="edge">
+<title>4->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M486.32,-143.88C465.63,-134.35 439.7,-122.41 417.72,-112.28"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="419.11,-109.07 408.56,-108.07 416.18,-115.43 419.11,-109.07"/>
</g>
<!-- 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="#d8ac56" stroke-width="2" d="M175,-252C175,-252 12,-252 12,-252 6,-252 0,-246 0,-240 0,-240 0,-228 0,-228 0,-222 6,-216 12,-216 12,-216 175,-216 175,-216 181,-216 187,-222 187,-228 187,-228 187,-240 187,-240 187,-246 181,-252 175,-252"/>
+<text text-anchor="middle" x="93.5" y="-231.5" font-family="sans" font-size="10.00">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="edge6" class="edge">
+<title>5->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M106.47,-215.84C131.37,-183.89 188.86,-114.66 250.5,-72 276.64,-53.91 309.94,-39.87 334.99,-30.8"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="336.22,-34.08 344.49,-27.45 333.9,-27.48 336.22,-34.08"/>
</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="#d85656" stroke-width="2" d="M363.5,-252C363.5,-252 217.5,-252 217.5,-252 211.5,-252 205.5,-246 205.5,-240 205.5,-240 205.5,-228 205.5,-228 205.5,-222 211.5,-216 217.5,-216 217.5,-216 363.5,-216 363.5,-216 369.5,-216 375.5,-222 375.5,-228 375.5,-228 375.5,-240 375.5,-240 375.5,-246 369.5,-252 363.5,-252"/>
+<text text-anchor="middle" x="290.5" y="-231.5" font-family="sans" font-size="10.00">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="edge2" class="edge">
+<title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M280.74,-215.53C264.7,-184.26 237.25,-117.72 265.5,-72 280.52,-47.7 310.44,-34.16 334.67,-26.87"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="335.6,-30.24 344.31,-24.2 333.73,-23.5 335.6,-30.24"/>
</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="#56d882" stroke-width="2" d="M952,-108C952,-108 857,-108 857,-108 851,-108 845,-102 845,-96 845,-96 845,-84 845,-84 845,-78 851,-72 857,-72 857,-72 952,-72 952,-72 958,-72 964,-78 964,-84 964,-84 964,-96 964,-96 964,-102 958,-108 952,-108"/>
+<text text-anchor="middle" x="904.5" y="-87.5" font-family="sans" font-size="10.00">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="edge7" class="edge">
+<title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M844.88,-77.28C834.44,-75.4 823.67,-73.56 813.5,-72 664.11,-49.11 485.04,-30.27 408.8,-22.64"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="409.04,-19.15 398.74,-21.64 408.35,-26.11 409.04,-19.15"/>
</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="edge10" class="edge">
+<title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M508.22,-71.88C477.48,-59.98 437,-44.33 408.08,-33.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="409.34,-29.88 398.75,-29.54 406.81,-36.41 409.34,-29.88"/>
</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="edge1" class="edge">
+<title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M371.5,-71.7C371.5,-63.98 371.5,-54.71 371.5,-46.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="375,-46.1 371.5,-36.1 368,-46.1 375,-46.1"/>
</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="#d86e56" stroke-width="2" d="M792,-108C792,-108 697,-108 697,-108 691,-108 685,-102 685,-96 685,-96 685,-84 685,-84 685,-78 691,-72 697,-72 697,-72 792,-72 792,-72 798,-72 804,-78 804,-84 804,-84 804,-96 804,-96 804,-102 798,-108 792,-108"/>
+<text text-anchor="middle" x="744.5" y="-87.5" font-family="sans" font-size="10.00">star_rpm_paired_end</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>
-<!-- 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>
-<!-- 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>
-</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->0 -->
+<g id="edge4" class="edge">
+<title>10->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M684.78,-75.01C679.96,-73.96 675.15,-72.95 670.5,-72 576.64,-52.91 465.4,-34.22 408.73,-24.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="409.23,-21.52 398.8,-23.37 408.11,-28.42 409.23,-21.52"/>
</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>
-<!-- 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="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M1371.5,-180C1371.5,-180 1277.5,-180 1277.5,-180 1271.5,-180 1265.5,-174 1265.5,-168 1265.5,-168 1265.5,-156 1265.5,-156 1265.5,-150 1271.5,-144 1277.5,-144 1277.5,-144 1371.5,-144 1371.5,-144 1377.5,-144 1383.5,-150 1383.5,-156 1383.5,-156 1383.5,-168 1383.5,-168 1383.5,-174 1377.5,-180 1371.5,-180"/>
+<text text-anchor="middle" x="1324.5" y="-159.5" font-family="sans" font-size="10.00">star_rpm_single_end</text>
</g>
-<!-- 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"/>
+<!-- 11->0 -->
+<g id="edge9" class="edge">
+<title>11->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1268.86,-143.94C1200.14,-123.55 1079.33,-89.96 973.5,-72 761.85,-36.09 503.95,-23.72 408.94,-20.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="408.82,-16.7 398.7,-19.84 408.57,-23.7 408.82,-16.7"/>
</g>
<!-- 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="#56c1d8" stroke-width="2" d="M467.5,-324C467.5,-324 339.5,-324 339.5,-324 333.5,-324 327.5,-318 327.5,-312 327.5,-312 327.5,-300 327.5,-300 327.5,-294 333.5,-288 339.5,-288 339.5,-288 467.5,-288 467.5,-288 473.5,-288 479.5,-294 479.5,-300 479.5,-300 479.5,-312 479.5,-312 479.5,-318 473.5,-324 467.5,-324"/>
+<text text-anchor="middle" x="403.5" y="-303.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+</g>
+<!-- 12->3 -->
+<g id="edge12" class="edge">
+<title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M400.01,-287.9C396.31,-269.96 390.22,-240.95 384.5,-216 382.56,-207.56 380.35,-198.39 378.31,-190.09"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="381.65,-189.02 375.85,-180.15 374.86,-190.7 381.65,-189.02"/>
+</g>
+<!-- 12->5 -->
+<g id="edge16" class="edge">
+<title>12->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M328.06,-287.97C282.97,-277.78 225.55,-264.82 178.81,-254.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="179.53,-250.84 169.01,-252.05 177.99,-257.67 179.53,-250.84"/>
</g>
-<!-- 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"/>
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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"/>
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-<!-- 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>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M791,-252C791,-252 690,-252 690,-252 684,-252 678,-246 678,-240 678,-240 678,-228 678,-228 678,-222 684,-216 690,-216 690,-216 791,-216 791,-216 797,-216 803,-222 803,-228 803,-228 803,-240 803,-240 803,-246 797,-252 791,-252"/>
+<text text-anchor="middle" x="740.5" y="-231.5" font-family="sans" font-size="10.00">pe_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->19 -->
+<g id="edge33" class="edge">
+<title>12->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M479.55,-289.2C535.93,-277.49 612.31,-261.63 667.86,-250.09"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="668.9,-253.45 677.98,-247.99 667.48,-246.59 668.9,-253.45"/>
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<!-- 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>
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-<!-- 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"/>
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-<!-- 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="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M541,-252C541,-252 444,-252 444,-252 438,-252 432,-246 432,-240 432,-240 432,-228 432,-228 432,-222 438,-216 444,-216 444,-216 541,-216 541,-216 547,-216 553,-222 553,-228 553,-228 553,-240 553,-240 553,-246 547,-252 541,-252"/>
+<text text-anchor="middle" x="492.5" y="-231.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+</g>
+<!-- 13->3 -->
+<g id="edge13" class="edge">
+<title>13->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M462.9,-215.88C446.93,-206.64 427.04,-195.13 409.89,-185.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="411.62,-182.17 401.21,-180.19 408.12,-188.23 411.62,-182.17"/>
+</g>
+<!-- 13->4 -->
+<g id="edge15" class="edge">
+<title>13->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M500.16,-215.7C503.69,-207.73 507.96,-198.1 511.87,-189.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="515.08,-190.67 515.93,-180.1 508.68,-187.83 515.08,-190.67"/>
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<!-- 14 -->
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-<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="#56d86b" stroke-width="2" d="M636.5,-324C636.5,-324 526.5,-324 526.5,-324 520.5,-324 514.5,-318 514.5,-312 514.5,-312 514.5,-300 514.5,-300 514.5,-294 520.5,-288 526.5,-288 526.5,-288 636.5,-288 636.5,-288 642.5,-288 648.5,-294 648.5,-300 648.5,-300 648.5,-312 648.5,-312 648.5,-318 642.5,-324 636.5,-324"/>
+<text text-anchor="middle" x="581.5" y="-303.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+</g>
+<!-- 14->4 -->
+<g id="edge14" class="edge">
+<title>14->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M580.02,-287.94C577.93,-269.51 573.12,-239.63 562.5,-216 558.14,-206.31 551.81,-196.66 545.5,-188.31"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="548.23,-186.11 539.28,-180.44 542.73,-190.45 548.23,-186.11"/>
+</g>
+<!-- 14->6 -->
+<g id="edge18" class="edge">
+<title>14->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M514.37,-288.85C471.68,-278.58 416.16,-265.23 371.09,-254.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="371.89,-250.98 361.35,-252.04 370.25,-257.78 371.89,-250.98"/>
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-<!-- 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"/>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1004,-252C1004,-252 921,-252 921,-252 915,-252 909,-246 909,-240 909,-240 909,-228 909,-228 909,-222 915,-216 921,-216 921,-216 1004,-216 1004,-216 1010,-216 1016,-222 1016,-228 1016,-228 1016,-240 1016,-240 1016,-246 1010,-252 1004,-252"/>
+<text text-anchor="middle" x="962.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
</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>
+<!-- 14->20 -->
+<g id="edge35" class="edge">
+<title>14->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M648.74,-292.65C719.39,-279.67 829.69,-259.4 898.93,-246.68"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="899.64,-250.11 908.84,-244.86 898.37,-243.22 899.64,-250.11"/>
</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"/>
+<!-- 15 -->
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M220,-324C220,-324 123,-324 123,-324 117,-324 111,-318 111,-312 111,-312 111,-300 111,-300 111,-294 117,-288 123,-288 123,-288 220,-288 220,-288 226,-288 232,-294 232,-300 232,-300 232,-312 232,-312 232,-318 226,-324 220,-324"/>
+<text text-anchor="middle" x="171.5" y="-303.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+</g>
+<!-- 15->5 -->
+<g id="edge17" class="edge">
+<title>15->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M152.22,-287.7C142.58,-279.05 130.77,-268.45 120.27,-259.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="122.34,-256.18 112.56,-252.1 117.66,-261.39 122.34,-256.18"/>
+</g>
+<!-- 15->6 -->
+<g id="edge19" class="edge">
+<title>15->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M200.61,-287.88C216.17,-278.72 235.52,-267.34 252.28,-257.48"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="254.43,-260.28 261.28,-252.19 250.88,-254.24 254.43,-260.28"/>
</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="#afd856" stroke-width="2" d="M1022,-180C1022,-180 833,-180 833,-180 827,-180 821,-174 821,-168 821,-168 821,-156 821,-156 821,-150 827,-144 833,-144 833,-144 1022,-144 1022,-144 1028,-144 1034,-150 1034,-156 1034,-156 1034,-168 1034,-168 1034,-174 1028,-180 1022,-180"/>
+<text text-anchor="middle" x="927.5" y="-159.5" font-family="sans" font-size="10.00">pe_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="edge21" class="edge">
+<title>16->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M921.81,-143.7C919.25,-135.9 916.17,-126.51 913.32,-117.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="916.57,-116.51 910.12,-108.1 909.92,-118.7 916.57,-116.51"/>
</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="#569ad8" stroke-width="2" d="M790.5,-180C790.5,-180 654.5,-180 654.5,-180 648.5,-180 642.5,-174 642.5,-168 642.5,-168 642.5,-156 642.5,-156 642.5,-150 648.5,-144 654.5,-144 654.5,-144 790.5,-144 790.5,-144 796.5,-144 802.5,-150 802.5,-156 802.5,-156 802.5,-168 802.5,-168 802.5,-174 796.5,-180 790.5,-180"/>
+<text text-anchor="middle" x="722.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</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"/>
+<!-- 17->7 -->
+<g id="edge22" class="edge">
+<title>17->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M767.02,-143.88C792.23,-134.18 823.95,-121.98 850.57,-111.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="852.05,-114.92 860.12,-108.07 849.53,-108.39 852.05,-114.92"/>
</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>
-<!-- 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 id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#80d856" stroke-width="2" d="M1235.5,-180C1235.5,-180 1063.5,-180 1063.5,-180 1057.5,-180 1051.5,-174 1051.5,-168 1051.5,-168 1051.5,-156 1051.5,-156 1051.5,-150 1057.5,-144 1063.5,-144 1063.5,-144 1235.5,-144 1235.5,-144 1241.5,-144 1247.5,-150 1247.5,-156 1247.5,-156 1247.5,-168 1247.5,-168 1247.5,-174 1241.5,-180 1235.5,-180"/>
+<text text-anchor="middle" x="1149.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+</g>
+<!-- 18->7 -->
+<g id="edge20" class="edge">
+<title>18->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1089.88,-143.97C1055.05,-134.01 1010.92,-121.41 974.46,-110.99"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="974.96,-107.49 964.39,-108.11 973.04,-114.22 974.96,-107.49"/>
+</g>
+<!-- 19->10 -->
+<g id="edge27" class="edge">
+<title>19->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M678.25,-215.95C660.75,-207.98 643.72,-196.47 633.5,-180 625.06,-166.41 624.96,-157.53 633.5,-144 643.3,-128.45 659.06,-117.37 675.66,-109.51"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="677.17,-112.67 684.94,-105.46 674.37,-106.25 677.17,-112.67"/>
+</g>
+<!-- 19->16 -->
+<g id="edge31" class="edge">
+<title>19->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M786.25,-215.88C812.26,-206.14 845.03,-193.87 872.45,-183.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="873.76,-186.85 881.9,-180.07 871.31,-180.3 873.76,-186.85"/>
+</g>
+<!-- 20->11 -->
+<g id="edge28" class="edge">
+<title>20->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1016.09,-224.44C1073.05,-215.1 1165.94,-199.16 1255.2,-180.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1256.17,-183.58 1265.22,-178.07 1254.71,-176.74 1256.17,-183.58"/>
+</g>
+<!-- 20->18 -->
+<g id="edge32" class="edge">
+<title>20->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1008.25,-215.88C1034.26,-206.14 1067.03,-193.87 1094.45,-183.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1095.76,-186.85 1103.9,-180.07 1093.31,-180.3 1095.76,-186.85"/>
</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"/>
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M475,-396C475,-396 332,-396 332,-396 326,-396 320,-390 320,-384 320,-384 320,-372 320,-372 320,-366 326,-360 332,-360 332,-360 475,-360 475,-360 481,-360 487,-366 487,-372 487,-372 487,-384 487,-384 487,-390 481,-396 475,-396"/>
+<text text-anchor="middle" x="403.5" y="-375.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 21->12 -->
+<g id="edge29" class="edge">
+<title>21->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M403.5,-359.7C403.5,-351.98 403.5,-342.71 403.5,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="407,-334.1 403.5,-324.1 400,-334.1 407,-334.1"/>
+</g>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M644.5,-396C644.5,-396 518.5,-396 518.5,-396 512.5,-396 506.5,-390 506.5,-384 506.5,-384 506.5,-372 506.5,-372 506.5,-366 512.5,-360 518.5,-360 518.5,-360 644.5,-360 644.5,-360 650.5,-360 656.5,-366 656.5,-372 656.5,-372 656.5,-384 656.5,-384 656.5,-390 650.5,-396 644.5,-396"/>
+<text text-anchor="middle" x="581.5" y="-375.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 22->14 -->
+<g id="edge30" class="edge">
+<title>22->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M581.5,-359.7C581.5,-351.98 581.5,-342.71 581.5,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="585,-334.1 581.5,-324.1 578,-334.1 585,-334.1"/>
+</g>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M847.5,-324C847.5,-324 767.5,-324 767.5,-324 761.5,-324 755.5,-318 755.5,-312 755.5,-312 755.5,-300 755.5,-300 755.5,-294 761.5,-288 767.5,-288 767.5,-288 847.5,-288 847.5,-288 853.5,-288 859.5,-294 859.5,-300 859.5,-300 859.5,-312 859.5,-312 859.5,-318 853.5,-324 847.5,-324"/>
+<text text-anchor="middle" x="807.5" y="-303.5" font-family="sans" font-size="10.00">create_index_star</text>
+</g>
+<!-- 23->19 -->
+<g id="edge34" class="edge">
+<title>23->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M790.94,-287.7C782.82,-279.22 772.91,-268.86 764.03,-259.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="766.31,-256.91 756.87,-252.1 761.26,-261.75 766.31,-256.91"/>
+</g>
+<!-- 23->20 -->
+<g id="edge36" class="edge">
+<title>23->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M845.42,-287.88C866.51,-278.35 892.96,-266.41 915.37,-256.28"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="917.03,-259.37 924.71,-252.07 914.15,-252.99 917.03,-259.37"/>
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diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index d5d5e83..1e0704d 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -78,3 +78,11 @@ 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
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str1.out.bg
+c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str2.out.bg
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str1.out.bg
+c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str2.out.bg
+ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str1.out.bg
+ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg
+ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
+ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index a0d87d1..7cccff1 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -338,3 +338,59 @@ rule pe_genome_quantification_kallisto:
{params.directionality} \
{input.reads1} {input.reads2} > {output.pseudoalignment}) &> {log}"
+rule star_rpm_paired_end:
+ ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
+ input:
+ bam = os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam")
+ output:
+ str1 = (os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str1.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str1.out.bg")),
+ str2 = (os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str2.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str2.out.bg"))
+ params:
+ out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
+ prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
+ str(wildcards.sample) + "_"),
+ stranded = "Stranded"
+ singularity:
+ "docker://zavolab/star:2.6.0a"
+ log: os.path.join(config["log_dir"], "paired_end", "{sample}", "star_rpm_paired_end.log")
+ threads: 4
+ shell:
+ """
+ (mkdir -p {params.out_dir}; \
+ chmod -R 777 {params.out_dir}; \
+ STAR \
+ --runMode inputAlignmentsFromBAM \
+ --runThreadN {threads} \
+ --inputBAMfile {input.bam} \
+ --outWigType "bedGraph" \
+ --outWigStrand "{params.stranded}" \
+ --outWigNorm "RPM" \
+ --outFileNamePrefix {params.prefix}) &> {log}
+ """
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index aa0ed10..352484e 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -264,3 +264,59 @@ rule genome_quantification_kallisto:
{params.directionality} \
{input.reads} > {output.pseudoalignment}) &> {log}"
+rule star_rpm_single_end:
+ ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
+ input:
+ bam = os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam")
+ output:
+ str1 = (os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str1.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str1.out.bg")),
+ str2 = (os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str2.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str2.out.bg"))
+ params:
+ out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
+ prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
+ str(wildcards.sample) + "_"),
+ stranded = "Stranded"
+ singularity:
+ "docker://zavolab/star:2.6.0a"
+ log: os.path.join(config["log_dir"], "single_end", "{sample}", "star_rpm_single_end.log")
+ threads: 4
+ shell:
+ """
+ (mkdir -p {params.out_dir}; \
+ chmod -R 777 {params.out_dir}; \
+ STAR \
+ --runMode inputAlignmentsFromBAM \
+ --runThreadN {threads} \
+ --inputBAMfile {input.bam} \
+ --outWigType "bedGraph" \
+ --outWigStrand {params.stranded} \
+ --outWigNorm "RPM" \
+ --outFileNamePrefix {params.prefix}) &> {log}
+ """
--
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