From 4e3cac0553b7f7057922d56e9fff3905c8a2ebff Mon Sep 17 00:00:00 2001
From: BIOPZ-Bak Maciej <maciej.bak@unibas.ch>
Date: Wed, 25 Mar 2020 20:44:29 +0100
Subject: [PATCH] Update salmon transcriptome index generation
---
Snakefile | 94 +-
images/dag_test_workflow.svg | 951 ++++++++----------
images/rule_graph.svg | 622 ++++++------
pipeline_documentation.md | 20 +-
tests/input_files/cluster.json | 12 +
.../expected_output.md5 | 2 +-
6 files changed, 829 insertions(+), 872 deletions(-)
diff --git a/Snakefile b/Snakefile
index cd36e9f..48e0b61 100644
--- a/Snakefile
+++ b/Snakefile
@@ -121,6 +121,7 @@ rule create_index_star:
--sjdbGTFfile {input.gtf}) \
1> {log.stdout} 2> {log.stderr}"
+
rule extract_transcriptome:
""" Create transcriptome from genome and gene annotations """
input:
@@ -154,9 +155,49 @@ rule extract_transcriptome:
-g {input.genome} {input.gtf}) \
1> {log.stdout} 2> {log.stderr}"
-rule create_index_salmon:
+
+rule extract_decoys_salmon:
"""
- Create index for Salmon quantification
+ Extract names of the genome targets
+ """
+ input:
+ genome = lambda wildcards:
+ samples_table['genome']
+ [samples_table['organism'] == wildcards.organism]
+ [0],
+
+ output:
+ decoys = os.path.join(
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "decoys.txt")
+
+ singularity:
+ "docker://bash:5.0.16"
+
+ log:
+ stderr = os.path.join(
+ config['log_dir'],
+ "{organism}_extract_decoys_salmon.stderr.log"),
+ stdout = os.path.join(
+ config['log_dir'],
+ "{organism}_extract_decoys_salmon.stdout.log")
+
+ threads: 1
+
+ shell:
+ """
+ (grep "^>" <{input.genome} \
+ | cut -d " " -f 1 > {output.decoys} && \
+ sed -i.bak -e 's/>//g' {output.decoys}) \
+ 1> {log.stdout} 2> {log.stderr}
+ """
+
+
+rule concatenate_transcriptome_and_genome:
+ """
+ Concatenate genome and transcriptome
"""
input:
transcriptome = os.path.join(
@@ -164,7 +205,53 @@ rule create_index_salmon:
"transcriptome",
"{organism}",
"transcriptome.fa",
+ ),
+ genome = lambda wildcards:
+ samples_table['genome']
+ [samples_table['organism'] == wildcards.organism]
+ [0],
+
+ output:
+ genome_transcriptome = os.path.join(
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "genome_transcriptome.fa",
)
+
+ singularity:
+ "docker://bash:5.0.16"
+
+ log:
+ stderr = os.path.join(
+ config['log_dir'],
+ "{organism}_concatenate_transcriptome_and_genome.stderr.log"),
+ stdout = os.path.join(
+ config['log_dir'],
+ "{organism}_concatenate_transcriptome_and_genome.stdout.log")
+
+ shell:
+ "(cat {input.transcriptome} {input.genome} \
+ 1> {output.genome_transcriptome}) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
+rule create_index_salmon:
+ """
+ Create index for Salmon quantification
+ """
+ input:
+ genome_transcriptome = os.path.join(
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "genome_transcriptome.fa",
+ ),
+ decoys = os.path.join(
+ config['output_dir'],
+ "transcriptome",
+ "{organism}",
+ "decoys.txt")
output:
index = directory(
os.path.join(
@@ -191,7 +278,8 @@ rule create_index_salmon:
shell:
"(salmon index \
- --transcripts {input.transcriptome} \
+ --transcripts {input.genome_transcriptome} \
+ --decoys {input.decoys} \
--index {output.index} \
--kmerLen {params.kmerLen} \
--threads {threads}) \
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index b4b01ad..11a9781 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,740 +1,641 @@
<?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 2.40.1 (20161225.0304)
+<!-- Generated by graphviz version 2.38.0 (20140413.2041)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="2395pt" height="913pt"
- viewBox="0.00 0.00 2395.06 913.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="2252pt" height="913pt"
+ viewBox="0.00 0.00 2252.45 913.00" 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(4 909)">
<title>snakemake_dag</title>
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+<polygon fill="white" stroke="none" points="-4,4 -4,-909 2248.45,-909 2248.45,4 -4,4"/>
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-<text text-anchor="middle" x="1272.5" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
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-<title>1</title>
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-<text text-anchor="middle" x="1272.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">MULTIQC_report</text>
+<g id="node2" class="node"><title>1</title>
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-<title>1->0</title>
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+<g id="edge1" class="edge"><title>1->0</title>
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<!-- 2->1 -->
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-<title>2->1</title>
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+<g id="edge2" class="edge"><title>2->1</title>
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-<text text-anchor="middle" x="1272.5" y="-226" font-family="sans" font-size="10.00" fill="#000000">output_dir: results</text>
+<g id="node4" class="node"><title>3</title>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M1198.5,-252C1198.5,-252 1103.5,-252 1103.5,-252 1097.5,-252 1091.5,-246 1091.5,-240 1091.5,-240 1091.5,-228 1091.5,-228 1091.5,-222 1097.5,-216 1103.5,-216 1103.5,-216 1198.5,-216 1198.5,-216 1204.5,-216 1210.5,-222 1210.5,-228 1210.5,-228 1210.5,-240 1210.5,-240 1210.5,-246 1204.5,-252 1198.5,-252"/>
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<!-- 3->2 -->
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-<title>3->2</title>
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+<g id="edge3" class="edge"><title>3->2</title>
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-<text text-anchor="middle" x="162.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node5" class="node"><title>4</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M280,-324C280,-324 12,-324 12,-324 6,-324 0,-318 0,-312 0,-312 0,-300 0,-300 0,-294 6,-288 12,-288 12,-288 280,-288 280,-288 286,-288 292,-294 292,-300 292,-300 292,-312 292,-312 292,-318 286,-324 280,-324"/>
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+<text text-anchor="middle" x="146" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
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-<title>4->3</title>
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+<path fill="none" stroke="#d86656" stroke-width="2" d="M1449.5,-396C1449.5,-396 1384.5,-396 1384.5,-396 1378.5,-396 1372.5,-390 1372.5,-384 1372.5,-384 1372.5,-372 1372.5,-372 1372.5,-366 1378.5,-360 1384.5,-360 1384.5,-360 1449.5,-360 1449.5,-360 1455.5,-360 1461.5,-366 1461.5,-372 1461.5,-372 1461.5,-384 1461.5,-384 1461.5,-390 1455.5,-396 1449.5,-396"/>
+<text text-anchor="middle" x="1417" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
</g>
<!-- 8->3 -->
-<g id="edge8" class="edge">
-<title>8->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1484.4705,-359.7055C1489.6974,-339.8988 1494.2501,-308.4109 1478.5,-288 1462.4863,-267.2475 1401.0119,-252.9172 1349.3505,-244.2616"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1349.5975,-240.7558 1339.1655,-242.6059 1348.4743,-247.6652 1349.5975,-240.7558"/>
+<g id="edge8" class="edge"><title>8->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1410.19,-359.799C1401.28,-339.516 1383.69,-306.261 1358,-288 1317.83,-259.444 1263.61,-246.253 1220.74,-240.17"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1221.03,-236.678 1210.66,-238.84 1220.11,-243.618 1221.03,-236.678"/>
</g>
<!-- 9 -->
-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M1068.5,-324C1068.5,-324 940.5,-324 940.5,-324 934.5,-324 928.5,-318 928.5,-312 928.5,-312 928.5,-300 928.5,-300 928.5,-294 934.5,-288 940.5,-288 940.5,-288 1068.5,-288 1068.5,-288 1074.5,-288 1080.5,-294 1080.5,-300 1080.5,-300 1080.5,-312 1080.5,-312 1080.5,-318 1074.5,-324 1068.5,-324"/>
-<text text-anchor="middle" x="1004.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1004.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M794,-324C794,-324 682,-324 682,-324 676,-324 670,-318 670,-312 670,-312 670,-300 670,-300 670,-294 676,-288 682,-288 682,-288 794,-288 794,-288 800,-288 806,-294 806,-300 806,-300 806,-312 806,-312 806,-318 800,-324 794,-324"/>
+<text text-anchor="middle" x="738" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="738" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
<!-- 9->3 -->
-<g id="edge9" class="edge">
-<title>9->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1071.7818,-287.9243C1109.5176,-277.7863 1156.7309,-265.1022 1195.8851,-254.5831"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1196.9058,-257.9331 1205.6553,-251.9583 1195.0896,-251.1728 1196.9058,-257.9331"/>
+<g id="edge9" class="edge"><title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M806.017,-289.934C809.389,-289.263 812.731,-288.614 816,-288 907.236,-270.855 1013.15,-254.726 1081.06,-244.865"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1081.82,-248.292 1091.21,-243.396 1080.82,-241.364 1081.82,-248.292"/>
</g>
<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M1248,-324C1248,-324 1111,-324 1111,-324 1105,-324 1099,-318 1099,-312 1099,-312 1099,-300 1099,-300 1099,-294 1105,-288 1111,-288 1111,-288 1248,-288 1248,-288 1254,-288 1260,-294 1260,-300 1260,-300 1260,-312 1260,-312 1260,-318 1254,-324 1248,-324"/>
-<text text-anchor="middle" x="1179.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1179.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M957.5,-324C957.5,-324 836.5,-324 836.5,-324 830.5,-324 824.5,-318 824.5,-312 824.5,-312 824.5,-300 824.5,-300 824.5,-294 830.5,-288 836.5,-288 836.5,-288 957.5,-288 957.5,-288 963.5,-288 969.5,-294 969.5,-300 969.5,-300 969.5,-312 969.5,-312 969.5,-318 963.5,-324 957.5,-324"/>
+<text text-anchor="middle" x="897" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="897" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
<!-- 10->3 -->
-<g id="edge10" class="edge">
-<title>10->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1202.9678,-287.8314C1214.5327,-278.8779 1228.6404,-267.9558 1241.1183,-258.2955"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1243.275,-261.0521 1249.0397,-252.1628 1238.9898,-255.5171 1243.275,-261.0521"/>
+<g id="edge10" class="edge"><title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M958.811,-287.966C995.746,-277.787 1042.77,-264.826 1081.06,-254.274"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1082.4,-257.537 1091.11,-251.506 1080.54,-250.789 1082.4,-257.537"/>
</g>
<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M1440.5,-324C1440.5,-324 1290.5,-324 1290.5,-324 1284.5,-324 1278.5,-318 1278.5,-312 1278.5,-312 1278.5,-300 1278.5,-300 1278.5,-294 1284.5,-288 1290.5,-288 1290.5,-288 1440.5,-288 1440.5,-288 1446.5,-288 1452.5,-294 1452.5,-300 1452.5,-300 1452.5,-312 1452.5,-312 1452.5,-318 1446.5,-324 1440.5,-324"/>
-<text text-anchor="middle" x="1365.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1365.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1130.5,-324C1130.5,-324 999.5,-324 999.5,-324 993.5,-324 987.5,-318 987.5,-312 987.5,-312 987.5,-300 987.5,-300 987.5,-294 993.5,-288 999.5,-288 999.5,-288 1130.5,-288 1130.5,-288 1136.5,-288 1142.5,-294 1142.5,-300 1142.5,-300 1142.5,-312 1142.5,-312 1142.5,-318 1136.5,-324 1130.5,-324"/>
+<text text-anchor="middle" x="1065" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1065" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
<!-- 11->3 -->
-<g id="edge11" class="edge">
-<title>11->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1342.0322,-287.8314C1330.4673,-278.8779 1316.3596,-267.9558 1303.8817,-258.2955"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1306.0102,-255.5171 1295.9603,-252.1628 1301.725,-261.0521 1306.0102,-255.5171"/>
+<g id="edge11" class="edge"><title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1086.26,-287.697C1097.09,-278.881 1110.42,-268.032 1122.16,-258.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1124.44,-261.132 1129.99,-252.104 1120.02,-255.703 1124.44,-261.132"/>
</g>
<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M898.5,-324C898.5,-324 748.5,-324 748.5,-324 742.5,-324 736.5,-318 736.5,-312 736.5,-312 736.5,-300 736.5,-300 736.5,-294 742.5,-288 748.5,-288 748.5,-288 898.5,-288 898.5,-288 904.5,-288 910.5,-294 910.5,-300 910.5,-300 910.5,-312 910.5,-312 910.5,-318 904.5,-324 898.5,-324"/>
-<text text-anchor="middle" x="823.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="823.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1303.5,-324C1303.5,-324 1172.5,-324 1172.5,-324 1166.5,-324 1160.5,-318 1160.5,-312 1160.5,-312 1160.5,-300 1160.5,-300 1160.5,-294 1166.5,-288 1172.5,-288 1172.5,-288 1303.5,-288 1303.5,-288 1309.5,-288 1315.5,-294 1315.5,-300 1315.5,-300 1315.5,-312 1315.5,-312 1315.5,-318 1309.5,-324 1303.5,-324"/>
+<text text-anchor="middle" x="1238" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1238" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
<!-- 12->3 -->
-<g id="edge12" class="edge">
-<title>12->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M910.5981,-289.5372C913.6005,-289.0118 916.5746,-288.4979 919.5,-288 1014.3082,-271.8648 1123.8293,-255.4566 1195.4227,-245.0306"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1196.3115,-248.4383 1205.7042,-243.5365 1195.3048,-241.5111 1196.3115,-248.4383"/>
+<g id="edge12" class="edge"><title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1216.49,-287.697C1205.54,-278.881 1192.05,-268.032 1180.18,-258.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1182.24,-255.646 1172.26,-252.104 1177.86,-261.1 1182.24,-255.646"/>
</g>
<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1732.5,-612C1732.5,-612 1696.5,-612 1696.5,-612 1690.5,-612 1684.5,-606 1684.5,-600 1684.5,-600 1684.5,-588 1684.5,-588 1684.5,-582 1690.5,-576 1696.5,-576 1696.5,-576 1732.5,-576 1732.5,-576 1738.5,-576 1744.5,-582 1744.5,-588 1744.5,-588 1744.5,-600 1744.5,-600 1744.5,-606 1738.5,-612 1732.5,-612"/>
-<text text-anchor="middle" x="1714.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1973.5,-612C1973.5,-612 1942.5,-612 1942.5,-612 1936.5,-612 1930.5,-606 1930.5,-600 1930.5,-600 1930.5,-588 1930.5,-588 1930.5,-582 1936.5,-576 1942.5,-576 1942.5,-576 1973.5,-576 1973.5,-576 1979.5,-576 1985.5,-582 1985.5,-588 1985.5,-588 1985.5,-600 1985.5,-600 1985.5,-606 1979.5,-612 1973.5,-612"/>
+<text text-anchor="middle" x="1958" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 13->3 -->
-<g id="edge13" class="edge">
-<title>13->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1684.3802,-579.7846C1681.3949,-578.4704 1678.398,-577.1878 1675.5,-576 1631.7921,-558.0856 1606.528,-575.617 1575.5,-540 1548.6464,-509.1748 1556.5,-490.8816 1556.5,-450 1556.5,-450 1556.5,-450 1556.5,-378 1556.5,-284.7709 1433.2511,-251.882 1349.1381,-240.2921"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1349.4539,-236.8038 1339.0854,-238.9817 1348.549,-243.745 1349.4539,-236.8038"/>
+<g id="edge13" class="edge"><title>13->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1985.7,-591.233C2046.65,-586.769 2189.61,-572.961 2223,-540 2251.78,-511.585 2242,-491.447 2242,-451 2242,-451 2242,-451 2242,-377 2242,-273.61 1461.59,-243.532 1220.86,-236.713"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1220.91,-233.214 1210.82,-236.434 1220.72,-240.211 1220.91,-233.214"/>
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-<!-- 40 -->
-<g id="node41" class="node">
-<title>40</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M1882.5,-540C1882.5,-540 1760.5,-540 1760.5,-540 1754.5,-540 1748.5,-534 1748.5,-528 1748.5,-528 1748.5,-516 1748.5,-516 1748.5,-510 1754.5,-504 1760.5,-504 1760.5,-504 1882.5,-504 1882.5,-504 1888.5,-504 1894.5,-510 1894.5,-516 1894.5,-516 1894.5,-528 1894.5,-528 1894.5,-534 1888.5,-540 1882.5,-540"/>
-<text text-anchor="middle" x="1821.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1821.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
-</g>
-<!-- 13->40 -->
-<g id="edge69" class="edge">
-<title>13->40</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1741.5006,-575.8314C1754.9331,-566.7927 1771.3473,-555.7476 1785.8039,-546.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1788.1654,-548.6494 1794.508,-540.1628 1784.2575,-542.8418 1788.1654,-548.6494"/>
-</g>
-<!-- 43 -->
-<g id="node44" class="node">
-<title>43</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M1718.5,-540C1718.5,-540 1596.5,-540 1596.5,-540 1590.5,-540 1584.5,-534 1584.5,-528 1584.5,-528 1584.5,-516 1584.5,-516 1584.5,-510 1590.5,-504 1596.5,-504 1596.5,-504 1718.5,-504 1718.5,-504 1724.5,-504 1730.5,-510 1730.5,-516 1730.5,-516 1730.5,-528 1730.5,-528 1730.5,-534 1724.5,-540 1718.5,-540"/>
-<text text-anchor="middle" x="1657.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1657.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
-</g>
-<!-- 13->43 -->
-<g id="edge72" class="edge">
-<title>13->43</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1700.1165,-575.8314C1693.5514,-567.5386 1685.6493,-557.557 1678.4422,-548.4533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1681.0284,-546.0813 1672.0772,-540.4133 1675.5401,-550.4262 1681.0284,-546.0813"/>
+<!-- 42 -->
+<g id="node43" class="node"><title>42</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M2202,-540C2202,-540 2096,-540 2096,-540 2090,-540 2084,-534 2084,-528 2084,-528 2084,-516 2084,-516 2084,-510 2090,-504 2096,-504 2096,-504 2202,-504 2202,-504 2208,-504 2214,-510 2214,-516 2214,-516 2214,-528 2214,-528 2214,-534 2208,-540 2202,-540"/>
+<text text-anchor="middle" x="2149" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="2149" y="-514" font-family="sans" font-size="10.00">unique: Unique</text>
+</g>
+<!-- 13->42 -->
+<g id="edge71" class="edge"><title>13->42</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1985.77,-582.821C2013.67,-572.597 2057.46,-556.549 2092.66,-543.648"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2094.16,-546.828 2102.34,-540.1 2091.75,-540.255 2094.16,-546.828"/>
+</g>
+<!-- 45 -->
+<g id="node46" class="node"><title>45</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1932,-540C1932,-540 1826,-540 1826,-540 1820,-540 1814,-534 1814,-528 1814,-528 1814,-516 1814,-516 1814,-510 1820,-504 1826,-504 1826,-504 1932,-504 1932,-504 1938,-504 1944,-510 1944,-516 1944,-516 1944,-528 1944,-528 1944,-534 1938,-540 1932,-540"/>
+<text text-anchor="middle" x="1879" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1879" y="-514" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
+</g>
+<!-- 13->45 -->
+<g id="edge74" class="edge"><title>13->45</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1938.47,-575.697C1928.62,-566.965 1916.51,-556.24 1905.8,-546.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1908.11,-544.117 1898.3,-540.104 1903.47,-549.356 1908.11,-544.117"/>
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-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M2094.5,-612C2094.5,-612 2058.5,-612 2058.5,-612 2052.5,-612 2046.5,-606 2046.5,-600 2046.5,-600 2046.5,-588 2046.5,-588 2046.5,-582 2052.5,-576 2058.5,-576 2058.5,-576 2094.5,-576 2094.5,-576 2100.5,-576 2106.5,-582 2106.5,-588 2106.5,-588 2106.5,-600 2106.5,-600 2106.5,-606 2100.5,-612 2094.5,-612"/>
-<text text-anchor="middle" x="2076.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1652.5,-612C1652.5,-612 1621.5,-612 1621.5,-612 1615.5,-612 1609.5,-606 1609.5,-600 1609.5,-600 1609.5,-588 1609.5,-588 1609.5,-582 1615.5,-576 1621.5,-576 1621.5,-576 1652.5,-576 1652.5,-576 1658.5,-576 1664.5,-582 1664.5,-588 1664.5,-588 1664.5,-600 1664.5,-600 1664.5,-606 1658.5,-612 1652.5,-612"/>
+<text text-anchor="middle" x="1637" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
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<!-- 14->3 -->
-<g id="edge14" class="edge">
-<title>14->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2106.6958,-592.4989C2173.1349,-588.564 2328.9892,-575.6686 2365.5,-540 2394.743,-511.4316 2384.5,-490.8816 2384.5,-450 2384.5,-450 2384.5,-450 2384.5,-378 2384.5,-273.4167 1600.9215,-242.9453 1349.2964,-235.8564"/>
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-<!-- 42 -->
-<g id="node43" class="node">
-<title>42</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M2344.5,-540C2344.5,-540 2222.5,-540 2222.5,-540 2216.5,-540 2210.5,-534 2210.5,-528 2210.5,-528 2210.5,-516 2210.5,-516 2210.5,-510 2216.5,-504 2222.5,-504 2222.5,-504 2344.5,-504 2344.5,-504 2350.5,-504 2356.5,-510 2356.5,-516 2356.5,-516 2356.5,-528 2356.5,-528 2356.5,-534 2350.5,-540 2344.5,-540"/>
-<text text-anchor="middle" x="2283.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="2283.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
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-<g id="edge71" class="edge">
-<title>14->42</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2106.5996,-583.5306C2136.7838,-573.0317 2184.1277,-556.5643 2222.2442,-543.3064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2223.4248,-546.6015 2231.72,-540.0104 2221.1252,-539.99 2223.4248,-546.6015"/>
+<g id="edge14" class="edge"><title>14->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1609.19,-580.028C1606.1,-578.645 1602.99,-577.277 1600,-576 1560,-558.914 1537.09,-573.204 1509,-540 1482.88,-509.122 1490,-491.447 1490,-451 1490,-451 1490,-451 1490,-377 1490,-261.448 1320.37,-238.32 1221.09,-234.678"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1220.93,-231.172 1210.83,-234.362 1220.71,-238.168 1220.93,-231.172"/>
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<!-- 44 -->
-<g id="node45" class="node">
-<title>44</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M2046.5,-540C2046.5,-540 1924.5,-540 1924.5,-540 1918.5,-540 1912.5,-534 1912.5,-528 1912.5,-528 1912.5,-516 1912.5,-516 1912.5,-510 1918.5,-504 1924.5,-504 1924.5,-504 2046.5,-504 2046.5,-504 2052.5,-504 2058.5,-510 2058.5,-516 2058.5,-516 2058.5,-528 2058.5,-528 2058.5,-534 2052.5,-540 2046.5,-540"/>
-<text text-anchor="middle" x="1985.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1985.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
+<g id="node45" class="node"><title>44</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1784,-540C1784,-540 1678,-540 1678,-540 1672,-540 1666,-534 1666,-528 1666,-528 1666,-516 1666,-516 1666,-510 1672,-504 1678,-504 1678,-504 1784,-504 1784,-504 1790,-504 1796,-510 1796,-516 1796,-516 1796,-528 1796,-528 1796,-534 1790,-540 1784,-540"/>
+<text text-anchor="middle" x="1731" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1731" y="-514" font-family="sans" font-size="10.00">unique: Unique</text>
</g>
<!-- 14->44 -->
-<g id="edge73" class="edge">
-<title>14->44</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2053.5369,-575.8314C2042.3285,-566.9632 2028.6791,-556.1637 2016.5561,-546.5718"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2018.4697,-543.6229 2008.4558,-540.1628 2014.1263,-549.1125 2018.4697,-543.6229"/>
+<g id="edge73" class="edge"><title>14->44</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1660.24,-575.697C1672.19,-566.796 1686.92,-555.823 1699.85,-546.199"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1702.1,-548.884 1708.03,-540.104 1697.92,-543.27 1702.1,-548.884"/>
+</g>
+<!-- 46 -->
+<g id="node47" class="node"><title>46</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1636,-540C1636,-540 1530,-540 1530,-540 1524,-540 1518,-534 1518,-528 1518,-528 1518,-516 1518,-516 1518,-510 1524,-504 1530,-504 1530,-504 1636,-504 1636,-504 1642,-504 1648,-510 1648,-516 1648,-516 1648,-528 1648,-528 1648,-534 1642,-540 1636,-540"/>
+<text text-anchor="middle" x="1583" y="-525" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1583" y="-514" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
+</g>
+<!-- 14->46 -->
+<g id="edge75" class="edge"><title>14->46</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1623.65,-575.697C1617.24,-567.389 1609.44,-557.277 1602.39,-548.141"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1605.07,-545.884 1596.19,-540.104 1599.53,-550.16 1605.07,-545.884"/>
</g>
<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1892,-324C1892,-324 1805,-324 1805,-324 1799,-324 1793,-318 1793,-312 1793,-312 1793,-300 1793,-300 1793,-294 1799,-288 1805,-288 1805,-288 1892,-288 1892,-288 1898,-288 1904,-294 1904,-300 1904,-300 1904,-312 1904,-312 1904,-318 1898,-324 1892,-324"/>
-<text text-anchor="middle" x="1848.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M1780.5,-324C1780.5,-324 1703.5,-324 1703.5,-324 1697.5,-324 1691.5,-318 1691.5,-312 1691.5,-312 1691.5,-300 1691.5,-300 1691.5,-294 1697.5,-288 1703.5,-288 1703.5,-288 1780.5,-288 1780.5,-288 1786.5,-288 1792.5,-294 1792.5,-300 1792.5,-300 1792.5,-312 1792.5,-312 1792.5,-318 1786.5,-324 1780.5,-324"/>
+<text text-anchor="middle" x="1742" y="-303.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
</g>
<!-- 15->3 -->
-<g id="edge15" class="edge">
-<title>15->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1792.7473,-299.0309C1689.1854,-286.0857 1466.9881,-258.311 1349.2964,-243.5996"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1349.6346,-240.1147 1339.2776,-242.3472 1348.7663,-247.0606 1349.6346,-240.1147"/>
+<g id="edge15" class="edge"><title>15->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1691.36,-299.002C1585.68,-286.485 1341.54,-257.568 1220.96,-243.287"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1221.09,-239.777 1210.74,-242.076 1220.26,-246.728 1221.09,-239.777"/>
</g>
<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1032.5,-830.5C1032.5,-830.5 904.5,-830.5 904.5,-830.5 898.5,-830.5 892.5,-824.5 892.5,-818.5 892.5,-818.5 892.5,-806.5 892.5,-806.5 892.5,-800.5 898.5,-794.5 904.5,-794.5 904.5,-794.5 1032.5,-794.5 1032.5,-794.5 1038.5,-794.5 1044.5,-800.5 1044.5,-806.5 1044.5,-806.5 1044.5,-818.5 1044.5,-818.5 1044.5,-824.5 1038.5,-830.5 1032.5,-830.5"/>
-<text text-anchor="middle" x="968.5" y="-810" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M1322,-830.5C1322,-830.5 1210,-830.5 1210,-830.5 1204,-830.5 1198,-824.5 1198,-818.5 1198,-818.5 1198,-806.5 1198,-806.5 1198,-800.5 1204,-794.5 1210,-794.5 1210,-794.5 1322,-794.5 1322,-794.5 1328,-794.5 1334,-800.5 1334,-806.5 1334,-806.5 1334,-818.5 1334,-818.5 1334,-824.5 1328,-830.5 1322,-830.5"/>
+<text text-anchor="middle" x="1266" y="-810" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 16->6 -->
-<g id="edge16" class="edge">
-<title>16->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M948.7584,-794.2151C923.0897,-768.348 881.5,-718.3581 881.5,-666 881.5,-666 881.5,-666 881.5,-522 881.5,-478.8617 859.4001,-433.0945 842.9668,-405.0255"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="845.8137,-402.9688 837.6512,-396.2143 839.82,-406.5847 845.8137,-402.9688"/>
+<g id="edge16" class="edge"><title>16->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1266,-794.151C1266,-767.022 1266,-712.909 1266,-667 1266,-667 1266,-667 1266,-593 1266,-549.905 1288.6,-504.262 1305.08,-476.697"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1308.13,-478.421 1310.4,-468.072 1302.17,-474.749 1308.13,-478.421"/>
</g>
<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M1067.5,-396C1067.5,-396 949.5,-396 949.5,-396 943.5,-396 937.5,-390 937.5,-384 937.5,-384 937.5,-372 937.5,-372 937.5,-366 943.5,-360 949.5,-360 949.5,-360 1067.5,-360 1067.5,-360 1073.5,-360 1079.5,-366 1079.5,-372 1079.5,-372 1079.5,-384 1079.5,-384 1079.5,-390 1073.5,-396 1067.5,-396"/>
-<text text-anchor="middle" x="1008.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M1108.5,-396C1108.5,-396 1005.5,-396 1005.5,-396 999.5,-396 993.5,-390 993.5,-384 993.5,-384 993.5,-372 993.5,-372 993.5,-366 999.5,-360 1005.5,-360 1005.5,-360 1108.5,-360 1108.5,-360 1114.5,-360 1120.5,-366 1120.5,-372 1120.5,-372 1120.5,-384 1120.5,-384 1120.5,-390 1114.5,-396 1108.5,-396"/>
+<text text-anchor="middle" x="1057" y="-375.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
<!-- 16->20 -->
-<g id="edge40" class="edge">
-<title>16->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M968.5,-794.4571C968.5,-766.8072 968.5,-712.2899 968.5,-666 968.5,-666 968.5,-666 968.5,-522 968.5,-480.2219 984.324,-434.0316 996.0664,-405.5067"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="999.3354,-406.7629 1000.017,-396.19 992.8908,-404.0301 999.3354,-406.7629"/>
+<g id="edge40" class="edge"><title>16->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1258.31,-794.093C1247.21,-767.328 1228,-714.21 1228,-667 1228,-667 1228,-667 1228,-593 1228,-552.553 1230.02,-538.557 1209,-504 1181.67,-459.06 1132.24,-422.965 1097.17,-401.329"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1098.96,-398.319 1088.59,-396.144 1095.34,-404.31 1098.96,-398.319"/>
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<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1716,-756C1716,-756 1615,-756 1615,-756 1609,-756 1603,-750 1603,-744 1603,-744 1603,-732 1603,-732 1603,-726 1609,-720 1615,-720 1615,-720 1716,-720 1716,-720 1722,-720 1728,-726 1728,-732 1728,-732 1728,-744 1728,-744 1728,-750 1722,-756 1716,-756"/>
-<text text-anchor="middle" x="1665.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1822.5,-756C1822.5,-756 1733.5,-756 1733.5,-756 1727.5,-756 1721.5,-750 1721.5,-744 1721.5,-744 1721.5,-732 1721.5,-732 1721.5,-726 1727.5,-720 1733.5,-720 1733.5,-720 1822.5,-720 1822.5,-720 1828.5,-720 1834.5,-726 1834.5,-732 1834.5,-732 1834.5,-744 1834.5,-744 1834.5,-750 1828.5,-756 1822.5,-756"/>
+<text text-anchor="middle" x="1778" y="-735.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 16->22 -->
-<g id="edge45" class="edge">
-<title>16->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1044.7512,-804.3498C1180.0467,-789.8885 1460.31,-759.9321 1592.9272,-745.7571"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1593.4149,-749.225 1602.9863,-744.6819 1592.6709,-742.2646 1593.4149,-749.225"/>
+<g id="edge45" class="edge"><title>16->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1334.25,-801.835C1432.73,-787.891 1613.53,-762.29 1711.19,-748.46"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1711.83,-751.905 1721.24,-747.037 1710.85,-744.974 1711.83,-751.905"/>
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<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M1245,-468C1245,-468 1148,-468 1148,-468 1142,-468 1136,-462 1136,-456 1136,-456 1136,-444 1136,-444 1136,-438 1142,-432 1148,-432 1148,-432 1245,-432 1245,-432 1251,-432 1257,-438 1257,-444 1257,-444 1257,-456 1257,-456 1257,-462 1251,-468 1245,-468"/>
-<text text-anchor="middle" x="1196.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M1188,-540C1188,-540 1104,-540 1104,-540 1098,-540 1092,-534 1092,-528 1092,-528 1092,-516 1092,-516 1092,-510 1098,-504 1104,-504 1104,-504 1188,-504 1188,-504 1194,-504 1200,-510 1200,-516 1200,-516 1200,-528 1200,-528 1200,-534 1194,-540 1188,-540"/>
+<text text-anchor="middle" x="1146" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 17->6 -->
-<g id="edge17" class="edge">
-<title>17->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1135.8593,-434.1133C1132.6991,-433.3773 1129.5651,-432.6681 1126.5,-432 1107.1924,-427.7918 1008.5364,-410.2141 929.3559,-396.241"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="929.7669,-392.7595 919.3109,-394.4692 928.5509,-399.6531 929.7669,-392.7595"/>
+<g id="edge17" class="edge"><title>17->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1189.05,-503.876C1213.33,-494.222 1243.84,-482.087 1269.51,-471.878"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1271.09,-475.016 1279.09,-468.068 1268.5,-468.512 1271.09,-475.016"/>
</g>
<!-- 17->7 -->
-<g id="edge19" class="edge">
-<title>17->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1229.3045,-431.8314C1246.0862,-422.5368 1266.6985,-411.1208 1284.6163,-401.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1286.6538,-404.0696 1293.706,-396.1628 1283.2623,-397.9461 1286.6538,-404.0696"/>
+<g id="edge19" class="edge"><title>17->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1091.82,-505.829C1088.85,-505.169 1085.89,-504.553 1083,-504 952.4,-479.05 798.675,-464.292 705.335,-456.922"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="705.339,-453.412 695.097,-456.124 704.795,-460.391 705.339,-453.412"/>
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<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M1378.5,-830.5C1378.5,-830.5 1268.5,-830.5 1268.5,-830.5 1262.5,-830.5 1256.5,-824.5 1256.5,-818.5 1256.5,-818.5 1256.5,-806.5 1256.5,-806.5 1256.5,-800.5 1262.5,-794.5 1268.5,-794.5 1268.5,-794.5 1378.5,-794.5 1378.5,-794.5 1384.5,-794.5 1390.5,-800.5 1390.5,-806.5 1390.5,-806.5 1390.5,-818.5 1390.5,-818.5 1390.5,-824.5 1384.5,-830.5 1378.5,-830.5"/>
-<text text-anchor="middle" x="1323.5" y="-810" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M755,-830.5C755,-830.5 659,-830.5 659,-830.5 653,-830.5 647,-824.5 647,-818.5 647,-818.5 647,-806.5 647,-806.5 647,-800.5 653,-794.5 659,-794.5 659,-794.5 755,-794.5 755,-794.5 761,-794.5 767,-800.5 767,-806.5 767,-806.5 767,-818.5 767,-818.5 767,-824.5 761,-830.5 755,-830.5"/>
+<text text-anchor="middle" x="707" y="-810" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 18->7 -->
-<g id="edge18" class="edge">
-<title>18->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1323.5,-794.4571C1323.5,-766.8072 1323.5,-712.2899 1323.5,-666 1323.5,-666 1323.5,-666 1323.5,-522 1323.5,-481.8673 1324.6792,-435.4566 1325.5589,-406.414"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1329.0645,-406.2872 1325.8784,-396.1828 1322.0679,-406.0687 1329.0645,-406.2872"/>
+<g id="edge18" class="edge"><title>18->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M692.155,-794.122C671.607,-768.23 637,-717.176 637,-667 637,-667 637,-667 637,-593 637,-552.931 630.244,-506.949 625.25,-478.433"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="628.661,-477.627 623.44,-468.408 621.773,-478.871 628.661,-477.627"/>
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<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1211,-396C1211,-396 1110,-396 1110,-396 1104,-396 1098,-390 1098,-384 1098,-384 1098,-372 1098,-372 1098,-366 1104,-360 1110,-360 1110,-360 1211,-360 1211,-360 1217,-360 1223,-366 1223,-372 1223,-372 1223,-384 1223,-384 1223,-390 1217,-396 1211,-396"/>
-<text text-anchor="middle" x="1160.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M948.5,-396C948.5,-396 861.5,-396 861.5,-396 855.5,-396 849.5,-390 849.5,-384 849.5,-384 849.5,-372 849.5,-372 849.5,-366 855.5,-360 861.5,-360 861.5,-360 948.5,-360 948.5,-360 954.5,-360 960.5,-366 960.5,-372 960.5,-372 960.5,-384 960.5,-384 960.5,-390 954.5,-396 948.5,-396"/>
+<text text-anchor="middle" x="905" y="-375.5" font-family="sans" font-size="10.00">quantification_salmon</text>
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<!-- 18->21 -->
-<g id="edge42" class="edge">
-<title>18->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1315.6264,-794.3912C1304.4959,-767.101 1285.5,-713.559 1285.5,-666 1285.5,-666 1285.5,-666 1285.5,-522 1285.5,-481.1184 1291.3659,-464.4499 1266.5,-432 1256.3571,-418.7635 1242.0678,-408.5049 1227.2566,-400.6623"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1228.5151,-397.3802 1217.9995,-396.0865 1225.4131,-403.6554 1228.5151,-397.3802"/>
+<g id="edge42" class="edge"><title>18->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M707,-794.151C707,-767.022 707,-712.909 707,-667 707,-667 707,-667 707,-593 707,-552.553 703.64,-537.704 726,-504 757.754,-456.137 814.637,-421.138 855.772,-400.545"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="857.372,-403.659 864.817,-396.121 854.296,-397.371 857.372,-403.659"/>
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<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
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-<text text-anchor="middle" x="1877.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<g id="node25" class="node"><title>24</title>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M1619.5,-756C1619.5,-756 1546.5,-756 1546.5,-756 1540.5,-756 1534.5,-750 1534.5,-744 1534.5,-744 1534.5,-732 1534.5,-732 1534.5,-726 1540.5,-720 1546.5,-720 1546.5,-720 1619.5,-720 1619.5,-720 1625.5,-720 1631.5,-726 1631.5,-732 1631.5,-732 1631.5,-744 1631.5,-744 1631.5,-750 1625.5,-756 1619.5,-756"/>
+<text text-anchor="middle" x="1583" y="-735.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 18->24 -->
-<g id="edge48" class="edge">
-<title>18->24</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1390.6012,-803.4765C1498.215,-789.0049 1707.988,-760.7954 1813.5612,-746.5983"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1814.3093,-750.0293 1823.7536,-745.2276 1813.3763,-743.0917 1814.3093,-750.0293"/>
+<g id="edge48" class="edge"><title>18->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M767.211,-806.517C927.87,-793.22 1365.27,-757.02 1524.24,-743.863"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1524.63,-747.343 1534.31,-743.03 1524.05,-740.367 1524.63,-747.343"/>
</g>
<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1516,-540C1516,-540 1433,-540 1433,-540 1427,-540 1421,-534 1421,-528 1421,-528 1421,-516 1421,-516 1421,-510 1427,-504 1433,-504 1433,-504 1516,-504 1516,-504 1522,-504 1528,-510 1528,-516 1528,-516 1528,-528 1528,-528 1528,-534 1522,-540 1516,-540"/>
-<text text-anchor="middle" x="1474.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M1450,-540C1450,-540 1374,-540 1374,-540 1368,-540 1362,-534 1362,-528 1362,-528 1362,-516 1362,-516 1362,-510 1368,-504 1374,-504 1374,-504 1450,-504 1450,-504 1456,-504 1462,-510 1462,-516 1462,-516 1462,-528 1462,-528 1462,-534 1456,-540 1450,-540"/>
+<text text-anchor="middle" x="1412" y="-519.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
</g>
<!-- 19->8 -->
-<g id="edge20" class="edge">
-<title>19->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1475.0066,-503.7623C1475.6889,-479.201 1476.9098,-435.2474 1477.7124,-406.3541"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1481.2184,-406.183 1477.9975,-396.0896 1474.2211,-405.9885 1481.2184,-406.183"/>
+<g id="edge20" class="edge"><title>19->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1412.67,-503.815C1413.06,-493.443 1413.57,-479.963 1414,-468 1414.74,-447.272 1415.53,-423.828 1416.11,-406.206"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1419.61,-406.172 1416.45,-396.063 1412.62,-405.942 1419.61,-406.172"/>
</g>
<!-- 20->9 -->
-<g id="edge21" class="edge">
-<title>20->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1007.4906,-359.8314C1007.0628,-352.131 1006.5541,-342.9743 1006.0787,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1009.5724,-334.2037 1005.523,-324.4133 1002.5831,-334.592 1009.5724,-334.2037"/>
+<g id="edge21" class="edge"><title>20->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M993.212,-363.003C942.204,-351.81 870.473,-336.069 816.041,-324.125"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="816.606,-320.666 806.088,-321.941 815.105,-327.503 816.606,-320.666"/>
</g>
<!-- 20->10 -->
-<g id="edge23" class="edge">
-<title>20->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1051.6505,-359.8314C1074.6224,-350.159 1103.0509,-338.1891 1127.2632,-327.9944"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1128.8016,-331.1443 1136.6598,-324.038 1126.0852,-324.6929 1128.8016,-331.1443"/>
+<g id="edge23" class="edge"><title>20->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1017.86,-359.876C995.987,-350.307 968.543,-338.3 945.338,-328.148"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="946.578,-324.87 936.013,-324.068 943.772,-331.283 946.578,-324.87"/>
</g>
<!-- 20->11 -->
-<g id="edge25" class="edge">
-<title>20->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1079.596,-362.0935C1082.9424,-361.3786 1086.2567,-360.6775 1089.5,-360 1148.7676,-347.6189 1215.3792,-334.5617 1268.3127,-324.3886"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1269.2099,-327.7804 1278.3712,-322.4586 1267.8907,-320.9058 1269.2099,-327.7804"/>
+<g id="edge25" class="edge"><title>20->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1058.98,-359.697C1059.86,-351.983 1060.92,-342.712 1061.9,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1065.39,-334.437 1063.05,-324.104 1058.43,-333.642 1065.39,-334.437"/>
</g>
<!-- 20->12 -->
-<g id="edge27" class="edge">
-<title>20->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M961.8167,-359.8314C936.7441,-350.0734 905.6633,-337.977 879.3191,-327.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="880.4362,-324.4033 869.8476,-324.038 877.8973,-330.9266 880.4362,-324.4033"/>
+<g id="edge27" class="edge"><title>20->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1101.28,-359.876C1126.35,-350.179 1157.9,-337.98 1184.37,-327.743"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1185.8,-330.94 1193.87,-324.068 1183.28,-324.411 1185.8,-330.94"/>
</g>
<!-- 21->9 -->
-<g id="edge22" class="edge">
-<title>21->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1121.1346,-359.8314C1100.3633,-350.2446 1074.7017,-338.4008 1052.7419,-328.2655"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1054.1286,-325.0508 1043.5823,-324.038 1051.1952,-331.4065 1054.1286,-325.0508"/>
+<g id="edge22" class="edge"><title>21->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M864.147,-359.876C841.216,-350.264 812.418,-338.193 788.13,-328.013"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="789.296,-324.706 778.72,-324.068 786.59,-331.162 789.296,-324.706"/>
</g>
<!-- 21->10 -->
-<g id="edge24" class="edge">
-<title>21->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1165.2945,-359.8314C1167.3489,-352.0463 1169.796,-342.7729 1172.0756,-334.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1175.4735,-334.9753 1174.6409,-324.4133 1168.7052,-333.1892 1175.4735,-334.9753"/>
+<g id="edge24" class="edge"><title>21->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M903.022,-359.697C902.141,-351.983 901.081,-342.712 900.099,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="903.568,-333.642 898.955,-324.104 896.613,-334.437 903.568,-333.642"/>
</g>
<!-- 21->11 -->
-<g id="edge26" class="edge">
-<title>21->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1211.9655,-359.9243C1239.9902,-350.0815 1274.8484,-337.8386 1304.264,-327.5073"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1305.7381,-330.6992 1314.0133,-324.0831 1303.4184,-324.0947 1305.7381,-330.6992"/>
+<g id="edge26" class="edge"><title>21->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M944.14,-359.876C966.013,-350.307 993.457,-338.3 1016.66,-328.148"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1018.23,-331.283 1025.99,-324.068 1015.42,-324.87 1018.23,-331.283"/>
</g>
<!-- 21->12 -->
-<g id="edge28" class="edge">
-<title>21->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1097.7102,-362.13C1094.5989,-361.3978 1091.5158,-360.6839 1088.5,-360 1033.0156,-347.4177 970.6855,-334.6484 920.4208,-324.6881"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="921.0232,-321.2395 910.5344,-322.7343 919.6661,-328.1067 921.0232,-321.2395"/>
+<g id="edge28" class="edge"><title>21->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M960.512,-365.182C968.722,-363.44 977.081,-361.671 985,-360 1040.05,-348.385 1101.85,-335.436 1150.6,-325.245"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1151.41,-328.652 1160.48,-323.179 1149.97,-321.8 1151.41,-328.652"/>
</g>
<!-- 22->13 -->
-<g id="edge29" class="edge">
-<title>22->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1728.0603,-720.2456C1745.4625,-712.1131 1762.3571,-700.4803 1772.5,-684 1780.8863,-670.3739 1778.8858,-662.6704 1772.5,-648 1767.6585,-636.8773 1759.2717,-627.0106 1750.3561,-618.8541"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1752.3456,-615.9515 1742.4609,-612.138 1747.81,-621.2833 1752.3456,-615.9515"/>
+<g id="edge29" class="edge"><title>22->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1834.89,-734.427C1872.5,-729.541 1919.73,-716.711 1947,-684 1961.13,-667.049 1962.99,-641.583 1961.83,-622.229"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1965.31,-621.847 1960.93,-612.198 1958.33,-622.469 1965.31,-621.847"/>
</g>
<!-- 23 -->
-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1751.5,-684C1751.5,-684 1579.5,-684 1579.5,-684 1573.5,-684 1567.5,-678 1567.5,-672 1567.5,-672 1567.5,-660 1567.5,-660 1567.5,-654 1573.5,-648 1579.5,-648 1579.5,-648 1751.5,-648 1751.5,-648 1757.5,-648 1763.5,-654 1763.5,-660 1763.5,-660 1763.5,-672 1763.5,-672 1763.5,-678 1757.5,-684 1751.5,-684"/>
-<text text-anchor="middle" x="1665.5" y="-669" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1665.5" y="-658" font-family="sans" font-size="10.00" fill="#000000">seqmode: paired_end</text>
+<g id="node24" class="node"><title>23</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1926,-684C1926,-684 1776,-684 1776,-684 1770,-684 1764,-678 1764,-672 1764,-672 1764,-660 1764,-660 1764,-654 1770,-648 1776,-648 1776,-648 1926,-648 1926,-648 1932,-648 1938,-654 1938,-660 1938,-660 1938,-672 1938,-672 1938,-678 1932,-684 1926,-684"/>
+<text text-anchor="middle" x="1851" y="-669" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1851" y="-658" font-family="sans" font-size="10.00">seqmode: paired_end</text>
</g>
<!-- 22->23 -->
-<g id="edge46" class="edge">
-<title>22->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1665.5,-719.8314C1665.5,-712.131 1665.5,-702.9743 1665.5,-694.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1669.0001,-694.4132 1665.5,-684.4133 1662.0001,-694.4133 1669.0001,-694.4132"/>
+<g id="edge46" class="edge"><title>22->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1796.04,-719.697C1805.06,-711.05 1816.12,-700.449 1825.94,-691.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1828.37,-693.552 1833.16,-684.104 1823.52,-688.499 1828.37,-693.552"/>
</g>
<!-- 31 -->
-<g id="node32" class="node">
-<title>31</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M1517,-612C1517,-612 1422,-612 1422,-612 1416,-612 1410,-606 1410,-600 1410,-600 1410,-588 1410,-588 1410,-582 1416,-576 1422,-576 1422,-576 1517,-576 1517,-576 1523,-576 1529,-582 1529,-588 1529,-588 1529,-600 1529,-600 1529,-606 1523,-612 1517,-612"/>
-<text text-anchor="middle" x="1469.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<g id="node32" class="node"><title>31</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1579,-612C1579,-612 1491,-612 1491,-612 1485,-612 1479,-606 1479,-600 1479,-600 1479,-588 1479,-588 1479,-582 1485,-576 1491,-576 1491,-576 1579,-576 1579,-576 1585,-576 1591,-582 1591,-588 1591,-588 1591,-600 1591,-600 1591,-606 1585,-612 1579,-612"/>
+<text text-anchor="middle" x="1535" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 22->31 -->
-<g id="edge54" class="edge">
-<title>22->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1602.8337,-735.1678C1527.6304,-730.302 1408.1672,-717.4016 1380.5,-684 1370.2936,-671.6781 1372.6512,-661.9426 1380.5,-648 1387.7034,-635.2038 1399.2994,-625.0907 1411.7742,-617.2465"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1413.6189,-620.2227 1420.5078,-612.1733 1410.1028,-614.1698 1413.6189,-620.2227"/>
+<g id="edge54" class="edge"><title>22->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1762.74,-719.786C1744.5,-700.11 1712.25,-668.045 1679,-648 1654.93,-633.488 1626.23,-621.935 1600.82,-613.367"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1601.85,-610.021 1591.25,-610.229 1599.67,-616.672 1601.85,-610.021"/>
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<!-- 23->13 -->
-<g id="edge30" class="edge">
-<title>23->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1677.8648,-647.8314C1683.4509,-639.6232 1690.163,-629.7606 1696.3072,-620.7323"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1699.236,-622.6496 1701.9687,-612.4133 1693.449,-618.7112 1699.236,-622.6496"/>
+<g id="edge30" class="edge"><title>23->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1877.18,-647.876C1891.04,-638.808 1908.24,-627.552 1923.21,-617.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1925.27,-620.593 1931.72,-612.19 1921.44,-614.735 1925.27,-620.593"/>
</g>
<!-- 23->31 -->
-<g id="edge55" class="edge">
-<title>23->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1616.2939,-647.9243C1589.6161,-638.1243 1556.4614,-625.945 1528.4148,-615.6422"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1529.3199,-612.246 1518.7263,-612.0831 1526.9062,-618.8167 1529.3199,-612.246"/>
+<g id="edge55" class="edge"><title>23->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1766.32,-647.996C1717.81,-638.018 1655.86,-624.873 1601,-612 1600.9,-611.976 1600.8,-611.953 1600.7,-611.929"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1601.67,-608.563 1591.13,-609.633 1600.04,-615.37 1601.67,-608.563"/>
</g>
<!-- 24->14 -->
-<g id="edge31" class="edge">
-<title>24->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1931.3273,-728.8736C1979.5156,-719.575 2045.1704,-703.7364 2062.5,-684 2077.1133,-667.3572 2079.9269,-641.985 2079.4782,-622.4174"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2082.9634,-622.0401 2078.9475,-612.2359 2075.9729,-622.4046 2082.9634,-622.0401"/>
+<g id="edge31" class="edge"><title>24->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1631.68,-722.094C1649.83,-713.907 1668.55,-701.707 1679,-684 1691.28,-663.202 1677.19,-638.237 1662.11,-620.048"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1664.44,-617.398 1655.21,-612.207 1659.19,-622.025 1664.44,-617.398"/>
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<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M2041.5,-684C2041.5,-684 1869.5,-684 1869.5,-684 1863.5,-684 1857.5,-678 1857.5,-672 1857.5,-672 1857.5,-660 1857.5,-660 1857.5,-654 1863.5,-648 1869.5,-648 1869.5,-648 2041.5,-648 2041.5,-648 2047.5,-648 2053.5,-654 2053.5,-660 2053.5,-660 2053.5,-672 2053.5,-672 2053.5,-678 2047.5,-684 2041.5,-684"/>
-<text text-anchor="middle" x="1955.5" y="-669" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1955.5" y="-658" font-family="sans" font-size="10.00" fill="#000000">seqmode: single_end</text>
+<g id="node26" class="node"><title>25</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1658,-684C1658,-684 1508,-684 1508,-684 1502,-684 1496,-678 1496,-672 1496,-672 1496,-660 1496,-660 1496,-654 1502,-648 1508,-648 1508,-648 1658,-648 1658,-648 1664,-648 1670,-654 1670,-660 1670,-660 1670,-672 1670,-672 1670,-678 1664,-684 1658,-684"/>
+<text text-anchor="middle" x="1583" y="-669" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1583" y="-658" font-family="sans" font-size="10.00">seqmode: single_end</text>
</g>
<!-- 24->25 -->
-<g id="edge49" class="edge">
-<title>24->25</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1897.1827,-719.8314C1906.6051,-711.1337 1918.0401,-700.5783 1928.2796,-691.1265"/>
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+<g id="edge49" class="edge"><title>24->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1583,-719.697C1583,-711.983 1583,-702.712 1583,-694.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1586.5,-694.104 1583,-684.104 1579.5,-694.104 1586.5,-694.104"/>
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<!-- 32 -->
-<g id="node33" class="node">
-<title>32</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M1654,-612C1654,-612 1559,-612 1559,-612 1553,-612 1547,-606 1547,-600 1547,-600 1547,-588 1547,-588 1547,-582 1553,-576 1559,-576 1559,-576 1654,-576 1654,-576 1660,-576 1666,-582 1666,-588 1666,-588 1666,-600 1666,-600 1666,-606 1660,-612 1654,-612"/>
-<text text-anchor="middle" x="1606.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<g id="node33" class="node"><title>32</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1449,-612C1449,-612 1361,-612 1361,-612 1355,-612 1349,-606 1349,-600 1349,-600 1349,-588 1349,-588 1349,-582 1355,-576 1361,-576 1361,-576 1449,-576 1449,-576 1455,-576 1461,-582 1461,-588 1461,-588 1461,-600 1461,-600 1461,-606 1455,-612 1449,-612"/>
+<text text-anchor="middle" x="1405" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 24->32 -->
-<g id="edge57" class="edge">
-<title>24->32</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1860.5781,-719.6848C1841.0852,-699.561 1807.253,-667.5109 1772.5,-648 1755.4585,-638.4326 1713.4539,-624.7991 1675.9648,-613.625"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1676.6257,-610.1707 1666.0438,-610.6929 1674.6417,-616.8837 1676.6257,-610.1707"/>
+<g id="edge57" class="edge"><title>24->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1534.42,-734.18C1466.9,-729.131 1350.04,-715.914 1324,-684 1313.88,-671.604 1316.39,-662.074 1324,-648 1330.82,-635.391 1342.09,-625.3 1354.08,-617.45"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1356.14,-620.294 1362.89,-612.126 1352.52,-614.303 1356.14,-620.294"/>
</g>
<!-- 25->14 -->
-<g id="edge32" class="edge">
-<title>25->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1986.0334,-647.8314C2001.6282,-638.5518 2020.7768,-627.1576 2037.4354,-617.2451"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2039.5916,-620.0348 2046.3955,-611.9134 2036.0121,-614.0193 2039.5916,-620.0348"/>
+<g id="edge32" class="edge"><title>25->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1596.35,-647.697C1602.76,-639.389 1610.56,-629.277 1617.61,-620.141"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1620.47,-622.16 1623.81,-612.104 1614.93,-617.884 1620.47,-622.16"/>
</g>
<!-- 25->32 -->
-<g id="edge58" class="edge">
-<title>25->32</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1857.3424,-648.6759C1806.1098,-639.2504 1742.2062,-626.8981 1676.4252,-612.1395"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1676.8068,-608.6376 1666.2813,-609.8477 1675.2641,-615.4655 1676.8068,-608.6376"/>
+<g id="edge58" class="edge"><title>25->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1539.46,-647.876C1514.8,-638.179 1483.78,-625.98 1457.75,-615.743"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1458.99,-612.471 1448.4,-612.068 1456.43,-618.985 1458.99,-612.471"/>
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<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M2028.5,-396C2028.5,-396 1936.5,-396 1936.5,-396 1930.5,-396 1924.5,-390 1924.5,-384 1924.5,-384 1924.5,-372 1924.5,-372 1924.5,-366 1930.5,-360 1936.5,-360 1936.5,-360 2028.5,-360 2028.5,-360 2034.5,-360 2040.5,-366 2040.5,-372 2040.5,-372 2040.5,-384 2040.5,-384 2040.5,-390 2034.5,-396 2028.5,-396"/>
-<text text-anchor="middle" x="1982.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+<g id="node27" class="node"><title>26</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1905.5,-396C1905.5,-396 1824.5,-396 1824.5,-396 1818.5,-396 1812.5,-390 1812.5,-384 1812.5,-384 1812.5,-372 1812.5,-372 1812.5,-366 1818.5,-360 1824.5,-360 1824.5,-360 1905.5,-360 1905.5,-360 1911.5,-360 1917.5,-366 1917.5,-372 1917.5,-372 1917.5,-384 1917.5,-384 1917.5,-390 1911.5,-396 1905.5,-396"/>
+<text text-anchor="middle" x="1865" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
<!-- 26->15 -->
-<g id="edge33" class="edge">
-<title>26->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1948.6861,-359.8314C1931.2293,-350.4516 1909.7513,-338.9112 1891.1648,-328.9244"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1892.7686,-325.8129 1882.303,-324.1628 1889.4554,-331.9792 1892.7686,-325.8129"/>
+<g id="edge33" class="edge"><title>26->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1834.91,-359.876C1818.68,-350.639 1798.46,-339.131 1781.03,-329.212"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1782.63,-326.094 1772.2,-324.19 1779.16,-332.178 1782.63,-326.094"/>
</g>
<!-- 27 -->
-<g id="node28" class="node">
-<title>27</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1894.5,-396C1894.5,-396 1802.5,-396 1802.5,-396 1796.5,-396 1790.5,-390 1790.5,-384 1790.5,-384 1790.5,-372 1790.5,-372 1790.5,-366 1796.5,-360 1802.5,-360 1802.5,-360 1894.5,-360 1894.5,-360 1900.5,-360 1906.5,-366 1906.5,-372 1906.5,-372 1906.5,-384 1906.5,-384 1906.5,-390 1900.5,-396 1894.5,-396"/>
-<text text-anchor="middle" x="1848.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+<g id="node28" class="node"><title>27</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1782.5,-396C1782.5,-396 1701.5,-396 1701.5,-396 1695.5,-396 1689.5,-390 1689.5,-384 1689.5,-384 1689.5,-372 1689.5,-372 1689.5,-366 1695.5,-360 1701.5,-360 1701.5,-360 1782.5,-360 1782.5,-360 1788.5,-360 1794.5,-366 1794.5,-372 1794.5,-372 1794.5,-384 1794.5,-384 1794.5,-390 1788.5,-396 1782.5,-396"/>
+<text text-anchor="middle" x="1742" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
<!-- 27->15 -->
-<g id="edge34" class="edge">
-<title>27->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1848.5,-359.8314C1848.5,-352.131 1848.5,-342.9743 1848.5,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1852.0001,-334.4132 1848.5,-324.4133 1845.0001,-334.4133 1852.0001,-334.4132"/>
+<g id="edge34" class="edge"><title>27->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1742,-359.697C1742,-351.983 1742,-342.712 1742,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1745.5,-334.104 1742,-324.104 1738.5,-334.104 1745.5,-334.104"/>
</g>
<!-- 28 -->
-<g id="node29" class="node">
-<title>28</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M1119,-905C1119,-905 818,-905 818,-905 812,-905 806,-899 806,-893 806,-893 806,-881 806,-881 806,-875 812,-869 818,-869 818,-869 1119,-869 1119,-869 1125,-869 1131,-875 1131,-881 1131,-881 1131,-893 1131,-893 1131,-899 1125,-905 1119,-905"/>
-<text text-anchor="middle" x="968.5" y="-890" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="968.5" y="-879" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node29" class="node"><title>28</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1400,-905C1400,-905 1132,-905 1132,-905 1126,-905 1120,-899 1120,-893 1120,-893 1120,-881 1120,-881 1120,-875 1126,-869 1132,-869 1132,-869 1400,-869 1400,-869 1406,-869 1412,-875 1412,-881 1412,-881 1412,-893 1412,-893 1412,-899 1406,-905 1400,-905"/>
+<text text-anchor="middle" x="1266" y="-890" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1266" y="-879" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 28->16 -->
-<g id="edge35" class="edge">
-<title>28->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M968.5,-868.9656C968.5,-860.5178 968.5,-850.2542 968.5,-840.8064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="972.0001,-840.6265 968.5,-830.6265 965.0001,-840.6265 972.0001,-840.6265"/>
+<g id="edge35" class="edge"><title>28->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1266,-868.819C1266,-860.422 1266,-850.116 1266,-840.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1269.5,-840.558 1266,-830.558 1262.5,-840.558 1269.5,-840.558"/>
</g>
<!-- 29 -->
-<g id="node30" class="node">
-<title>29</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M1185,-540C1185,-540 1070,-540 1070,-540 1064,-540 1058,-534 1058,-528 1058,-528 1058,-516 1058,-516 1058,-510 1064,-504 1070,-504 1070,-504 1185,-504 1185,-504 1191,-504 1197,-510 1197,-516 1197,-516 1197,-528 1197,-528 1197,-534 1191,-540 1185,-540"/>
-<text text-anchor="middle" x="1127.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
-<text text-anchor="middle" x="1127.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<g id="node30" class="node"><title>29</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1106.5,-612C1106.5,-612 1005.5,-612 1005.5,-612 999.5,-612 993.5,-606 993.5,-600 993.5,-600 993.5,-588 993.5,-588 993.5,-582 999.5,-576 1005.5,-576 1005.5,-576 1106.5,-576 1106.5,-576 1112.5,-576 1118.5,-582 1118.5,-588 1118.5,-588 1118.5,-600 1118.5,-600 1118.5,-606 1112.5,-612 1106.5,-612"/>
+<text text-anchor="middle" x="1056" y="-597" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<text text-anchor="middle" x="1056" y="-586" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 29->17 -->
-<g id="edge36" class="edge">
-<title>29->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1144.9116,-503.8314C1153.021,-495.3694 1162.8156,-485.1489 1171.682,-475.8971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1174.4618,-478.0549 1178.854,-468.4133 1169.4079,-473.2115 1174.4618,-478.0549"/>
+<g id="edge36" class="edge"><title>29->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1078.25,-575.697C1089.58,-566.881 1103.53,-556.032 1115.82,-546.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.26,-549.007 1124.01,-540.104 1113.97,-543.481 1118.26,-549.007"/>
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-<!-- 33 -->
-<g id="node34" class="node">
-<title>33</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M1106,-468C1106,-468 1009,-468 1009,-468 1003,-468 997,-462 997,-456 997,-456 997,-444 997,-444 997,-438 1003,-432 1009,-432 1009,-432 1106,-432 1106,-432 1112,-432 1118,-438 1118,-444 1118,-444 1118,-456 1118,-456 1118,-462 1112,-468 1106,-468"/>
-<text text-anchor="middle" x="1057.5" y="-453" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
-<text text-anchor="middle" x="1057.5" y="-442" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
-</g>
-<!-- 29->33 -->
-<g id="edge60" class="edge">
-<title>29->33</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1109.836,-503.8314C1101.5268,-495.2848 1091.4736,-484.9443 1082.4082,-475.6198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1084.8821,-473.1435 1075.4018,-468.4133 1079.8631,-478.023 1084.8821,-473.1435"/>
+<!-- 40 -->
+<g id="node41" class="node"><title>40</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M1061.5,-540C1061.5,-540 890.5,-540 890.5,-540 884.5,-540 878.5,-534 878.5,-528 878.5,-528 878.5,-516 878.5,-516 878.5,-510 884.5,-504 890.5,-504 890.5,-504 1061.5,-504 1061.5,-504 1067.5,-504 1073.5,-510 1073.5,-516 1073.5,-516 1073.5,-528 1073.5,-528 1073.5,-534 1067.5,-540 1061.5,-540"/>
+<text text-anchor="middle" x="976" y="-519.5" font-family="sans" font-size="10.00">concatenate_transcriptome_and_genome</text>
+</g>
+<!-- 29->40 -->
+<g id="edge70" class="edge"><title>29->40</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1036.22,-575.697C1026.25,-566.965 1013.99,-556.24 1003.14,-546.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1005.38,-544.055 995.548,-540.104 1000.77,-549.323 1005.38,-544.055"/>
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<!-- 30 -->
-<g id="node31" class="node">
-<title>30</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M1480,-905C1480,-905 1167,-905 1167,-905 1161,-905 1155,-899 1155,-893 1155,-893 1155,-881 1155,-881 1155,-875 1161,-869 1167,-869 1167,-869 1480,-869 1480,-869 1486,-869 1492,-875 1492,-881 1492,-881 1492,-893 1492,-893 1492,-899 1486,-905 1480,-905"/>
-<text text-anchor="middle" x="1323.5" y="-890" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1323.5" y="-879" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<g id="node31" class="node"><title>30</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M847,-905C847,-905 567,-905 567,-905 561,-905 555,-899 555,-893 555,-893 555,-881 555,-881 555,-875 561,-869 567,-869 567,-869 847,-869 847,-869 853,-869 859,-875 859,-881 859,-881 859,-893 859,-893 859,-899 853,-905 847,-905"/>
+<text text-anchor="middle" x="707" y="-890" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="707" y="-879" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
<!-- 30->18 -->
-<g id="edge37" class="edge">
-<title>30->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1323.5,-868.9656C1323.5,-860.5178 1323.5,-850.2542 1323.5,-840.8064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1327.0001,-840.6265 1323.5,-830.6265 1320.0001,-840.6265 1327.0001,-840.6265"/>
+<g id="edge37" class="edge"><title>30->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M707,-868.819C707,-860.422 707,-850.116 707,-840.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="710.5,-840.558 707,-830.558 703.5,-840.558 710.5,-840.558"/>
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<!-- 31->19 -->
-<g id="edge38" class="edge">
-<title>31->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1470.7617,-575.8314C1471.2965,-568.131 1471.9323,-558.9743 1472.5266,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1476.02,-550.6317 1473.2213,-540.4133 1469.0368,-550.1467 1476.02,-550.6317"/>
+<g id="edge38" class="edge"><title>31->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1504.91,-575.876C1488.68,-566.639 1468.46,-555.131 1451.03,-545.212"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1452.63,-542.094 1442.2,-540.19 1449.16,-548.178 1452.63,-542.094"/>
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<!-- 32->19 -->
-<g id="edge39" class="edge">
-<title>32->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1573.1908,-575.8314C1556.0727,-566.4942 1535.0294,-555.016 1516.7778,-545.0606"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1518.2535,-541.8788 1507.7985,-540.1628 1514.9015,-548.024 1518.2535,-541.8788"/>
+<g id="edge39" class="edge"><title>32->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1406.73,-575.697C1407.5,-567.983 1408.43,-558.712 1409.29,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1412.78,-550.403 1410.29,-540.104 1405.81,-549.706 1412.78,-550.403"/>
+</g>
+<!-- 33 -->
+<g id="node34" class="node"><title>33</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M979.5,-468C979.5,-468 894.5,-468 894.5,-468 888.5,-468 882.5,-462 882.5,-456 882.5,-456 882.5,-444 882.5,-444 882.5,-438 888.5,-432 894.5,-432 894.5,-432 979.5,-432 979.5,-432 985.5,-432 991.5,-438 991.5,-444 991.5,-444 991.5,-456 991.5,-456 991.5,-462 985.5,-468 979.5,-468"/>
+<text text-anchor="middle" x="937" y="-447.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 33->20 -->
-<g id="edge41" class="edge">
-<title>33->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1045.1352,-431.8314C1039.5491,-423.6232 1032.837,-413.7606 1026.6928,-404.7323"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1029.551,-402.7112 1021.0313,-396.4133 1023.764,-406.6496 1029.551,-402.7112"/>
+<g id="edge41" class="edge"><title>33->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M966.355,-431.876C982.045,-422.724 1001.56,-411.342 1018.45,-401.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1020.66,-404.252 1027.53,-396.19 1017.13,-398.205 1020.66,-404.252"/>
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<!-- 33->21 -->
-<g id="edge43" class="edge">
-<title>33->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1083.4912,-431.8314C1096.4216,-422.7927 1112.2222,-411.7476 1126.1383,-402.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1128.3263,-404.7608 1134.5171,-396.1628 1124.3157,-399.0235 1128.3263,-404.7608"/>
+<g id="edge43" class="edge"><title>33->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M929.09,-431.697C925.447,-423.728 921.046,-414.1 917.006,-405.264"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="920.16,-403.744 912.819,-396.104 913.794,-406.654 920.16,-403.744"/>
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<!-- 34 -->
-<g id="node35" class="node">
-<title>34</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M1935,-833C1935,-833 1820,-833 1820,-833 1814,-833 1808,-827 1808,-821 1808,-821 1808,-804 1808,-804 1808,-798 1814,-792 1820,-792 1820,-792 1935,-792 1935,-792 1941,-792 1947,-798 1947,-804 1947,-804 1947,-821 1947,-821 1947,-827 1941,-833 1935,-833"/>
-<text text-anchor="middle" x="1877.5" y="-821" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
-<text text-anchor="middle" x="1877.5" y="-810" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
-<text text-anchor="middle" x="1877.5" y="-799" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<g id="node35" class="node"><title>34</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M1828.5,-833C1828.5,-833 1727.5,-833 1727.5,-833 1721.5,-833 1715.5,-827 1715.5,-821 1715.5,-821 1715.5,-804 1715.5,-804 1715.5,-798 1721.5,-792 1727.5,-792 1727.5,-792 1828.5,-792 1828.5,-792 1834.5,-792 1840.5,-798 1840.5,-804 1840.5,-804 1840.5,-821 1840.5,-821 1840.5,-827 1834.5,-833 1828.5,-833"/>
+<text text-anchor="middle" x="1778" y="-821" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1778" y="-810" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1778" y="-799" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 34->22 -->
-<g id="edge44" class="edge">
-<title>34->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1819.0089,-791.9453C1790.2695,-781.8459 1755.6554,-769.682 1726.576,-759.463"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1727.5378,-756.0912 1716.9429,-756.0778 1725.2169,-762.6953 1727.5378,-756.0912"/>
+<g id="edge44" class="edge"><title>34->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1778,-791.689C1778,-783.907 1778,-774.842 1778,-766.447"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1781.5,-766.319 1778,-756.319 1774.5,-766.32 1781.5,-766.319"/>
</g>
<!-- 34->24 -->
-<g id="edge47" class="edge">
-<title>34->24</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1877.5,-791.7476C1877.5,-783.8767 1877.5,-774.7743 1877.5,-766.3232"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1881.0001,-766.1086 1877.5,-756.1087 1874.0001,-766.1087 1881.0001,-766.1086"/>
+<g id="edge47" class="edge"><title>34->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1725.49,-791.976C1698.54,-781.959 1665.73,-769.76 1638.39,-759.594"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1639.56,-756.294 1628.96,-756.09 1637.12,-762.855 1639.56,-756.294"/>
</g>
-<!-- 41 -->
-<g id="node42" class="node">
-<title>41</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M2180.5,-540C2180.5,-540 2088.5,-540 2088.5,-540 2082.5,-540 2076.5,-534 2076.5,-528 2076.5,-528 2076.5,-516 2076.5,-516 2076.5,-510 2082.5,-504 2088.5,-504 2088.5,-504 2180.5,-504 2180.5,-504 2186.5,-504 2192.5,-510 2192.5,-516 2192.5,-516 2192.5,-528 2192.5,-528 2192.5,-534 2186.5,-540 2180.5,-540"/>
-<text text-anchor="middle" x="2134.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
+<!-- 43 -->
+<g id="node44" class="node"><title>43</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M2054,-540C2054,-540 1974,-540 1974,-540 1968,-540 1962,-534 1962,-528 1962,-528 1962,-516 1962,-516 1962,-510 1968,-504 1974,-504 1974,-504 2054,-504 2054,-504 2060,-504 2066,-510 2066,-516 2066,-516 2066,-528 2066,-528 2066,-534 2060,-540 2054,-540"/>
+<text text-anchor="middle" x="2014" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
-<!-- 34->41 -->
-<g id="edge70" class="edge">
-<title>34->41</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1927.0531,-791.9156C1972.8687,-770.722 2040.2186,-733.7833 2083.5,-684 2116.8987,-645.584 2128.4448,-585.3066 2132.4228,-550.1245"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2135.9164,-550.3626 2133.4302,-540.0636 2128.9512,-549.6651 2135.9164,-550.3626"/>
+<!-- 34->43 -->
+<g id="edge72" class="edge"><title>34->43</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1821.52,-791.833C1863.92,-770.678 1927.59,-733.322 1967,-684 1998.41,-644.69 2008.83,-585.094 2012.29,-550.508"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2015.8,-550.48 2013.18,-540.215 2008.83,-549.874 2015.8,-550.48"/>
</g>
<!-- 35 -->
-<g id="node36" class="node">
-<title>35</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M1966.5,-468C1966.5,-468 1936.5,-468 1936.5,-468 1930.5,-468 1924.5,-462 1924.5,-456 1924.5,-456 1924.5,-444 1924.5,-444 1924.5,-438 1930.5,-432 1936.5,-432 1936.5,-432 1966.5,-432 1966.5,-432 1972.5,-432 1978.5,-438 1978.5,-444 1978.5,-444 1978.5,-456 1978.5,-456 1978.5,-462 1972.5,-468 1966.5,-468"/>
-<text text-anchor="middle" x="1951.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+<g id="node36" class="node"><title>35</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M2029,-468C2029,-468 1999,-468 1999,-468 1993,-468 1987,-462 1987,-456 1987,-456 1987,-444 1987,-444 1987,-438 1993,-432 1999,-432 1999,-432 2029,-432 2029,-432 2035,-432 2041,-438 2041,-444 2041,-444 2041,-456 2041,-456 2041,-462 2035,-468 2029,-468"/>
+<text text-anchor="middle" x="2014" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 35->26 -->
-<g id="edge50" class="edge">
-<title>35->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1959.3226,-431.8314C1962.7109,-423.9617 1966.7541,-414.5712 1970.5076,-405.8533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1973.8321,-406.9822 1974.5721,-396.4133 1967.4027,-404.214 1973.8321,-406.9822"/>
+<g id="edge50" class="edge"><title>35->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1986.67,-436.161C1965.44,-426.186 1935.53,-412.133 1910.67,-400.456"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1911.96,-397.196 1901.42,-396.111 1908.99,-403.531 1911.96,-397.196"/>
</g>
<!-- 36 -->
-<g id="node37" class="node">
-<title>36</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M2149.5,-468C2149.5,-468 2119.5,-468 2119.5,-468 2113.5,-468 2107.5,-462 2107.5,-456 2107.5,-456 2107.5,-444 2107.5,-444 2107.5,-438 2113.5,-432 2119.5,-432 2119.5,-432 2149.5,-432 2149.5,-432 2155.5,-432 2161.5,-438 2161.5,-444 2161.5,-444 2161.5,-456 2161.5,-456 2161.5,-462 2155.5,-468 2149.5,-468"/>
-<text text-anchor="middle" x="2134.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+<g id="node37" class="node"><title>36</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1854,-468C1854,-468 1824,-468 1824,-468 1818,-468 1812,-462 1812,-456 1812,-456 1812,-444 1812,-444 1812,-438 1818,-432 1824,-432 1824,-432 1854,-432 1854,-432 1860,-432 1866,-438 1866,-444 1866,-444 1866,-456 1866,-456 1866,-462 1860,-468 1854,-468"/>
+<text text-anchor="middle" x="1839" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 36->26 -->
-<g id="edge51" class="edge">
-<title>36->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2107.3254,-437.1278C2085.8027,-426.9329 2055.2203,-412.4465 2029.7138,-400.3645"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2031.1083,-397.1522 2020.5725,-396.0344 2028.1116,-403.4784 2031.1083,-397.1522"/>
+<g id="edge51" class="edge"><title>36->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1845.43,-431.697C1848.36,-423.813 1851.89,-414.304 1855.14,-405.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1858.45,-406.697 1858.65,-396.104 1851.88,-404.26 1858.45,-406.697"/>
</g>
<!-- 37 -->
-<g id="node38" class="node">
-<title>37</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M1863.5,-468C1863.5,-468 1833.5,-468 1833.5,-468 1827.5,-468 1821.5,-462 1821.5,-456 1821.5,-456 1821.5,-444 1821.5,-444 1821.5,-438 1827.5,-432 1833.5,-432 1833.5,-432 1863.5,-432 1863.5,-432 1869.5,-432 1875.5,-438 1875.5,-444 1875.5,-444 1875.5,-456 1875.5,-456 1875.5,-462 1869.5,-468 1863.5,-468"/>
-<text text-anchor="middle" x="1848.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+<g id="node38" class="node"><title>37</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1926,-468C1926,-468 1896,-468 1896,-468 1890,-468 1884,-462 1884,-456 1884,-456 1884,-444 1884,-444 1884,-438 1890,-432 1896,-432 1896,-432 1926,-432 1926,-432 1932,-432 1938,-438 1938,-444 1938,-444 1938,-456 1938,-456 1938,-462 1932,-468 1926,-468"/>
+<text text-anchor="middle" x="1911" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 37->27 -->
-<g id="edge52" class="edge">
-<title>37->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1848.5,-431.8314C1848.5,-424.131 1848.5,-414.9743 1848.5,-406.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1852.0001,-406.4132 1848.5,-396.4133 1845.0001,-406.4133 1852.0001,-406.4132"/>
+<g id="edge52" class="edge"><title>37->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1883.96,-436.009C1880.95,-434.629 1877.92,-433.268 1875,-432 1849.34,-420.843 1820.54,-409.251 1796.31,-399.763"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1797.51,-396.475 1786.92,-396.102 1794.97,-402.997 1797.51,-396.475"/>
</g>
<!-- 38 -->
-<g id="node39" class="node">
-<title>38</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M2038.5,-468C2038.5,-468 2008.5,-468 2008.5,-468 2002.5,-468 1996.5,-462 1996.5,-456 1996.5,-456 1996.5,-444 1996.5,-444 1996.5,-438 2002.5,-432 2008.5,-432 2008.5,-432 2038.5,-432 2038.5,-432 2044.5,-432 2050.5,-438 2050.5,-444 2050.5,-444 2050.5,-456 2050.5,-456 2050.5,-462 2044.5,-468 2038.5,-468"/>
-<text text-anchor="middle" x="2023.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+<g id="node39" class="node"><title>38</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1757,-468C1757,-468 1727,-468 1727,-468 1721,-468 1715,-462 1715,-456 1715,-456 1715,-444 1715,-444 1715,-438 1721,-432 1727,-432 1727,-432 1757,-432 1757,-432 1763,-432 1769,-438 1769,-444 1769,-444 1769,-456 1769,-456 1769,-462 1763,-468 1757,-468"/>
+<text text-anchor="middle" x="1742" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 38->27 -->
-<g id="edge53" class="edge">
-<title>38->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1996.1081,-435.975C1993.2192,-434.5947 1990.311,-433.2455 1987.5,-432 1961.6937,-420.5654 1932.6567,-409.076 1907.8216,-399.6524"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1908.7628,-396.2668 1898.171,-396.0138 1906.2933,-402.8168 1908.7628,-396.2668"/>
+<g id="edge53" class="edge"><title>38->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1742,-431.697C1742,-423.983 1742,-414.712 1742,-406.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1745.5,-406.104 1742,-396.104 1738.5,-406.104 1745.5,-406.104"/>
</g>
<!-- 39 -->
-<g id="node40" class="node">
-<title>39</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1537.5,-684C1537.5,-684 1401.5,-684 1401.5,-684 1395.5,-684 1389.5,-678 1389.5,-672 1389.5,-672 1389.5,-660 1389.5,-660 1389.5,-654 1395.5,-648 1401.5,-648 1401.5,-648 1537.5,-648 1537.5,-648 1543.5,-648 1549.5,-654 1549.5,-660 1549.5,-660 1549.5,-672 1549.5,-672 1549.5,-678 1543.5,-684 1537.5,-684"/>
-<text text-anchor="middle" x="1469.5" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<g id="node40" class="node"><title>39</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M1465.5,-684C1465.5,-684 1344.5,-684 1344.5,-684 1338.5,-684 1332.5,-678 1332.5,-672 1332.5,-672 1332.5,-660 1332.5,-660 1332.5,-654 1338.5,-648 1344.5,-648 1344.5,-648 1465.5,-648 1465.5,-648 1471.5,-648 1477.5,-654 1477.5,-660 1477.5,-660 1477.5,-672 1477.5,-672 1477.5,-678 1471.5,-684 1465.5,-684"/>
+<text text-anchor="middle" x="1405" y="-663.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 39->31 -->
-<g id="edge56" class="edge">
-<title>39->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1469.5,-647.8314C1469.5,-640.131 1469.5,-630.9743 1469.5,-622.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1473.0001,-622.4132 1469.5,-612.4133 1466.0001,-622.4133 1473.0001,-622.4132"/>
+<g id="edge56" class="edge"><title>39->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1436.8,-647.876C1454.11,-638.554 1475.72,-626.919 1494.26,-616.939"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1495.93,-620.012 1503.08,-612.19 1492.61,-613.849 1495.93,-620.012"/>
</g>
<!-- 39->32 -->
-<g id="edge59" class="edge">
-<title>39->32</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1504.0709,-647.8314C1521.9185,-638.4516 1543.8774,-626.9112 1562.88,-616.9244"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1564.7164,-619.9132 1571.9402,-612.1628 1561.4599,-613.7168 1564.7164,-619.9132"/>
-</g>
-<!-- 40->35 -->
-<g id="edge61" class="edge">
-<title>40->35</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1854.3045,-503.8314C1873.0055,-493.4739 1896.4632,-480.4819 1915.6483,-469.8563"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1917.3538,-472.9127 1924.406,-465.0059 1913.9623,-466.7892 1917.3538,-472.9127"/>
-</g>
-<!-- 41->35 -->
-<g id="edge62" class="edge">
-<title>41->35</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2080.8637,-503.9168C2055.067,-494.8474 2023.6154,-483.2493 1988.3984,-468.1973"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1989.4363,-464.833 1978.8684,-464.0786 1986.6593,-471.2586 1989.4363,-464.833"/>
-</g>
-<!-- 41->36 -->
-<g id="edge64" class="edge">
-<title>41->36</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2134.5,-503.8314C2134.5,-496.131 2134.5,-486.9743 2134.5,-478.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2138.0001,-478.4132 2134.5,-468.4133 2131.0001,-478.4133 2138.0001,-478.4132"/>
-</g>
-<!-- 41->37 -->
-<g id="edge66" class="edge">
-<title>41->37</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2076.4231,-506.2834C2073.4075,-505.503 2070.4193,-504.7377 2067.5,-504 2000.1912,-486.9918 1982.8088,-485.0082 1915.5,-468 1905.7065,-465.5253 1895.139,-462.7402 1885.3557,-460.1136"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1886.0765,-456.6829 1875.5097,-457.4536 1884.2507,-463.4407 1886.0765,-456.6829"/>
-</g>
-<!-- 41->38 -->
-<g id="edge68" class="edge">
-<title>41->38</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2106.49,-503.8314C2092.2091,-494.5681 2074.6795,-483.1975 2059.4166,-473.2972"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2061.0279,-470.1706 2050.7336,-467.665 2057.2185,-476.0434 2061.0279,-470.1706"/>
-</g>
-<!-- 42->36 -->
-<g id="edge63" class="edge">
-<title>42->36</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2245.901,-503.8314C2222.8665,-492.7006 2193.5355,-478.5272 2170.7526,-467.5181"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2172.2689,-464.3636 2161.7422,-463.164 2169.2233,-470.6663 2172.2689,-464.3636"/>
+<g id="edge59" class="edge"><title>39->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1405,-647.697C1405,-639.983 1405,-630.712 1405,-622.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1408.5,-622.104 1405,-612.104 1401.5,-622.104 1408.5,-622.104"/>
+</g>
+<!-- 40->33 -->
+<g id="edge60" class="edge"><title>40->33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M966.36,-503.697C961.873,-495.644 956.441,-485.894 951.476,-476.982"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="954.454,-475.137 946.53,-468.104 948.339,-478.544 954.454,-475.137"/>
+</g>
+<!-- 41 -->
+<g id="node42" class="node"><title>41</title>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M848.5,-540C848.5,-540 747.5,-540 747.5,-540 741.5,-540 735.5,-534 735.5,-528 735.5,-528 735.5,-516 735.5,-516 735.5,-510 741.5,-504 747.5,-504 747.5,-504 848.5,-504 848.5,-504 854.5,-504 860.5,-510 860.5,-516 860.5,-516 860.5,-528 860.5,-528 860.5,-534 854.5,-540 848.5,-540"/>
+<text text-anchor="middle" x="798" y="-525" font-family="sans" font-size="10.00">extract_decoys_salmon</text>
+<text text-anchor="middle" x="798" y="-514" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 41->33 -->
+<g id="edge61" class="edge"><title>41->33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M832.003,-503.876C850.598,-494.512 873.827,-482.814 893.706,-472.803"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="895.509,-475.814 902.866,-468.19 892.36,-469.562 895.509,-475.814"/>
+</g>
+<!-- 42->35 -->
+<g id="edge62" class="edge"><title>42->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2115.98,-503.876C2096.07,-493.557 2070.71,-480.403 2050.25,-469.797"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2051.73,-466.619 2041.24,-465.123 2048.5,-472.833 2051.73,-466.619"/>
+</g>
+<!-- 43->35 -->
+<g id="edge63" class="edge"><title>43->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2014,-503.697C2014,-495.983 2014,-486.712 2014,-478.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2017.5,-478.104 2014,-468.104 2010.5,-478.104 2017.5,-478.104"/>
+</g>
+<!-- 43->36 -->
+<g id="edge65" class="edge"><title>43->36</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1966.67,-503.982C1941.84,-494.818 1910.78,-482.99 1875.56,-468.1"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1876.6,-464.736 1866.03,-464.035 1873.85,-471.176 1876.6,-464.736"/>
</g>
<!-- 43->37 -->
-<g id="edge65" class="edge">
-<title>43->37</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1705.6974,-503.8314C1738.5618,-491.4427 1781.4249,-475.2849 1811.5846,-463.9158"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1813.1702,-467.0585 1821.2929,-460.2561 1810.701,-460.5085 1813.1702,-467.0585"/>
-</g>
-<!-- 44->38 -->
-<g id="edge67" class="edge">
-<title>44->38</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1946.53,-470.916 1936.29,-468.19 1942.6,-476.705 1946.53,-470.916"/>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1805.99,-476.566 1812.48,-468.19 1802.18,-470.692 1805.99,-476.566"/>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="1902.21,-478.654 1903.18,-468.104 1895.84,-475.744 1902.21,-478.654"/>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index d5f3ea2..c2634ec 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,505 +1,443 @@
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<title>snakemake_dag</title>
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+<text text-anchor="middle" x="472" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
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-<text text-anchor="middle" x="338.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_MultiQC_config</text>
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+<path fill="none" stroke="#56d88a" stroke-width="2" d="M521,-180C521,-180 423,-180 423,-180 417,-180 411,-174 411,-168 411,-168 411,-156 411,-156 411,-150 417,-144 423,-144 423,-144 521,-144 521,-144 527,-144 533,-150 533,-156 533,-156 533,-168 533,-168 533,-174 527,-180 521,-180"/>
+<text text-anchor="middle" x="472" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
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+<g id="edge2" class="edge"><title>2->1</title>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="475.5,-118.104 472,-108.104 468.5,-118.104 475.5,-118.104"/>
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+<path fill="none" stroke="#88d856" stroke-width="2" d="M519.5,-252C519.5,-252 424.5,-252 424.5,-252 418.5,-252 412.5,-246 412.5,-240 412.5,-240 412.5,-228 412.5,-228 412.5,-222 418.5,-216 424.5,-216 424.5,-216 519.5,-216 519.5,-216 525.5,-216 531.5,-222 531.5,-228 531.5,-228 531.5,-240 531.5,-240 531.5,-246 525.5,-252 519.5,-252"/>
+<text text-anchor="middle" x="472" y="-231.5" font-family="sans" font-size="10.00">prepare_files_for_report</text>
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+<polygon fill="grey" stroke="grey" stroke-width="2" points="475.5,-190.104 472,-180.104 468.5,-190.104 475.5,-190.104"/>
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-<text text-anchor="middle" x="64.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
+<g id="node5" class="node"><title>4</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M89.5,-324C89.5,-324 54.5,-324 54.5,-324 48.5,-324 42.5,-318 42.5,-312 42.5,-312 42.5,-300 42.5,-300 42.5,-294 48.5,-288 54.5,-288 54.5,-288 89.5,-288 89.5,-288 95.5,-288 101.5,-294 101.5,-300 101.5,-300 101.5,-312 101.5,-312 101.5,-318 95.5,-324 89.5,-324"/>
+<text text-anchor="middle" x="72" y="-303.5" font-family="sans" font-size="10.00">pe_fastqc</text>
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+<g id="edge12" class="edge"><title>4->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M101.511,-291.172C104.673,-289.982 107.875,-288.893 111,-288 209.889,-259.733 328.553,-246.003 402.13,-239.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="402.53,-243.219 412.206,-238.905 401.951,-236.243 402.53,-243.219"/>
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-<text text-anchor="middle" x="141.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
+<g id="node6" class="node"><title>5</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M162,-324C162,-324 132,-324 132,-324 126,-324 120,-318 120,-312 120,-312 120,-300 120,-300 120,-294 126,-288 132,-288 132,-288 162,-288 162,-288 168,-288 174,-294 174,-300 174,-300 174,-312 174,-312 174,-318 168,-324 162,-324"/>
+<text text-anchor="middle" x="147" y="-303.5" font-family="sans" font-size="10.00">fastqc</text>
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+<path fill="none" stroke="grey" stroke-width="2" d="M174.06,-292.852C178.654,-291.059 183.42,-289.361 188,-288 259.664,-266.71 344.151,-252.245 402.237,-243.874"/>
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-<text text-anchor="middle" x="93.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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+<g id="edge4" class="edge"><title>6->3</title>
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+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M463,-756C463,-756 337,-756 337,-756 331,-756 325,-750 325,-744 325,-744 325,-732 325,-732 325,-726 331,-720 337,-720 337,-720 463,-720 463,-720 469,-720 475,-726 475,-732 475,-732 475,-744 475,-744 475,-750 469,-756 463,-756"/>
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-<title>9->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M338.5,-647.8146C338.5,-620.4983 338.5,-567.25 338.5,-522 338.5,-522 338.5,-522 338.5,-378 338.5,-337.876 338.5,-291.4631 338.5,-262.4177"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="342.0001,-262.1853 338.5,-252.1854 335.0001,-262.1854 342.0001,-262.1853"/>
+<g id="edge6" class="edge"><title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M472,-575.951C472,-549.292 472,-496.115 472,-451 472,-451 472,-451 472,-377 472,-336.996 472,-290.653 472,-262.08"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="475.5,-262.049 472,-252.049 468.5,-262.049 475.5,-262.049"/>
</g>
<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M594.5,-684C594.5,-684 444.5,-684 444.5,-684 438.5,-684 432.5,-678 432.5,-672 432.5,-672 432.5,-660 432.5,-660 432.5,-654 438.5,-648 444.5,-648 444.5,-648 594.5,-648 594.5,-648 600.5,-648 606.5,-654 606.5,-660 606.5,-660 606.5,-672 606.5,-672 606.5,-678 600.5,-684 594.5,-684"/>
-<text text-anchor="middle" x="519.5" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M373.5,-612C373.5,-612 242.5,-612 242.5,-612 236.5,-612 230.5,-606 230.5,-600 230.5,-600 230.5,-588 230.5,-588 230.5,-582 236.5,-576 242.5,-576 242.5,-576 373.5,-576 373.5,-576 379.5,-576 385.5,-582 385.5,-588 385.5,-588 385.5,-600 385.5,-600 385.5,-606 379.5,-612 373.5,-612"/>
+<text text-anchor="middle" x="308" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
<!-- 10->3 -->
-<g id="edge11" class="edge">
-<title>10->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M503.7428,-647.8597C482.8256,-621.8524 448.5,-571.6151 448.5,-522 448.5,-522 448.5,-522 448.5,-378 448.5,-327.5369 405.3128,-283.7768 373.0594,-258.1321"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="375.1825,-255.3495 365.1279,-252.0095 370.9051,-260.8907 375.1825,-255.3495"/>
+<g id="edge5" class="edge"><title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M321.361,-575.721C339.854,-550.027 371,-499.546 371,-451 371,-451 371,-451 371,-377 371,-328.193 411.113,-284.506 440.78,-258.87"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="443.41,-261.233 448.829,-252.129 438.915,-255.867 443.41,-261.233"/>
</g>
<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M989.5,-612C989.5,-612 953.5,-612 953.5,-612 947.5,-612 941.5,-606 941.5,-600 941.5,-600 941.5,-588 941.5,-588 941.5,-582 947.5,-576 953.5,-576 953.5,-576 989.5,-576 989.5,-576 995.5,-576 1001.5,-582 1001.5,-588 1001.5,-588 1001.5,-600 1001.5,-600 1001.5,-606 995.5,-612 989.5,-612"/>
-<text text-anchor="middle" x="971.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M942.5,-612C942.5,-612 911.5,-612 911.5,-612 905.5,-612 899.5,-606 899.5,-600 899.5,-600 899.5,-588 899.5,-588 899.5,-582 905.5,-576 911.5,-576 911.5,-576 942.5,-576 942.5,-576 948.5,-576 954.5,-582 954.5,-588 954.5,-588 954.5,-600 954.5,-600 954.5,-606 948.5,-612 942.5,-612"/>
+<text text-anchor="middle" x="927" y="-591.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 11->3 -->
-<g id="edge12" class="edge">
-<title>11->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M941.3162,-586.1618C866.1306,-565.7547 676.5,-508.4873 676.5,-450 676.5,-450 676.5,-450 676.5,-378 676.5,-321.5184 514.7343,-274.2676 415.0242,-250.5076"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="415.8139,-247.0979 405.2779,-248.2127 414.2095,-253.9116 415.8139,-247.0979"/>
+<g id="edge8" class="edge"><title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M899.442,-579.32C860.486,-557.807 794,-512.137 794,-451 794,-451 794,-451 794,-377 794,-267.649 636.61,-241.792 541.903,-236.132"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="541.984,-232.631 531.811,-235.59 541.609,-239.621 541.984,-232.631"/>
</g>
-<!-- 31 -->
-<g id="node32" class="node">
-<title>31</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M1032.5,-540C1032.5,-540 910.5,-540 910.5,-540 904.5,-540 898.5,-534 898.5,-528 898.5,-528 898.5,-516 898.5,-516 898.5,-510 904.5,-504 910.5,-504 910.5,-504 1032.5,-504 1032.5,-504 1038.5,-504 1044.5,-510 1044.5,-516 1044.5,-516 1044.5,-528 1044.5,-528 1044.5,-534 1038.5,-540 1032.5,-540"/>
-<text text-anchor="middle" x="971.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<!-- 33 -->
+<g id="node34" class="node"><title>33</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M980,-540C980,-540 874,-540 874,-540 868,-540 862,-534 862,-528 862,-528 862,-516 862,-516 862,-510 868,-504 874,-504 874,-504 980,-504 980,-504 986,-504 992,-510 992,-516 992,-516 992,-528 992,-528 992,-534 986,-540 980,-540"/>
+<text text-anchor="middle" x="927" y="-519.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
-<!-- 11->31 -->
-<g id="edge48" class="edge">
-<title>11->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M971.5,-575.8314C971.5,-568.131 971.5,-558.9743 971.5,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="975.0001,-550.4132 971.5,-540.4133 968.0001,-550.4133 975.0001,-550.4132"/>
+<!-- 11->33 -->
+<g id="edge50" class="edge"><title>11->33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M927,-575.697C927,-567.983 927,-558.712 927,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="930.5,-550.104 927,-540.104 923.5,-550.104 930.5,-550.104"/>
</g>
<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M889,-324C889,-324 802,-324 802,-324 796,-324 790,-318 790,-312 790,-312 790,-300 790,-300 790,-294 796,-288 802,-288 802,-288 889,-288 889,-288 895,-288 901,-294 901,-300 901,-300 901,-312 901,-312 901,-318 895,-324 889,-324"/>
-<text text-anchor="middle" x="845.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M925.5,-324C925.5,-324 848.5,-324 848.5,-324 842.5,-324 836.5,-318 836.5,-312 836.5,-312 836.5,-300 836.5,-300 836.5,-294 842.5,-288 848.5,-288 848.5,-288 925.5,-288 925.5,-288 931.5,-288 937.5,-294 937.5,-300 937.5,-300 937.5,-312 937.5,-312 937.5,-318 931.5,-324 925.5,-324"/>
+<text text-anchor="middle" x="887" y="-303.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
</g>
<!-- 12->3 -->
-<g id="edge9" class="edge">
-<title>12->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M789.7918,-298.0888C698.802,-285.1672 518.1379,-259.5107 415.1331,-244.8828"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="415.5004,-241.3999 405.1076,-243.4591 414.5161,-248.3304 415.5004,-241.3999"/>
+<g id="edge11" class="edge"><title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M836.088,-293.61C826.763,-291.647 817.103,-289.696 808,-288 716.334,-270.921 609.924,-254.748 541.829,-244.86"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="542.05,-241.356 531.652,-243.388 541.047,-248.284 542.05,-241.356"/>
</g>
<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M446.5,-828C446.5,-828 318.5,-828 318.5,-828 312.5,-828 306.5,-822 306.5,-816 306.5,-816 306.5,-804 306.5,-804 306.5,-798 312.5,-792 318.5,-792 318.5,-792 446.5,-792 446.5,-792 452.5,-792 458.5,-798 458.5,-804 458.5,-804 458.5,-816 458.5,-816 458.5,-822 452.5,-828 446.5,-828"/>
-<text text-anchor="middle" x="382.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M744,-828C744,-828 632,-828 632,-828 626,-828 620,-822 620,-816 620,-816 620,-804 620,-804 620,-798 626,-792 632,-792 632,-792 744,-792 744,-792 750,-792 756,-798 756,-804 756,-804 756,-816 756,-816 756,-822 750,-828 744,-828"/>
+<text text-anchor="middle" x="688" y="-807.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 13->6 -->
-<g id="edge13" class="edge">
-<title>13->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M309.9461,-791.9243C269.0723,-781.7412 217.8873,-768.9892 175.5552,-758.4428"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="176.3826,-755.042 165.833,-756.0207 174.6903,-761.8344 176.3826,-755.042"/>
+<g id="edge13" class="edge"><title>13->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M679.101,-791.697C675.003,-783.728 670.051,-774.1 665.507,-765.264"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="668.483,-763.396 660.797,-756.104 662.258,-766.598 668.483,-763.396"/>
</g>
<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M523.5,-756C523.5,-756 405.5,-756 405.5,-756 399.5,-756 393.5,-750 393.5,-744 393.5,-744 393.5,-732 393.5,-732 393.5,-726 399.5,-720 405.5,-720 405.5,-720 523.5,-720 523.5,-720 529.5,-720 535.5,-726 535.5,-732 535.5,-732 535.5,-744 535.5,-744 535.5,-750 529.5,-756 523.5,-756"/>
-<text text-anchor="middle" x="464.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M513.5,-684C513.5,-684 410.5,-684 410.5,-684 404.5,-684 398.5,-678 398.5,-672 398.5,-672 398.5,-660 398.5,-660 398.5,-654 404.5,-648 410.5,-648 410.5,-648 513.5,-648 513.5,-648 519.5,-648 525.5,-654 525.5,-660 525.5,-660 525.5,-672 525.5,-672 525.5,-678 519.5,-684 513.5,-684"/>
+<text text-anchor="middle" x="462" y="-663.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
<!-- 13->17 -->
-<g id="edge30" class="edge">
-<title>13->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M403.1921,-791.8314C413.1948,-783.0485 425.355,-772.3712 436.1999,-762.8489"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="438.6094,-765.3909 443.8146,-756.1628 433.9908,-760.1308 438.6094,-765.3909"/>
+<g id="edge30" class="edge"><title>13->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M635.545,-791.953C611.565,-783.007 583.362,-770.808 560,-756 544.498,-746.174 510.194,-713.967 486.583,-691.13"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="488.941,-688.542 479.33,-684.085 484.064,-693.563 488.941,-688.542"/>
</g>
<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M981,-756C981,-756 880,-756 880,-756 874,-756 868,-750 868,-744 868,-744 868,-732 868,-732 868,-726 874,-720 880,-720 880,-720 981,-720 981,-720 987,-720 993,-726 993,-732 993,-732 993,-744 993,-744 993,-750 987,-756 981,-756"/>
-<text text-anchor="middle" x="930.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M1039.5,-756C1039.5,-756 950.5,-756 950.5,-756 944.5,-756 938.5,-750 938.5,-744 938.5,-744 938.5,-732 938.5,-732 938.5,-726 944.5,-720 950.5,-720 950.5,-720 1039.5,-720 1039.5,-720 1045.5,-720 1051.5,-726 1051.5,-732 1051.5,-732 1051.5,-744 1051.5,-744 1051.5,-750 1045.5,-756 1039.5,-756"/>
+<text text-anchor="middle" x="995" y="-735.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 13->19 -->
-<g id="edge35" class="edge">
-<title>13->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M458.8927,-793.4742C461.795,-792.9571 464.6717,-792.4634 467.5,-792 604.7105,-769.5199 766.2912,-752.8915 857.7293,-744.3857"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="858.0763,-747.8686 867.7119,-743.4635 857.4323,-740.8983 858.0763,-747.8686"/>
+<g id="edge34" class="edge"><title>13->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M756.189,-794.681C802.17,-784.869 864.435,-771.279 928.304,-756.126"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="929.234,-759.502 938.15,-753.78 927.611,-752.693 929.234,-759.502"/>
</g>
<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M272,-828C272,-828 175,-828 175,-828 169,-828 163,-822 163,-816 163,-816 163,-804 163,-804 163,-798 169,-792 175,-792 175,-792 272,-792 272,-792 278,-792 284,-798 284,-804 284,-804 284,-816 284,-816 284,-822 278,-828 272,-828"/>
-<text text-anchor="middle" x="223.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#d87556" stroke-width="2" d="M448,-828C448,-828 364,-828 364,-828 358,-828 352,-822 352,-816 352,-816 352,-804 352,-804 352,-798 358,-792 364,-792 364,-792 448,-792 448,-792 454,-792 460,-798 460,-804 460,-804 460,-816 460,-816 460,-822 454,-828 448,-828"/>
+<text text-anchor="middle" x="406" y="-807.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 14->6 -->
-<g id="edge14" class="edge">
-<title>14->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M190.6955,-791.8314C173.9138,-782.5368 153.3015,-771.1208 135.3837,-761.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="136.7377,-757.9461 126.294,-756.1628 133.3462,-764.0696 136.7377,-757.9461"/>
+<g id="edge14" class="edge"><title>14->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M460.29,-793.552C496.291,-783.307 543.855,-769.773 582.599,-758.748"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="583.586,-762.106 592.247,-756.003 581.671,-755.374 583.586,-762.106"/>
</g>
<!-- 14->7 -->
-<g id="edge15" class="edge">
-<title>14->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M240.4069,-791.8314C248.2813,-783.3694 257.792,-773.1489 266.4013,-763.8971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="269.1153,-766.1183 273.3654,-756.4133 263.9908,-761.3497 269.1153,-766.1183"/>
+<g id="edge16" class="edge"><title>14->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M404.517,-791.697C403.856,-783.983 403.061,-774.712 402.324,-766.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="405.807,-765.769 401.466,-756.104 398.833,-766.367 405.807,-765.769"/>
</g>
<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M738.5,-828C738.5,-828 628.5,-828 628.5,-828 622.5,-828 616.5,-822 616.5,-816 616.5,-816 616.5,-804 616.5,-804 616.5,-798 622.5,-792 628.5,-792 628.5,-792 738.5,-792 738.5,-792 744.5,-792 750.5,-798 750.5,-804 750.5,-804 750.5,-816 750.5,-816 750.5,-822 744.5,-828 738.5,-828"/>
-<text text-anchor="middle" x="683.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M586,-828C586,-828 490,-828 490,-828 484,-828 478,-822 478,-816 478,-816 478,-804 478,-804 478,-798 484,-792 490,-792 490,-792 586,-792 586,-792 592,-792 598,-798 598,-804 598,-804 598,-816 598,-816 598,-822 592,-828 586,-828"/>
+<text text-anchor="middle" x="538" y="-807.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 15->7 -->
-<g id="edge16" class="edge">
-<title>15->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M616.3672,-794.0196C613.0352,-793.3165 609.7323,-792.6391 606.5,-792 511.6028,-773.2369 484.649,-773.3713 385.6674,-756.1726"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="385.9887,-752.6756 375.5344,-754.3954 384.7794,-759.5704 385.9887,-752.6756"/>
+<g id="edge15" class="edge"><title>15->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M504.241,-791.876C485.78,-782.512 462.718,-770.814 442.983,-760.803"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="444.39,-757.592 433.888,-756.19 441.223,-763.835 444.39,-757.592"/>
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<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M667,-756C667,-756 566,-756 566,-756 560,-756 554,-750 554,-744 554,-744 554,-732 554,-732 554,-726 560,-720 566,-720 566,-720 667,-720 667,-720 673,-720 679,-726 679,-732 679,-732 679,-744 679,-744 679,-750 673,-756 667,-756"/>
-<text text-anchor="middle" x="616.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M355.5,-684C355.5,-684 268.5,-684 268.5,-684 262.5,-684 256.5,-678 256.5,-672 256.5,-672 256.5,-660 256.5,-660 256.5,-654 262.5,-648 268.5,-648 268.5,-648 355.5,-648 355.5,-648 361.5,-648 367.5,-654 367.5,-660 367.5,-660 367.5,-672 367.5,-672 367.5,-678 361.5,-684 355.5,-684"/>
+<text text-anchor="middle" x="312" y="-663.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
<!-- 15->18 -->
-<g id="edge33" class="edge">
-<title>15->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M666.5931,-791.8314C658.7187,-783.3694 649.208,-773.1489 640.5987,-763.8971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="643.0092,-761.3497 633.6346,-756.4133 637.8847,-766.1183 643.0092,-761.3497"/>
+<g id="edge32" class="edge"><title>15->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M531.875,-791.656C523.906,-771.551 508.088,-738.779 484,-720 467.061,-706.794 418.711,-692.487 377.572,-682.07"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="378.387,-678.666 367.837,-679.642 376.693,-685.458 378.387,-678.666"/>
</g>
<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M1106,-756C1106,-756 1023,-756 1023,-756 1017,-756 1011,-750 1011,-744 1011,-744 1011,-732 1011,-732 1011,-726 1017,-720 1023,-720 1023,-720 1106,-720 1106,-720 1112,-720 1118,-726 1118,-732 1118,-732 1118,-744 1118,-744 1118,-750 1112,-756 1106,-756"/>
-<text text-anchor="middle" x="1064.5" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M908.5,-756C908.5,-756 835.5,-756 835.5,-756 829.5,-756 823.5,-750 823.5,-744 823.5,-744 823.5,-732 823.5,-732 823.5,-726 829.5,-720 835.5,-720 835.5,-720 908.5,-720 908.5,-720 914.5,-720 920.5,-726 920.5,-732 920.5,-732 920.5,-744 920.5,-744 920.5,-750 914.5,-756 908.5,-756"/>
+<text text-anchor="middle" x="872" y="-735.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 15->21 -->
-<g id="edge39" class="edge">
-<title>15->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M750.5367,-800.9396C813.1135,-791.9636 909.2168,-776.8572 1000.835,-756.2636"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1001.8553,-759.621 1010.8302,-753.9907 1000.303,-752.7953 1001.8553,-759.621"/>
+<g id="edge38" class="edge"><title>15->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M598.122,-794.856C602.477,-793.875 606.804,-792.914 611,-792 680.392,-776.878 760.474,-760.822 813.437,-750.397"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="814.191,-753.816 823.329,-748.454 812.842,-746.947 814.191,-753.816"/>
</g>
<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M615,-540C615,-540 532,-540 532,-540 526,-540 520,-534 520,-528 520,-528 520,-516 520,-516 520,-510 526,-504 532,-504 532,-504 615,-504 615,-504 621,-504 627,-510 627,-516 627,-516 627,-528 627,-528 627,-534 621,-540 615,-540"/>
-<text text-anchor="middle" x="573.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M714,-540C714,-540 638,-540 638,-540 632,-540 626,-534 626,-528 626,-528 626,-516 626,-516 626,-510 632,-504 638,-504 638,-504 714,-504 714,-504 720,-504 726,-510 726,-516 726,-516 726,-528 726,-528 726,-534 720,-540 714,-540"/>
+<text text-anchor="middle" x="676" y="-519.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
</g>
<!-- 16->8 -->
-<g id="edge17" class="edge">
-<title>16->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M570.2071,-503.7623C565.7529,-479.0928 557.7663,-434.8598 552.5507,-405.9731"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="555.9874,-405.3086 550.7662,-396.0896 549.0988,-406.5524 555.9874,-405.3086"/>
+<g id="edge17" class="edge"><title>16->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M673.226,-503.871C669.306,-479.67 662.105,-435.211 657.437,-406.393"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="660.838,-405.501 655.784,-396.189 653.928,-406.62 660.838,-405.501"/>
</g>
<!-- 17->9 -->
-<g id="edge19" class="edge">
-<title>17->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M432.7049,-719.8314C416.4395,-710.5368 396.4614,-699.1208 379.0949,-689.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="380.7039,-686.0854 370.2849,-684.1628 377.2309,-692.1631 380.7039,-686.0854"/>
+<g id="edge18" class="edge"><title>17->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M464.472,-647.697C465.574,-639.983 466.898,-630.712 468.127,-622.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="471.607,-622.499 469.557,-612.104 464.677,-621.509 471.607,-622.499"/>
</g>
<!-- 17->10 -->
-<g id="edge21" class="edge">
-<title>17->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M478.3788,-719.8314C484.7136,-711.5386 492.3384,-701.557 499.2926,-692.4533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="502.1452,-694.4847 505.4343,-684.4133 496.5825,-690.2353 502.1452,-694.4847"/>
+<g id="edge20" class="edge"><title>17->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M424.327,-647.876C403.368,-638.349 377.095,-626.407 354.823,-616.283"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="356.102,-613.02 345.55,-612.068 353.206,-619.393 356.102,-613.02"/>
</g>
<!-- 18->9 -->
-<g id="edge18" class="edge">
-<title>18->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M553.7647,-721.752C513.6508,-711.3628 461.2633,-697.7948 418.2129,-686.6451"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="418.8911,-683.2053 408.3329,-684.0862 417.136,-689.9817 418.8911,-683.2053"/>
+<g id="edge19" class="edge"><title>18->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M351.14,-647.876C373.013,-638.307 400.457,-626.3 423.662,-616.148"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="425.228,-619.283 432.987,-612.068 422.422,-612.87 425.228,-619.283"/>
</g>
<!-- 18->10 -->
-<g id="edge20" class="edge">
-<title>18->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M592.0228,-719.8314C579.9605,-710.8779 565.246,-699.9558 552.2314,-690.2955"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="554.0852,-687.3127 543.9694,-684.1628 549.913,-692.9335 554.0852,-687.3127"/>
+<g id="edge21" class="edge"><title>18->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M311.011,-647.697C310.57,-639.983 310.041,-630.712 309.549,-622.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="313.042,-621.888 308.977,-612.104 306.054,-622.288 313.042,-621.888"/>
</g>
<!-- 19->11 -->
-<g id="edge22" class="edge">
-<title>19->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M993.0894,-723.1441C1013.3376,-715.0538 1033.6146,-702.7114 1045.5,-684 1054.0788,-670.4943 1052.749,-662.2637 1045.5,-648 1037.9342,-633.1129 1024.1258,-621.3535 1010.4685,-612.6606"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1011.9689,-609.4812 1001.5827,-607.3889 1008.3972,-615.5014 1011.9689,-609.4812"/>
+<g id="edge24" class="edge"><title>19->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M998.427,-719.921C1001.3,-701.221 1003.33,-670.855 992,-648 985.547,-634.983 974.25,-624.061 962.865,-615.579"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="964.832,-612.685 954.627,-609.839 960.83,-618.428 964.832,-612.685"/>
</g>
<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1024.5,-684C1024.5,-684 852.5,-684 852.5,-684 846.5,-684 840.5,-678 840.5,-672 840.5,-672 840.5,-660 840.5,-660 840.5,-654 846.5,-648 852.5,-648 852.5,-648 1024.5,-648 1024.5,-648 1030.5,-648 1036.5,-654 1036.5,-660 1036.5,-660 1036.5,-672 1036.5,-672 1036.5,-678 1030.5,-684 1024.5,-684"/>
-<text text-anchor="middle" x="938.5" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M955,-684C955,-684 805,-684 805,-684 799,-684 793,-678 793,-672 793,-672 793,-660 793,-660 793,-654 799,-648 805,-648 805,-648 955,-648 955,-648 961,-648 967,-654 967,-660 967,-660 967,-672 967,-672 967,-678 961,-684 955,-684"/>
+<text text-anchor="middle" x="880" y="-663.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 19->20 -->
-<g id="edge36" class="edge">
-<title>19->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M932.5187,-719.8314C933.3743,-712.131 934.3917,-702.9743 935.3426,-694.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="938.8283,-694.7386 936.4541,-684.4133 931.8711,-693.9656 938.8283,-694.7386"/>
+<g id="edge37" class="edge"><title>19->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M966.868,-719.876C951.832,-710.724 933.133,-699.342 916.94,-689.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="918.602,-686.4 908.24,-684.19 914.962,-692.379 918.602,-686.4"/>
</g>
<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M860,-612C860,-612 765,-612 765,-612 759,-612 753,-606 753,-600 753,-600 753,-588 753,-588 753,-582 759,-576 765,-576 765,-576 860,-576 860,-576 866,-576 872,-582 872,-588 872,-588 872,-600 872,-600 872,-606 866,-612 860,-612"/>
-<text text-anchor="middle" x="812.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<g id="node27" class="node"><title>26</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M746,-612C746,-612 658,-612 658,-612 652,-612 646,-606 646,-600 646,-600 646,-588 646,-588 646,-582 652,-576 658,-576 658,-576 746,-576 746,-576 752,-576 758,-582 758,-588 758,-588 758,-600 758,-600 758,-606 752,-612 746,-612"/>
+<text text-anchor="middle" x="702" y="-591.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 19->26 -->
-<g id="edge41" class="edge">
-<title>19->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M878.2953,-719.9048C861.0278,-711.4985 843.2465,-699.7849 831.5,-684 818.2888,-666.2468 813.8129,-641.3423 812.4865,-622.2306"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="815.9733,-621.8532 812.0325,-612.0186 808.9802,-622.1642 815.9733,-621.8532"/>
+<g id="edge44" class="edge"><title>19->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M996.5,-719.984C997.261,-699.884 995.174,-666.809 976,-648 947.195,-619.744 839.886,-605.821 768.42,-599.541"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="768.409,-596.027 758.149,-598.669 767.817,-603.002 768.409,-596.027"/>
</g>
<!-- 20->11 -->
-<g id="edge24" class="edge">
-<title>20->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M946.8273,-647.8314C950.473,-639.8771 954.8309,-630.369 958.8627,-621.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="962.0757,-622.9622 963.0606,-612.4133 955.7123,-620.0456 962.0757,-622.9622"/>
+<g id="edge23" class="edge"><title>20->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M891.618,-647.697C897.139,-639.474 903.847,-629.483 909.932,-620.421"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="912.847,-622.358 915.516,-612.104 907.035,-618.456 912.847,-622.358"/>
</g>
<!-- 20->26 -->
-<g id="edge43" class="edge">
-<title>20->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M906.7049,-647.8314C890.4395,-638.5368 870.4614,-627.1208 853.0949,-617.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="854.7039,-614.0854 844.2849,-612.1628 851.2309,-620.1631 854.7039,-614.0854"/>
+<g id="edge43" class="edge"><title>20->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M836.456,-647.876C811.798,-638.179 780.777,-625.98 754.746,-615.743"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="755.989,-612.471 745.402,-612.068 753.428,-618.985 755.989,-612.471"/>
</g>
<!-- 21->11 -->
-<g id="edge23" class="edge">
-<title>21->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1068.7164,-719.6926C1072.1057,-700.4444 1074.4231,-669.963 1061.5,-648 1050.3537,-629.0567 1029.7305,-615.9763 1011.0356,-607.4394"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1012.3518,-604.1958 1001.7802,-603.4952 1009.6075,-610.6355 1012.3518,-604.1958"/>
+<g id="edge22" class="edge"><title>21->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M916.362,-719.889C941.372,-709.243 968.986,-695.447 976,-684 984.359,-670.357 981.832,-662.899 976,-648 971.803,-637.279 964.308,-627.427 956.422,-619.201"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="958.76,-616.592 949.153,-612.125 953.877,-621.608 958.76,-616.592"/>
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<!-- 21->20 -->
-<g id="edge37" class="edge">
-<title>21->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1032.7049,-719.8314C1016.4395,-710.5368 996.4614,-699.1208 979.0949,-689.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="980.7039,-686.0854 970.2849,-684.1628 977.2309,-692.1631 980.7039,-686.0854"/>
+<g id="edge36" class="edge"><title>21->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M873.978,-719.697C874.859,-711.983 875.919,-702.712 876.901,-694.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="880.387,-694.437 878.045,-684.104 873.432,-693.642 880.387,-694.437"/>
</g>
<!-- 21->26 -->
-<g id="edge42" class="edge">
-<title>21->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1065.9775,-719.8347C1066.5678,-699.5401 1064.1713,-667.0424 1045.5,-648 1033.9274,-636.1973 946.6077,-618.1855 882.2472,-606.255"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="882.5982,-602.7609 872.13,-604.3943 881.3319,-609.6454 882.5982,-602.7609"/>
+<g id="edge41" class="edge"><title>21->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M823.356,-730.106C753.776,-719.753 632.766,-699.73 620,-684 609.918,-671.576 612.35,-662.053 620,-648 626.913,-635.301 638.322,-625.181 650.465,-617.33"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="652.587,-620.14 659.382,-612.011 649.001,-614.128 652.587,-620.14"/>
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<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M971.5,-396C971.5,-396 879.5,-396 879.5,-396 873.5,-396 867.5,-390 867.5,-384 867.5,-384 867.5,-372 867.5,-372 867.5,-366 873.5,-360 879.5,-360 879.5,-360 971.5,-360 971.5,-360 977.5,-360 983.5,-366 983.5,-372 983.5,-372 983.5,-384 983.5,-384 983.5,-390 977.5,-396 971.5,-396"/>
-<text text-anchor="middle" x="925.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M941.5,-396C941.5,-396 860.5,-396 860.5,-396 854.5,-396 848.5,-390 848.5,-384 848.5,-384 848.5,-372 848.5,-372 848.5,-366 854.5,-360 860.5,-360 860.5,-360 941.5,-360 941.5,-360 947.5,-360 953.5,-366 953.5,-372 953.5,-372 953.5,-384 953.5,-384 953.5,-390 947.5,-396 941.5,-396"/>
+<text text-anchor="middle" x="901" y="-375.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
<!-- 22->12 -->
-<g id="edge25" class="edge">
-<title>22->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M905.3126,-359.8314C895.6486,-351.1337 883.9204,-340.5783 873.4184,-331.1265"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="875.4553,-328.251 865.6809,-324.1628 870.7725,-333.454 875.4553,-328.251"/>
+<g id="edge25" class="edge"><title>22->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M897.539,-359.697C895.997,-351.983 894.142,-342.712 892.422,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="895.814,-333.224 890.421,-324.104 888.95,-334.597 895.814,-333.224"/>
</g>
<!-- 23 -->
-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M459,-900C459,-900 316,-900 316,-900 310,-900 304,-894 304,-888 304,-888 304,-876 304,-876 304,-870 310,-864 316,-864 316,-864 459,-864 459,-864 465,-864 471,-870 471,-876 471,-876 471,-888 471,-888 471,-894 465,-900 459,-900"/>
-<text text-anchor="middle" x="387.5" y="-879.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+<g id="node24" class="node"><title>23</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M758,-900C758,-900 632,-900 632,-900 626,-900 620,-894 620,-888 620,-888 620,-876 620,-876 620,-870 626,-864 632,-864 632,-864 758,-864 758,-864 764,-864 770,-870 770,-876 770,-876 770,-888 770,-888 770,-894 764,-900 758,-900"/>
+<text text-anchor="middle" x="695" y="-879.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 23->13 -->
-<g id="edge26" class="edge">
-<title>23->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M386.2383,-863.8314C385.7035,-856.131 385.0677,-846.9743 384.4734,-838.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="387.9632,-838.1467 383.7787,-828.4133 380.98,-838.6317 387.9632,-838.1467"/>
+<g id="edge26" class="edge"><title>23->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M693.27,-863.697C692.498,-855.983 691.571,-846.712 690.711,-838.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="694.188,-837.706 689.71,-828.104 687.223,-838.403 694.188,-837.706"/>
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<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
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-<text text-anchor="middle" x="223.5" y="-879.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<g id="node25" class="node"><title>24</title>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M359.5,-900C359.5,-900 272.5,-900 272.5,-900 266.5,-900 260.5,-894 260.5,-888 260.5,-888 260.5,-876 260.5,-876 260.5,-870 266.5,-864 272.5,-864 272.5,-864 359.5,-864 359.5,-864 365.5,-864 371.5,-870 371.5,-876 371.5,-876 371.5,-888 371.5,-888 371.5,-894 365.5,-900 359.5,-900"/>
+<text text-anchor="middle" x="316" y="-879.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
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<!-- 24->14 -->
-<g id="edge27" class="edge">
-<title>24->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M223.5,-863.8314C223.5,-856.131 223.5,-846.9743 223.5,-838.4166"/>
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+<g id="edge27" class="edge"><title>24->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M338.247,-863.697C349.582,-854.881 363.53,-844.032 375.819,-834.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="378.264,-837.007 384.009,-828.104 373.966,-831.481 378.264,-837.007"/>
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-<g id="node28" class="node">
-<title>27</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M586,-828C586,-828 489,-828 489,-828 483,-828 477,-822 477,-816 477,-816 477,-804 477,-804 477,-798 483,-792 489,-792 489,-792 586,-792 586,-792 592,-792 598,-798 598,-804 598,-804 598,-816 598,-816 598,-822 592,-828 586,-828"/>
-<text text-anchor="middle" x="537.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+<!-- 31 -->
+<g id="node32" class="node"><title>31</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M321.5,-828C321.5,-828 150.5,-828 150.5,-828 144.5,-828 138.5,-822 138.5,-816 138.5,-816 138.5,-804 138.5,-804 138.5,-798 144.5,-792 150.5,-792 150.5,-792 321.5,-792 321.5,-792 327.5,-792 333.5,-798 333.5,-804 333.5,-804 333.5,-816 333.5,-816 333.5,-822 327.5,-828 321.5,-828"/>
+<text text-anchor="middle" x="236" y="-807.5" font-family="sans" font-size="10.00">concatenate_transcriptome_and_genome</text>
</g>
-<!-- 24->27 -->
-<g id="edge45" class="edge">
-<title>24->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M286.1843,-865.9522C288.9922,-865.2826 291.774,-864.6289 294.5,-864 368.0367,-847.0355 389.357,-845.8541 467.0718,-828.0404"/>
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+<!-- 24->31 -->
+<g id="edge49" class="edge"><title>24->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M296.225,-863.697C286.246,-854.965 273.989,-844.24 263.143,-834.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="265.378,-832.055 255.548,-828.104 260.769,-837.323 265.378,-832.055"/>
</g>
<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#80d856" stroke-width="2" d="M746.5,-900C746.5,-900 620.5,-900 620.5,-900 614.5,-900 608.5,-894 608.5,-888 608.5,-888 608.5,-876 608.5,-876 608.5,-870 614.5,-864 620.5,-864 620.5,-864 746.5,-864 746.5,-864 752.5,-864 758.5,-870 758.5,-876 758.5,-876 758.5,-888 758.5,-888 758.5,-894 752.5,-900 746.5,-900"/>
-<text text-anchor="middle" x="683.5" y="-879.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<g id="node26" class="node"><title>25</title>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M590,-900C590,-900 480,-900 480,-900 474,-900 468,-894 468,-888 468,-888 468,-876 468,-876 468,-870 474,-864 480,-864 480,-864 590,-864 590,-864 596,-864 602,-870 602,-876 602,-876 602,-888 602,-888 602,-894 596,-900 590,-900"/>
+<text text-anchor="middle" x="535" y="-879.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
</g>
<!-- 25->15 -->
-<g id="edge28" class="edge">
-<title>25->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M683.5,-863.8314C683.5,-856.131 683.5,-846.9743 683.5,-838.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="687.0001,-838.4132 683.5,-828.4133 680.0001,-838.4133 687.0001,-838.4132"/>
+<g id="edge28" class="edge"><title>25->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M535.742,-863.697C536.072,-855.983 536.469,-846.712 536.838,-838.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="540.335,-838.245 537.267,-828.104 533.342,-837.945 540.335,-838.245"/>
</g>
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-<g id="edge29" class="edge">
-<title>26->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M752.8067,-576.0171C717.5467,-565.3948 672.9268,-551.9529 637.0192,-541.1355"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="637.722,-537.6919 627.1374,-538.1586 635.7028,-544.3944 637.722,-537.6919"/>
+<g id="edge29" class="edge"><title>26->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M695.573,-575.697C692.645,-567.813 689.113,-558.304 685.86,-549.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="689.116,-548.26 682.353,-540.104 682.554,-550.697 689.116,-548.26"/>
+</g>
+<!-- 27 -->
+<g id="node28" class="node"><title>27</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M283.5,-756C283.5,-756 198.5,-756 198.5,-756 192.5,-756 186.5,-750 186.5,-744 186.5,-744 186.5,-732 186.5,-732 186.5,-726 192.5,-720 198.5,-720 198.5,-720 283.5,-720 283.5,-720 289.5,-720 295.5,-726 295.5,-732 295.5,-732 295.5,-744 295.5,-744 295.5,-750 289.5,-756 283.5,-756"/>
+<text text-anchor="middle" x="241" y="-735.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 27->17 -->
-<g id="edge31" class="edge">
-<title>27->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M519.079,-791.8314C510.3471,-783.219 499.7683,-772.7851 490.2577,-763.4048"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="492.4925,-760.6931 482.9151,-756.1628 487.577,-765.6769 492.4925,-760.6931"/>
+<g id="edge31" class="edge"><title>27->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M294.78,-719.966C325.927,-710.1 365.323,-697.622 398.052,-687.255"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="399.502,-690.467 407.979,-684.111 397.389,-683.794 399.502,-690.467"/>
</g>
<!-- 27->18 -->
-<g id="edge32" class="edge">
-<title>27->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M557.435,-791.8314C566.9783,-783.1337 578.5599,-772.5783 588.9306,-763.1265"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="591.538,-765.4857 596.5713,-756.1628 586.8228,-760.3121 591.538,-765.4857"/>
+<g id="edge33" class="edge"><title>27->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M258.551,-719.697C267.234,-711.135 277.863,-700.656 287.348,-691.304"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="289.988,-693.617 294.651,-684.104 285.073,-688.633 289.988,-693.617"/>
</g>
<!-- 28 -->
-<g id="node29" class="node">
-<title>28</title>
-<path fill="none" stroke="#ced856" stroke-width="2" d="M1104.5,-828C1104.5,-828 1024.5,-828 1024.5,-828 1018.5,-828 1012.5,-822 1012.5,-816 1012.5,-816 1012.5,-804 1012.5,-804 1012.5,-798 1018.5,-792 1024.5,-792 1024.5,-792 1104.5,-792 1104.5,-792 1110.5,-792 1116.5,-798 1116.5,-804 1116.5,-804 1116.5,-816 1116.5,-816 1116.5,-822 1110.5,-828 1104.5,-828"/>
-<text text-anchor="middle" x="1064.5" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<g id="node29" class="node"><title>28</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M1030,-828C1030,-828 960,-828 960,-828 954,-828 948,-822 948,-816 948,-816 948,-804 948,-804 948,-798 954,-792 960,-792 960,-792 1030,-792 1030,-792 1036,-792 1042,-798 1042,-804 1042,-804 1042,-816 1042,-816 1042,-822 1036,-828 1030,-828"/>
+<text text-anchor="middle" x="995" y="-807.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
<!-- 28->19 -->
-<g id="edge34" class="edge">
-<title>28->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1030.6861,-791.8314C1013.2293,-782.4516 991.7513,-770.9112 973.1648,-760.9244"/>
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+<g id="edge35" class="edge"><title>28->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M995,-791.697C995,-783.983 995,-774.712 995,-766.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="998.5,-766.104 995,-756.104 991.5,-766.104 998.5,-766.104"/>
</g>
<!-- 28->21 -->
-<g id="edge38" class="edge">
-<title>28->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1064.5,-791.8314C1064.5,-784.131 1064.5,-774.9743 1064.5,-766.4166"/>
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+<g id="edge39" class="edge"><title>28->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M964.911,-791.876C948.68,-782.639 928.458,-771.131 911.029,-761.212"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="912.627,-758.094 902.205,-756.19 909.165,-764.178 912.627,-758.094"/>
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-<!-- 32 -->
-<g id="node33" class="node">
-<title>32</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M1190.5,-612C1190.5,-612 1098.5,-612 1098.5,-612 1092.5,-612 1086.5,-606 1086.5,-600 1086.5,-600 1086.5,-588 1086.5,-588 1086.5,-582 1092.5,-576 1098.5,-576 1098.5,-576 1190.5,-576 1190.5,-576 1196.5,-576 1202.5,-582 1202.5,-588 1202.5,-588 1202.5,-600 1202.5,-600 1202.5,-606 1196.5,-612 1190.5,-612"/>
-<text text-anchor="middle" x="1144.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
+<!-- 34 -->
+<g id="node35" class="node"><title>34</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1126,-540C1126,-540 1046,-540 1046,-540 1040,-540 1034,-534 1034,-528 1034,-528 1034,-516 1034,-516 1034,-510 1040,-504 1046,-504 1046,-504 1126,-504 1126,-504 1132,-504 1138,-510 1138,-516 1138,-516 1138,-528 1138,-528 1138,-534 1132,-540 1126,-540"/>
+<text text-anchor="middle" x="1086" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
-<!-- 28->32 -->
-<g id="edge49" class="edge">
-<title>28->32</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1094.4299,-791.7677C1106.7731,-782.6238 1119.9345,-770.4134 1127.5,-756 1149.7961,-713.5226 1150.0078,-656.2043 1147.6133,-622.3666"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1151.089,-621.9281 1146.769,-612.254 1144.1132,-622.5105 1151.089,-621.9281"/>
+<!-- 28->34 -->
+<g id="edge51" class="edge"><title>28->34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1025.63,-791.97C1038.75,-783.028 1052.89,-770.827 1061,-756 1097.51,-689.252 1094.02,-595.687 1089.49,-550.104"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1092.96,-549.666 1088.4,-540.104 1086,-550.425 1092.96,-549.666"/>
</g>
<!-- 29 -->
-<g id="node30" class="node">
-<title>29</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M986.5,-468C986.5,-468 956.5,-468 956.5,-468 950.5,-468 944.5,-462 944.5,-456 944.5,-456 944.5,-444 944.5,-444 944.5,-438 950.5,-432 956.5,-432 956.5,-432 986.5,-432 986.5,-432 992.5,-432 998.5,-438 998.5,-444 998.5,-444 998.5,-456 998.5,-456 998.5,-462 992.5,-468 986.5,-468"/>
-<text text-anchor="middle" x="971.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+<g id="node30" class="node"><title>29</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M942,-468C942,-468 912,-468 912,-468 906,-468 900,-462 900,-456 900,-456 900,-444 900,-444 900,-438 906,-432 912,-432 912,-432 942,-432 942,-432 948,-432 954,-438 954,-444 954,-444 954,-456 954,-456 954,-462 948,-468 942,-468"/>
+<text text-anchor="middle" x="927" y="-447.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 29->22 -->
-<g id="edge40" class="edge">
-<title>29->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M959.8923,-431.8314C954.7022,-423.7079 948.4768,-413.9637 942.7575,-405.0118"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="945.5974,-402.9559 937.264,-396.4133 939.6985,-406.7246 945.5974,-402.9559"/>
+<g id="edge40" class="edge"><title>29->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M920.573,-431.697C917.645,-423.813 914.113,-414.304 910.86,-405.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="914.116,-404.26 907.353,-396.104 907.554,-406.697 914.116,-404.26"/>
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<!-- 30 -->
-<g id="node31" class="node">
-<title>30</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M772.5,-684C772.5,-684 636.5,-684 636.5,-684 630.5,-684 624.5,-678 624.5,-672 624.5,-672 624.5,-660 624.5,-660 624.5,-654 630.5,-648 636.5,-648 636.5,-648 772.5,-648 772.5,-648 778.5,-648 784.5,-654 784.5,-660 784.5,-660 784.5,-672 784.5,-672 784.5,-678 778.5,-684 772.5,-684"/>
-<text text-anchor="middle" x="704.5" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<g id="node31" class="node"><title>30</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M762.5,-684C762.5,-684 641.5,-684 641.5,-684 635.5,-684 629.5,-678 629.5,-672 629.5,-672 629.5,-660 629.5,-660 629.5,-654 635.5,-648 641.5,-648 641.5,-648 762.5,-648 762.5,-648 768.5,-648 774.5,-654 774.5,-660 774.5,-660 774.5,-672 774.5,-672 774.5,-678 768.5,-684 762.5,-684"/>
+<text text-anchor="middle" x="702" y="-663.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 30->26 -->
-<g id="edge44" class="edge">
-<title>30->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M731.753,-647.8314C745.4389,-638.7074 762.1915,-627.539 776.8827,-617.7449"/>
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-</g>
-<!-- 31->29 -->
-<g id="edge47" class="edge">
-<title>31->29</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M971.5,-503.8314C971.5,-496.131 971.5,-486.9743 971.5,-478.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="975.0001,-478.4132 971.5,-468.4133 968.0001,-478.4133 975.0001,-478.4132"/>
-</g>
-<!-- 32->29 -->
-<g id="edge46" class="edge">
-<title>32->29</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1128.0138,-575.6758C1110.4778,-556.6857 1081.4648,-526.6656 1053.5,-504 1039.1341,-492.3564 1022.2183,-480.8839 1007.4936,-471.5284"/>
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+<g id="edge42" class="edge"><title>30->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M702,-647.697C702,-639.983 702,-630.712 702,-622.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="705.5,-622.104 702,-612.104 698.5,-622.104 705.5,-622.104"/>
+</g>
+<!-- 31->27 -->
+<g id="edge45" class="edge"><title>31->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M237.236,-791.697C237.787,-783.983 238.449,-774.712 239.063,-766.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="242.557,-766.328 239.778,-756.104 235.575,-765.83 242.557,-766.328"/>
+</g>
+<!-- 32 -->
+<g id="node33" class="node"><title>32</title>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M108,-828C108,-828 12,-828 12,-828 6,-828 0,-822 0,-816 0,-816 0,-804 0,-804 0,-798 6,-792 12,-792 12,-792 108,-792 108,-792 114,-792 120,-798 120,-804 120,-804 120,-816 120,-816 120,-822 114,-828 108,-828"/>
+<text text-anchor="middle" x="60" y="-807.5" font-family="sans" font-size="10.00">extract_decoys_salmon</text>
+</g>
+<!-- 32->27 -->
+<g id="edge46" class="edge"><title>32->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M104.278,-791.876C129.351,-782.179 160.896,-769.98 187.365,-759.743"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="188.802,-762.94 196.866,-756.068 186.277,-756.411 188.802,-762.94"/>
+</g>
+<!-- 33->29 -->
+<g id="edge47" class="edge"><title>33->29</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M927,-503.697C927,-495.983 927,-486.712 927,-478.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="930.5,-478.104 927,-468.104 923.5,-478.104 930.5,-478.104"/>
+</g>
+<!-- 34->29 -->
+<g id="edge48" class="edge"><title>34->29</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1047.1,-503.876C1021.51,-492.607 988.231,-477.957 963.198,-466.936"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="964.604,-463.731 954.041,-462.905 961.783,-470.138 964.604,-463.731"/>
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diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index 9f33fc3..b34ee66 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -7,6 +7,8 @@ This document describes the individual rules of the pipeline for information pur
* create log directories
* **create_index_star**
* **extract_transcriptome**
+* **extract_decoys_salmon**
+* **concatenate_transcriptome_and_genome**
* **create_index_salmon**
* **create_index_kallisto**
* **extract_transcripts_as_bed12**
@@ -98,7 +100,23 @@ Create transcriptome from genome and gene annotations using [gffread](https://gi
**Input:** `genome` and `gtf` of the input samples table
**Output:** transcriptome fasta file.
-
+
+#### extract_decoys_salmon
+Salmon indexing requires the names of the genome targets (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/). Extract target names from the genome.
+
+
+**Input:** `genome` of the input samples table
+**Output:** text file with the genome targert names
+
+
+#### concatenate_transcriptome_and_genome
+Salmon indexing requires concatenated transcriptome and genome reference file (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/).
+
+
+**Input:** `genome` of the input samples table and extracted transcriptome
+**Output:** fasta file with concatenated genome and transcriptome
+
+
#### create_index_salmon
Create index for [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) quantification. Salmon index of transcriptome, required for mapping-based mode of Salmon. The index is created via an auxiliary k-mer hash over k-mers of length 31. While mapping algorithms will make use of arbitrarily long matches between the query and reference, the k-mer size selected here will act as the minimum acceptable length for a valid match. A k-mer size of 31 seems to work well for reads of 75bp or longer, although smaller size might improve sensitivity. A smaller k-mer size is suggested when working with shorter reads.
diff --git a/tests/input_files/cluster.json b/tests/input_files/cluster.json
index 0734b24..6df74cd 100644
--- a/tests/input_files/cluster.json
+++ b/tests/input_files/cluster.json
@@ -26,6 +26,18 @@
"threads":"1",
"mem":"1G"
},
+ "extract_decoys_salmon":
+ {
+ "time": "00:30:00",
+ "threads":"1",
+ "mem":"10G"
+ },
+ "concatenate_transcriptome_and_genome":
+ {
+ "time": "00:30:00",
+ "threads":"1",
+ "mem":"10G"
+ },
"create_index_salmon":
{
"time": "03:00:00",
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 93f8a66..e3166e7 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -1,7 +1,7 @@
cbaebdb67aee4784b64aff7fec9fda42 results/kallisto_indexes/homo_sapiens/kallisto.idx
0ac1afd9a4f380afd70be75b21814c64 results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
51b5292e3a874119c0e1aa566e95d70c results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
-4c1ab7841bbd1a1e8e3b15e7750ecc38 results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
+7f8679a6e6622e1b611642b5735f357c results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
dee7cdc194d5d0617552b7a3b5ad8dfb results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
8e2e96e2d6b7f29940ad5de40662b7cb results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
d0826904b8afa45352906ad9591f2bfb results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt
--
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