From f5e2f6ac80145f4f13b111a260acc28b67998460 Mon Sep 17 00:00:00 2001
From: Dominik Burri <dominik.burri@unibas.ch>
Date: Fri, 20 Mar 2020 15:14:14 +0100
Subject: [PATCH] extend ALFA functionality
- generate nucleotide distribution for unique reads only
- new rule to generate PNG image for MultiQC
---
Snakefile | 78 +-
images/dag_test_workflow.svg | 1058 ++++++++++-------
images/rule_graph.svg | 713 ++++++-----
tests/test_alfa/expected_output.md5 | 36 +-
tests/test_alfa/test.sh | 2 +-
.../expected_output.md5 | 18 +-
tests/test_integration_workflow/test.local.sh | 2 +-
7 files changed, 1119 insertions(+), 788 deletions(-)
diff --git a/Snakefile b/Snakefile
index c3b7de0..44bf7b5 100644
--- a/Snakefile
+++ b/Snakefile
@@ -53,6 +53,7 @@ rule finish:
"multiqc_summary"),
output_dir=config["output_dir"])
+
rule create_index_star:
"""
Create index for STAR alignments
@@ -398,13 +399,13 @@ rule rename_star_rpm_for_alfa:
"{seqmode}",
"{sample}",
"STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str1.out.bg"),
+ "{sample}_Signal.{unique}.str1.out.bg"),
str2 = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str2.out.bg")
+ "{sample}_Signal.{unique}.str2.out.bg")
output:
plus = os.path.join(
@@ -412,13 +413,15 @@ rule rename_star_rpm_for_alfa:
"{seqmode}",
"{sample}",
"ALFA",
- "{sample}_Signal.UniqueMultiple.out.plus.bg"),
+ "{unique}",
+ "{sample}_Signal.{unique}.out.plus.bg"),
minus = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
- "{sample}_Signal.UniqueMultiple.out.minus.bg")
+ "{unique}",
+ "{sample}_Signal.{unique}.out.minus.bg")
params:
orientation = lambda wildcards: samples_table.loc[wildcards.sample, "kallisto_directionality"]
@@ -763,13 +766,15 @@ rule alfa_qc:
"{seqmode}",
"{sample}",
"ALFA",
- "{sample}_Signal.UniqueMultiple.out.plus.bg"),
+ "{unique}",
+ "{sample}_Signal.{unique}.out.plus.bg"),
minus = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
- "{sample}_Signal.UniqueMultiple.out.minus.bg"),
+ "{unique}",
+ "{sample}_Signal.{unique}.out.minus.bg"),
gtf = lambda wildcards: os.path.join(config["alfa_indexes"],
samples_table.loc[wildcards.sample, "organism"],
str(samples_table.loc[wildcards.sample, "index_size"]),
@@ -782,18 +787,21 @@ rule alfa_qc:
"{seqmode}",
"{sample}",
"ALFA",
+ "{unique}",
"ALFA_plots.Biotypes.pdf"),
categories = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
+ "{unique}",
"ALFA_plots.Categories.pdf"),
table = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
+ "{unique}",
"{sample}.ALFA_feature_counts.tsv")
params:
@@ -812,7 +820,7 @@ rule alfa_qc:
config["log_dir"],
"{seqmode}",
"{sample}",
- "alfa_qc.log"))
+ "alfa_qc.{unique}.log"))
shell:
"""
@@ -831,6 +839,7 @@ rule alfa_qc_all_samples:
samples_table.loc[sample1, "seqmode"],
str(sample1),
"ALFA",
+ "{unique}",
sample1 + ".ALFA_feature_counts.tsv")
for sample1 in list(samples_table.index.values)]
@@ -838,10 +847,12 @@ rule alfa_qc_all_samples:
biotypes = os.path.join(
config["output_dir"],
"ALFA",
+ "{unique}",
"ALFA_plots.Biotypes.pdf"),
categories = os.path.join(
config["output_dir"],
"ALFA",
+ "{unique}",
"ALFA_plots.Categories.pdf")
params:
@@ -850,7 +861,7 @@ rule alfa_qc_all_samples:
log:
os.path.abspath(
os.path.join(config["log_dir"],
- "alfa_qc_all_samples.log"))
+ "alfa_qc_all_samples.{unique}.log"))
singularity:
"docker://zavolab/alfa:1.1.1"
@@ -861,6 +872,40 @@ rule alfa_qc_all_samples:
"""
+rule alfa_concat_results:
+ input:
+ expand(os.path.join(
+ config["output_dir"],
+ "ALFA",
+ "{unique_type}",
+ "ALFA_plots.{annotation}.pdf"),
+ unique_type = ["Unique", "UniqueMultiple"],
+ annotation = ["Categories", "Biotypes"])
+
+ output:
+ expand(os.path.join(
+ config["output_dir"],
+ "ALFA",
+ "ALFA_plots.concat.png"))
+
+ params:
+ density = 300
+
+ log:
+ os.path.abspath(
+ os.path.join(config["log_dir"],
+ "alfa_qc_all_samples.concat.log"))
+
+ singularity:
+ "docker://zavolab/imagemagick:7.0.8"
+
+ shell:
+ """
+ convert -append -density {params.density} \
+ {input} {output} &> {log}
+ """
+
+
rule prepare_files_for_report:
'''
Re-structure the results and add comments for MultiQC parsing
@@ -918,21 +963,10 @@ rule prepare_files_for_report:
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)]),
- alfa_reports = expand(os.path.join(
+ alfa_concat_out = expand(os.path.join(
config["output_dir"],
- "{seqmode}",
- "{sample}",
"ALFA",
- "ALFA_plots.Biotypes.pdf"),
- zip,
- sample= [i for i in list(samples_table.index.values)],
- seqmode= [
- samples_table.loc[i,"seqmode"]
- for i in list(samples_table.index.values)]),
- alfa_all_samples = os.path.join(
- config["output_dir"],
- "ALFA",
- "ALFA_plots.Categories.pdf")
+ "ALFA_plots.concat.png"))
output:
samples_dir = directory(os.path.join(
@@ -1232,4 +1266,4 @@ rule MULTIQC_report:
{params.results_dir} \
{params.log_dir} \
&> {log.LOG_local_log};
- """
\ No newline at end of file
+ """
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 1214e0a..5a911b6 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,548 +1,740 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.38.0 (20140413.2041)
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1912pt" height="841pt"
- viewBox="0.00 0.00 1911.56 841.00" 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(4 837)">
+<svg width="2395pt" height="913pt"
+ viewBox="0.00 0.00 2395.00 913.00" 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>
-<polygon fill="white" stroke="none" points="-4,4 -4,-837 1907.56,-837 1907.56,4 -4,4"/>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-909 2391,-909 2391,4 -4,4"/>
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-<text text-anchor="middle" x="1294" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
+<title>0</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1287.5,-36C1287.5,-36 1257.5,-36 1257.5,-36 1251.5,-36 1245.5,-30 1245.5,-24 1245.5,-24 1245.5,-12 1245.5,-12 1245.5,-6 1251.5,0 1257.5,0 1257.5,0 1287.5,0 1287.5,0 1293.5,0 1299.5,-6 1299.5,-12 1299.5,-12 1299.5,-24 1299.5,-24 1299.5,-30 1293.5,-36 1287.5,-36"/>
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</g>
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-<text text-anchor="middle" x="1294" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
+<g id="node2" class="node">
+<title>1</title>
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</g>
<!-- 1->0 -->
-<g id="edge1" class="edge"><title>1->0</title>
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+<title>1->0</title>
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-<text text-anchor="middle" x="1294" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
+<g id="node3" class="node">
+<title>2</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1326.5,-180C1326.5,-180 1218.5,-180 1218.5,-180 1212.5,-180 1206.5,-174 1206.5,-168 1206.5,-168 1206.5,-156 1206.5,-156 1206.5,-150 1212.5,-144 1218.5,-144 1218.5,-144 1326.5,-144 1326.5,-144 1332.5,-144 1338.5,-150 1338.5,-156 1338.5,-156 1338.5,-168 1338.5,-168 1338.5,-174 1332.5,-180 1326.5,-180"/>
+<text text-anchor="middle" x="1272.5" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
</g>
<!-- 2->1 -->
-<g id="edge2" class="edge"><title>2->1</title>
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+<g id="edge2" class="edge">
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<!-- 3 -->
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-<text text-anchor="middle" x="1294" y="-226" font-family="sans" font-size="10.00">output_dir: results</text>
+<g id="node4" class="node">
+<title>3</title>
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+<text text-anchor="middle" x="1272.5" y="-226" font-family="sans" font-size="10.00">output_dir: results</text>
</g>
<!-- 3->2 -->
-<g id="edge3" class="edge"><title>3->2</title>
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+<g id="edge3" class="edge">
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<!-- 4 -->
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-<text text-anchor="middle" x="146" y="-309" font-family="sans" font-size="10.00">pe_fastqc</text>
-<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 id="node5" class="node">
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+<text text-anchor="middle" x="162.5" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
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-<text text-anchor="middle" x="462" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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+<text text-anchor="middle" x="511.5" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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-<g id="edge7" class="edge"><title>7->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1280.09,-359.929C1298.08,-352.036 1315.35,-340.579 1326,-324 1338.64,-304.323 1327.31,-278.989 1314.77,-260.386"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1317.49,-258.175 1308.81,-252.102 1311.81,-262.264 1317.49,-258.175"/>
+<g id="edge7" class="edge">
+<title>7->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1411.65,-360.9C1431.18,-353.05 1449.66,-341.37 1461.5,-324 1470.51,-310.78 1471.17,-300.75 1461.5,-288 1447.55,-269.59 1395.38,-255.82 1349.38,-246.93"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1349.84,-243.46 1339.37,-245.06 1348.55,-250.34 1349.84,-243.46"/>
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<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1462.5,-396C1462.5,-396 1397.5,-396 1397.5,-396 1391.5,-396 1385.5,-390 1385.5,-384 1385.5,-384 1385.5,-372 1385.5,-372 1385.5,-366 1391.5,-360 1397.5,-360 1397.5,-360 1462.5,-360 1462.5,-360 1468.5,-360 1474.5,-366 1474.5,-372 1474.5,-372 1474.5,-384 1474.5,-384 1474.5,-390 1468.5,-396 1462.5,-396"/>
-<text text-anchor="middle" x="1430" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1513.5,-396C1513.5,-396 1443.5,-396 1443.5,-396 1437.5,-396 1431.5,-390 1431.5,-384 1431.5,-384 1431.5,-372 1431.5,-372 1431.5,-366 1437.5,-360 1443.5,-360 1443.5,-360 1513.5,-360 1513.5,-360 1519.5,-360 1525.5,-366 1525.5,-372 1525.5,-372 1525.5,-384 1525.5,-384 1525.5,-390 1519.5,-396 1513.5,-396"/>
+<text text-anchor="middle" x="1478.5" 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="grey" stroke-width="2" d="M1427.43,-359.676C1423.74,-340.193 1415.26,-308.593 1397,-288 1385.29,-274.792 1369.5,-264.41 1353.81,-256.47"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1355.14,-253.228 1344.61,-252.074 1352.12,-259.544 1355.14,-253.228"/>
+<g id="edge8" class="edge">
+<title>8->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1484.14,-359.95C1489.43,-340.43 1494.4,-308.52 1478.5,-288 1462.46,-267.31 1400.99,-253.28 1349.33,-244.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1349.57,-241.37 1339.15,-243.27 1348.48,-248.29 1349.57,-241.37"/>
</g>
<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#568ad8" stroke-width="2" d="M1141,-324C1141,-324 1029,-324 1029,-324 1023,-324 1017,-318 1017,-312 1017,-312 1017,-300 1017,-300 1017,-294 1023,-288 1029,-288 1029,-288 1141,-288 1141,-288 1147,-288 1153,-294 1153,-300 1153,-300 1153,-312 1153,-312 1153,-318 1147,-324 1141,-324"/>
-<text text-anchor="middle" x="1085" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1085" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#56d85b" 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">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1004.5" 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="grey" stroke-width="2" d="M1135.86,-287.966C1165.19,-278.142 1202.25,-265.729 1233.12,-255.389"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1234.54,-258.606 1242.91,-252.111 1232.32,-251.968 1234.54,-258.606"/>
+<g id="edge9" class="edge">
+<title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1069.72,-287.97C1108.22,-277.91 1157.12,-265.14 1197.25,-254.65"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1198.2,-258.02 1206.99,-252.11 1196.43,-251.25 1198.2,-258.02"/>
</g>
<!-- 10 -->
-<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#568ad8" stroke-width="2" d="M1304.5,-324C1304.5,-324 1183.5,-324 1183.5,-324 1177.5,-324 1171.5,-318 1171.5,-312 1171.5,-312 1171.5,-300 1171.5,-300 1171.5,-294 1177.5,-288 1183.5,-288 1183.5,-288 1304.5,-288 1304.5,-288 1310.5,-288 1316.5,-294 1316.5,-300 1316.5,-300 1316.5,-312 1316.5,-312 1316.5,-318 1310.5,-324 1304.5,-324"/>
-<text text-anchor="middle" x="1244" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1244" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#56d85b" 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">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1179.5" 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="grey" stroke-width="2" d="M1256.36,-287.697C1262.23,-279.474 1269.37,-269.483 1275.84,-260.421"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1278.82,-262.276 1281.78,-252.104 1273.12,-258.207 1278.82,-262.276"/>
+<g id="edge10" class="edge">
+<title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1202.49,-287.7C1214.31,-278.8 1228.89,-267.82 1241.68,-258.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1243.89,-260.91 1249.78,-252.1 1239.68,-255.32 1243.89,-260.91"/>
</g>
<!-- 11 -->
-<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#567bd8" stroke-width="2" d="M813.5,-324C813.5,-324 682.5,-324 682.5,-324 676.5,-324 670.5,-318 670.5,-312 670.5,-312 670.5,-300 670.5,-300 670.5,-294 676.5,-288 682.5,-288 682.5,-288 813.5,-288 813.5,-288 819.5,-288 825.5,-294 825.5,-300 825.5,-300 825.5,-312 825.5,-312 825.5,-318 819.5,-324 813.5,-324"/>
-<text text-anchor="middle" x="748" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="748" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#56c1d8" 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">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1365.5" 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="grey" stroke-width="2" d="M825.735,-289.499C828.861,-288.974 831.958,-288.472 835,-288 972.388,-266.678 1134.14,-249.934 1224.29,-241.342"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1224.76,-244.813 1234.38,-240.385 1224.1,-237.844 1224.76,-244.813"/>
+<g id="edge11" class="edge">
+<title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1342.51,-287.7C1330.69,-278.8 1316.11,-267.82 1303.32,-258.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1305.32,-255.32 1295.22,-252.1 1301.11,-260.91 1305.32,-255.32"/>
</g>
<!-- 12 -->
-<g id="node13" class="node"><title>12</title>
-<path fill="none" stroke="#567bd8" stroke-width="2" d="M986.5,-324C986.5,-324 855.5,-324 855.5,-324 849.5,-324 843.5,-318 843.5,-312 843.5,-312 843.5,-300 843.5,-300 843.5,-294 849.5,-288 855.5,-288 855.5,-288 986.5,-288 986.5,-288 992.5,-288 998.5,-294 998.5,-300 998.5,-300 998.5,-312 998.5,-312 998.5,-318 992.5,-324 986.5,-324"/>
-<text text-anchor="middle" x="921" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="921" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#56c1d8" 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">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="823.5" 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="grey" stroke-width="2" d="M998.781,-289.763C1001.89,-289.165 1004.98,-288.576 1008,-288 1081.71,-273.97 1166.2,-258.372 1224.12,-247.753"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1225.06,-251.141 1234.26,-245.896 1223.79,-244.255 1225.06,-251.141"/>
+<g id="edge12" class="edge">
+<title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M910.6,-289.47C913.6,-288.97 916.58,-288.48 919.5,-288 1014.37,-272.48 1123.88,-256.31 1195.45,-245.97"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1196.33,-249.38 1205.73,-244.49 1195.33,-242.46 1196.33,-249.38"/>
</g>
<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1358.5,-540C1358.5,-540 1327.5,-540 1327.5,-540 1321.5,-540 1315.5,-534 1315.5,-528 1315.5,-528 1315.5,-516 1315.5,-516 1315.5,-510 1321.5,-504 1327.5,-504 1327.5,-504 1358.5,-504 1358.5,-504 1364.5,-504 1370.5,-510 1370.5,-516 1370.5,-516 1370.5,-528 1370.5,-528 1370.5,-534 1364.5,-540 1358.5,-540"/>
-<text text-anchor="middle" x="1343" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#8fd856" 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">star_rpm</text>
</g>
<!-- 13->3 -->
-<g id="edge13" class="edge"><title>13->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1346.95,-503.853C1355.25,-464.209 1371.41,-363.802 1342,-288 1337.87,-277.367 1330.53,-267.54 1322.8,-259.309"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1325.24,-256.797 1315.68,-252.222 1320.3,-261.758 1325.24,-256.797"/>
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-<!-- 28 -->
-<g id="node29" class="node"><title>28</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1489,-468C1489,-468 1383,-468 1383,-468 1377,-468 1371,-462 1371,-456 1371,-456 1371,-444 1371,-444 1371,-438 1377,-432 1383,-432 1383,-432 1489,-432 1489,-432 1495,-432 1501,-438 1501,-444 1501,-444 1501,-456 1501,-456 1501,-462 1495,-468 1489,-468"/>
-<text text-anchor="middle" x="1436" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-</g>
-<!-- 13->28 -->
-<g id="edge56" class="edge"><title>13->28</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1365.99,-503.697C1377.81,-494.796 1392.39,-483.823 1405.18,-474.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1407.39,-476.915 1413.28,-468.104 1403.18,-471.322 1407.39,-476.915"/>
+<g id="edge13" class="edge">
+<title>13->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1684.35,-579.62C1681.37,-578.37 1678.38,-577.15 1675.5,-576 1631.6,-558.55 1606.57,-575.58 1575.5,-540 1548.9,-509.53 1556.5,-491.45 1556.5,-451 1556.5,-451 1556.5,-451 1556.5,-377 1556.5,-284.03 1433.25,-251.93 1349.14,-240.84"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1349.44,-237.36 1339.09,-239.59 1348.58,-244.3 1349.44,-237.36"/>
+</g>
+<!-- 40 -->
+<g id="node41" class="node">
+<title>40</title>
+<path fill="none" stroke="#d87556" 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">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1821.5" y="-514" font-family="sans" font-size="10.00">unique: Unique</text>
+</g>
+<!-- 13->40 -->
+<g id="edge69" class="edge">
+<title>13->40</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1740.68,-575.88C1754.54,-566.81 1771.74,-555.55 1786.71,-545.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1788.77,-548.59 1795.22,-540.19 1784.94,-542.74 1788.77,-548.59"/>
+</g>
+<!-- 43 -->
+<g id="node44" class="node">
+<title>43</title>
+<path fill="none" stroke="#d87556" 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">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1657.5" y="-514" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
+</g>
+<!-- 13->43 -->
+<g id="edge72" class="edge">
+<title>13->43</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1700.41,-575.7C1693.58,-567.3 1685.24,-557.07 1677.74,-547.86"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1680.46,-545.65 1671.43,-540.1 1675.03,-550.07 1680.46,-545.65"/>
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<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1863.5,-540C1863.5,-540 1832.5,-540 1832.5,-540 1826.5,-540 1820.5,-534 1820.5,-528 1820.5,-528 1820.5,-516 1820.5,-516 1820.5,-510 1826.5,-504 1832.5,-504 1832.5,-504 1863.5,-504 1863.5,-504 1869.5,-504 1875.5,-510 1875.5,-516 1875.5,-516 1875.5,-528 1875.5,-528 1875.5,-534 1869.5,-540 1863.5,-540"/>
-<text text-anchor="middle" x="1848" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#8fd856" 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">star_rpm</text>
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<!-- 14->3 -->
-<g id="edge14" class="edge"><title>14->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1870.6,-503.963C1881.06,-494.635 1892.4,-482.107 1898,-468 1903.91,-453.13 1906.17,-445.758 1898,-432 1829.77,-317.072 1760.57,-330.929 1634,-288 1543.54,-257.32 1433.45,-244.289 1363.54,-238.829"/>
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-<!-- 30 -->
-<g id="node31" class="node"><title>30</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1877,-468C1877,-468 1771,-468 1771,-468 1765,-468 1759,-462 1759,-456 1759,-456 1759,-444 1759,-444 1759,-438 1765,-432 1771,-432 1771,-432 1877,-432 1877,-432 1883,-432 1889,-438 1889,-444 1889,-444 1889,-456 1889,-456 1889,-462 1883,-468 1877,-468"/>
-<text text-anchor="middle" x="1824" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
-</g>
-<!-- 14->30 -->
-<g id="edge58" class="edge"><title>14->30</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1842.07,-503.697C1839.39,-495.898 1836.17,-486.509 1833.2,-477.829"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1836.42,-476.429 1829.86,-468.104 1829.8,-478.699 1836.42,-476.429"/>
+<g id="edge14" class="edge">
+<title>14->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2106.68,-591.6C2173.1,-587.9 2328.91,-575.54 2365.5,-540 2394.51,-511.82 2384.5,-491.45 2384.5,-451 2384.5,-451 2384.5,-451 2384.5,-377 2384.5,-272.44 1600.92,-243.36 1349.3,-236.72"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1349.23,-233.22 1339.14,-236.46 1349.05,-240.21 1349.23,-233.22"/>
+</g>
+<!-- 42 -->
+<g id="node43" class="node">
+<title>42</title>
+<path fill="none" stroke="#d87556" 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">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="2283.5" y="-514" font-family="sans" font-size="10.00">unique: Unique</text>
+</g>
+<!-- 14->42 -->
+<g id="edge71" class="edge">
+<title>14->42</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2106.6,-582.82C2137.09,-572.51 2185.1,-556.27 2223.42,-543.32"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2224.58,-546.62 2232.93,-540.1 2222.34,-539.99 2224.58,-546.62"/>
+</g>
+<!-- 44 -->
+<g id="node45" class="node">
+<title>44</title>
+<path fill="none" stroke="#d87556" 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">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1985.5" y="-514" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
+</g>
+<!-- 14->44 -->
+<g id="edge73" class="edge">
+<title>14->44</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2054.01,-575.7C2042.54,-566.88 2028.44,-556.03 2016.02,-546.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2017.8,-543.43 2007.74,-540.1 2013.53,-548.98 2017.8,-543.43"/>
</g>
<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M1549,-396C1549,-396 1519,-396 1519,-396 1513,-396 1507,-390 1507,-384 1507,-384 1507,-372 1507,-372 1507,-366 1513,-360 1519,-360 1519,-360 1549,-360 1549,-360 1555,-360 1561,-366 1561,-372 1561,-372 1561,-384 1561,-384 1561,-390 1555,-396 1549,-396"/>
-<text text-anchor="middle" x="1534" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#afd856" 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">alfa_concat_results</text>
</g>
<!-- 15->3 -->
-<g id="edge15" class="edge"><title>15->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1515.56,-359.869C1494.09,-340.564 1456.96,-309.127 1421,-288 1399.74,-275.506 1374.97,-264.471 1352.99,-255.749"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1354.02,-252.395 1343.43,-252.032 1351.48,-258.919 1354.02,-252.395"/>
+<g id="edge15" class="edge">
+<title>15->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1792.75,-298.22C1689.19,-285.64 1466.99,-258.64 1349.3,-244.33"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1349.63,-240.85 1339.28,-243.12 1348.78,-247.8 1349.63,-240.85"/>
</g>
-<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#56d863" stroke-width="2" d="M1580.5,-324C1580.5,-324 1499.5,-324 1499.5,-324 1493.5,-324 1487.5,-318 1487.5,-312 1487.5,-312 1487.5,-300 1487.5,-300 1487.5,-294 1493.5,-288 1499.5,-288 1499.5,-288 1580.5,-288 1580.5,-288 1586.5,-288 1592.5,-294 1592.5,-300 1592.5,-300 1592.5,-312 1592.5,-312 1592.5,-318 1586.5,-324 1580.5,-324"/>
-<text text-anchor="middle" x="1540" y="-303.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<!-- 16 -->
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#5682d8" 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">pe_remove_polya_cutadapt</text>
</g>
-<!-- 15->17 -->
-<g id="edge39" class="edge"><title>15->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1535.48,-359.697C1536.14,-351.983 1536.94,-342.712 1537.68,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1541.17,-334.367 1538.53,-324.104 1534.19,-333.769 1541.17,-334.367"/>
+<!-- 16->6 -->
+<g id="edge16" class="edge">
+<title>16->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M949.62,-794.37C924.03,-769.18 881.5,-719.42 881.5,-667 881.5,-667 881.5,-667 881.5,-521 881.5,-477.91 858.9,-432.26 842.42,-404.7"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="845.33,-402.75 837.1,-396.07 839.37,-406.42 845.33,-402.75"/>
</g>
-<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M1684,-396C1684,-396 1654,-396 1654,-396 1648,-396 1642,-390 1642,-384 1642,-384 1642,-372 1642,-372 1642,-366 1648,-360 1654,-360 1654,-360 1684,-360 1684,-360 1690,-360 1696,-366 1696,-372 1696,-372 1696,-384 1696,-384 1696,-390 1690,-396 1684,-396"/>
-<text text-anchor="middle" x="1669" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#ced856" 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">pe_quantification_salmon</text>
+</g>
+<!-- 16->20 -->
+<g id="edge40" class="edge">
+<title>16->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M968.5,-794.15C968.5,-767.02 968.5,-712.91 968.5,-667 968.5,-667 968.5,-667 968.5,-521 968.5,-479.48 984.54,-433.61 996.3,-405.54"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="999.65,-406.62 1000.41,-396.05 993.23,-403.84 999.65,-406.62"/>
</g>
-<!-- 16->3 -->
-<g id="edge16" class="edge"><title>16->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1661.08,-359.778C1650.64,-339.151 1630.23,-305.229 1602,-288 1563.05,-264.229 1442.32,-248.815 1364.09,-241.038"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1364.12,-237.524 1353.83,-240.037 1363.44,-244.491 1364.12,-237.524"/>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#d85656" 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">pe_map_genome_star</text>
</g>
-<!-- 16->17 -->
-<g id="edge40" class="edge"><title>16->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1641.96,-362.326C1624.15,-352.661 1600.5,-339.831 1580.47,-328.96"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1582.01,-325.815 1571.55,-324.122 1578.67,-331.968 1582.01,-325.815"/>
+<!-- 16->22 -->
+<g id="edge45" class="edge">
+<title>16->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1044.75,-803.57C1180.05,-789.5 1460.31,-760.34 1592.93,-746.55"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1593.4,-750.02 1602.99,-745.5 1592.68,-743.06 1593.4,-750.02"/>
</g>
-<!-- 17->3 -->
-<g id="edge17" class="edge"><title>17->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1487.23,-289.983C1451.05,-279.688 1402.67,-265.923 1363.38,-254.742"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1364.17,-251.329 1353.6,-251.958 1362.26,-258.062 1364.17,-251.329"/>
+<!-- 17 -->
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#56b1d8" 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">create_index_kallisto</text>
+</g>
+<!-- 17->6 -->
+<g id="edge17" class="edge">
+<title>17->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1135.85,-434.02C1132.69,-433.32 1129.56,-432.64 1126.5,-432 1089.55,-424.27 1000.66,-408.75 929.01,-396.5"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="929.46,-393.03 919.02,-394.79 928.28,-399.93 929.46,-393.03"/>
+</g>
+<!-- 17->7 -->
+<g id="edge19" class="edge">
+<title>17->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1228.3,-431.88C1245.61,-422.55 1267.22,-410.92 1285.76,-400.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1287.43,-404.01 1294.58,-396.19 1284.11,-397.85 1287.43,-404.01"/>
</g>
<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M916,-758.5C916,-758.5 804,-758.5 804,-758.5 798,-758.5 792,-752.5 792,-746.5 792,-746.5 792,-734.5 792,-734.5 792,-728.5 798,-722.5 804,-722.5 804,-722.5 916,-722.5 916,-722.5 922,-722.5 928,-728.5 928,-734.5 928,-734.5 928,-746.5 928,-746.5 928,-752.5 922,-758.5 916,-758.5"/>
-<text text-anchor="middle" x="860" y="-738" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#d8a456" 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">remove_polya_cutadapt</text>
</g>
-<!-- 18->6 -->
-<g id="edge18" class="edge"><title>18->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M845.155,-722.122C824.607,-696.23 790,-645.176 790,-595 790,-595 790,-595 790,-521 790,-480.098 777.572,-434.063 768.454,-405.793"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="771.749,-404.61 765.273,-396.224 765.106,-406.817 771.749,-404.61"/>
+<!-- 18->7 -->
+<g id="edge18" class="edge">
+<title>18->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1323.5,-794.15C1323.5,-767.02 1323.5,-712.91 1323.5,-667 1323.5,-667 1323.5,-667 1323.5,-521 1323.5,-480.99 1324.71,-434.65 1325.59,-406.08"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1329.09,-406.15 1325.91,-396.05 1322.09,-405.93 1329.09,-406.15"/>
</g>
-<!-- 22 -->
-<g id="node23" class="node"><title>22</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M975.5,-396C975.5,-396 872.5,-396 872.5,-396 866.5,-396 860.5,-390 860.5,-384 860.5,-384 860.5,-372 860.5,-372 860.5,-366 866.5,-360 872.5,-360 872.5,-360 975.5,-360 975.5,-360 981.5,-360 987.5,-366 987.5,-372 987.5,-372 987.5,-384 987.5,-384 987.5,-390 981.5,-396 975.5,-396"/>
-<text text-anchor="middle" x="924" y="-375.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#9fd856" 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">quantification_salmon</text>
</g>
-<!-- 18->22 -->
-<g id="edge46" class="edge"><title>18->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M860,-722.151C860,-695.022 860,-640.909 860,-595 860,-595 860,-595 860,-521 860,-480.458 862.112,-468.382 880,-432 884.958,-421.915 892.205,-412.093 899.392,-403.699"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="902.113,-405.907 906.188,-396.127 896.904,-401.232 902.113,-405.907"/>
+<!-- 18->21 -->
+<g id="edge42" class="edge">
+<title>18->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1315.81,-794.09C1304.71,-767.33 1285.5,-714.21 1285.5,-667 1285.5,-667 1285.5,-667 1285.5,-521 1285.5,-480.55 1291.26,-463.98 1266.5,-432 1256.12,-418.59 1241.44,-408.33 1226.31,-400.57"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1227.39,-397.21 1216.86,-396.05 1224.37,-403.52 1227.39,-397.21"/>
</g>
<!-- 24 -->
-<g id="node25" class="node"><title>24</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1387.5,-684C1387.5,-684 1298.5,-684 1298.5,-684 1292.5,-684 1286.5,-678 1286.5,-672 1286.5,-672 1286.5,-660 1286.5,-660 1286.5,-654 1292.5,-648 1298.5,-648 1298.5,-648 1387.5,-648 1387.5,-648 1393.5,-648 1399.5,-654 1399.5,-660 1399.5,-660 1399.5,-672 1399.5,-672 1399.5,-678 1393.5,-684 1387.5,-684"/>
-<text text-anchor="middle" x="1343" y="-663.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M1919,-756C1919,-756 1836,-756 1836,-756 1830,-756 1824,-750 1824,-744 1824,-744 1824,-732 1824,-732 1824,-726 1830,-720 1836,-720 1836,-720 1919,-720 1919,-720 1925,-720 1931,-726 1931,-732 1931,-732 1931,-744 1931,-744 1931,-750 1925,-756 1919,-756"/>
+<text text-anchor="middle" x="1877.5" y="-735.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 18->24 -->
-<g id="edge51" class="edge"><title>18->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M928.178,-729.266C1020.66,-715.384 1184.83,-690.742 1276.46,-676.988"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1277.08,-680.433 1286.45,-675.488 1276.05,-673.511 1277.08,-680.433"/>
+<g id="edge48" class="edge">
+<title>18->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1390.6,-802.72C1498.21,-788.64 1707.99,-761.18 1813.56,-747.37"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1814.29,-750.8 1823.75,-746.03 1813.38,-743.86 1814.29,-750.8"/>
</g>
<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#68d856" stroke-width="2" d="M1112,-468C1112,-468 1028,-468 1028,-468 1022,-468 1016,-462 1016,-456 1016,-456 1016,-444 1016,-444 1016,-438 1022,-432 1028,-432 1028,-432 1112,-432 1112,-432 1118,-432 1124,-438 1124,-444 1124,-444 1124,-456 1124,-456 1124,-462 1118,-468 1112,-468"/>
-<text text-anchor="middle" x="1070" y="-447.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
-</g>
-<!-- 19->6 -->
-<g id="edge19" class="edge"><title>19->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1015.75,-434.165C1012.79,-433.418 1009.86,-432.692 1007,-432 956.065,-419.694 898.887,-407.375 852.28,-397.715"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="852.7,-394.228 842.199,-395.632 851.284,-401.083 852.7,-394.228"/>
-</g>
-<!-- 19->7 -->
-<g id="edge21" class="edge"><title>19->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1104.25,-431.876C1123.06,-422.469 1146.58,-410.708 1166.67,-400.667"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1168.24,-403.792 1175.62,-396.19 1165.11,-397.531 1168.24,-403.792"/>
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-<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1238,-758.5C1238,-758.5 1142,-758.5 1142,-758.5 1136,-758.5 1130,-752.5 1130,-746.5 1130,-746.5 1130,-734.5 1130,-734.5 1130,-728.5 1136,-722.5 1142,-722.5 1142,-722.5 1238,-722.5 1238,-722.5 1244,-722.5 1250,-728.5 1250,-734.5 1250,-734.5 1250,-746.5 1250,-746.5 1250,-752.5 1244,-758.5 1238,-758.5"/>
-<text text-anchor="middle" x="1190" y="-738" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
-</g>
-<!-- 20->7 -->
-<g id="edge20" class="edge"><title>20->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1190,-722.151C1190,-695.022 1190,-640.909 1190,-595 1190,-595 1190,-595 1190,-521 1190,-480.822 1197.95,-434.869 1203.82,-406.389"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1207.3,-406.887 1205.95,-396.378 1200.45,-405.431 1207.3,-406.887"/>
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#70d856" 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">merge_TIN_scores</text>
+</g>
+<!-- 19->8 -->
+<g id="edge20" class="edge">
+<title>19->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1474.98,-503.87C1475.66,-479.67 1476.92,-435.21 1477.73,-406.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1481.23,-406.28 1478.02,-396.19 1474.24,-406.09 1481.23,-406.28"/>
+</g>
+<!-- 20->9 -->
+<g id="edge21" class="edge">
+<title>20->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1007.51,-359.7C1007.07,-351.98 1006.54,-342.71 1006.05,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1009.54,-333.89 1005.48,-324.1 1002.55,-334.29 1009.54,-333.89"/>
+</g>
+<!-- 20->10 -->
+<g id="edge23" class="edge">
+<title>20->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1050.33,-359.88C1073.92,-350.22 1103.56,-338.09 1128.5,-327.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1129.88,-331.1 1137.8,-324.07 1127.22,-324.62 1129.88,-331.1"/>
+</g>
+<!-- 20->11 -->
+<g id="edge25" class="edge">
+<title>20->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1079.6,-362C1082.95,-361.32 1086.26,-360.65 1089.5,-360 1148.82,-348.08 1215.43,-335.27 1268.35,-325.23"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1269.24,-328.63 1278.41,-323.33 1267.93,-321.75 1269.24,-328.63"/>
+</g>
+<!-- 20->12 -->
+<g id="edge27" class="edge">
+<title>20->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M963.24,-359.88C937.5,-350.14 905.09,-337.87 877.96,-327.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="879.2,-324.33 868.61,-324.07 876.72,-330.88 879.2,-324.33"/>
+</g>
+<!-- 21->9 -->
+<g id="edge22" class="edge">
+<title>21->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1122.34,-359.88C1101.11,-350.35 1074.49,-338.41 1051.93,-328.28"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1053.09,-324.97 1042.54,-324.07 1050.23,-331.36 1053.09,-324.97"/>
+</g>
+<!-- 21->10 -->
+<g id="edge24" class="edge">
+<title>21->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1165.2,-359.7C1167.31,-351.9 1169.86,-342.51 1172.22,-333.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1175.62,-334.67 1174.86,-324.1 1168.86,-332.84 1175.62,-334.67"/>
+</g>
+<!-- 21->11 -->
+<g id="edge26" class="edge">
+<title>21->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1210.39,-359.97C1239.15,-350.14 1275.51,-337.73 1305.79,-327.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1307.06,-330.65 1315.39,-324.11 1304.8,-324.03 1307.06,-330.65"/>
+</g>
+<!-- 21->12 -->
+<g id="edge28" class="edge">
+<title>21->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1097.7,-362.04C1094.59,-361.34 1091.51,-360.66 1088.5,-360 1033.06,-347.91 970.86,-335.42 920.66,-325.6"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="921.27,-322.15 910.79,-323.67 919.93,-329.02 921.27,-322.15"/>
+</g>
+<!-- 22->13 -->
+<g id="edge29" class="edge">
+<title>22->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1727.75,-719.95C1745.25,-711.98 1762.28,-700.47 1772.5,-684 1780.94,-670.41 1778.95,-662.64 1772.5,-648 1767.51,-636.69 1758.79,-626.74 1749.6,-618.62"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1751.78,-615.88 1741.84,-612.23 1747.33,-621.28 1751.78,-615.88"/>
</g>
<!-- 23 -->
-<g id="node24" class="node"><title>23</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1104.5,-396C1104.5,-396 1017.5,-396 1017.5,-396 1011.5,-396 1005.5,-390 1005.5,-384 1005.5,-384 1005.5,-372 1005.5,-372 1005.5,-366 1011.5,-360 1017.5,-360 1017.5,-360 1104.5,-360 1104.5,-360 1110.5,-360 1116.5,-366 1116.5,-372 1116.5,-372 1116.5,-384 1116.5,-384 1116.5,-390 1110.5,-396 1104.5,-396"/>
-<text text-anchor="middle" x="1061" y="-375.5" font-family="sans" font-size="10.00">quantification_salmon</text>
-</g>
-<!-- 20->23 -->
-<g id="edge48" class="edge"><title>20->23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1182.31,-722.093C1171.21,-695.328 1152,-642.21 1152,-595 1152,-595 1152,-595 1152,-521 1152,-480.553 1154.94,-465.98 1133,-432 1125.28,-420.038 1113.84,-409.843 1102.35,-401.685"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1104.28,-398.765 1094.02,-396.109 1100.39,-404.581 1104.28,-398.765"/>
-</g>
-<!-- 26 -->
-<g id="node27" class="node"><title>26</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M1753.5,-684C1753.5,-684 1680.5,-684 1680.5,-684 1674.5,-684 1668.5,-678 1668.5,-672 1668.5,-672 1668.5,-660 1668.5,-660 1668.5,-654 1674.5,-648 1680.5,-648 1680.5,-648 1753.5,-648 1753.5,-648 1759.5,-648 1765.5,-654 1765.5,-660 1765.5,-660 1765.5,-672 1765.5,-672 1765.5,-678 1759.5,-684 1753.5,-684"/>
-<text text-anchor="middle" x="1717" y="-663.5" font-family="sans" font-size="10.00">map_genome_star</text>
-</g>
-<!-- 20->26 -->
-<g id="edge54" class="edge"><title>20->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1250.2,-731.219C1352.16,-717.192 1557.56,-688.934 1658.42,-675.059"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1659,-678.512 1668.43,-673.682 1658.05,-671.577 1659,-678.512"/>
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#56d87b" 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">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1665.5" 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="grey" stroke-width="2" d="M1665.5,-719.7C1665.5,-711.98 1665.5,-702.71 1665.5,-694.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1669,-694.1 1665.5,-684.1 1662,-694.1 1669,-694.1"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M1607,-468C1607,-468 1531,-468 1531,-468 1525,-468 1519,-462 1519,-456 1519,-456 1519,-444 1519,-444 1519,-438 1525,-432 1531,-432 1531,-432 1607,-432 1607,-432 1613,-432 1619,-438 1619,-444 1619,-444 1619,-456 1619,-456 1619,-462 1613,-468 1607,-468"/>
-<text text-anchor="middle" x="1569" y="-447.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
-</g>
-<!-- 21->8 -->
-<g id="edge22" class="edge"><title>21->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1535,-431.876C1516.4,-422.512 1493.17,-410.814 1473.29,-400.803"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1474.64,-397.562 1464.13,-396.19 1471.49,-403.814 1474.64,-397.562"/>
-</g>
-<!-- 22->9 -->
-<g id="edge23" class="edge"><title>22->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M963.385,-359.876C985.395,-350.307 1013.01,-338.3 1036.36,-328.148"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1037.97,-331.265 1045.74,-324.068 1035.18,-324.846 1037.97,-331.265"/>
-</g>
-<!-- 22->10 -->
-<g id="edge25" class="edge"><title>22->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M987.686,-362.1C990.834,-361.385 993.952,-360.682 997,-360 1051.64,-347.776 1113.21,-334.563 1161.21,-324.387"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1162.19,-327.759 1171.24,-322.264 1160.74,-320.911 1162.19,-327.759"/>
-</g>
-<!-- 22->11 -->
-<g id="edge27" class="edge"><title>22->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M880.946,-359.876C856.671,-350.222 826.16,-338.087 800.492,-327.878"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="801.5,-324.512 790.915,-324.068 798.913,-331.016 801.5,-324.512"/>
-</g>
-<!-- 22->12 -->
-<g id="edge29" class="edge"><title>22->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M923.258,-359.697C922.928,-351.983 922.531,-342.712 922.162,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="925.658,-333.945 921.733,-324.104 918.665,-334.245 925.658,-333.945"/>
-</g>
-<!-- 23->9 -->
-<g id="edge24" class="edge"><title>23->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1066.93,-359.697C1069.61,-351.898 1072.83,-342.509 1075.8,-333.829"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1079.2,-334.699 1079.14,-324.104 1072.58,-332.429 1079.2,-334.699"/>
-</g>
-<!-- 23->10 -->
-<g id="edge26" class="edge"><title>23->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1105.77,-359.876C1131.12,-350.179 1163.01,-337.98 1189.77,-327.743"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1191.29,-330.91 1199.38,-324.068 1188.79,-324.372 1191.29,-330.91"/>
-</g>
-<!-- 23->11 -->
-<g id="edge28" class="edge"><title>23->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1005.19,-362.001C1002.43,-361.312 999.684,-360.642 997,-360 943.625,-347.239 883.449,-334.389 835.625,-324.537"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="836.114,-321.065 825.615,-322.482 834.706,-327.922 836.114,-321.065"/>
-</g>
-<!-- 23->12 -->
-<g id="edge30" class="edge"><title>23->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1026.75,-359.876C1007.94,-350.469 984.415,-338.708 964.334,-328.667"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="965.889,-325.531 955.38,-324.19 962.759,-331.792 965.889,-325.531"/>
-</g>
-<!-- 24->13 -->
-<g id="edge31" class="edge"><title>24->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1289.78,-647.963C1273.11,-639.835 1256.58,-628.231 1247,-612 1238.87,-598.221 1238.87,-589.779 1247,-576 1259.61,-554.628 1284.27,-541.279 1305.44,-533.324"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1306.88,-536.53 1315.17,-529.94 1304.58,-529.918 1306.88,-536.53"/>
+<!-- 31 -->
+<g id="node32" class="node">
+<title>31</title>
+<path fill="none" stroke="#d8c356" 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">calculate_TIN_scores</text>
+</g>
+<!-- 22->31 -->
+<g id="edge54" class="edge">
+<title>22->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1602.85,-734.4C1527.66,-729.8 1408.21,-717.33 1380.5,-684 1370.27,-671.7 1372.59,-661.91 1380.5,-648 1387.86,-635.04 1399.79,-624.92 1412.55,-617.16"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1414.46,-620.1 1421.47,-612.15 1411.03,-613.99 1414.46,-620.1"/>
+</g>
+<!-- 23->13 -->
+<g id="edge30" class="edge">
+<title>23->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1677.61,-647.7C1683.37,-639.47 1690.36,-629.48 1696.71,-620.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1699.66,-622.3 1702.53,-612.1 1693.92,-618.29 1699.66,-622.3"/>
+</g>
+<!-- 23->31 -->
+<g id="edge55" class="edge">
+<title>23->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1617.8,-647.97C1590.42,-638.19 1555.84,-625.84 1526.97,-615.52"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1528,-612.18 1517.41,-612.11 1525.65,-618.77 1528,-612.18"/>
+</g>
+<!-- 24->14 -->
+<g id="edge31" class="edge">
+<title>24->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1931.01,-736.44C1973.04,-732.97 2029.75,-721.05 2062.5,-684 2077.18,-667.39 2079.9,-641.89 2079.4,-622.43"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2082.89,-622.13 2078.84,-612.34 2075.9,-622.52 2082.89,-622.13"/>
</g>
<!-- 25 -->
-<g id="node26" class="node"><title>25</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M1418,-612C1418,-612 1268,-612 1268,-612 1262,-612 1256,-606 1256,-600 1256,-600 1256,-588 1256,-588 1256,-582 1262,-576 1268,-576 1268,-576 1418,-576 1418,-576 1424,-576 1430,-582 1430,-588 1430,-588 1430,-600 1430,-600 1430,-606 1424,-612 1418,-612"/>
-<text text-anchor="middle" x="1343" y="-597" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1343" y="-586" font-family="sans" font-size="10.00">seqmode: paired_end</text>
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#56d87b" 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">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1955.5" y="-658" font-family="sans" font-size="10.00">seqmode: single_end</text>
</g>
<!-- 24->25 -->
-<g id="edge52" class="edge"><title>24->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1343,-647.697C1343,-639.983 1343,-630.712 1343,-622.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-622.104 1343,-612.104 1339.5,-622.104 1346.5,-622.104"/>
+<g id="edge49" class="edge">
+<title>24->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1896.78,-719.7C1906.42,-711.05 1918.23,-700.45 1928.73,-691.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1931.34,-693.39 1936.44,-684.1 1926.66,-688.18 1931.34,-693.39"/>
</g>
-<!-- 34 -->
-<g id="node35" class="node"><title>34</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M1520,-540C1520,-540 1432,-540 1432,-540 1426,-540 1420,-534 1420,-528 1420,-528 1420,-516 1420,-516 1420,-510 1426,-504 1432,-504 1432,-504 1520,-504 1520,-504 1526,-504 1532,-510 1532,-516 1532,-516 1532,-528 1532,-528 1532,-534 1526,-540 1520,-540"/>
-<text text-anchor="middle" x="1476" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
-</g>
-<!-- 24->34 -->
-<g id="edge59" class="edge"><title>24->34</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1387.92,-647.937C1405.7,-639.364 1425.16,-627.461 1439,-612 1454.73,-594.433 1464.35,-569.241 1469.82,-550.14"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1473.27,-550.805 1472.45,-540.242 1466.5,-549.01 1473.27,-550.805"/>
-</g>
-<!-- 25->13 -->
-<g id="edge32" class="edge"><title>25->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1343,-575.697C1343,-567.983 1343,-558.712 1343,-550.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-550.104 1343,-540.104 1339.5,-550.104 1346.5,-550.104"/>
-</g>
-<!-- 25->34 -->
-<g id="edge60" class="edge"><title>25->34</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1375.54,-575.876C1393.25,-566.554 1415.35,-554.919 1434.32,-544.939"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1436.12,-547.944 1443.34,-540.19 1432.86,-541.75 1436.12,-547.944"/>
-</g>
-<!-- 26->14 -->
-<g id="edge33" class="edge"><title>26->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1765.69,-662.525C1801.26,-657.86 1847.27,-645.261 1871,-612 1884.22,-593.466 1875.57,-567.952 1865.31,-548.991"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1868.29,-547.152 1860.23,-540.269 1862.24,-550.673 1868.29,-547.152"/>
+<!-- 32 -->
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#d8c356" 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">calculate_TIN_scores</text>
+</g>
+<!-- 24->32 -->
+<g id="edge57" class="edge">
+<title>24->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1861.6,-719.93C1842.27,-700.09 1807.82,-667.58 1772.5,-648 1755.44,-638.54 1713.43,-625.16 1675.95,-614.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1676.61,-610.76 1666.03,-611.34 1674.66,-617.48 1676.61,-610.76"/>
+</g>
+<!-- 25->14 -->
+<g id="edge32" class="edge">
+<title>25->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1985.1,-647.88C2001.07,-638.64 2020.96,-627.13 2038.11,-617.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2039.88,-620.23 2046.79,-612.19 2036.38,-614.17 2039.88,-620.23"/>
+</g>
+<!-- 25->32 -->
+<g id="edge58" class="edge">
+<title>25->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1858.37,-647.96C1806.91,-638.61 1742.42,-626.39 1676.09,-612.07"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1676.81,-608.64 1666.29,-609.94 1675.32,-615.49 1676.81,-608.64"/>
+</g>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#56d8a9" 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">alfa_qc_all_samples</text>
+</g>
+<!-- 26->15 -->
+<g id="edge33" class="edge">
+<title>26->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1949.72,-359.88C1931.87,-350.55 1909.6,-338.92 1890.5,-328.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1891.89,-325.72 1881.41,-324.19 1888.65,-331.92 1891.89,-325.72"/>
</g>
<!-- 27 -->
-<g id="node28" class="node"><title>27</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M1850,-612C1850,-612 1700,-612 1700,-612 1694,-612 1688,-606 1688,-600 1688,-600 1688,-588 1688,-588 1688,-582 1694,-576 1700,-576 1700,-576 1850,-576 1850,-576 1856,-576 1862,-582 1862,-588 1862,-588 1862,-600 1862,-600 1862,-606 1856,-612 1850,-612"/>
-<text text-anchor="middle" x="1775" y="-597" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1775" y="-586" font-family="sans" font-size="10.00">seqmode: single_end</text>
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#56d8a9" 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">alfa_qc_all_samples</text>
</g>
-<!-- 26->27 -->
-<g id="edge55" class="edge"><title>26->27</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1731.34,-647.697C1738.29,-639.305 1746.77,-629.07 1754.4,-619.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1757.14,-622.038 1760.83,-612.104 1751.75,-617.571 1757.14,-622.038"/>
+<!-- 27->15 -->
+<g id="edge34" class="edge">
+<title>27->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1848.5,-359.7C1848.5,-351.98 1848.5,-342.71 1848.5,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1852,-334.1 1848.5,-324.1 1845,-334.1 1852,-334.1"/>
</g>
-<!-- 35 -->
-<g id="node36" class="node"><title>35</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M1668,-540C1668,-540 1580,-540 1580,-540 1574,-540 1568,-534 1568,-528 1568,-528 1568,-516 1568,-516 1568,-510 1574,-504 1580,-504 1580,-504 1668,-504 1668,-504 1674,-504 1680,-510 1680,-516 1680,-516 1680,-528 1680,-528 1680,-534 1674,-540 1668,-540"/>
-<text text-anchor="middle" x="1624" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
-</g>
-<!-- 26->35 -->
-<g id="edge62" class="edge"><title>26->35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1704.03,-647.545C1696.54,-637.31 1687.04,-624.06 1679,-612 1665.11,-591.148 1650.21,-566.925 1639.44,-549.019"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1642.34,-547.061 1634.2,-540.282 1636.34,-550.659 1642.34,-547.061"/>
-</g>
-<!-- 27->14 -->
-<g id="edge34" class="edge"><title>27->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1793.04,-575.697C1802.06,-567.05 1813.12,-556.449 1822.94,-547.027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1825.37,-549.552 1830.16,-540.104 1820.52,-544.499 1825.37,-549.552"/>
-</g>
-<!-- 27->35 -->
-<g id="edge63" class="edge"><title>27->35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1738.06,-575.876C1717.51,-566.349 1691.75,-554.407 1669.91,-544.283"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1671.36,-541.099 1660.82,-540.068 1668.42,-547.45 1671.36,-541.099"/>
-</g>
-<!-- 28->15 -->
-<g id="edge35" class="edge"><title>28->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1459.97,-431.876C1472.55,-422.893 1488.13,-411.763 1501.75,-402.034"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.83,-404.85 1509.93,-396.19 1499.76,-399.154 1503.83,-404.85"/>
+<!-- 28 -->
+<g id="node29" class="node">
+<title>28</title>
+<path fill="none" stroke="#d88556" 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">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="968.5" 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="grey" stroke-width="2" d="M968.5,-868.82C968.5,-860.42 968.5,-850.12 968.5,-840.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="972,-840.56 968.5,-830.56 965,-840.56 972,-840.56"/>
</g>
<!-- 29 -->
-<g id="node30" class="node"><title>29</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M1729,-468C1729,-468 1649,-468 1649,-468 1643,-468 1637,-462 1637,-456 1637,-456 1637,-444 1637,-444 1637,-438 1643,-432 1649,-432 1649,-432 1729,-432 1729,-432 1735,-432 1741,-438 1741,-444 1741,-444 1741,-456 1741,-456 1741,-462 1735,-468 1729,-468"/>
-<text text-anchor="middle" x="1689" y="-447.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#bed856" 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">extract_transcriptome</text>
+<text text-anchor="middle" x="1127.5" y="-514" 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="grey" stroke-width="2" d="M1144.56,-503.7C1153,-495.14 1163.32,-484.66 1172.54,-475.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1175.11,-477.68 1179.64,-468.1 1170.13,-472.77 1175.11,-477.68"/>
</g>
-<!-- 29->15 -->
-<g id="edge36" class="edge"><title>29->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1651.08,-431.876C1626.56,-420.799 1594.8,-406.457 1570.55,-395.504"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1571.87,-392.264 1561.32,-391.338 1568.99,-398.643 1571.87,-392.264"/>
-</g>
-<!-- 29->16 -->
-<g id="edge38" class="edge"><title>29->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1684.06,-431.697C1681.83,-423.898 1679.15,-414.509 1676.67,-405.829"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1680,-404.758 1673.89,-396.104 1673.27,-406.681 1680,-404.758"/>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#d86656" 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">create_index_salmon</text>
+<text text-anchor="middle" x="1057.5" y="-442" font-family="sans" font-size="10.00">kmer: 31</text>
+</g>
+<!-- 29->33 -->
+<g id="edge60" class="edge">
+<title>29->33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1110.2,-503.7C1101.64,-495.14 1091.16,-484.66 1081.8,-475.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1084.15,-472.7 1074.6,-468.1 1079.2,-477.65 1084.15,-472.7"/>
</g>
-<!-- 30->16 -->
-<g id="edge37" class="edge"><title>30->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1786.08,-431.876C1761.56,-420.799 1729.8,-406.457 1705.55,-395.504"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1706.87,-392.264 1696.32,-391.338 1703.99,-398.643 1706.87,-392.264"/>
+<!-- 30 -->
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#d89556" 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">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1323.5" 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="grey" stroke-width="2" d="M1323.5,-868.82C1323.5,-860.42 1323.5,-850.12 1323.5,-840.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1327,-840.56 1323.5,-830.56 1320,-840.56 1327,-840.56"/>
+</g>
+<!-- 31->19 -->
+<g id="edge38" class="edge">
+<title>31->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1470.74,-575.7C1471.29,-567.98 1471.95,-558.71 1472.56,-550.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1476.06,-550.33 1473.28,-540.1 1469.07,-549.83 1476.06,-550.33"/>
</g>
-<!-- 31 -->
-<g id="node32" class="node"><title>31</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M994,-833C994,-833 726,-833 726,-833 720,-833 714,-827 714,-821 714,-821 714,-809 714,-809 714,-803 720,-797 726,-797 726,-797 994,-797 994,-797 1000,-797 1006,-803 1006,-809 1006,-809 1006,-821 1006,-821 1006,-827 1000,-833 994,-833"/>
-<text text-anchor="middle" x="860" y="-818" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="860" y="-807" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<!-- 32->19 -->
+<g id="edge39" class="edge">
+<title>32->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1574.21,-575.88C1556.63,-566.55 1534.69,-554.92 1515.87,-544.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1517.39,-541.78 1506.91,-540.19 1514.11,-547.97 1517.39,-541.78"/>
</g>
-<!-- 31->18 -->
-<g id="edge41" class="edge"><title>31->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M860,-796.819C860,-788.422 860,-778.116 860,-768.686"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="863.5,-768.558 860,-758.558 856.5,-768.558 863.5,-768.558"/>
+<!-- 33->20 -->
+<g id="edge41" class="edge">
+<title>33->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1045.39,-431.7C1039.63,-423.47 1032.64,-413.48 1026.29,-404.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1029.08,-402.29 1020.47,-396.1 1023.34,-406.3 1029.08,-402.29"/>
</g>
-<!-- 32 -->
-<g id="node33" class="node"><title>32</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M1056.5,-540C1056.5,-540 955.5,-540 955.5,-540 949.5,-540 943.5,-534 943.5,-528 943.5,-528 943.5,-516 943.5,-516 943.5,-510 949.5,-504 955.5,-504 955.5,-504 1056.5,-504 1056.5,-504 1062.5,-504 1068.5,-510 1068.5,-516 1068.5,-516 1068.5,-528 1068.5,-528 1068.5,-534 1062.5,-540 1056.5,-540"/>
-<text text-anchor="middle" x="1006" y="-525" font-family="sans" font-size="10.00">extract_transcriptome</text>
-<text text-anchor="middle" x="1006" y="-514" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<!-- 33->21 -->
+<g id="edge43" class="edge">
+<title>33->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1082.7,-431.88C1095.91,-422.89 1112.29,-411.76 1126.61,-402.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1128.9,-404.71 1135.21,-396.19 1124.97,-398.92 1128.9,-404.71"/>
</g>
-<!-- 32->19 -->
-<g id="edge42" class="edge"><title>32->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1021.82,-503.697C1029.57,-495.22 1039.04,-484.864 1047.52,-475.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1050.2,-477.846 1054.36,-468.104 1045.03,-473.123 1050.2,-477.846"/>
+<!-- 34 -->
+<g id="node35" class="node">
+<title>34</title>
+<path fill="none" stroke="#56d88a" 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">create_index_star</text>
+<text text-anchor="middle" x="1877.5" y="-810" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1877.5" 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="grey" stroke-width="2" d="M1820.41,-791.98C1790.86,-781.87 1754.82,-769.55 1724.94,-759.33"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1726.07,-756.01 1715.47,-756.09 1723.8,-762.64 1726.07,-756.01"/>
+</g>
+<!-- 34->24 -->
+<g id="edge47" class="edge">
+<title>34->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1877.5,-791.69C1877.5,-783.91 1877.5,-774.84 1877.5,-766.45"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1881,-766.32 1877.5,-756.32 1874,-766.32 1881,-766.32"/>
+</g>
+<!-- 41 -->
+<g id="node42" class="node">
+<title>41</title>
+<path fill="none" stroke="#5692d8" 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">generate_alfa_index</text>
+</g>
+<!-- 34->41 -->
+<g id="edge70" class="edge">
+<title>34->41</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1925.31,-791.96C1971.15,-771.14 2039.67,-734.23 2083.5,-684 2116.9,-645.72 2128.45,-585.52 2132.43,-550.59"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2135.95,-550.5 2133.47,-540.2 2128.99,-549.8 2135.95,-550.5"/>
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-<!-- 36 -->
-<g id="node37" class="node"><title>36</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M985.5,-468C985.5,-468 900.5,-468 900.5,-468 894.5,-468 888.5,-462 888.5,-456 888.5,-456 888.5,-444 888.5,-444 888.5,-438 894.5,-432 900.5,-432 900.5,-432 985.5,-432 985.5,-432 991.5,-432 997.5,-438 997.5,-444 997.5,-444 997.5,-456 997.5,-456 997.5,-462 991.5,-468 985.5,-468"/>
-<text text-anchor="middle" x="943" y="-453" font-family="sans" font-size="10.00">create_index_salmon</text>
-<text text-anchor="middle" x="943" y="-442" font-family="sans" font-size="10.00">kmer: 31</text>
+<!-- 35 -->
+<g id="node36" class="node">
+<title>35</title>
+<path fill="none" stroke="#56a2d8" 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">alfa_qc</text>
</g>
-<!-- 32->36 -->
-<g id="edge65" class="edge"><title>32->36</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M990.427,-503.697C982.798,-495.22 973.477,-484.864 965.124,-475.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="967.685,-473.196 958.394,-468.104 962.482,-477.879 967.685,-473.196"/>
+<!-- 35->26 -->
+<g id="edge50" class="edge">
+<title>35->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1959.16,-431.7C1962.69,-423.73 1966.96,-414.1 1970.87,-405.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1974.08,-406.67 1974.93,-396.1 1967.68,-403.83 1974.08,-406.67"/>
</g>
-<!-- 33 -->
-<g id="node34" class="node"><title>33</title>
-<path fill="none" stroke="#56b9d8" stroke-width="2" d="M1330,-833C1330,-833 1050,-833 1050,-833 1044,-833 1038,-827 1038,-821 1038,-821 1038,-809 1038,-809 1038,-803 1044,-797 1050,-797 1050,-797 1330,-797 1330,-797 1336,-797 1342,-803 1342,-809 1342,-809 1342,-821 1342,-821 1342,-827 1336,-833 1330,-833"/>
-<text text-anchor="middle" x="1190" y="-818" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1190" y="-807" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<!-- 36 -->
+<g id="node37" class="node">
+<title>36</title>
+<path fill="none" stroke="#56a2d8" 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">alfa_qc</text>
</g>
-<!-- 33->20 -->
-<g id="edge43" class="edge"><title>33->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1190,-796.819C1190,-788.422 1190,-778.116 1190,-768.686"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.5,-768.558 1190,-758.558 1186.5,-768.558 1193.5,-768.558"/>
-</g>
-<!-- 34->21 -->
-<g id="edge44" class="edge"><title>34->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1498.99,-503.697C1510.81,-494.796 1525.39,-483.823 1538.18,-474.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1540.39,-476.915 1546.28,-468.104 1536.18,-471.322 1540.39,-476.915"/>
-</g>
-<!-- 35->21 -->
-<g id="edge45" class="edge"><title>35->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1610.4,-503.697C1603.88,-495.389 1595.93,-485.277 1588.75,-476.141"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1591.37,-473.805 1582.44,-468.104 1585.87,-478.13 1591.37,-473.805"/>
-</g>
-<!-- 36->22 -->
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.21,-404.302 1032.02,-396.19 1021.64,-398.282 1025.21,-404.302"/>
+<!-- 36->26 -->
+<g id="edge51" class="edge">
+<title>36->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2107.33,-436.49C2085.5,-426.43 2054.35,-412.09 2028.64,-400.25"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2029.98,-397.01 2019.43,-396.01 2027.05,-403.37 2029.98,-397.01"/>
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<!-- 37 -->
-<g id="node38" class="node"><title>37</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1767.5,-761C1767.5,-761 1666.5,-761 1666.5,-761 1660.5,-761 1654.5,-755 1654.5,-749 1654.5,-749 1654.5,-732 1654.5,-732 1654.5,-726 1660.5,-720 1666.5,-720 1666.5,-720 1767.5,-720 1767.5,-720 1773.5,-720 1779.5,-726 1779.5,-732 1779.5,-732 1779.5,-749 1779.5,-749 1779.5,-755 1773.5,-761 1767.5,-761"/>
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-<text text-anchor="middle" x="1717" y="-738" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="1717" y="-727" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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-<g id="edge50" class="edge"><title>37->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1654.4,-727.365C1586.62,-714.225 1478.92,-693.349 1409.61,-679.913"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1410.16,-676.453 1399.67,-677.986 1408.82,-683.325 1410.16,-676.453"/>
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-<g id="edge53" class="edge"><title>37->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1717,-719.689C1717,-711.907 1717,-702.842 1717,-694.447"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1720.5,-694.319 1717,-684.319 1713.5,-694.32 1720.5,-694.319"/>
-</g>
-<!-- 37->29 -->
-<g id="edge57" class="edge"><title>37->29</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1763.03,-719.97C1804.26,-699.684 1862.09,-663.634 1888,-612 1896.33,-595.398 1897.01,-518.975 1885,-504 1848.05,-457.922 1813.46,-481.709 1751.06,-468.017"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1751.78,-464.589 1741.23,-465.598 1750.11,-471.386 1751.78,-464.589"/>
+<g id="node38" class="node">
+<title>37</title>
+<path fill="none" stroke="#56a2d8" 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">alfa_qc</text>
+</g>
+<!-- 37->27 -->
+<g id="edge52" class="edge">
+<title>37->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1848.5,-431.7C1848.5,-423.98 1848.5,-414.71 1848.5,-406.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1852,-406.1 1848.5,-396.1 1845,-406.1 1852,-406.1"/>
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-<g id="node39" class="node"><title>38</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M1619.5,-612C1619.5,-612 1498.5,-612 1498.5,-612 1492.5,-612 1486.5,-606 1486.5,-600 1486.5,-600 1486.5,-588 1486.5,-588 1486.5,-582 1492.5,-576 1498.5,-576 1498.5,-576 1619.5,-576 1619.5,-576 1625.5,-576 1631.5,-582 1631.5,-588 1631.5,-588 1631.5,-600 1631.5,-600 1631.5,-606 1625.5,-612 1619.5,-612"/>
-<text text-anchor="middle" x="1559" y="-591.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
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-<!-- 38->34 -->
-<g id="edge61" class="edge"><title>38->34</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1506.18,-543.876 1496.28,-540.104 1501.67,-549.227 1506.18,-543.876"/>
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-<g id="edge64" class="edge"><title>38->35</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1575.07,-575.697C1582.94,-567.22 1592.56,-556.864 1601.17,-547.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1603.88,-549.814 1608.12,-540.104 1598.75,-545.051 1603.88,-549.814"/>
+<g id="node39" class="node">
+<title>38</title>
+<path fill="none" stroke="#56a2d8" 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">alfa_qc</text>
+</g>
+<!-- 38->27 -->
+<g id="edge53" class="edge">
+<title>38->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1996.47,-435.96C1993.46,-434.59 1990.43,-433.25 1987.5,-432 1960.74,-420.6 1930.63,-408.97 1905.29,-399.53"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1906.42,-396.21 1895.83,-396.02 1903.99,-402.78 1906.42,-396.21"/>
+</g>
+<!-- 39 -->
+<g id="node40" class="node">
+<title>39</title>
+<path fill="none" stroke="#56d89a" 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">extract_transcripts_as_bed12</text>
+</g>
+<!-- 39->31 -->
+<g id="edge56" class="edge">
+<title>39->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1469.5,-647.7C1469.5,-639.98 1469.5,-630.71 1469.5,-622.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1473,-622.1 1469.5,-612.1 1466,-622.1 1473,-622.1"/>
+</g>
+<!-- 39->32 -->
+<g id="edge59" class="edge">
+<title>39->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1503.01,-647.88C1521.34,-638.51 1544.24,-626.81 1563.83,-616.8"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1565.54,-619.86 1572.86,-612.19 1562.36,-613.62 1565.54,-619.86"/>
+</g>
+<!-- 40->35 -->
+<g id="edge61" class="edge">
+<title>40->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1853.3,-503.88C1872.12,-493.74 1896.01,-480.88 1915.52,-470.37"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1917.27,-473.4 1924.42,-465.58 1913.96,-467.24 1917.27,-473.4"/>
+</g>
+<!-- 41->35 -->
+<g id="edge62" class="edge">
+<title>41->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2083.36,-503.9C2057.11,-494.82 2024.51,-483.07 1987.9,-467.99"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1989.08,-464.7 1978.5,-464.09 1986.39,-471.16 1989.08,-464.7"/>
+</g>
+<!-- 41->36 -->
+<g id="edge64" class="edge">
+<title>41->36</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2134.5,-503.7C2134.5,-495.98 2134.5,-486.71 2134.5,-478.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2138,-478.1 2134.5,-468.1 2131,-478.1 2138,-478.1"/>
+</g>
+<!-- 41->37 -->
+<g id="edge66" class="edge">
+<title>41->37</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2076.41,-506.2C2073.4,-505.45 2070.41,-504.71 2067.5,-504 2000.07,-487.46 1982.93,-484.54 1915.5,-468 1905.73,-465.6 1895.16,-462.95 1885.38,-460.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1886.09,-457.04 1875.53,-457.96 1884.36,-463.82 1886.09,-457.04"/>
+</g>
+<!-- 41->38 -->
+<g id="edge68" class="edge">
+<title>41->38</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2107.35,-503.88C2092.97,-494.81 2075.12,-483.55 2059.59,-473.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2061.08,-470.56 2050.76,-468.19 2057.35,-476.48 2061.08,-470.56"/>
+</g>
+<!-- 42->36 -->
+<g id="edge63" class="edge">
+<title>42->36</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2247.05,-503.88C2223.88,-492.99 2194,-478.95 2170.85,-468.07"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2172.23,-464.86 2161.69,-463.78 2169.26,-471.2 2172.23,-464.86"/>
+</g>
+<!-- 43->37 -->
+<g id="edge65" class="edge">
+<title>43->37</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1704.22,-503.88C1737.41,-491.71 1781.34,-475.62 1811.97,-464.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1813.23,-467.65 1821.41,-460.93 1810.82,-461.08 1813.23,-467.65"/>
+</g>
+<!-- 44->38 -->
+<g id="edge67" class="edge">
+<title>44->38</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1994.89,-503.7C1999.26,-495.64 2004.56,-485.89 2009.4,-476.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2012.52,-478.56 2014.21,-468.1 2006.37,-475.22 2012.52,-478.56"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 8de684c..0ee1545 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,418 +1,505 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.38.0 (20140413.2041)
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
-->
<!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 1074.00 836.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 832)">
+<svg width="1211pt" height="908pt"
+ viewBox="0.00 0.00 1210.50 908.00" 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(4 904)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-832 1070,-832 1070,4 -4,4"/>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-904 1206.5,-904 1206.5,4 -4,4"/>
<!-- 0 -->
-<g id="node1" class="node"><title>0</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M339,-36C339,-36 309,-36 309,-36 303,-36 297,-30 297,-24 297,-24 297,-12 297,-12 297,-6 303,-0 309,-0 309,-0 339,-0 339,-0 345,-0 351,-6 351,-12 351,-12 351,-24 351,-24 351,-30 345,-36 339,-36"/>
-<text text-anchor="middle" x="324" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
+<title>0</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M353.5,-36C353.5,-36 323.5,-36 323.5,-36 317.5,-36 311.5,-30 311.5,-24 311.5,-24 311.5,-12 311.5,-12 311.5,-6 317.5,0 323.5,0 323.5,0 353.5,0 353.5,0 359.5,0 365.5,-6 365.5,-12 365.5,-12 365.5,-24 365.5,-24 365.5,-30 359.5,-36 353.5,-36"/>
+<text text-anchor="middle" x="338.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
-<g id="node2" class="node"><title>1</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M358,-108C358,-108 290,-108 290,-108 284,-108 278,-102 278,-96 278,-96 278,-84 278,-84 278,-78 284,-72 290,-72 290,-72 358,-72 358,-72 364,-72 370,-78 370,-84 370,-84 370,-96 370,-96 370,-102 364,-108 358,-108"/>
-<text text-anchor="middle" x="324" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
+<g id="node2" class="node">
+<title>1</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M373.5,-108C373.5,-108 303.5,-108 303.5,-108 297.5,-108 291.5,-102 291.5,-96 291.5,-96 291.5,-84 291.5,-84 291.5,-78 297.5,-72 303.5,-72 303.5,-72 373.5,-72 373.5,-72 379.5,-72 385.5,-78 385.5,-84 385.5,-84 385.5,-96 385.5,-96 385.5,-102 379.5,-108 373.5,-108"/>
+<text text-anchor="middle" x="338.5" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
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<!-- 1->0 -->
-<g id="edge1" class="edge"><title>1->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="327.5,-46.1043 324,-36.1043 320.5,-46.1044 327.5,-46.1043"/>
+<g id="edge1" class="edge">
+<title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M338.5,-71.7C338.5,-63.98 338.5,-54.71 338.5,-46.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="342,-46.1 338.5,-36.1 335,-46.1 342,-46.1"/>
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-<text text-anchor="middle" x="324" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
+<g id="node3" class="node">
+<title>2</title>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M392.5,-180C392.5,-180 284.5,-180 284.5,-180 278.5,-180 272.5,-174 272.5,-168 272.5,-168 272.5,-156 272.5,-156 272.5,-150 278.5,-144 284.5,-144 284.5,-144 392.5,-144 392.5,-144 398.5,-144 404.5,-150 404.5,-156 404.5,-156 404.5,-168 404.5,-168 404.5,-174 398.5,-180 392.5,-180"/>
+<text text-anchor="middle" x="338.5" 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="327.5,-118.104 324,-108.104 320.5,-118.104 327.5,-118.104"/>
+<g id="edge2" class="edge">
+<title>2->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M338.5,-143.7C338.5,-135.98 338.5,-126.71 338.5,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="342,-118.1 338.5,-108.1 335,-118.1 342,-118.1"/>
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-<g id="node4" class="node"><title>3</title>
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-<text text-anchor="middle" x="324" y="-231.5" font-family="sans" font-size="10.00">prepare_files_for_report</text>
+<g id="node4" class="node">
+<title>3</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M393,-252C393,-252 284,-252 284,-252 278,-252 272,-246 272,-240 272,-240 272,-228 272,-228 272,-222 278,-216 284,-216 284,-216 393,-216 393,-216 399,-216 405,-222 405,-228 405,-228 405,-240 405,-240 405,-246 399,-252 393,-252"/>
+<text text-anchor="middle" x="338.5" 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="327.5,-190.104 324,-180.104 320.5,-190.104 327.5,-190.104"/>
+<g id="edge3" class="edge">
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+<path fill="none" stroke="grey" stroke-width="2" d="M338.5,-215.7C338.5,-207.98 338.5,-198.71 338.5,-190.11"/>
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-<text text-anchor="middle" x="39" y="-303.5" font-family="sans" font-size="10.00">pe_fastqc</text>
+<g id="node5" class="node">
+<title>4</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M84.5,-324C84.5,-324 44.5,-324 44.5,-324 38.5,-324 32.5,-318 32.5,-312 32.5,-312 32.5,-300 32.5,-300 32.5,-294 38.5,-288 44.5,-288 44.5,-288 84.5,-288 84.5,-288 90.5,-288 96.5,-294 96.5,-300 96.5,-300 96.5,-312 96.5,-312 96.5,-318 90.5,-324 84.5,-324"/>
+<text text-anchor="middle" x="64.5" y="-303.5" font-family="sans" font-size="10.00">pe_fastqc</text>
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-<g id="edge7" class="edge"><title>4->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M68.5755,-291.384C71.7245,-290.153 74.9066,-288.996 78,-288 136.356,-269.202 204.655,-255.087 254.46,-246.169"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="255.242,-249.586 264.481,-244.4 254.025,-242.692 255.242,-249.586"/>
+<g id="edge10" class="edge">
+<title>4->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M96.54,-291.11C99.54,-289.99 102.56,-288.94 105.5,-288 156.87,-271.64 216.14,-258.23 262.04,-248.99"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="262.79,-252.41 271.92,-247.03 261.43,-245.54 262.79,-252.41"/>
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-<g id="node6" class="node"><title>5</title>
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-<text text-anchor="middle" x="114" y="-303.5" font-family="sans" font-size="10.00">fastqc</text>
+<g id="node6" class="node">
+<title>5</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M156.5,-324C156.5,-324 126.5,-324 126.5,-324 120.5,-324 114.5,-318 114.5,-312 114.5,-312 114.5,-300 114.5,-300 114.5,-294 120.5,-288 126.5,-288 126.5,-288 156.5,-288 156.5,-288 162.5,-288 168.5,-294 168.5,-300 168.5,-300 168.5,-312 168.5,-312 168.5,-318 162.5,-324 156.5,-324"/>
+<text text-anchor="middle" x="141.5" y="-303.5" font-family="sans" font-size="10.00">fastqc</text>
</g>
<!-- 5->3 -->
-<g id="edge13" class="edge"><title>5->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M141.214,-293.319C145.789,-291.47 150.51,-289.631 155,-288 187.729,-276.11 224.572,-264.368 255.485,-254.97"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="256.741,-258.247 265.301,-252.003 254.716,-251.546 256.741,-258.247"/>
+<g id="edge7" class="edge">
+<title>5->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M168.75,-293.41C173.32,-291.55 178.03,-289.68 182.5,-288 212.91,-276.54 247.05,-264.82 275.62,-255.32"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="277.09,-258.52 285.48,-252.05 274.89,-251.87 277.09,-258.52"/>
</g>
<!-- 6 -->
-<g id="node7" class="node"><title>6</title>
-<path fill="none" stroke="#568ad8" stroke-width="2" d="M154,-684C154,-684 12,-684 12,-684 6,-684 0,-678 0,-672 0,-672 0,-660 0,-660 0,-654 6,-648 12,-648 12,-648 154,-648 154,-648 160,-648 166,-654 166,-660 166,-660 166,-672 166,-672 166,-678 160,-684 154,-684"/>
-<text text-anchor="middle" x="83" y="-663.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M175,-756C175,-756 12,-756 12,-756 6,-756 0,-750 0,-744 0,-744 0,-732 0,-732 0,-726 6,-720 12,-720 12,-720 175,-720 175,-720 181,-720 187,-726 187,-732 187,-732 187,-744 187,-744 187,-750 181,-756 175,-756"/>
+<text text-anchor="middle" x="93.5" y="-735.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 6->3 -->
-<g id="edge10" class="edge"><title>6->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M102.086,-647.773C127.422,-622.914 169,-574.302 169,-523 169,-523 169,-523 169,-377 169,-331.41 186.982,-319.437 220,-288 233.622,-275.031 251.036,-264.499 267.703,-256.342"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="269.285,-259.466 276.857,-252.054 266.316,-253.127 269.285,-259.466"/>
+<g id="edge5" class="edge">
+<title>6->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M117.13,-719.97C147.54,-695.89 196.5,-648.75 196.5,-595 196.5,-595 196.5,-595 196.5,-377 196.5,-331.63 214.59,-320.25 246.5,-288 258.74,-275.63 274.46,-265.17 289.44,-256.91"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="291.42,-259.81 298.62,-252.04 288.15,-253.63 291.42,-259.81"/>
</g>
<!-- 7 -->
-<g id="node8" class="node"><title>7</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M322,-684C322,-684 196,-684 196,-684 190,-684 184,-678 184,-672 184,-672 184,-660 184,-660 184,-654 190,-648 196,-648 196,-648 322,-648 322,-648 328,-648 334,-654 334,-660 334,-660 334,-672 334,-672 334,-678 328,-684 322,-684"/>
-<text text-anchor="middle" x="259" y="-663.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M363.5,-756C363.5,-756 217.5,-756 217.5,-756 211.5,-756 205.5,-750 205.5,-744 205.5,-744 205.5,-732 205.5,-732 205.5,-726 211.5,-720 217.5,-720 217.5,-720 363.5,-720 363.5,-720 369.5,-720 375.5,-726 375.5,-732 375.5,-732 375.5,-744 375.5,-744 375.5,-750 369.5,-756 363.5,-756"/>
+<text text-anchor="middle" x="290.5" y="-735.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 7->3 -->
-<g id="edge5" class="edge"><title>7->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M246.068,-647.677C239.186,-637.702 231.112,-624.665 226,-612 210.862,-574.493 207,-563.447 207,-523 207,-523 207,-523 207,-377 207,-325.614 253.2,-282.737 287.537,-257.966"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="289.787,-260.664 295.976,-252.064 285.775,-254.927 289.787,-260.664"/>
+<g id="edge11" class="edge">
+<title>7->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M275.93,-719.91C268.19,-710.01 259.13,-696.97 253.5,-684 237.38,-646.9 234.5,-635.45 234.5,-595 234.5,-595 234.5,-595 234.5,-377 234.5,-327.63 275.92,-284.02 306.48,-258.56"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="308.8,-261.19 314.38,-252.18 304.4,-255.74 308.8,-261.19"/>
</g>
<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#68d856" stroke-width="2" d="M510.5,-396C510.5,-396 445.5,-396 445.5,-396 439.5,-396 433.5,-390 433.5,-384 433.5,-384 433.5,-372 433.5,-372 433.5,-366 439.5,-360 445.5,-360 445.5,-360 510.5,-360 510.5,-360 516.5,-360 522.5,-366 522.5,-372 522.5,-372 522.5,-384 522.5,-384 522.5,-390 516.5,-396 510.5,-396"/>
-<text text-anchor="middle" x="478" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M582.5,-396C582.5,-396 512.5,-396 512.5,-396 506.5,-396 500.5,-390 500.5,-384 500.5,-384 500.5,-372 500.5,-372 500.5,-366 506.5,-360 512.5,-360 512.5,-360 582.5,-360 582.5,-360 588.5,-360 594.5,-366 594.5,-372 594.5,-372 594.5,-384 594.5,-384 594.5,-390 588.5,-396 582.5,-396"/>
+<text text-anchor="middle" x="547.5" 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="grey" stroke-width="2" d="M459.424,-359.871C432.137,-334.711 381.103,-287.654 350.073,-259.042"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="352.366,-256.395 342.642,-252.189 347.621,-261.541 352.366,-256.395"/>
+<g id="edge12" class="edge">
+<title>8->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M534.73,-359.93C519.39,-340.39 492,-308.45 462.5,-288 443.65,-274.93 421.06,-264.1 400.35,-255.71"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="401.58,-252.43 391,-252.03 399.02,-258.95 401.58,-252.43"/>
</g>
<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M359,-612C359,-612 247,-612 247,-612 241,-612 235,-606 235,-600 235,-600 235,-588 235,-588 235,-582 241,-576 247,-576 247,-576 359,-576 359,-576 365,-576 371,-582 371,-588 371,-588 371,-600 371,-600 371,-606 365,-612 359,-612"/>
-<text text-anchor="middle" x="303" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M402.5,-684C402.5,-684 274.5,-684 274.5,-684 268.5,-684 262.5,-678 262.5,-672 262.5,-672 262.5,-660 262.5,-660 262.5,-654 268.5,-648 274.5,-648 274.5,-648 402.5,-648 402.5,-648 408.5,-648 414.5,-654 414.5,-660 414.5,-660 414.5,-672 414.5,-672 414.5,-678 408.5,-684 402.5,-684"/>
+<text text-anchor="middle" x="338.5" y="-663.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
<!-- 9->3 -->
-<g id="edge9" class="edge"><title>9->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M303.198,-575.951C303.489,-549.292 304,-496.116 304,-451 304,-451 304,-451 304,-377 304,-336.822 311.948,-290.869 317.823,-262.389"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="321.296,-262.887 319.953,-252.378 314.449,-261.431 321.296,-262.887"/>
+<g id="edge9" class="edge">
+<title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M338.5,-647.95C338.5,-621.29 338.5,-568.11 338.5,-523 338.5,-523 338.5,-523 338.5,-377 338.5,-337 338.5,-290.65 338.5,-262.08"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="342,-262.05 338.5,-252.05 335,-262.05 342,-262.05"/>
</g>
<!-- 10 -->
-<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M532.5,-612C532.5,-612 401.5,-612 401.5,-612 395.5,-612 389.5,-606 389.5,-600 389.5,-600 389.5,-588 389.5,-588 389.5,-582 395.5,-576 401.5,-576 401.5,-576 532.5,-576 532.5,-576 538.5,-576 544.5,-582 544.5,-588 544.5,-588 544.5,-600 544.5,-600 544.5,-606 538.5,-612 532.5,-612"/>
-<text text-anchor="middle" x="467" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#56d8c9" 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">salmon_quantmerge_transcripts</text>
</g>
<!-- 10->3 -->
-<g id="edge4" class="edge"><title>10->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M436.911,-575.894C400.497,-552.696 344,-507.588 344,-451 344,-451 344,-451 344,-377 344,-336.822 336.052,-290.869 330.177,-262.389"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="333.551,-261.431 328.047,-252.378 326.704,-262.887 333.551,-261.431"/>
+<g id="edge6" class="edge">
+<title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M504.09,-647.58C483.21,-622.1 448.5,-572.34 448.5,-523 448.5,-523 448.5,-523 448.5,-377 448.5,-326.76 404.94,-283.52 372.64,-258.36"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="374.38,-255.29 364.29,-252.06 370.16,-260.88 374.38,-255.29"/>
</g>
<!-- 11 -->
-<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M866.5,-540C866.5,-540 835.5,-540 835.5,-540 829.5,-540 823.5,-534 823.5,-528 823.5,-528 823.5,-516 823.5,-516 823.5,-510 829.5,-504 835.5,-504 835.5,-504 866.5,-504 866.5,-504 872.5,-504 878.5,-510 878.5,-516 878.5,-516 878.5,-528 878.5,-528 878.5,-534 872.5,-540 866.5,-540"/>
-<text text-anchor="middle" x="851" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#56d86b" 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">star_rpm</text>
</g>
<!-- 11->3 -->
-<g id="edge11" class="edge"><title>11->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M823.408,-506.026C736.345,-458.777 467.135,-312.679 364.403,-256.927"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="366.024,-253.824 355.566,-252.131 362.686,-259.977 366.024,-253.824"/>
+<g id="edge8" class="edge">
+<title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M941.32,-585.35C866.13,-565.41 676.5,-509.33 676.5,-451 676.5,-451 676.5,-451 676.5,-377 676.5,-264.39 515.06,-239.61 415.33,-235.04"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="415.41,-231.54 405.28,-234.64 415.13,-238.54 415.41,-231.54"/>
</g>
-<!-- 23 -->
-<g id="node24" class="node"><title>23</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M903,-468C903,-468 797,-468 797,-468 791,-468 785,-462 785,-456 785,-456 785,-444 785,-444 785,-438 791,-432 797,-432 797,-432 903,-432 903,-432 909,-432 915,-438 915,-444 915,-444 915,-456 915,-456 915,-462 909,-468 903,-468"/>
-<text text-anchor="middle" x="850" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<!-- 31 -->
+<g id="node32" class="node">
+<title>31</title>
+<path fill="none" stroke="#afd856" 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">rename_star_rpm_for_alfa</text>
</g>
-<!-- 11->23 -->
-<g id="edge43" class="edge"><title>11->23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M850.753,-503.697C850.643,-495.983 850.51,-486.712 850.387,-478.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="853.887,-478.053 850.244,-468.104 846.888,-478.153 853.887,-478.053"/>
+<!-- 11->31 -->
+<g id="edge48" class="edge">
+<title>11->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M971.5,-575.7C971.5,-567.98 971.5,-558.71 971.5,-550.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="975,-550.1 971.5,-540.1 968,-550.1 975,-550.1"/>
</g>
<!-- 12 -->
-<g id="node13" class="node"><title>12</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M850,-396C850,-396 820,-396 820,-396 814,-396 808,-390 808,-384 808,-384 808,-372 808,-372 808,-366 814,-360 820,-360 820,-360 850,-360 850,-360 856,-360 862,-366 862,-372 862,-372 862,-384 862,-384 862,-390 856,-396 850,-396"/>
-<text text-anchor="middle" x="835" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#d8b456" 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">alfa_concat_results</text>
</g>
<!-- 12->3 -->
-<g id="edge12" class="edge"><title>12->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M807.667,-361.655C789.461,-351.295 765.097,-337.159 744,-324 719.526,-308.735 716.935,-298.32 690,-288 591.798,-250.373 469.428,-239.198 394.018,-236.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="393.823,-232.52 383.697,-235.634 393.555,-239.515 393.823,-232.52"/>
+<g id="edge4" class="edge">
+<title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M789.79,-297.31C698.8,-284.75 518.14,-259.8 415.13,-245.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="415.49,-242.1 405.11,-244.2 414.53,-249.03 415.49,-242.1"/>
</g>
<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M846.5,-324C846.5,-324 765.5,-324 765.5,-324 759.5,-324 753.5,-318 753.5,-312 753.5,-312 753.5,-300 753.5,-300 753.5,-294 759.5,-288 765.5,-288 765.5,-288 846.5,-288 846.5,-288 852.5,-288 858.5,-294 858.5,-300 858.5,-300 858.5,-312 858.5,-312 858.5,-318 852.5,-324 846.5,-324"/>
-<text text-anchor="middle" x="806" y="-303.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#d8a456" 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">pe_remove_polya_cutadapt</text>
</g>
-<!-- 12->13 -->
-<g id="edge28" class="edge"><title>12->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M827.831,-359.697C824.565,-351.813 820.626,-342.304 816.998,-333.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="820.147,-332.003 813.086,-324.104 813.68,-334.683 820.147,-332.003"/>
+<!-- 13->6 -->
+<g id="edge14" class="edge">
+<title>13->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M312.17,-791.97C270.4,-781.85 217.28,-768.98 173.85,-758.46"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="174.44,-755 163.89,-756.05 172.79,-761.81 174.44,-755"/>
</g>
-<!-- 13->3 -->
-<g id="edge6" class="edge"><title>13->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M753.403,-291.745C747.22,-290.383 740.984,-289.099 735,-288 615.786,-266.106 475.48,-250.075 393.473,-241.672"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="393.825,-238.19 383.522,-240.661 393.117,-245.154 393.825,-238.19"/>
+<!-- 17 -->
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#d86656" 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">pe_quantification_salmon</text>
</g>
-<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M395,-756C395,-756 283,-756 283,-756 277,-756 271,-750 271,-744 271,-744 271,-732 271,-732 271,-726 277,-720 283,-720 283,-720 395,-720 395,-720 401,-720 407,-726 407,-732 407,-732 407,-744 407,-744 407,-750 401,-756 395,-756"/>
-<text text-anchor="middle" x="339" y="-735.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<!-- 13->17 -->
+<g id="edge31" class="edge">
+<title>13->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M402.77,-791.7C413,-782.97 425.56,-772.24 436.68,-762.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="439.13,-765.26 444.46,-756.1 434.59,-759.94 439.13,-765.26"/>
</g>
-<!-- 14->6 -->
-<g id="edge15" class="edge"><title>14->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M276.703,-719.966C240.156,-709.972 193.806,-697.298 155.609,-686.854"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="156.146,-683.372 145.577,-684.111 154.299,-690.124 156.146,-683.372"/>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#56d8a9" 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">pe_map_genome_star</text>
</g>
-<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M467.5,-684C467.5,-684 364.5,-684 364.5,-684 358.5,-684 352.5,-678 352.5,-672 352.5,-672 352.5,-660 352.5,-660 352.5,-654 358.5,-648 364.5,-648 364.5,-648 467.5,-648 467.5,-648 473.5,-648 479.5,-654 479.5,-660 479.5,-660 479.5,-672 479.5,-672 479.5,-678 473.5,-684 467.5,-684"/>
-<text text-anchor="middle" x="416" y="-663.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<!-- 13->19 -->
+<g id="edge35" class="edge">
+<title>13->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M458.9,-793.41C461.8,-792.91 464.68,-792.44 467.5,-792 604.82,-770.45 766.37,-753.95 857.77,-745.43"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="858.11,-748.92 867.74,-744.51 857.46,-741.95 858.11,-748.92"/>
</g>
-<!-- 14->18 -->
-<g id="edge34" class="edge"><title>14->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M358.034,-719.697C367.545,-711.05 379.207,-700.449 389.57,-691.027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="392.14,-693.421 397.185,-684.104 387.431,-688.241 392.14,-693.421"/>
+<!-- 14 -->
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#56d88a" 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">create_index_kallisto</text>
</g>
-<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M887.5,-684C887.5,-684 798.5,-684 798.5,-684 792.5,-684 786.5,-678 786.5,-672 786.5,-672 786.5,-660 786.5,-660 786.5,-654 792.5,-648 798.5,-648 798.5,-648 887.5,-648 887.5,-648 893.5,-648 899.5,-654 899.5,-660 899.5,-660 899.5,-672 899.5,-672 899.5,-678 893.5,-684 887.5,-684"/>
-<text text-anchor="middle" x="843" y="-663.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 14->6 -->
+<g id="edge13" class="edge">
+<title>14->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M191.7,-791.88C174.39,-782.55 152.78,-770.92 134.24,-760.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="135.89,-757.85 125.42,-756.19 132.57,-764.01 135.89,-757.85"/>
</g>
-<!-- 14->20 -->
-<g id="edge38" class="edge"><title>14->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M407.368,-721.557C410.28,-721.009 413.167,-720.487 416,-720 542.678,-698.204 691.979,-681.763 776.257,-673.326"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="776.852,-676.784 786.456,-672.312 776.159,-669.819 776.852,-676.784"/>
+<!-- 14->7 -->
+<g id="edge15" class="edge">
+<title>14->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M240.06,-791.7C248.18,-783.22 258.09,-772.86 266.97,-763.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="269.74,-765.75 274.13,-756.1 264.69,-760.91 269.74,-765.75"/>
</g>
<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#56a9d8" stroke-width="2" d="M237,-756C237,-756 153,-756 153,-756 147,-756 141,-750 141,-744 141,-744 141,-732 141,-732 141,-726 147,-720 153,-720 153,-720 237,-720 237,-720 243,-720 249,-726 249,-732 249,-732 249,-744 249,-744 249,-750 243,-756 237,-756"/>
-<text text-anchor="middle" x="195" y="-735.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
-</g>
-<!-- 15->6 -->
-<g id="edge14" class="edge"><title>15->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M167.602,-719.876C153.093,-710.808 135.084,-699.552 119.415,-689.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="120.839,-686.522 110.504,-684.19 117.129,-692.458 120.839,-686.522"/>
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#d88556" 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">remove_polya_cutadapt</text>
</g>
<!-- 15->7 -->
-<g id="edge16" class="edge"><title>15->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M210.82,-719.697C218.57,-711.22 228.039,-700.864 236.524,-691.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="239.197,-693.846 243.362,-684.104 234.031,-689.123 239.197,-693.846"/>
+<g id="edge16" class="edge">
+<title>15->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M616.35,-793.94C613.03,-793.27 609.73,-792.62 606.5,-792 511.49,-773.82 484.72,-772.93 385.68,-756.18"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="385.99,-752.68 375.54,-754.45 384.81,-759.58 385.99,-752.68"/>
</g>
-<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M661,-756C661,-756 565,-756 565,-756 559,-756 553,-750 553,-744 553,-744 553,-732 553,-732 553,-726 559,-720 565,-720 565,-720 661,-720 661,-720 667,-720 673,-726 673,-732 673,-732 673,-744 673,-744 673,-750 667,-756 661,-756"/>
-<text text-anchor="middle" x="613" y="-735.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
-</g>
-<!-- 16->7 -->
-<g id="edge17" class="edge"><title>16->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M552.723,-722.118C549.439,-721.383 546.181,-720.672 543,-720 457.739,-701.99 433.404,-701.008 344.115,-684.184"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="344.567,-680.707 334.09,-682.28 343.261,-687.585 344.567,-680.707"/>
-</g>
-<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M596.5,-684C596.5,-684 509.5,-684 509.5,-684 503.5,-684 497.5,-678 497.5,-672 497.5,-672 497.5,-660 497.5,-660 497.5,-654 503.5,-648 509.5,-648 509.5,-648 596.5,-648 596.5,-648 602.5,-648 608.5,-654 608.5,-660 608.5,-660 608.5,-672 608.5,-672 608.5,-678 602.5,-684 596.5,-684"/>
-<text text-anchor="middle" x="553" y="-663.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<!-- 18 -->
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#d8c356" 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">quantification_salmon</text>
</g>
-<!-- 16->19 -->
-<g id="edge36" class="edge"><title>16->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M598.169,-719.697C590.975,-711.305 582.203,-701.07 574.31,-691.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="576.826,-689.419 567.661,-684.104 571.511,-693.975 576.826,-689.419"/>
+<!-- 15->18 -->
+<g id="edge33" class="edge">
+<title>15->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M666.94,-791.7C658.82,-783.22 648.91,-772.86 640.03,-763.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="642.31,-760.91 632.87,-756.1 637.26,-765.75 642.31,-760.91"/>
</g>
-<!-- 22 -->
-<g id="node23" class="node"><title>22</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1002.5,-684C1002.5,-684 929.5,-684 929.5,-684 923.5,-684 917.5,-678 917.5,-672 917.5,-672 917.5,-660 917.5,-660 917.5,-654 923.5,-648 929.5,-648 929.5,-648 1002.5,-648 1002.5,-648 1008.5,-648 1014.5,-654 1014.5,-660 1014.5,-660 1014.5,-672 1014.5,-672 1014.5,-678 1008.5,-684 1002.5,-684"/>
-<text text-anchor="middle" x="966" y="-663.5" font-family="sans" font-size="10.00">map_genome_star</text>
-</g>
-<!-- 16->22 -->
-<g id="edge42" class="edge"><title>16->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M673.279,-728.113C731.011,-719.162 820.701,-704.115 907.607,-683.955"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="908.43,-687.357 917.367,-681.666 906.832,-680.542 908.43,-687.357"/>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#56b1d8" 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">map_genome_star</text>
</g>
-<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M577,-468C577,-468 501,-468 501,-468 495,-468 489,-462 489,-456 489,-456 489,-444 489,-444 489,-438 495,-432 501,-432 501,-432 577,-432 577,-432 583,-432 589,-438 589,-444 589,-444 589,-456 589,-456 589,-462 583,-468 577,-468"/>
-<text text-anchor="middle" x="539" y="-447.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
+<!-- 15->21 -->
+<g id="edge39" class="edge">
+<title>15->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M750.79,-799.88C813.33,-790.93 909.24,-776.03 1000.82,-756.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1001.79,-759.63 1010.82,-754.08 1000.3,-752.8 1001.79,-759.63"/>
</g>
-<!-- 17->8 -->
-<g id="edge18" class="edge"><title>17->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M523.921,-431.697C516.608,-423.305 507.69,-413.07 499.665,-403.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="502.114,-401.344 492.905,-396.104 496.836,-405.943 502.114,-401.344"/>
+<!-- 16 -->
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#5692d8" 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">merge_TIN_scores</text>
+</g>
+<!-- 16->8 -->
+<g id="edge17" class="edge">
+<title>16->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M570.36,-503.87C565.93,-479.67 557.79,-435.21 552.52,-406.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="555.89,-405.4 550.65,-396.19 549.01,-406.66 555.89,-405.4"/>
+</g>
+<!-- 17->9 -->
+<g id="edge18" class="edge">
+<title>17->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M433.68,-719.88C417.05,-710.64 396.34,-699.13 378.48,-689.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="379.88,-685.99 369.44,-684.19 376.48,-692.11 379.88,-685.99"/>
+</g>
+<!-- 17->10 -->
+<g id="edge20" class="edge">
+<title>17->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M478.1,-719.7C484.62,-711.39 492.57,-701.28 499.75,-692.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="502.63,-694.13 506.06,-684.1 497.13,-689.81 502.63,-694.13"/>
</g>
<!-- 18->9 -->
-<g id="edge20" class="edge"><title>18->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M388.357,-647.876C373.582,-638.724 355.209,-627.342 339.297,-617.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="341.093,-614.481 330.749,-612.19 337.407,-620.431 341.093,-614.481"/>
+<g id="edge19" class="edge">
+<title>18->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M553.76,-721.2C513.06,-710.95 459.71,-697.52 416.31,-686.59"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="416.91,-683.13 406.36,-684.09 415.2,-689.92 416.91,-683.13"/>
</g>
<!-- 18->10 -->
-<g id="edge22" class="edge"><title>18->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M428.607,-647.697C434.597,-639.474 441.876,-629.483 448.479,-620.421"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="451.478,-622.248 454.538,-612.104 445.821,-618.126 451.478,-622.248"/>
+<g id="edge21" class="edge">
+<title>18->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M592.52,-719.7C580.19,-710.8 564.98,-699.82 551.65,-690.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="553.36,-687.12 543.2,-684.1 549.26,-692.79 553.36,-687.12"/>
</g>
-<!-- 19->9 -->
-<g id="edge19" class="edge"><title>19->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M497.206,-649.378C460.723,-639.163 412.756,-625.732 373.621,-614.774"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="374.447,-611.371 363.874,-612.045 372.56,-618.111 374.447,-611.371"/>
+<!-- 19->11 -->
+<g id="edge22" class="edge">
+<title>19->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M993.06,-722.69C1013.3,-714.77 1033.59,-702.61 1045.5,-684 1054.13,-670.53 1052.81,-662.23 1045.5,-648 1037.92,-633.24 1024.11,-621.67 1010.45,-613.16"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1011.97,-610 1001.57,-608.01 1008.46,-616.05 1011.97,-610"/>
</g>
-<!-- 19->10 -->
-<g id="edge21" class="edge"><title>19->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M531.742,-647.697C520.911,-638.881 507.582,-628.032 495.84,-618.474"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="497.979,-615.703 488.014,-612.104 493.56,-621.132 497.979,-615.703"/>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#d87556" 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">index_genomic_alignment_samtools</text>
</g>
-<!-- 20->11 -->
-<g id="edge24" class="edge"><title>20->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M899.722,-649.313C918.045,-641.265 936.359,-629.365 947,-612 955.359,-598.357 955.132,-589.779 947,-576 934.386,-554.628 909.727,-541.279 888.56,-533.324"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="889.422,-529.918 878.828,-529.94 887.123,-536.53 889.422,-529.918"/>
+<!-- 19->20 -->
+<g id="edge36" class="edge">
+<title>19->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M932.48,-719.7C933.36,-711.98 934.42,-702.71 935.4,-694.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="938.89,-694.44 936.55,-684.1 931.93,-693.64 938.89,-694.44"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#56b9d8" stroke-width="2" d="M926,-612C926,-612 776,-612 776,-612 770,-612 764,-606 764,-600 764,-600 764,-588 764,-588 764,-582 770,-576 776,-576 776,-576 926,-576 926,-576 932,-576 938,-582 938,-588 938,-588 938,-600 938,-600 938,-606 932,-612 926,-612"/>
-<text text-anchor="middle" x="851" y="-591.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#8fd856" 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">calculate_TIN_scores</text>
</g>
-<!-- 20->21 -->
-<g id="edge40" class="edge"><title>20->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M844.978,-647.697C845.859,-639.983 846.919,-630.712 847.901,-622.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="851.387,-622.437 849.045,-612.104 844.432,-621.642 851.387,-622.437"/>
+<!-- 19->26 -->
+<g id="edge42" class="edge">
+<title>19->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M879.36,-719.91C861.77,-711.65 843.51,-699.97 831.5,-684 818.18,-666.29 813.75,-641.27 812.47,-622.27"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="815.96,-621.99 812.04,-612.15 808.97,-622.28 815.96,-621.99"/>
</g>
-<!-- 28 -->
-<g id="node29" class="node"><title>28</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M780,-540C780,-540 692,-540 692,-540 686,-540 680,-534 680,-528 680,-528 680,-516 680,-516 680,-510 686,-504 692,-504 692,-504 780,-504 780,-504 786,-504 792,-510 792,-516 792,-516 792,-528 792,-528 792,-534 786,-540 780,-540"/>
-<text text-anchor="middle" x="736" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<!-- 20->11 -->
+<g id="edge23" class="edge">
+<title>20->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M946.66,-647.7C950.41,-639.73 954.95,-630.1 959.12,-621.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="962.34,-622.64 963.44,-612.1 956.01,-619.66 962.34,-622.64"/>
</g>
-<!-- 20->28 -->
-<g id="edge46" class="edge"><title>20->28</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M799.53,-647.827C783.272,-639.345 766.08,-627.537 755,-612 742.133,-593.959 737.662,-568.972 736.249,-550.065"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="739.741,-549.812 735.737,-540.002 732.75,-550.167 739.741,-549.812"/>
+<!-- 20->26 -->
+<g id="edge43" class="edge">
+<title>20->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M907.68,-647.88C891.05,-638.64 870.34,-627.13 852.48,-617.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="853.88,-613.99 843.44,-612.19 850.48,-620.11 853.88,-613.99"/>
</g>
<!-- 21->11 -->
-<g id="edge23" class="edge"><title>21->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M851,-575.697C851,-567.983 851,-558.712 851,-550.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="854.5,-550.104 851,-540.104 847.5,-550.104 854.5,-550.104"/>
-</g>
-<!-- 21->28 -->
-<g id="edge45" class="edge"><title>21->28</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M822.868,-575.876C807.832,-566.724 789.133,-555.342 772.94,-545.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="774.602,-542.4 764.24,-540.19 770.962,-548.379 774.602,-542.4"/>
-</g>
-<!-- 22->11 -->
-<g id="edge25" class="edge"><title>22->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M970.876,-647.724C975.205,-628.573 978.916,-597.548 965,-576 948.17,-549.94 914.888,-536.48 888.609,-529.662"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="889.107,-526.183 878.57,-527.284 887.494,-532.994 889.107,-526.183"/>
-</g>
-<!-- 22->21 -->
-<g id="edge39" class="edge"><title>22->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M937.868,-647.876C922.832,-638.724 904.133,-627.342 887.94,-617.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="889.602,-614.4 879.24,-612.19 885.962,-620.379 889.602,-614.4"/>
-</g>
-<!-- 22->28 -->
-<g id="edge48" class="edge"><title>22->28</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M967.332,-647.807C967.882,-627.847 965.54,-595.215 947,-576 941.799,-570.609 861.991,-551.541 802.055,-537.821"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="802.775,-534.395 792.247,-535.582 801.217,-541.22 802.775,-534.395"/>
-</g>
-<!-- 23->12 -->
-<g id="edge27" class="edge"><title>23->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M846.292,-431.697C844.639,-423.983 842.653,-414.712 840.81,-406.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="844.183,-405.149 838.665,-396.104 837.338,-406.616 844.183,-405.149"/>
+<g id="edge24" class="edge">
+<title>21->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1068.51,-719.91C1071.98,-700.93 1074.61,-670.06 1061.5,-648 1050.33,-629.2 1029.7,-616.35 1011.01,-608.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1012.34,-604.77 1001.76,-604.17 1009.65,-611.24 1012.34,-604.77"/>
+</g>
+<!-- 21->20 -->
+<g id="edge37" class="edge">
+<title>21->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1033.68,-719.88C1017.05,-710.64 996.34,-699.13 978.48,-689.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="979.88,-685.99 969.44,-684.19 976.48,-692.11 979.88,-685.99"/>
+</g>
+<!-- 21->26 -->
+<g id="edge44" class="edge">
+<title>21->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1065.91,-719.73C1066.53,-699.7 1064.25,-667.01 1045.5,-648 1033.9,-636.25 946.59,-618.61 882.24,-606.95"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="882.58,-603.46 872.12,-605.14 881.34,-610.35 882.58,-603.46"/>
</g>
-<!-- 24 -->
-<g id="node25" class="node"><title>24</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M1054,-540C1054,-540 974,-540 974,-540 968,-540 962,-534 962,-528 962,-528 962,-516 962,-516 962,-510 968,-504 974,-504 974,-504 1054,-504 1054,-504 1060,-504 1066,-510 1066,-516 1066,-516 1066,-528 1066,-528 1066,-534 1060,-540 1054,-540"/>
-<text text-anchor="middle" x="1014" y="-519.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
-</g>
-<!-- 24->12 -->
-<g id="edge26" class="edge"><title>24->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M998.839,-503.668C981.776,-484.746 952.678,-454.186 924,-432 907.558,-419.28 887.819,-407.241 871.112,-397.862"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="872.629,-394.702 862.182,-392.937 869.249,-400.831 872.629,-394.702"/>
-</g>
-<!-- 25 -->
-<g id="node26" class="node"><title>25</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M407,-828C407,-828 281,-828 281,-828 275,-828 269,-822 269,-816 269,-816 269,-804 269,-804 269,-798 275,-792 281,-792 281,-792 407,-792 407,-792 413,-792 419,-798 419,-804 419,-804 419,-816 419,-816 419,-822 413,-828 407,-828"/>
-<text text-anchor="middle" x="344" y="-807.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#9fd856" 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">alfa_qc_all_samples</text>
</g>
-<!-- 25->14 -->
-<g id="edge29" class="edge"><title>25->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M342.764,-791.697C342.213,-783.983 341.551,-774.712 340.937,-766.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="344.425,-765.83 340.222,-756.104 337.443,-766.328 344.425,-765.83"/>
+<!-- 22->12 -->
+<g id="edge25" class="edge">
+<title>22->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M905.72,-359.7C895.75,-350.97 883.49,-340.24 872.64,-330.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="874.88,-328.06 865.05,-324.1 870.27,-333.32 874.88,-328.06"/>
</g>
-<!-- 26 -->
-<g id="node27" class="node"><title>26</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M238.5,-828C238.5,-828 151.5,-828 151.5,-828 145.5,-828 139.5,-822 139.5,-816 139.5,-816 139.5,-804 139.5,-804 139.5,-798 145.5,-792 151.5,-792 151.5,-792 238.5,-792 238.5,-792 244.5,-792 250.5,-798 250.5,-804 250.5,-804 250.5,-816 250.5,-816 250.5,-822 244.5,-828 238.5,-828"/>
-<text text-anchor="middle" x="195" y="-807.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#d89556" 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">pe_remove_adapters_cutadapt</text>
</g>
-<!-- 26->15 -->
-<g id="edge30" class="edge"><title>26->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M195,-791.697C195,-783.983 195,-774.712 195,-766.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="198.5,-766.104 195,-756.104 191.5,-766.104 198.5,-766.104"/>
+<!-- 23->13 -->
+<g id="edge26" class="edge">
+<title>23->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M386.26,-863.7C385.71,-855.98 385.05,-846.71 384.44,-838.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="387.93,-837.83 383.72,-828.1 380.94,-838.33 387.93,-837.83"/>
</g>
-<!-- 29 -->
-<g id="node30" class="node"><title>29</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M522.5,-756C522.5,-756 437.5,-756 437.5,-756 431.5,-756 425.5,-750 425.5,-744 425.5,-744 425.5,-732 425.5,-732 425.5,-726 431.5,-720 437.5,-720 437.5,-720 522.5,-720 522.5,-720 528.5,-720 534.5,-726 534.5,-732 534.5,-732 534.5,-744 534.5,-744 534.5,-750 528.5,-756 522.5,-756"/>
-<text text-anchor="middle" x="480" y="-735.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M274,-900C274,-900 173,-900 173,-900 167,-900 161,-894 161,-888 161,-888 161,-876 161,-876 161,-870 167,-864 173,-864 173,-864 274,-864 274,-864 280,-864 286,-870 286,-876 286,-876 286,-888 286,-888 286,-894 280,-900 274,-900"/>
+<text text-anchor="middle" x="223.5" y="-879.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
-<!-- 26->29 -->
-<g id="edge49" class="edge"><title>26->29</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M250.642,-794.334C253.806,-793.536 256.942,-792.753 260,-792 326.125,-775.727 345.31,-773.324 415.453,-756.091"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="416.35,-759.475 425.218,-753.678 414.67,-752.68 416.35,-759.475"/>
+<!-- 24->14 -->
+<g id="edge27" class="edge">
+<title>24->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M223.5,-863.7C223.5,-855.98 223.5,-846.71 223.5,-838.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="227,-838.1 223.5,-828.1 220,-838.1 227,-838.1"/>
</g>
<!-- 27 -->
-<g id="node28" class="node"><title>27</title>
-<path fill="none" stroke="#567bd8" stroke-width="2" d="M668,-828C668,-828 558,-828 558,-828 552,-828 546,-822 546,-816 546,-816 546,-804 546,-804 546,-798 552,-792 558,-792 558,-792 668,-792 668,-792 674,-792 680,-798 680,-804 680,-804 680,-816 680,-816 680,-822 674,-828 668,-828"/>
-<text text-anchor="middle" x="613" y="-807.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-</g>
-<!-- 27->16 -->
-<g id="edge31" class="edge"><title>27->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M613,-791.697C613,-783.983 613,-774.712 613,-766.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="616.5,-766.104 613,-756.104 609.5,-766.104 616.5,-766.104"/>
-</g>
-<!-- 28->17 -->
-<g id="edge32" class="edge"><title>28->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M688.06,-503.966C660.535,-494.185 625.783,-481.836 596.759,-471.524"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="597.749,-468.161 587.155,-468.111 595.406,-474.757 597.749,-468.161"/>
-</g>
-<!-- 29->18 -->
-<g id="edge33" class="edge"><title>29->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M464.18,-719.697C456.43,-711.22 446.961,-700.864 438.476,-691.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="440.969,-689.123 431.638,-684.104 435.803,-693.846 440.969,-689.123"/>
-</g>
-<!-- 29->19 -->
-<g id="edge35" class="edge"><title>29->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M498.045,-719.697C507.062,-711.05 518.118,-700.449 527.943,-691.027"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="530.367,-693.552 535.163,-684.104 525.522,-688.499 530.367,-693.552"/>
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#d85656" 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">create_index_salmon</text>
</g>
-<!-- 30 -->
-<g id="node31" class="node"><title>30</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1001,-756C1001,-756 931,-756 931,-756 925,-756 919,-750 919,-744 919,-744 919,-732 919,-732 919,-726 925,-720 931,-720 931,-720 1001,-720 1001,-720 1007,-720 1013,-726 1013,-732 1013,-732 1013,-744 1013,-744 1013,-750 1007,-756 1001,-756"/>
-<text text-anchor="middle" x="966" y="-735.5" font-family="sans" font-size="10.00">create_index_star</text>
+<!-- 24->27 -->
+<g id="edge45" class="edge">
+<title>24->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M286.2,-865.88C289,-865.24 291.78,-864.61 294.5,-864 368.15,-847.52 389.26,-845.42 467.05,-828.06"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="467.83,-831.47 476.82,-825.87 466.3,-824.64 467.83,-831.47"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#56a2d8" 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">remove_adapters_cutadapt</text>
+</g>
+<!-- 25->15 -->
+<g id="edge28" class="edge">
+<title>25->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M683.5,-863.7C683.5,-855.98 683.5,-846.71 683.5,-838.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="687,-838.1 683.5,-828.1 680,-838.1 687,-838.1"/>
+</g>
+<!-- 26->16 -->
+<g id="edge29" class="edge">
+<title>26->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M754.34,-575.97C718.85,-565.57 673.46,-552.28 637.03,-541.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="637.59,-538.12 627.01,-538.67 635.62,-544.84 637.59,-538.12"/>
+</g>
+<!-- 27->17 -->
+<g id="edge30" class="edge">
+<title>27->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M519.46,-791.7C510.44,-783.05 499.38,-772.45 489.56,-763.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="491.98,-760.5 482.34,-756.1 487.13,-765.55 491.98,-760.5"/>
+</g>
+<!-- 27->18 -->
+<g id="edge32" class="edge">
+<title>27->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M557.03,-791.7C566.88,-782.97 578.99,-772.24 589.7,-762.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="592.03,-765.36 597.2,-756.1 587.39,-760.12 592.03,-765.36"/>
</g>
-<!-- 30->20 -->
-<g id="edge37" class="edge"><title>30->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M935.911,-719.876C919.68,-710.639 899.458,-699.131 882.029,-689.212"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="883.627,-686.094 873.205,-684.19 880.165,-692.178 883.627,-686.094"/>
+<!-- 28 -->
+<g id="node29" class="node">
+<title>28</title>
+<path fill="none" stroke="#61d856" 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">create_index_star</text>
+</g>
+<!-- 28->19 -->
+<g id="edge34" class="edge">
+<title>28->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1031.72,-791.88C1013.87,-782.55 991.6,-770.92 972.5,-760.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="973.89,-757.72 963.41,-756.19 970.65,-763.92 973.89,-757.72"/>
+</g>
+<!-- 28->21 -->
+<g id="edge38" class="edge">
+<title>28->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1064.5,-791.7C1064.5,-783.98 1064.5,-774.71 1064.5,-766.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1068,-766.1 1064.5,-756.1 1061,-766.1 1068,-766.1"/>
+</g>
+<!-- 32 -->
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#80d856" 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">generate_alfa_index</text>
+</g>
+<!-- 28->32 -->
+<g id="edge49" class="edge">
+<title>28->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1093.44,-791.92C1106.06,-782.9 1119.72,-770.64 1127.5,-756 1150.11,-713.44 1150.06,-655.68 1147.56,-622.16"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1151.05,-621.84 1146.69,-612.18 1144.07,-622.45 1151.05,-621.84"/>
</g>
-<!-- 30->22 -->
-<g id="edge41" class="edge"><title>30->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M966,-719.697C966,-711.983 966,-702.712 966,-694.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="969.5,-694.104 966,-684.104 962.5,-694.104 969.5,-694.104"/>
+<!-- 29 -->
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#56c1d8" 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">alfa_qc</text>
</g>
-<!-- 30->24 -->
-<g id="edge44" class="edge"><title>30->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M993.34,-719.775C1005.11,-710.718 1017.62,-698.478 1024,-684 1043.27,-640.297 1032.42,-583.371 1023.04,-550.235"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1026.3,-548.935 1020.08,-540.359 1019.6,-550.943 1026.3,-548.935"/>
+<!-- 29->22 -->
+<g id="edge40" class="edge">
+<title>29->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M960.13,-431.7C954.78,-423.56 948.3,-413.69 942.39,-404.7"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="945.16,-402.54 936.74,-396.1 939.31,-406.38 945.16,-402.54"/>
</g>
-<!-- 31 -->
-<g id="node32" class="node"><title>31</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M695.5,-612C695.5,-612 574.5,-612 574.5,-612 568.5,-612 562.5,-606 562.5,-600 562.5,-600 562.5,-588 562.5,-588 562.5,-582 568.5,-576 574.5,-576 574.5,-576 695.5,-576 695.5,-576 701.5,-576 707.5,-582 707.5,-588 707.5,-588 707.5,-600 707.5,-600 707.5,-606 701.5,-612 695.5,-612"/>
-<text text-anchor="middle" x="635" y="-591.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
-</g>
-<!-- 31->28 -->
-<g id="edge47" class="edge"><title>31->28</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M659.707,-575.876C672.669,-566.893 688.728,-555.763 702.765,-546.034"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="704.972,-548.763 711.198,-540.19 700.985,-543.009 704.972,-548.763"/>
+<!-- 30 -->
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#5682d8" 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">extract_transcripts_as_bed12</text>
+</g>
+<!-- 30->26 -->
+<g id="edge41" class="edge">
+<title>30->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M730.92,-647.88C744.91,-638.81 762.28,-627.55 777.39,-617.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="779.49,-620.57 785.98,-612.19 775.68,-614.69 779.49,-620.57"/>
+</g>
+<!-- 31->29 -->
+<g id="edge47" class="edge">
+<title>31->29</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M971.5,-503.7C971.5,-495.98 971.5,-486.71 971.5,-478.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="975,-478.1 971.5,-468.1 968,-478.1 975,-478.1"/>
+</g>
+<!-- 32->29 -->
+<g id="edge46" class="edge">
+<title>32->29</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1128.98,-575.88C1111.56,-557.15 1081.99,-526.76 1053.5,-504 1039.13,-492.52 1022.22,-481.25 1007.49,-472.08"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1009,-468.9 998.65,-466.66 1005.34,-474.87 1009,-468.9"/>
</g>
</g>
</svg>
diff --git a/tests/test_alfa/expected_output.md5 b/tests/test_alfa/expected_output.md5
index 57f9dfd..7b2472f 100644
--- a/tests/test_alfa/expected_output.md5
+++ b/tests/test_alfa/expected_output.md5
@@ -1,5 +1,29 @@
90e42aa46890e9cd0a47800428699fbf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
ccc3cf5a57fddb0d469e597d4376b1bf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.plus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.plus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense_Signal.Unique.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense_Signal.Unique.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense_Signal.Unique.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense_Signal.Unique.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense_Signal.Unique.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense_Signal.Unique.out.plus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense_Signal.Unique.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense_Signal.Unique.out.plus.bg
5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str1.out.bg
8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str2.out.bg
5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.Unique.str1.out.bg
@@ -16,15 +40,3 @@ ccc3cf5a57fddb0d469e597d4376b1bf results/alfa_indexes/homo_sapiens/75/ALFA/sort
5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.str2.out.bg
8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str1.out.bg
5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str2.out.bg
-5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.minus.bg
-8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.plus.bg
-8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.minus.bg
-5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.plus.bg
-8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.minus.bg
-5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.plus.bg
-5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.minus.bg
-8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.plus.bg
-e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
-c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
-c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
-e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
diff --git a/tests/test_alfa/test.sh b/tests/test_alfa/test.sh
index 2f45621..523eea4 100755
--- a/tests/test_alfa/test.sh
+++ b/tests/test_alfa/test.sh
@@ -33,7 +33,7 @@ snakemake \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose \
- results/ALFA/ALFA_plots.Categories.pdf
+ results/ALFA/ALFA_plots.concat.png
# Check md5 sum of some output files
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 31cbf64..93f8a66 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -89,9 +89,15 @@ bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synt
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
-53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
-90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
-16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
-c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
-bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
-ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
\ No newline at end of file
+bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
+ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
+bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.out.minus.bg
+ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.out.plus.bg
+90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
+16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
+90ae442ebf35015eab2dd4e804c2bafb results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.out.minus.bg
+16652c037090f3eed1123618a2e75107 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.out.plus.bg
+c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+53fd53f884352d0493b2ca99cef5d76d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
\ No newline at end of file
diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh
index 6b641f2..ac6e45e 100755
--- a/tests/test_integration_workflow/test.local.sh
+++ b/tests/test_integration_workflow/test.local.sh
@@ -7,7 +7,7 @@ cleanup () {
rm -rf .java/
rm -rf .snakemake/
rm -rf logs/
- # rm -rf results/
+ rm -rf results/
cd $user_dir
echo "Exit status: $rc"
}
--
GitLab