diff --git a/Snakefile b/Snakefile
index 5075e82e1ae2e8f35cc829efccdacc52ed25cb5c..97db0e37a7318235ecc8c990e8e94662a3d89e3b 100644
--- a/Snakefile
+++ b/Snakefile
@@ -65,17 +65,12 @@ rule finish:
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)]),
- TIN_score = expand(
- os.path.join(
- config['output_dir'],
- "{seqmode}",
- "{sample}",
- "TIN",
- "TIN_score.tsv"),
- 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)]),
+ TIN_boxplot_PNG = os.path.join(
+ config['output_dir'],
+ "TIN_scores_boxplot.png"),
+ TIN_boxplot_PDF = os.path.join(
+ config['output_dir'],
+ "TIN_scores_boxplot.pdf"),
salmon_merge_genes = expand(
os.path.join(
config["output_dir"],
@@ -541,7 +536,7 @@ rule calculate_TIN_scores:
threads: 8
singularity:
- "docker://zavolab/tin_score_calculation:0.1.0-slim"
+ "docker://zavolab/tin_score_calculation:0.2.0-slim"
shell:
"(tin_score_calculation.py \
@@ -552,6 +547,103 @@ rule calculate_TIN_scores:
-n 100 > {output.TIN_score};) 2> {log.stderr}"
+rule merge_TIN_scores:
+ """
+ Merge TIN scores tables
+ """
+ input:
+ TIN_score = expand(
+ os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "TIN",
+ "TIN_score.tsv"),
+ 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)])
+
+ output:
+ TIN_scores_merged = os.path.join(
+ config['output_dir'],
+ "TIN_scores_merged.tsv")
+
+ params:
+ TIN_score_merged_paths = ",".join(expand(
+ os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "TIN",
+ "TIN_score.tsv"),
+ 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)]))
+
+ log:
+ stderr = os.path.join(
+ config['log_dir'],
+ "merge_TIN_scores.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "merge_TIN_scores.stdout.log")
+
+ threads: 1
+
+ singularity:
+ "docker://zavolab/tin_score_calculation:0.2.0-slim"
+
+ shell:
+ "(tin_score_merge.py \
+ --input-files {params.TIN_score_merged_paths} \
+ --output-file {output.TIN_scores_merged}) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
+rule plot_TIN_scores:
+ """
+ Generate TIN scores boxplots
+ """
+ input:
+ TIN_scores_merged = os.path.join(
+ config['output_dir'],
+ "TIN_scores_merged.tsv"),
+
+ output:
+ TIN_boxplot_PNG = os.path.join(
+ config['output_dir'],
+ "TIN_scores_boxplot.png"),
+ TIN_boxplot_PDF = os.path.join(
+ config['output_dir'],
+ "TIN_scores_boxplot.pdf")
+
+ params:
+ TIN_boxplot_prefix = os.path.join(
+ config['output_dir'],
+ "TIN_scores_boxplot")
+
+ log:
+ stderr = os.path.join(
+ config['log_dir'],
+ "plot_TIN_scores.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "plot_TIN_scores.stdout.log")
+
+ threads: 1
+
+ singularity:
+ "docker://zavolab/tin_score_calculation:0.2.0-slim"
+
+ shell:
+ "(tin_score_plot.py \
+ --input-file {input.TIN_scores_merged} \
+ --output-file-prefix {params.TIN_boxplot_prefix}) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
rule salmon_quantmerge_genes:
'''
Merge gene quantifications into a single file
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 720c5f02a83574369148ce65600ce833d0b3a919..208139ab6dde973074b9b277c60d3f339b2cec89 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,591 +1,517 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+<!-- Generated by graphviz version 2.38.0 (20140413.2041)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="2113pt" height="625pt"
- viewBox="0.00 0.00 2112.50 625.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1912pt" height="625pt"
+ viewBox="0.00 0.00 1911.56 625.00" 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(4 621)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="transparent" points="-4,4 -4,-621 2108.5,-621 2108.5,4 -4,4"/>
+<polygon fill="white" stroke="none" points="-4,4 -4,-621 1907.56,-621 1907.56,4 -4,4"/>
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-<g id="node1" class="node">
-<title>0</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M1495.5,-36C1495.5,-36 1465.5,-36 1465.5,-36 1459.5,-36 1453.5,-30 1453.5,-24 1453.5,-24 1453.5,-12 1453.5,-12 1453.5,-6 1459.5,0 1465.5,0 1465.5,0 1495.5,0 1495.5,0 1501.5,0 1507.5,-6 1507.5,-12 1507.5,-12 1507.5,-24 1507.5,-24 1507.5,-30 1501.5,-36 1495.5,-36"/>
-<text text-anchor="middle" x="1480.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node"><title>0</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M1309,-36C1309,-36 1279,-36 1279,-36 1273,-36 1267,-30 1267,-24 1267,-24 1267,-12 1267,-12 1267,-6 1273,-0 1279,-0 1279,-0 1309,-0 1309,-0 1315,-0 1321,-6 1321,-12 1321,-12 1321,-24 1321,-24 1321,-30 1315,-36 1309,-36"/>
+<text text-anchor="middle" x="1294" 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="#5692d8" stroke-width="2" d="M313,-108C313,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 313,-72 313,-72 319,-72 325,-78 325,-84 325,-84 325,-96 325,-96 325,-102 319,-108 313,-108"/>
-<text text-anchor="middle" x="162.5" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
-<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node2" class="node"><title>1</title>
+<path fill="none" stroke="#80d856" stroke-width="2" d="M280,-108C280,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 280,-72 280,-72 286,-72 292,-78 292,-84 292,-84 292,-96 292,-96 292,-102 286,-108 280,-108"/>
+<text text-anchor="middle" x="146" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
+<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 1->0 -->
-<g id="edge1" class="edge">
-<title>1->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M325.4,-72.61C328.12,-72.4 330.82,-72.19 333.5,-72 769.44,-40.28 1300.04,-24.02 1443.35,-20"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1443.47,-23.5 1453.37,-19.72 1443.28,-16.5 1443.47,-23.5"/>
+<g id="edge1" class="edge"><title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M292.011,-72.7558C295.033,-72.4942 298.032,-72.2418 301,-72 672.971,-41.6987 1124.8,-24.7799 1256.38,-20.249"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1256.84,-23.7356 1266.71,-19.8963 1256.6,-16.7397 1256.84,-23.7356"/>
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-<g id="node3" class="node">
-<title>2</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M668,-108C668,-108 355,-108 355,-108 349,-108 343,-102 343,-96 343,-96 343,-84 343,-84 343,-78 349,-72 355,-72 355,-72 668,-72 668,-72 674,-72 680,-78 680,-84 680,-84 680,-96 680,-96 680,-102 674,-108 668,-108"/>
-<text text-anchor="middle" x="511.5" y="-93" font-family="sans" font-size="10.00">fastqc</text>
-<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<g id="node3" class="node"><title>2</title>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M602,-108C602,-108 322,-108 322,-108 316,-108 310,-102 310,-96 310,-96 310,-84 310,-84 310,-78 316,-72 322,-72 322,-72 602,-72 602,-72 608,-72 614,-78 614,-84 614,-84 614,-96 614,-96 614,-102 608,-108 602,-108"/>
+<text text-anchor="middle" x="462" y="-93" font-family="sans" font-size="10.00">fastqc</text>
+<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
<!-- 2->0 -->
-<g id="edge2" class="edge">
-<title>2->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M680,-73.18C684.89,-72.78 689.73,-72.38 694.5,-72 982.41,-48.92 1330.21,-27.85 1443.14,-21.18"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1443.55,-24.66 1453.33,-20.58 1443.14,-17.68 1443.55,-24.66"/>
+<g id="edge2" class="edge"><title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M614.408,-73.2567C618.989,-72.8268 623.528,-72.4069 628,-72 867.307,-50.2271 1155.45,-28.9846 1256.67,-21.6729"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1256.98,-25.1597 1266.7,-20.9496 1256.48,-18.1778 1256.98,-25.1597"/>
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-<g id="node4" class="node">
-<title>3</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M922,-180C922,-180 759,-180 759,-180 753,-180 747,-174 747,-168 747,-168 747,-156 747,-156 747,-150 753,-144 759,-144 759,-144 922,-144 922,-144 928,-144 934,-150 934,-156 934,-156 934,-168 934,-168 934,-174 928,-180 922,-180"/>
-<text text-anchor="middle" x="840.5" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<g id="node4" class="node"><title>3</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M830,-180C830,-180 688,-180 688,-180 682,-180 676,-174 676,-168 676,-168 676,-156 676,-156 676,-150 682,-144 688,-144 688,-144 830,-144 830,-144 836,-144 842,-150 842,-156 842,-156 842,-168 842,-168 842,-174 836,-180 830,-180"/>
+<text text-anchor="middle" x="759" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 3->0 -->
-<g id="edge3" class="edge">
-<title>3->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M773.07,-143.94C755.22,-136.02 738.02,-124.55 727.5,-108 718.92,-94.5 716.59,-83.7 727.5,-72 776.64,-19.27 1297.41,-18.03 1442.92,-18.72"/>
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+<g id="edge3" class="edge"><title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M704.98,-143.962C688.226,-135.851 671.643,-124.258 662,-108 653.838,-94.2387 651.169,-83.777 662,-72 702.371,-28.1018 1127.09,-20.5458 1256.67,-19.2602"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1256.92,-22.7581 1266.89,-19.1659 1256.85,-15.7584 1256.92,-22.7581"/>
</g>
<!-- 4 -->
-<g id="node5" class="node">
-<title>4</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M1414.5,-180C1414.5,-180 1268.5,-180 1268.5,-180 1262.5,-180 1256.5,-174 1256.5,-168 1256.5,-168 1256.5,-156 1256.5,-156 1256.5,-150 1262.5,-144 1268.5,-144 1268.5,-144 1414.5,-144 1414.5,-144 1420.5,-144 1426.5,-150 1426.5,-156 1426.5,-156 1426.5,-168 1426.5,-168 1426.5,-174 1420.5,-180 1414.5,-180"/>
-<text text-anchor="middle" x="1341.5" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node5" class="node"><title>4</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1273,-180C1273,-180 1147,-180 1147,-180 1141,-180 1135,-174 1135,-168 1135,-168 1135,-156 1135,-156 1135,-150 1141,-144 1147,-144 1147,-144 1273,-144 1273,-144 1279,-144 1285,-150 1285,-156 1285,-156 1285,-168 1285,-168 1285,-174 1279,-180 1273,-180"/>
+<text text-anchor="middle" x="1210" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 4->0 -->
-<g id="edge4" class="edge">
-<title>4->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1409.25,-143.89C1428.65,-135.92 1448.14,-124.43 1461.5,-108 1475.56,-90.7 1479.9,-65.44 1480.95,-46.24"/>
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+<g id="edge4" class="edge"><title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1280.09,-143.929C1298.08,-136.036 1315.35,-124.579 1326,-108 1338.64,-88.3232 1327.31,-62.9893 1314.77,-44.3855"/>
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-<g id="node6" class="node">
-<title>5</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M1487,-324C1487,-324 1392,-324 1392,-324 1386,-324 1380,-318 1380,-312 1380,-312 1380,-300 1380,-300 1380,-294 1386,-288 1392,-288 1392,-288 1487,-288 1487,-288 1493,-288 1499,-294 1499,-300 1499,-300 1499,-312 1499,-312 1499,-318 1493,-324 1487,-324"/>
-<text text-anchor="middle" x="1439.5" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<g id="node6" class="node"><title>5</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M1462.5,-180C1462.5,-180 1397.5,-180 1397.5,-180 1391.5,-180 1385.5,-174 1385.5,-168 1385.5,-168 1385.5,-156 1385.5,-156 1385.5,-150 1391.5,-144 1397.5,-144 1397.5,-144 1462.5,-144 1462.5,-144 1468.5,-144 1474.5,-150 1474.5,-156 1474.5,-156 1474.5,-168 1474.5,-168 1474.5,-174 1468.5,-180 1462.5,-180"/>
+<text text-anchor="middle" x="1430" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
</g>
<!-- 5->0 -->
-<g id="edge5" class="edge">
-<title>5->0</title>
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+<g id="edge5" class="edge"><title>5->0</title>
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-<g id="node7" class="node">
-<title>6</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M1766,-324C1766,-324 1671,-324 1671,-324 1665,-324 1659,-318 1659,-312 1659,-312 1659,-300 1659,-300 1659,-294 1665,-288 1671,-288 1671,-288 1766,-288 1766,-288 1772,-288 1778,-294 1778,-300 1778,-300 1778,-312 1778,-312 1778,-318 1772,-324 1766,-324"/>
-<text text-anchor="middle" x="1718.5" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<g id="node7" class="node"><title>6</title>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M1141,-108C1141,-108 1029,-108 1029,-108 1023,-108 1017,-102 1017,-96 1017,-96 1017,-84 1017,-84 1017,-78 1023,-72 1029,-72 1029,-72 1141,-72 1141,-72 1147,-72 1153,-78 1153,-84 1153,-84 1153,-96 1153,-96 1153,-102 1147,-108 1141,-108"/>
+<text text-anchor="middle" x="1085" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1085" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
<!-- 6->0 -->
-<g id="edge6" class="edge">
-<title>6->0</title>
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+<g id="edge6" class="edge"><title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1135.86,-71.9656C1173.31,-59.4227 1223.37,-42.6564 1257.05,-31.3763"/>
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-<title>7</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M1440.5,-108C1440.5,-108 1312.5,-108 1312.5,-108 1306.5,-108 1300.5,-102 1300.5,-96 1300.5,-96 1300.5,-84 1300.5,-84 1300.5,-78 1306.5,-72 1312.5,-72 1312.5,-72 1440.5,-72 1440.5,-72 1446.5,-72 1452.5,-78 1452.5,-84 1452.5,-84 1452.5,-96 1452.5,-96 1452.5,-102 1446.5,-108 1440.5,-108"/>
-<text text-anchor="middle" x="1376.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1376.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<g id="node8" class="node"><title>7</title>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M1304.5,-108C1304.5,-108 1183.5,-108 1183.5,-108 1177.5,-108 1171.5,-102 1171.5,-96 1171.5,-96 1171.5,-84 1171.5,-84 1171.5,-78 1177.5,-72 1183.5,-72 1183.5,-72 1304.5,-72 1304.5,-72 1310.5,-72 1316.5,-78 1316.5,-84 1316.5,-84 1316.5,-96 1316.5,-96 1316.5,-102 1310.5,-108 1304.5,-108"/>
+<text text-anchor="middle" x="1244" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1244" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<!-- 7->0 -->
-<g id="edge7" class="edge">
-<title>7->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="1448.62,-44.68 1454.96,-36.19 1444.71,-38.87 1448.62,-44.68"/>
+<g id="edge7" class="edge"><title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1256.36,-71.6966C1262.23,-63.4741 1269.37,-53.4832 1275.84,-44.4207"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1278.82,-46.276 1281.78,-36.1043 1273.12,-42.2073 1278.82,-46.276"/>
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<!-- 8 -->
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-<title>8</title>
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-<text text-anchor="middle" x="817.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="817.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<g id="node9" class="node"><title>8</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M813.5,-108C813.5,-108 682.5,-108 682.5,-108 676.5,-108 670.5,-102 670.5,-96 670.5,-96 670.5,-84 670.5,-84 670.5,-78 676.5,-72 682.5,-72 682.5,-72 813.5,-72 813.5,-72 819.5,-72 825.5,-78 825.5,-84 825.5,-84 825.5,-96 825.5,-96 825.5,-102 819.5,-108 813.5,-108"/>
+<text text-anchor="middle" x="748" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="748" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
<!-- 8->0 -->
-<g id="edge8" class="edge">
-<title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M898.39,-73.35C901.46,-72.87 904.51,-72.42 907.5,-72 1108.54,-43.78 1351.45,-26.97 1443.09,-21.23"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1443.49,-24.71 1453.25,-20.6 1443.06,-17.73 1443.49,-24.71"/>
+<g id="edge8" class="edge"><title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M825.735,-73.4985C828.861,-72.9741 831.958,-72.472 835,-72 990.957,-47.7965 1178.31,-29.4911 1256.68,-22.3138"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.36,-25.7666 1267,-21.3755 1256.72,-18.7954 1257.36,-25.7666"/>
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<!-- 9 -->
-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1078.5,-108C1078.5,-108 928.5,-108 928.5,-108 922.5,-108 916.5,-102 916.5,-96 916.5,-96 916.5,-84 916.5,-84 916.5,-78 922.5,-72 928.5,-72 928.5,-72 1078.5,-72 1078.5,-72 1084.5,-72 1090.5,-78 1090.5,-84 1090.5,-84 1090.5,-96 1090.5,-96 1090.5,-102 1084.5,-108 1078.5,-108"/>
-<text text-anchor="middle" x="1003.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1003.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M986.5,-108C986.5,-108 855.5,-108 855.5,-108 849.5,-108 843.5,-102 843.5,-96 843.5,-96 843.5,-84 843.5,-84 843.5,-78 849.5,-72 855.5,-72 855.5,-72 986.5,-72 986.5,-72 992.5,-72 998.5,-78 998.5,-84 998.5,-84 998.5,-96 998.5,-96 998.5,-102 992.5,-108 986.5,-108"/>
+<text text-anchor="middle" x="921" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="921" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
<!-- 9->0 -->
-<g id="edge9" class="edge">
-<title>9->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1090.6,-73.43C1093.6,-72.94 1096.57,-72.46 1099.5,-72 1225.04,-52.16 1374.5,-32.53 1442.92,-23.76"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1443.72,-27.19 1453.19,-22.45 1442.83,-20.24 1443.72,-27.19"/>
+<g id="edge9" class="edge"><title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M998.781,-73.7625C1001.89,-73.165 1004.98,-72.5756 1008,-72 1097.25,-55.0116 1202.3,-35.7258 1256.87,-25.7615"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.56,-29.1926 1266.77,-23.9542 1256.31,-22.3063 1257.56,-29.1926"/>
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<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1270.5,-108C1270.5,-108 1120.5,-108 1120.5,-108 1114.5,-108 1108.5,-102 1108.5,-96 1108.5,-96 1108.5,-84 1108.5,-84 1108.5,-78 1114.5,-72 1120.5,-72 1120.5,-72 1270.5,-72 1270.5,-72 1276.5,-72 1282.5,-78 1282.5,-84 1282.5,-84 1282.5,-96 1282.5,-96 1282.5,-102 1276.5,-108 1270.5,-108"/>
-<text text-anchor="middle" x="1195.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1195.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1358.5,-324C1358.5,-324 1327.5,-324 1327.5,-324 1321.5,-324 1315.5,-318 1315.5,-312 1315.5,-312 1315.5,-300 1315.5,-300 1315.5,-294 1321.5,-288 1327.5,-288 1327.5,-288 1358.5,-288 1358.5,-288 1364.5,-288 1370.5,-294 1370.5,-300 1370.5,-300 1370.5,-312 1370.5,-312 1370.5,-318 1364.5,-324 1358.5,-324"/>
+<text text-anchor="middle" x="1343" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 10->0 -->
-<g id="edge10" class="edge">
-<title>10->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1264.85,-71.97C1321.11,-58.15 1398.22,-39.21 1443.37,-28.12"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1444.43,-31.46 1453.31,-25.68 1442.76,-24.66 1444.43,-31.46"/>
+<g id="edge10" class="edge"><title>10->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1346.95,-287.853C1355.25,-248.209 1371.41,-147.802 1342,-72 1337.87,-61.3668 1330.53,-51.5395 1322.8,-43.3091"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1325.24,-40.7972 1315.68,-36.2223 1320.3,-45.758 1325.24,-40.7972"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node"><title>25</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M1489,-252C1489,-252 1383,-252 1383,-252 1377,-252 1371,-246 1371,-240 1371,-240 1371,-228 1371,-228 1371,-222 1377,-216 1383,-216 1383,-216 1489,-216 1489,-216 1495,-216 1501,-222 1501,-228 1501,-228 1501,-240 1501,-240 1501,-246 1495,-252 1489,-252"/>
+<text text-anchor="middle" x="1436" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+</g>
+<!-- 10->25 -->
+<g id="edge53" class="edge"><title>10->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1365.99,-287.697C1377.81,-278.796 1392.39,-267.823 1405.18,-258.199"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1407.39,-260.915 1413.28,-252.104 1403.18,-255.322 1407.39,-260.915"/>
</g>
<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1574.5,-324C1574.5,-324 1538.5,-324 1538.5,-324 1532.5,-324 1526.5,-318 1526.5,-312 1526.5,-312 1526.5,-300 1526.5,-300 1526.5,-294 1532.5,-288 1538.5,-288 1538.5,-288 1574.5,-288 1574.5,-288 1580.5,-288 1586.5,-294 1586.5,-300 1586.5,-300 1586.5,-312 1586.5,-312 1586.5,-318 1580.5,-324 1574.5,-324"/>
-<text text-anchor="middle" x="1556.5" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1863.5,-324C1863.5,-324 1832.5,-324 1832.5,-324 1826.5,-324 1820.5,-318 1820.5,-312 1820.5,-312 1820.5,-300 1820.5,-300 1820.5,-294 1826.5,-288 1832.5,-288 1832.5,-288 1863.5,-288 1863.5,-288 1869.5,-288 1875.5,-294 1875.5,-300 1875.5,-300 1875.5,-312 1875.5,-312 1875.5,-318 1869.5,-324 1863.5,-324"/>
+<text text-anchor="middle" x="1848" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 11->0 -->
-<g id="edge11" class="edge">
-<title>11->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1552.37,-287.98C1542.96,-249.41 1518.99,-152.46 1496.5,-72 1494.11,-63.44 1491.36,-54.16 1488.82,-45.79"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1492.14,-44.67 1485.87,-36.13 1485.45,-46.72 1492.14,-44.67"/>
+<g id="edge11" class="edge"><title>11->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1870.6,-287.963C1881.06,-278.635 1892.4,-266.107 1898,-252 1903.91,-237.13 1906.17,-229.758 1898,-216 1829.77,-101.072 1760.57,-114.929 1634,-72 1528.11,-36.0846 1395.31,-24.3556 1331.55,-20.6448"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.38,-17.13 1321.2,-20.0782 1330.99,-24.1196 1331.38,-17.13"/>
</g>
-<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M1794.5,-252C1794.5,-252 1672.5,-252 1672.5,-252 1666.5,-252 1660.5,-246 1660.5,-240 1660.5,-240 1660.5,-228 1660.5,-228 1660.5,-222 1666.5,-216 1672.5,-216 1672.5,-216 1794.5,-216 1794.5,-216 1800.5,-216 1806.5,-222 1806.5,-228 1806.5,-228 1806.5,-240 1806.5,-240 1806.5,-246 1800.5,-252 1794.5,-252"/>
-<text text-anchor="middle" x="1733.5" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<!-- 27 -->
+<g id="node28" class="node"><title>27</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M1877,-252C1877,-252 1771,-252 1771,-252 1765,-252 1759,-246 1759,-240 1759,-240 1759,-228 1759,-228 1759,-222 1765,-216 1771,-216 1771,-216 1877,-216 1877,-216 1883,-216 1889,-222 1889,-228 1889,-228 1889,-240 1889,-240 1889,-246 1883,-252 1877,-252"/>
+<text text-anchor="middle" x="1824" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
-<!-- 11->26 -->
-<g id="edge57" class="edge">
-<title>11->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1586.53,-293.13C1612.36,-282.91 1650.22,-267.94 1681.05,-255.74"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1682.35,-258.99 1690.37,-252.06 1679.78,-252.48 1682.35,-258.99"/>
+<!-- 11->27 -->
+<g id="edge55" class="edge"><title>11->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1842.07,-287.697C1839.39,-279.898 1836.17,-270.509 1833.2,-261.829"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1836.42,-260.429 1829.86,-252.104 1829.8,-262.699 1836.42,-260.429"/>
</g>
<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1969.5,-324C1969.5,-324 1933.5,-324 1933.5,-324 1927.5,-324 1921.5,-318 1921.5,-312 1921.5,-312 1921.5,-300 1921.5,-300 1921.5,-294 1927.5,-288 1933.5,-288 1933.5,-288 1969.5,-288 1969.5,-288 1975.5,-288 1981.5,-294 1981.5,-300 1981.5,-300 1981.5,-312 1981.5,-312 1981.5,-318 1975.5,-324 1969.5,-324"/>
-<text text-anchor="middle" x="1951.5" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M1549,-180C1549,-180 1519,-180 1519,-180 1513,-180 1507,-174 1507,-168 1507,-168 1507,-156 1507,-156 1507,-150 1513,-144 1519,-144 1519,-144 1549,-144 1549,-144 1555,-144 1561,-150 1561,-156 1561,-156 1561,-168 1561,-168 1561,-174 1555,-180 1549,-180"/>
+<text text-anchor="middle" x="1534" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 12->0 -->
-<g id="edge12" class="edge">
-<title>12->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1921.02,-302.73C1853.83,-297.23 1695.43,-281.45 1651.5,-252 1612.17,-225.64 1567.75,-108.42 1537.5,-72 1529.07,-61.85 1518.77,-51.73 1509.27,-43.1"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1511.33,-40.24 1501.52,-36.22 1506.68,-45.48 1511.33,-40.24"/>
+<g id="edge12" class="edge"><title>12->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1515.56,-143.869C1494.09,-124.564 1456.96,-93.1274 1421,-72 1392.05,-54.9889 1356.61,-40.6817 1330.53,-31.2367"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.62,-27.91 1321.03,-27.8593 1329.28,-34.5059 1331.62,-27.91"/>
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-<!-- 28 -->
-<g id="node29" class="node">
-<title>28</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M2092.5,-252C2092.5,-252 1970.5,-252 1970.5,-252 1964.5,-252 1958.5,-246 1958.5,-240 1958.5,-240 1958.5,-228 1958.5,-228 1958.5,-222 1964.5,-216 1970.5,-216 1970.5,-216 2092.5,-216 2092.5,-216 2098.5,-216 2104.5,-222 2104.5,-228 2104.5,-228 2104.5,-240 2104.5,-240 2104.5,-246 2098.5,-252 2092.5,-252"/>
-<text text-anchor="middle" x="2031.5" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<!-- 14 -->
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M1580.5,-108C1580.5,-108 1499.5,-108 1499.5,-108 1493.5,-108 1487.5,-102 1487.5,-96 1487.5,-96 1487.5,-84 1487.5,-84 1487.5,-78 1493.5,-72 1499.5,-72 1499.5,-72 1580.5,-72 1580.5,-72 1586.5,-72 1592.5,-78 1592.5,-84 1592.5,-84 1592.5,-96 1592.5,-96 1592.5,-102 1586.5,-108 1580.5,-108"/>
+<text text-anchor="middle" x="1540" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
-<!-- 12->28 -->
-<g id="edge59" class="edge">
-<title>12->28</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1971.28,-287.7C1981.25,-278.97 1993.51,-268.24 2004.36,-258.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="2006.73,-261.32 2011.95,-252.1 2002.12,-256.06 2006.73,-261.32"/>
+<!-- 12->14 -->
+<g id="edge36" class="edge"><title>12->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1535.48,-143.697C1536.14,-135.983 1536.94,-126.712 1537.68,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1541.17,-118.367 1538.53,-108.104 1534.19,-117.769 1541.17,-118.367"/>
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<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1760.5,-180C1760.5,-180 1730.5,-180 1730.5,-180 1724.5,-180 1718.5,-174 1718.5,-168 1718.5,-168 1718.5,-156 1718.5,-156 1718.5,-150 1724.5,-144 1730.5,-144 1730.5,-144 1760.5,-144 1760.5,-144 1766.5,-144 1772.5,-150 1772.5,-156 1772.5,-156 1772.5,-168 1772.5,-168 1772.5,-174 1766.5,-180 1760.5,-180"/>
-<text text-anchor="middle" x="1745.5" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M1684,-180C1684,-180 1654,-180 1654,-180 1648,-180 1642,-174 1642,-168 1642,-168 1642,-156 1642,-156 1642,-150 1648,-144 1654,-144 1654,-144 1684,-144 1684,-144 1690,-144 1696,-150 1696,-156 1696,-156 1696,-168 1696,-168 1696,-174 1690,-180 1684,-180"/>
+<text text-anchor="middle" x="1669" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 13->0 -->
-<g id="edge13" class="edge">
-<title>13->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1727.32,-143.9C1701.31,-119.54 1655.57,-77.2 1646.5,-72 1605.47,-48.47 1552.65,-33.92 1517.74,-26.15"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1518.02,-22.63 1507.51,-23.95 1516.55,-29.47 1518.02,-22.63"/>
+<g id="edge13" class="edge"><title>13->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1661.08,-143.778C1650.64,-123.151 1630.23,-89.2286 1602,-72 1557.07,-44.5771 1403.3,-28.2763 1331.5,-21.9921"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.38,-18.4689 1321.11,-21.1033 1330.78,-25.4434 1331.38,-18.4689"/>
+</g>
+<!-- 13->14 -->
+<g id="edge37" class="edge"><title>13->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1641.96,-146.326C1624.15,-136.661 1600.5,-123.831 1580.47,-112.96"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1582.01,-109.815 1571.55,-108.122 1578.67,-115.968 1582.01,-109.815"/>
+</g>
+<!-- 14->0 -->
+<g id="edge14" class="edge"><title>14->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1487.23,-73.9832C1440.14,-60.5856 1372.41,-41.3131 1330.91,-29.5036"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.78,-26.1127 1321.21,-26.7421 1329.87,-32.8454 1331.78,-26.1127"/>
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<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#56d8d0" stroke-width="2" d="M1802.5,-108C1802.5,-108 1710.5,-108 1710.5,-108 1704.5,-108 1698.5,-102 1698.5,-96 1698.5,-96 1698.5,-84 1698.5,-84 1698.5,-78 1704.5,-72 1710.5,-72 1710.5,-72 1802.5,-72 1802.5,-72 1808.5,-72 1814.5,-78 1814.5,-84 1814.5,-84 1814.5,-96 1814.5,-96 1814.5,-102 1808.5,-108 1802.5,-108"/>
-<text text-anchor="middle" x="1756.5" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M916,-542.5C916,-542.5 804,-542.5 804,-542.5 798,-542.5 792,-536.5 792,-530.5 792,-530.5 792,-518.5 792,-518.5 792,-512.5 798,-506.5 804,-506.5 804,-506.5 916,-506.5 916,-506.5 922,-506.5 928,-512.5 928,-518.5 928,-518.5 928,-530.5 928,-530.5 928,-536.5 922,-542.5 916,-542.5"/>
+<text text-anchor="middle" x="860" y="-522" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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-<!-- 13->15 -->
-<g id="edge42" class="edge">
-<title>13->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1748.22,-143.7C1749.43,-135.98 1750.89,-126.71 1752.24,-118.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1755.72,-118.53 1753.81,-108.1 1748.8,-117.44 1755.72,-118.53"/>
+<!-- 15->3 -->
+<g id="edge15" class="edge"><title>15->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M845.155,-506.122C824.607,-480.23 790,-429.176 790,-379 790,-379 790,-379 790,-305 790,-264.098 777.572,-218.063 768.454,-189.793"/>
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-<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1887.5,-180C1887.5,-180 1857.5,-180 1857.5,-180 1851.5,-180 1845.5,-174 1845.5,-168 1845.5,-168 1845.5,-156 1845.5,-156 1845.5,-150 1851.5,-144 1857.5,-144 1857.5,-144 1887.5,-144 1887.5,-144 1893.5,-144 1899.5,-150 1899.5,-156 1899.5,-156 1899.5,-168 1899.5,-168 1899.5,-174 1893.5,-180 1887.5,-180"/>
-<text text-anchor="middle" x="1872.5" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<!-- 19 -->
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M975.5,-180C975.5,-180 872.5,-180 872.5,-180 866.5,-180 860.5,-174 860.5,-168 860.5,-168 860.5,-156 860.5,-156 860.5,-150 866.5,-144 872.5,-144 872.5,-144 975.5,-144 975.5,-144 981.5,-144 987.5,-150 987.5,-156 987.5,-156 987.5,-168 987.5,-168 987.5,-174 981.5,-180 975.5,-180"/>
+<text text-anchor="middle" x="924" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
-<!-- 14->0 -->
-<g id="edge14" class="edge">
-<title>14->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1868.06,-143.8C1861.78,-123.19 1848.21,-89.29 1823.5,-72 1774.63,-37.82 1596.27,-24.81 1517.89,-20.67"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1517.68,-17.15 1507.51,-20.14 1517.32,-24.14 1517.68,-17.15"/>
-</g>
-<!-- 14->15 -->
-<g id="edge43" class="edge">
-<title>14->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1845.3,-144.59C1829.93,-135.31 1810.5,-123.59 1793.74,-113.47"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1795.11,-110.21 1784.74,-108.04 1791.49,-116.2 1795.11,-110.21"/>
-</g>
-<!-- 15->0 -->
-<g id="edge15" class="edge">
-<title>15->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1698.3,-74.24C1643.75,-60.41 1563.86,-40.14 1517.52,-28.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1518.16,-24.94 1507.61,-25.87 1516.44,-31.73 1518.16,-24.94"/>
+<!-- 15->19 -->
+<g id="edge43" class="edge"><title>15->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M860,-506.151C860,-479.022 860,-424.909 860,-379 860,-379 860,-379 860,-305 860,-264.458 862.112,-252.382 880,-216 884.958,-205.915 892.205,-196.093 899.392,-187.699"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="902.113,-189.907 906.188,-180.127 896.904,-185.232 902.113,-189.907"/>
+</g>
+<!-- 21 -->
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M1387.5,-468C1387.5,-468 1298.5,-468 1298.5,-468 1292.5,-468 1286.5,-462 1286.5,-456 1286.5,-456 1286.5,-444 1286.5,-444 1286.5,-438 1292.5,-432 1298.5,-432 1298.5,-432 1387.5,-432 1387.5,-432 1393.5,-432 1399.5,-438 1399.5,-444 1399.5,-444 1399.5,-456 1399.5,-456 1399.5,-462 1393.5,-468 1387.5,-468"/>
+<text text-anchor="middle" x="1343" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+</g>
+<!-- 15->21 -->
+<g id="edge48" class="edge"><title>15->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M928.178,-513.266C1020.66,-499.384 1184.83,-474.742 1276.46,-460.988"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1277.08,-464.433 1286.45,-459.488 1276.05,-457.511 1277.08,-464.433"/>
</g>
<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M975.5,-542.5C975.5,-542.5 847.5,-542.5 847.5,-542.5 841.5,-542.5 835.5,-536.5 835.5,-530.5 835.5,-530.5 835.5,-518.5 835.5,-518.5 835.5,-512.5 841.5,-506.5 847.5,-506.5 847.5,-506.5 975.5,-506.5 975.5,-506.5 981.5,-506.5 987.5,-512.5 987.5,-518.5 987.5,-518.5 987.5,-530.5 987.5,-530.5 987.5,-536.5 981.5,-542.5 975.5,-542.5"/>
-<text text-anchor="middle" x="911.5" y="-522" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1112,-252C1112,-252 1028,-252 1028,-252 1022,-252 1016,-246 1016,-240 1016,-240 1016,-228 1016,-228 1016,-222 1022,-216 1028,-216 1028,-216 1112,-216 1112,-216 1118,-216 1124,-222 1124,-228 1124,-228 1124,-240 1124,-240 1124,-246 1118,-252 1112,-252"/>
+<text text-anchor="middle" x="1070" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 16->3 -->
-<g id="edge16" class="edge">
-<title>16->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M902.6,-506.22C889.74,-479.63 867.5,-426.73 867.5,-379 867.5,-379 867.5,-379 867.5,-305 867.5,-264.5 856.77,-218.63 848.84,-190.26"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="852.1,-188.93 845.96,-180.29 845.37,-190.87 852.1,-188.93"/>
+<g id="edge16" class="edge"><title>16->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1015.75,-218.165C1012.79,-217.418 1009.86,-216.692 1007,-216 956.065,-203.694 898.887,-191.375 852.28,-181.715"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="852.7,-178.228 842.199,-179.632 851.284,-185.083 852.7,-178.228"/>
</g>
-<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#56b9d8" stroke-width="2" d="M1481,-468C1481,-468 1380,-468 1380,-468 1374,-468 1368,-462 1368,-456 1368,-456 1368,-444 1368,-444 1368,-438 1374,-432 1380,-432 1380,-432 1481,-432 1481,-432 1487,-432 1493,-438 1493,-444 1493,-444 1493,-456 1493,-456 1493,-462 1487,-468 1481,-468"/>
-<text text-anchor="middle" x="1430.5" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 16->4 -->
+<g id="edge18" class="edge"><title>16->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1104.25,-215.876C1123.06,-206.469 1146.58,-194.708 1166.67,-184.667"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1168.24,-187.792 1175.62,-180.19 1165.11,-181.531 1168.24,-187.792"/>
</g>
-<!-- 16->19 -->
-<g id="edge48" class="edge">
-<title>16->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M987.52,-512.88C1086.91,-499 1259.83,-474.84 1357.63,-461.18"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1358.31,-464.62 1367.73,-459.77 1357.34,-457.69 1358.31,-464.62"/>
+<!-- 17 -->
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1238,-542.5C1238,-542.5 1142,-542.5 1142,-542.5 1136,-542.5 1130,-536.5 1130,-530.5 1130,-530.5 1130,-518.5 1130,-518.5 1130,-512.5 1136,-506.5 1142,-506.5 1142,-506.5 1238,-506.5 1238,-506.5 1244,-506.5 1250,-512.5 1250,-518.5 1250,-518.5 1250,-530.5 1250,-530.5 1250,-536.5 1244,-542.5 1238,-542.5"/>
+<text text-anchor="middle" x="1190" y="-522" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
-<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M1082.5,-180C1082.5,-180 964.5,-180 964.5,-180 958.5,-180 952.5,-174 952.5,-168 952.5,-168 952.5,-156 952.5,-156 952.5,-150 958.5,-144 964.5,-144 964.5,-144 1082.5,-144 1082.5,-144 1088.5,-144 1094.5,-150 1094.5,-156 1094.5,-156 1094.5,-168 1094.5,-168 1094.5,-174 1088.5,-180 1082.5,-180"/>
-<text text-anchor="middle" x="1023.5" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<!-- 17->4 -->
+<g id="edge17" class="edge"><title>17->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1190,-506.151C1190,-479.022 1190,-424.909 1190,-379 1190,-379 1190,-379 1190,-305 1190,-264.822 1197.95,-218.869 1203.82,-190.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1207.3,-190.887 1205.95,-180.378 1200.45,-189.431 1207.3,-190.887"/>
</g>
-<!-- 16->24 -->
-<g id="edge53" class="edge">
-<title>16->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M911.5,-506.15C911.5,-479.02 911.5,-424.91 911.5,-379 911.5,-379 911.5,-379 911.5,-305 911.5,-264.55 906.62,-248.64 930.5,-216 939.95,-203.08 953.57,-192.86 967.48,-184.97"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="969.43,-187.9 976.63,-180.13 966.15,-181.72 969.43,-187.9"/>
+<!-- 20 -->
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M1104.5,-180C1104.5,-180 1017.5,-180 1017.5,-180 1011.5,-180 1005.5,-174 1005.5,-168 1005.5,-168 1005.5,-156 1005.5,-156 1005.5,-150 1011.5,-144 1017.5,-144 1017.5,-144 1104.5,-144 1104.5,-144 1110.5,-144 1116.5,-150 1116.5,-156 1116.5,-156 1116.5,-168 1116.5,-168 1116.5,-174 1110.5,-180 1104.5,-180"/>
+<text text-anchor="middle" x="1061" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1049,-252C1049,-252 952,-252 952,-252 946,-252 940,-246 940,-240 940,-240 940,-228 940,-228 940,-222 946,-216 952,-216 952,-216 1049,-216 1049,-216 1055,-216 1061,-222 1061,-228 1061,-228 1061,-240 1061,-240 1061,-246 1055,-252 1049,-252"/>
-<text text-anchor="middle" x="1000.5" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<!-- 17->20 -->
+<g id="edge45" class="edge"><title>17->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1182.31,-506.093C1171.21,-479.328 1152,-426.21 1152,-379 1152,-379 1152,-379 1152,-305 1152,-264.553 1154.94,-249.98 1133,-216 1125.28,-204.038 1113.84,-193.843 1102.35,-185.685"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1104.28,-182.765 1094.02,-180.109 1100.39,-188.581 1104.28,-182.765"/>
</g>
-<!-- 17->3 -->
-<g id="edge17" class="edge">
-<title>17->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M961.36,-215.88C939.49,-206.31 912.04,-194.3 888.84,-184.15"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="890.08,-180.87 879.51,-180.07 887.27,-187.28 890.08,-180.87"/>
+<!-- 23 -->
+<g id="node24" class="node"><title>23</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1753.5,-468C1753.5,-468 1680.5,-468 1680.5,-468 1674.5,-468 1668.5,-462 1668.5,-456 1668.5,-456 1668.5,-444 1668.5,-444 1668.5,-438 1674.5,-432 1680.5,-432 1680.5,-432 1753.5,-432 1753.5,-432 1759.5,-432 1765.5,-438 1765.5,-444 1765.5,-444 1765.5,-456 1765.5,-456 1765.5,-462 1759.5,-468 1753.5,-468"/>
+<text text-anchor="middle" x="1717" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
-<!-- 17->4 -->
-<g id="edge19" class="edge">
-<title>17->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1061.04,-217.91C1063.9,-217.25 1066.73,-216.61 1069.5,-216 1128.09,-203.08 1194.15,-190.17 1246.49,-180.33"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1247.25,-183.75 1256.44,-178.46 1245.96,-176.87 1247.25,-183.75"/>
+<!-- 17->23 -->
+<g id="edge51" class="edge"><title>17->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1250.2,-515.219C1352.16,-501.192 1557.56,-472.934 1658.42,-459.059"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1659,-462.512 1668.43,-457.682 1658.05,-455.577 1659,-462.512"/>
</g>
<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#d87d56" stroke-width="2" d="M1321.5,-542.5C1321.5,-542.5 1211.5,-542.5 1211.5,-542.5 1205.5,-542.5 1199.5,-536.5 1199.5,-530.5 1199.5,-530.5 1199.5,-518.5 1199.5,-518.5 1199.5,-512.5 1205.5,-506.5 1211.5,-506.5 1211.5,-506.5 1321.5,-506.5 1321.5,-506.5 1327.5,-506.5 1333.5,-512.5 1333.5,-518.5 1333.5,-518.5 1333.5,-530.5 1333.5,-530.5 1333.5,-536.5 1327.5,-542.5 1321.5,-542.5"/>
-<text text-anchor="middle" x="1266.5" y="-522" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
-</g>
-<!-- 18->4 -->
-<g id="edge18" class="edge">
-<title>18->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1266.5,-506.15C1266.5,-479.02 1266.5,-424.91 1266.5,-379 1266.5,-379 1266.5,-379 1266.5,-305 1266.5,-259.77 1296.62,-214.85 1318.68,-188"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1321.44,-190.16 1325.23,-180.27 1316.09,-185.64 1321.44,-190.16"/>
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1607,-252C1607,-252 1531,-252 1531,-252 1525,-252 1519,-246 1519,-240 1519,-240 1519,-228 1519,-228 1519,-222 1525,-216 1531,-216 1531,-216 1607,-216 1607,-216 1613,-216 1619,-222 1619,-228 1619,-228 1619,-240 1619,-240 1619,-246 1613,-252 1607,-252"/>
+<text text-anchor="middle" x="1569" y="-231.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
+</g>
+<!-- 18->5 -->
+<g id="edge19" class="edge"><title>18->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1535,-215.876C1516.4,-206.512 1493.17,-194.814 1473.29,-184.803"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1474.64,-181.562 1464.13,-180.19 1471.49,-187.814 1474.64,-181.562"/>
+</g>
+<!-- 19->6 -->
+<g id="edge20" class="edge"><title>19->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M963.385,-143.876C985.395,-134.307 1013.01,-122.3 1036.36,-112.148"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1037.97,-115.265 1045.74,-108.068 1035.18,-108.846 1037.97,-115.265"/>
+</g>
+<!-- 19->7 -->
+<g id="edge22" class="edge"><title>19->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M987.686,-146.1C990.834,-145.385 993.952,-144.682 997,-144 1051.64,-131.776 1113.21,-118.563 1161.21,-108.387"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1162.19,-111.759 1171.24,-106.264 1160.74,-104.911 1162.19,-111.759"/>
+</g>
+<!-- 19->8 -->
+<g id="edge24" class="edge"><title>19->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M880.946,-143.876C856.671,-134.222 826.16,-122.087 800.492,-111.878"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="801.5,-108.512 790.915,-108.068 798.913,-115.016 801.5,-108.512"/>
+</g>
+<!-- 19->9 -->
+<g id="edge26" class="edge"><title>19->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M923.258,-143.697C922.928,-135.983 922.531,-126.712 922.162,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="925.658,-117.945 921.733,-108.104 918.665,-118.245 925.658,-117.945"/>
+</g>
+<!-- 20->6 -->
+<g id="edge21" class="edge"><title>20->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1066.93,-143.697C1069.61,-135.898 1072.83,-126.509 1075.8,-117.829"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1079.2,-118.699 1079.14,-108.104 1072.58,-116.429 1079.2,-118.699"/>
+</g>
+<!-- 20->7 -->
+<g id="edge23" class="edge"><title>20->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1105.77,-143.876C1131.12,-134.179 1163.01,-121.98 1189.77,-111.743"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1191.29,-114.91 1199.38,-108.068 1188.79,-108.372 1191.29,-114.91"/>
+</g>
+<!-- 20->8 -->
+<g id="edge25" class="edge"><title>20->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1005.19,-146.001C1002.43,-145.312 999.684,-144.642 997,-144 943.625,-131.239 883.449,-118.389 835.625,-108.537"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="836.114,-105.065 825.615,-106.482 834.706,-111.922 836.114,-105.065"/>
+</g>
+<!-- 20->9 -->
+<g id="edge27" class="edge"><title>20->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1026.75,-143.876C1007.94,-134.469 984.415,-122.708 964.334,-112.667"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="965.889,-109.531 955.38,-108.19 962.759,-115.792 965.889,-109.531"/>
+</g>
+<!-- 21->10 -->
+<g id="edge28" class="edge"><title>21->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1289.78,-431.963C1273.11,-423.835 1256.58,-412.231 1247,-396 1238.87,-382.221 1238.87,-373.779 1247,-360 1259.61,-338.628 1284.27,-325.279 1305.44,-317.324"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1306.88,-320.53 1315.17,-313.94 1304.58,-313.918 1306.88,-320.53"/>
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<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#56d863" stroke-width="2" d="M1877,-468C1877,-468 1794,-468 1794,-468 1788,-468 1782,-462 1782,-456 1782,-456 1782,-444 1782,-444 1782,-438 1788,-432 1794,-432 1794,-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="1835.5" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M1418,-396C1418,-396 1268,-396 1268,-396 1262,-396 1256,-390 1256,-384 1256,-384 1256,-372 1256,-372 1256,-366 1262,-360 1268,-360 1268,-360 1418,-360 1418,-360 1424,-360 1430,-366 1430,-372 1430,-372 1430,-384 1430,-384 1430,-390 1424,-396 1418,-396"/>
+<text text-anchor="middle" x="1343" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1343" y="-370" font-family="sans" font-size="10.00">seqmode: paired_end</text>
</g>
-<!-- 18->22 -->
-<g id="edge51" class="edge">
-<title>18->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1333.73,-514.93C1444.4,-500.83 1663.5,-472.92 1771.81,-459.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1772.46,-462.56 1781.94,-457.82 1771.58,-455.62 1772.46,-462.56"/>
+<!-- 21->22 -->
+<g id="edge49" class="edge"><title>21->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1343,-431.697C1343,-423.983 1343,-414.712 1343,-406.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-406.104 1343,-396.104 1339.5,-406.104 1346.5,-406.104"/>
</g>
-<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M1226,-180C1226,-180 1125,-180 1125,-180 1119,-180 1113,-174 1113,-168 1113,-168 1113,-156 1113,-156 1113,-150 1119,-144 1125,-144 1125,-144 1226,-144 1226,-144 1232,-144 1238,-150 1238,-156 1238,-156 1238,-168 1238,-168 1238,-174 1232,-180 1226,-180"/>
-<text text-anchor="middle" x="1175.5" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
-</g>
-<!-- 18->25 -->
-<g id="edge55" class="edge">
-<title>18->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1258.81,-506.09C1247.71,-479.33 1228.5,-426.21 1228.5,-379 1228.5,-379 1228.5,-379 1228.5,-305 1228.5,-264.46 1223.88,-253.51 1208.5,-216 1204.7,-206.72 1199.33,-197.22 1194.03,-188.88"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1196.82,-186.75 1188.38,-180.34 1190.98,-190.62 1196.82,-186.75"/>
-</g>
-<!-- 19->5 -->
-<g id="edge20" class="edge">
-<title>19->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1368.25,-431.95C1350.75,-423.98 1333.72,-412.47 1323.5,-396 1315.06,-382.41 1314.85,-373.46 1323.5,-360 1334.35,-343.11 1352.07,-331.53 1370.43,-323.63"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1371.76,-326.87 1379.76,-319.93 1369.18,-320.36 1371.76,-326.87"/>
-</g>
-<!-- 19->11 -->
-<g id="edge34" class="edge">
-<title>19->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1487.66,-431.93C1506.05,-423.8 1524.91,-412.21 1537.5,-396 1551.1,-378.5 1555.5,-353.46 1556.7,-334.4"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1560.2,-334.36 1557.08,-324.24 1553.21,-334.1 1560.2,-334.36"/>
+<!-- 31 -->
+<g id="node32" class="node"><title>31</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M1520,-324C1520,-324 1432,-324 1432,-324 1426,-324 1420,-318 1420,-312 1420,-312 1420,-300 1420,-300 1420,-294 1426,-288 1432,-288 1432,-288 1520,-288 1520,-288 1526,-288 1532,-294 1532,-300 1532,-300 1532,-312 1532,-312 1532,-318 1526,-324 1520,-324"/>
+<text text-anchor="middle" x="1476" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+</g>
+<!-- 21->31 -->
+<g id="edge56" class="edge"><title>21->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1387.92,-431.937C1405.7,-423.364 1425.16,-411.461 1439,-396 1454.73,-378.433 1464.35,-353.241 1469.82,-334.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1473.27,-334.805 1472.45,-324.242 1466.5,-333.01 1473.27,-334.805"/>
+</g>
+<!-- 22->10 -->
+<g id="edge29" class="edge"><title>22->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1343,-359.697C1343,-351.983 1343,-342.712 1343,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-334.104 1343,-324.104 1339.5,-334.104 1346.5,-334.104"/>
+</g>
+<!-- 22->31 -->
+<g id="edge57" class="edge"><title>22->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1375.54,-359.876C1393.25,-350.554 1415.35,-338.919 1434.32,-328.939"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1436.12,-331.944 1443.34,-324.19 1432.86,-325.75 1436.12,-331.944"/>
+</g>
+<!-- 23->11 -->
+<g id="edge30" class="edge"><title>23->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1765.69,-446.525C1801.26,-441.86 1847.27,-429.261 1871,-396 1884.22,-377.466 1875.57,-351.952 1865.31,-332.991"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1868.29,-331.152 1860.23,-324.269 1862.24,-334.673 1868.29,-331.152"/>
</g>
-<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1516.5,-396C1516.5,-396 1344.5,-396 1344.5,-396 1338.5,-396 1332.5,-390 1332.5,-384 1332.5,-384 1332.5,-372 1332.5,-372 1332.5,-366 1338.5,-360 1344.5,-360 1344.5,-360 1516.5,-360 1516.5,-360 1522.5,-360 1528.5,-366 1528.5,-372 1528.5,-372 1528.5,-384 1528.5,-384 1528.5,-390 1522.5,-396 1516.5,-396"/>
-<text text-anchor="middle" x="1430.5" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1430.5" y="-370" font-family="sans" font-size="10.00">seqmode: paired_end</text>
-</g>
-<!-- 19->20 -->
-<g id="edge49" class="edge">
-<title>19->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1430.5,-431.7C1430.5,-423.98 1430.5,-414.71 1430.5,-406.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1434,-406.1 1430.5,-396.1 1427,-406.1 1434,-406.1"/>
-</g>
-<!-- 20->5 -->
-<g id="edge21" class="edge">
-<title>20->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1432.72,-359.7C1433.72,-351.98 1434.91,-342.71 1436.01,-334.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1439.5,-334.47 1437.3,-324.1 1432.55,-333.58 1439.5,-334.47"/>
-</g>
-<!-- 20->11 -->
-<g id="edge35" class="edge">
-<title>20->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1461.32,-359.88C1478.2,-350.5 1499.28,-338.79 1517.32,-328.77"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1519.39,-331.62 1526.43,-323.71 1515.99,-325.5 1519.39,-331.62"/>
+<!-- 24 -->
+<g id="node25" class="node"><title>24</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M1850,-396C1850,-396 1700,-396 1700,-396 1694,-396 1688,-390 1688,-384 1688,-384 1688,-372 1688,-372 1688,-366 1694,-360 1700,-360 1700,-360 1850,-360 1850,-360 1856,-360 1862,-366 1862,-372 1862,-372 1862,-384 1862,-384 1862,-390 1856,-396 1850,-396"/>
+<text text-anchor="middle" x="1775" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1775" y="-370" font-family="sans" font-size="10.00">seqmode: single_end</text>
</g>
-<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M1732.5,-396C1732.5,-396 1596.5,-396 1596.5,-396 1590.5,-396 1584.5,-390 1584.5,-384 1584.5,-384 1584.5,-372 1584.5,-372 1584.5,-366 1590.5,-360 1596.5,-360 1596.5,-360 1732.5,-360 1732.5,-360 1738.5,-360 1744.5,-366 1744.5,-372 1744.5,-372 1744.5,-384 1744.5,-384 1744.5,-390 1738.5,-396 1732.5,-396"/>
-<text text-anchor="middle" x="1664.5" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
-</g>
-<!-- 21->5 -->
-<g id="edge22" class="edge">
-<title>21->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1609.75,-359.97C1577.9,-350.06 1537.58,-337.51 1504.17,-327.12"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1505.09,-323.74 1494.5,-324.11 1503.01,-330.42 1505.09,-323.74"/>
-</g>
-<!-- 21->6 -->
-<g id="edge25" class="edge">
-<title>21->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1677.85,-359.7C1684.26,-351.39 1692.06,-341.28 1699.11,-332.14"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1701.97,-334.16 1705.31,-324.1 1696.43,-329.88 1701.97,-334.16"/>
-</g>
-<!-- 22->6 -->
-<g id="edge23" class="edge">
-<title>22->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1821.21,-431.84C1812.59,-421.47 1801.4,-407.99 1791.5,-396 1773.79,-374.54 1753.76,-350.1 1739.16,-332.27"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1741.51,-329.61 1732.46,-324.09 1736.09,-334.04 1741.51,-329.61"/>
-</g>
-<!-- 22->12 -->
-<g id="edge36" class="edge">
-<title>22->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1889.09,-448.07C1928.28,-444.23 1979.03,-431.98 2005.5,-396 2020.98,-374.96 2001.77,-349.31 1982.1,-330.96"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1984.41,-328.33 1974.61,-324.31 1979.77,-333.57 1984.41,-328.33"/>
+<!-- 23->24 -->
+<g id="edge52" class="edge"><title>23->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1731.34,-431.697C1738.29,-423.305 1746.77,-413.07 1754.4,-403.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1757.14,-406.038 1760.83,-396.104 1751.75,-401.571 1757.14,-406.038"/>
</g>
-<!-- 23 -->
-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M1984.5,-396C1984.5,-396 1812.5,-396 1812.5,-396 1806.5,-396 1800.5,-390 1800.5,-384 1800.5,-384 1800.5,-372 1800.5,-372 1800.5,-366 1806.5,-360 1812.5,-360 1812.5,-360 1984.5,-360 1984.5,-360 1990.5,-360 1996.5,-366 1996.5,-372 1996.5,-372 1996.5,-384 1996.5,-384 1996.5,-390 1990.5,-396 1984.5,-396"/>
-<text text-anchor="middle" x="1898.5" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1898.5" y="-370" font-family="sans" font-size="10.00">seqmode: single_end</text>
-</g>
-<!-- 22->23 -->
-<g id="edge52" class="edge">
-<title>22->23</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1851.07,-431.7C1858.7,-423.22 1868.02,-412.86 1876.38,-403.58"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1879.02,-405.88 1883.11,-396.1 1873.81,-401.2 1879.02,-405.88"/>
-</g>
-<!-- 23->6 -->
-<g id="edge24" class="edge">
-<title>23->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1854.47,-359.88C1829.53,-350.18 1798.16,-337.98 1771.84,-327.74"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1772.98,-324.43 1762.39,-324.07 1770.44,-330.95 1772.98,-324.43"/>
-</g>
-<!-- 23->12 -->
-<g id="edge37" class="edge">
-<title>23->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1911.6,-359.7C1917.89,-351.39 1925.55,-341.28 1932.46,-332.14"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1935.3,-334.19 1938.55,-324.1 1929.72,-329.96 1935.3,-334.19"/>
-</g>
-<!-- 24->7 -->
-<g id="edge26" class="edge">
-<title>24->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1094.58,-145.82C1097.6,-145.2 1100.58,-144.59 1103.5,-144 1183.8,-127.78 1206.36,-124.57 1290.09,-108.27"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1290.91,-111.67 1300.05,-106.32 1289.56,-104.8 1290.91,-111.67"/>
-</g>
-<!-- 24->8 -->
-<g id="edge28" class="edge">
-<title>24->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M973.37,-143.97C944.46,-134.14 907.93,-121.73 877.5,-111.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="878.45,-108.01 867.85,-108.11 876.2,-114.64 878.45,-108.01"/>
-</g>
-<!-- 24->9 -->
-<g id="edge30" class="edge">
-<title>24->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1018.56,-143.7C1016.33,-135.9 1013.65,-126.51 1011.17,-117.83"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1014.5,-116.76 1008.39,-108.1 1007.77,-118.68 1014.5,-116.76"/>
-</g>
-<!-- 24->10 -->
-<g id="edge32" class="edge">
-<title>24->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1065.58,-143.88C1089.3,-134.22 1119.12,-122.09 1144.2,-111.88"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1145.62,-115.08 1153.56,-108.07 1142.98,-108.6 1145.62,-115.08"/>
-</g>
-<!-- 25->7 -->
-<g id="edge27" class="edge">
-<title>25->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1224.41,-143.97C1252.5,-134.19 1287.96,-121.84 1317.57,-111.52"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1319.07,-114.71 1327.37,-108.11 1316.77,-108.09 1319.07,-114.71"/>
-</g>
-<!-- 25->8 -->
-<g id="edge29" class="edge">
-<title>25->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1112.71,-145.98C1109.6,-145.3 1106.52,-144.63 1103.5,-144 1019.87,-126.46 996.21,-124.35 908.32,-108.14"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="908.92,-104.69 898.45,-106.31 907.64,-111.57 908.92,-104.69"/>
-</g>
-<!-- 25->9 -->
-<g id="edge31" class="edge">
-<title>25->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1133.42,-143.88C1109.7,-134.22 1079.88,-122.09 1054.8,-111.88"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1056.02,-108.6 1045.44,-108.07 1053.38,-115.08 1056.02,-108.6"/>
-</g>
-<!-- 25->10 -->
-<g id="edge33" class="edge">
-<title>25->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1180.44,-143.7C1182.67,-135.9 1185.35,-126.51 1187.83,-117.83"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1191.23,-118.68 1190.61,-108.1 1184.5,-116.76 1191.23,-118.68"/>
+<!-- 32 -->
+<g id="node33" class="node"><title>32</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M1668,-324C1668,-324 1580,-324 1580,-324 1574,-324 1568,-318 1568,-312 1568,-312 1568,-300 1568,-300 1568,-294 1574,-288 1580,-288 1580,-288 1668,-288 1668,-288 1674,-288 1680,-294 1680,-300 1680,-300 1680,-312 1680,-312 1680,-318 1674,-324 1668,-324"/>
+<text text-anchor="middle" x="1624" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+</g>
+<!-- 23->32 -->
+<g id="edge59" class="edge"><title>23->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1704.03,-431.545C1696.54,-421.31 1687.04,-408.06 1679,-396 1665.11,-375.148 1650.21,-350.925 1639.44,-333.019"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1642.34,-331.061 1634.2,-324.282 1636.34,-334.659 1642.34,-331.061"/>
+</g>
+<!-- 24->11 -->
+<g id="edge31" class="edge"><title>24->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1793.04,-359.697C1802.06,-351.05 1813.12,-340.449 1822.94,-331.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1825.37,-333.552 1830.16,-324.104 1820.52,-328.499 1825.37,-333.552"/>
+</g>
+<!-- 24->32 -->
+<g id="edge60" class="edge"><title>24->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1738.06,-359.876C1717.51,-350.349 1691.75,-338.407 1669.91,-328.283"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1671.36,-325.099 1660.82,-324.068 1668.42,-331.45 1671.36,-325.099"/>
+</g>
+<!-- 25->12 -->
+<g id="edge32" class="edge"><title>25->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1459.97,-215.876C1472.55,-206.893 1488.13,-195.763 1501.75,-186.034"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.83,-188.85 1509.93,-180.19 1499.76,-183.154 1503.83,-188.85"/>
</g>
-<!-- 26->13 -->
-<g id="edge38" class="edge">
-<title>26->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1736.47,-215.7C1737.79,-207.98 1739.38,-198.71 1740.85,-190.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1744.33,-190.55 1742.57,-180.1 1737.43,-189.37 1744.33,-190.55"/>
+<!-- 26 -->
+<g id="node27" class="node"><title>26</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M1729,-252C1729,-252 1649,-252 1649,-252 1643,-252 1637,-246 1637,-240 1637,-240 1637,-228 1637,-228 1637,-222 1643,-216 1649,-216 1649,-216 1729,-216 1729,-216 1735,-216 1741,-222 1741,-228 1741,-228 1741,-240 1741,-240 1741,-246 1735,-252 1729,-252"/>
+<text text-anchor="middle" x="1689" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
-<!-- 27 -->
-<g id="node28" class="node">
-<title>27</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1928.5,-252C1928.5,-252 1836.5,-252 1836.5,-252 1830.5,-252 1824.5,-246 1824.5,-240 1824.5,-240 1824.5,-228 1824.5,-228 1824.5,-222 1830.5,-216 1836.5,-216 1836.5,-216 1928.5,-216 1928.5,-216 1934.5,-216 1940.5,-222 1940.5,-228 1940.5,-228 1940.5,-240 1940.5,-240 1940.5,-246 1934.5,-252 1928.5,-252"/>
-<text text-anchor="middle" x="1882.5" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+<!-- 26->12 -->
+<g id="edge33" class="edge"><title>26->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1651.08,-215.876C1626.56,-204.799 1594.8,-190.457 1570.55,-179.504"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1571.87,-176.264 1561.32,-175.338 1568.99,-182.643 1571.87,-176.264"/>
+</g>
+<!-- 26->13 -->
+<g id="edge35" class="edge"><title>26->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1684.06,-215.697C1681.83,-207.898 1679.15,-198.509 1676.67,-189.829"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1680,-188.758 1673.89,-180.104 1673.27,-190.681 1680,-188.758"/>
</g>
<!-- 27->13 -->
-<g id="edge39" class="edge">
-<title>27->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1848.99,-215.88C1828.65,-205.49 1802.7,-192.22 1781.87,-181.58"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1783.19,-178.33 1772.69,-176.9 1780.01,-184.56 1783.19,-178.33"/>
-</g>
-<!-- 27->14 -->
-<g id="edge41" class="edge">
-<title>27->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1880.03,-215.7C1878.93,-207.98 1877.6,-198.71 1876.37,-190.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1879.82,-189.51 1874.94,-180.1 1872.89,-190.5 1879.82,-189.51"/>
-</g>
-<!-- 28->14 -->
-<g id="edge40" class="edge">
-<title>28->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1992.6,-215.88C1967.01,-204.61 1933.73,-189.96 1908.7,-178.94"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1910.1,-175.73 1899.54,-174.9 1907.28,-182.14 1910.1,-175.73"/>
+<g id="edge34" class="edge"><title>27->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1786.08,-215.876C1761.56,-204.799 1729.8,-190.457 1705.55,-179.504"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1706.87,-176.264 1696.32,-175.338 1703.99,-182.643 1706.87,-176.264"/>
+</g>
+<!-- 28 -->
+<g id="node29" class="node"><title>28</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M994,-617C994,-617 726,-617 726,-617 720,-617 714,-611 714,-605 714,-605 714,-593 714,-593 714,-587 720,-581 726,-581 726,-581 994,-581 994,-581 1000,-581 1006,-587 1006,-593 1006,-593 1006,-605 1006,-605 1006,-611 1000,-617 994,-617"/>
+<text text-anchor="middle" x="860" y="-602" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="860" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 28->15 -->
+<g id="edge38" class="edge"><title>28->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M860,-580.819C860,-572.422 860,-562.116 860,-552.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="863.5,-552.558 860,-542.558 856.5,-552.558 863.5,-552.558"/>
</g>
<!-- 29 -->
-<g id="node30" class="node">
-<title>29</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M1062,-617C1062,-617 761,-617 761,-617 755,-617 749,-611 749,-605 749,-605 749,-593 749,-593 749,-587 755,-581 761,-581 761,-581 1062,-581 1062,-581 1068,-581 1074,-587 1074,-593 1074,-593 1074,-605 1074,-605 1074,-611 1068,-617 1062,-617"/>
-<text text-anchor="middle" x="911.5" y="-602" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="911.5" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node30" class="node"><title>29</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1056.5,-324C1056.5,-324 955.5,-324 955.5,-324 949.5,-324 943.5,-318 943.5,-312 943.5,-312 943.5,-300 943.5,-300 943.5,-294 949.5,-288 955.5,-288 955.5,-288 1056.5,-288 1056.5,-288 1062.5,-288 1068.5,-294 1068.5,-300 1068.5,-300 1068.5,-312 1068.5,-312 1068.5,-318 1062.5,-324 1056.5,-324"/>
+<text text-anchor="middle" x="1006" y="-309" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<text text-anchor="middle" x="1006" y="-298" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 29->16 -->
-<g id="edge44" class="edge">
-<title>29->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M911.5,-580.82C911.5,-572.42 911.5,-562.12 911.5,-552.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="915,-552.56 911.5,-542.56 908,-552.56 915,-552.56"/>
+<g id="edge39" class="edge"><title>29->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1021.82,-287.697C1029.57,-279.22 1039.04,-268.864 1047.52,-259.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1050.2,-261.846 1054.36,-252.104 1045.03,-257.123 1050.2,-261.846"/>
</g>
-<!-- 30 -->
-<g id="node31" class="node">
-<title>30</title>
-<path fill="none" stroke="#567bd8" stroke-width="2" d="M1128,-324C1128,-324 1013,-324 1013,-324 1007,-324 1001,-318 1001,-312 1001,-312 1001,-300 1001,-300 1001,-294 1007,-288 1013,-288 1013,-288 1128,-288 1128,-288 1134,-288 1140,-294 1140,-300 1140,-300 1140,-312 1140,-312 1140,-318 1134,-324 1128,-324"/>
-<text text-anchor="middle" x="1070.5" y="-309" font-family="sans" font-size="10.00">extract_transcriptome</text>
-<text text-anchor="middle" x="1070.5" y="-298" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<!-- 33 -->
+<g id="node34" class="node"><title>33</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M985.5,-252C985.5,-252 900.5,-252 900.5,-252 894.5,-252 888.5,-246 888.5,-240 888.5,-240 888.5,-228 888.5,-228 888.5,-222 894.5,-216 900.5,-216 900.5,-216 985.5,-216 985.5,-216 991.5,-216 997.5,-222 997.5,-228 997.5,-228 997.5,-240 997.5,-240 997.5,-246 991.5,-252 985.5,-252"/>
+<text text-anchor="middle" x="943" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="943" y="-226" font-family="sans" font-size="10.00">kmer: 31</text>
</g>
-<!-- 30->17 -->
-<g id="edge45" class="edge">
-<title>30->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1053.2,-287.7C1044.64,-279.14 1034.16,-268.66 1024.8,-259.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1027.15,-256.7 1017.6,-252.1 1022.2,-261.65 1027.15,-256.7"/>
+<!-- 29->33 -->
+<g id="edge62" class="edge"><title>29->33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M990.427,-287.697C982.798,-279.22 973.477,-268.864 965.124,-259.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="967.685,-257.196 958.394,-252.104 962.482,-261.879 967.685,-257.196"/>
</g>
-<!-- 33 -->
-<g id="node34" class="node">
-<title>33</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M1188,-252C1188,-252 1091,-252 1091,-252 1085,-252 1079,-246 1079,-240 1079,-240 1079,-228 1079,-228 1079,-222 1085,-216 1091,-216 1091,-216 1188,-216 1188,-216 1194,-216 1200,-222 1200,-228 1200,-228 1200,-240 1200,-240 1200,-246 1194,-252 1188,-252"/>
-<text text-anchor="middle" x="1139.5" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text>
-<text text-anchor="middle" x="1139.5" y="-226" font-family="sans" font-size="10.00">kmer: 31</text>
-</g>
-<!-- 30->33 -->
-<g id="edge60" class="edge">
-<title>30->33</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1087.56,-287.7C1096,-279.14 1106.32,-268.66 1115.54,-259.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.11,-261.68 1122.64,-252.1 1113.13,-256.77 1118.11,-261.68"/>
+<!-- 30 -->
+<g id="node31" class="node"><title>30</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1330,-617C1330,-617 1050,-617 1050,-617 1044,-617 1038,-611 1038,-605 1038,-605 1038,-593 1038,-593 1038,-587 1044,-581 1050,-581 1050,-581 1330,-581 1330,-581 1336,-581 1342,-587 1342,-593 1342,-593 1342,-605 1342,-605 1342,-611 1336,-617 1330,-617"/>
+<text text-anchor="middle" x="1190" y="-602" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1190" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
-<!-- 31 -->
-<g id="node32" class="node">
-<title>31</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M1423,-617C1423,-617 1110,-617 1110,-617 1104,-617 1098,-611 1098,-605 1098,-605 1098,-593 1098,-593 1098,-587 1104,-581 1110,-581 1110,-581 1423,-581 1423,-581 1429,-581 1435,-587 1435,-593 1435,-593 1435,-605 1435,-605 1435,-611 1429,-617 1423,-617"/>
-<text text-anchor="middle" x="1266.5" y="-602" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1266.5" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<!-- 30->17 -->
+<g id="edge40" class="edge"><title>30->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1190,-580.819C1190,-572.422 1190,-562.116 1190,-552.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.5,-552.558 1190,-542.558 1186.5,-552.558 1193.5,-552.558"/>
</g>
<!-- 31->18 -->
-<g id="edge46" class="edge">
-<title>31->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1266.5,-580.82C1266.5,-572.42 1266.5,-562.12 1266.5,-552.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1270,-552.56 1266.5,-542.56 1263,-552.56 1270,-552.56"/>
-</g>
-<!-- 32 -->
-<g id="node33" class="node">
-<title>32</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M1893,-545C1893,-545 1778,-545 1778,-545 1772,-545 1766,-539 1766,-533 1766,-533 1766,-516 1766,-516 1766,-510 1772,-504 1778,-504 1778,-504 1893,-504 1893,-504 1899,-504 1905,-510 1905,-516 1905,-516 1905,-533 1905,-533 1905,-539 1899,-545 1893,-545"/>
-<text text-anchor="middle" x="1835.5" y="-533" font-family="sans" font-size="10.00">create_index_star</text>
-<text text-anchor="middle" x="1835.5" y="-522" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="1835.5" y="-511" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
-</g>
-<!-- 32->19 -->
-<g id="edge47" class="edge">
-<title>32->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1765.88,-511.04C1692.65,-497.93 1577.92,-477.39 1503.47,-464.06"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.69,-460.55 1493.23,-462.23 1502.46,-467.44 1503.69,-460.55"/>
-</g>
-<!-- 32->22 -->
-<g id="edge50" class="edge">
-<title>32->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1835.5,-503.69C1835.5,-495.91 1835.5,-486.84 1835.5,-478.45"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1839,-478.32 1835.5,-468.32 1832,-478.32 1839,-478.32"/>
-</g>
-<!-- 32->27 -->
-<g id="edge58" class="edge">
-<title>32->27</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1888.04,-503.93C1932.59,-484.19 1993.58,-448.99 2021.5,-396 2044.78,-351.82 2024.92,-324.18 1990.5,-288 1977.81,-274.66 1961.04,-264.22 1944.52,-256.27"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1945.95,-253.07 1935.4,-252.1 1943.04,-259.44 1945.95,-253.07"/>
-</g>
-<!-- 33->24 -->
-<g id="edge54" class="edge">
-<title>33->24</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1111.12,-215.88C1095.96,-206.72 1077.09,-195.34 1060.76,-185.48"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1062.36,-182.36 1051.99,-180.19 1058.74,-188.35 1062.36,-182.36"/>
-</g>
-<!-- 33->25 -->
-<g id="edge56" class="edge">
-<title>33->25</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1148.4,-215.7C1152.5,-207.73 1157.45,-198.1 1161.99,-189.26"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1165.24,-190.6 1166.7,-180.1 1159.02,-187.4 1165.24,-190.6"/>
+<g id="edge41" class="edge"><title>31->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1498.99,-287.697C1510.81,-278.796 1525.39,-267.823 1538.18,-258.199"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1540.39,-260.915 1546.28,-252.104 1536.18,-255.322 1540.39,-260.915"/>
+</g>
+<!-- 32->18 -->
+<g id="edge42" class="edge"><title>32->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1610.4,-287.697C1603.88,-279.389 1595.93,-269.277 1588.75,-260.141"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1591.37,-257.805 1582.44,-252.104 1585.87,-262.13 1591.37,-257.805"/>
+</g>
+<!-- 33->19 -->
+<g id="edge44" class="edge"><title>33->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M938.303,-215.697C936.187,-207.898 933.638,-198.509 931.282,-189.829"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="934.64,-188.838 928.643,-180.104 927.884,-190.672 934.64,-188.838"/>
+</g>
+<!-- 33->20 -->
+<g id="edge46" class="edge"><title>33->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M971.866,-215.876C987.295,-206.724 1006.48,-195.342 1023.1,-185.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.21,-188.302 1032.02,-180.19 1021.64,-182.282 1025.21,-188.302"/>
+</g>
+<!-- 34 -->
+<g id="node35" class="node"><title>34</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1767.5,-545C1767.5,-545 1666.5,-545 1666.5,-545 1660.5,-545 1654.5,-539 1654.5,-533 1654.5,-533 1654.5,-516 1654.5,-516 1654.5,-510 1660.5,-504 1666.5,-504 1666.5,-504 1767.5,-504 1767.5,-504 1773.5,-504 1779.5,-510 1779.5,-516 1779.5,-516 1779.5,-533 1779.5,-533 1779.5,-539 1773.5,-545 1767.5,-545"/>
+<text text-anchor="middle" x="1717" y="-533" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1717" y="-522" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1717" y="-511" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 34->21 -->
+<g id="edge47" class="edge"><title>34->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1654.4,-511.365C1586.62,-498.225 1478.92,-477.349 1409.61,-463.913"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1410.16,-460.453 1399.67,-461.986 1408.82,-467.325 1410.16,-460.453"/>
+</g>
+<!-- 34->23 -->
+<g id="edge50" class="edge"><title>34->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1717,-503.689C1717,-495.907 1717,-486.842 1717,-478.447"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1720.5,-478.319 1717,-468.319 1713.5,-478.32 1720.5,-478.319"/>
+</g>
+<!-- 34->26 -->
+<g id="edge54" class="edge"><title>34->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1763.03,-503.97C1804.26,-483.684 1862.09,-447.634 1888,-396 1896.33,-379.398 1897.01,-302.975 1885,-288 1848.05,-241.922 1813.46,-265.709 1751.06,-252.017"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1751.78,-248.589 1741.23,-249.598 1750.11,-255.386 1751.78,-248.589"/>
+</g>
+<!-- 35 -->
+<g id="node36" class="node"><title>35</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M1619.5,-396C1619.5,-396 1498.5,-396 1498.5,-396 1492.5,-396 1486.5,-390 1486.5,-384 1486.5,-384 1486.5,-372 1486.5,-372 1486.5,-366 1492.5,-360 1498.5,-360 1498.5,-360 1619.5,-360 1619.5,-360 1625.5,-360 1631.5,-366 1631.5,-372 1631.5,-372 1631.5,-384 1631.5,-384 1631.5,-390 1625.5,-396 1619.5,-396"/>
+<text text-anchor="middle" x="1559" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 35->31 -->
+<g id="edge58" class="edge"><title>35->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1538.48,-359.697C1528.13,-350.965 1515.41,-340.24 1504.16,-330.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1506.18,-327.876 1496.28,-324.104 1501.67,-333.227 1506.18,-327.876"/>
+</g>
+<!-- 35->32 -->
+<g id="edge61" class="edge"><title>35->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1575.07,-359.697C1582.94,-351.22 1592.56,-340.864 1601.17,-331.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1603.88,-333.814 1608.12,-324.104 1598.75,-329.051 1603.88,-333.814"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 2cd57eb5e4559967bd92fae1fbe82566094a064c..ef56730d2ad5048d97675c173e2a3ed530ee1447 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,439 +1,388 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+<!-- Generated by graphviz version 2.38.0 (20140413.2041)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="987pt" height="620pt"
- viewBox="0.00 0.00 987.00 620.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1074pt" height="620pt"
+ viewBox="0.00 0.00 1074.00 620.00" 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(4 616)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="transparent" points="-4,4 -4,-616 983,-616 983,4 -4,4"/>
+<polygon fill="white" stroke="none" points="-4,4 -4,-616 1070,-616 1070,4 -4,4"/>
<!-- 0 -->
-<g id="node1" class="node">
-<title>0</title>
-<path fill="none" stroke="#d8a456" stroke-width="2" d="M506,-36C506,-36 476,-36 476,-36 470,-36 464,-30 464,-24 464,-24 464,-12 464,-12 464,-6 470,0 476,0 476,0 506,0 506,0 512,0 518,-6 518,-12 518,-12 518,-24 518,-24 518,-30 512,-36 506,-36"/>
-<text text-anchor="middle" x="491" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<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>
<!-- 1 -->
-<g id="node2" class="node">
-<title>1</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M188,-108C188,-108 148,-108 148,-108 142,-108 136,-102 136,-96 136,-96 136,-84 136,-84 136,-78 142,-72 148,-72 148,-72 188,-72 188,-72 194,-72 200,-78 200,-84 200,-84 200,-96 200,-96 200,-102 194,-108 188,-108"/>
-<text text-anchor="middle" x="168" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
+<g id="node2" class="node"><title>1</title>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M56.5,-108C56.5,-108 21.5,-108 21.5,-108 15.5,-108 9.5,-102 9.5,-96 9.5,-96 9.5,-84 9.5,-84 9.5,-78 15.5,-72 21.5,-72 21.5,-72 56.5,-72 56.5,-72 62.5,-72 68.5,-78 68.5,-84 68.5,-84 68.5,-96 68.5,-96 68.5,-102 62.5,-108 56.5,-108"/>
+<text text-anchor="middle" x="39" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
</g>
<!-- 1->0 -->
-<g id="edge4" class="edge">
-<title>1->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M200,-74.99C203.01,-73.9 206.05,-72.88 209,-72 294.71,-46.48 398.9,-30.69 453.49,-23.53"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="454.26,-26.96 463.73,-22.21 453.36,-20.02 454.26,-26.96"/>
+<g id="edge3" class="edge"><title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M68.5755,-75.3841C71.7245,-74.1526 74.9066,-72.9965 78,-72 150.446,-48.6629 238.217,-32.5434 286.903,-24.626"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="287.646,-28.0518 296.968,-23.016 286.54,-21.1396 287.646,-28.0518"/>
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-<title>2</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M260,-108C260,-108 230,-108 230,-108 224,-108 218,-102 218,-96 218,-96 218,-84 218,-84 218,-78 224,-72 230,-72 230,-72 260,-72 260,-72 266,-72 272,-78 272,-84 272,-84 272,-96 272,-96 272,-102 266,-108 260,-108"/>
-<text text-anchor="middle" x="245" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
+<g id="node3" class="node"><title>2</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M129,-108C129,-108 99,-108 99,-108 93,-108 87,-102 87,-96 87,-96 87,-84 87,-84 87,-78 93,-72 99,-72 99,-72 129,-72 129,-72 135,-72 141,-78 141,-84 141,-84 141,-96 141,-96 141,-102 135,-108 129,-108"/>
+<text text-anchor="middle" x="114" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
</g>
<!-- 2->0 -->
-<g id="edge2" class="edge">
-<title>2->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M272.15,-77.12C276.73,-75.3 281.47,-73.52 286,-72 343.68,-52.69 412.45,-36.2 453.87,-26.95"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="454.78,-30.33 463.79,-24.76 453.27,-23.5 454.78,-30.33"/>
+<g id="edge4" class="edge"><title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M141.214,-77.319C145.789,-75.4697 150.51,-73.6314 155,-72 199.981,-55.6584 252.733,-39.5974 287.182,-29.5158"/>
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-<g id="node4" class="node">
-<title>3</title>
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-<text text-anchor="middle" x="390" y="-447.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<g id="node4" class="node"><title>3</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M154,-468C154,-468 12,-468 12,-468 6,-468 0,-462 0,-456 0,-456 0,-444 0,-444 0,-438 6,-432 12,-432 12,-432 154,-432 154,-432 160,-432 166,-438 166,-444 166,-444 166,-456 166,-456 166,-462 160,-468 154,-468"/>
+<text text-anchor="middle" x="83" y="-447.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 3->0 -->
-<g id="edge6" class="edge">
-<title>3->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M450.25,-431.97C470.89,-423.78 492.82,-412.12 509,-396 539.72,-365.39 549,-350.37 549,-307 549,-307 549,-307 549,-161 549,-117.7 525.6,-72.11 508.52,-44.61"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="511.36,-42.55 503.02,-36.01 505.46,-46.32 511.36,-42.55"/>
+<g id="edge8" class="edge"><title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M102.086,-431.773C127.422,-406.914 169,-358.302 169,-307 169,-307 169,-307 169,-161 169,-115.41 186.982,-103.437 220,-72 239.091,-53.8231 265.632,-40.4345 287.123,-31.6611"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="288.56,-34.8574 296.597,-27.9542 286.01,-28.3386 288.56,-34.8574"/>
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<!-- 4 -->
-<g id="node5" class="node">
-<title>4</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M660,-468C660,-468 514,-468 514,-468 508,-468 502,-462 502,-456 502,-456 502,-444 502,-444 502,-438 508,-432 514,-432 514,-432 660,-432 660,-432 666,-432 672,-438 672,-444 672,-444 672,-456 672,-456 672,-462 666,-468 660,-468"/>
-<text text-anchor="middle" x="587" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node5" class="node"><title>4</title>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M322,-468C322,-468 196,-468 196,-468 190,-468 184,-462 184,-456 184,-456 184,-444 184,-444 184,-438 190,-432 196,-432 196,-432 322,-432 322,-432 328,-432 334,-438 334,-444 334,-444 334,-456 334,-456 334,-462 328,-468 322,-468"/>
+<text text-anchor="middle" x="259" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 4->0 -->
-<g id="edge8" class="edge">
-<title>4->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M587,-431.95C587,-405.29 587,-352.11 587,-307 587,-307 587,-307 587,-161 587,-120.03 586.13,-105.82 563,-72 553.82,-58.57 540.08,-47.25 527.07,-38.57"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="528.56,-35.37 518.23,-32.99 524.82,-41.29 528.56,-35.37"/>
+<g id="edge6" class="edge"><title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M246.068,-431.677C239.186,-421.702 231.112,-408.665 226,-396 210.862,-358.493 207,-347.447 207,-307 207,-307 207,-307 207,-161 207,-109.172 253.998,-66.0006 288.42,-41.3312"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="290.649,-44.0444 296.864,-35.4639 286.654,-38.2958 290.649,-44.0444"/>
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<!-- 5 -->
-<g id="node6" class="node">
-<title>5</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M450.5,-324C450.5,-324 355.5,-324 355.5,-324 349.5,-324 343.5,-318 343.5,-312 343.5,-312 343.5,-300 343.5,-300 343.5,-294 349.5,-288 355.5,-288 355.5,-288 450.5,-288 450.5,-288 456.5,-288 462.5,-294 462.5,-300 462.5,-300 462.5,-312 462.5,-312 462.5,-318 456.5,-324 450.5,-324"/>
-<text text-anchor="middle" x="403" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<g id="node6" class="node"><title>5</title>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M510.5,-180C510.5,-180 445.5,-180 445.5,-180 439.5,-180 433.5,-174 433.5,-168 433.5,-168 433.5,-156 433.5,-156 433.5,-150 439.5,-144 445.5,-144 445.5,-144 510.5,-144 510.5,-144 516.5,-144 522.5,-150 522.5,-156 522.5,-156 522.5,-168 522.5,-168 522.5,-174 516.5,-180 510.5,-180"/>
+<text text-anchor="middle" x="478" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
</g>
<!-- 5->0 -->
-<g id="edge7" class="edge">
-<title>5->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M446.39,-287.77C461.66,-279.38 477.21,-267.65 486,-252 523.15,-185.9 508.59,-91.71 498.12,-45.99"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="501.51,-45.12 495.77,-36.22 494.7,-46.76 501.51,-45.12"/>
+<g id="edge9" class="edge"><title>5->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M459.424,-143.871C432.137,-118.711 381.103,-71.6535 350.073,-43.0415"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="352.366,-40.395 342.642,-36.1893 347.621,-45.5412 352.366,-40.395"/>
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<!-- 6 -->
-<g id="node7" class="node">
-<title>6</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M775,-396C775,-396 647,-396 647,-396 641,-396 635,-390 635,-384 635,-384 635,-372 635,-372 635,-366 641,-360 647,-360 647,-360 775,-360 775,-360 781,-360 787,-366 787,-372 787,-372 787,-384 787,-384 787,-390 781,-396 775,-396"/>
-<text text-anchor="middle" x="711" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<g id="node7" class="node"><title>6</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M359,-396C359,-396 247,-396 247,-396 241,-396 235,-390 235,-384 235,-384 235,-372 235,-372 235,-366 241,-360 247,-360 247,-360 359,-360 359,-360 365,-360 371,-366 371,-372 371,-372 371,-384 371,-384 371,-390 365,-396 359,-396"/>
+<text text-anchor="middle" x="303" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
<!-- 6->0 -->
-<g id="edge5" class="edge">
-<title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M700.02,-359.84C684.49,-333.89 658,-282.63 658,-235 658,-235 658,-235 658,-161 658,-93.03 576.72,-50.79 527.57,-31.45"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="528.79,-28.17 518.2,-27.89 526.31,-34.72 528.79,-28.17"/>
+<g id="edge7" class="edge"><title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M303.198,-359.951C303.489,-333.292 304,-280.116 304,-235 304,-235 304,-235 304,-161 304,-120.822 311.948,-74.8689 317.823,-46.3889"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="321.296,-46.887 319.953,-36.3777 314.449,-45.4307 321.296,-46.887"/>
</g>
<!-- 7 -->
-<g id="node8" class="node">
-<title>7</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M967,-396C967,-396 817,-396 817,-396 811,-396 805,-390 805,-384 805,-384 805,-372 805,-372 805,-366 811,-360 817,-360 817,-360 967,-360 967,-360 973,-360 979,-366 979,-372 979,-372 979,-384 979,-384 979,-390 973,-396 967,-396"/>
-<text text-anchor="middle" x="892" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<g id="node8" class="node"><title>7</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M532.5,-396C532.5,-396 401.5,-396 401.5,-396 395.5,-396 389.5,-390 389.5,-384 389.5,-384 389.5,-372 389.5,-372 389.5,-366 395.5,-360 401.5,-360 401.5,-360 532.5,-360 532.5,-360 538.5,-360 544.5,-366 544.5,-372 544.5,-372 544.5,-384 544.5,-384 544.5,-390 538.5,-396 532.5,-396"/>
+<text text-anchor="middle" x="467" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
<!-- 7->0 -->
-<g id="edge3" class="edge">
-<title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M871.12,-359.63C843.98,-334.97 800,-286.99 800,-235 800,-235 800,-235 800,-161 800,-42.65 610.53,-22.58 528.32,-19.44"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="528.26,-15.94 518.15,-19.12 528.04,-22.93 528.26,-15.94"/>
+<g id="edge1" class="edge"><title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M436.911,-359.894C400.497,-336.696 344,-291.588 344,-235 344,-235 344,-235 344,-161 344,-120.822 336.052,-74.8689 330.177,-46.3889"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="333.551,-45.4307 328.047,-36.3777 326.704,-46.887 333.551,-45.4307"/>
</g>
<!-- 8 -->
-<g id="node9" class="node">
-<title>8</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M313,-324C313,-324 277,-324 277,-324 271,-324 265,-318 265,-312 265,-312 265,-300 265,-300 265,-294 271,-288 277,-288 277,-288 313,-288 313,-288 319,-288 325,-294 325,-300 325,-300 325,-312 325,-312 325,-318 319,-324 313,-324"/>
-<text text-anchor="middle" x="295" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node9" class="node"><title>8</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M866.5,-324C866.5,-324 835.5,-324 835.5,-324 829.5,-324 823.5,-318 823.5,-312 823.5,-312 823.5,-300 823.5,-300 823.5,-294 829.5,-288 835.5,-288 835.5,-288 866.5,-288 866.5,-288 872.5,-288 878.5,-294 878.5,-300 878.5,-300 878.5,-312 878.5,-312 878.5,-318 872.5,-324 866.5,-324"/>
+<text text-anchor="middle" x="851" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 8->0 -->
-<g id="edge1" class="edge">
-<title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M325.02,-290.82C342.15,-281.6 363.11,-268.27 378,-252 435.3,-189.42 469.53,-92.48 483.56,-45.85"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="486.94,-46.75 486.4,-36.17 480.23,-44.78 486.94,-46.75"/>
+<g id="edge10" class="edge"><title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M823.408,-290.026C735.084,-242.093 459.299,-92.4259 360.045,-38.5615"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="361.462,-35.3482 351.003,-33.6545 358.123,-41.5006 361.462,-35.3482"/>
</g>
<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M357,-252C357,-252 235,-252 235,-252 229,-252 223,-246 223,-240 223,-240 223,-228 223,-228 223,-222 229,-216 235,-216 235,-216 357,-216 357,-216 363,-216 369,-222 369,-228 369,-228 369,-240 369,-240 369,-246 363,-252 357,-252"/>
-<text text-anchor="middle" x="296" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M903,-252C903,-252 797,-252 797,-252 791,-252 785,-246 785,-240 785,-240 785,-228 785,-228 785,-222 791,-216 797,-216 797,-216 903,-216 903,-216 909,-216 915,-222 915,-228 915,-228 915,-240 915,-240 915,-246 909,-252 903,-252"/>
+<text text-anchor="middle" x="850" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
<!-- 8->20 -->
-<g id="edge42" class="edge">
-<title>8->20</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M295.25,-287.7C295.36,-279.98 295.49,-270.71 295.61,-262.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="299.11,-262.15 295.76,-252.1 292.11,-262.05 299.11,-262.15"/>
+<g id="edge40" class="edge"><title>8->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M850.753,-287.697C850.643,-279.983 850.51,-270.712 850.387,-262.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="853.887,-262.053 850.244,-252.104 846.888,-262.153 853.887,-262.053"/>
</g>
<!-- 9 -->
-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M314,-180C314,-180 284,-180 284,-180 278,-180 272,-174 272,-168 272,-168 272,-156 272,-156 272,-150 278,-144 284,-144 284,-144 314,-144 314,-144 320,-144 326,-150 326,-156 326,-156 326,-168 326,-168 326,-174 320,-180 314,-180"/>
-<text text-anchor="middle" x="299" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M850,-180C850,-180 820,-180 820,-180 814,-180 808,-174 808,-168 808,-168 808,-156 808,-156 808,-150 814,-144 820,-144 820,-144 850,-144 850,-144 856,-144 862,-150 862,-156 862,-156 862,-168 862,-168 862,-174 856,-180 850,-180"/>
+<text text-anchor="middle" x="835" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 9->0 -->
-<g id="edge9" class="edge">
-<title>9->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M298.06,-143.96C297.93,-124.14 300.83,-91.65 319,-72 353.79,-34.39 414.57,-23.22 453.78,-20.04"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="454.24,-23.52 463.99,-19.36 453.77,-16.53 454.24,-23.52"/>
+<g id="edge5" class="edge"><title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M807.667,-145.655C789.461,-135.295 765.097,-121.159 744,-108 719.526,-92.7346 716.935,-82.3204 690,-72 575.896,-28.28 429.165,-20.273 361.382,-19.0424"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="361.247,-15.5402 351.199,-18.8986 361.148,-22.5395 361.247,-15.5402"/>
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<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M432,-108C432,-108 340,-108 340,-108 334,-108 328,-102 328,-96 328,-96 328,-84 328,-84 328,-78 334,-72 340,-72 340,-72 432,-72 432,-72 438,-72 444,-78 444,-84 444,-84 444,-96 444,-96 444,-102 438,-108 432,-108"/>
-<text text-anchor="middle" x="386" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M846.5,-108C846.5,-108 765.5,-108 765.5,-108 759.5,-108 753.5,-102 753.5,-96 753.5,-96 753.5,-84 753.5,-84 753.5,-78 759.5,-72 765.5,-72 765.5,-72 846.5,-72 846.5,-72 852.5,-72 858.5,-78 858.5,-84 858.5,-84 858.5,-96 858.5,-96 858.5,-102 852.5,-108 846.5,-108"/>
+<text text-anchor="middle" x="806" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
<!-- 9->10 -->
-<g id="edge28" class="edge">
-<title>9->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M320.51,-143.7C331.46,-134.88 344.95,-124.03 356.82,-114.47"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="359.14,-117.1 364.74,-108.1 354.76,-111.65 359.14,-117.1"/>
+<g id="edge25" class="edge"><title>9->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M827.831,-143.697C824.565,-135.813 820.626,-126.304 816.998,-117.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="820.147,-116.003 813.086,-108.104 813.68,-118.683 820.147,-116.003"/>
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<!-- 10->0 -->
-<g id="edge10" class="edge">
-<title>10->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M411.69,-71.88C425.29,-62.81 442.17,-51.55 456.86,-41.76"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="458.84,-44.65 465.22,-36.19 454.95,-38.82 458.84,-44.65"/>
+<g id="edge2" class="edge"><title>10->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M753.403,-75.7453C747.22,-74.3834 740.984,-73.0989 735,-72 598.087,-46.8556 433.355,-29.4441 361.065,-22.4398"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="361.372,-18.9533 351.084,-21.4822 360.704,-25.9213 361.372,-18.9533"/>
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<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#56d863" stroke-width="2" d="M413,-540C413,-540 285,-540 285,-540 279,-540 273,-534 273,-528 273,-528 273,-516 273,-516 273,-510 279,-504 285,-504 285,-504 413,-504 413,-504 419,-504 425,-510 425,-516 425,-516 425,-528 425,-528 425,-534 419,-540 413,-540"/>
-<text text-anchor="middle" x="349" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M395,-540C395,-540 283,-540 283,-540 277,-540 271,-534 271,-528 271,-528 271,-516 271,-516 271,-510 277,-504 283,-504 283,-504 395,-504 395,-504 401,-504 407,-510 407,-516 407,-516 407,-528 407,-528 407,-534 401,-540 395,-540"/>
+<text text-anchor="middle" x="339" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 11->3 -->
-<g id="edge11" class="edge">
-<title>11->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M359.13,-503.7C363.85,-495.64 369.56,-485.89 374.78,-476.98"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="377.95,-478.5 379.98,-468.1 371.91,-474.96 377.95,-478.5"/>
+<g id="edge11" class="edge"><title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M276.703,-503.966C240.156,-493.972 193.806,-481.298 155.609,-470.854"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="156.146,-467.372 145.577,-468.111 154.299,-474.124 156.146,-467.372"/>
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-<g id="node15" class="node">
-<title>14</title>
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-<text text-anchor="middle" x="91" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 15 -->
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M467.5,-468C467.5,-468 364.5,-468 364.5,-468 358.5,-468 352.5,-462 352.5,-456 352.5,-456 352.5,-444 352.5,-444 352.5,-438 358.5,-432 364.5,-432 364.5,-432 467.5,-432 467.5,-432 473.5,-432 479.5,-438 479.5,-444 479.5,-444 479.5,-456 479.5,-456 479.5,-462 473.5,-468 467.5,-468"/>
+<text text-anchor="middle" x="416" y="-447.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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-<!-- 11->14 -->
-<g id="edge33" class="edge">
-<title>11->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M286.22,-503.97C249.25,-493.94 202.32,-481.2 163.75,-470.74"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="164.19,-467.23 153.62,-467.99 162.35,-473.99 164.19,-467.23"/>
+<!-- 11->15 -->
+<g id="edge31" class="edge"><title>11->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M358.034,-503.697C367.545,-495.05 379.207,-484.449 389.57,-475.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="392.14,-477.421 397.185,-468.104 387.431,-472.241 392.14,-477.421"/>
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-<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M820,-468C820,-468 702,-468 702,-468 696,-468 690,-462 690,-456 690,-456 690,-444 690,-444 690,-438 696,-432 702,-432 702,-432 820,-432 820,-432 826,-432 832,-438 832,-444 832,-444 832,-456 832,-456 832,-462 826,-468 820,-468"/>
-<text text-anchor="middle" x="761" y="-447.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<!-- 17 -->
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M887.5,-468C887.5,-468 798.5,-468 798.5,-468 792.5,-468 786.5,-462 786.5,-456 786.5,-456 786.5,-444 786.5,-444 786.5,-438 792.5,-432 798.5,-432 798.5,-432 887.5,-432 887.5,-432 893.5,-432 899.5,-438 899.5,-444 899.5,-444 899.5,-456 899.5,-456 899.5,-462 893.5,-468 887.5,-468"/>
+<text text-anchor="middle" x="843" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
-<!-- 11->18 -->
-<g id="edge38" class="edge">
-<title>11->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M425.27,-506.7C430.59,-505.77 435.87,-504.86 441,-504 544.26,-486.72 573.19,-487.17 680.05,-468.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="680.72,-471.55 689.94,-466.33 679.48,-464.66 680.72,-471.55"/>
+<!-- 11->17 -->
+<g id="edge35" class="edge"><title>11->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M407.368,-505.557C410.28,-505.009 413.167,-504.487 416,-504 542.678,-482.204 691.979,-465.763 776.257,-457.326"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="776.852,-460.784 786.456,-456.312 776.159,-453.819 776.852,-460.784"/>
</g>
<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M711.5,-540C711.5,-540 614.5,-540 614.5,-540 608.5,-540 602.5,-534 602.5,-528 602.5,-528 602.5,-516 602.5,-516 602.5,-510 608.5,-504 614.5,-504 614.5,-504 711.5,-504 711.5,-504 717.5,-504 723.5,-510 723.5,-516 723.5,-516 723.5,-528 723.5,-528 723.5,-534 717.5,-540 711.5,-540"/>
-<text text-anchor="middle" x="663" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M237,-540C237,-540 153,-540 153,-540 147,-540 141,-534 141,-528 141,-528 141,-516 141,-516 141,-510 147,-504 153,-504 153,-504 237,-504 237,-504 243,-504 249,-510 249,-516 249,-516 249,-528 249,-528 249,-534 243,-540 237,-540"/>
+<text text-anchor="middle" x="195" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 12->3 -->
-<g id="edge12" class="edge">
-<title>12->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M602.41,-505.46C562.34,-495.19 509.46,-481.63 466.49,-470.61"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="467.19,-467.18 456.64,-468.09 465.45,-473.96 467.19,-467.18"/>
+<g id="edge12" class="edge"><title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M167.602,-503.876C153.093,-494.808 135.084,-483.552 119.415,-473.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="120.839,-470.522 110.504,-468.19 117.129,-476.458 120.839,-470.522"/>
</g>
<!-- 12->4 -->
-<g id="edge13" class="edge">
-<title>12->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M644.21,-503.7C634.83,-495.05 623.32,-484.45 613.09,-475.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="615.3,-472.3 605.57,-468.1 610.55,-477.45 615.3,-472.3"/>
+<g id="edge14" class="edge"><title>12->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M210.82,-503.697C218.57,-495.22 228.039,-484.864 236.524,-475.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="239.197,-477.846 243.362,-468.104 234.031,-473.123 239.197,-477.846"/>
</g>
<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M572,-540C572,-540 462,-540 462,-540 456,-540 450,-534 450,-528 450,-528 450,-516 450,-516 450,-510 456,-504 462,-504 462,-504 572,-504 572,-504 578,-504 584,-510 584,-516 584,-516 584,-528 584,-528 584,-534 578,-540 572,-540"/>
-<text text-anchor="middle" x="517" y="-519.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M661,-540C661,-540 565,-540 565,-540 559,-540 553,-534 553,-528 553,-528 553,-516 553,-516 553,-510 559,-504 565,-504 565,-504 661,-504 661,-504 667,-504 673,-510 673,-516 673,-516 673,-528 673,-528 673,-534 667,-540 661,-540"/>
+<text text-anchor="middle" x="613" y="-519.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 13->4 -->
-<g id="edge14" class="edge">
-<title>13->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M534.3,-503.7C542.86,-495.14 553.34,-484.66 562.7,-475.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="565.3,-477.65 569.9,-468.1 560.35,-472.7 565.3,-477.65"/>
+<g id="edge13" class="edge"><title>13->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M552.723,-506.118C549.439,-505.383 546.181,-504.672 543,-504 457.739,-485.99 433.404,-485.008 344.115,-468.184"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="344.567,-464.707 334.09,-466.28 343.261,-471.585 344.567,-464.707"/>
</g>
-<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M266.5,-468C266.5,-468 183.5,-468 183.5,-468 177.5,-468 171.5,-462 171.5,-456 171.5,-456 171.5,-444 171.5,-444 171.5,-438 177.5,-432 183.5,-432 183.5,-432 266.5,-432 266.5,-432 272.5,-432 278.5,-438 278.5,-444 278.5,-444 278.5,-456 278.5,-456 278.5,-462 272.5,-468 266.5,-468"/>
-<text text-anchor="middle" x="225" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<!-- 16 -->
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M596.5,-468C596.5,-468 509.5,-468 509.5,-468 503.5,-468 497.5,-462 497.5,-456 497.5,-456 497.5,-444 497.5,-444 497.5,-438 503.5,-432 509.5,-432 509.5,-432 596.5,-432 596.5,-432 602.5,-432 608.5,-438 608.5,-444 608.5,-444 608.5,-456 608.5,-456 608.5,-462 602.5,-468 596.5,-468"/>
+<text text-anchor="middle" x="553" y="-447.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 13->17 -->
-<g id="edge37" class="edge">
-<title>13->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M449.71,-506.1C406.41,-496.35 348.7,-483.08 288.63,-468.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="289.13,-464.63 278.58,-465.6 287.43,-471.42 289.13,-464.63"/>
+<!-- 13->16 -->
+<g id="edge33" class="edge"><title>13->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M598.169,-503.697C590.975,-495.305 582.203,-485.07 574.31,-475.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="576.826,-473.419 567.661,-468.104 571.511,-477.975 576.826,-473.419"/>
</g>
<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M963.5,-468C963.5,-468 862.5,-468 862.5,-468 856.5,-468 850.5,-462 850.5,-456 850.5,-456 850.5,-444 850.5,-444 850.5,-438 856.5,-432 862.5,-432 862.5,-432 963.5,-432 963.5,-432 969.5,-432 975.5,-438 975.5,-444 975.5,-444 975.5,-456 975.5,-456 975.5,-462 969.5,-468 963.5,-468"/>
-<text text-anchor="middle" x="913" y="-447.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M1002.5,-468C1002.5,-468 929.5,-468 929.5,-468 923.5,-468 917.5,-462 917.5,-456 917.5,-456 917.5,-444 917.5,-444 917.5,-438 923.5,-432 929.5,-432 929.5,-432 1002.5,-432 1002.5,-432 1008.5,-432 1014.5,-438 1014.5,-444 1014.5,-444 1014.5,-456 1014.5,-456 1014.5,-462 1008.5,-468 1002.5,-468"/>
+<text text-anchor="middle" x="966" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 13->19 -->
-<g id="edge41" class="edge">
-<title>13->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M584.13,-505.88C587.47,-505.22 590.77,-504.59 594,-504 700.03,-484.59 730.32,-488.52 840.41,-468.01"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="841.06,-471.45 850.24,-466.16 839.76,-464.57 841.06,-471.45"/>
+<g id="edge39" class="edge"><title>13->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M673.279,-512.113C731.011,-503.162 820.701,-488.115 907.607,-467.955"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="908.43,-471.357 917.367,-465.666 906.832,-464.542 908.43,-471.357"/>
+</g>
+<!-- 14 -->
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M577,-252C577,-252 501,-252 501,-252 495,-252 489,-246 489,-240 489,-240 489,-228 489,-228 489,-222 495,-216 501,-216 501,-216 577,-216 577,-216 583,-216 589,-222 589,-228 589,-228 589,-240 589,-240 589,-246 583,-252 577,-252"/>
+<text text-anchor="middle" x="539" y="-231.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
</g>
<!-- 14->5 -->
-<g id="edge17" class="edge">
-<title>14->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M144.14,-431.97C172.41,-422.38 207.54,-409.62 238,-396 283.09,-375.85 332.69,-348.32 365.62,-329.24"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="367.57,-332.15 374.45,-324.09 364.05,-326.1 367.57,-332.15"/>
+<g id="edge15" class="edge"><title>14->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M523.921,-215.697C516.608,-207.305 507.69,-197.07 499.665,-187.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="502.114,-185.344 492.905,-180.104 496.836,-189.943 502.114,-185.344"/>
+</g>
+<!-- 15->6 -->
+<g id="edge16" class="edge"><title>15->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M388.357,-431.876C373.582,-422.724 355.209,-411.342 339.297,-401.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="341.093,-398.481 330.749,-396.19 337.407,-404.431 341.093,-398.481"/>
+</g>
+<!-- 15->7 -->
+<g id="edge18" class="edge"><title>15->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M428.607,-431.697C434.597,-423.474 441.876,-413.483 448.479,-404.421"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="451.478,-406.248 454.538,-396.104 445.821,-402.126 451.478,-406.248"/>
+</g>
+<!-- 16->6 -->
+<g id="edge17" class="edge"><title>16->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M497.206,-433.378C460.723,-423.163 412.756,-409.732 373.621,-398.774"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="374.447,-395.371 363.874,-396.045 372.56,-402.111 374.447,-395.371"/>
+</g>
+<!-- 16->7 -->
+<g id="edge19" class="edge"><title>16->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M531.742,-431.697C520.911,-422.881 507.582,-412.032 495.84,-402.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="497.979,-399.703 488.014,-396.104 493.56,-405.132 497.979,-399.703"/>
</g>
-<!-- 14->8 -->
-<g id="edge25" class="edge">
-<title>14->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M58.47,-431.98C45.21,-423.18 31.3,-411.09 24,-396 17.03,-381.6 13.83,-372.35 24,-360 52.71,-325.13 185.96,-312.88 254.32,-308.84"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="254.91,-312.31 264.7,-308.26 254.52,-305.32 254.91,-312.31"/>
+<!-- 17->8 -->
+<g id="edge20" class="edge"><title>17->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M899.722,-433.313C918.045,-425.265 936.359,-413.365 947,-396 955.359,-382.357 955.132,-373.779 947,-360 934.386,-338.628 909.727,-325.279 888.56,-317.324"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.422,-313.918 878.828,-313.94 887.123,-320.53 889.422,-313.918"/>
</g>
-<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#56d8c1" stroke-width="2" d="M217,-396C217,-396 45,-396 45,-396 39,-396 33,-390 33,-384 33,-384 33,-372 33,-372 33,-366 39,-360 45,-360 45,-360 217,-360 217,-360 223,-360 229,-366 229,-372 229,-372 229,-384 229,-384 229,-390 223,-396 217,-396"/>
-<text text-anchor="middle" x="131" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
-</g>
-<!-- 14->15 -->
-<g id="edge35" class="edge">
-<title>14->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M100.89,-431.7C105.49,-423.64 111.06,-413.89 116.15,-404.98"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="119.3,-406.52 121.23,-396.1 113.23,-403.05 119.3,-406.52"/>
-</g>
-<!-- 15->5 -->
-<g id="edge15" class="edge">
-<title>15->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M197.19,-359.97C238.54,-349.33 291.69,-335.65 333.62,-324.85"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="334.67,-328.2 343.48,-322.32 332.92,-321.42 334.67,-328.2"/>
-</g>
-<!-- 15->8 -->
-<g id="edge23" class="edge">
-<title>15->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M171.12,-359.88C196.77,-348.93 229.88,-334.79 255.42,-323.89"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="256.99,-327.03 264.81,-319.89 254.24,-320.59 256.99,-327.03"/>
+<!-- 18 -->
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M926,-396C926,-396 776,-396 776,-396 770,-396 764,-390 764,-384 764,-384 764,-372 764,-372 764,-366 770,-360 776,-360 776,-360 926,-360 926,-360 932,-360 938,-366 938,-372 938,-372 938,-384 938,-384 938,-390 932,-396 926,-396"/>
+<text text-anchor="middle" x="851" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
-<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M471,-396C471,-396 335,-396 335,-396 329,-396 323,-390 323,-384 323,-384 323,-372 323,-372 323,-366 329,-360 335,-360 335,-360 471,-360 471,-360 477,-360 483,-366 483,-372 483,-372 483,-384 483,-384 483,-390 477,-396 471,-396"/>
-<text text-anchor="middle" x="403" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
-</g>
-<!-- 16->5 -->
-<g id="edge18" class="edge">
-<title>16->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M403,-359.7C403,-351.98 403,-342.71 403,-334.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="406.5,-334.1 403,-324.1 399.5,-334.1 406.5,-334.1"/>
-</g>
-<!-- 17->5 -->
-<g id="edge16" class="edge">
-<title>17->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M278.54,-434.21C281.73,-433.43 284.9,-432.69 288,-432 332.93,-421.99 462.41,-431.27 492,-396 502.28,-383.74 499.91,-373.91 492,-360 484.64,-347.04 472.71,-336.92 459.95,-329.16"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="461.47,-325.99 451.03,-324.15 458.04,-332.1 461.47,-325.99"/>
+<!-- 17->18 -->
+<g id="edge36" class="edge"><title>17->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M844.978,-431.697C845.859,-423.983 846.919,-414.712 847.901,-406.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="851.387,-406.437 849.045,-396.104 844.432,-405.642 851.387,-406.437"/>
</g>
-<!-- 17->8 -->
-<g id="edge24" class="edge">
-<title>17->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M233.44,-431.87C245.53,-407.35 267.87,-362.03 282.06,-333.26"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="285.24,-334.71 286.53,-324.19 278.97,-331.61 285.24,-334.71"/>
-</g>
-<!-- 17->15 -->
-<g id="edge34" class="edge">
-<title>17->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M201.76,-431.7C189.81,-422.8 175.08,-411.82 162.15,-402.2"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="164.08,-399.27 153.97,-396.1 159.9,-404.88 164.08,-399.27"/>
-</g>
-<!-- 18->6 -->
-<g id="edge19" class="edge">
-<title>18->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M748.64,-431.7C742.77,-423.47 735.63,-413.48 729.16,-404.42"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="731.88,-402.21 723.22,-396.1 726.18,-406.28 731.88,-402.21"/>
-</g>
-<!-- 18->7 -->
-<g id="edge21" class="edge">
-<title>18->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M793.05,-431.88C810.49,-422.55 832.27,-410.92 850.94,-400.94"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="852.66,-403.99 859.83,-396.19 849.36,-397.82 852.66,-403.99"/>
-</g>
-<!-- 19->6 -->
-<g id="edge20" class="edge">
-<title>19->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M863.84,-431.97C835.5,-422.14 799.68,-409.73 769.84,-399.39"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="770.97,-396.08 760.38,-396.11 768.68,-402.69 770.97,-396.08"/>
-</g>
-<!-- 19->7 -->
-<g id="edge22" class="edge">
-<title>19->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M907.81,-431.7C905.47,-423.9 902.65,-414.51 900.05,-405.83"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="903.36,-404.68 897.13,-396.1 896.65,-406.69 903.36,-404.68"/>
+<!-- 25 -->
+<g id="node26" class="node"><title>25</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M780,-324C780,-324 692,-324 692,-324 686,-324 680,-318 680,-312 680,-312 680,-300 680,-300 680,-294 686,-288 692,-288 692,-288 780,-288 780,-288 786,-288 792,-294 792,-300 792,-300 792,-312 792,-312 792,-318 786,-324 780,-324"/>
+<text text-anchor="middle" x="736" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+</g>
+<!-- 17->25 -->
+<g id="edge42" class="edge"><title>17->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M799.53,-431.827C783.272,-423.345 766.08,-411.537 755,-396 742.133,-377.959 737.662,-352.972 736.249,-334.065"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="739.741,-333.812 735.737,-324.002 732.75,-334.167 739.741,-333.812"/>
+</g>
+<!-- 18->8 -->
+<g id="edge21" class="edge"><title>18->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M851,-359.697C851,-351.983 851,-342.712 851,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="854.5,-334.104 851,-324.104 847.5,-334.104 854.5,-334.104"/>
+</g>
+<!-- 18->25 -->
+<g id="edge44" class="edge"><title>18->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M822.868,-359.876C807.832,-350.724 789.133,-339.342 772.94,-329.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="774.602,-326.4 764.24,-324.19 770.962,-332.379 774.602,-326.4"/>
+</g>
+<!-- 19->8 -->
+<g id="edge22" class="edge"><title>19->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M970.876,-431.724C975.205,-412.573 978.916,-381.548 965,-360 948.17,-333.94 914.888,-320.48 888.609,-313.662"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.107,-310.183 878.57,-311.284 887.494,-316.994 889.107,-310.183"/>
+</g>
+<!-- 19->18 -->
+<g id="edge37" class="edge"><title>19->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M937.868,-431.876C922.832,-422.724 904.133,-411.342 887.94,-401.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.602,-398.4 879.24,-396.19 885.962,-404.379 889.602,-398.4"/>
+</g>
+<!-- 19->25 -->
+<g id="edge45" class="edge"><title>19->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M967.332,-431.807C967.882,-411.847 965.54,-379.215 947,-360 941.799,-354.609 861.991,-335.541 802.055,-321.821"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="802.775,-318.395 792.247,-319.582 801.217,-325.22 802.775,-318.395"/>
</g>
<!-- 20->9 -->
-<g id="edge26" class="edge">
-<title>20->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M296.74,-215.7C297.07,-207.98 297.47,-198.71 297.84,-190.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="301.34,-190.25 298.27,-180.1 294.34,-189.95 301.34,-190.25"/>
+<g id="edge23" class="edge"><title>20->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M846.292,-215.697C844.639,-207.983 842.653,-198.712 840.81,-190.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="844.183,-189.149 838.665,-180.104 837.338,-190.616 844.183,-189.149"/>
</g>
<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#56d8d0" stroke-width="2" d="M104,-252C104,-252 12,-252 12,-252 6,-252 0,-246 0,-240 0,-240 0,-228 0,-228 0,-222 6,-216 12,-216 12,-216 104,-216 104,-216 110,-216 116,-222 116,-228 116,-228 116,-240 116,-240 116,-246 110,-252 104,-252"/>
-<text text-anchor="middle" x="58" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#80d856" stroke-width="2" d="M1054,-324C1054,-324 974,-324 974,-324 968,-324 962,-318 962,-312 962,-312 962,-300 962,-300 962,-294 968,-288 974,-288 974,-288 1054,-288 1054,-288 1060,-288 1066,-294 1066,-300 1066,-300 1066,-312 1066,-312 1066,-318 1060,-324 1054,-324"/>
+<text text-anchor="middle" x="1014" y="-303.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
<!-- 21->9 -->
-<g id="edge27" class="edge">
-<title>21->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M116.03,-216.14C161.42,-202.96 223.15,-185.03 262.04,-173.74"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="263.26,-177.03 271.89,-170.88 261.31,-170.3 263.26,-177.03"/>
+<g id="edge24" class="edge"><title>21->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M998.839,-287.668C981.776,-268.746 952.678,-238.186 924,-216 907.558,-203.28 887.819,-191.241 871.112,-181.862"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="872.629,-178.702 862.182,-176.937 869.249,-184.831 872.629,-178.702"/>
</g>
<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#d87d56" stroke-width="2" d="M416.5,-612C416.5,-612 273.5,-612 273.5,-612 267.5,-612 261.5,-606 261.5,-600 261.5,-600 261.5,-588 261.5,-588 261.5,-582 267.5,-576 273.5,-576 273.5,-576 416.5,-576 416.5,-576 422.5,-576 428.5,-582 428.5,-588 428.5,-588 428.5,-600 428.5,-600 428.5,-606 422.5,-612 416.5,-612"/>
-<text text-anchor="middle" x="345" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M407,-612C407,-612 281,-612 281,-612 275,-612 269,-606 269,-600 269,-600 269,-588 269,-588 269,-582 275,-576 281,-576 281,-576 407,-576 407,-576 413,-576 419,-582 419,-588 419,-588 419,-600 419,-600 419,-606 413,-612 407,-612"/>
+<text text-anchor="middle" x="344" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 22->11 -->
-<g id="edge29" class="edge">
-<title>22->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M345.99,-575.7C346.43,-567.98 346.96,-558.71 347.45,-550.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="350.95,-550.29 348.02,-540.1 343.96,-549.89 350.95,-550.29"/>
+<g id="edge26" class="edge"><title>22->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M342.764,-575.697C342.213,-567.983 341.551,-558.712 340.937,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="344.425,-549.83 340.222,-540.104 337.443,-550.328 344.425,-549.83"/>
</g>
<!-- 23 -->
-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M783.5,-612C783.5,-612 682.5,-612 682.5,-612 676.5,-612 670.5,-606 670.5,-600 670.5,-600 670.5,-588 670.5,-588 670.5,-582 676.5,-576 682.5,-576 682.5,-576 783.5,-576 783.5,-576 789.5,-576 795.5,-582 795.5,-588 795.5,-588 795.5,-600 795.5,-600 795.5,-606 789.5,-612 783.5,-612"/>
-<text text-anchor="middle" x="733" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<g id="node24" class="node"><title>23</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M238.5,-612C238.5,-612 151.5,-612 151.5,-612 145.5,-612 139.5,-606 139.5,-600 139.5,-600 139.5,-588 139.5,-588 139.5,-582 145.5,-576 151.5,-576 151.5,-576 238.5,-576 238.5,-576 244.5,-576 250.5,-582 250.5,-588 250.5,-588 250.5,-600 250.5,-600 250.5,-606 244.5,-612 238.5,-612"/>
+<text text-anchor="middle" x="195" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
<!-- 23->12 -->
-<g id="edge30" class="edge">
-<title>23->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M715.7,-575.7C707.14,-567.14 696.66,-556.66 687.3,-547.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="689.65,-544.7 680.1,-540.1 684.7,-549.65 689.65,-544.7"/>
+<g id="edge27" class="edge"><title>23->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M195,-575.697C195,-567.983 195,-558.712 195,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="198.5,-550.104 195,-540.104 191.5,-550.104 198.5,-550.104"/>
</g>
<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#567bd8" stroke-width="2" d="M850.5,-540C850.5,-540 753.5,-540 753.5,-540 747.5,-540 741.5,-534 741.5,-528 741.5,-528 741.5,-516 741.5,-516 741.5,-510 747.5,-504 753.5,-504 753.5,-504 850.5,-504 850.5,-504 856.5,-504 862.5,-510 862.5,-516 862.5,-516 862.5,-528 862.5,-528 862.5,-534 856.5,-540 850.5,-540"/>
-<text text-anchor="middle" x="802" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+<g id="node27" class="node"><title>26</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M522.5,-540C522.5,-540 437.5,-540 437.5,-540 431.5,-540 425.5,-534 425.5,-528 425.5,-528 425.5,-516 425.5,-516 425.5,-510 431.5,-504 437.5,-504 437.5,-504 522.5,-504 522.5,-504 528.5,-504 534.5,-510 534.5,-516 534.5,-516 534.5,-528 534.5,-528 534.5,-534 528.5,-540 522.5,-540"/>
+<text text-anchor="middle" x="480" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 23->26 -->
-<g id="edge44" class="edge">
-<title>23->26</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M750.06,-575.7C758.5,-567.14 768.82,-556.66 778.04,-547.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="780.61,-549.68 785.14,-540.1 775.63,-544.77 780.61,-549.68"/>
+<g id="edge46" class="edge"><title>23->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M250.642,-578.334C253.806,-577.536 256.942,-576.753 260,-576 326.125,-559.727 345.31,-557.324 415.453,-540.091"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="416.35,-543.475 425.218,-537.678 414.67,-536.68 416.35,-543.475"/>
</g>
<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M584,-612C584,-612 458,-612 458,-612 452,-612 446,-606 446,-600 446,-600 446,-588 446,-588 446,-582 452,-576 458,-576 458,-576 584,-576 584,-576 590,-576 596,-582 596,-588 596,-588 596,-600 596,-600 596,-606 590,-612 584,-612"/>
-<text text-anchor="middle" x="521" y="-591.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<g id="node25" class="node"><title>24</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M668,-612C668,-612 558,-612 558,-612 552,-612 546,-606 546,-600 546,-600 546,-588 546,-588 546,-582 552,-576 558,-576 558,-576 668,-576 668,-576 674,-576 680,-582 680,-588 680,-588 680,-600 680,-600 680,-606 674,-612 668,-612"/>
+<text text-anchor="middle" x="613" y="-591.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
</g>
<!-- 24->13 -->
-<g id="edge31" class="edge">
-<title>24->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M520.01,-575.7C519.57,-567.98 519.04,-558.71 518.55,-550.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="522.04,-549.89 517.98,-540.1 515.05,-550.29 522.04,-549.89"/>
-</g>
-<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M131,-540C131,-540 51,-540 51,-540 45,-540 39,-534 39,-528 39,-528 39,-516 39,-516 39,-510 45,-504 51,-504 51,-504 131,-504 131,-504 137,-504 143,-510 143,-516 143,-516 143,-528 143,-528 143,-534 137,-540 131,-540"/>
-<text text-anchor="middle" x="91" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text>
+<g id="edge28" class="edge"><title>24->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M613,-575.697C613,-567.983 613,-558.712 613,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="616.5,-550.104 613,-540.104 609.5,-550.104 616.5,-550.104"/>
</g>
<!-- 25->14 -->
-<g id="edge32" class="edge">
-<title>25->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M91,-503.7C91,-495.98 91,-486.71 91,-478.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="94.5,-478.1 91,-468.1 87.5,-478.1 94.5,-478.1"/>
-</g>
-<!-- 25->17 -->
-<g id="edge36" class="edge">
-<title>25->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M123.78,-503.88C141.63,-494.55 163.9,-482.92 183,-472.94"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="184.85,-475.92 192.09,-468.19 181.61,-469.72 184.85,-475.92"/>
-</g>
-<!-- 25->21 -->
-<g id="edge43" class="edge">
-<title>25->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M55.86,-503.78C41.94,-495.07 27.3,-483.1 19,-468 -18.19,-400.37 20.37,-306.26 43.41,-261.15"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="46.65,-262.52 48.2,-252.04 40.45,-259.26 46.65,-262.52"/>
-</g>
-<!-- 26->18 -->
-<g id="edge39" class="edge">
-<title>26->18</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M791.87,-503.7C787.15,-495.64 781.44,-485.89 776.22,-476.98"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="779.09,-474.96 771.02,-468.1 773.05,-478.5 779.09,-474.96"/>
-</g>
-<!-- 26->19 -->
-<g id="edge40" class="edge">
-<title>26->19</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M829.15,-503.88C843.53,-494.81 861.38,-483.55 876.91,-473.76"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="879.15,-476.48 885.74,-468.19 875.42,-470.56 879.15,-476.48"/>
+<g id="edge29" class="edge"><title>25->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M688.06,-287.966C660.535,-278.185 625.783,-265.836 596.759,-255.524"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="597.749,-252.161 587.155,-252.111 595.406,-258.757 597.749,-252.161"/>
+</g>
+<!-- 26->15 -->
+<g id="edge30" class="edge"><title>26->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M464.18,-503.697C456.43,-495.22 446.961,-484.864 438.476,-475.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="440.969,-473.123 431.638,-468.104 435.803,-477.846 440.969,-473.123"/>
+</g>
+<!-- 26->16 -->
+<g id="edge32" class="edge"><title>26->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M498.045,-503.697C507.062,-495.05 518.118,-484.449 527.943,-475.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="530.367,-477.552 535.163,-468.104 525.522,-472.499 530.367,-477.552"/>
+</g>
+<!-- 27 -->
+<g id="node28" class="node"><title>27</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1001,-540C1001,-540 931,-540 931,-540 925,-540 919,-534 919,-528 919,-528 919,-516 919,-516 919,-510 925,-504 931,-504 931,-504 1001,-504 1001,-504 1007,-504 1013,-510 1013,-516 1013,-516 1013,-528 1013,-528 1013,-534 1007,-540 1001,-540"/>
+<text text-anchor="middle" x="966" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text>
+</g>
+<!-- 27->17 -->
+<g id="edge34" class="edge"><title>27->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M935.911,-503.876C919.68,-494.639 899.458,-483.131 882.029,-473.212"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="883.627,-470.094 873.205,-468.19 880.165,-476.178 883.627,-470.094"/>
+</g>
+<!-- 27->19 -->
+<g id="edge38" class="edge"><title>27->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M966,-503.697C966,-495.983 966,-486.712 966,-478.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="969.5,-478.104 966,-468.104 962.5,-478.104 969.5,-478.104"/>
+</g>
+<!-- 27->21 -->
+<g id="edge41" class="edge"><title>27->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M993.34,-503.775C1005.11,-494.718 1017.62,-482.478 1024,-468 1043.27,-424.297 1032.42,-367.371 1023.04,-334.235"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1026.3,-332.935 1020.08,-324.359 1019.6,-334.943 1026.3,-332.935"/>
+</g>
+<!-- 28 -->
+<g id="node29" class="node"><title>28</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M695.5,-396C695.5,-396 574.5,-396 574.5,-396 568.5,-396 562.5,-390 562.5,-384 562.5,-384 562.5,-372 562.5,-372 562.5,-366 568.5,-360 574.5,-360 574.5,-360 695.5,-360 695.5,-360 701.5,-360 707.5,-366 707.5,-372 707.5,-372 707.5,-384 707.5,-384 707.5,-390 701.5,-396 695.5,-396"/>
+<text text-anchor="middle" x="635" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 28->25 -->
+<g id="edge43" class="edge"><title>28->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M659.707,-359.876C672.669,-350.893 688.728,-339.763 702.765,-330.034"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="704.972,-332.763 711.198,-324.19 700.985,-327.009 704.972,-332.763"/>
</g>
</g>
</svg>
diff --git a/tests/input_files/cluster.json b/tests/input_files/cluster.json
index f0456181eb00ec2ee961050096d07b6422c48930..46bc56c8852e63d7e0aff68ad0046934eab1d240 100644
--- a/tests/input_files/cluster.json
+++ b/tests/input_files/cluster.json
@@ -43,5 +43,17 @@
"time": "06:00:00",
"threads":"8",
"mem":"32G"
+ },
+ "merge_TIN_scores":
+ {
+ "time": "00:05:00",
+ "threads":"1",
+ "mem":"4G"
+ },
+ "plot_TIN_scores":
+ {
+ "time": "00:05:00",
+ "threads":"1",
+ "mem":"4G"
}
}