diff --git a/Snakefile b/Snakefile
index f26b9e17097a273ae4757edd4949e38469c28963..156e12466bde2f3ca24b00cc14ade8cb70aa97cb 100644
--- a/Snakefile
+++ b/Snakefile
@@ -99,7 +99,18 @@ rule finish:
"summary_salmon",
"quantmerge",
"transcripts_{salmon_merge_on}.tsv"),
- salmon_merge_on=["tpm", "numreads"])
+ salmon_merge_on=["tpm", "numreads"]),
+ star_rpm = expand(
+ os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str1.out.bg"),
+ zip,
+ sample=[i for i in list(samples_table.index.values)],
+ seqmode=[samples_table.loc[i, 'seqmode']
+ for i in list(samples_table.index.values)])
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 2b1194f1f10f6655c79ae1be9212f1ce3fe84f58..5b222ac1b8de89838e844ccb08792b141a3d0888 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -4,432 +4,480 @@
<!-- Generated by graphviz version 2.40.1 (20161225.0304)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="2046pt" height="409pt"
- viewBox="0.00 0.00 2046.00 409.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1950pt" height="409pt"
+ viewBox="0.00 0.00 1949.50 409.00" 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(4 405)">
<title>snakemake_dag</title>
-<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-405 2042,-405 2042,4 -4,4"/>
+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-405 1945.5,-405 1945.5,4 -4,4"/>
<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M1181,-36C1181,-36 1151,-36 1151,-36 1145,-36 1139,-30 1139,-24 1139,-24 1139,-12 1139,-12 1139,-6 1145,0 1151,0 1151,0 1181,0 1181,0 1187,0 1193,-6 1193,-12 1193,-12 1193,-24 1193,-24 1193,-30 1187,-36 1181,-36"/>
-<text text-anchor="middle" x="1166" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M1088,-36C1088,-36 1058,-36 1058,-36 1052,-36 1046,-30 1046,-24 1046,-24 1046,-12 1046,-12 1046,-6 1052,0 1058,0 1058,0 1088,0 1088,0 1094,0 1100,-6 1100,-12 1100,-12 1100,-24 1100,-24 1100,-30 1094,-36 1088,-36"/>
+<text text-anchor="middle" x="1073" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
</g>
<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
-<path fill="none" stroke="#56d863" 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"/>
+<path fill="none" stroke="#b6d856" 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" fill="#000000">pe_fastqc</text>
<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00" fill="#000000">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="#c0c0c0" stroke-width="2" d="M292.0103,-72.8245C295.0326,-72.5401 298.0318,-72.2648 301,-72 620.6922,-43.4788 1008.1917,-24.9957 1128.5335,-19.6246"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M292.0131,-72.855C295.0345,-72.5614 298.0328,-72.2759 301,-72 583.1987,-45.7585 924.507,-26.0981 1035.9032,-19.9907"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1036.1616,-23.4819 1045.956,-19.4422 1035.7802,-16.4922 1036.1616,-23.4819"/>
</g>
<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
-<path fill="none" stroke="#56d8d0" 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"/>
+<path fill="none" stroke="#56d863" 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" fill="#000000">fastqc</text>
<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00" fill="#000000">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="#c0c0c0" stroke-width="2" d="M614.4157,-73.4253C618.9948,-72.9426 623.5311,-72.4666 628,-72 816.1827,-52.3535 1041.5419,-30.1696 1128.8848,-21.6224"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M614.2117,-72.0634C754.7588,-55.5014 953.7298,-32.0548 1035.5979,-22.4075"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1036.3793,-25.8397 1045.9009,-21.1933 1035.56,-18.8878 1036.3793,-25.8397"/>
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<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M980.5,-180C980.5,-180 877.5,-180 877.5,-180 871.5,-180 865.5,-174 865.5,-168 865.5,-168 865.5,-156 865.5,-156 865.5,-150 871.5,-144 877.5,-144 877.5,-144 980.5,-144 980.5,-144 986.5,-144 992.5,-150 992.5,-156 992.5,-156 992.5,-168 992.5,-168 992.5,-174 986.5,-180 980.5,-180"/>
-<text text-anchor="middle" x="929" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1038.5,-180C1038.5,-180 935.5,-180 935.5,-180 929.5,-180 923.5,-174 923.5,-168 923.5,-168 923.5,-156 923.5,-156 923.5,-150 929.5,-144 935.5,-144 935.5,-144 1038.5,-144 1038.5,-144 1044.5,-144 1050.5,-150 1050.5,-156 1050.5,-156 1050.5,-168 1050.5,-168 1050.5,-174 1044.5,-180 1038.5,-180"/>
+<text text-anchor="middle" x="987" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
</g>
<!-- 3->0 -->
<g id="edge3" class="edge">
<title>3->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M865.3527,-158.2313C794.421,-152.5464 686.3294,-138.9422 661,-108 650.8651,-95.6193 650.3047,-83.9 661,-72 692.19,-37.297 1017.0548,-23.0637 1128.6246,-19.175"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M923.207,-147.3698C918.0643,-146.2194 912.9466,-145.0842 908,-144 827.4499,-126.3457 683.5164,-134.7655 737,-72 756.2467,-49.4131 952.2269,-29.0197 1035.6878,-21.2881"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1036.1172,-24.7636 1045.7565,-20.3664 1035.479,-17.7927 1036.1172,-24.7636"/>
</g>
<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1304,-108C1304,-108 1192,-108 1192,-108 1186,-108 1180,-102 1180,-96 1180,-96 1180,-84 1180,-84 1180,-78 1186,-72 1192,-72 1192,-72 1304,-72 1304,-72 1310,-72 1316,-78 1316,-84 1316,-84 1316,-96 1316,-96 1316,-102 1310,-108 1304,-108"/>
-<text text-anchor="middle" x="1248" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1248" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M1380,-108C1380,-108 1268,-108 1268,-108 1262,-108 1256,-102 1256,-96 1256,-96 1256,-84 1256,-84 1256,-78 1262,-72 1268,-72 1268,-72 1380,-72 1380,-72 1386,-72 1392,-78 1392,-84 1392,-84 1392,-96 1392,-96 1392,-102 1386,-108 1380,-108"/>
+<text text-anchor="middle" x="1324" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1324" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
</g>
<!-- 3->9 -->
-<g id="edge25" class="edge">
+<g id="edge27" class="edge">
<title>3->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M992.574,-145.978C995.4196,-145.3014 998.2384,-144.6391 1001,-144 1075.8188,-126.6844 1095.0269,-124.6348 1170,-108 1170.1018,-107.9774 1170.2036,-107.9548 1170.3055,-107.9322"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1050.6778,-149.1163C1103.1545,-138.4046 1179.4904,-122.6059 1246,-108 1246.1018,-107.9776 1246.2037,-107.9553 1246.3056,-107.9329"/>
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</g>
<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M803.5,-108C803.5,-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,-72 803.5,-72 803.5,-72 809.5,-72 815.5,-78 815.5,-84 815.5,-84 815.5,-96 815.5,-96 815.5,-102 809.5,-108 803.5,-108"/>
-<text text-anchor="middle" x="743" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="743" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M879.5,-108C879.5,-108 758.5,-108 758.5,-108 752.5,-108 746.5,-102 746.5,-96 746.5,-96 746.5,-84 746.5,-84 746.5,-78 752.5,-72 758.5,-72 758.5,-72 879.5,-72 879.5,-72 885.5,-72 891.5,-78 891.5,-84 891.5,-84 891.5,-96 891.5,-96 891.5,-102 885.5,-108 879.5,-108"/>
+<text text-anchor="middle" x="819" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="819" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
</g>
<!-- 3->10 -->
-<g id="edge27" class="edge">
+<g id="edge29" class="edge">
<title>3->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M882.0643,-143.8314C856.8563,-134.0734 825.6074,-121.977 799.1209,-111.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="800.1873,-108.384 789.5981,-108.038 797.6603,-114.912 800.1873,-108.384"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M944.6065,-143.8314C922.0376,-134.159 894.1079,-122.1891 870.3204,-111.9944"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="871.6588,-108.7602 861.0886,-108.038 868.9014,-115.1943 871.6588,-108.7602"/>
</g>
<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M976.5,-108C976.5,-108 845.5,-108 845.5,-108 839.5,-108 833.5,-102 833.5,-96 833.5,-96 833.5,-84 833.5,-84 833.5,-78 839.5,-72 845.5,-72 845.5,-72 976.5,-72 976.5,-72 982.5,-72 988.5,-78 988.5,-84 988.5,-84 988.5,-96 988.5,-96 988.5,-102 982.5,-108 976.5,-108"/>
-<text text-anchor="middle" x="911" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="911" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1052.5,-108C1052.5,-108 921.5,-108 921.5,-108 915.5,-108 909.5,-102 909.5,-96 909.5,-96 909.5,-84 909.5,-84 909.5,-78 915.5,-72 921.5,-72 921.5,-72 1052.5,-72 1052.5,-72 1058.5,-72 1064.5,-78 1064.5,-84 1064.5,-84 1064.5,-96 1064.5,-96 1064.5,-102 1058.5,-108 1052.5,-108"/>
+<text text-anchor="middle" x="987" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="987" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
</g>
<!-- 3->11 -->
-<g id="edge29" class="edge">
+<g id="edge31" class="edge">
<title>3->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M924.4578,-143.8314C922.5116,-136.0463 920.1932,-126.7729 918.0337,-118.1347"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M987,-143.8314C987,-136.131 987,-126.9743 987,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="990.5001,-118.4132 987,-108.4133 983.5001,-118.4133 990.5001,-118.4132"/>
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<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M1149.5,-108C1149.5,-108 1018.5,-108 1018.5,-108 1012.5,-108 1006.5,-102 1006.5,-96 1006.5,-96 1006.5,-84 1006.5,-84 1006.5,-78 1012.5,-72 1018.5,-72 1018.5,-72 1149.5,-72 1149.5,-72 1155.5,-72 1161.5,-78 1161.5,-84 1161.5,-84 1161.5,-96 1161.5,-96 1161.5,-102 1155.5,-108 1149.5,-108"/>
-<text text-anchor="middle" x="1084" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1084" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1225.5,-108C1225.5,-108 1094.5,-108 1094.5,-108 1088.5,-108 1082.5,-102 1082.5,-96 1082.5,-96 1082.5,-84 1082.5,-84 1082.5,-78 1088.5,-72 1094.5,-72 1094.5,-72 1225.5,-72 1225.5,-72 1231.5,-72 1237.5,-78 1237.5,-84 1237.5,-84 1237.5,-96 1237.5,-96 1237.5,-102 1231.5,-108 1225.5,-108"/>
+<text text-anchor="middle" x="1160" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1160" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
</g>
<!-- 3->12 -->
-<g id="edge31" class="edge">
+<g id="edge33" class="edge">
<title>3->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M968.113,-143.8314C988.7512,-134.2446 1014.2484,-122.4008 1036.0673,-112.2655"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1037.5734,-115.4251 1045.1682,-108.038 1034.6244,-109.0766 1037.5734,-115.4251"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1030.6552,-143.8314C1053.8958,-134.159 1082.6568,-122.1891 1107.1523,-111.9944"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1108.7712,-115.1117 1116.6587,-108.038 1106.0815,-108.6491 1108.7712,-115.1117"/>
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<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1109.5,-180C1109.5,-180 1022.5,-180 1022.5,-180 1016.5,-180 1010.5,-174 1010.5,-168 1010.5,-168 1010.5,-156 1010.5,-156 1010.5,-150 1016.5,-144 1022.5,-144 1022.5,-144 1109.5,-144 1109.5,-144 1115.5,-144 1121.5,-150 1121.5,-156 1121.5,-156 1121.5,-168 1121.5,-168 1121.5,-174 1115.5,-180 1109.5,-180"/>
-<text text-anchor="middle" x="1066" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M1203.5,-180C1203.5,-180 1116.5,-180 1116.5,-180 1110.5,-180 1104.5,-174 1104.5,-168 1104.5,-168 1104.5,-156 1104.5,-156 1104.5,-150 1110.5,-144 1116.5,-144 1116.5,-144 1203.5,-144 1203.5,-144 1209.5,-144 1215.5,-150 1215.5,-156 1215.5,-156 1215.5,-168 1215.5,-168 1215.5,-174 1209.5,-180 1203.5,-180"/>
+<text text-anchor="middle" x="1160" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
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<!-- 4->0 -->
<g id="edge4" class="edge">
<title>4->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1121.5883,-146.2651C1124.7656,-145.4722 1127.9194,-144.711 1131,-144 1173.7241,-134.1398 1296.9662,-141.7146 1325,-108 1362.7844,-62.559 1261.3527,-35.5901 1203.3308,-24.2747"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1215.6074,-157.444C1279.4185,-150.9274 1378.2197,-136.4495 1401,-108 1411.0007,-95.5105 1411.3541,-84.1981 1401,-72 1382.3059,-49.9765 1192.2107,-29.3705 1110.2636,-21.4368"/>
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<!-- 4->9 -->
-<g id="edge26" class="edge">
+<g id="edge28" class="edge">
<title>4->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1111.9263,-143.8314C1136.5923,-134.0734 1167.1691,-121.977 1193.086,-111.7242"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1201.3841,-143.8314C1223.3182,-134.2018 1250.4392,-122.295 1273.5931,-112.1299"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1275.164,-115.2627 1282.9135,-108.038 1272.35,-108.8532 1275.164,-115.2627"/>
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+<g id="edge32" class="edge">
<title>4->11</title>
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+<g id="edge34" class="edge">
<title>4->12</title>
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<g id="node6" class="node">
<title>5</title>
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-<text text-anchor="middle" x="1223" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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+<text text-anchor="middle" x="648" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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<!-- 5->0 -->
<g id="edge5" class="edge">
<title>5->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M655.3856,-143.7578C664.9136,-122.7498 683.5895,-88.9596 711,-72 764.8472,-38.6833 954.2591,-24.513 1035.5187,-19.8704"/>
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<g id="node7" class="node">
<title>6</title>
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-<text text-anchor="middle" x="1399" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
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+<text text-anchor="middle" x="824" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
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<g id="edge6" class="edge">
<title>6->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M764.8288,-143.88C748.0479,-135.7024 731.715,-124.1357 722,-108 713.7471,-94.2927 711.5819,-84.1434 722,-72 742.3046,-48.3328 949.7311,-28.3477 1035.8409,-21.0061"/>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
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-<text text-anchor="middle" x="1587" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: paired_end</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1674,-108C1674,-108 1586,-108 1586,-108 1580,-108 1574,-102 1574,-96 1574,-96 1574,-84 1574,-84 1574,-78 1580,-72 1586,-72 1586,-72 1674,-72 1674,-72 1680,-72 1686,-78 1686,-84 1686,-84 1686,-96 1686,-96 1686,-102 1680,-108 1674,-108"/>
+<text text-anchor="middle" x="1630" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<text text-anchor="middle" x="1630" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: paired_end</text>
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<!-- 7->0 -->
<g id="edge7" class="edge">
<title>7->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1573.7608,-73.8301C1570.808,-73.168 1567.8748,-72.5521 1565,-72 1397.0468,-39.7453 1192.867,-25.0044 1110.3037,-20.0406"/>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
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-<text text-anchor="middle" x="1773" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
-<text text-anchor="middle" x="1773" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: single_end</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1804,-108C1804,-108 1716,-108 1716,-108 1710,-108 1704,-102 1704,-96 1704,-96 1704,-84 1704,-84 1704,-78 1710,-72 1716,-72 1716,-72 1804,-72 1804,-72 1810,-72 1816,-78 1816,-84 1816,-84 1816,-96 1816,-96 1816,-102 1810,-108 1804,-108"/>
+<text text-anchor="middle" x="1760" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<text text-anchor="middle" x="1760" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: single_end</text>
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<!-- 8->0 -->
<g id="edge8" class="edge">
<title>8->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1703.7757,-73.7502C1700.819,-73.109 1697.8809,-72.5194 1695,-72 1475.7405,-32.4691 1207.5916,-21.6058 1110.4092,-18.8593"/>
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<!-- 9->0 -->
<g id="edge9" class="edge">
<title>9->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1260.9861,-71.9243C1213.2951,-58.244 1149.4414,-39.9274 1109.7811,-28.5508"/>
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<!-- 10->0 -->
<g id="edge10" class="edge">
<title>10->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M882.7671,-71.9243C931.1305,-58.215 995.9194,-39.8496 1036.0346,-28.4784"/>
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<!-- 11->0 -->
<g id="edge11" class="edge">
<title>11->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1008.7014,-71.8314C1019.1921,-63.0485 1031.9455,-52.3712 1043.3194,-42.8489"/>
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<!-- 12->0 -->
<g id="edge12" class="edge">
<title>12->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1104.6921,-71.8314C1114.6948,-63.0485 1126.855,-52.3712 1137.6999,-42.8489"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1138.0462,-71.8314C1127.3305,-62.9632 1114.2811,-52.1637 1102.691,-42.5718"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1104.8822,-39.8422 1094.9467,-36.1628 1100.4192,-45.2349 1104.8822,-39.8422"/>
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<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
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-<text text-anchor="middle" x="1101" y="-306" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M1543.5,-108C1543.5,-108 1460.5,-108 1460.5,-108 1454.5,-108 1448.5,-102 1448.5,-96 1448.5,-96 1448.5,-84 1448.5,-84 1448.5,-78 1454.5,-72 1460.5,-72 1460.5,-72 1543.5,-72 1543.5,-72 1549.5,-72 1555.5,-78 1555.5,-84 1555.5,-84 1555.5,-96 1555.5,-96 1555.5,-102 1549.5,-108 1543.5,-108"/>
+<text text-anchor="middle" x="1502" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_paired_end</text>
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-<!-- 13->3 -->
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<g id="edge13" class="edge">
-<title>13->3</title>
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-<g id="edge17" class="edge">
-<title>13->5</title>
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-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M1569.5,-252C1569.5,-252 1480.5,-252 1480.5,-252 1474.5,-252 1468.5,-246 1468.5,-240 1468.5,-240 1468.5,-228 1468.5,-228 1468.5,-222 1474.5,-216 1480.5,-216 1480.5,-216 1569.5,-216 1569.5,-216 1575.5,-216 1581.5,-222 1581.5,-228 1581.5,-228 1581.5,-240 1581.5,-240 1581.5,-246 1575.5,-252 1569.5,-252"/>
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-<g id="edge40" class="edge">
-<title>13->23</title>
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+<title>13->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1448.308,-75.2021C1443.4857,-74.0506 1438.6643,-72.9631 1434,-72 1317.0102,-47.8429 1176.5727,-29.9825 1110.6523,-22.2439"/>
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<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
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+<path fill="none" stroke="#56d873" stroke-width="2" d="M1929.5,-108C1929.5,-108 1846.5,-108 1846.5,-108 1840.5,-108 1834.5,-102 1834.5,-96 1834.5,-96 1834.5,-84 1834.5,-84 1834.5,-78 1840.5,-72 1846.5,-72 1846.5,-72 1929.5,-72 1929.5,-72 1935.5,-72 1941.5,-78 1941.5,-84 1941.5,-84 1941.5,-96 1941.5,-96 1941.5,-102 1935.5,-108 1929.5,-108"/>
+<text text-anchor="middle" x="1888" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_single_end</text>
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<g id="edge14" class="edge">
-<title>14->3</title>
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-<title>14->4</title>
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+<title>14->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1834.2148,-73.8421C1831.1116,-73.1569 1828.0244,-72.5347 1825,-72 1685.2143,-47.2858 1242.4607,-25.6858 1110.482,-19.6645"/>
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<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M1449,-326.5C1449,-326.5 1353,-326.5 1353,-326.5 1347,-326.5 1341,-320.5 1341,-314.5 1341,-314.5 1341,-302.5 1341,-302.5 1341,-296.5 1347,-290.5 1353,-290.5 1353,-290.5 1449,-290.5 1449,-290.5 1455,-290.5 1461,-296.5 1461,-302.5 1461,-302.5 1461,-314.5 1461,-314.5 1461,-320.5 1455,-326.5 1449,-326.5"/>
-<text text-anchor="middle" x="1401" y="-306" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M918,-326.5C918,-326.5 806,-326.5 806,-326.5 800,-326.5 794,-320.5 794,-314.5 794,-314.5 794,-302.5 794,-302.5 794,-296.5 800,-290.5 806,-290.5 806,-290.5 918,-290.5 918,-290.5 924,-290.5 930,-296.5 930,-302.5 930,-302.5 930,-314.5 930,-314.5 930,-320.5 924,-326.5 918,-326.5"/>
+<text text-anchor="middle" x="862" y="-306" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
</g>
-<!-- 15->4 -->
+<!-- 15->3 -->
<g id="edge15" class="edge">
-<title>15->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1340.9243,-291.6426C1285.695,-276.0737 1211.4147,-254.9235 1205,-252 1165.8152,-234.1413 1124.8978,-206.3691 1097.6905,-186.3986"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1099.4735,-183.3631 1089.3583,-180.2112 1095.3002,-188.9831 1099.4735,-183.3631"/>
+<title>15->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M877.5786,-290.2419C899.5931,-264.4409 939.9104,-217.189 964.9793,-187.8083"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="967.7895,-189.907 971.6177,-180.028 962.4644,-185.3634 967.7895,-189.907"/>
</g>
-<!-- 15->6 -->
+<!-- 15->5 -->
<g id="edge19" class="edge">
-<title>15->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1400.7507,-290.2419C1400.4075,-265.1025 1399.7863,-219.5981 1399.3837,-190.1029"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1402.8824,-189.9793 1399.2461,-180.028 1395.883,-190.0749 1402.8824,-189.9793"/>
+<title>15->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M825.7098,-290.3394C805.8181,-279.9088 781.007,-266.1075 760,-252 729.9375,-231.8113 697.9539,-205.5778 675.8955,-186.6474"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="678.0935,-183.921 668.2397,-180.0282 673.5152,-189.2163 678.0935,-183.921"/>
</g>
-<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M1684.5,-252C1684.5,-252 1611.5,-252 1611.5,-252 1605.5,-252 1599.5,-246 1599.5,-240 1599.5,-240 1599.5,-228 1599.5,-228 1599.5,-222 1605.5,-216 1611.5,-216 1611.5,-216 1684.5,-216 1684.5,-216 1690.5,-216 1696.5,-222 1696.5,-228 1696.5,-228 1696.5,-240 1696.5,-240 1696.5,-246 1690.5,-252 1684.5,-252"/>
-<text text-anchor="middle" x="1648" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1455.5,-252C1455.5,-252 1366.5,-252 1366.5,-252 1360.5,-252 1354.5,-246 1354.5,-240 1354.5,-240 1354.5,-228 1354.5,-228 1354.5,-222 1360.5,-216 1366.5,-216 1366.5,-216 1455.5,-216 1455.5,-216 1461.5,-216 1467.5,-222 1467.5,-228 1467.5,-228 1467.5,-240 1467.5,-240 1467.5,-246 1461.5,-252 1455.5,-252"/>
+<text text-anchor="middle" x="1411" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
</g>
-<!-- 15->24 -->
-<g id="edge42" class="edge">
-<title>15->24</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1461.4049,-290.8195C1496.4471,-280.4971 1541.6598,-267.068 1589.5811,-252.4162"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.6628,-255.7455 1599.1992,-249.4702 1588.6126,-249.0524 1590.6628,-255.7455"/>
+<!-- 15->22 -->
+<g id="edge46" class="edge">
+<title>15->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M930.3123,-290.7169C934.9305,-289.7326 939.5245,-288.8146 944,-288 1085.2977,-262.2809 1252.997,-246.4049 1344.041,-238.9922"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1344.5331,-242.464 1354.22,-238.1727 1343.9713,-235.4865 1344.5331,-242.464"/>
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<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M1310,-252C1310,-252 1226,-252 1226,-252 1220,-252 1214,-246 1214,-240 1214,-240 1214,-228 1214,-228 1214,-222 1220,-216 1226,-216 1226,-216 1310,-216 1310,-216 1316,-216 1322,-222 1322,-228 1322,-228 1322,-240 1322,-240 1322,-246 1316,-252 1310,-252"/>
-<text text-anchor="middle" x="1268" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M1068.5,-252C1068.5,-252 983.5,-252 983.5,-252 977.5,-252 971.5,-246 971.5,-240 971.5,-240 971.5,-228 971.5,-228 971.5,-222 977.5,-216 983.5,-216 983.5,-216 1068.5,-216 1068.5,-216 1074.5,-216 1080.5,-222 1080.5,-228 1080.5,-228 1080.5,-240 1080.5,-240 1080.5,-246 1074.5,-252 1068.5,-252"/>
+<text text-anchor="middle" x="1026" y="-237" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
+<text text-anchor="middle" x="1026" y="-226" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
</g>
-<!-- 16->5 -->
-<g id="edge18" class="edge">
-<title>16->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1256.6446,-215.8314C1251.5674,-207.7079 1245.4773,-197.9637 1239.8824,-189.0118"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1242.7763,-187.0383 1234.5083,-180.4133 1236.8403,-190.7483 1242.7763,-187.0383"/>
+<!-- 16->3 -->
+<g id="edge16" class="edge">
+<title>16->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1016.1587,-215.8314C1011.8043,-207.7925 1006.5902,-198.1666 1001.7831,-189.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1004.8143,-187.5392 996.9739,-180.4133 998.6592,-190.8732 1004.8143,-187.5392"/>
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-<!-- 16->6 -->
-<g id="edge20" class="edge">
-<title>16->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1301.0568,-215.8314C1317.9677,-206.5368 1338.7385,-195.1208 1356.7941,-185.1971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1358.876,-188.0468 1365.9537,-180.1628 1355.5043,-181.9122 1358.876,-188.0468"/>
+<!-- 16->4 -->
+<g id="edge18" class="edge">
+<title>16->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1059.8139,-215.8314C1077.2707,-206.4516 1098.7487,-194.9112 1117.3352,-184.9244"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1119.0446,-187.9792 1126.197,-180.1628 1115.7314,-181.8129 1119.0446,-187.9792"/>
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<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1670,-180C1670,-180 1504,-180 1504,-180 1498,-180 1492,-174 1492,-168 1492,-168 1492,-156 1492,-156 1492,-150 1498,-144 1504,-144 1504,-144 1670,-144 1670,-144 1676,-144 1682,-150 1682,-156 1682,-156 1682,-168 1682,-168 1682,-174 1676,-180 1670,-180"/>
-<text text-anchor="middle" x="1587" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1210,-326.5C1210,-326.5 1114,-326.5 1114,-326.5 1108,-326.5 1102,-320.5 1102,-314.5 1102,-314.5 1102,-302.5 1102,-302.5 1102,-296.5 1108,-290.5 1114,-290.5 1114,-290.5 1210,-290.5 1210,-290.5 1216,-290.5 1222,-296.5 1222,-302.5 1222,-302.5 1222,-314.5 1222,-314.5 1222,-320.5 1216,-326.5 1210,-326.5"/>
+<text text-anchor="middle" x="1162" y="-306" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
-<!-- 17->7 -->
+<!-- 17->4 -->
+<g id="edge17" class="edge">
+<title>17->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1161.7507,-290.2419C1161.4075,-265.1025 1160.7863,-219.5981 1160.3837,-190.1029"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1163.8824,-189.9793 1160.2461,-180.028 1156.883,-190.0749 1163.8824,-189.9793"/>
+</g>
+<!-- 17->6 -->
<g id="edge21" class="edge">
-<title>17->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1587,-143.8314C1587,-136.131 1587,-126.9743 1587,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.5001,-118.4132 1587,-108.4133 1583.5001,-118.4133 1590.5001,-118.4132"/>
+<title>17->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1101.7546,-291.9557C1045.2913,-276.3765 968.5797,-254.9907 962,-252 922.9956,-234.2714 882.3898,-206.4771 855.4101,-186.4657"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="857.2474,-183.4685 847.1486,-180.2647 853.0452,-189.0669 857.2474,-183.4685"/>
+</g>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1752.5,-252C1752.5,-252 1679.5,-252 1679.5,-252 1673.5,-252 1667.5,-246 1667.5,-240 1667.5,-240 1667.5,-228 1667.5,-228 1667.5,-222 1673.5,-216 1679.5,-216 1679.5,-216 1752.5,-216 1752.5,-216 1758.5,-216 1764.5,-222 1764.5,-228 1764.5,-228 1764.5,-240 1764.5,-240 1764.5,-246 1758.5,-252 1752.5,-252"/>
+<text text-anchor="middle" x="1716" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+</g>
+<!-- 17->23 -->
+<g id="edge48" class="edge">
+<title>17->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1222.078,-300.4209C1329.0221,-286.0395 1551.1122,-256.1735 1657.1603,-241.9126"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1657.9155,-245.3426 1667.3598,-240.541 1656.9825,-238.405 1657.9155,-245.3426"/>
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<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1833.5,-180C1833.5,-180 1712.5,-180 1712.5,-180 1706.5,-180 1700.5,-174 1700.5,-168 1700.5,-168 1700.5,-156 1700.5,-156 1700.5,-150 1706.5,-144 1712.5,-144 1712.5,-144 1833.5,-144 1833.5,-144 1839.5,-144 1845.5,-150 1845.5,-156 1845.5,-156 1845.5,-168 1845.5,-168 1845.5,-174 1839.5,-180 1833.5,-180"/>
-<text text-anchor="middle" x="1773" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M865,-252C865,-252 781,-252 781,-252 775,-252 769,-246 769,-240 769,-240 769,-228 769,-228 769,-222 775,-216 781,-216 781,-216 865,-216 865,-216 871,-216 877,-222 877,-228 877,-228 877,-240 877,-240 877,-246 871,-252 865,-252"/>
+<text text-anchor="middle" x="823" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
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-<!-- 18->7 -->
-<g id="edge22" class="edge">
-<title>18->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1726.0643,-143.8314C1700.8563,-134.0734 1669.6074,-121.977 1643.1209,-111.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1644.1873,-108.384 1633.5981,-108.038 1641.6603,-114.912 1644.1873,-108.384"/>
+<!-- 18->5 -->
+<g id="edge20" class="edge">
+<title>18->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M778.8401,-215.8314C755.2268,-206.1162 725.9798,-194.0831 701.13,-183.8592"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="702.4219,-180.6061 691.8423,-180.038 699.7585,-187.0797 702.4219,-180.6061"/>
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-<!-- 18->8 -->
-<g id="edge24" class="edge">
-<title>18->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1773,-143.8314C1773,-136.131 1773,-126.9743 1773,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1776.5001,-118.4132 1773,-108.4133 1769.5001,-118.4133 1776.5001,-118.4132"/>
+<!-- 18->6 -->
+<g id="edge22" class="edge">
+<title>18->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M823.2523,-215.8314C823.3593,-208.131 823.4865,-198.9743 823.6053,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="827.1049,-190.4609 823.7443,-180.4133 820.1056,-190.3637 827.1049,-190.4609"/>
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<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M2026,-180C2026,-180 1876,-180 1876,-180 1870,-180 1864,-174 1864,-168 1864,-168 1864,-156 1864,-156 1864,-150 1870,-144 1876,-144 1876,-144 2026,-144 2026,-144 2032,-144 2038,-150 2038,-156 2038,-156 2038,-168 2038,-168 2038,-174 2032,-180 2026,-180"/>
-<text text-anchor="middle" x="1951" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1556,-180C1556,-180 1390,-180 1390,-180 1384,-180 1378,-174 1378,-168 1378,-168 1378,-156 1378,-156 1378,-150 1384,-144 1390,-144 1390,-144 1556,-144 1556,-144 1562,-144 1568,-150 1568,-156 1568,-156 1568,-168 1568,-168 1568,-174 1562,-180 1556,-180"/>
+<text text-anchor="middle" x="1473" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
</g>
-<!-- 19->8 -->
+<!-- 19->7 -->
<g id="edge23" class="edge">
-<title>19->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1906.0831,-143.8314C1882.065,-134.1162 1852.3166,-122.0831 1827.0408,-111.8592"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1828.1767,-108.5432 1817.5939,-108.038 1825.5518,-115.0325 1828.1767,-108.5432"/>
+<title>19->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1512.6177,-143.8314C1533.5222,-134.2446 1559.3483,-122.4008 1581.4488,-112.2655"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1583.0364,-115.388 1590.6672,-108.038 1580.1184,-109.0252 1583.0364,-115.388"/>
+</g>
+<!-- 19->13 -->
+<g id="edge36" class="edge">
+<title>19->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1480.3179,-143.8314C1483.4876,-135.9617 1487.27,-126.5712 1490.7813,-117.8533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1494.0939,-118.9968 1494.5835,-108.4133 1487.6008,-116.3815 1494.0939,-118.9968"/>
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<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
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-<text text-anchor="middle" x="1088" y="-386" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1088" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1719.5,-180C1719.5,-180 1598.5,-180 1598.5,-180 1592.5,-180 1586.5,-174 1586.5,-168 1586.5,-168 1586.5,-156 1586.5,-156 1586.5,-150 1592.5,-144 1598.5,-144 1598.5,-144 1719.5,-144 1719.5,-144 1725.5,-144 1731.5,-150 1731.5,-156 1731.5,-156 1731.5,-168 1731.5,-168 1731.5,-174 1725.5,-180 1719.5,-180"/>
+<text text-anchor="middle" x="1659" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
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-<g id="edge33" class="edge">
-<title>20->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1091.1469,-364.9656C1092.6369,-356.427 1094.4506,-346.0333 1096.1138,-336.502"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1099.5658,-337.0793 1097.837,-326.6265 1092.67,-335.876 1099.5658,-337.0793"/>
+<!-- 20->7 -->
+<g id="edge24" class="edge">
+<title>20->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1651.6821,-143.8314C1648.5124,-135.9617 1644.73,-126.5712 1641.2187,-117.8533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1644.3992,-116.3815 1637.4165,-108.4133 1637.9061,-118.9968 1644.3992,-116.3815"/>
+</g>
+<!-- 20->8 -->
+<g id="edge26" class="edge">
+<title>20->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1684.4866,-143.8314C1697.1659,-134.7927 1712.6596,-123.7476 1726.3055,-114.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1728.4105,-116.8176 1734.5216,-108.1628 1724.3471,-111.1176 1728.4105,-116.8176"/>
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<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M1306.5,-326.5C1306.5,-326.5 1205.5,-326.5 1205.5,-326.5 1199.5,-326.5 1193.5,-320.5 1193.5,-314.5 1193.5,-314.5 1193.5,-302.5 1193.5,-302.5 1193.5,-296.5 1199.5,-290.5 1205.5,-290.5 1205.5,-290.5 1306.5,-290.5 1306.5,-290.5 1312.5,-290.5 1318.5,-296.5 1318.5,-302.5 1318.5,-302.5 1318.5,-314.5 1318.5,-314.5 1318.5,-320.5 1312.5,-326.5 1306.5,-326.5"/>
-<text text-anchor="middle" x="1256" y="-311.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
-<text text-anchor="middle" x="1256" y="-300.5" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1912,-180C1912,-180 1762,-180 1762,-180 1756,-180 1750,-174 1750,-168 1750,-168 1750,-156 1750,-156 1750,-150 1756,-144 1762,-144 1762,-144 1912,-144 1912,-144 1918,-144 1924,-150 1924,-156 1924,-156 1924,-168 1924,-168 1924,-174 1918,-180 1912,-180"/>
+<text text-anchor="middle" x="1837" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+</g>
+<!-- 21->8 -->
+<g id="edge25" class="edge">
+<title>21->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1817.5696,-143.8314C1808.268,-135.1337 1796.9796,-124.5783 1786.8714,-115.1265"/>
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</g>
<!-- 21->14 -->
-<g id="edge34" class="edge">
+<g id="edge38" class="edge">
<title>21->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1209.7642,-290.4656C1182.9826,-280.0194 1149.0828,-266.7967 1120.8216,-255.7734"/>
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-</g>
-<!-- 21->16 -->
-<g id="edge36" class="edge">
-<title>21->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1258.9049,-290.4656C1260.2802,-281.927 1261.9544,-271.5333 1263.4896,-262.002"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1849.8695,-143.8314C1855.6835,-135.6232 1862.6696,-125.7606 1869.0646,-116.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1872.0331,-118.5966 1874.9573,-108.4133 1866.321,-114.5505 1872.0331,-118.5966"/>
</g>
-<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1544,-401C1544,-401 1264,-401 1264,-401 1258,-401 1252,-395 1252,-389 1252,-389 1252,-377 1252,-377 1252,-371 1258,-365 1264,-365 1264,-365 1544,-365 1544,-365 1550,-365 1556,-371 1556,-377 1556,-377 1556,-389 1556,-389 1556,-395 1550,-401 1544,-401"/>
-<text text-anchor="middle" x="1404" y="-386" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1404" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
-</g>
-<!-- 22->15 -->
+<!-- 22->13 -->
<g id="edge35" class="edge">
-<title>22->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1403.2738,-364.9656C1402.9336,-356.5178 1402.5203,-346.2542 1402.1399,-336.8064"/>
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+<title>22->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1391.8604,-215.8802C1374.3626,-197.0568 1353.3998,-167.1709 1369,-144 1377.5714,-131.269 1408.6828,-118.2882 1438.6606,-108.2451"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1439.903,-111.5213 1448.3238,-105.0916 1437.7313,-104.8667 1439.903,-111.5213"/>
</g>
-<!-- 23->17 -->
+<!-- 22->19 -->
+<g id="edge43" class="edge">
+<title>22->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1426.6452,-215.8314C1433.8591,-207.454 1442.557,-197.3531 1450.4605,-188.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1453.2711,-190.2748 1457.1441,-180.4133 1447.9667,-185.7071 1453.2711,-190.2748"/>
+</g>
+<!-- 23->14 -->
<g id="edge37" class="edge">
-<title>23->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1540.6452,-215.8314C1547.8591,-207.454 1556.557,-197.3531 1564.4605,-188.1749"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1567.2711,-190.2748 1571.1441,-180.4133 1561.9667,-185.7071 1567.2711,-190.2748"/>
+<title>23->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1764.6187,-228.8067C1822.0772,-221.5499 1912.4985,-206.2285 1933,-180 1948.4125,-160.2821 1932.4822,-134.4478 1915.4622,-115.5178"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1917.8661,-112.9664 1908.4443,-108.1207 1912.7879,-117.7842 1917.8661,-112.9664"/>
</g>
-<!-- 24->19 -->
-<g id="edge38" class="edge">
-<title>24->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1696.6822,-222.432C1742.0379,-211.6543 1810.6724,-195.3452 1865.2132,-182.385"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1866.3044,-185.7232 1875.2243,-180.0061 1864.6861,-178.9129 1866.3044,-185.7232"/>
+<!-- 23->21 -->
+<g id="edge44" class="edge">
+<title>23->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1746.5334,-215.8314C1762.0101,-206.6221 1780.9869,-195.3301 1797.5563,-185.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1799.6724,-188.2843 1806.4764,-180.1628 1796.0929,-182.2687 1799.6724,-188.2843"/>
+</g>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M983,-401C983,-401 715,-401 715,-401 709,-401 703,-395 703,-389 703,-389 703,-377 703,-377 703,-371 709,-365 715,-365 715,-365 983,-365 983,-365 989,-365 995,-371 995,-377 995,-377 995,-389 995,-389 995,-395 989,-401 983,-401"/>
+<text text-anchor="middle" x="849" y="-386" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="849" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 24->15 -->
+<g id="edge39" class="edge">
+<title>24->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M852.1469,-364.9656C853.6369,-356.427 855.4506,-346.0333 857.1138,-336.502"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="860.5658,-337.0793 858.837,-326.6265 853.67,-335.876 860.5658,-337.0793"/>
</g>
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<g id="node26" class="node">
<title>25</title>
-<path fill="none" stroke="#8fd856" stroke-width="2" d="M1615.5,-329C1615.5,-329 1514.5,-329 1514.5,-329 1508.5,-329 1502.5,-323 1502.5,-317 1502.5,-317 1502.5,-300 1502.5,-300 1502.5,-294 1508.5,-288 1514.5,-288 1514.5,-288 1615.5,-288 1615.5,-288 1621.5,-288 1627.5,-294 1627.5,-300 1627.5,-300 1627.5,-317 1627.5,-317 1627.5,-323 1621.5,-329 1615.5,-329"/>
-<text text-anchor="middle" x="1565" y="-317" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
-<text text-anchor="middle" x="1565" y="-306" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
-<text text-anchor="middle" x="1565" y="-295" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1066.5,-326.5C1066.5,-326.5 965.5,-326.5 965.5,-326.5 959.5,-326.5 953.5,-320.5 953.5,-314.5 953.5,-314.5 953.5,-302.5 953.5,-302.5 953.5,-296.5 959.5,-290.5 965.5,-290.5 965.5,-290.5 1066.5,-290.5 1066.5,-290.5 1072.5,-290.5 1078.5,-296.5 1078.5,-302.5 1078.5,-302.5 1078.5,-314.5 1078.5,-314.5 1078.5,-320.5 1072.5,-326.5 1066.5,-326.5"/>
+<text text-anchor="middle" x="1016" y="-311.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<text text-anchor="middle" x="1016" y="-300.5" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
</g>
-<!-- 25->23 -->
-<g id="edge39" class="edge">
-<title>25->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1553.8578,-287.7476C1549.397,-279.4394 1544.1995,-269.7591 1539.4543,-260.9211"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1542.5369,-259.2634 1534.7228,-252.1087 1536.3696,-262.5747 1542.5369,-259.2634"/>
+<!-- 25->16 -->
+<g id="edge40" class="edge">
+<title>25->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1018.4207,-290.4656C1019.5547,-282.0178 1020.9323,-271.7542 1022.2005,-262.3064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1025.7054,-262.5033 1023.5669,-252.1265 1018.7676,-261.572 1025.7054,-262.5033"/>
</g>
-<!-- 25->24 -->
+<!-- 25->18 -->
+<g id="edge42" class="edge">
+<title>25->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M969.2801,-290.4656C942.218,-280.0194 907.9633,-266.7967 879.4062,-255.7734"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="880.5481,-252.4625 869.9586,-252.1265 878.0273,-258.9929 880.5481,-252.4625"/>
+</g>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M1305,-401C1305,-401 1025,-401 1025,-401 1019,-401 1013,-395 1013,-389 1013,-389 1013,-377 1013,-377 1013,-371 1019,-365 1025,-365 1025,-365 1305,-365 1305,-365 1311,-365 1317,-371 1317,-377 1317,-377 1317,-389 1317,-389 1317,-395 1311,-401 1305,-401"/>
+<text text-anchor="middle" x="1165" y="-386" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1165" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+</g>
+<!-- 26->17 -->
<g id="edge41" class="edge">
-<title>25->24</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1588.1201,-287.7476C1598.0583,-278.8272 1609.7587,-268.3251 1620.1677,-258.982"/>
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+<title>26->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1164.2738,-364.9656C1163.9336,-356.5178 1163.5203,-346.2542 1163.1399,-336.8064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1166.6295,-336.4776 1162.7299,-326.6265 1159.6352,-336.7593 1166.6295,-336.4776"/>
+</g>
+<!-- 27 -->
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M1613.5,-329C1613.5,-329 1512.5,-329 1512.5,-329 1506.5,-329 1500.5,-323 1500.5,-317 1500.5,-317 1500.5,-300 1500.5,-300 1500.5,-294 1506.5,-288 1512.5,-288 1512.5,-288 1613.5,-288 1613.5,-288 1619.5,-288 1625.5,-294 1625.5,-300 1625.5,-300 1625.5,-317 1625.5,-317 1625.5,-323 1619.5,-329 1613.5,-329"/>
+<text text-anchor="middle" x="1563" y="-317" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<text text-anchor="middle" x="1563" y="-306" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
+<text text-anchor="middle" x="1563" y="-295" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+</g>
+<!-- 27->22 -->
+<g id="edge45" class="edge">
+<title>27->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1521.063,-287.9453C1501.1741,-278.1972 1477.3611,-266.5256 1456.98,-256.5362"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1458.4035,-253.3362 1447.8836,-252.0778 1455.3227,-259.6218 1458.4035,-253.3362"/>
+</g>
+<!-- 27->23 -->
+<g id="edge47" class="edge">
+<title>27->23</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1605.2129,-287.9453C1625.2327,-278.1972 1649.2024,-266.5256 1669.7175,-256.5362"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1671.4152,-259.6025 1678.8737,-252.0778 1668.3507,-253.309 1671.4152,-259.6025"/>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 05617e7f160d0153366fcebea2ce39d454716a5e..9ba29ef63af3646654959d2305a4f8db3cfc8a20 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -4,352 +4,400 @@
<!-- Generated by graphviz version 2.40.1 (20161225.0304)
-->
<!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 1180.00 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1235pt" height="404pt"
+ viewBox="0.00 0.00 1234.93 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 400)">
<title>snakemake_dag</title>
-<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-400 1176,-400 1176,4 -4,4"/>
+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-400 1230.93,-400 1230.93,4 -4,4"/>
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<g id="node1" class="node">
<title>0</title>
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-<text text-anchor="middle" x="297" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M416,-36C416,-36 386,-36 386,-36 380,-36 374,-30 374,-24 374,-24 374,-12 374,-12 374,-6 380,0 386,0 386,0 416,0 416,0 422,0 428,-6 428,-12 428,-12 428,-24 428,-24 428,-30 422,-36 416,-36"/>
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<g id="node2" class="node">
<title>1</title>
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-<text text-anchor="middle" x="91" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M106.5,-108C106.5,-108 71.5,-108 71.5,-108 65.5,-108 59.5,-102 59.5,-96 59.5,-96 59.5,-84 59.5,-84 59.5,-78 65.5,-72 71.5,-72 71.5,-72 106.5,-72 106.5,-72 112.5,-72 118.5,-78 118.5,-84 118.5,-84 118.5,-96 118.5,-96 118.5,-102 112.5,-108 106.5,-108"/>
+<text text-anchor="middle" x="89" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
</g>
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+<g id="edge8" class="edge">
<title>1->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M120.6523,-75.8697C123.7863,-74.51 126.9439,-73.1944 130,-72 173.8524,-54.8612 225.6071,-38.7391 259.7492,-28.6502"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M118.5189,-75.4965C121.6789,-74.2094 124.8791,-73.013 128,-72 210.0713,-45.362 310.4979,-29.6097 363.726,-22.5192"/>
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<g id="node3" class="node">
<title>2</title>
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-<text text-anchor="middle" x="166" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M179,-108C179,-108 149,-108 149,-108 143,-108 137,-102 137,-96 137,-96 137,-84 137,-84 137,-78 143,-72 149,-72 149,-72 179,-72 179,-72 185,-72 191,-78 191,-84 191,-84 191,-96 191,-96 191,-102 185,-108 179,-108"/>
+<text text-anchor="middle" x="164" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
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-<g id="edge8" class="edge">
+<g id="edge3" class="edge">
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-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M193.1433,-75.0816C212.8158,-64.2692 239.6157,-49.5395 261.0636,-37.7513"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M191.1255,-77.435C195.7115,-75.5006 200.4582,-73.6131 205,-72 259.4623,-52.6571 324.4424,-35.9659 364.203,-26.4479"/>
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-<text text-anchor="middle" x="416" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
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+<text text-anchor="middle" x="545" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
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<g id="node9" class="node">
<title>8</title>
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-<text text-anchor="middle" x="393" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
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+<text text-anchor="middle" x="565" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
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<!-- 9 -->
<g id="node10" class="node">
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-<text text-anchor="middle" x="557" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
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+<text text-anchor="middle" x="401" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
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+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="447.5855,-109.3797 437.076,-108.038 444.455,-115.6407 447.5855,-109.3797"/>
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<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
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-<text text-anchor="middle" x="553" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
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<title>4->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M355.3375,-143.9237C339.1801,-135.618 323.2394,-123.9631 314,-108 305.985,-94.1523 306.222,-85.9822 314,-72 324.7443,-52.6853 345.5726,-39.3947 364.1559,-30.8325"/>
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<!-- 4->8 -->
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+<g id="edge24" class="edge">
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+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="518.0364,-115.388 525.6672,-108.038 515.1184,-109.0252 518.0364,-115.388"/>
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<!-- 4->9 -->
-<g id="edge24" class="edge">
+<g id="edge26" class="edge">
<title>4->9</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M406.2336,-143.8314C405.485,-136.131 404.5947,-126.9743 403.7627,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="407.2415,-118.0276 402.7902,-108.4133 400.2744,-118.7051 407.2415,-118.0276"/>
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<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
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-<text text-anchor="middle" x="83" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M322,-180C322,-180 180,-180 180,-180 174,-180 168,-174 168,-168 168,-168 168,-156 168,-156 168,-150 174,-144 180,-144 180,-144 322,-144 322,-144 328,-144 334,-150 334,-156 334,-156 334,-168 334,-168 334,-174 328,-180 322,-180"/>
+<text text-anchor="middle" x="251" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
</g>
<!-- 5->0 -->
-<g id="edge4" class="edge">
+<g id="edge2" class="edge">
<title>5->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M132.4149,-143.9133C154.5952,-134.7238 180.5404,-122.4364 202,-108 229.3371,-89.6096 256.1879,-63.1737 274.3309,-43.709"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M258.4479,-143.9136C267.2426,-124.2889 283.4444,-92.9597 305,-72 322.0837,-55.3886 345.2816,-42.1543 364.5938,-32.9452"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="366.0943,-36.1076 373.7184,-28.7506 363.1705,-29.7474 366.0943,-36.1076"/>
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<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
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-<text text-anchor="middle" x="259" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M138,-180C138,-180 12,-180 12,-180 6,-180 0,-174 0,-168 0,-168 0,-156 0,-156 0,-150 6,-144 12,-144 12,-144 138,-144 138,-144 144,-144 150,-150 150,-156 150,-156 150,-168 150,-168 150,-174 144,-180 138,-180"/>
+<text text-anchor="middle" x="75" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
</g>
<!-- 6->0 -->
-<g id="edge7" class="edge">
+<g id="edge4" class="edge">
<title>6->0</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="293.0589,-46.6517 292.2264,-36.0896 286.2906,-44.8656 293.0589,-46.6517"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M117.9968,-143.9241C142.1918,-133.6278 172.8963,-120.3534 200,-108 233.6446,-92.6654 241.3332,-87.2859 275,-72 304.844,-58.4497 339.043,-43.8507 364.2744,-33.2528"/>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
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-<text text-anchor="middle" x="816" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M942,-108C942,-108 854,-108 854,-108 848,-108 842,-102 842,-96 842,-96 842,-84 842,-84 842,-78 848,-72 854,-72 854,-72 942,-72 942,-72 948,-72 954,-78 954,-84 954,-84 954,-96 954,-96 954,-102 948,-108 942,-108"/>
+<text text-anchor="middle" x="898" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
</g>
<!-- 7->0 -->
-<g id="edge2" class="edge">
+<g id="edge10" class="edge">
<title>7->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M759.9648,-82.2263C653.3136,-67.4308 423.786,-35.5888 334.0397,-23.1385"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M841.6588,-78.4156C829.8991,-76.1554 817.5629,-73.9002 806,-72 671.1794,-49.8439 509.9668,-30.4589 438.3975,-22.2175"/>
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<!-- 8->0 -->
-<g id="edge5" class="edge">
+<g id="edge1" class="edge">
<title>8->0</title>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M523.6159,-71.8314C497.1957,-60.2323 463.2497,-45.3291 437.7762,-34.1457"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="439.0249,-30.8715 428.4615,-30.0563 436.2109,-37.281 439.0249,-30.8715"/>
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<!-- 9->0 -->
-<g id="edge6" class="edge">
+<g id="edge5" class="edge">
<title>9->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M491.7266,-71.9243C441.9434,-58.1382 375.1578,-39.6437 334.1509,-28.2879"/>
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+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="404.5001,-46.4132 401,-36.4133 397.5001,-46.4133 404.5001,-46.4132"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
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-<text text-anchor="middle" x="293" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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-<title>10->3</title>
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-<g id="edge14" class="edge">
-<title>10->5</title>
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+<text text-anchor="middle" x="1116" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_paired_end</text>
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-<g id="node21" class="node">
-<title>20</title>
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-<g id="edge31" class="edge">
-<title>10->20</title>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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-<g id="edge11" class="edge">
-<title>11->3</title>
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-<g id="edge12" class="edge">
-<title>11->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M480.4772,-215.8314C492.5395,-206.8779 507.254,-195.9558 520.2686,-186.2955"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="522.587,-188.9335 528.5306,-180.1628 518.4148,-183.3127 522.587,-188.9335"/>
+<!-- 11->0 -->
+<g id="edge6" class="edge">
+<title>11->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M689.2575,-75.4333C684.446,-74.2324 679.6409,-73.0704 675,-72 590.8464,-52.5906 491.1471,-34.0478 438.2775,-24.5626"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="438.8061,-21.1017 428.3464,-22.7887 437.5752,-27.9926 438.8061,-21.1017"/>
</g>
<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
-<path fill="none" stroke="#56d863" stroke-width="2" d="M617,-324C617,-324 521,-324 521,-324 515,-324 509,-318 509,-312 509,-312 509,-300 509,-300 509,-294 515,-288 521,-288 521,-288 617,-288 617,-288 623,-288 629,-294 629,-300 629,-300 629,-312 629,-312 629,-318 623,-324 617,-324"/>
-<text text-anchor="middle" x="569" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M602,-324C602,-324 490,-324 490,-324 484,-324 478,-318 478,-312 478,-312 478,-300 478,-300 478,-294 484,-288 490,-288 490,-288 602,-288 602,-288 608,-288 614,-294 614,-300 614,-300 614,-312 614,-312 614,-318 608,-324 602,-324"/>
+<text text-anchor="middle" x="546" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
</g>
-<!-- 12->4 -->
+<!-- 12->3 -->
<g id="edge13" class="edge">
-<title>12->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M566.9736,-287.7623C564.2446,-263.201 559.3608,-219.2474 556.1505,-190.3541"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="559.593,-189.6419 555.01,-180.0896 552.6358,-190.415 559.593,-189.6419"/>
+<title>12->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M545.8733,-287.7623C545.7028,-263.201 545.3976,-219.2474 545.1969,-190.3541"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="548.6951,-190.065 545.1256,-180.0896 541.6952,-190.1137 548.6951,-190.065"/>
</g>
-<!-- 12->6 -->
+<!-- 12->5 -->
<g id="edge17" class="edge">
-<title>12->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M508.9935,-289.7599C466.2685,-277.8079 412.8739,-261.968 392,-252 354.315,-234.0041 315.1964,-206.2553 289.2236,-186.3277"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="291.3169,-183.5219 281.2713,-180.1548 287.0246,-189.0515 291.3169,-183.5219"/>
+<title>12->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M489.0978,-287.9875C461.3893,-278.493 427.8994,-265.9316 399,-252 358.6163,-232.5322 315.0772,-205.2176 285.7526,-185.797"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="287.3881,-182.6806 277.1274,-180.0408 283.5023,-188.5031 287.3881,-182.6806"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M895.5,-252C895.5,-252 822.5,-252 822.5,-252 816.5,-252 810.5,-246 810.5,-240 810.5,-240 810.5,-228 810.5,-228 810.5,-222 816.5,-216 822.5,-216 822.5,-216 895.5,-216 895.5,-216 901.5,-216 907.5,-222 907.5,-228 907.5,-228 907.5,-240 907.5,-240 907.5,-246 901.5,-252 895.5,-252"/>
-<text text-anchor="middle" x="859" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1039.5,-252C1039.5,-252 950.5,-252 950.5,-252 944.5,-252 938.5,-246 938.5,-240 938.5,-240 938.5,-228 938.5,-228 938.5,-222 944.5,-216 950.5,-216 950.5,-216 1039.5,-216 1039.5,-216 1045.5,-216 1051.5,-222 1051.5,-228 1051.5,-228 1051.5,-240 1051.5,-240 1051.5,-246 1045.5,-252 1039.5,-252"/>
+<text text-anchor="middle" x="995" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
</g>
-<!-- 12->21 -->
-<g id="edge34" class="edge">
-<title>12->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M629.1827,-293.4061C674.1156,-283.6937 737.1966,-269.4079 800.5071,-252.3215"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="801.5267,-255.6714 810.2566,-249.6682 799.6884,-248.917 801.5267,-255.6714"/>
+<!-- 12->19 -->
+<g id="edge37" class="edge">
+<title>12->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M614.1934,-295.0647C699.2963,-281.418 843.8898,-258.2315 928.293,-244.6969"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="928.96,-248.1347 938.2796,-243.0955 927.8516,-241.223 928.96,-248.1347"/>
</g>
<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M295,-252C295,-252 211,-252 211,-252 205,-252 199,-246 199,-240 199,-240 199,-228 199,-228 199,-222 205,-216 211,-216 211,-216 295,-216 295,-216 301,-216 307,-222 307,-228 307,-228 307,-240 307,-240 307,-246 301,-252 295,-252"/>
-<text text-anchor="middle" x="253" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<path fill="none" stroke="#d89556" stroke-width="2" d="M505.5,-252C505.5,-252 420.5,-252 420.5,-252 414.5,-252 408.5,-246 408.5,-240 408.5,-240 408.5,-228 408.5,-228 408.5,-222 414.5,-216 420.5,-216 420.5,-216 505.5,-216 505.5,-216 511.5,-216 517.5,-222 517.5,-228 517.5,-228 517.5,-240 517.5,-240 517.5,-246 511.5,-252 505.5,-252"/>
+<text text-anchor="middle" x="463" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
</g>
-<!-- 13->5 -->
-<g id="edge15" class="edge">
-<title>13->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M210.1018,-215.8314C187.2643,-206.159 159.002,-194.1891 134.9313,-183.9944"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="136.1629,-180.7151 125.5897,-180.038 133.4329,-187.1608 136.1629,-180.7151"/>
+<!-- 13->3 -->
+<g id="edge12" class="edge">
+<title>13->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M483.6921,-215.8314C493.6948,-207.0485 505.855,-196.3712 516.6999,-186.8489"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="519.1094,-189.3909 524.3146,-180.1628 514.4908,-184.1308 519.1094,-189.3909"/>
</g>
-<!-- 13->6 -->
-<g id="edge16" class="edge">
-<title>13->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M254.5141,-215.8314C255.1558,-208.131 255.9188,-198.9743 256.6319,-190.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="260.1229,-190.6694 257.4656,-180.4133 253.1471,-190.088 260.1229,-190.6694"/>
+<!-- 13->4 -->
+<g id="edge15" class="edge">
+<title>13->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M449.1212,-215.8314C442.7864,-207.5386 435.1616,-197.557 428.2074,-188.4533"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="430.9175,-186.2353 422.0657,-180.4133 425.3548,-190.4847 430.9175,-186.2353"/>
</g>
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M968,-180C968,-180 802,-180 802,-180 796,-180 790,-174 790,-168 790,-168 790,-156 790,-156 790,-150 796,-144 802,-144 802,-144 968,-144 968,-144 974,-144 980,-150 980,-156 980,-156 980,-168 980,-168 980,-174 974,-180 968,-180"/>
-<text text-anchor="middle" x="885" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M431,-324C431,-324 335,-324 335,-324 329,-324 323,-318 323,-312 323,-312 323,-300 323,-300 323,-294 329,-288 335,-288 335,-288 431,-288 431,-288 437,-288 443,-294 443,-300 443,-300 443,-312 443,-312 443,-318 437,-324 431,-324"/>
+<text text-anchor="middle" x="383" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
</g>
-<!-- 14->7 -->
+<!-- 14->4 -->
+<g id="edge14" class="edge">
+<title>14->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M386.1663,-287.7623C390.4492,-263.0928 398.1285,-218.8598 403.1436,-189.9731"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="406.5973,-190.541 404.8594,-180.0896 399.7004,-189.3435 406.5973,-190.541"/>
+</g>
+<!-- 14->6 -->
<g id="edge19" class="edge">
-<title>14->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M867.5884,-143.8314C859.479,-135.3694 849.6844,-125.1489 840.818,-115.8971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="843.0921,-113.2115 833.646,-108.4133 838.0382,-118.0549 843.0921,-113.2115"/>
+<title>14->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M322.8075,-290.1425C267.2147,-275.3972 192.2896,-255.2299 186,-252 153.1752,-235.1432 121.024,-207.494 99.8437,-187.2831"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="102.1687,-184.6621 92.5559,-180.2072 97.2925,-189.6843 102.1687,-184.6621"/>
+</g>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M730.5,-252C730.5,-252 657.5,-252 657.5,-252 651.5,-252 645.5,-246 645.5,-240 645.5,-240 645.5,-228 645.5,-228 645.5,-222 651.5,-216 657.5,-216 657.5,-216 730.5,-216 730.5,-216 736.5,-216 742.5,-222 742.5,-228 742.5,-228 742.5,-240 742.5,-240 742.5,-246 736.5,-252 730.5,-252"/>
+<text text-anchor="middle" x="694" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+</g>
+<!-- 14->20 -->
+<g id="edge39" class="edge">
+<title>14->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M443.3327,-292.0323C498.7078,-279.2123 580.245,-260.3356 635.1476,-247.625"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="636.124,-250.9916 645.0768,-245.3263 634.5451,-244.172 636.124,-250.9916"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#8fd856" stroke-width="2" d="M759.5,-180C759.5,-180 638.5,-180 638.5,-180 632.5,-180 626.5,-174 626.5,-168 626.5,-168 626.5,-156 626.5,-156 626.5,-150 632.5,-144 638.5,-144 638.5,-144 759.5,-144 759.5,-144 765.5,-144 771.5,-150 771.5,-156 771.5,-156 771.5,-168 771.5,-168 771.5,-174 765.5,-180 759.5,-180"/>
-<text text-anchor="middle" x="699" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M291,-252C291,-252 207,-252 207,-252 201,-252 195,-246 195,-240 195,-240 195,-228 195,-228 195,-222 201,-216 207,-216 207,-216 291,-216 291,-216 297,-216 303,-222 303,-228 303,-228 303,-240 303,-240 303,-246 297,-252 291,-252"/>
+<text text-anchor="middle" x="249" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
</g>
-<!-- 15->7 -->
-<g id="edge20" class="edge">
-<title>15->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M728.524,-143.8314C743.4891,-134.6221 761.8386,-123.3301 777.8603,-113.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="779.8032,-116.3847 786.4854,-108.1628 776.1345,-110.423 779.8032,-116.3847"/>
+<!-- 15->5 -->
+<g id="edge16" class="edge">
+<title>15->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M249.5047,-215.8314C249.7186,-208.131 249.9729,-198.9743 250.2106,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="253.7094,-190.5066 250.4885,-180.4133 246.7121,-190.3122 253.7094,-190.5066"/>
+</g>
+<!-- 15->6 -->
+<g id="edge18" class="edge">
+<title>15->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M205.0925,-215.8314C181.7176,-206.159 152.7903,-194.1891 128.1532,-183.9944"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="129.1702,-180.6275 118.5918,-180.038 126.4937,-187.0956 129.1702,-180.6275"/>
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<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1160,-180C1160,-180 1010,-180 1010,-180 1004,-180 998,-174 998,-168 998,-168 998,-156 998,-156 998,-150 1004,-144 1010,-144 1010,-144 1160,-144 1160,-144 1166,-144 1172,-150 1172,-156 1172,-156 1172,-168 1172,-168 1172,-174 1166,-180 1160,-180"/>
-<text text-anchor="middle" x="1085" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M1199,-180C1199,-180 1033,-180 1033,-180 1027,-180 1021,-174 1021,-168 1021,-168 1021,-156 1021,-156 1021,-150 1027,-144 1033,-144 1033,-144 1199,-144 1199,-144 1205,-144 1211,-150 1211,-156 1211,-156 1211,-168 1211,-168 1211,-174 1205,-180 1199,-180"/>
+<text text-anchor="middle" x="1116" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 16->7 -->
-<g id="edge18" class="edge">
+<g id="edge21" class="edge">
<title>16->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1017.4672,-143.9243C975.9721,-132.8178 923.0599,-118.6554 881.8743,-107.6318"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="882.7719,-104.2489 872.207,-105.0442 880.9619,-111.0109 882.7719,-104.2489"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1061.2708,-143.9243C1031.2098,-133.9959 993.755,-121.6255 962.3046,-111.2382"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="963.3449,-107.8959 952.7517,-108.0831 961.1496,-114.5428 963.3449,-107.8959"/>
+</g>
+<!-- 16->10 -->
+<g id="edge28" class="edge">
+<title>16->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1116,-143.8314C1116,-136.131 1116,-126.9743 1116,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1119.5001,-118.4132 1116,-108.4133 1112.5001,-118.4133 1119.5001,-118.4132"/>
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<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M356,-396C356,-396 230,-396 230,-396 224,-396 218,-390 218,-384 218,-384 218,-372 218,-372 218,-366 224,-360 230,-360 230,-360 356,-360 356,-360 362,-360 368,-366 368,-372 368,-372 368,-384 368,-384 368,-390 362,-396 356,-396"/>
-<text text-anchor="middle" x="293" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M990.5,-180C990.5,-180 869.5,-180 869.5,-180 863.5,-180 857.5,-174 857.5,-168 857.5,-168 857.5,-156 857.5,-156 857.5,-150 863.5,-144 869.5,-144 869.5,-144 990.5,-144 990.5,-144 996.5,-144 1002.5,-150 1002.5,-156 1002.5,-156 1002.5,-168 1002.5,-168 1002.5,-174 996.5,-180 990.5,-180"/>
+<text text-anchor="middle" x="930" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
</g>
-<!-- 17->10 -->
-<g id="edge25" class="edge">
-<title>17->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M293,-359.8314C293,-352.131 293,-342.9743 293,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="296.5001,-334.4132 293,-324.4133 289.5001,-334.4133 296.5001,-334.4132"/>
+<!-- 17->7 -->
+<g id="edge22" class="edge">
+<title>17->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M921.925,-143.8314C918.3898,-135.8771 914.164,-126.369 910.2544,-117.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="913.4435,-116.1299 906.1837,-108.4133 907.0468,-118.9729 913.4435,-116.1299"/>
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<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M478.5,-324C478.5,-324 391.5,-324 391.5,-324 385.5,-324 379.5,-318 379.5,-312 379.5,-312 379.5,-300 379.5,-300 379.5,-294 385.5,-288 391.5,-288 391.5,-288 478.5,-288 478.5,-288 484.5,-288 490.5,-294 490.5,-300 490.5,-300 490.5,-312 490.5,-312 490.5,-318 484.5,-324 478.5,-324"/>
-<text text-anchor="middle" x="435" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M827,-180C827,-180 677,-180 677,-180 671,-180 665,-174 665,-168 665,-168 665,-156 665,-156 665,-150 671,-144 677,-144 677,-144 827,-144 827,-144 833,-144 839,-150 839,-156 839,-156 839,-168 839,-168 839,-174 833,-180 827,-180"/>
+<text text-anchor="middle" x="752" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+</g>
+<!-- 18->7 -->
+<g id="edge20" class="edge">
+<title>18->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M788.842,-143.8314C808.1082,-134.3302 831.8699,-122.6121 852.2992,-112.5374"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="854.0023,-115.6 861.423,-108.038 850.9062,-109.3219 854.0023,-115.6"/>
</g>
<!-- 18->11 -->
-<g id="edge26" class="edge">
+<g id="edge29" class="edge">
<title>18->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M440.2992,-287.8314C442.5698,-280.0463 445.2746,-270.7729 447.794,-262.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="451.1894,-262.9933 450.6295,-252.4133 444.4694,-261.0332 451.1894,-262.9933"/>
-</g>
-<!-- 18->13 -->
-<g id="edge28" class="edge">
-<title>18->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M389.0737,-287.8314C364.4077,-278.0734 333.8309,-265.977 307.914,-255.7242"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M749.7289,-143.8314C748.7664,-136.131 747.6218,-126.9743 746.5521,-118.4166"/>
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-<!-- 19 -->
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-<title>19</title>
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-</g>
-<!-- 19->12 -->
+<!-- 19->10 -->
<g id="edge27" class="edge">
-<title>19->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M569,-359.8314C569,-352.131 569,-342.9743 569,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="572.5001,-334.4132 569,-324.4133 565.5001,-334.4133 572.5001,-334.4132"/>
+<title>19->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1051.7598,-228.313C1111.4117,-221.0258 1199.419,-206.1048 1220,-180 1229.906,-167.4353 1228.3076,-157.6742 1220,-144 1210.64,-128.5934 1195.2997,-117.3827 1179.2404,-109.3089"/>
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-<!-- 20->14 -->
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-<title>20->14</title>
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+<!-- 19->16 -->
+<g id="edge35" class="edge">
+<title>19->16</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1025.5334,-215.8314C1041.0101,-206.6221 1059.9869,-195.3301 1076.5563,-185.4706"/>
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</g>
-<!-- 21->16 -->
+<!-- 20->11 -->
<g id="edge30" class="edge">
-<title>21->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M907.7604,-218.4657C940.1409,-208.1498 983.0597,-194.4766 1018.5527,-183.169"/>
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+<title>20->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M676.7008,-215.8753C661.1777,-197.3079 642.7255,-167.863 656,-144 663.0918,-131.2514 674.5767,-121.1272 686.9096,-113.255"/>
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+</g>
+<!-- 20->18 -->
+<g id="edge36" class="edge">
+<title>20->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M708.6358,-215.8314C715.3161,-207.5386 723.3568,-197.557 730.6904,-188.4533"/>
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+</g>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#56d8b1" stroke-width="2" d="M609,-396C609,-396 483,-396 483,-396 477,-396 471,-390 471,-384 471,-384 471,-372 471,-372 471,-366 477,-360 483,-360 483,-360 609,-360 609,-360 615,-360 621,-366 621,-372 621,-372 621,-384 621,-384 621,-390 615,-396 609,-396"/>
+<text text-anchor="middle" x="546" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 21->12 -->
+<g id="edge31" class="edge">
+<title>21->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M546,-359.8314C546,-352.131 546,-342.9743 546,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="549.5001,-334.4132 546,-324.4133 542.5001,-334.4133 549.5001,-334.4132"/>
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<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M832,-324C832,-324 762,-324 762,-324 756,-324 750,-318 750,-312 750,-312 750,-300 750,-300 750,-294 756,-288 762,-288 762,-288 832,-288 832,-288 838,-288 844,-294 844,-300 844,-300 844,-312 844,-312 844,-318 838,-324 832,-324"/>
-<text text-anchor="middle" x="797" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M292.5,-324C292.5,-324 205.5,-324 205.5,-324 199.5,-324 193.5,-318 193.5,-312 193.5,-312 193.5,-300 193.5,-300 193.5,-294 199.5,-288 205.5,-288 205.5,-288 292.5,-288 292.5,-288 298.5,-288 304.5,-294 304.5,-300 304.5,-300 304.5,-312 304.5,-312 304.5,-318 298.5,-324 292.5,-324"/>
+<text text-anchor="middle" x="249" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
</g>
-<!-- 22->20 -->
+<!-- 22->13 -->
<g id="edge32" class="edge">
-<title>22->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M781.6071,-287.8314C774.5096,-279.454 765.952,-269.3531 758.176,-260.1749"/>
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+<title>22->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M302.725,-287.9243C332.1073,-278.0387 368.6852,-265.7321 399.4758,-255.3726"/>
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+</g>
+<!-- 22->15 -->
+<g id="edge34" class="edge">
+<title>22->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M249,-287.8314C249,-280.131 249,-270.9743 249,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="252.5001,-262.4132 249,-252.4133 245.5001,-262.4133 252.5001,-262.4132"/>
+</g>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M438,-396C438,-396 328,-396 328,-396 322,-396 316,-390 316,-384 316,-384 316,-372 316,-372 316,-366 322,-360 328,-360 328,-360 438,-360 438,-360 444,-360 450,-366 450,-372 450,-372 450,-384 450,-384 450,-390 444,-396 438,-396"/>
+<text text-anchor="middle" x="383" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
</g>
-<!-- 22->21 -->
+<!-- 23->14 -->
<g id="edge33" class="edge">
-<title>22->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M812.6452,-287.8314C819.8591,-279.454 828.557,-269.3531 836.4605,-260.1749"/>
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+<title>23->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M383,-359.8314C383,-352.131 383,-342.9743 383,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="386.5001,-334.4132 383,-324.4133 379.5001,-334.4133 386.5001,-334.4132"/>
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+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M844,-324C844,-324 774,-324 774,-324 768,-324 762,-318 762,-312 762,-312 762,-300 762,-300 762,-294 768,-288 774,-288 774,-288 844,-288 844,-288 850,-288 856,-294 856,-300 856,-300 856,-312 856,-312 856,-318 850,-324 844,-324"/>
+<text text-anchor="middle" x="809" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+</g>
+<!-- 24->19 -->
+<g id="edge38" class="edge">
+<title>24->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M855.9357,-287.8314C881.1437,-278.0734 912.3926,-265.977 938.8791,-255.7242"/>
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+</g>
+<!-- 24->20 -->
+<g id="edge40" class="edge">
+<title>24->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M779.9806,-287.8314C765.2714,-278.6221 747.2356,-267.3301 731.4878,-257.4706"/>
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diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 9bf33eb15ed0e651c8601f5ca31a0f5dc0603234..93a8f667794f5919a49f468da6303c262016d900 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -78,4 +78,12 @@ e72f5d798c99272f8c0166dc77247db1 results/single_end/synthetic_10_reads_mate_1_s
92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias
92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias_3p
d41d8cd98f00b204e9800998ecf8427e results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/unmapped_names.txt
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str1.out.bg
+c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str2.out.bg
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str1.out.bg
+c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str2.out.bg
+ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str1.out.bg
+ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg
+ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
+ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
79fc3e46b3ac1a72b80cb7bebf6058cd results/transcriptome/homo_sapiens/transcriptome.fa
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 77869565b586e138c5b555dd0052c3ccfae1912a..89c4f7e6bc94d5eca659d8c88add19fc3c0b02b0 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -453,3 +453,77 @@ rule pe_genome_quantification_kallisto:
{params.directionality} \
{input.reads1} {input.reads2} > {output.pseudoalignment}) \
2> {log.stderr}"
+
+rule star_rpm_paired_end:
+ ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
+ input:
+ bam = os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam"),
+ bai = os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam.bai")
+ output:
+ str1 = (os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str1.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str1.out.bg")),
+ str2 = (os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str2.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "paired_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str2.out.bg"))
+ params:
+ out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
+ prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
+ str(wildcards.sample) + "_"),
+ stranded = "Stranded"
+ singularity:
+ "docker://zavolab/star:2.7.3a-slim"
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "paired_end",
+ "{sample}",
+ "star_rpm_paired_end.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "paired_end",
+ "{sample}",
+ "star_rpm_paired_end.stdout.log")
+ threads: 4
+ shell:
+ """
+ (mkdir -p {params.out_dir}; \
+ chmod -R 777 {params.out_dir}; \
+ STAR \
+ --runMode inputAlignmentsFromBAM \
+ --runThreadN {threads} \
+ --inputBAMfile {input.bam} \
+ --outWigType "bedGraph" \
+ --outWigStrand "{params.stranded}" \
+ --outWigNorm "RPM" \
+ --outFileNamePrefix {params.prefix}) \
+ 1> {log.stdout} 2> {log.stderr}
+ """
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index eaebe797ebc3a17f707a1e49e5e62695581a05dc..cf4c7c4eb1611b8bc4f5c55dda56a20222592aed 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -412,3 +412,77 @@ rule genome_quantification_kallisto:
{params.directionality} \
{input.reads} > {output.pseudoalignment};) \
2> {log.stderr}"
+
+rule star_rpm_single_end:
+ ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
+ input:
+ bam = os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam"),
+ bai = os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam.bai")
+ output:
+ str1 = (os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str1.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str1.out.bg")),
+ str2 = (os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str2.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "single_end",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str2.out.bg"))
+ params:
+ out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
+ prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
+ str(wildcards.sample) + "_"),
+ stranded = "Stranded"
+ singularity:
+ "docker://zavolab/star:2.7.3a-slim"
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "single_end",
+ "{sample}",
+ "star_rpm_single_end.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "single_end",
+ "{sample}",
+ "star_rpm_single_end.stdout.log")
+ threads: 4
+ shell:
+ """
+ (mkdir -p {params.out_dir}; \
+ chmod -R 777 {params.out_dir}; \
+ STAR \
+ --runMode inputAlignmentsFromBAM \
+ --runThreadN {threads} \
+ --inputBAMfile {input.bam} \
+ --outWigType "bedGraph" \
+ --outWigStrand {params.stranded} \
+ --outWigNorm "RPM" \
+ --outFileNamePrefix {params.prefix}) \
+ 1> {log.stdout} 2> {log.stderr}
+ """