diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index c4c04887e7095f24b48e45428a6df615378f1d69..5b222ac1b8de89838e844ccb08792b141a3d0888 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -4,468 +4,480 @@
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-->
<!-- Title: snakemake_dag Pages: 1 -->
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<title>snakemake_dag</title>
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<g id="node1" class="node">
<title>0</title>
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<g id="node2" class="node">
<title>1</title>
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<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>
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<g id="edge1" class="edge">
<title>1->0</title>
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<g id="node3" class="node">
<title>2</title>
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<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>
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<!-- 2->0 -->
<g id="edge2" class="edge">
<title>2->0</title>
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<title>3</title>
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+<text text-anchor="middle" x="987" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
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<g id="edge3" class="edge">
<title>3->0</title>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
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-<text text-anchor="middle" x="1161" 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>
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<!-- 3->9 -->
<g id="edge27" class="edge">
<title>3->9</title>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1380.5,-108C1380.5,-108 1259.5,-108 1259.5,-108 1253.5,-108 1247.5,-102 1247.5,-96 1247.5,-96 1247.5,-84 1247.5,-84 1247.5,-78 1253.5,-72 1259.5,-72 1259.5,-72 1380.5,-72 1380.5,-72 1386.5,-72 1392.5,-78 1392.5,-84 1392.5,-84 1392.5,-96 1392.5,-96 1392.5,-102 1386.5,-108 1380.5,-108"/>
-<text text-anchor="middle" x="1320" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="1320" 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>
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<!-- 3->10 -->
<g id="edge29" class="edge">
<title>3->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1176.4497,-143.8314C1202.5851,-134.0306 1235.0109,-121.8709 1262.4283,-111.5894"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M944.6065,-143.8314C922.0376,-134.159 894.1079,-122.1891 870.3204,-111.9944"/>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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-<text text-anchor="middle" x="824" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="824" 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>
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<!-- 3->11 -->
<g id="edge31" class="edge">
<title>3->11</title>
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<!-- 12 -->
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<title>12</title>
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-<text text-anchor="middle" x="997" 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>
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<g id="edge33" class="edge">
<title>3->12</title>
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<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
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-<text text-anchor="middle" x="991" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
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+<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>
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<g id="edge28" class="edge">
<title>4->9</title>
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<title>4->10</title>
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<!-- 4->11 -->
<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="829" 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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<g id="edge5" class="edge">
<title>5->0</title>
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<g id="node7" class="node">
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-<text text-anchor="middle" x="653" 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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<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="1673" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
-<text text-anchor="middle" x="1673" 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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<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="1543" 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 -->
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<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>
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<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
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-<text text-anchor="middle" x="1855" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_paired_end</text>
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+<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->0 -->
<g id="edge13" class="edge">
<title>13->0</title>
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<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
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-<text text-anchor="middle" x="1263" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_single_end</text>
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+<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->0</title>
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-<text text-anchor="middle" x="1154" y="-306" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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+<text text-anchor="middle" x="862" y="-306" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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<g id="edge15" class="edge">
<title>15->3</title>
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-<text text-anchor="middle" x="1635" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+<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>
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<!-- 15->22 -->
-<g id="edge44" class="edge">
+<g id="edge46" class="edge">
<title>15->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1222.1499,-297.9446C1314.2011,-283.6871 1477.2202,-258.4378 1568.4438,-244.3086"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1569.0464,-247.7571 1578.3928,-242.7676 1567.9749,-240.8396 1569.0464,-247.7571"/>
+<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"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1053.5,-252C1053.5,-252 968.5,-252 968.5,-252 962.5,-252 956.5,-246 956.5,-240 956.5,-240 956.5,-228 956.5,-228 956.5,-222 962.5,-216 968.5,-216 968.5,-216 1053.5,-216 1053.5,-216 1059.5,-216 1065.5,-222 1065.5,-228 1065.5,-228 1065.5,-240 1065.5,-240 1065.5,-246 1059.5,-252 1053.5,-252"/>
-<text text-anchor="middle" x="1011" y="-237" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
-<text text-anchor="middle" x="1011" y="-226" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</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->3 -->
<g id="edge16" class="edge">
<title>16->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1040.524,-215.8314C1055.4891,-206.6221 1073.8386,-195.3301 1089.8603,-185.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1091.8032,-188.3847 1098.4854,-180.1628 1088.1345,-182.423 1091.8032,-188.3847"/>
+<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->4 -->
<g id="edge18" class="edge">
<title>16->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1005.9532,-215.8314C1003.7906,-208.0463 1001.2147,-198.7729 998.8152,-190.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1002.1636,-189.1117 996.1148,-180.4133 995.419,-190.9852 1002.1636,-189.1117"/>
+<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"/>
</g>
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M903,-326.5C903,-326.5 807,-326.5 807,-326.5 801,-326.5 795,-320.5 795,-314.5 795,-314.5 795,-302.5 795,-302.5 795,-296.5 801,-290.5 807,-290.5 807,-290.5 903,-290.5 903,-290.5 909,-290.5 915,-296.5 915,-302.5 915,-302.5 915,-314.5 915,-314.5 915,-320.5 909,-326.5 903,-326.5"/>
-<text text-anchor="middle" x="855" y="-306" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</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->4 -->
<g id="edge17" class="edge">
<title>17->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M871.9495,-290.2419C896.0036,-264.3307 940.1418,-216.7848 967.3902,-187.4326"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="970.0256,-189.7381 974.2641,-180.028 964.8954,-184.9756 970.0256,-189.7381"/>
+<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"/>
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<!-- 17->6 -->
<g id="edge21" class="edge">
<title>17->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M812.8113,-290.4821C791.5896,-280.5296 765.9881,-267.1251 745,-252 718.8712,-233.1702 692.9998,-207.0124 675.3793,-187.7482"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="677.883,-185.2982 668.587,-180.2154 672.6843,-189.9859 677.883,-185.2982"/>
+<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"/>
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<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
-<path fill="none" stroke="#56d863" stroke-width="2" d="M1355.5,-252C1355.5,-252 1282.5,-252 1282.5,-252 1276.5,-252 1270.5,-246 1270.5,-240 1270.5,-240 1270.5,-228 1270.5,-228 1270.5,-222 1276.5,-216 1282.5,-216 1282.5,-216 1355.5,-216 1355.5,-216 1361.5,-216 1367.5,-222 1367.5,-228 1367.5,-228 1367.5,-240 1367.5,-240 1367.5,-246 1361.5,-252 1355.5,-252"/>
-<text text-anchor="middle" x="1319" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<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="edge46" class="edge">
+<g id="edge48" class="edge">
<title>17->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M915.0114,-291.3649C920.0625,-290.1458 925.1075,-289.0039 930,-288 1045.9392,-264.211 1183.5021,-247.8552 1260.0579,-239.7898"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1260.8635,-243.2249 1270.4467,-238.7068 1260.1377,-236.2626 1260.8635,-243.2249"/>
+<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="#78d856" stroke-width="2" d="M850,-252C850,-252 766,-252 766,-252 760,-252 754,-246 754,-240 754,-240 754,-228 754,-228 754,-222 760,-216 766,-216 766,-216 850,-216 850,-216 856,-216 862,-222 862,-228 862,-228 862,-240 862,-240 862,-246 856,-252 850,-252"/>
-<text text-anchor="middle" x="808" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</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>
</g>
<!-- 18->5 -->
<g id="edge20" class="edge">
<title>18->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M813.2992,-215.8314C815.5698,-208.0463 818.2746,-198.7729 820.794,-190.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="824.1894,-190.9933 823.6295,-180.4133 817.4694,-189.0332 824.1894,-190.9933"/>
+<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->6 -->
<g id="edge22" class="edge">
<title>18->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M768.887,-215.8314C748.2488,-206.2446 722.7516,-194.4008 700.9327,-184.2655"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="702.3756,-181.0766 691.8318,-180.038 699.4266,-187.4251 702.3756,-181.0766"/>
+<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="#56d8c9" stroke-width="2" d="M1869,-180C1869,-180 1703,-180 1703,-180 1697,-180 1691,-174 1691,-168 1691,-168 1691,-156 1691,-156 1691,-150 1697,-144 1703,-144 1703,-144 1869,-144 1869,-144 1875,-144 1881,-150 1881,-156 1881,-156 1881,-168 1881,-168 1881,-174 1875,-180 1869,-180"/>
-<text text-anchor="middle" x="1786" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_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->7 -->
<g id="edge23" class="edge">
<title>19->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1757.4853,-143.8314C1743.1658,-134.7074 1725.6376,-123.539 1710.2662,-113.7449"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1711.8199,-110.5847 1701.5055,-108.1628 1708.0583,-116.4882 1711.8199,-110.5847"/>
+<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>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1660.5,-180C1660.5,-180 1539.5,-180 1539.5,-180 1533.5,-180 1527.5,-174 1527.5,-168 1527.5,-168 1527.5,-156 1527.5,-156 1527.5,-150 1533.5,-144 1539.5,-144 1539.5,-144 1660.5,-144 1660.5,-144 1666.5,-144 1672.5,-150 1672.5,-156 1672.5,-156 1672.5,-168 1672.5,-168 1672.5,-174 1666.5,-180 1660.5,-180"/>
-<text text-anchor="middle" x="1600" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</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>
</g>
<!-- 20->7 -->
<g id="edge24" class="edge">
<title>20->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1618.421,-143.8314C1627.1529,-135.219 1637.7317,-124.7851 1647.2423,-115.4048"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1649.923,-117.6769 1654.5849,-108.1628 1645.0075,-112.6931 1649.923,-117.6769"/>
+<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"/>
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<!-- 20->8 -->
<g id="edge26" class="edge">
<title>20->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1585.6165,-143.8314C1579.0514,-135.5386 1571.1493,-125.557 1563.9422,-116.4533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1566.5284,-114.0813 1557.5772,-108.4133 1561.0401,-118.4262 1566.5284,-114.0813"/>
+<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>
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-<text text-anchor="middle" x="1422" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</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>
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<!-- 21->8 -->
<g id="edge25" class="edge">
<title>21->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1452.5334,-143.8314C1468.0101,-134.6221 1486.9869,-123.3301 1503.5563,-113.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1505.6724,-116.2843 1512.4764,-108.1628 1502.0929,-110.2687 1505.6724,-116.2843"/>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1817.5696,-143.8314C1808.268,-135.1337 1796.9796,-124.5783 1786.8714,-115.1265"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1789.1189,-112.4363 1779.4241,-108.1628 1784.3379,-117.5493 1789.1189,-112.4363"/>
+</g>
+<!-- 21->14 -->
+<g id="edge38" class="edge">
+<title>21->14</title>
+<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"/>
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<!-- 22->13 -->
<g id="edge35" class="edge">
<title>22->13</title>
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+<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"/>
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</g>
<!-- 22->19 -->
-<g id="edge41" class="edge">
+<g id="edge43" class="edge">
<title>22->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1673.1037,-215.8314C1693.1195,-206.2874 1717.8267,-194.5065 1739.0194,-184.4013"/>
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1426.6452,-215.8314C1433.8591,-207.454 1442.557,-197.3531 1450.4605,-188.1749"/>
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</g>
<!-- 23->14 -->
-<g id="edge36" class="edge">
+<g id="edge37" class="edge">
<title>23->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1304.8688,-215.8314C1298.4189,-207.5386 1290.6555,-197.557 1283.5748,-188.4533"/>
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+<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"/>
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</g>
<!-- 23->21 -->
-<g id="edge42" class="edge">
+<g id="edge44" class="edge">
<title>23->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1344.9912,-215.8314C1357.9216,-206.7927 1373.7222,-195.7476 1387.6383,-186.0198"/>
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+<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="#5682d8" stroke-width="2" d="M1292,-401C1292,-401 1024,-401 1024,-401 1018,-401 1012,-395 1012,-389 1012,-389 1012,-377 1012,-377 1012,-371 1018,-365 1024,-365 1024,-365 1292,-365 1292,-365 1298,-365 1304,-371 1304,-377 1304,-377 1304,-389 1304,-389 1304,-395 1298,-401 1292,-401"/>
-<text text-anchor="middle" x="1158" y="-386" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1158" 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="#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="edge37" class="edge">
+<g id="edge39" class="edge">
<title>24->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1157.0317,-364.9656C1156.5781,-356.5178 1156.0271,-346.2542 1155.5198,-336.8064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1159.0044,-336.4244 1154.9732,-326.6265 1152.0145,-336.7998 1159.0044,-336.4244"/>
+<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>
<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M1052.5,-326.5C1052.5,-326.5 951.5,-326.5 951.5,-326.5 945.5,-326.5 939.5,-320.5 939.5,-314.5 939.5,-314.5 939.5,-302.5 939.5,-302.5 939.5,-296.5 945.5,-290.5 951.5,-290.5 951.5,-290.5 1052.5,-290.5 1052.5,-290.5 1058.5,-290.5 1064.5,-296.5 1064.5,-302.5 1064.5,-302.5 1064.5,-314.5 1064.5,-314.5 1064.5,-320.5 1058.5,-326.5 1052.5,-326.5"/>
-<text text-anchor="middle" x="1002" y="-311.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
-<text text-anchor="middle" x="1002" y="-300.5" 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->16 -->
-<g id="edge38" class="edge">
+<g id="edge40" class="edge">
<title>25->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1004.1786,-290.4656C1005.1992,-282.0178 1006.4391,-271.7542 1007.5804,-262.3064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1011.0855,-262.4741 1008.8102,-252.1265 1004.1361,-261.6345 1011.0855,-262.4741"/>
+<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->18 -->
-<g id="edge40" class="edge">
+<g id="edge42" class="edge">
<title>25->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M955.038,-290.4656C927.8357,-280.0194 893.4035,-266.7967 864.6984,-255.7734"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="865.792,-252.4442 855.2019,-252.1265 863.2825,-258.9789 865.792,-252.4442"/>
+<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="#56d0d8" stroke-width="2" d="M982,-401C982,-401 702,-401 702,-401 696,-401 690,-395 690,-389 690,-389 690,-377 690,-377 690,-371 696,-365 702,-365 702,-365 982,-365 982,-365 988,-365 994,-371 994,-377 994,-377 994,-389 994,-389 994,-395 988,-401 982,-401"/>
-<text text-anchor="middle" x="842" y="-386" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="842" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<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="edge39" class="edge">
+<g id="edge41" class="edge">
<title>26->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M845.1469,-364.9656C846.6369,-356.427 848.4506,-346.0333 850.1138,-336.502"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="853.5658,-337.0793 851.837,-326.6265 846.67,-335.876 853.5658,-337.0793"/>
+<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="#c6d856" stroke-width="2" d="M1425.5,-329C1425.5,-329 1324.5,-329 1324.5,-329 1318.5,-329 1312.5,-323 1312.5,-317 1312.5,-317 1312.5,-300 1312.5,-300 1312.5,-294 1318.5,-288 1324.5,-288 1324.5,-288 1425.5,-288 1425.5,-288 1431.5,-288 1437.5,-294 1437.5,-300 1437.5,-300 1437.5,-317 1437.5,-317 1437.5,-323 1431.5,-329 1425.5,-329"/>
-<text text-anchor="middle" x="1375" y="-317" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
-<text text-anchor="middle" x="1375" y="-306" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
-<text text-anchor="middle" x="1375" y="-295" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<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="edge43" class="edge">
+<g id="edge45" class="edge">
<title>27->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1437.6073,-290.5606C1477.1698,-279.2244 1528.2421,-264.5902 1568.5247,-253.0477"/>
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+<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="edge45" class="edge">
+<g id="edge47" class="edge">
<title>27->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1359.4009,-287.7476C1353.0243,-279.2645 1345.5725,-269.3509 1338.8173,-260.364"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1341.4183,-257.9992 1332.6119,-252.1087 1335.8227,-262.2053 1341.4183,-257.9992"/>
+<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 d5cd5f2b98e7adb7d41f3c78b88d9d006a9c37b5..9ba29ef63af3646654959d2305a4f8db3cfc8a20 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -5,387 +5,399 @@
-->
<!-- Title: snakemake_dag Pages: 1 -->
<svg width="1235pt" height="404pt"
- viewBox="0.00 0.00 1234.84 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+ 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 1230.8447,-400 1230.8447,4 -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="395" 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"/>
+<text text-anchor="middle" x="401" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
</g>
<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
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-<text text-anchor="middle" x="83" 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="edge6" class="edge">
+<g id="edge8" class="edge">
<title>1->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M112.5189,-75.4965C115.6789,-74.2094 118.8791,-73.013 122,-72 204.0713,-45.362 304.4979,-29.6097 357.726,-22.5192"/>
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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"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="364.2593,-25.9794 373.7229,-21.216 363.3544,-19.0381 364.2593,-25.9794"/>
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<g id="node3" class="node">
<title>2</title>
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-<text text-anchor="middle" x="158" 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>
</g>
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-<g id="edge4" class="edge">
+<g id="edge3" class="edge">
<title>2->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M185.1255,-77.435C189.7115,-75.5006 194.4582,-73.6131 199,-72 253.4623,-52.6571 318.4424,-35.9659 358.203,-26.4479"/>
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<g id="node4" class="node">
<title>3</title>
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+<path fill="none" stroke="#d86e56" stroke-width="2" d="M596.5,-180C596.5,-180 493.5,-180 493.5,-180 487.5,-180 481.5,-174 481.5,-168 481.5,-168 481.5,-156 481.5,-156 481.5,-150 487.5,-144 493.5,-144 493.5,-144 596.5,-144 596.5,-144 602.5,-144 608.5,-150 608.5,-156 608.5,-156 608.5,-168 608.5,-168 608.5,-174 602.5,-180 596.5,-180"/>
<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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<title>3->0</title>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
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-<text text-anchor="middle" x="559" 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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<g id="edge23" class="edge">
<title>3->8</title>
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+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="560.581,-118.9852 559.8852,-108.4133 553.8364,-117.1117 560.581,-118.9852"/>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
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-<text text-anchor="middle" x="395" 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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<!-- 3->9 -->
<g id="edge25" class="edge">
<title>3->9</title>
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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="408" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
</g>
<!-- 4->0 -->
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+<g id="edge9" class="edge">
<title>4->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M352.3262,-144.7845C335.0549,-136.5321 317.9559,-124.6909 308,-108 299.8036,-94.2589 300.222,-85.9822 308,-72 318.7443,-52.6853 339.5726,-39.3947 358.1559,-30.8325"/>
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<!-- 4->8 -->
<g id="edge24" class="edge">
<title>4->8</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="513.6503,-115.5013 521.1703,-108.038 510.6375,-109.1828 513.6503,-115.5013"/>
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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="edge26" class="edge">
<title>4->9</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="403.5458,-117.6322 398.3246,-108.4133 396.6572,-118.8761 403.5458,-117.6322"/>
+<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="251" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
</g>
<!-- 5->0 -->
-<g id="edge9" class="edge">
+<g id="edge2" class="edge">
<title>5->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M257.14,-143.8876C264.537,-124.2402 278.5723,-92.8912 299,-72 315.7741,-54.8454 339.1659,-41.5348 358.6594,-32.4209"/>
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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>
-<path fill="none" stroke="#61d856" 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"/>
+<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="edge2" class="edge">
+<g id="edge4" class="edge">
<title>6->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M114.9897,-143.9896C138.1064,-133.5443 167.7271,-120.1023 194,-108 228.3124,-92.1944 236.5678,-87.5431 271,-72 300.2844,-58.7807 333.6905,-44.2651 358.4453,-33.6158"/>
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+<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="897" 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="edge10" class="edge">
<title>7->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M840.8525,-79.201C827.1802,-76.7058 812.5826,-74.1538 799,-72 664.3844,-50.6538 503.6344,-30.86 432.2816,-22.3665"/>
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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>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M517.6159,-71.8314C491.1957,-60.2323 457.2497,-45.3291 431.7762,-34.1457"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="433.0249,-30.8715 422.4615,-30.0563 430.2109,-37.281 433.0249,-30.8715"/>
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+<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="edge8" class="edge">
+<g id="edge5" class="edge">
<title>9->0</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="398.5001,-46.4132 395,-36.4133 391.5001,-46.4133 398.5001,-46.4132"/>
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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="1132" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_paired_end</text>
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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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<!-- 10->0 -->
-<g id="edge3" class="edge">
+<g id="edge11" class="edge">
<title>10->0</title>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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-<text text-anchor="middle" x="737" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_single_end</text>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M784.5,-108C784.5,-108 701.5,-108 701.5,-108 695.5,-108 689.5,-102 689.5,-96 689.5,-96 689.5,-84 689.5,-84 689.5,-78 695.5,-72 701.5,-72 701.5,-72 784.5,-72 784.5,-72 790.5,-72 796.5,-78 796.5,-84 796.5,-84 796.5,-96 796.5,-96 796.5,-102 790.5,-108 784.5,-108"/>
+<text text-anchor="middle" x="743" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_single_end</text>
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<!-- 11->0 -->
-<g id="edge7" class="edge">
+<g id="edge6" class="edge">
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<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
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-<text text-anchor="middle" x="566" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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+<text text-anchor="middle" x="546" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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+<g id="edge13" class="edge">
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+<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"/>
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<g id="edge17" class="edge">
<title>12->5</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="279.2201,-184.397 269.4987,-180.1845 274.4713,-189.5399 279.2201,-184.397"/>
+<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"/>
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<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
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-<text text-anchor="middle" x="967" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+<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->19 -->
-<g id="edge35" class="edge">
+<g id="edge37" class="edge">
<title>12->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M634.0242,-293.7862C708.2921,-280.4513 826.4539,-259.2352 900.2251,-245.9895"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="901.1067,-249.3873 910.3307,-244.175 899.8696,-242.4975 901.1067,-249.3873"/>
+<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>
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-<text text-anchor="middle" x="431" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</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->3 -->
-<g id="edge13" class="edge">
+<g id="edge12" class="edge">
<title>13->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M459.767,-215.8314C474.2133,-206.7074 491.8965,-195.539 507.404,-185.7449"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="509.6563,-188.462 516.2422,-180.1628 505.9183,-182.5436 509.6563,-188.462"/>
+<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->4 -->
<g id="edge15" class="edge">
<title>13->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M425.1961,-215.8314C422.7092,-208.0463 419.7469,-198.7729 416.9875,-190.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="420.2591,-188.874 413.882,-180.4133 413.591,-191.0041 420.2591,-188.874"/>
+<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"/>
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<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M338,-324C338,-324 242,-324 242,-324 236,-324 230,-318 230,-312 230,-312 230,-300 230,-300 230,-294 236,-288 242,-288 242,-288 338,-288 338,-288 344,-288 350,-294 350,-300 350,-300 350,-312 350,-312 350,-318 344,-324 338,-324"/>
-<text text-anchor="middle" x="290" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</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->4 -->
<g id="edge14" class="edge">
<title>14->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M304.9448,-287.7623C325.6033,-262.5518 363.004,-216.9103 386.6165,-188.0952"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="389.5455,-190.0428 393.1766,-180.0896 384.1311,-185.606 389.5455,-190.0428"/>
+<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"/>
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<!-- 14->6 -->
<g id="edge19" class="edge">
<title>14->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M236.3238,-287.9628C213.3286,-278.9616 186.8051,-266.8088 165,-252 138.4905,-233.9962 113.1341,-207.5089 96.1314,-187.927"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="98.7503,-185.6041 89.5981,-180.2667 93.4243,-190.1465 98.7503,-185.6041"/>
+<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"/>
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<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M723.5,-252C723.5,-252 650.5,-252 650.5,-252 644.5,-252 638.5,-246 638.5,-240 638.5,-240 638.5,-228 638.5,-228 638.5,-222 644.5,-216 650.5,-216 650.5,-216 723.5,-216 723.5,-216 729.5,-216 735.5,-222 735.5,-228 735.5,-228 735.5,-240 735.5,-240 735.5,-246 729.5,-252 723.5,-252"/>
-<text text-anchor="middle" x="687" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<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="edge37" class="edge">
+<g id="edge39" class="edge">
<title>14->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M350.1333,-289.9651C353.1256,-289.2765 356.0935,-288.617 359,-288 452.5081,-268.15 562.3266,-251.3802 628.2026,-242.0148"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="628.9766,-245.4402 638.3888,-240.5759 627.9975,-238.5091 628.9766,-245.4402"/>
+<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"/>
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<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M270,-252C270,-252 186,-252 186,-252 180,-252 174,-246 174,-240 174,-240 174,-228 174,-228 174,-222 180,-216 186,-216 186,-216 270,-216 270,-216 276,-216 282,-222 282,-228 282,-228 282,-240 282,-240 282,-246 276,-252 270,-252"/>
-<text text-anchor="middle" x="228" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</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->5 -->
<g id="edge16" class="edge">
<title>15->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M233.8039,-215.8314C236.2908,-208.0463 239.2531,-198.7729 242.0125,-190.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="245.409,-191.0041 245.118,-180.4133 238.7409,-188.874 245.409,-191.0041"/>
+<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="M189.3916,-215.8314C169.1107,-206.2874 144.0762,-194.5065 122.6029,-184.4013"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="123.8692,-181.1291 113.3307,-180.038 120.8886,-187.4629 123.8692,-181.1291"/>
+<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="#56d88a" 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"/>
+<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="edge20" class="edge">
+<g id="edge21" class="edge">
<title>16->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1061.0197,-143.9243C1030.8208,-133.9959 993.1942,-121.6255 961.5996,-111.2382"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="962.5958,-107.8815 952.0029,-108.0831 960.4095,-114.5313 962.5958,-107.8815"/>
+<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="#d85656" 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"/>
+<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>
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<!-- 17->7 -->
<g id="edge22" class="edge">
<title>17->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M921.6727,-143.8314C918.027,-135.8771 913.6691,-126.369 909.6373,-117.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="912.7877,-116.0456 905.4394,-108.4133 906.4243,-118.9622 912.7877,-116.0456"/>
+<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="#56d8a2" 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"/>
+<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="edge21" class="edge">
+<g id="edge20" class="edge">
<title>18->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M788.5896,-143.8314C807.7239,-134.3302 831.3229,-122.6121 851.6122,-112.5374"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="853.2735,-115.6203 860.6735,-108.038 850.1603,-109.3506 853.2735,-115.6203"/>
+<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"/>
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+<!-- 18->11 -->
+<g id="edge29" class="edge">
+<title>18->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M749.7289,-143.8314C748.7664,-136.131 747.6218,-126.9743 746.5521,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="750.0151,-117.9019 745.3017,-108.4133 743.0691,-118.7702 750.0151,-117.9019"/>
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<!-- 19->10 -->
<g id="edge27" class="edge">
<title>19->10</title>
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+<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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<!-- 19->16 -->
-<g id="edge33" class="edge">
+<g id="edge35" class="edge">
<title>19->16</title>
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+<g id="edge30" class="edge">
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</g>
<!-- 20->18 -->
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+<g id="edge36" class="edge">
<title>20->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M703.4022,-215.8314C711.0415,-207.3694 720.2683,-197.1489 728.6207,-187.8971"/>
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<g id="node22" class="node">
<title>21</title>
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+<text text-anchor="middle" x="546" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
</g>
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+<g id="edge31" class="edge">
<title>21->12</title>
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+<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>
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-<text text-anchor="middle" x="424" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</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->13 -->
-<g id="edge30" class="edge">
+<g id="edge32" class="edge">
<title>22->13</title>
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<!-- 22->15 -->
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+<g id="edge34" class="edge">
<title>22->15</title>
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<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
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-<text text-anchor="middle" x="290" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
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+<g id="edge33" class="edge">
<title>23->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M290,-359.8314C290,-352.131 290,-342.9743 290,-334.4166"/>
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<g id="node25" class="node">
<title>24</title>
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-<text text-anchor="middle" x="736" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
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</g>
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-<g id="edge36" class="edge">
+<g id="edge38" class="edge">
<title>24->19</title>
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+<g id="edge40" class="edge">
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diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 38b24d3ae6d4b9b1c57d01bb1b10bd0cced86c75..89c4f7e6bc94d5eca659d8c88add19fc3c0b02b0 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -462,7 +462,13 @@ rule star_rpm_paired_end:
"paired_end",
"{sample}",
"map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam")
+ "{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"],
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 7a9bcc6bdef17859c3f56aa5239296d91fd8fcbe..cf4c7c4eb1611b8bc4f5c55dda56a20222592aed 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -421,7 +421,13 @@ rule star_rpm_single_end:
"single_end",
"{sample}",
"map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam")
+ "{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"],