From c538fe8b3bbfc8ab672dc7fd86a526b14cee2ff1 Mon Sep 17 00:00:00 2001
From: BIOPZ-Bak Maciej <maciej.bak@unibas.ch>
Date: Mon, 17 Feb 2020 23:56:34 +0100
Subject: [PATCH] add TIN score calculation
- add rule for input preparation (GTF to BED12)
- add rule for TIN score calculation
- update rule graph and DAG image
- update Slurm cluster config
---
Snakefile | 71 ++++-
images/dag_test_workflow.svg | 399 ++++++++++++------------
images/rule_graph.svg | 378 +++++++++++-----------
tests/input_files/cluster.json | 6 +
workflow/rules/paired_end.snakefile.smk | 7 -
5 files changed, 448 insertions(+), 413 deletions(-)
diff --git a/Snakefile b/Snakefile
index 2e489ce..17137c9 100644
--- a/Snakefile
+++ b/Snakefile
@@ -29,10 +29,6 @@ rule finish:
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)]),
- bai_index_map = expand(os.path.join(config["output_dir"], "{seqmode}", "{sample}", "map_genome", "{sample}_Aligned.sortedByCoord.out.bam.bai"),
- 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)]),
salmon_gn_estimates = expand(os.path.join(config["output_dir"],"{seqmode}","{sample}","salmon_quant","quant.genes.sf"),
zip,
sample= [i for i in list(samples_table.index.values)],
@@ -41,6 +37,10 @@ rule finish:
zip,
sample= [i for i in list(samples_table.index.values)],
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
+ TIN_score = expand(os.path.join(config["output_dir"], "{seqmode}", "{sample}", "TIN", "TIN_score.tsv"),
+ zip,
+ sample= [i for i in list(samples_table.index.values)],
+ seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
rule create_index_star:
@@ -139,3 +139,66 @@ rule create_index_kallisto:
chmod -R 777 {params.output_dir}; \
kallisto index -i {output.index} {input.transcriptome}) &> {log}"
+
+rule extract_transcripts_as_bed12:
+ ''' Extract transcripts: from GTF into BED12 format'''
+ input:
+ gtf =lambda wildcards: samples_table["gtf"][0]
+ output:
+ bed12 = os.path.join(
+ config["output_dir"],
+ "full_transcripts_protein_coding.bed")
+ singularity:
+ "docker://zavolab/gtf_transcript_type_to_bed12:0.1.0"
+ threads: 1
+ log:
+ os.path.join( config["local_log"], "extract_transcripts_as_bed12.log")
+ shell:
+ "gtf_transcript_type_to_bed12.pl \
+ --anno={input.gtf} \
+ --type=protein_coding \
+ 1> {output.bed12} \
+ 2> {log}"
+
+
+rule calculate_TIN_scores:
+ '''Calculate TIN score'''
+ input:
+ bai = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam.bai"),
+ transcripts_bed12 = os.path.join(
+ config["output_dir"],
+ "full_transcripts_protein_coding.bed")
+ output:
+ TIN_score = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "TIN",
+ "TIN_score.tsv")
+ params:
+ bam = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam"),
+ sample = "{sample}"
+ log:
+ os.path.join(config["local_log"], "{seqmode}", "{sample}", "calculate_TIN_scores.log")
+ threads: 8
+ singularity:
+ "docker://zavolab/tin_score_calculation:0.1.0"
+ shell:
+ "tin_score_calculation.py \
+ -i {params.bam} \
+ -r {input.transcripts_bed12} \
+ -c 0 \
+ --names {params.sample} \
+ -n 100 \
+ 1> {output.TIN_score} \
+ 2> {log}"
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index c53d0db..6b992f3 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,274 +1,269 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+<!-- Generated by graphviz version 2.38.0 (20140413.2041)
-->
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-<path fill="none" stroke="grey" stroke-width="2" d="M1532.96,-143.94C1427.4,-114.2 1212.71,-53.71 1126.53,-29.43"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1127.24,-26 1116.67,-26.65 1125.34,-32.74 1127.24,-26"/>
+<g id="edge8" class="edge"><title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1008.61,-78.2159C933.016,-63.7572 800.875,-38.4843 736.452,-26.1629"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="736.823,-22.6705 726.343,-24.2296 735.508,-29.5459 736.823,-22.6705"/>
</g>
<!-- 9 -->
-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M844,-180C844,-180 743,-180 743,-180 737,-180 731,-174 731,-168 731,-168 731,-156 731,-156 731,-150 737,-144 743,-144 743,-144 844,-144 844,-144 850,-144 856,-150 856,-156 856,-156 856,-168 856,-168 856,-174 850,-180 844,-180"/>
-<text text-anchor="middle" x="793.5" y="-159.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M726,-326.5C726,-326.5 614,-326.5 614,-326.5 608,-326.5 602,-320.5 602,-314.5 602,-314.5 602,-302.5 602,-302.5 602,-296.5 608,-290.5 614,-290.5 614,-290.5 726,-290.5 726,-290.5 732,-290.5 738,-296.5 738,-302.5 738,-302.5 738,-314.5 738,-314.5 738,-320.5 732,-326.5 726,-326.5"/>
+<text text-anchor="middle" x="670" y="-306" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
<!-- 9->3 -->
-<g id="edge9" class="edge">
-<title>9->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M796.22,-143.7C797.43,-135.98 798.89,-126.71 800.24,-118.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="803.72,-118.53 801.81,-108.1 796.8,-117.44 803.72,-118.53"/>
+<g id="edge9" class="edge"><title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M620.97,-290.41C590.929,-279.939 552.3,-266.475 520.644,-255.441"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="521.655,-252.087 511.061,-252.1 519.351,-258.697 521.655,-252.087"/>
+</g>
+<!-- 9->5 -->
+<g id="edge13" class="edge"><title>9->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M690.381,-290.319C701.627,-280.838 715.758,-268.925 728.024,-258.585"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="730.376,-261.18 735.765,-252.058 725.864,-255.828 730.376,-261.18"/>
+</g>
+<!-- 18 -->
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M1126.5,-252C1126.5,-252 1037.5,-252 1037.5,-252 1031.5,-252 1025.5,-246 1025.5,-240 1025.5,-240 1025.5,-228 1025.5,-228 1025.5,-222 1031.5,-216 1037.5,-216 1037.5,-216 1126.5,-216 1126.5,-216 1132.5,-216 1138.5,-222 1138.5,-228 1138.5,-228 1138.5,-240 1138.5,-240 1138.5,-246 1132.5,-252 1126.5,-252"/>
+<text text-anchor="middle" x="1082" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+</g>
+<!-- 9->18 -->
+<g id="edge26" class="edge"><title>9->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M738.35,-290.717C742.959,-289.749 747.541,-288.832 752,-288 865.226,-266.87 898.018,-274.364 1015.13,-252.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1016.06,-255.415 1025.21,-250.075 1014.73,-248.543 1016.06,-255.415"/>
</g>
<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M969,-180C969,-180 886,-180 886,-180 880,-180 874,-174 874,-168 874,-168 874,-156 874,-156 874,-150 880,-144 886,-144 886,-144 969,-144 969,-144 975,-144 981,-150 981,-156 981,-156 981,-168 981,-168 981,-174 975,-180 969,-180"/>
-<text text-anchor="middle" x="927.5" y="-159.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M541.5,-329C541.5,-329 440.5,-329 440.5,-329 434.5,-329 428.5,-323 428.5,-317 428.5,-317 428.5,-300 428.5,-300 428.5,-294 434.5,-288 440.5,-288 440.5,-288 541.5,-288 541.5,-288 547.5,-288 553.5,-294 553.5,-300 553.5,-300 553.5,-317 553.5,-317 553.5,-323 547.5,-329 541.5,-329"/>
+<text text-anchor="middle" x="491" y="-317" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="491" y="-306" font-family="sans" font-size="10.00">kmer: 31</text>
+<text text-anchor="middle" x="491" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 10->3 -->
+<g id="edge10" class="edge"><title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M483.076,-287.689C479.859,-279.647 476.094,-270.236 472.644,-261.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="475.891,-260.304 468.928,-252.319 469.392,-262.904 475.891,-260.304"/>
</g>
<!-- 10->4 -->
-<g id="edge10" class="edge">
-<title>10->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M951.72,-143.88C964.42,-134.89 980.16,-123.76 993.92,-114.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="996.04,-116.82 1002.19,-108.19 992,-111.11 996.04,-116.82"/>
+<g id="edge12" class="edge"><title>10->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M520.226,-287.88C533.987,-278.643 550.489,-267.565 564.825,-257.941"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="567.076,-260.646 573.428,-252.166 563.174,-254.834 567.076,-260.646"/>
</g>
<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1096.5,-254.5C1096.5,-254.5 968.5,-254.5 968.5,-254.5 962.5,-254.5 956.5,-248.5 956.5,-242.5 956.5,-242.5 956.5,-230.5 956.5,-230.5 956.5,-224.5 962.5,-218.5 968.5,-218.5 968.5,-218.5 1096.5,-218.5 1096.5,-218.5 1102.5,-218.5 1108.5,-224.5 1108.5,-230.5 1108.5,-230.5 1108.5,-242.5 1108.5,-242.5 1108.5,-248.5 1102.5,-254.5 1096.5,-254.5"/>
-<text text-anchor="middle" x="1032.5" y="-234" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
-</g>
-<!-- 11->5 -->
-<g id="edge11" class="edge">
-<title>11->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1041.51,-218.32C1046.1,-209.56 1051.77,-198.73 1056.89,-188.97"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1060.02,-190.54 1061.56,-180.06 1053.82,-187.29 1060.02,-190.54"/>
-</g>
-<!-- 11->7 -->
-<g id="edge15" class="edge">
-<title>11->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1108.81,-220.3C1164.79,-209.15 1241.19,-193.93 1301.19,-181.98"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1301.93,-185.4 1311.06,-180.02 1300.57,-178.54 1301.93,-185.4"/>
-</g>
-<!-- 11->9 -->
-<g id="edge20" class="edge">
-<title>11->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M976.16,-218.41C941.2,-207.8 896.11,-194.13 859.48,-183.01"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="860.46,-179.65 849.87,-180.1 858.43,-186.35 860.46,-179.65"/>
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M1015,-326.5C1015,-326.5 919,-326.5 919,-326.5 913,-326.5 907,-320.5 907,-314.5 907,-314.5 907,-302.5 907,-302.5 907,-296.5 913,-290.5 919,-290.5 919,-290.5 1015,-290.5 1015,-290.5 1021,-290.5 1027,-296.5 1027,-302.5 1027,-302.5 1027,-314.5 1027,-314.5 1027,-320.5 1021,-326.5 1015,-326.5"/>
+<text text-anchor="middle" x="967" y="-306" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+</g>
+<!-- 11->4 -->
+<g id="edge11" class="edge"><title>11->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M906.62,-290.63C902.698,-289.695 898.8,-288.808 895,-288 796.444,-267.04 767.467,-272.788 664.451,-251.962"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="665.082,-248.518 654.582,-249.932 663.672,-255.375 665.082,-248.518"/>
+</g>
+<!-- 11->6 -->
+<g id="edge15" class="edge"><title>11->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M958.705,-290.319C954.521,-281.651 949.355,-270.949 944.685,-261.276"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="947.734,-259.542 940.235,-252.058 941.431,-262.585 947.734,-259.542"/>
+</g>
+<!-- 19 -->
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M1241.5,-252C1241.5,-252 1168.5,-252 1168.5,-252 1162.5,-252 1156.5,-246 1156.5,-240 1156.5,-240 1156.5,-228 1156.5,-228 1156.5,-222 1162.5,-216 1168.5,-216 1168.5,-216 1241.5,-216 1241.5,-216 1247.5,-216 1253.5,-222 1253.5,-228 1253.5,-228 1253.5,-240 1253.5,-240 1253.5,-246 1247.5,-252 1241.5,-252"/>
+<text text-anchor="middle" x="1205" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
+</g>
+<!-- 11->19 -->
+<g id="edge28" class="edge"><title>11->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1023.1,-290.41C1060.19,-279.112 1108.72,-264.329 1146.32,-252.874"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1147.58,-256.15 1156.13,-249.888 1145.54,-249.454 1147.58,-256.15"/>
</g>
<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1267,-257C1267,-257 1152,-257 1152,-257 1146,-257 1140,-251 1140,-245 1140,-245 1140,-228 1140,-228 1140,-222 1146,-216 1152,-216 1152,-216 1267,-216 1267,-216 1273,-216 1279,-222 1279,-228 1279,-228 1279,-245 1279,-245 1279,-251 1273,-257 1267,-257"/>
-<text text-anchor="middle" x="1209.5" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
-<text text-anchor="middle" x="1209.5" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
-<text text-anchor="middle" x="1209.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M873.5,-326.5C873.5,-326.5 772.5,-326.5 772.5,-326.5 766.5,-326.5 760.5,-320.5 760.5,-314.5 760.5,-314.5 760.5,-302.5 760.5,-302.5 760.5,-296.5 766.5,-290.5 772.5,-290.5 772.5,-290.5 873.5,-290.5 873.5,-290.5 879.5,-290.5 885.5,-296.5 885.5,-302.5 885.5,-302.5 885.5,-314.5 885.5,-314.5 885.5,-320.5 879.5,-326.5 873.5,-326.5"/>
+<text text-anchor="middle" x="823" y="-311.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<text text-anchor="middle" x="823" y="-300.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 12->5 -->
-<g id="edge12" class="edge">
-<title>12->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1171.88,-215.88C1153.51,-206.29 1131.33,-194.73 1112.41,-184.86"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1113.9,-181.69 1103.41,-180.17 1110.66,-187.89 1113.9,-181.69"/>
+<g id="edge14" class="edge"><title>12->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M807.122,-290.319C798.611,-281.109 787.979,-269.604 778.618,-259.475"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="781.122,-257.027 771.764,-252.058 775.981,-261.778 781.122,-257.027"/>
</g>
<!-- 12->6 -->
-<g id="edge14" class="edge">
-<title>12->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1213.05,-215.69C1214.46,-207.82 1216.11,-198.64 1217.63,-190.17"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1221.07,-190.78 1219.39,-180.32 1214.18,-189.54 1221.07,-190.78"/>
+<g id="edge16" class="edge"><title>12->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M848.831,-290.319C863.492,-280.567 882.022,-268.242 897.868,-257.702"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="899.966,-260.511 906.354,-252.058 896.089,-254.682 899.966,-260.511"/>
</g>
<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#56a9d8" stroke-width="2" d="M1427.5,-254.5C1427.5,-254.5 1317.5,-254.5 1317.5,-254.5 1311.5,-254.5 1305.5,-248.5 1305.5,-242.5 1305.5,-242.5 1305.5,-230.5 1305.5,-230.5 1305.5,-224.5 1311.5,-218.5 1317.5,-218.5 1317.5,-218.5 1427.5,-218.5 1427.5,-218.5 1433.5,-218.5 1439.5,-224.5 1439.5,-230.5 1439.5,-230.5 1439.5,-242.5 1439.5,-242.5 1439.5,-248.5 1433.5,-254.5 1427.5,-254.5"/>
-<text text-anchor="middle" x="1372.5" y="-234" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
-</g>
-<!-- 13->6 -->
-<g id="edge13" class="edge">
-<title>13->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1336.95,-218.32C1316.03,-208.21 1289.38,-195.33 1267.06,-184.54"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1268.32,-181.26 1257.79,-180.06 1265.27,-187.56 1268.32,-181.26"/>
-</g>
-<!-- 13->8 -->
-<g id="edge17" class="edge">
-<title>13->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1424.59,-218.41C1456.65,-207.89 1497.91,-194.36 1531.63,-183.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1532.96,-186.54 1541.37,-180.1 1530.78,-179.89 1532.96,-186.54"/>
-</g>
-<!-- 13->10 -->
-<g id="edge22" class="edge">
-<title>13->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1305.35,-219.41C1299.33,-218.18 1293.32,-217.02 1287.5,-216 1159.72,-193.66 1122.81,-204.81 991.39,-180"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="991.82,-176.52 981.34,-178.07 990.5,-183.4 991.82,-176.52"/>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M962,-180C962,-180 796,-180 796,-180 790,-180 784,-174 784,-168 784,-168 784,-156 784,-156 784,-150 790,-144 796,-144 796,-144 962,-144 962,-144 968,-144 974,-150 974,-156 974,-156 974,-168 974,-168 974,-174 968,-180 962,-180"/>
+<text text-anchor="middle" x="879" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
+</g>
+<!-- 13->7 -->
+<g id="edge17" class="edge"><title>13->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M879,-143.697C879,-135.983 879,-126.712 879,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="882.5,-118.104 879,-108.104 875.5,-118.104 882.5,-118.104"/>
</g>
<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M1618,-254.5C1618,-254.5 1503,-254.5 1503,-254.5 1497,-254.5 1491,-248.5 1491,-242.5 1491,-242.5 1491,-230.5 1491,-230.5 1491,-224.5 1497,-218.5 1503,-218.5 1503,-218.5 1618,-218.5 1618,-218.5 1624,-218.5 1630,-224.5 1630,-230.5 1630,-230.5 1630,-242.5 1630,-242.5 1630,-248.5 1624,-254.5 1618,-254.5"/>
-<text text-anchor="middle" x="1560.5" y="-239.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
-<text text-anchor="middle" x="1560.5" y="-228.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M1125.5,-180C1125.5,-180 1004.5,-180 1004.5,-180 998.5,-180 992.5,-174 992.5,-168 992.5,-168 992.5,-156 992.5,-156 992.5,-150 998.5,-144 1004.5,-144 1004.5,-144 1125.5,-144 1125.5,-144 1131.5,-144 1137.5,-150 1137.5,-156 1137.5,-156 1137.5,-168 1137.5,-168 1137.5,-174 1131.5,-180 1125.5,-180"/>
+<text text-anchor="middle" x="1065" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 14->7 -->
-<g id="edge16" class="edge">
-<title>14->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1521.63,-218.32C1498.45,-208.07 1468.84,-194.98 1444.24,-184.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1445.65,-180.9 1435.09,-180.06 1442.82,-187.3 1445.65,-180.9"/>
+<g id="edge18" class="edge"><title>14->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1019.5,-143.876C993.62,-134.137 961.033,-121.872 933.759,-111.608"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="934.945,-108.315 924.353,-108.068 932.479,-114.866 934.945,-108.315"/>
</g>
<!-- 14->8 -->
-<g id="edge18" class="edge">
-<title>14->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1568.32,-218.32C1572.27,-209.65 1577.14,-198.95 1581.54,-189.28"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1584.78,-190.61 1585.74,-180.06 1578.41,-187.71 1584.78,-190.61"/>
+<g id="edge20" class="edge"><title>14->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1065,-143.697C1065,-135.983 1065,-126.712 1065,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1068.5,-118.104 1065,-108.104 1061.5,-118.104 1068.5,-118.104"/>
</g>
<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M901,-257C901,-257 786,-257 786,-257 780,-257 774,-251 774,-245 774,-245 774,-228 774,-228 774,-222 780,-216 786,-216 786,-216 901,-216 901,-216 907,-216 913,-222 913,-228 913,-228 913,-245 913,-245 913,-251 907,-257 901,-257"/>
-<text text-anchor="middle" x="843.5" y="-245" font-family="sans" font-size="10.00">create_index_star</text>
-<text text-anchor="middle" x="843.5" y="-234" font-family="sans" font-size="10.00">index_size: 75</text>
-<text text-anchor="middle" x="843.5" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
-</g>
-<!-- 15->9 -->
-<g id="edge19" class="edge">
-<title>15->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M829.84,-215.69C824.11,-207.39 817.38,-197.63 811.28,-188.78"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="814,-186.56 805.44,-180.32 808.24,-190.54 814,-186.56"/>
-</g>
-<!-- 15->10 -->
-<g id="edge21" class="edge">
-<title>15->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M866.45,-215.69C876.85,-206.72 889.22,-196.04 900.1,-186.65"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="902.43,-189.26 907.71,-180.08 897.86,-183.96 902.43,-189.26"/>
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1318,-180C1318,-180 1168,-180 1168,-180 1162,-180 1156,-174 1156,-168 1156,-168 1156,-156 1156,-156 1156,-150 1162,-144 1168,-144 1168,-144 1318,-144 1318,-144 1324,-144 1330,-150 1330,-156 1330,-156 1330,-168 1330,-168 1330,-174 1324,-180 1318,-180"/>
+<text text-anchor="middle" x="1243" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+</g>
+<!-- 15->8 -->
+<g id="edge19" class="edge"><title>15->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1199.46,-143.876C1174.8,-134.179 1143.78,-121.98 1117.75,-111.743"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.99,-108.471 1108.4,-108.068 1116.43,-114.985 1118.99,-108.471"/>
</g>
<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#8fd856" stroke-width="2" d="M1179,-329C1179,-329 878,-329 878,-329 872,-329 866,-323 866,-317 866,-317 866,-305 866,-305 866,-299 872,-293 878,-293 878,-293 1179,-293 1179,-293 1185,-293 1191,-299 1191,-305 1191,-305 1191,-317 1191,-317 1191,-323 1185,-329 1179,-329"/>
-<text text-anchor="middle" x="1028.5" y="-314" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1028.5" y="-303" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
-</g>
-<!-- 16->11 -->
-<g id="edge23" class="edge">
-<title>16->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1029.45,-292.82C1029.91,-284.42 1030.48,-274.12 1031,-264.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1034.5,-264.74 1031.56,-254.56 1027.51,-264.35 1034.5,-264.74"/>
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M791,-401C791,-401 523,-401 523,-401 517,-401 511,-395 511,-389 511,-389 511,-377 511,-377 511,-371 517,-365 523,-365 523,-365 791,-365 791,-365 797,-365 803,-371 803,-377 803,-377 803,-389 803,-389 803,-395 797,-401 791,-401"/>
+<text text-anchor="middle" x="657" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="657" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 16->9 -->
+<g id="edge21" class="edge"><title>16->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M660.081,-364.819C661.586,-356.422 663.434,-346.116 665.125,-336.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="668.621,-337.019 666.941,-326.558 661.731,-335.783 668.621,-337.019"/>
</g>
<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M1534,-329C1534,-329 1221,-329 1221,-329 1215,-329 1209,-323 1209,-317 1209,-317 1209,-305 1209,-305 1209,-299 1215,-293 1221,-293 1221,-293 1534,-293 1534,-293 1540,-293 1546,-299 1546,-305 1546,-305 1546,-317 1546,-317 1546,-323 1540,-329 1534,-329"/>
-<text text-anchor="middle" x="1377.5" y="-314" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1377.5" y="-303" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
-</g>
-<!-- 17->13 -->
-<g id="edge24" class="edge">
-<title>17->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1376.32,-292.82C1375.74,-284.42 1375.03,-274.12 1374.37,-264.69"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1377.86,-264.29 1373.68,-254.56 1370.87,-264.78 1377.86,-264.29"/>
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M1113,-401C1113,-401 833,-401 833,-401 827,-401 821,-395 821,-389 821,-389 821,-377 821,-377 821,-371 827,-365 833,-365 833,-365 1113,-365 1113,-365 1119,-365 1125,-371 1125,-377 1125,-377 1125,-389 1125,-389 1125,-395 1119,-401 1113,-401"/>
+<text text-anchor="middle" x="973" y="-386" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="973" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+</g>
+<!-- 17->11 -->
+<g id="edge22" class="edge"><title>17->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M971.578,-364.819C970.883,-356.422 970.03,-346.116 969.25,-336.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="972.725,-336.235 968.412,-326.558 965.748,-336.813 972.725,-336.235"/>
+</g>
+<!-- 18->13 -->
+<g id="edge23" class="edge"><title>18->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1032.6,-215.966C1004.11,-206.142 968.114,-193.729 938.129,-183.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="939.216,-180.062 928.621,-180.111 936.934,-186.68 939.216,-180.062"/>
+</g>
+<!-- 19->15 -->
+<g id="edge24" class="edge"><title>19->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1214.39,-215.697C1218.76,-207.644 1224.06,-197.894 1228.9,-188.982"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1232.02,-190.563 1233.71,-180.104 1225.87,-187.223 1232.02,-190.563"/>
+</g>
+<!-- 20 -->
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M1193.5,-329C1193.5,-329 1092.5,-329 1092.5,-329 1086.5,-329 1080.5,-323 1080.5,-317 1080.5,-317 1080.5,-300 1080.5,-300 1080.5,-294 1086.5,-288 1092.5,-288 1092.5,-288 1193.5,-288 1193.5,-288 1199.5,-288 1205.5,-294 1205.5,-300 1205.5,-300 1205.5,-317 1205.5,-317 1205.5,-323 1199.5,-329 1193.5,-329"/>
+<text text-anchor="middle" x="1143" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1143" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1143" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 20->18 -->
+<g id="edge25" class="edge"><title>20->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1126.33,-287.689C1119.2,-279.215 1110.79,-269.22 1103.22,-260.226"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1105.69,-257.718 1096.57,-252.319 1100.33,-262.225 1105.69,-257.718"/>
+</g>
+<!-- 20->19 -->
+<g id="edge27" class="edge"><title>20->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1159.94,-287.689C1167.26,-279.128 1175.91,-269.016 1183.66,-259.951"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1186.35,-262.194 1190.19,-252.319 1181.03,-257.645 1186.35,-262.194"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 11a2f35..5c845f5 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,265 +1,243 @@
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<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.42.3 (20191010.1750)
+<!-- Generated by graphviz version 2.38.0 (20140413.2041)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1143pt" height="332pt"
- viewBox="0.00 0.00 1143.00 332.00" 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(4 328)">
+<svg width="940pt" height="404pt"
+ viewBox="0.00 0.00 939.50 404.00" 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="white" stroke="transparent" points="-4,4 -4,-328 1139,-328 1139,4 -4,4"/>
+<polygon fill="white" stroke="none" points="-4,4 -4,-400 935.5,-400 935.5,4 -4,4"/>
<!-- 0 -->
-<g id="node1" class="node">
-<title>0</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M561,-36C561,-36 531,-36 531,-36 525,-36 519,-30 519,-24 519,-24 519,-12 519,-12 519,-6 525,0 531,0 531,0 561,0 561,0 567,0 573,-6 573,-12 573,-12 573,-24 573,-24 573,-30 567,-36 561,-36"/>
-<text text-anchor="middle" x="546" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node"><title>0</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M296.5,-36C296.5,-36 266.5,-36 266.5,-36 260.5,-36 254.5,-30 254.5,-24 254.5,-24 254.5,-12 254.5,-12 254.5,-6 260.5,-0 266.5,-0 266.5,-0 296.5,-0 296.5,-0 302.5,-0 308.5,-6 308.5,-12 308.5,-12 308.5,-24 308.5,-24 308.5,-30 302.5,-36 296.5,-36"/>
+<text text-anchor="middle" x="281.5" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
-<g id="node2" class="node">
-<title>1</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M52,-108C52,-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 52,-72 52,-72 58,-72 64,-78 64,-84 64,-84 64,-96 64,-96 64,-102 58,-108 52,-108"/>
-<text text-anchor="middle" x="32" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
+<g id="node2" class="node"><title>1</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M131,-108C131,-108 96,-108 96,-108 90,-108 84,-102 84,-96 84,-96 84,-84 84,-84 84,-78 90,-72 96,-72 96,-72 131,-72 131,-72 137,-72 143,-78 143,-84 143,-84 143,-96 143,-96 143,-102 137,-108 131,-108"/>
+<text text-anchor="middle" x="113.5" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
</g>
<!-- 1->0 -->
-<g id="edge3" class="edge">
-<title>1->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M64.39,-74.6C67.27,-73.62 70.16,-72.73 73,-72 231.51,-31.13 427.95,-21.78 508.69,-19.64"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="508.94,-23.13 518.85,-19.39 508.77,-16.13 508.94,-23.13"/>
+<g id="edge5" class="edge"><title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M143.282,-75.9405C146.391,-74.6005 149.507,-73.2669 152.5,-72 183.541,-58.86 218.97,-44.3377 244.835,-33.8224"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="246.302,-37.0044 254.25,-29.9997 243.668,-30.5186 246.302,-37.0044"/>
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-<g id="node3" class="node">
-<title>2</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M124,-108C124,-108 94,-108 94,-108 88,-108 82,-102 82,-96 82,-96 82,-84 82,-84 82,-78 88,-72 94,-72 94,-72 124,-72 124,-72 130,-72 136,-78 136,-84 136,-84 136,-96 136,-96 136,-102 130,-108 124,-108"/>
-<text text-anchor="middle" x="109" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
+<g id="node3" class="node"><title>2</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M203.5,-108C203.5,-108 173.5,-108 173.5,-108 167.5,-108 161.5,-102 161.5,-96 161.5,-96 161.5,-84 161.5,-84 161.5,-78 167.5,-72 173.5,-72 173.5,-72 203.5,-72 203.5,-72 209.5,-72 215.5,-78 215.5,-84 215.5,-84 215.5,-96 215.5,-96 215.5,-102 209.5,-108 203.5,-108"/>
+<text text-anchor="middle" x="188.5" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
</g>
<!-- 2->0 -->
-<g id="edge8" class="edge">
-<title>2->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M136.17,-75.1C139.1,-73.92 142.08,-72.86 145,-72 274.75,-33.8 436.26,-23.08 508.28,-20.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="508.79,-23.6 518.65,-19.72 508.53,-16.6 508.79,-23.6"/>
+<g id="edge6" class="edge"><title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M211.489,-71.6966C223.314,-62.796 237.892,-51.8232 250.679,-42.1989"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="252.891,-44.9145 258.776,-36.1043 248.681,-39.3217 252.891,-44.9145"/>
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-<g id="node4" class="node">
-<title>3</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M355.5,-108C355.5,-108 166.5,-108 166.5,-108 160.5,-108 154.5,-102 154.5,-96 154.5,-96 154.5,-84 154.5,-84 154.5,-78 160.5,-72 166.5,-72 166.5,-72 355.5,-72 355.5,-72 361.5,-72 367.5,-78 367.5,-84 367.5,-84 367.5,-96 367.5,-96 367.5,-102 361.5,-108 355.5,-108"/>
-<text text-anchor="middle" x="261" y="-87.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
+<g id="node4" class="node"><title>3</title>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M115,-252C115,-252 12,-252 12,-252 6,-252 -7.10543e-15,-246 -7.10543e-15,-240 -7.10543e-15,-240 -7.10543e-15,-228 -7.10543e-15,-228 -7.10543e-15,-222 6,-216 12,-216 12,-216 115,-216 115,-216 121,-216 127,-222 127,-228 127,-228 127,-240 127,-240 127,-246 121,-252 115,-252"/>
+<text text-anchor="middle" x="63.5" y="-231.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
<!-- 3->0 -->
-<g id="edge4" class="edge">
-<title>3->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M330.35,-71.97C386.61,-58.15 463.72,-39.21 508.87,-28.12"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="509.93,-31.46 518.81,-25.68 508.26,-24.66 509.93,-31.46"/>
+<g id="edge7" class="edge"><title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M90.8692,-215.973C124.885,-193.92 183.454,-152.942 224.5,-108 241.966,-88.8761 257.5,-63.7838 267.923,-45.1186"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="271.035,-46.723 272.753,-36.2684 264.89,-43.3697 271.035,-46.723"/>
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-<title>4</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M569,-108C569,-108 397,-108 397,-108 391,-108 385,-102 385,-96 385,-96 385,-84 385,-84 385,-78 391,-72 397,-72 397,-72 569,-72 569,-72 575,-72 581,-78 581,-84 581,-84 581,-96 581,-96 581,-102 575,-108 569,-108"/>
-<text text-anchor="middle" x="483" y="-87.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<g id="node5" class="node"><title>4</title>
+<path fill="none" stroke="#d8bc56" stroke-width="2" d="M244,-252C244,-252 157,-252 157,-252 151,-252 145,-246 145,-240 145,-240 145,-228 145,-228 145,-222 151,-216 157,-216 157,-216 244,-216 244,-216 250,-216 256,-222 256,-228 256,-228 256,-240 256,-240 256,-246 250,-252 244,-252"/>
+<text text-anchor="middle" x="200.5" y="-231.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
<!-- 4->0 -->
-<g id="edge6" class="edge">
-<title>4->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M498.57,-71.7C506.2,-63.22 515.52,-52.86 523.88,-43.58"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="526.52,-45.88 530.61,-36.1 521.31,-41.2 526.52,-45.88"/>
+<g id="edge3" class="edge"><title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M225.562,-215.933C237.162,-206.679 250.005,-194.227 257.5,-180 279.985,-137.319 283.155,-79.9722 282.771,-46.4954"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="286.261,-46.0283 282.527,-36.1132 279.263,-46.1926 286.261,-46.0283"/>
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<!-- 5 -->
-<g id="node6" class="node">
-<title>5</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M586,-180C586,-180 468,-180 468,-180 462,-180 456,-174 456,-168 456,-168 456,-156 456,-156 456,-150 462,-144 468,-144 468,-144 586,-144 586,-144 592,-144 598,-150 598,-156 598,-156 598,-168 598,-168 598,-174 592,-180 586,-180"/>
-<text text-anchor="middle" x="527" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<g id="node6" class="node"><title>5</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M428.5,-252C428.5,-252 286.5,-252 286.5,-252 280.5,-252 274.5,-246 274.5,-240 274.5,-240 274.5,-228 274.5,-228 274.5,-222 280.5,-216 286.5,-216 286.5,-216 428.5,-216 428.5,-216 434.5,-216 440.5,-222 440.5,-228 440.5,-228 440.5,-240 440.5,-240 440.5,-246 434.5,-252 428.5,-252"/>
+<text text-anchor="middle" x="357.5" y="-231.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 5->0 -->
-<g id="edge5" class="edge">
-<title>5->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M557.3,-143.8C569.88,-134.9 583.12,-122.77 590,-108 596.75,-93.49 595.43,-87.05 590,-72 586.25,-61.6 579.46,-51.8 572.33,-43.52"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="574.83,-41.06 565.47,-36.08 569.68,-45.81 574.83,-41.06"/>
+<g id="edge4" class="edge"><title>5->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M351.409,-215.849C338.207,-178.675 306.871,-90.4388 291.025,-45.8204"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="294.265,-44.4845 287.62,-36.2325 287.668,-46.8272 294.265,-44.4845"/>
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-<g id="node7" class="node">
-<title>6</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M729.5,-180C729.5,-180 628.5,-180 628.5,-180 622.5,-180 616.5,-174 616.5,-168 616.5,-168 616.5,-156 616.5,-156 616.5,-150 622.5,-144 628.5,-144 628.5,-144 729.5,-144 729.5,-144 735.5,-144 741.5,-150 741.5,-156 741.5,-156 741.5,-168 741.5,-168 741.5,-174 735.5,-180 729.5,-180"/>
-<text text-anchor="middle" x="679" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<g id="node7" class="node"><title>6</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M596.5,-252C596.5,-252 470.5,-252 470.5,-252 464.5,-252 458.5,-246 458.5,-240 458.5,-240 458.5,-228 458.5,-228 458.5,-222 464.5,-216 470.5,-216 470.5,-216 596.5,-216 596.5,-216 602.5,-216 608.5,-222 608.5,-228 608.5,-228 608.5,-240 608.5,-240 608.5,-246 602.5,-252 596.5,-252"/>
+<text text-anchor="middle" x="533.5" y="-231.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 6->0 -->
-<g id="edge2" class="edge">
-<title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M666.56,-143.86C652.82,-125.38 629.64,-95.45 607,-72 597.14,-61.79 585.54,-51.36 575.12,-42.5"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="577.34,-39.79 567.43,-36.05 572.84,-45.15 577.34,-39.79"/>
+<g id="edge2" class="edge"><title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M466.704,-215.888C430.604,-205.599 390.594,-192.18 376.5,-180 335.744,-144.78 350.057,-117.673 321.5,-72 315.633,-62.6164 308.541,-52.8174 301.968,-44.2341"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="304.545,-41.8464 295.633,-36.1164 299.026,-46.1532 304.545,-41.8464"/>
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<!-- 7 -->
-<g id="node8" class="node">
-<title>7</title>
-<path fill="none" stroke="#56d8a9" stroke-width="2" d="M934.5,-180C934.5,-180 771.5,-180 771.5,-180 765.5,-180 759.5,-174 759.5,-168 759.5,-168 759.5,-156 759.5,-156 759.5,-150 765.5,-144 771.5,-144 771.5,-144 934.5,-144 934.5,-144 940.5,-144 946.5,-150 946.5,-156 946.5,-156 946.5,-168 946.5,-168 946.5,-174 940.5,-180 934.5,-180"/>
-<text text-anchor="middle" x="853" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<g id="node8" class="node"><title>7</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M617.5,-108C617.5,-108 529.5,-108 529.5,-108 523.5,-108 517.5,-102 517.5,-96 517.5,-96 517.5,-84 517.5,-84 517.5,-78 523.5,-72 529.5,-72 529.5,-72 617.5,-72 617.5,-72 623.5,-72 629.5,-78 629.5,-84 629.5,-84 629.5,-96 629.5,-96 629.5,-102 623.5,-108 617.5,-108"/>
+<text text-anchor="middle" x="573.5" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 7->0 -->
-<g id="edge7" class="edge">
-<title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M815.97,-143.87C756.75,-116.48 641.43,-63.14 582.53,-35.9"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="583.78,-32.62 573.24,-31.6 580.84,-38.97 583.78,-32.62"/>
+<g id="edge1" class="edge"><title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M517.199,-75.5033C458.593,-61.4537 368.502,-39.8566 318.378,-27.8405"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="319.151,-24.4268 308.61,-25.4991 317.519,-31.2339 319.151,-24.4268"/>
</g>
<!-- 8 -->
-<g id="node9" class="node">
-<title>8</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M1123,-180C1123,-180 977,-180 977,-180 971,-180 965,-174 965,-168 965,-168 965,-156 965,-156 965,-150 971,-144 977,-144 977,-144 1123,-144 1123,-144 1129,-144 1135,-150 1135,-156 1135,-156 1135,-168 1135,-168 1135,-174 1129,-180 1123,-180"/>
-<text text-anchor="middle" x="1050" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node9" class="node"><title>8</title>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M360.5,-324C360.5,-324 248.5,-324 248.5,-324 242.5,-324 236.5,-318 236.5,-312 236.5,-312 236.5,-300 236.5,-300 236.5,-294 242.5,-288 248.5,-288 248.5,-288 360.5,-288 360.5,-288 366.5,-288 372.5,-294 372.5,-300 372.5,-300 372.5,-312 372.5,-312 372.5,-318 366.5,-324 360.5,-324"/>
+<text text-anchor="middle" x="304.5" y="-303.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
-<!-- 8->0 -->
-<g id="edge1" class="edge">
-<title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M989.46,-143.94C883.9,-114.2 669.21,-53.71 583.03,-29.43"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="583.74,-26 573.17,-26.65 581.84,-32.74 583.74,-26"/>
+<!-- 8->3 -->
+<g id="edge9" class="edge"><title>8->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M245.853,-287.966C211.594,-278.015 168.184,-265.406 132.314,-254.987"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="132.989,-251.539 122.41,-252.111 131.037,-258.261 132.989,-251.539"/>
+</g>
+<!-- 8->5 -->
+<g id="edge13" class="edge"><title>8->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M317.601,-287.697C323.891,-279.389 331.547,-269.277 338.465,-260.141"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="341.304,-262.19 344.55,-252.104 335.723,-257.964 341.304,-262.19"/>
+</g>
+<!-- 17 -->
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#59d856" stroke-width="2" d="M728,-252C728,-252 639,-252 639,-252 633,-252 627,-246 627,-240 627,-240 627,-228 627,-228 627,-222 633,-216 639,-216 639,-216 728,-216 728,-216 734,-216 740,-222 740,-228 740,-228 740,-240 740,-240 740,-246 734,-252 728,-252"/>
+<text text-anchor="middle" x="683.5" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+</g>
+<!-- 8->17 -->
+<g id="edge24" class="edge"><title>8->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M372.886,-289.657C375.793,-289.082 378.674,-288.527 381.5,-288 482.647,-269.141 511.799,-272.997 616.656,-252.052"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="617.597,-255.433 626.703,-250.017 616.207,-248.572 617.597,-255.433"/>
</g>
<!-- 9 -->
-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M300.5,-180C300.5,-180 199.5,-180 199.5,-180 193.5,-180 187.5,-174 187.5,-168 187.5,-168 187.5,-156 187.5,-156 187.5,-150 193.5,-144 199.5,-144 199.5,-144 300.5,-144 300.5,-144 306.5,-144 312.5,-150 312.5,-156 312.5,-156 312.5,-168 312.5,-168 312.5,-174 306.5,-180 300.5,-180"/>
-<text text-anchor="middle" x="250" y="-159.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M156,-324C156,-324 71,-324 71,-324 65,-324 59,-318 59,-312 59,-312 59,-300 59,-300 59,-294 65,-288 71,-288 71,-288 156,-288 156,-288 162,-288 168,-294 168,-300 168,-300 168,-312 168,-312 168,-318 162,-324 156,-324"/>
+<text text-anchor="middle" x="113.5" y="-303.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 9->3 -->
-<g id="edge9" class="edge">
-<title>9->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M252.72,-143.7C253.93,-135.98 255.39,-126.71 256.74,-118.11"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="260.22,-118.53 258.31,-108.1 253.3,-117.44 260.22,-118.53"/>
+<g id="edge8" class="edge"><title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M101.14,-287.697C95.2672,-279.474 88.1309,-269.483 81.6576,-260.421"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="84.3779,-258.207 75.7174,-252.104 78.6817,-262.276 84.3779,-258.207"/>
+</g>
+<!-- 9->4 -->
+<g id="edge11" class="edge"><title>9->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M135.006,-287.697C145.963,-278.881 159.446,-268.032 171.325,-258.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="173.645,-261.1 179.242,-252.104 169.256,-255.646 173.645,-261.1"/>
</g>
<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M425.5,-180C425.5,-180 342.5,-180 342.5,-180 336.5,-180 330.5,-174 330.5,-168 330.5,-168 330.5,-156 330.5,-156 330.5,-150 336.5,-144 342.5,-144 342.5,-144 425.5,-144 425.5,-144 431.5,-144 437.5,-150 437.5,-156 437.5,-156 437.5,-168 437.5,-168 437.5,-174 431.5,-180 425.5,-180"/>
-<text text-anchor="middle" x="384" y="-159.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M624.5,-324C624.5,-324 528.5,-324 528.5,-324 522.5,-324 516.5,-318 516.5,-312 516.5,-312 516.5,-300 516.5,-300 516.5,-294 522.5,-288 528.5,-288 528.5,-288 624.5,-288 624.5,-288 630.5,-288 636.5,-294 636.5,-300 636.5,-300 636.5,-312 636.5,-312 636.5,-318 630.5,-324 624.5,-324"/>
+<text text-anchor="middle" x="576.5" y="-303.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 10->4 -->
-<g id="edge10" class="edge">
-<title>10->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M408.22,-143.88C420.92,-134.89 436.66,-123.76 450.42,-114.03"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="452.54,-116.82 458.69,-108.19 448.5,-111.11 452.54,-116.82"/>
+<g id="edge10" class="edge"><title>10->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M516.363,-289.831C513.372,-289.187 510.405,-288.573 507.5,-288 403.939,-267.586 373.787,-273.413 266.048,-251.975"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="266.572,-248.51 256.077,-249.958 265.184,-255.371 266.572,-248.51"/>
+</g>
+<!-- 10->6 -->
+<g id="edge14" class="edge"><title>10->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M565.871,-287.697C560.872,-279.559 554.809,-269.689 549.288,-260.701"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="552.223,-258.793 544.007,-252.104 546.259,-262.457 552.223,-258.793"/>
+</g>
+<!-- 18 -->
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M843,-252C843,-252 770,-252 770,-252 764,-252 758,-246 758,-240 758,-240 758,-228 758,-228 758,-222 764,-216 770,-216 770,-216 843,-216 843,-216 849,-216 855,-222 855,-228 855,-228 855,-240 855,-240 855,-246 849,-252 843,-252"/>
+<text text-anchor="middle" x="806.5" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
+</g>
+<!-- 10->18 -->
+<g id="edge25" class="edge"><title>10->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M632.47,-287.966C667.475,-277.312 712.49,-263.612 747.968,-252.814"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="749.158,-256.111 757.705,-249.851 747.119,-249.414 749.158,-256.111"/>
</g>
<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M528,-252C528,-252 400,-252 400,-252 394,-252 388,-246 388,-240 388,-240 388,-228 388,-228 388,-222 394,-216 400,-216 400,-216 528,-216 528,-216 534,-216 540,-222 540,-228 540,-228 540,-240 540,-240 540,-246 534,-252 528,-252"/>
-<text text-anchor="middle" x="464" y="-231.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#56d8c1" stroke-width="2" d="M486.5,-324C486.5,-324 402.5,-324 402.5,-324 396.5,-324 390.5,-318 390.5,-312 390.5,-312 390.5,-300 390.5,-300 390.5,-294 396.5,-288 402.5,-288 402.5,-288 486.5,-288 486.5,-288 492.5,-288 498.5,-294 498.5,-300 498.5,-300 498.5,-312 498.5,-312 498.5,-318 492.5,-324 486.5,-324"/>
+<text text-anchor="middle" x="444.5" y="-303.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
<!-- 11->5 -->
-<g id="edge11" class="edge">
-<title>11->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M479.57,-215.7C487.2,-207.22 496.52,-196.86 504.88,-187.58"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="507.52,-189.88 511.61,-180.1 502.31,-185.2 507.52,-189.88"/>
-</g>
-<!-- 11->7 -->
-<g id="edge15" class="edge">
-<title>11->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M540.44,-217.62C543.33,-217.07 546.19,-216.53 549,-216 615.58,-203.54 690.55,-190.46 749.38,-180.41"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="750.15,-183.83 759.42,-178.7 748.97,-176.93 750.15,-183.83"/>
-</g>
-<!-- 11->9 -->
-<g id="edge19" class="edge">
-<title>11->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M411.92,-215.97C381.76,-206.1 343.61,-193.62 311.92,-183.25"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="312.9,-179.89 302.31,-180.11 310.73,-186.55 312.9,-179.89"/>
+<g id="edge12" class="edge"><title>11->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M422.994,-287.697C412.037,-278.881 398.554,-268.032 386.675,-258.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="388.744,-255.646 378.758,-252.104 384.355,-261.1 388.744,-255.646"/>
+</g>
+<!-- 11->6 -->
+<g id="edge15" class="edge"><title>11->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M466.5,-287.697C477.709,-278.881 491.502,-268.032 503.654,-258.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="506.057,-261.038 511.753,-252.104 501.729,-255.535 506.057,-261.038"/>
</g>
<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M667.5,-252C667.5,-252 570.5,-252 570.5,-252 564.5,-252 558.5,-246 558.5,-240 558.5,-240 558.5,-228 558.5,-228 558.5,-222 564.5,-216 570.5,-216 570.5,-216 667.5,-216 667.5,-216 673.5,-216 679.5,-222 679.5,-228 679.5,-228 679.5,-240 679.5,-240 679.5,-246 673.5,-252 667.5,-252"/>
-<text text-anchor="middle" x="619" y="-231.5" font-family="sans" font-size="10.00">create_index_salmon</text>
-</g>
-<!-- 12->5 -->
-<g id="edge12" class="edge">
-<title>12->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M596.26,-215.7C584.56,-206.8 570.14,-195.82 557.49,-186.2"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="559.56,-183.37 549.48,-180.1 555.32,-188.94 559.56,-183.37"/>
-</g>
-<!-- 12->6 -->
-<g id="edge14" class="edge">
-<title>12->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M633.83,-215.7C641.02,-207.3 649.8,-197.07 657.69,-187.86"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="660.49,-189.97 664.34,-180.1 655.17,-185.42 660.49,-189.97"/>
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M563.5,-180C563.5,-180 397.5,-180 397.5,-180 391.5,-180 385.5,-174 385.5,-168 385.5,-168 385.5,-156 385.5,-156 385.5,-150 391.5,-144 397.5,-144 397.5,-144 563.5,-144 563.5,-144 569.5,-144 575.5,-150 575.5,-156 575.5,-156 575.5,-168 575.5,-168 575.5,-174 569.5,-180 563.5,-180"/>
+<text text-anchor="middle" x="480.5" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
+</g>
+<!-- 12->7 -->
+<g id="edge17" class="edge"><title>12->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M503.489,-143.697C515.314,-134.796 529.892,-123.823 542.679,-114.199"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="544.891,-116.915 550.776,-108.104 540.681,-111.322 544.891,-116.915"/>
</g>
<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M820,-252C820,-252 710,-252 710,-252 704,-252 698,-246 698,-240 698,-240 698,-228 698,-228 698,-222 704,-216 710,-216 710,-216 820,-216 820,-216 826,-216 832,-222 832,-228 832,-228 832,-240 832,-240 832,-246 826,-252 820,-252"/>
-<text text-anchor="middle" x="765" y="-231.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
-</g>
-<!-- 13->6 -->
-<g id="edge13" class="edge">
-<title>13->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M743.74,-215.7C732.91,-206.88 719.58,-196.03 707.84,-186.47"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="709.98,-183.7 700.01,-180.1 705.56,-189.13 709.98,-183.7"/>
-</g>
-<!-- 13->8 -->
-<g id="edge17" class="edge">
-<title>13->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M832.18,-216.5C873.55,-206.34 926.82,-193.26 970.32,-182.57"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="971.42,-185.9 980.29,-180.12 969.75,-179.11 971.42,-185.9"/>
-</g>
-<!-- 13->10 -->
-<g id="edge21" class="edge">
-<title>13->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M697.86,-217.89C694.53,-217.23 691.23,-216.6 688,-216 584.62,-196.89 554.75,-201.82 447.45,-179.95"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="448.02,-176.49 437.52,-177.89 446.6,-183.35 448.02,-176.49"/>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M727,-180C727,-180 606,-180 606,-180 600,-180 594,-174 594,-168 594,-168 594,-156 594,-156 594,-150 600,-144 606,-144 606,-144 727,-144 727,-144 733,-144 739,-150 739,-156 739,-156 739,-168 739,-168 739,-174 733,-180 727,-180"/>
+<text text-anchor="middle" x="666.5" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 13->7 -->
+<g id="edge18" class="edge"><title>13->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M643.511,-143.697C631.686,-134.796 617.108,-123.823 604.321,-114.199"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="606.319,-111.322 596.224,-108.104 602.109,-116.915 606.319,-111.322"/>
</g>
<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M961.5,-252C961.5,-252 864.5,-252 864.5,-252 858.5,-252 852.5,-246 852.5,-240 852.5,-240 852.5,-228 852.5,-228 852.5,-222 858.5,-216 864.5,-216 864.5,-216 961.5,-216 961.5,-216 967.5,-216 973.5,-222 973.5,-228 973.5,-228 973.5,-240 973.5,-240 973.5,-246 967.5,-252 961.5,-252"/>
-<text text-anchor="middle" x="913" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M919.5,-180C919.5,-180 769.5,-180 769.5,-180 763.5,-180 757.5,-174 757.5,-168 757.5,-168 757.5,-156 757.5,-156 757.5,-150 763.5,-144 769.5,-144 769.5,-144 919.5,-144 919.5,-144 925.5,-144 931.5,-150 931.5,-156 931.5,-156 931.5,-168 931.5,-168 931.5,-174 925.5,-180 919.5,-180"/>
+<text text-anchor="middle" x="844.5" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 14->7 -->
-<g id="edge16" class="edge">
-<title>14->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M898.17,-215.7C890.98,-207.3 882.2,-197.07 874.31,-187.86"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="876.83,-185.42 867.66,-180.1 871.51,-189.97 876.83,-185.42"/>
-</g>
-<!-- 14->8 -->
-<g id="edge18" class="edge">
-<title>14->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M946.51,-215.88C964.84,-206.51 987.74,-194.81 1007.33,-184.8"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1009.04,-187.86 1016.36,-180.19 1005.86,-181.62 1009.04,-187.86"/>
+<g id="edge16" class="edge"><title>14->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M778.552,-143.966C736.344,-133.063 681.783,-118.97 639.554,-108.062"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="640.206,-104.615 629.648,-105.503 638.455,-111.393 640.206,-104.615"/>
</g>
<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#56a9d8" stroke-width="2" d="M353,-252C353,-252 273,-252 273,-252 267,-252 261,-246 261,-240 261,-240 261,-228 261,-228 261,-222 267,-216 273,-216 273,-216 353,-216 353,-216 359,-216 365,-222 365,-228 365,-228 365,-240 365,-240 365,-246 359,-252 353,-252"/>
-<text text-anchor="middle" x="313" y="-231.5" font-family="sans" font-size="10.00">create_index_star</text>
-</g>
-<!-- 15->9 -->
-<g id="edge20" class="edge">
-<title>15->9</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="274.69,-185.2 265.39,-180.1 269.48,-189.88 274.69,-185.2"/>
-</g>
-<!-- 15->10 -->
-<g id="edge22" class="edge">
-<title>15->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M330.55,-215.7C339.23,-207.14 349.86,-196.66 359.35,-187.3"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="361.99,-189.62 366.65,-180.1 357.07,-184.63 361.99,-189.62"/>
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M367.5,-396C367.5,-396 241.5,-396 241.5,-396 235.5,-396 229.5,-390 229.5,-384 229.5,-384 229.5,-372 229.5,-372 229.5,-366 235.5,-360 241.5,-360 241.5,-360 367.5,-360 367.5,-360 373.5,-360 379.5,-366 379.5,-372 379.5,-372 379.5,-384 379.5,-384 379.5,-390 373.5,-396 367.5,-396"/>
+<text text-anchor="middle" x="304.5" y="-375.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
-<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
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-<text text-anchor="middle" x="464" y="-303.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-</g>
-<!-- 16->11 -->
-<g id="edge23" class="edge">
-<title>16->11</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="467.5,-262.1 464,-252.1 460.5,-262.1 467.5,-262.1"/>
+<!-- 15->8 -->
+<g id="edge19" class="edge"><title>15->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M304.5,-359.697C304.5,-351.983 304.5,-342.712 304.5,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="308,-334.104 304.5,-324.104 301,-334.104 308,-334.104"/>
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-<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
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-<text text-anchor="middle" x="765" y="-303.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
-</g>
-<!-- 17->13 -->
-<g id="edge24" class="edge">
-<title>17->13</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="768.5,-262.1 765,-252.1 761.5,-262.1 768.5,-262.1"/>
+<!-- 16 -->
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M631.5,-396C631.5,-396 521.5,-396 521.5,-396 515.5,-396 509.5,-390 509.5,-384 509.5,-384 509.5,-372 509.5,-372 509.5,-366 515.5,-360 521.5,-360 521.5,-360 631.5,-360 631.5,-360 637.5,-360 643.5,-366 643.5,-372 643.5,-372 643.5,-384 643.5,-384 643.5,-390 637.5,-396 631.5,-396"/>
+<text text-anchor="middle" x="576.5" y="-375.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 16->10 -->
+<g id="edge20" class="edge"><title>16->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M576.5,-359.697C576.5,-351.983 576.5,-342.712 576.5,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="580,-334.104 576.5,-324.104 573,-334.104 580,-334.104"/>
+</g>
+<!-- 17->12 -->
+<g id="edge21" class="edge"><title>17->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M634.1,-215.966C605.613,-206.142 569.614,-193.729 539.629,-183.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="540.716,-180.062 530.121,-180.111 538.434,-186.68 540.716,-180.062"/>
+</g>
+<!-- 18->14 -->
+<g id="edge22" class="edge"><title>18->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M815.893,-215.697C820.265,-207.644 825.557,-197.894 830.395,-188.982"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="833.52,-190.563 835.215,-180.104 827.368,-187.223 833.52,-190.563"/>
+</g>
+<!-- 19 -->
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M779.5,-324C779.5,-324 709.5,-324 709.5,-324 703.5,-324 697.5,-318 697.5,-312 697.5,-312 697.5,-300 697.5,-300 697.5,-294 703.5,-288 709.5,-288 709.5,-288 779.5,-288 779.5,-288 785.5,-288 791.5,-294 791.5,-300 791.5,-300 791.5,-312 791.5,-312 791.5,-318 785.5,-324 779.5,-324"/>
+<text text-anchor="middle" x="744.5" y="-303.5" font-family="sans" font-size="10.00">create_index_star</text>
+</g>
+<!-- 19->17 -->
+<g id="edge23" class="edge"><title>19->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M729.421,-287.697C722.108,-279.305 713.19,-269.07 705.165,-259.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="707.614,-257.344 698.405,-252.104 702.336,-261.943 707.614,-257.344"/>
+</g>
+<!-- 19->18 -->
+<g id="edge26" class="edge"><title>19->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M759.826,-287.697C767.259,-279.305 776.323,-269.07 784.48,-259.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="787.34,-261.911 791.35,-252.104 782.1,-257.27 787.34,-261.911"/>
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</svg>
diff --git a/tests/input_files/cluster.json b/tests/input_files/cluster.json
index eb681fc..eaafcd3 100644
--- a/tests/input_files/cluster.json
+++ b/tests/input_files/cluster.json
@@ -37,5 +37,11 @@
"time": "02:00:00",
"threads":"6",
"mem":"32G"
+ },
+ "calculate_TIN_scores":
+ {
+ "time": "06:00:00",
+ "threads":"8",
+ "mem":"32G"
}
}
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 8805f20..53ef308 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -339,10 +339,3 @@ rule pe_genome_quantification_kallisto:
{params.directionality} \
{input.reads1} {input.reads2} > {output.pseudoalignment}) &> {log}"
-
-
-
-
-
-
-
--
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