diff --git a/Snakefile b/Snakefile
index 725b195733410364ecee341bf56c90bedc892780..00c113880e880f8fe889baf4ca7ba64b131b4e32 100644
--- a/Snakefile
+++ b/Snakefile
@@ -86,7 +86,6 @@ rule finish:
"summary_kallisto",
"genes_tpm.tsv")
-
rule start:
'''
Get samples
@@ -808,10 +807,14 @@ rule kallisto_merge_genes:
gtf = get_sample('gtf')
output:
- gn_out = os.path.join(
+ gn_tpm = os.path.join(
config["output_dir"],
"summary_kallisto",
- "genes_tpm.tsv")
+ "genes_tpm.tsv"),
+ gn_counts = os.path.join(
+ config["output_dir"],
+ "summary_kallisto",
+ "genes_counts.tsv")
params:
dir_out = os.path.join(
@@ -874,10 +877,14 @@ rule kallisto_merge_transcripts:
for i in pd.unique(samples_table.index.values)]),
output:
- tx_out = os.path.join(
+ tx_tpm = os.path.join(
config["output_dir"],
"summary_kallisto",
- "transcripts_tpm.tsv")
+ "transcripts_tpm.tsv"),
+ tx_counts = os.path.join(
+ config["output_dir"],
+ "summary_kallisto",
+ "transcripts_counts.tsv")
params:
dir_out = os.path.join(
@@ -917,6 +924,87 @@ rule kallisto_merge_transcripts:
1> {log.stdout} 2> {log.stderr}"
+rule pca_salmon:
+ input:
+ tpm = os.path.join(
+ config["output_dir"],
+ "summary_salmon",
+ "quantmerge",
+ "{molecule}_tpm.tsv"),
+
+ params:
+ tpm_filter = "0",
+ tpm_pseudocount = "1"
+
+ output:
+ out = directory(os.path.join(
+ config["output_dir"],
+ "zpca",
+ "pca_salmon_{molecule}"))
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "pca_salmon_{molecule}.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "pca_salmon_{molecule}.stdout.log")
+
+ threads: 1
+
+ singularity:
+ "docker://zavolab/zpca:0.8"
+
+ shell:
+ "(zpca-tpm \
+ --tpm {input.tpm} \
+ --tpm-filter {params.tpm_filter} \
+ --tpm-pseudocount {params.tpm_pseudocount} \
+ --out {output.out} \
+ --verbose) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
+rule pca_kallisto:
+ input:
+ tpm = os.path.join(
+ config["output_dir"],
+ "summary_kallisto",
+ "{molecule}_tpm.tsv")
+
+ params:
+ tpm_filter = "0",
+ tpm_pseudocount = "1"
+
+ output:
+ out = directory(os.path.join(
+ config["output_dir"],
+ "zpca",
+ "pca_kallisto_{molecule}"))
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "pca_kallisto_{molecule}.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "pca_kallisto_{molecule}.stdout.log")
+
+ threads: 1
+
+ singularity:
+ "docker://zavolab/zpca:0.8"
+
+ shell:
+ "(zpca-tpm \
+ --tpm {input.tpm} \
+ --tpm-filter {params.tpm_filter} \
+ --tpm-pseudocount {params.tpm_pseudocount} \
+ --out {output.out} \
+ --verbose) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
rule star_rpm:
'''
Create stranded bedgraph coverage with STARs RPM normalisation
@@ -1238,7 +1326,6 @@ rule alfa_qc:
-s {params.alfa_orientation}) &> {log}"
-# cd {params.out_dir};
rule alfa_qc_all_samples:
'''
Run ALFA from stranded bedgraph files on all samples
@@ -1405,6 +1492,19 @@ rule multiqc_report:
"ALFA",
"ALFA_plots_mqc.png"),
+ zpca_salmon = expand(os.path.join(
+ config["output_dir"],
+ "zpca",
+ "pca_salmon_{molecule}"),
+ molecule=["genes", "transcripts"]),
+
+ zpca_kallisto = expand(os.path.join(
+ config["output_dir"],
+ "zpca",
+ "pca_kallisto_{molecule}"),
+ molecule=["genes", "transcripts"]
+ ),
+
multiqc_config = os.path.join(
config["output_dir"],
"multiqc_config.yaml")
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 2a883aeb204a3d2a52c4b9735d7fe47c24852e51..b7f09262796896e834f9d99e656d6658af4d71bd 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,1097 +1,1221 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
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+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
-->
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- viewBox="0.00 0.00 2325.50 846.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="2753pt" height="846pt"
+ viewBox="0.00 0.00 2752.62 846.00" 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(4 842)">
<title>snakemake_dag</title>
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<g id="node10" class="node">
<title>9</title>
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<title>9->0</title>
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<g id="node11" class="node">
<title>10</title>
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-<text text-anchor="middle" x="707.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
-<text text-anchor="middle" x="707.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1166.5,-252C1166.5,-252 1038.5,-252 1038.5,-252 1032.5,-252 1026.5,-246 1026.5,-240 1026.5,-240 1026.5,-228 1026.5,-228 1026.5,-222 1032.5,-216 1038.5,-216 1038.5,-216 1166.5,-216 1166.5,-216 1172.5,-216 1178.5,-222 1178.5,-228 1178.5,-228 1178.5,-240 1178.5,-240 1178.5,-246 1172.5,-252 1166.5,-252"/>
+<text text-anchor="middle" x="1102.5" y="-237" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1102.5" y="-226" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 10->0 -->
<g id="edge10" class="edge">
<title>10->0</title>
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+<g id="node24" class="node">
+<title>23</title>
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+<text text-anchor="middle" x="1205.5" y="-165" font-family="sans" font-size="10.00">pca_salmon</text>
+<text text-anchor="middle" x="1205.5" y="-154" font-family="sans" font-size="10.00">molecule: genes</text>
+</g>
+<!-- 10->23 -->
+<g id="edge66" class="edge">
+<title>10->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1127.7,-215.88C1140.91,-206.89 1157.29,-195.76 1171.61,-186.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1173.9,-188.71 1180.21,-180.19 1169.97,-182.92 1173.9,-188.71"/>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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-<text text-anchor="middle" x="882.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M1346,-252C1346,-252 1209,-252 1209,-252 1203,-252 1197,-246 1197,-240 1197,-240 1197,-228 1197,-228 1197,-222 1203,-216 1209,-216 1209,-216 1346,-216 1346,-216 1352,-216 1358,-222 1358,-228 1358,-228 1358,-240 1358,-240 1358,-246 1352,-252 1346,-252"/>
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+<text text-anchor="middle" x="1277.5" y="-226" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<g id="edge11" class="edge">
<title>11->0</title>
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<g id="node13" class="node">
<title>12</title>
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-<text text-anchor="middle" x="1068.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1068.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: tpm</text>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M996.5,-252C996.5,-252 846.5,-252 846.5,-252 840.5,-252 834.5,-246 834.5,-240 834.5,-240 834.5,-228 834.5,-228 834.5,-222 840.5,-216 846.5,-216 846.5,-216 996.5,-216 996.5,-216 1002.5,-216 1008.5,-222 1008.5,-228 1008.5,-228 1008.5,-240 1008.5,-240 1008.5,-246 1002.5,-252 996.5,-252"/>
+<text text-anchor="middle" x="921.5" y="-237" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="921.5" y="-226" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 12->0 -->
<g id="edge12" class="edge">
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+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1127,-180C1127,-180 1032,-180 1032,-180 1026,-180 1020,-174 1020,-168 1020,-168 1020,-156 1020,-156 1020,-150 1026,-144 1032,-144 1032,-144 1127,-144 1127,-144 1133,-144 1139,-150 1139,-156 1139,-156 1139,-168 1139,-168 1139,-174 1133,-180 1127,-180"/>
+<text text-anchor="middle" x="1079.5" y="-165" font-family="sans" font-size="10.00">pca_salmon</text>
+<text text-anchor="middle" x="1079.5" y="-154" font-family="sans" font-size="10.00">molecule: transcripts</text>
+</g>
+<!-- 12->24 -->
+<g id="edge67" class="edge">
+<title>12->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M960.15,-215.88C981.75,-206.31 1008.85,-194.3 1031.77,-184.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1033.25,-187.32 1040.97,-180.07 1030.41,-180.92 1033.25,-187.32"/>
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<g id="node14" class="node">
<title>13</title>
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-<text text-anchor="middle" x="1260.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
-<text text-anchor="middle" x="1260.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">salmon_merge_on: numreads</text>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1538.5,-252C1538.5,-252 1388.5,-252 1388.5,-252 1382.5,-252 1376.5,-246 1376.5,-240 1376.5,-240 1376.5,-228 1376.5,-228 1376.5,-222 1382.5,-216 1388.5,-216 1388.5,-216 1538.5,-216 1538.5,-216 1544.5,-216 1550.5,-222 1550.5,-228 1550.5,-228 1550.5,-240 1550.5,-240 1550.5,-246 1544.5,-252 1538.5,-252"/>
+<text text-anchor="middle" x="1463.5" y="-237" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1463.5" y="-226" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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-<text text-anchor="middle" x="161.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
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+<text text-anchor="middle" x="636.5" y="-231.5" font-family="sans" font-size="10.00">kallisto_merge_transcripts</text>
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+<title>26</title>
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+<text text-anchor="middle" x="642.5" y="-165" font-family="sans" font-size="10.00">pca_kallisto</text>
+<text text-anchor="middle" x="642.5" y="-154" font-family="sans" font-size="10.00">molecule: transcripts</text>
+</g>
+<!-- 14->26 -->
+<g id="edge69" class="edge">
+<title>14->26</title>
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-<text text-anchor="middle" x="216.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
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+<text text-anchor="middle" x="477.5" y="-231.5" font-family="sans" font-size="10.00">kallisto_merge_genes</text>
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+<title>15->0</title>
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+<title>25</title>
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+<text text-anchor="middle" x="477.5" y="-154" font-family="sans" font-size="10.00">molecule: genes</text>
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+<g id="edge68" class="edge">
+<title>15->25</title>
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-<text text-anchor="middle" x="1020.5" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M284.5,-612C284.5,-612 254.5,-612 254.5,-612 248.5,-612 242.5,-606 242.5,-600 242.5,-600 242.5,-588 242.5,-588 242.5,-582 248.5,-576 254.5,-576 254.5,-576 284.5,-576 284.5,-576 290.5,-576 296.5,-582 296.5,-588 296.5,-588 296.5,-600 296.5,-600 296.5,-606 290.5,-612 284.5,-612"/>
+<text text-anchor="middle" x="269.5" y="-591.5" font-family="sans" font-size="10.00">fastqc</text>
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<g id="edge16" class="edge">
<title>16->1</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M271.08,-575.97C273.41,-549.33 277.5,-496.19 277.5,-451 277.5,-451 277.5,-451 277.5,-233 277.5,-190.81 277.26,-169.98 310.5,-144 374.78,-93.76 620.61,-89.43 731.12,-90.12"/>
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<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
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-<text text-anchor="middle" x="375.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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+<text text-anchor="middle" x="552.5" y="-666" font-family="sans" font-size="10.00">fastqc</text>
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<!-- 17->1 -->
<g id="edge17" class="edge">
<title>17->1</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="539.1856,-116.8602 545.1293,-108.0896 535.0135,-111.2394 539.1856,-116.8602"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M525.45,-663.4C465.06,-652.55 324.5,-617.2 324.5,-523 324.5,-523 324.5,-523 324.5,-233 324.5,-179.52 358.2,-168.96 405.5,-144 460.88,-114.78 639.86,-99.89 731.04,-94.05"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="731.41,-97.53 741.18,-93.41 730.98,-90.54 731.41,-97.53"/>
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<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
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-<text text-anchor="middle" x="572.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M192.5,-761C192.5,-761 162.5,-761 162.5,-761 156.5,-761 150.5,-755 150.5,-749 150.5,-749 150.5,-737 150.5,-737 150.5,-731 156.5,-725 162.5,-725 162.5,-725 192.5,-725 192.5,-725 198.5,-725 204.5,-731 204.5,-737 204.5,-737 204.5,-749 204.5,-749 204.5,-755 198.5,-761 192.5,-761"/>
+<text text-anchor="middle" x="177.5" y="-740.5" font-family="sans" font-size="10.00">fastqc</text>
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<!-- 18->1 -->
<g id="edge18" class="edge">
<title>18->1</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="573.5845,-118.0145 569.8769,-108.0896 566.586,-118.1604 573.5845,-118.0145"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M183.43,-724.59C192.17,-697.3 207.5,-642.67 207.5,-595 207.5,-595 207.5,-595 207.5,-233 207.5,-182.12 234.79,-168.28 279.5,-144 356.28,-102.31 616.55,-93.4 730.88,-91.51"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="731.2,-95 741.15,-91.35 731.1,-88 731.2,-95"/>
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<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
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-<text text-anchor="middle" x="676.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">plot_TIN_scores</text>
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+<text text-anchor="middle" x="477.5" y="-303.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 19->1 -->
<g id="edge19" class="edge">
<title>19->1</title>
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+<path fill="none" stroke="grey" stroke-width="2" d="M442.33,-287.94C428.52,-279.25 414.15,-267.26 406.5,-252 394.64,-228.34 415.56,-147.8 419.5,-144 462.97,-102.02 640.41,-93.12 731.29,-91.35"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="731.46,-94.85 741.4,-91.18 731.34,-87.85 731.46,-94.85"/>
+</g>
+<!-- 19->14 -->
+<g id="edge52" class="edge">
+<title>19->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M516.4,-287.88C538.13,-278.31 565.4,-266.3 588.46,-256.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="589.99,-259.3 597.73,-252.07 587.17,-252.89 589.99,-259.3"/>
+</g>
+<!-- 19->15 -->
+<g id="edge54" class="edge">
+<title>19->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M477.5,-287.7C477.5,-279.98 477.5,-270.71 477.5,-262.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="481,-262.1 477.5,-252.1 474,-262.1 481,-262.1"/>
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<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
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-<text text-anchor="middle" x="1368.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M747.5,-324C747.5,-324 601.5,-324 601.5,-324 595.5,-324 589.5,-318 589.5,-312 589.5,-312 589.5,-300 589.5,-300 589.5,-294 595.5,-288 601.5,-288 601.5,-288 747.5,-288 747.5,-288 753.5,-288 759.5,-294 759.5,-300 759.5,-300 759.5,-312 759.5,-312 759.5,-318 753.5,-324 747.5,-324"/>
+<text text-anchor="middle" x="674.5" y="-303.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 20->1 -->
<g id="edge20" class="edge">
<title>20->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1312.9658,-158.1697C1153.4844,-147.147 701.0407,-115.708 623.7686,-107.2571"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="623.8901,-103.7423 613.5145,-105.8863 622.9625,-110.6806 623.8901,-103.7423"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M695.09,-287.87C718.08,-269.13 756.78,-238.72 792.5,-216 821.35,-197.65 842.86,-209.3 860.5,-180 868.75,-166.29 867.86,-158.21 860.5,-144 854.13,-131.7 843.45,-121.65 832.12,-113.73"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="833.68,-110.58 823.38,-108.09 829.89,-116.46 833.68,-110.58"/>
+</g>
+<!-- 20->14 -->
+<g id="edge53" class="edge">
+<title>20->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M665.11,-287.7C660.74,-279.64 655.44,-269.89 650.6,-260.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="653.63,-259.22 645.79,-252.1 647.48,-262.56 653.63,-259.22"/>
+</g>
+<!-- 20->15 -->
+<g id="edge55" class="edge">
+<title>20->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M626.56,-287.97C599.03,-278.19 564.28,-265.84 535.26,-255.52"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="536.25,-252.16 525.65,-252.11 533.91,-258.76 536.25,-252.16"/>
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<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M138,-180C138,-180 31,-180 31,-180 25,-180 19,-174 19,-168 19,-168 19,-156 19,-156 19,-150 25,-144 31,-144 31,-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="84.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M989.5,-180C989.5,-180 919.5,-180 919.5,-180 913.5,-180 907.5,-174 907.5,-168 907.5,-168 907.5,-156 907.5,-156 907.5,-150 913.5,-144 919.5,-144 919.5,-144 989.5,-144 989.5,-144 995.5,-144 1001.5,-150 1001.5,-156 1001.5,-156 1001.5,-168 1001.5,-168 1001.5,-174 995.5,-180 989.5,-180"/>
+<text text-anchor="middle" x="954.5" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
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<!-- 21->1 -->
<g id="edge21" class="edge">
<title>21->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M150.3272,-146.7025C155.1138,-145.7397 159.8754,-144.8269 164.5,-144 289.2993,-121.6855 437.2428,-104.2085 515.186,-95.6907"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M913.16,-143.88C889.95,-134.26 860.81,-122.19 836.23,-112.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="837.29,-108.66 826.71,-108.07 834.61,-115.13 837.29,-108.66"/>
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<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M926.5,-324C926.5,-324 860.5,-324 860.5,-324 854.5,-324 848.5,-318 848.5,-312 848.5,-312 848.5,-300 848.5,-300 848.5,-294 854.5,-288 860.5,-288 860.5,-288 926.5,-288 926.5,-288 932.5,-288 938.5,-294 938.5,-300 938.5,-300 938.5,-312 938.5,-312 938.5,-318 932.5,-324 926.5,-324"/>
-<text text-anchor="middle" x="893.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
-<text text-anchor="middle" x="893.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1893,-180C1893,-180 1806,-180 1806,-180 1800,-180 1794,-174 1794,-168 1794,-168 1794,-156 1794,-156 1794,-150 1800,-144 1806,-144 1806,-144 1893,-144 1893,-144 1899,-144 1905,-150 1905,-156 1905,-156 1905,-168 1905,-168 1905,-174 1899,-180 1893,-180"/>
+<text text-anchor="middle" x="1849.5" y="-159.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
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-<!-- 22->2 -->
+<!-- 22->1 -->
<g id="edge22" class="edge">
-<title>22->2</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M938.9252,-289.4817C967.5656,-279.0671 1004.7665,-265.5395 1035.2645,-254.4493"/>
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-<g id="node24" class="node">
-<title>23</title>
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-<text text-anchor="middle" x="1672.5" y="-677" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
-<text text-anchor="middle" x="1672.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
-<text text-anchor="middle" x="1672.5" y="-655" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<title>22->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1793.79,-157.34C1609.66,-145.22 1021.97,-106.56 839.84,-94.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="839.91,-91.07 829.7,-93.91 839.45,-98.06 839.91,-91.07"/>
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-<!-- 23->2 -->
+<!-- 23->1 -->
<g id="edge23" class="edge">
-<title>23->2</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1602.6493,-661.3903C1521.4699,-648.8199 1398.5,-614.5106 1398.5,-522 1398.5,-522 1398.5,-522 1398.5,-450 1398.5,-373.5246 1401.0548,-334.7077 1340.5,-288 1273.9045,-236.6329 1234.9739,-270.718 1148.0991,-251.8284"/>
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-<!-- 23->3 -->
-<g id="edge25" class="edge">
-<title>23->3</title>
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-<g id="edge27" class="edge">
-<title>23->4</title>
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-<!-- 23->5 -->
-<g id="edge29" class="edge">
-<title>23->5</title>
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-<!-- 23->6 -->
-<g id="edge31" class="edge">
-<title>23->6</title>
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-<g id="edge33" class="edge">
-<title>23->7</title>
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-<g id="edge35" class="edge">
-<title>23->8</title>
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-<title>23->9</title>
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-<!-- 46 -->
-<g id="node47" class="node">
-<title>46</title>
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-<text text-anchor="middle" x="872.5" y="-237" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
-<text text-anchor="middle" x="872.5" y="-226" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
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-<!-- 23->46 -->
-<g id="edge82" class="edge">
-<title>23->46</title>
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-<!-- 59 -->
-<g id="node60" class="node">
-<title>59</title>
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-<title>23->59</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="763.4771,-596.0265 753.241,-598.7599 762.9475,-603.0064 763.4771,-596.0265"/>
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-<!-- 62 -->
-<g id="node63" class="node">
-<title>62</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M1238,-612C1238,-612 1155,-612 1155,-612 1149,-612 1143,-606 1143,-600 1143,-600 1143,-588 1143,-588 1143,-582 1149,-576 1155,-576 1155,-576 1238,-576 1238,-576 1244,-576 1250,-582 1250,-588 1250,-588 1250,-600 1250,-600 1250,-606 1244,-612 1238,-612"/>
-<text text-anchor="middle" x="1196.5" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
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-<!-- 23->62 -->
-<g id="edge108" class="edge">
-<title>23->62</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1602.7014,-657.7795C1529.4145,-646.4967 1410.832,-628.165 1308.5,-612 1292.8618,-609.5297 1276.0006,-606.8359 1260.2267,-604.3025"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1260.4706,-600.7968 1250.0418,-602.6648 1259.3593,-607.708 1260.4706,-600.7968"/>
+<title>23->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1156.8,-145.97C1154,-145.27 1151.22,-144.6 1148.5,-144 1040.18,-120.07 911.21,-104.17 839.84,-96.45"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="840.05,-92.95 829.74,-95.37 839.31,-99.91 840.05,-92.95"/>
</g>
-<!-- 64 -->
-<g id="node65" class="node">
-<title>64</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1320.5,-396C1320.5,-396 1228.5,-396 1228.5,-396 1222.5,-396 1216.5,-390 1216.5,-384 1216.5,-384 1216.5,-372 1216.5,-372 1216.5,-366 1222.5,-360 1228.5,-360 1228.5,-360 1320.5,-360 1320.5,-360 1326.5,-360 1332.5,-366 1332.5,-372 1332.5,-372 1332.5,-384 1332.5,-384 1332.5,-390 1326.5,-396 1320.5,-396"/>
-<text text-anchor="middle" x="1274.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
-</g>
-<!-- 23->64 -->
-<g id="edge111" class="edge">
-<title>23->64</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1602.9448,-664.838C1518.7744,-659.0115 1383.6827,-644.7404 1346.5,-612 1330.6633,-598.0553 1296.0731,-464.9468 1281.3522,-405.9339"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1284.7293,-405.0101 1278.9239,-396.1474 1277.9353,-406.696 1284.7293,-405.0101"/>
-</g>
-<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1214.5,-324C1214.5,-324 1148.5,-324 1148.5,-324 1142.5,-324 1136.5,-318 1136.5,-312 1136.5,-312 1136.5,-300 1136.5,-300 1136.5,-294 1142.5,-288 1148.5,-288 1148.5,-288 1214.5,-288 1214.5,-288 1220.5,-288 1226.5,-294 1226.5,-300 1226.5,-300 1226.5,-312 1226.5,-312 1226.5,-318 1220.5,-324 1214.5,-324"/>
-<text text-anchor="middle" x="1181.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
-<text text-anchor="middle" x="1181.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
-</g>
-<!-- 24->3 -->
+<!-- 24->1 -->
<g id="edge24" class="edge">
-<title>24->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1226.688,-290.2113C1229.6527,-289.4008 1232.6083,-288.6534 1235.5,-288 1359.9314,-259.8859 1398.0239,-279.4596 1526.0782,-252.0882"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1526.8448,-255.5034 1535.8636,-249.9436 1525.3462,-248.6656 1526.8448,-255.5034"/>
+<title>24->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1019.67,-146.22C1016.57,-145.47 1013.5,-144.72 1010.5,-144 952.1,-129.93 885.08,-114.19 839.47,-103.55"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="840.04,-100.09 829.51,-101.23 838.45,-106.91 840.04,-100.09"/>
</g>
-<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1106.5,-324C1106.5,-324 1040.5,-324 1040.5,-324 1034.5,-324 1028.5,-318 1028.5,-312 1028.5,-312 1028.5,-300 1028.5,-300 1028.5,-294 1034.5,-288 1040.5,-288 1040.5,-288 1106.5,-288 1106.5,-288 1112.5,-288 1118.5,-294 1118.5,-300 1118.5,-300 1118.5,-312 1118.5,-312 1118.5,-318 1112.5,-324 1106.5,-324"/>
-<text text-anchor="middle" x="1073.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
-<text text-anchor="middle" x="1073.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
+<!-- 25->1 -->
+<g id="edge25" class="edge">
+<title>25->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M526.3,-149.91C582.15,-137.22 673.35,-116.49 731.34,-103.31"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="732.44,-106.65 741.42,-101.02 730.89,-99.82 732.44,-106.65"/>
</g>
-<!-- 25->4 -->
+<!-- 26->1 -->
<g id="edge26" class="edge">
-<title>25->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1118.6893,-290.217C1121.6537,-289.4051 1124.6088,-288.6558 1127.5,-288 1250.1063,-260.1896 1287.6495,-278.8542 1414.8044,-251.8897"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1415.9003,-255.2332 1424.9279,-249.6877 1414.4125,-248.3932 1415.9003,-255.2332"/>
-</g>
-<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1470.5,-324C1470.5,-324 1404.5,-324 1404.5,-324 1398.5,-324 1392.5,-318 1392.5,-312 1392.5,-312 1392.5,-300 1392.5,-300 1392.5,-294 1398.5,-288 1404.5,-288 1404.5,-288 1470.5,-288 1470.5,-288 1476.5,-288 1482.5,-294 1482.5,-300 1482.5,-300 1482.5,-312 1482.5,-312 1482.5,-318 1476.5,-324 1470.5,-324"/>
-<text text-anchor="middle" x="1437.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
-<text text-anchor="middle" x="1437.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
-</g>
-<!-- 26->5 -->
-<g id="edge28" class="edge">
-<title>26->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1482.7893,-290.6056C1485.7292,-289.6986 1488.6516,-288.822 1491.5,-288 1553.0972,-270.2234 1572.0606,-270.4122 1636.8627,-252.3623"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1638.096,-255.6509 1646.7668,-249.5625 1636.1918,-248.9148 1638.096,-255.6509"/>
+<title>26->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M677.48,-143.88C696.7,-134.47 720.73,-122.71 741.24,-112.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="742.94,-115.73 750.38,-108.19 739.86,-109.44 742.94,-115.73"/>
</g>
<!-- 27 -->
<g id="node28" class="node">
<title>27</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1838.5,-324C1838.5,-324 1772.5,-324 1772.5,-324 1766.5,-324 1760.5,-318 1760.5,-312 1760.5,-312 1760.5,-300 1760.5,-300 1760.5,-294 1766.5,-288 1772.5,-288 1772.5,-288 1838.5,-288 1838.5,-288 1844.5,-288 1850.5,-294 1850.5,-300 1850.5,-300 1850.5,-312 1850.5,-312 1850.5,-318 1844.5,-324 1838.5,-324"/>
-<text text-anchor="middle" x="1805.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
-<text text-anchor="middle" x="1805.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M839,-180C839,-180 732,-180 732,-180 726,-180 720,-174 720,-168 720,-168 720,-156 720,-156 720,-150 726,-144 732,-144 732,-144 839,-144 839,-144 845,-144 851,-150 851,-156 851,-156 851,-168 851,-168 851,-174 845,-180 839,-180"/>
+<text text-anchor="middle" x="785.5" y="-159.5" font-family="sans" font-size="10.00">prepare_multiqc_config</text>
</g>
-<!-- 27->6 -->
-<g id="edge30" class="edge">
-<title>27->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1805.2477,-287.8314C1805.1407,-280.131 1805.0135,-270.9743 1804.8947,-262.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1808.3944,-262.3637 1804.7557,-252.4133 1801.3951,-262.4609 1808.3944,-262.3637"/>
+<!-- 27->1 -->
+<g id="edge27" class="edge">
+<title>27->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M785.5,-143.7C785.5,-135.98 785.5,-126.71 785.5,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="789,-118.1 785.5,-108.1 782,-118.1 789,-118.1"/>
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<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M2239.5,-324C2239.5,-324 2173.5,-324 2173.5,-324 2167.5,-324 2161.5,-318 2161.5,-312 2161.5,-312 2161.5,-300 2161.5,-300 2161.5,-294 2167.5,-288 2173.5,-288 2173.5,-288 2239.5,-288 2239.5,-288 2245.5,-288 2251.5,-294 2251.5,-300 2251.5,-300 2251.5,-312 2251.5,-312 2251.5,-318 2245.5,-324 2239.5,-324"/>
-<text text-anchor="middle" x="2206.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
-<text text-anchor="middle" x="2206.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: plus</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1394.5,-324C1394.5,-324 1328.5,-324 1328.5,-324 1322.5,-324 1316.5,-318 1316.5,-312 1316.5,-312 1316.5,-300 1316.5,-300 1316.5,-294 1322.5,-288 1328.5,-288 1328.5,-288 1394.5,-288 1394.5,-288 1400.5,-288 1406.5,-294 1406.5,-300 1406.5,-300 1406.5,-312 1406.5,-312 1406.5,-318 1400.5,-324 1394.5,-324"/>
+<text text-anchor="middle" x="1361.5" y="-309" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<text text-anchor="middle" x="1361.5" y="-298" font-family="sans" font-size="10.00">strand: plus</text>
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-<!-- 28->7 -->
-<g id="edge32" class="edge">
-<title>28->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2206.5,-287.8314C2206.5,-280.131 2206.5,-270.9743 2206.5,-262.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2210.0001,-262.4132 2206.5,-252.4133 2203.0001,-262.4133 2210.0001,-262.4132"/>
+<!-- 28->2 -->
+<g id="edge28" class="edge">
+<title>28->2</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1406.52,-290.6C1409.55,-289.7 1412.57,-288.83 1415.5,-288 1476.02,-270.93 1494.23,-269.67 1558.91,-252.08"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1560.08,-255.39 1568.8,-249.37 1558.23,-248.64 1560.08,-255.39"/>
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<!-- 29 -->
<g id="node30" class="node">
<title>29</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M2055.5,-324C2055.5,-324 1989.5,-324 1989.5,-324 1983.5,-324 1977.5,-318 1977.5,-312 1977.5,-312 1977.5,-300 1977.5,-300 1977.5,-294 1983.5,-288 1989.5,-288 1989.5,-288 2055.5,-288 2055.5,-288 2061.5,-288 2067.5,-294 2067.5,-300 2067.5,-300 2067.5,-312 2067.5,-312 2067.5,-318 2061.5,-324 2055.5,-324"/>
-<text text-anchor="middle" x="2022.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
-<text text-anchor="middle" x="2022.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M2037,-689C2037,-689 1922,-689 1922,-689 1916,-689 1910,-683 1910,-677 1910,-677 1910,-660 1910,-660 1910,-654 1916,-648 1922,-648 1922,-648 2037,-648 2037,-648 2043,-648 2049,-654 2049,-660 2049,-660 2049,-677 2049,-677 2049,-683 2043,-689 2037,-689"/>
+<text text-anchor="middle" x="1979.5" y="-677" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1979.5" y="-666" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1979.5" y="-655" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 29->2 -->
+<g id="edge29" class="edge">
+<title>29->2</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1933.47,-647.77C1916.03,-638.7 1896.92,-626.66 1882.5,-612 1850.83,-579.81 1833.5,-568.15 1833.5,-523 1833.5,-523 1833.5,-523 1833.5,-449 1833.5,-408.55 1828.5,-397.95 1814.5,-360 1801.91,-325.86 1803.4,-311.36 1775.5,-288 1771.25,-284.44 1716.07,-266.56 1671.69,-252.54"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1672.71,-249.19 1662.12,-249.52 1670.6,-255.86 1672.71,-249.19"/>
+</g>
+<!-- 29->3 -->
+<g id="edge31" class="edge">
+<title>29->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2007.85,-647.84C2040.15,-622.88 2088.5,-576.58 2088.5,-523 2088.5,-523 2088.5,-523 2088.5,-449 2088.5,-393.05 2099.22,-379.79 2103.5,-324 2105.09,-303.32 2105.83,-279.87 2106.19,-262.24"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2109.69,-262.14 2106.36,-252.09 2102.69,-262.02 2109.69,-262.14"/>
+</g>
+<!-- 29->4 -->
+<g id="edge33" class="edge">
+<title>29->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1951.41,-647.78C1919.41,-622.77 1871.5,-576.4 1871.5,-523 1871.5,-523 1871.5,-523 1871.5,-449 1871.5,-372.16 1860.69,-344.39 1808.5,-288 1797.45,-276.06 1783.16,-265.62 1769.61,-257.24"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1771.24,-254.14 1760.86,-252.03 1767.66,-260.15 1771.24,-254.14"/>
+</g>
+<!-- 29->5 -->
+<g id="edge35" class="edge">
+<title>29->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2049.29,-664.88C2140.99,-657.28 2290.5,-628.68 2290.5,-523 2290.5,-523 2290.5,-523 2290.5,-449 2290.5,-408.55 2297.68,-390.83 2271.5,-360 2243.08,-326.53 2204.25,-360.27 2179.5,-324 2165.89,-304.05 2179.54,-278.45 2194.13,-259.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2196.89,-261.99 2200.58,-252.06 2191.5,-257.52 2196.89,-261.99"/>
+</g>
+<!-- 29->6 -->
+<g id="edge37" class="edge">
+<title>29->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2049.1,-663.58C2195.62,-653.41 2522.5,-619.88 2522.5,-523 2522.5,-523 2522.5,-523 2522.5,-377 2522.5,-336.55 2530.88,-317.77 2503.5,-288 2468.14,-249.56 2440.55,-265.95 2385.15,-251.95"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2385.82,-248.5 2375.25,-249.2 2383.95,-255.25 2385.82,-248.5"/>
+</g>
+<!-- 29->7 -->
+<g id="edge39" class="edge">
+<title>29->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2049.15,-668.42C2158.87,-668.17 2377.73,-660.83 2555.5,-612 2645.03,-587.41 2744.5,-615.85 2744.5,-523 2744.5,-523 2744.5,-523 2744.5,-377 2744.5,-336.55 2744.98,-323.45 2725.5,-288 2719.58,-277.23 2710.77,-267.25 2701.98,-258.92"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2704.1,-256.13 2694.33,-252.05 2699.43,-261.34 2704.1,-256.13"/>
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<!-- 29->8 -->
-<g id="edge34" class="edge">
+<g id="edge41" class="edge">
<title>29->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2023.5094,-287.8314C2023.9372,-280.131 2024.4459,-270.9743 2024.9213,-262.4166"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M2049.08,-665.88C2173.55,-662.06 2428.79,-649.74 2508.5,-612 2559.34,-587.93 2598.5,-579.26 2598.5,-523 2598.5,-523 2598.5,-523 2598.5,-377 2598.5,-334.87 2579.3,-289.23 2565.19,-261.37"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2568.18,-259.54 2560.45,-252.29 2561.97,-262.78 2568.18,-259.54"/>
+</g>
+<!-- 29->9 -->
+<g id="edge43" class="edge">
+<title>29->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2049.34,-664.26C2163.21,-658.15 2383.32,-642.72 2454.5,-612 2510.98,-587.63 2560.5,-584.52 2560.5,-523 2560.5,-523 2560.5,-523 2560.5,-377 2560.5,-334.66 2553.59,-320.54 2526.5,-288 2516.2,-275.62 2502.22,-265.35 2488.48,-257.24"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2489.96,-254.06 2479.53,-252.23 2486.54,-260.17 2489.96,-254.06"/>
+</g>
+<!-- 52 -->
+<g id="node53" class="node">
+<title>52</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M1284,-396C1284,-396 1187,-396 1187,-396 1181,-396 1175,-390 1175,-384 1175,-384 1175,-372 1175,-372 1175,-366 1181,-360 1187,-360 1187,-360 1284,-360 1284,-360 1290,-360 1296,-366 1296,-372 1296,-372 1296,-384 1296,-384 1296,-390 1290,-396 1284,-396"/>
+<text text-anchor="middle" x="1235.5" y="-381" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="1235.5" y="-370" font-family="sans" font-size="10.00">kmer: 31</text>
+</g>
+<!-- 29->52 -->
+<g id="edge96" class="edge">
+<title>29->52</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1909.91,-651.92C1873.02,-642.52 1827.41,-629.04 1788.5,-612 1703.39,-574.72 1693.85,-542.96 1609.5,-504 1507.49,-456.88 1382.55,-418.8 1306.01,-397.54"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1306.58,-394.06 1296,-394.77 1304.71,-400.81 1306.58,-394.06"/>
+</g>
+<!-- 65 -->
+<g id="node66" class="node">
+<title>65</title>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1009,-612C1009,-612 908,-612 908,-612 902,-612 896,-606 896,-600 896,-600 896,-588 896,-588 896,-582 902,-576 908,-576 908,-576 1009,-576 1009,-576 1015,-576 1021,-582 1021,-588 1021,-588 1021,-600 1021,-600 1021,-606 1015,-612 1009,-612"/>
+<text text-anchor="middle" x="958.5" y="-591.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+</g>
+<!-- 29->65 -->
+<g id="edge119" class="edge">
+<title>29->65</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1909.72,-662.55C1724.27,-649.38 1220.41,-613.6 1031.41,-600.18"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1031.53,-596.68 1021.31,-599.46 1031.03,-603.66 1031.53,-596.68"/>
+</g>
+<!-- 68 -->
+<g id="node69" class="node">
+<title>68</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M1544,-612C1544,-612 1461,-612 1461,-612 1455,-612 1449,-606 1449,-600 1449,-600 1449,-588 1449,-588 1449,-582 1455,-576 1461,-576 1461,-576 1544,-576 1544,-576 1550,-576 1556,-582 1556,-588 1556,-588 1556,-600 1556,-600 1556,-606 1550,-612 1544,-612"/>
+<text text-anchor="middle" x="1502.5" y="-591.5" font-family="sans" font-size="10.00">map_genome_star</text>
+</g>
+<!-- 29->68 -->
+<g id="edge122" class="edge">
+<title>29->68</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1909.88,-656.92C1817.51,-642.88 1655.72,-618.29 1566.35,-604.7"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1566.76,-601.23 1556.34,-603.18 1565.7,-608.15 1566.76,-601.23"/>
+</g>
+<!-- 70 -->
+<g id="node71" class="node">
+<title>70</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M1793.5,-396C1793.5,-396 1701.5,-396 1701.5,-396 1695.5,-396 1689.5,-390 1689.5,-384 1689.5,-384 1689.5,-372 1689.5,-372 1689.5,-366 1695.5,-360 1701.5,-360 1701.5,-360 1793.5,-360 1793.5,-360 1799.5,-360 1805.5,-366 1805.5,-372 1805.5,-372 1805.5,-384 1805.5,-384 1805.5,-390 1799.5,-396 1793.5,-396"/>
+<text text-anchor="middle" x="1747.5" y="-375.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+</g>
+<!-- 29->70 -->
+<g id="edge125" class="edge">
+<title>29->70</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1909.95,-657.96C1878.58,-650.34 1843.3,-636.63 1819.5,-612 1763.82,-554.38 1751.11,-454.61 1748.28,-406.5"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1751.76,-406.07 1747.78,-396.25 1744.77,-406.41 1751.76,-406.07"/>
</g>
<!-- 30 -->
<g id="node31" class="node">
<title>30</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1947.5,-324C1947.5,-324 1881.5,-324 1881.5,-324 1875.5,-324 1869.5,-318 1869.5,-312 1869.5,-312 1869.5,-300 1869.5,-300 1869.5,-294 1875.5,-288 1881.5,-288 1881.5,-288 1947.5,-288 1947.5,-288 1953.5,-288 1959.5,-294 1959.5,-300 1959.5,-300 1959.5,-312 1959.5,-312 1959.5,-318 1953.5,-324 1947.5,-324"/>
-<text text-anchor="middle" x="1914.5" y="-309" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
-<text text-anchor="middle" x="1914.5" y="-298" font-family="sans" font-size="10.00" fill="#000000">strand: minus</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1682.5,-324C1682.5,-324 1616.5,-324 1616.5,-324 1610.5,-324 1604.5,-318 1604.5,-312 1604.5,-312 1604.5,-300 1604.5,-300 1604.5,-294 1610.5,-288 1616.5,-288 1616.5,-288 1682.5,-288 1682.5,-288 1688.5,-288 1694.5,-294 1694.5,-300 1694.5,-300 1694.5,-312 1694.5,-312 1694.5,-318 1688.5,-324 1682.5,-324"/>
+<text text-anchor="middle" x="1649.5" y="-309" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<text text-anchor="middle" x="1649.5" y="-298" font-family="sans" font-size="10.00">strand: plus</text>
</g>
-<!-- 30->9 -->
-<g id="edge36" class="edge">
-<title>30->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1914.7523,-287.8314C1914.8593,-280.131 1914.9865,-270.9743 1915.1053,-262.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1918.6049,-262.4609 1915.2443,-252.4133 1911.6056,-262.3637 1918.6049,-262.4609"/>
+<!-- 30->3 -->
+<g id="edge30" class="edge">
+<title>30->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1694.7,-290.04C1697.66,-289.29 1700.61,-288.6 1703.5,-288 1852.07,-257.24 1896.61,-281.56 2049.68,-251.9"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2050.79,-255.25 2059.92,-249.87 2049.43,-248.38 2050.79,-255.25"/>
</g>
<!-- 31 -->
<g id="node32" class="node">
<title>31</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M941.5,-180C941.5,-180 823.5,-180 823.5,-180 817.5,-180 811.5,-174 811.5,-168 811.5,-168 811.5,-156 811.5,-156 811.5,-150 817.5,-144 823.5,-144 823.5,-144 941.5,-144 941.5,-144 947.5,-144 953.5,-150 953.5,-156 953.5,-156 953.5,-168 953.5,-168 953.5,-174 947.5,-180 941.5,-180"/>
-<text text-anchor="middle" x="882.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1502.5,-324C1502.5,-324 1436.5,-324 1436.5,-324 1430.5,-324 1424.5,-318 1424.5,-312 1424.5,-312 1424.5,-300 1424.5,-300 1424.5,-294 1430.5,-288 1436.5,-288 1436.5,-288 1502.5,-288 1502.5,-288 1508.5,-288 1514.5,-294 1514.5,-300 1514.5,-300 1514.5,-312 1514.5,-312 1514.5,-318 1508.5,-324 1502.5,-324"/>
+<text text-anchor="middle" x="1469.5" y="-309" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<text text-anchor="middle" x="1469.5" y="-298" font-family="sans" font-size="10.00">strand: minus</text>
</g>
-<!-- 31->10 -->
-<g id="edge38" class="edge">
-<title>31->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M838.3401,-143.8314C814.7268,-134.1162 785.4798,-122.0831 760.63,-111.8592"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="761.9219,-108.6061 751.3423,-108.038 759.2585,-115.0797 761.9219,-108.6061"/>
-</g>
-<!-- 31->11 -->
-<g id="edge40" class="edge">
-<title>31->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M882.5,-143.8314C882.5,-136.131 882.5,-126.9743 882.5,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="886.0001,-118.4132 882.5,-108.4133 879.0001,-118.4133 886.0001,-118.4132"/>
-</g>
-<!-- 31->12 -->
-<g id="edge42" class="edge">
-<title>31->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M929.4357,-143.8314C954.6437,-134.0734 985.8926,-121.977 1012.3791,-111.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1013.8397,-114.912 1021.9019,-108.038 1011.3127,-108.384 1013.8397,-114.912"/>
-</g>
-<!-- 31->13 -->
-<g id="edge44" class="edge">
-<title>31->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M953.5828,-146.029C956.9328,-145.3314 960.2514,-144.6516 963.5,-144 1049.3543,-126.7799 1073.5509,-124.5084 1163.3062,-108.2054"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1164.1757,-111.6046 1173.3848,-106.366 1162.9189,-104.7184 1164.1757,-111.6046"/>
+<!-- 31->4 -->
+<g id="edge32" class="edge">
+<title>31->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1514.51,-290.58C1517.55,-289.69 1520.56,-288.82 1523.5,-288 1585.65,-270.68 1604.49,-270.03 1669.77,-252.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1671.03,-255.68 1679.75,-249.66 1669.18,-248.93 1671.03,-255.68"/>
</g>
<!-- 32 -->
<g id="node33" class="node">
<title>32</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1085,-180C1085,-180 984,-180 984,-180 978,-180 972,-174 972,-168 972,-168 972,-156 972,-156 972,-150 978,-144 984,-144 984,-144 1085,-144 1085,-144 1091,-144 1097,-150 1097,-156 1097,-156 1097,-168 1097,-168 1097,-174 1091,-180 1085,-180"/>
-<text text-anchor="middle" x="1034.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1938.5,-324C1938.5,-324 1872.5,-324 1872.5,-324 1866.5,-324 1860.5,-318 1860.5,-312 1860.5,-312 1860.5,-300 1860.5,-300 1860.5,-294 1866.5,-288 1872.5,-288 1872.5,-288 1938.5,-288 1938.5,-288 1944.5,-288 1950.5,-294 1950.5,-300 1950.5,-300 1950.5,-312 1950.5,-312 1950.5,-318 1944.5,-324 1938.5,-324"/>
+<text text-anchor="middle" x="1905.5" y="-309" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<text text-anchor="middle" x="1905.5" y="-298" font-family="sans" font-size="10.00">strand: minus</text>
</g>
-<!-- 32->10 -->
-<g id="edge39" class="edge">
-<title>32->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M971.7037,-146.1584C968.5941,-145.4187 965.5131,-144.6954 962.5,-144 945.9258,-140.1746 860.8578,-122.2153 793.4697,-108.0441"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="794.1719,-104.6153 783.6657,-105.9829 792.7316,-111.4656 794.1719,-104.6153"/>
-</g>
-<!-- 32->11 -->
-<g id="edge41" class="edge">
-<title>32->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M996.144,-143.8314C975.9956,-134.2874 951.1248,-122.5065 929.7917,-112.4013"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="931.1159,-109.1558 920.5802,-108.038 928.1193,-115.482 931.1159,-109.1558"/>
-</g>
-<!-- 32->12 -->
-<g id="edge43" class="edge">
-<title>32->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1043.0796,-143.8314C1046.8358,-135.8771 1051.3257,-126.369 1055.4798,-117.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1058.6996,-118.9503 1059.8048,-108.4133 1052.3699,-115.9612 1058.6996,-118.9503"/>
-</g>
-<!-- 32->13 -->
-<g id="edge45" class="edge">
-<title>32->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1091.2376,-143.9243C1122.4018,-133.9959 1161.2311,-121.6255 1193.8356,-111.2382"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1195.2733,-114.4536 1203.739,-108.0831 1193.1484,-107.7839 1195.2733,-114.4536"/>
+<!-- 32->5 -->
+<g id="edge34" class="edge">
+<title>32->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1950.75,-290.29C1953.7,-289.47 1956.64,-288.7 1959.5,-288 2045.46,-266.94 2071.67,-273.1 2161.07,-252.19"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2161.89,-255.59 2170.8,-249.87 2160.26,-248.78 2161.89,-255.59"/>
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<!-- 33 -->
<g id="node34" class="node">
<title>33</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M313,-838C313,-838 12,-838 12,-838 6,-838 0,-832 0,-826 0,-826 0,-809 0,-809 0,-803 6,-797 12,-797 12,-797 313,-797 313,-797 319,-797 325,-803 325,-809 325,-809 325,-826 325,-826 325,-832 319,-838 313,-838"/>
-<text text-anchor="middle" x="162.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
-<text text-anchor="middle" x="162.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq1</text>
-<text text-anchor="middle" x="162.5" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M2266.5,-324C2266.5,-324 2200.5,-324 2200.5,-324 2194.5,-324 2188.5,-318 2188.5,-312 2188.5,-312 2188.5,-300 2188.5,-300 2188.5,-294 2194.5,-288 2200.5,-288 2200.5,-288 2266.5,-288 2266.5,-288 2272.5,-288 2278.5,-294 2278.5,-300 2278.5,-300 2278.5,-312 2278.5,-312 2278.5,-318 2272.5,-324 2266.5,-324"/>
+<text text-anchor="middle" x="2233.5" y="-309" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<text text-anchor="middle" x="2233.5" y="-298" font-family="sans" font-size="10.00">strand: plus</text>
</g>
-<!-- 33->14 -->
-<g id="edge46" class="edge">
-<title>33->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M162.4077,-796.8743C162.2278,-756.6563 161.8298,-667.7154 161.6259,-622.1329"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="165.1256,-622.0376 161.5808,-612.0534 158.1257,-622.069 165.1256,-622.0376"/>
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-<!-- 47 -->
-<g id="node48" class="node">
-<title>47</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M409,-761C409,-761 266,-761 266,-761 260,-761 254,-755 254,-749 254,-749 254,-737 254,-737 254,-731 260,-725 266,-725 266,-725 409,-725 409,-725 415,-725 421,-731 421,-737 421,-737 421,-749 421,-749 421,-755 415,-761 409,-761"/>
-<text text-anchor="middle" x="337.5" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-</g>
-<!-- 33->47 -->
-<g id="edge83" class="edge">
-<title>33->47</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M210.7828,-796.9453C234.0937,-787.0215 262.0869,-775.1044 285.827,-764.9979"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="287.2053,-768.2152 295.0353,-761.0778 284.4634,-761.7745 287.2053,-768.2152"/>
+<!-- 33->6 -->
+<g id="edge36" class="edge">
+<title>33->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2256.98,-287.7C2269.06,-278.8 2283.95,-267.82 2297.02,-258.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2299.31,-260.85 2305.29,-252.1 2295.16,-255.22 2299.31,-260.85"/>
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<!-- 34 -->
<g id="node35" class="node">
<title>34</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M676,-838C676,-838 363,-838 363,-838 357,-838 351,-832 351,-826 351,-826 351,-809 351,-809 351,-803 357,-797 363,-797 363,-797 676,-797 676,-797 682,-797 688,-803 688,-809 688,-809 688,-826 688,-826 688,-832 682,-838 676,-838"/>
-<text text-anchor="middle" x="519.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
-<text text-anchor="middle" x="519.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq1</text>
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-<!-- 34->15 -->
-<g id="edge47" class="edge">
-<title>34->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M350.662,-797.1539C304.1026,-788.4729 261.6457,-776.6476 244.5,-761 226.6642,-744.7226 220.0329,-717.5137 217.6452,-696.808"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="221.1155,-696.3174 216.7465,-686.6654 214.1429,-696.9353 221.1155,-696.3174"/>
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-<!-- 49 -->
-<g id="node50" class="node">
-<title>49</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M583.5,-761C583.5,-761 457.5,-761 457.5,-761 451.5,-761 445.5,-755 445.5,-749 445.5,-749 445.5,-737 445.5,-737 445.5,-731 451.5,-725 457.5,-725 457.5,-725 583.5,-725 583.5,-725 589.5,-725 595.5,-731 595.5,-737 595.5,-737 595.5,-749 595.5,-749 595.5,-755 589.5,-761 583.5,-761"/>
-<text text-anchor="middle" x="520.5" y="-740.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M2704.5,-324C2704.5,-324 2638.5,-324 2638.5,-324 2632.5,-324 2626.5,-318 2626.5,-312 2626.5,-312 2626.5,-300 2626.5,-300 2626.5,-294 2632.5,-288 2638.5,-288 2638.5,-288 2704.5,-288 2704.5,-288 2710.5,-288 2716.5,-294 2716.5,-300 2716.5,-300 2716.5,-312 2716.5,-312 2716.5,-318 2710.5,-324 2704.5,-324"/>
+<text text-anchor="middle" x="2671.5" y="-309" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<text text-anchor="middle" x="2671.5" y="-298" font-family="sans" font-size="10.00">strand: plus</text>
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-<!-- 34->49 -->
-<g id="edge85" class="edge">
-<title>34->49</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M519.7786,-796.7476C519.8842,-788.8767 520.0064,-779.7743 520.1198,-771.3232"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="523.6223,-771.1548 520.2569,-761.1087 516.6229,-771.0608 523.6223,-771.1548"/>
+<!-- 34->7 -->
+<g id="edge38" class="edge">
+<title>34->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2671.5,-287.7C2671.5,-279.98 2671.5,-270.71 2671.5,-262.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2675,-262.1 2671.5,-252.1 2668,-262.1 2675,-262.1"/>
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<!-- 35 -->
<g id="node36" class="node">
<title>35</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M1070,-838C1070,-838 769,-838 769,-838 763,-838 757,-832 757,-826 757,-826 757,-809 757,-809 757,-803 763,-797 769,-797 769,-797 1070,-797 1070,-797 1076,-797 1082,-803 1082,-809 1082,-809 1082,-826 1082,-826 1082,-832 1076,-838 1070,-838"/>
-<text text-anchor="middle" x="919.5" y="-826" font-family="sans" font-size="10.00" fill="#000000">start</text>
-<text text-anchor="middle" x="919.5" y="-815" font-family="sans" font-size="10.00" fill="#000000">mate: fq2</text>
-<text text-anchor="middle" x="919.5" y="-804" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
-</g>
-<!-- 35->16 -->
-<g id="edge48" class="edge">
-<title>35->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M947.3661,-796.9453C959.8194,-787.7594 974.5882,-776.8656 987.5823,-767.2809"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="989.853,-769.9552 995.8229,-761.2024 985.6977,-764.3219 989.853,-769.9552"/>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M2482.5,-324C2482.5,-324 2416.5,-324 2416.5,-324 2410.5,-324 2404.5,-318 2404.5,-312 2404.5,-312 2404.5,-300 2404.5,-300 2404.5,-294 2410.5,-288 2416.5,-288 2416.5,-288 2482.5,-288 2482.5,-288 2488.5,-288 2494.5,-294 2494.5,-300 2494.5,-300 2494.5,-312 2494.5,-312 2494.5,-318 2488.5,-324 2482.5,-324"/>
+<text text-anchor="middle" x="2449.5" y="-309" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<text text-anchor="middle" x="2449.5" y="-298" font-family="sans" font-size="10.00">strand: minus</text>
</g>
-<!-- 35->47 -->
-<g id="edge84" class="edge">
-<title>35->47</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M756.7818,-801.0648C662.9526,-790.9385 542.8595,-776.8736 436.5,-761 434.7776,-760.7429 433.0392,-760.4786 431.2887,-760.208"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="431.5834,-756.7109 421.1575,-758.5954 430.483,-763.6239 431.5834,-756.7109"/>
+<!-- 35->8 -->
+<g id="edge40" class="edge">
+<title>35->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2474.21,-287.88C2487.17,-278.89 2503.23,-267.76 2517.27,-258.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2519.47,-260.76 2525.7,-252.19 2515.48,-255.01 2519.47,-260.76"/>
</g>
<!-- 36 -->
<g id="node37" class="node">
<title>36</title>
-<path fill="none" stroke="#56d86b" stroke-width="2" d="M401.5,-686.5C401.5,-686.5 273.5,-686.5 273.5,-686.5 267.5,-686.5 261.5,-680.5 261.5,-674.5 261.5,-674.5 261.5,-662.5 261.5,-662.5 261.5,-656.5 267.5,-650.5 273.5,-650.5 273.5,-650.5 401.5,-650.5 401.5,-650.5 407.5,-650.5 413.5,-656.5 413.5,-662.5 413.5,-662.5 413.5,-674.5 413.5,-674.5 413.5,-680.5 407.5,-686.5 401.5,-686.5"/>
-<text text-anchor="middle" x="337.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M2374.5,-324C2374.5,-324 2308.5,-324 2308.5,-324 2302.5,-324 2296.5,-318 2296.5,-312 2296.5,-312 2296.5,-300 2296.5,-300 2296.5,-294 2302.5,-288 2308.5,-288 2308.5,-288 2374.5,-288 2374.5,-288 2380.5,-288 2386.5,-294 2386.5,-300 2386.5,-300 2386.5,-312 2386.5,-312 2386.5,-318 2380.5,-324 2374.5,-324"/>
+<text text-anchor="middle" x="2341.5" y="-309" font-family="sans" font-size="10.00">sort_bed_4_big</text>
+<text text-anchor="middle" x="2341.5" y="-298" font-family="sans" font-size="10.00">strand: minus</text>
</g>
-<!-- 36->17 -->
-<g id="edge49" class="edge">
-<title>36->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M327.9567,-650.0941C314.7473,-622.8634 292.5,-569.8923 292.5,-522 292.5,-522 292.5,-522 292.5,-378 292.5,-337.1184 290.5164,-323.0856 311.5,-288 318.2711,-276.6784 328.2832,-266.5982 338.3879,-258.3019"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="340.6991,-260.9385 346.4513,-252.0412 336.4062,-255.4094 340.6991,-260.9385"/>
-</g>
-<!-- 36->31 -->
-<g id="edge64" class="edge">
-<title>36->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M319.0796,-650.4784C294.6271,-624.5348 254.5,-574.0336 254.5,-522 254.5,-522 254.5,-522 254.5,-306 254.5,-265.2078 241.9874,-243.0737 272.5,-216 310.8481,-181.974 681.4824,-185.0552 732.5,-180 754.7947,-177.7909 778.9112,-175.052 801.1518,-172.3828"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="801.7182,-175.8399 811.2251,-171.1635 800.877,-168.8906 801.7182,-175.8399"/>
-</g>
-<!-- 36->59 -->
-<g id="edge106" class="edge">
-<title>36->59</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M413.6611,-652.4263C474.1098,-639.6688 558.0713,-621.9488 617.6412,-609.3767"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="618.6639,-612.7381 627.7256,-607.2484 617.2184,-605.8889 618.6639,-612.7381"/>
+<!-- 36->9 -->
+<g id="edge42" class="edge">
+<title>36->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2365.47,-287.88C2378.05,-278.89 2393.63,-267.76 2407.25,-258.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2409.33,-260.85 2415.43,-252.19 2405.26,-255.15 2409.33,-260.85"/>
</g>
<!-- 37 -->
<g id="node38" class="node">
<title>37</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M430,-324C430,-324 333,-324 333,-324 327,-324 321,-318 321,-312 321,-312 321,-300 321,-300 321,-294 327,-288 333,-288 333,-288 430,-288 430,-288 436,-288 442,-294 442,-300 442,-300 442,-312 442,-312 442,-318 436,-324 430,-324"/>
-<text text-anchor="middle" x="381.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M1142.5,-324C1142.5,-324 1024.5,-324 1024.5,-324 1018.5,-324 1012.5,-318 1012.5,-312 1012.5,-312 1012.5,-300 1012.5,-300 1012.5,-294 1018.5,-288 1024.5,-288 1024.5,-288 1142.5,-288 1142.5,-288 1148.5,-288 1154.5,-294 1154.5,-300 1154.5,-300 1154.5,-312 1154.5,-312 1154.5,-318 1148.5,-324 1142.5,-324"/>
+<text text-anchor="middle" x="1083.5" y="-303.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
-<!-- 37->17 -->
-<g id="edge50" class="edge">
-<title>37->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M379.9859,-287.8314C379.3442,-280.131 378.5812,-270.9743 377.8681,-262.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="381.3529,-262.088 377.0344,-252.4133 374.3771,-262.6694 381.3529,-262.088"/>
+<!-- 37->10 -->
+<g id="edge44" class="edge">
+<title>37->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1088.2,-287.7C1090.31,-279.9 1092.86,-270.51 1095.22,-261.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1098.62,-262.67 1097.86,-252.1 1091.86,-260.84 1098.62,-262.67"/>
</g>
-<!-- 37->18 -->
-<g id="edge52" class="edge">
-<title>37->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M429.6974,-287.8314C455.6966,-278.0306 487.9536,-265.8709 515.2281,-255.5894"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="516.5266,-258.8404 524.6492,-252.038 514.0574,-252.2904 516.5266,-258.8404"/>
+<!-- 37->11 -->
+<g id="edge46" class="edge">
+<title>37->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1130.96,-287.88C1158.07,-278.09 1192.24,-265.77 1220.76,-255.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1221.98,-258.75 1230.2,-252.07 1219.6,-252.17 1221.98,-258.75"/>
+</g>
+<!-- 37->12 -->
+<g id="edge48" class="edge">
+<title>37->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1043.87,-287.88C1021.72,-278.31 993.94,-266.3 970.44,-256.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="971.57,-252.82 961,-252.07 968.79,-259.25 971.57,-252.82"/>
+</g>
+<!-- 37->13 -->
+<g id="edge50" class="edge">
+<title>37->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1154.59,-289.95C1157.94,-289.28 1161.26,-288.63 1164.5,-288 1167.05,-287.51 1280.23,-267.45 1366.58,-252.16"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1367.2,-255.61 1376.44,-250.42 1365.98,-248.71 1367.2,-255.61"/>
</g>
<!-- 38 -->
<g id="node39" class="node">
<title>38</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M577.5,-686.5C577.5,-686.5 467.5,-686.5 467.5,-686.5 461.5,-686.5 455.5,-680.5 455.5,-674.5 455.5,-674.5 455.5,-662.5 455.5,-662.5 455.5,-656.5 461.5,-650.5 467.5,-650.5 467.5,-650.5 577.5,-650.5 577.5,-650.5 583.5,-650.5 589.5,-656.5 589.5,-662.5 589.5,-662.5 589.5,-674.5 589.5,-674.5 589.5,-680.5 583.5,-686.5 577.5,-686.5"/>
-<text text-anchor="middle" x="522.5" y="-666" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M1286,-324C1286,-324 1185,-324 1185,-324 1179,-324 1173,-318 1173,-312 1173,-312 1173,-300 1173,-300 1173,-294 1179,-288 1185,-288 1185,-288 1286,-288 1286,-288 1292,-288 1298,-294 1298,-300 1298,-300 1298,-312 1298,-312 1298,-318 1292,-324 1286,-324"/>
+<text text-anchor="middle" x="1235.5" y="-303.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 38->18 -->
-<g id="edge51" class="edge">
-<title>38->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M515.4552,-650.314C505.4964,-622.9252 488.5,-569.2591 488.5,-522 488.5,-522 488.5,-522 488.5,-450 488.5,-377.9986 454.9753,-351.1842 489.5,-288 496.3321,-275.4964 507.4404,-265.4289 519.3399,-257.5306"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="521.4015,-260.372 528.0945,-252.159 517.7406,-254.4056 521.4015,-260.372"/>
+<!-- 38->10 -->
+<g id="edge45" class="edge">
+<title>38->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1202.96,-287.88C1185.25,-278.55 1163.15,-266.92 1144.18,-256.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1145.64,-253.75 1135.16,-252.19 1142.38,-259.94 1145.64,-253.75"/>
</g>
-<!-- 38->32 -->
-<g id="edge66" class="edge">
-<title>38->32</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M525.0999,-650.0328C530.2013,-618.2821 543.6371,-552.1246 572.5,-504 651.0069,-373.1014 700.9451,-352.0338 839.5,-288 883.5197,-267.6561 901.2938,-277.5667 942.5,-252 970.2007,-234.8129 996.2093,-207.9838 1013.4571,-188.0855"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1016.2642,-190.187 1020.0688,-180.2988 1010.9283,-185.6562 1016.2642,-190.187"/>
+<!-- 38->11 -->
+<g id="edge47" class="edge">
+<title>38->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1245.88,-287.7C1250.76,-279.56 1256.69,-269.69 1262.08,-260.7"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1265.09,-262.48 1267.24,-252.1 1259.09,-258.88 1265.09,-262.48"/>
</g>
-<!-- 38->62 -->
-<g id="edge109" class="edge">
-<title>38->62</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M589.5898,-661.0843C719.7521,-646.6969 1004.9461,-615.1732 1132.5611,-601.0674"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1133.0212,-604.538 1142.5761,-599.9604 1132.2521,-597.5804 1133.0212,-604.538"/>
+<!-- 38->12 -->
+<g id="edge49" class="edge">
+<title>38->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1172.69,-290.11C1169.58,-289.39 1166.51,-288.68 1163.5,-288 1113,-276.51 1056.47,-264.1 1010.75,-254.18"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1011.38,-250.74 1000.86,-252.04 1009.9,-257.58 1011.38,-250.74"/>
+</g>
+<!-- 38->13 -->
+<g id="edge51" class="edge">
+<title>38->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1290.98,-287.97C1323.26,-278.06 1364.11,-265.51 1397.96,-255.12"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1399.24,-258.39 1407.77,-252.11 1397.18,-251.7 1399.24,-258.39"/>
</g>
<!-- 39 -->
<g id="node40" class="node">
<title>39</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M820,-396C820,-396 737,-396 737,-396 731,-396 725,-390 725,-384 725,-384 725,-372 725,-372 725,-366 731,-360 737,-360 737,-360 820,-360 820,-360 826,-360 832,-366 832,-372 832,-372 832,-384 832,-384 832,-390 826,-396 820,-396"/>
-<text text-anchor="middle" x="778.5" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M656,-838C656,-838 355,-838 355,-838 349,-838 343,-832 343,-826 343,-826 343,-809 343,-809 343,-803 349,-797 355,-797 355,-797 656,-797 656,-797 662,-797 668,-803 668,-809 668,-809 668,-826 668,-826 668,-832 662,-838 656,-838"/>
+<text text-anchor="middle" x="505.5" y="-826" font-family="sans" font-size="10.00">start</text>
+<text text-anchor="middle" x="505.5" y="-815" font-family="sans" font-size="10.00">mate: fq1</text>
+<text text-anchor="middle" x="505.5" y="-804" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
-<!-- 39->19 -->
-<g id="edge53" class="edge">
-<title>39->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M769.979,-359.9555C752.0915,-322.0762 710.5386,-234.0818 689.3794,-189.274"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="692.5035,-187.693 685.0685,-180.1451 686.1737,-190.6821 692.5035,-187.693"/>
+<!-- 39->16 -->
+<g id="edge56" class="edge">
+<title>39->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M503.78,-796.82C501.17,-776.94 494.65,-746.22 478.5,-725 454.94,-694.05 359.18,-641.37 305.83,-613.52"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="307.19,-610.28 296.7,-608.78 303.97,-616.5 307.19,-610.28"/>
+</g>
+<!-- 53 -->
+<g id="node54" class="node">
+<title>53</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M458,-761C458,-761 315,-761 315,-761 309,-761 303,-755 303,-749 303,-749 303,-737 303,-737 303,-731 309,-725 315,-725 315,-725 458,-725 458,-725 464,-725 470,-731 470,-737 470,-737 470,-749 470,-749 470,-755 464,-761 458,-761"/>
+<text text-anchor="middle" x="386.5" y="-740.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 39->53 -->
+<g id="edge97" class="edge">
+<title>39->53</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M473.3,-796.88C457.85,-787.47 439.27,-776.15 423.26,-766.4"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="425.04,-763.38 414.68,-761.17 421.4,-769.36 425.04,-763.38"/>
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<!-- 40 -->
<g id="node41" class="node">
<title>40</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M1260.5,-252C1260.5,-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 1260.5,-216 1260.5,-216 1266.5,-216 1272.5,-222 1272.5,-228 1272.5,-228 1272.5,-240 1272.5,-240 1272.5,-246 1266.5,-252 1260.5,-252"/>
-<text text-anchor="middle" x="1214.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M1119,-838C1119,-838 806,-838 806,-838 800,-838 794,-832 794,-826 794,-826 794,-809 794,-809 794,-803 800,-797 806,-797 806,-797 1119,-797 1119,-797 1125,-797 1131,-803 1131,-809 1131,-809 1131,-826 1131,-826 1131,-832 1125,-838 1119,-838"/>
+<text text-anchor="middle" x="962.5" y="-826" font-family="sans" font-size="10.00">start</text>
+<text text-anchor="middle" x="962.5" y="-815" font-family="sans" font-size="10.00">mate: fq1</text>
+<text text-anchor="middle" x="962.5" y="-804" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
-<!-- 40->20 -->
-<g id="edge54" class="edge">
-<title>40->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1253.3607,-215.8314C1273.7742,-206.2874 1298.9723,-194.5065 1320.586,-184.4013"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1322.3423,-187.4439 1329.9187,-180.038 1319.3775,-181.1027 1322.3423,-187.4439"/>
+<!-- 40->17 -->
+<g id="edge57" class="edge">
+<title>40->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M893.98,-796.93C820.05,-774.96 699.19,-736.61 589.04,-688.93"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="590.35,-685.68 579.78,-684.89 587.54,-692.1 590.35,-685.68"/>
+</g>
+<!-- 55 -->
+<g id="node56" class="node">
+<title>55</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1132.5,-761C1132.5,-761 1006.5,-761 1006.5,-761 1000.5,-761 994.5,-755 994.5,-749 994.5,-749 994.5,-737 994.5,-737 994.5,-731 1000.5,-725 1006.5,-725 1006.5,-725 1132.5,-725 1132.5,-725 1138.5,-725 1144.5,-731 1144.5,-737 1144.5,-737 1144.5,-749 1144.5,-749 1144.5,-755 1138.5,-761 1132.5,-761"/>
+<text text-anchor="middle" x="1069.5" y="-740.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 40->55 -->
+<g id="edge99" class="edge">
+<title>40->55</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M991.46,-796.88C1005.09,-787.64 1021.44,-776.57 1035.64,-766.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1037.85,-769.67 1044.16,-761.17 1033.92,-763.88 1037.85,-769.67"/>
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<!-- 41 -->
<g id="node42" class="node">
<title>41</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M1394.5,-252C1394.5,-252 1302.5,-252 1302.5,-252 1296.5,-252 1290.5,-246 1290.5,-240 1290.5,-240 1290.5,-228 1290.5,-228 1290.5,-222 1296.5,-216 1302.5,-216 1302.5,-216 1394.5,-216 1394.5,-216 1400.5,-216 1406.5,-222 1406.5,-228 1406.5,-228 1406.5,-240 1406.5,-240 1406.5,-246 1400.5,-252 1394.5,-252"/>
-<text text-anchor="middle" x="1348.5" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M313,-838C313,-838 12,-838 12,-838 6,-838 0,-832 0,-826 0,-826 0,-809 0,-809 0,-803 6,-797 12,-797 12,-797 313,-797 313,-797 319,-797 325,-803 325,-809 325,-809 325,-826 325,-826 325,-832 319,-838 313,-838"/>
+<text text-anchor="middle" x="162.5" y="-826" font-family="sans" font-size="10.00">start</text>
+<text text-anchor="middle" x="162.5" y="-815" font-family="sans" font-size="10.00">mate: fq2</text>
+<text text-anchor="middle" x="162.5" y="-804" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
-<!-- 41->20 -->
-<g id="edge55" class="edge">
-<title>41->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1353.5468,-215.8314C1355.7094,-208.0463 1358.2853,-198.7729 1360.6848,-190.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1364.081,-190.9852 1363.3852,-180.4133 1357.3364,-189.1117 1364.081,-190.9852"/>
+<!-- 41->18 -->
+<g id="edge58" class="edge">
+<title>41->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M166.6,-796.69C168.23,-788.82 170.13,-779.64 171.88,-771.17"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="175.32,-771.82 173.92,-761.32 168.46,-770.4 175.32,-771.82"/>
+</g>
+<!-- 41->53 -->
+<g id="edge98" class="edge">
+<title>41->53</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M222.82,-796.98C254.18,-786.83 292.45,-774.44 324.1,-764.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="325.26,-767.5 333.7,-761.09 323.11,-760.84 325.26,-767.5"/>
</g>
<!-- 42 -->
<g id="node43" class="node">
<title>42</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M1022.5,-396C1022.5,-396 900.5,-396 900.5,-396 894.5,-396 888.5,-390 888.5,-384 888.5,-384 888.5,-372 888.5,-372 888.5,-366 894.5,-360 900.5,-360 900.5,-360 1022.5,-360 1022.5,-360 1028.5,-360 1034.5,-366 1034.5,-372 1034.5,-372 1034.5,-384 1034.5,-384 1034.5,-390 1028.5,-396 1022.5,-396"/>
-<text text-anchor="middle" x="961.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="961.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M737.5,-686.5C737.5,-686.5 609.5,-686.5 609.5,-686.5 603.5,-686.5 597.5,-680.5 597.5,-674.5 597.5,-674.5 597.5,-662.5 597.5,-662.5 597.5,-656.5 603.5,-650.5 609.5,-650.5 609.5,-650.5 737.5,-650.5 737.5,-650.5 743.5,-650.5 749.5,-656.5 749.5,-662.5 749.5,-662.5 749.5,-674.5 749.5,-674.5 749.5,-680.5 743.5,-686.5 737.5,-686.5"/>
+<text text-anchor="middle" x="673.5" y="-666" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
-<!-- 42->22 -->
-<g id="edge56" class="edge">
-<title>42->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M944.3407,-359.8314C936.3489,-351.3694 926.6962,-341.1489 917.9584,-331.8971"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="920.3011,-329.2802 910.8903,-324.4133 915.212,-334.0866 920.3011,-329.2802"/>
+<!-- 42->19 -->
+<g id="edge59" class="edge">
+<title>42->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M611.75,-650.41C554.3,-630.3 477.5,-590.75 477.5,-523 477.5,-523 477.5,-523 477.5,-449 477.5,-409 477.5,-362.65 477.5,-334.08"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="481,-334.05 477.5,-324.05 474,-334.05 481,-334.05"/>
</g>
-<!-- 42->25 -->
-<g id="edge58" class="edge">
-<title>42->25</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M989.7623,-359.8314C1003.9552,-350.7074 1021.3282,-339.539 1036.5636,-329.7449"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1038.7276,-332.5146 1045.2467,-324.1628 1034.9422,-326.6263 1038.7276,-332.5146"/>
+<!-- 42->37 -->
+<g id="edge78" class="edge">
+<title>42->37</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M673.5,-650.15C673.5,-623.02 673.5,-568.91 673.5,-523 673.5,-523 673.5,-523 673.5,-449 673.5,-380.2 882.27,-337.28 1001.86,-318.34"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1002.74,-321.75 1012.08,-316.75 1001.66,-314.83 1002.74,-321.75"/>
</g>
-<!-- 52 -->
-<g id="node53" class="node">
-<title>52</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M998.5,-324C998.5,-324 968.5,-324 968.5,-324 962.5,-324 956.5,-318 956.5,-312 956.5,-312 956.5,-300 956.5,-300 956.5,-294 962.5,-288 968.5,-288 968.5,-288 998.5,-288 998.5,-288 1004.5,-288 1010.5,-294 1010.5,-300 1010.5,-300 1010.5,-312 1010.5,-312 1010.5,-318 1004.5,-324 998.5,-324"/>
-<text text-anchor="middle" x="983.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
-</g>
-<!-- 42->52 -->
-<g id="edge92" class="edge">
-<title>42->52</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M967.0515,-359.8314C969.4303,-352.0463 972.2638,-342.7729 974.9033,-334.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="978.2987,-334.9996 977.8737,-324.4133 971.6042,-332.954 978.2987,-334.9996"/>
+<!-- 42->65 -->
+<g id="edge120" class="edge">
+<title>42->65</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M740.68,-650.41C784.28,-639.32 841.09,-624.87 885.76,-613.5"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="886.85,-616.84 895.68,-610.98 885.12,-610.06 886.85,-616.84"/>
</g>
<!-- 43 -->
<g id="node44" class="node">
<title>43</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M1186.5,-396C1186.5,-396 1064.5,-396 1064.5,-396 1058.5,-396 1052.5,-390 1052.5,-384 1052.5,-384 1052.5,-372 1052.5,-372 1052.5,-366 1058.5,-360 1064.5,-360 1064.5,-360 1186.5,-360 1186.5,-360 1192.5,-360 1198.5,-366 1198.5,-372 1198.5,-372 1198.5,-384 1198.5,-384 1198.5,-390 1192.5,-396 1186.5,-396"/>
-<text text-anchor="middle" x="1125.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1125.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
-</g>
-<!-- 43->24 -->
-<g id="edge57" class="edge">
-<title>43->24</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1139.6312,-359.8314C1146.0811,-351.5386 1153.8445,-341.557 1160.9252,-332.4533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1163.8019,-334.4556 1167.1786,-324.4133 1158.2764,-330.158 1163.8019,-334.4556"/>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M624,-396C624,-396 527,-396 527,-396 521,-396 515,-390 515,-384 515,-384 515,-372 515,-372 515,-366 521,-360 527,-360 527,-360 624,-360 624,-360 630,-360 636,-366 636,-372 636,-372 636,-384 636,-384 636,-390 630,-396 624,-396"/>
+<text text-anchor="middle" x="575.5" y="-375.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
-<!-- 43->26 -->
-<g id="edge59" class="edge">
-<title>43->26</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1198.6501,-361.1192C1254.8791,-348.1433 1331.3385,-330.4988 1382.4526,-318.7032"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1383.3671,-322.0843 1392.324,-316.4252 1381.793,-315.2635 1383.3671,-322.0843"/>
-</g>
-<!-- 54 -->
-<g id="node55" class="node">
-<title>54</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1286.5,-324C1286.5,-324 1256.5,-324 1256.5,-324 1250.5,-324 1244.5,-318 1244.5,-312 1244.5,-312 1244.5,-300 1244.5,-300 1244.5,-294 1250.5,-288 1256.5,-288 1256.5,-288 1286.5,-288 1286.5,-288 1292.5,-288 1298.5,-294 1298.5,-300 1298.5,-300 1298.5,-312 1298.5,-312 1298.5,-318 1292.5,-324 1286.5,-324"/>
-<text text-anchor="middle" x="1271.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+<!-- 43->19 -->
+<g id="edge60" class="edge">
+<title>43->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M551.53,-359.88C538.95,-350.89 523.37,-339.76 509.75,-330.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="511.74,-327.15 501.57,-324.19 507.67,-332.85 511.74,-327.15"/>
</g>
-<!-- 43->54 -->
-<g id="edge96" class="edge">
-<title>43->54</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1162.4507,-359.9439C1181.8115,-350.4643 1206.1139,-338.536 1235.2027,-324.1337"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1236.9773,-327.1606 1244.3838,-319.5846 1233.8694,-320.8883 1236.9773,-327.1606"/>
+<!-- 43->20 -->
+<g id="edge62" class="edge">
+<title>43->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M599.72,-359.88C612.42,-350.89 628.16,-339.76 641.92,-330.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="644.04,-332.82 650.19,-324.19 640,-327.11 644.04,-332.82"/>
</g>
<!-- 44 -->
<g id="node45" class="node">
<title>44</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M1891.5,-396C1891.5,-396 1769.5,-396 1769.5,-396 1763.5,-396 1757.5,-390 1757.5,-384 1757.5,-384 1757.5,-372 1757.5,-372 1757.5,-366 1763.5,-360 1769.5,-360 1769.5,-360 1891.5,-360 1891.5,-360 1897.5,-360 1903.5,-366 1903.5,-372 1903.5,-372 1903.5,-384 1903.5,-384 1903.5,-390 1897.5,-396 1891.5,-396"/>
-<text text-anchor="middle" x="1830.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1830.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: Unique</text>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M1304.5,-686.5C1304.5,-686.5 1194.5,-686.5 1194.5,-686.5 1188.5,-686.5 1182.5,-680.5 1182.5,-674.5 1182.5,-674.5 1182.5,-662.5 1182.5,-662.5 1182.5,-656.5 1188.5,-650.5 1194.5,-650.5 1194.5,-650.5 1304.5,-650.5 1304.5,-650.5 1310.5,-650.5 1316.5,-656.5 1316.5,-662.5 1316.5,-662.5 1316.5,-674.5 1316.5,-674.5 1316.5,-680.5 1310.5,-686.5 1304.5,-686.5"/>
+<text text-anchor="middle" x="1249.5" y="-666" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
-<!-- 44->27 -->
-<g id="edge60" class="edge">
-<title>44->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1824.1914,-359.8314C1821.4883,-352.0463 1818.2684,-342.7729 1815.269,-334.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1818.48,-332.7119 1811.8935,-324.4133 1811.8673,-335.0081 1818.48,-332.7119"/>
-</g>
-<!-- 44->29 -->
-<g id="edge62" class="edge">
-<title>44->29</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1878.9497,-359.8314C1905.9795,-349.6952 1939.7376,-337.0359 1967.7249,-326.5407"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1969.2289,-329.7147 1977.3632,-322.9263 1966.771,-323.1604 1969.2289,-329.7147"/>
+<!-- 44->20 -->
+<g id="edge61" class="edge">
+<title>44->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1234.43,-650.34C1204.95,-617.72 1136.34,-546.24 1065.5,-504 1025.29,-480.02 1006.33,-492.61 966.5,-468 946.71,-455.77 947.6,-445.29 928.5,-432 864.18,-387.25 781.46,-349.76 728.21,-327.84"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="729.52,-324.6 718.94,-324.06 726.88,-331.08 729.52,-324.6"/>
</g>
-<!-- 53 -->
-<g id="node54" class="node">
-<title>53</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1542.5,-324C1542.5,-324 1512.5,-324 1512.5,-324 1506.5,-324 1500.5,-318 1500.5,-312 1500.5,-312 1500.5,-300 1500.5,-300 1500.5,-294 1506.5,-288 1512.5,-288 1512.5,-288 1542.5,-288 1542.5,-288 1548.5,-288 1554.5,-294 1554.5,-300 1554.5,-300 1554.5,-312 1554.5,-312 1554.5,-318 1548.5,-324 1542.5,-324"/>
-<text text-anchor="middle" x="1527.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
+<!-- 44->38 -->
+<g id="edge80" class="edge">
+<title>44->38</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1262.79,-650.14C1279.84,-626.67 1308.52,-582.81 1319.5,-540 1331.42,-493.5 1324.1,-479.78 1319.5,-432 1316.37,-399.55 1322.74,-387.66 1305.5,-360 1298.17,-348.25 1287.23,-338.16 1276.17,-330.04"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1277.95,-327.02 1267.73,-324.22 1273.97,-332.78 1277.95,-327.02"/>
</g>
-<!-- 44->53 -->
-<g id="edge94" class="edge">
-<title>44->53</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1757.4501,-368.5501C1705.4431,-360.6099 1634.0877,-347.2475 1564.4994,-323.8908"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1565.2888,-320.4614 1554.6942,-320.5282 1563.018,-327.0829 1565.2888,-320.4614"/>
+<!-- 44->68 -->
+<g id="edge123" class="edge">
+<title>44->68</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1309.14,-650.41C1348.28,-639.19 1399.4,-624.54 1439.25,-613.13"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1440.21,-616.49 1448.86,-610.37 1438.28,-609.76 1440.21,-616.49"/>
</g>
<!-- 45 -->
<g id="node46" class="node">
<title>45</title>
-<path fill="none" stroke="#5663d8" stroke-width="2" d="M2055.5,-396C2055.5,-396 1933.5,-396 1933.5,-396 1927.5,-396 1921.5,-390 1921.5,-384 1921.5,-384 1921.5,-372 1921.5,-372 1921.5,-366 1927.5,-360 1933.5,-360 1933.5,-360 2055.5,-360 2055.5,-360 2061.5,-360 2067.5,-366 2067.5,-372 2067.5,-372 2067.5,-384 2067.5,-384 2067.5,-390 2061.5,-396 2055.5,-396"/>
-<text text-anchor="middle" x="1994.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
-<text text-anchor="middle" x="1994.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">unique: UniqueMultiple</text>
-</g>
-<!-- 45->28 -->
-<g id="edge61" class="edge">
-<title>45->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M2047.7229,-359.9243C2079.402,-349.1654 2119.5245,-335.5388 2151.5103,-324.6757"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="2152.8141,-327.9294 2161.1574,-321.3994 2150.563,-321.3012 2152.8141,-327.9294"/>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M1145,-396C1145,-396 1062,-396 1062,-396 1056,-396 1050,-390 1050,-384 1050,-384 1050,-372 1050,-372 1050,-366 1056,-360 1062,-360 1062,-360 1145,-360 1145,-360 1151,-360 1157,-366 1157,-372 1157,-372 1157,-384 1157,-384 1157,-390 1151,-396 1145,-396"/>
+<text text-anchor="middle" x="1103.5" y="-375.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
</g>
-<!-- 45->30 -->
+<!-- 45->21 -->
<g id="edge63" class="edge">
-<title>45->30</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1974.3126,-359.8314C1964.6486,-351.1337 1952.9204,-340.5783 1942.4184,-331.1265"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1944.4553,-328.251 1934.6809,-324.1628 1939.7725,-333.454 1944.4553,-328.251"/>
+<title>45->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1049.89,-370.24C984.07,-358.76 875.08,-328.65 825.5,-252 816.81,-238.57 816.59,-229.29 825.5,-216 834.23,-202.98 867.13,-189.57 897.52,-179.5"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="898.82,-182.75 907.26,-176.35 896.67,-176.09 898.82,-182.75"/>
</g>
-<!-- 55 -->
-<g id="node56" class="node">
-<title>55</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1614.5,-324C1614.5,-324 1584.5,-324 1584.5,-324 1578.5,-324 1572.5,-318 1572.5,-312 1572.5,-312 1572.5,-300 1572.5,-300 1572.5,-294 1578.5,-288 1584.5,-288 1584.5,-288 1614.5,-288 1614.5,-288 1620.5,-288 1626.5,-294 1626.5,-300 1626.5,-300 1626.5,-312 1626.5,-312 1626.5,-318 1620.5,-324 1614.5,-324"/>
-<text text-anchor="middle" x="1599.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
-</g>
-<!-- 45->55 -->
-<g id="edge98" class="edge">
-<title>45->55</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1921.2166,-361.7413C1918.2748,-361.1432 1915.3606,-360.5604 1912.5,-360 1813.2092,-340.5476 1695.4586,-321.2394 1636.7158,-311.8616"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1637.2156,-308.3971 1626.7897,-310.2819 1636.1154,-315.3101 1637.2156,-308.3971"/>
+<!-- 46 -->
+<g id="node47" class="node">
+<title>46</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M1895.5,-252C1895.5,-252 1803.5,-252 1803.5,-252 1797.5,-252 1791.5,-246 1791.5,-240 1791.5,-240 1791.5,-228 1791.5,-228 1791.5,-222 1797.5,-216 1803.5,-216 1803.5,-216 1895.5,-216 1895.5,-216 1901.5,-216 1907.5,-222 1907.5,-228 1907.5,-228 1907.5,-240 1907.5,-240 1907.5,-246 1901.5,-252 1895.5,-252"/>
+<text text-anchor="middle" x="1849.5" y="-231.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
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-<!-- 46->31 -->
-<g id="edge65" class="edge">
-<title>46->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M875.0234,-215.8314C876.0929,-208.131 877.3647,-198.9743 878.5532,-190.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="882.0336,-190.7997 879.9426,-180.4133 875.1001,-189.8367 882.0336,-190.7997"/>
+<!-- 46->22 -->
+<g id="edge64" class="edge">
+<title>46->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1849.5,-215.7C1849.5,-207.98 1849.5,-198.71 1849.5,-190.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1853,-190.1 1849.5,-180.1 1846,-190.1 1853,-190.1"/>
</g>
-<!-- 46->32 -->
-<g id="edge67" class="edge">
-<title>46->32</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M913.3794,-215.8314C935.046,-206.2018 961.8363,-194.295 984.7078,-184.1299"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="986.1979,-187.2978 993.9145,-180.038 983.3549,-180.9011 986.1979,-187.2978"/>
+<!-- 47 -->
+<g id="node48" class="node">
+<title>47</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M2029.5,-252C2029.5,-252 1937.5,-252 1937.5,-252 1931.5,-252 1925.5,-246 1925.5,-240 1925.5,-240 1925.5,-228 1925.5,-228 1925.5,-222 1931.5,-216 1937.5,-216 1937.5,-216 2029.5,-216 2029.5,-216 2035.5,-216 2041.5,-222 2041.5,-228 2041.5,-228 2041.5,-240 2041.5,-240 2041.5,-246 2035.5,-252 2029.5,-252"/>
+<text text-anchor="middle" x="1983.5" y="-231.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
-<!-- 47->36 -->
-<g id="edge68" class="edge">
-<title>47->36</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M337.5,-724.9656C337.5,-716.5178 337.5,-706.2542 337.5,-696.8064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="341.0001,-696.6265 337.5,-686.6265 334.0001,-696.6265 341.0001,-696.6265"/>
+<!-- 47->22 -->
+<g id="edge65" class="edge">
+<title>47->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1950.72,-215.88C1932.87,-206.55 1910.6,-194.92 1891.5,-184.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1892.89,-181.72 1882.41,-180.19 1889.65,-187.92 1892.89,-181.72"/>
</g>
<!-- 48 -->
<g id="node49" class="node">
<title>48</title>
-<path fill="none" stroke="#56a2d8" stroke-width="2" d="M448,-396C448,-396 333,-396 333,-396 327,-396 321,-390 321,-384 321,-384 321,-372 321,-372 321,-366 327,-360 333,-360 333,-360 448,-360 448,-360 454,-360 460,-366 460,-372 460,-372 460,-384 460,-384 460,-390 454,-396 448,-396"/>
-<text text-anchor="middle" x="390.5" y="-381" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
-<text text-anchor="middle" x="390.5" y="-370" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1495.5,-396C1495.5,-396 1373.5,-396 1373.5,-396 1367.5,-396 1361.5,-390 1361.5,-384 1361.5,-384 1361.5,-372 1361.5,-372 1361.5,-366 1367.5,-360 1373.5,-360 1373.5,-360 1495.5,-360 1495.5,-360 1501.5,-360 1507.5,-366 1507.5,-372 1507.5,-372 1507.5,-384 1507.5,-384 1507.5,-390 1501.5,-396 1495.5,-396"/>
+<text text-anchor="middle" x="1434.5" y="-381" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1434.5" y="-370" font-family="sans" font-size="10.00">unique: Unique</text>
</g>
-<!-- 48->37 -->
-<g id="edge69" class="edge">
-<title>48->37</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M388.2289,-359.8314C387.2664,-352.131 386.1218,-342.9743 385.0521,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="388.5151,-333.9019 383.8017,-324.4133 381.5691,-334.7702 388.5151,-333.9019"/>
+<!-- 48->28 -->
+<g id="edge70" class="edge">
+<title>48->28</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1416.46,-359.7C1407.44,-351.05 1396.38,-340.45 1386.56,-331.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1388.98,-328.5 1379.34,-324.1 1384.13,-333.55 1388.98,-328.5"/>
+</g>
+<!-- 48->31 -->
+<g id="edge72" class="edge">
+<title>48->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1443.15,-359.7C1447.14,-351.73 1451.95,-342.1 1456.37,-333.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1459.61,-334.61 1460.95,-324.1 1453.35,-331.48 1459.61,-334.61"/>
</g>
<!-- 58 -->
<g id="node59" class="node">
<title>58</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M704.5,-324C704.5,-324 510.5,-324 510.5,-324 504.5,-324 498.5,-318 498.5,-312 498.5,-312 498.5,-300 498.5,-300 498.5,-294 504.5,-288 510.5,-288 510.5,-288 704.5,-288 704.5,-288 710.5,-288 716.5,-294 716.5,-300 716.5,-300 716.5,-312 716.5,-312 716.5,-318 710.5,-324 704.5,-324"/>
-<text text-anchor="middle" x="607.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">concatenate_transcriptome_and_genome</text>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M1574.5,-324C1574.5,-324 1544.5,-324 1544.5,-324 1538.5,-324 1532.5,-318 1532.5,-312 1532.5,-312 1532.5,-300 1532.5,-300 1532.5,-294 1538.5,-288 1544.5,-288 1544.5,-288 1574.5,-288 1574.5,-288 1580.5,-288 1586.5,-294 1586.5,-300 1586.5,-300 1586.5,-312 1586.5,-312 1586.5,-318 1580.5,-324 1574.5,-324"/>
+<text text-anchor="middle" x="1559.5" y="-303.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
<!-- 48->58 -->
-<g id="edge104" class="edge">
+<g id="edge106" class="edge">
<title>48->58</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M444.9782,-359.9243C474.9013,-349.9959 512.1843,-337.6255 543.4904,-327.2382"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="544.6104,-330.5543 552.9994,-324.0831 542.406,-323.9104 544.6104,-330.5543"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1465.08,-359.88C1482.72,-350 1505,-337.52 1523.48,-327.17"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1525.2,-330.22 1532.22,-322.28 1521.78,-324.11 1525.2,-330.22"/>
</g>
-<!-- 49->38 -->
-<g id="edge70" class="edge">
-<title>49->38</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M520.9841,-724.9656C521.2109,-716.5178 521.4865,-706.2542 521.7401,-696.8064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="525.2437,-696.7169 522.0134,-686.6265 518.2462,-696.5289 525.2437,-696.7169"/>
+<!-- 49 -->
+<g id="node50" class="node">
+<title>49</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1659.5,-396C1659.5,-396 1537.5,-396 1537.5,-396 1531.5,-396 1525.5,-390 1525.5,-384 1525.5,-384 1525.5,-372 1525.5,-372 1525.5,-366 1531.5,-360 1537.5,-360 1537.5,-360 1659.5,-360 1659.5,-360 1665.5,-360 1671.5,-366 1671.5,-372 1671.5,-372 1671.5,-384 1671.5,-384 1671.5,-390 1665.5,-396 1659.5,-396"/>
+<text text-anchor="middle" x="1598.5" y="-381" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1598.5" y="-370" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
+</g>
+<!-- 49->30 -->
+<g id="edge71" class="edge">
+<title>49->30</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1611.11,-359.7C1617.1,-351.47 1624.38,-341.48 1630.98,-332.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1633.98,-334.25 1637.04,-324.1 1628.32,-330.13 1633.98,-334.25"/>
+</g>
+<!-- 49->32 -->
+<g id="edge73" class="edge">
+<title>49->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1671.64,-360.32C1726.56,-347.8 1800.6,-330.92 1850.53,-319.53"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1851.52,-322.9 1860.5,-317.26 1849.97,-316.07 1851.52,-322.9"/>
+</g>
+<!-- 60 -->
+<g id="node61" class="node">
+<title>60</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M1754.5,-324C1754.5,-324 1724.5,-324 1724.5,-324 1718.5,-324 1712.5,-318 1712.5,-312 1712.5,-312 1712.5,-300 1712.5,-300 1712.5,-294 1718.5,-288 1724.5,-288 1724.5,-288 1754.5,-288 1754.5,-288 1760.5,-288 1766.5,-294 1766.5,-300 1766.5,-300 1766.5,-312 1766.5,-312 1766.5,-318 1760.5,-324 1754.5,-324"/>
+<text text-anchor="middle" x="1739.5" y="-303.5" font-family="sans" font-size="10.00">alfa_qc</text>
+</g>
+<!-- 49->60 -->
+<g id="edge110" class="edge">
+<title>49->60</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1632.99,-359.88C1654.3,-349.3 1681.6,-335.74 1703.23,-325.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1705.02,-328.03 1712.42,-320.44 1701.91,-321.76 1705.02,-328.03"/>
</g>
<!-- 50 -->
<g id="node51" class="node">
<title>50</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M859,-468C859,-468 764,-468 764,-468 758,-468 752,-462 752,-456 752,-456 752,-444 752,-444 752,-438 758,-432 764,-432 764,-432 859,-432 859,-432 865,-432 871,-438 871,-444 871,-444 871,-456 871,-456 871,-462 865,-468 859,-468"/>
-<text text-anchor="middle" x="811.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M2048.5,-396C2048.5,-396 1926.5,-396 1926.5,-396 1920.5,-396 1914.5,-390 1914.5,-384 1914.5,-384 1914.5,-372 1914.5,-372 1914.5,-366 1920.5,-360 1926.5,-360 1926.5,-360 2048.5,-360 2048.5,-360 2054.5,-360 2060.5,-366 2060.5,-372 2060.5,-372 2060.5,-384 2060.5,-384 2060.5,-390 2054.5,-396 2048.5,-396"/>
+<text text-anchor="middle" x="1987.5" y="-381" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="1987.5" y="-370" font-family="sans" font-size="10.00">unique: Unique</text>
</g>
-<!-- 50->39 -->
-<g id="edge71" class="edge">
-<title>50->39</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M803.1727,-431.8314C799.527,-423.8771 795.1691,-414.369 791.1373,-405.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="794.2877,-404.0456 786.9394,-396.4133 787.9243,-406.9622 794.2877,-404.0456"/>
+<!-- 50->33 -->
+<g id="edge74" class="edge">
+<title>50->33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2047.36,-359.97C2087.31,-348.6 2139.45,-333.76 2178.38,-322.68"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2179.83,-325.91 2188.49,-319.81 2177.91,-319.18 2179.83,-325.91"/>
+</g>
+<!-- 50->35 -->
+<g id="edge76" class="edge">
+<title>50->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2060.77,-366.43C2076.2,-364.25 2092.38,-362.02 2107.5,-360 2232.12,-343.39 2267.67,-351.06 2394.21,-324.07"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2395.25,-327.42 2404.29,-321.89 2393.77,-320.58 2395.25,-327.42"/>
+</g>
+<!-- 59 -->
+<g id="node60" class="node">
+<title>59</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M2010.5,-324C2010.5,-324 1980.5,-324 1980.5,-324 1974.5,-324 1968.5,-318 1968.5,-312 1968.5,-312 1968.5,-300 1968.5,-300 1968.5,-294 1974.5,-288 1980.5,-288 1980.5,-288 2010.5,-288 2010.5,-288 2016.5,-288 2022.5,-294 2022.5,-300 2022.5,-300 2022.5,-312 2022.5,-312 2022.5,-318 2016.5,-324 2010.5,-324"/>
+<text text-anchor="middle" x="1995.5" y="-303.5" font-family="sans" font-size="10.00">alfa_qc</text>
+</g>
+<!-- 50->59 -->
+<g id="edge108" class="edge">
+<title>50->59</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1989.48,-359.7C1990.36,-351.98 1991.42,-342.71 1992.4,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1995.89,-334.44 1993.55,-324.1 1988.93,-333.64 1995.89,-334.44"/>
</g>
<!-- 51 -->
<g id="node52" class="node">
<title>51</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M1015,-468C1015,-468 920,-468 920,-468 914,-468 908,-462 908,-456 908,-456 908,-444 908,-444 908,-438 914,-432 920,-432 920,-432 1015,-432 1015,-432 1021,-432 1027,-438 1027,-444 1027,-444 1027,-456 1027,-456 1027,-462 1021,-468 1015,-468"/>
-<text text-anchor="middle" x="967.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M2250.5,-396C2250.5,-396 2128.5,-396 2128.5,-396 2122.5,-396 2116.5,-390 2116.5,-384 2116.5,-384 2116.5,-372 2116.5,-372 2116.5,-366 2122.5,-360 2128.5,-360 2128.5,-360 2250.5,-360 2250.5,-360 2256.5,-360 2262.5,-366 2262.5,-372 2262.5,-372 2262.5,-384 2262.5,-384 2262.5,-390 2256.5,-396 2250.5,-396"/>
+<text text-anchor="middle" x="2189.5" y="-381" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+<text text-anchor="middle" x="2189.5" y="-370" font-family="sans" font-size="10.00">unique: UniqueMultiple</text>
</g>
-<!-- 51->39 -->
-<g id="edge72" class="edge">
-<title>51->39</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M919.8073,-431.8314C894.1927,-422.0734 862.4398,-409.977 835.526,-399.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="836.4406,-396.3273 825.8497,-396.038 833.9486,-402.8687 836.4406,-396.3273"/>
+<!-- 51->34 -->
+<g id="edge75" class="edge">
+<title>51->34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2262.71,-366.37C2359.86,-352.26 2529.22,-327.66 2616.31,-315.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2616.87,-318.47 2626.26,-313.57 2615.86,-311.54 2616.87,-318.47"/>
</g>
-<!-- 52->40 -->
-<g id="edge73" class="edge">
-<title>52->40</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1010.7706,-291.6816C1013.6832,-290.3585 1016.63,-289.1029 1019.5,-288 1025.7027,-285.6163 1092.7135,-267.1809 1146.473,-252.5042"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1147.6133,-255.8211 1156.3393,-249.8122 1145.7706,-249.068 1147.6133,-255.8211"/>
+<!-- 51->36 -->
+<g id="edge77" class="edge">
+<title>51->36</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2226.68,-359.88C2247.37,-350.35 2273.3,-338.41 2295.28,-328.28"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2296.82,-331.43 2304.44,-324.07 2293.89,-325.07 2296.82,-331.43"/>
</g>
-<!-- 53->40 -->
-<g id="edge74" class="edge">
-<title>53->40</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1500.3358,-291.3825C1497.4025,-290.1177 1494.4217,-288.9576 1491.5,-288 1404.5027,-259.487 1375.8885,-271.4378 1282.3915,-252.0524"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1283.0348,-248.6109 1272.5239,-249.9413 1281.5703,-255.456 1283.0348,-248.6109"/>
+<!-- 61 -->
+<g id="node62" class="node">
+<title>61</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M2082.5,-324C2082.5,-324 2052.5,-324 2052.5,-324 2046.5,-324 2040.5,-318 2040.5,-312 2040.5,-312 2040.5,-300 2040.5,-300 2040.5,-294 2046.5,-288 2052.5,-288 2052.5,-288 2082.5,-288 2082.5,-288 2088.5,-288 2094.5,-294 2094.5,-300 2094.5,-300 2094.5,-312 2094.5,-312 2094.5,-318 2088.5,-324 2082.5,-324"/>
+<text text-anchor="middle" x="2067.5" y="-303.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
-<!-- 54->41 -->
-<g id="edge75" class="edge">
-<title>54->41</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1290.9304,-287.8314C1300.232,-279.1337 1311.5204,-268.5783 1321.6286,-259.1265"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1324.1621,-261.5493 1329.0759,-252.1628 1319.3811,-256.4363 1324.1621,-261.5493"/>
+<!-- 51->61 -->
+<g id="edge112" class="edge">
+<title>51->61</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2159.66,-359.88C2142.72,-350.16 2121.39,-337.92 2103.53,-327.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2104.95,-324.46 2094.54,-322.51 2101.47,-330.53 2104.95,-324.46"/>
</g>
-<!-- 55->41 -->
-<g id="edge76" class="edge">
-<title>55->41</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1572.2628,-291.5928C1569.3437,-290.287 1566.3862,-289.0598 1563.5,-288 1500.3582,-264.8147 1481.6817,-268.6069 1416.5,-252 1416.4001,-251.9746 1416.3002,-251.9491 1416.2002,-251.9236"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1417.2765,-248.5865 1406.72,-249.4873 1415.5342,-255.3662 1417.2765,-248.5865"/>
+<!-- 52->37 -->
+<g id="edge79" class="edge">
+<title>52->37</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1198.32,-359.88C1177.63,-350.35 1151.7,-338.41 1129.72,-328.28"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1131.11,-325.07 1120.56,-324.07 1128.18,-331.43 1131.11,-325.07"/>
+</g>
+<!-- 52->38 -->
+<g id="edge81" class="edge">
+<title>52->38</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1235.5,-359.7C1235.5,-351.98 1235.5,-342.71 1235.5,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1239,-334.1 1235.5,-324.1 1232,-334.1 1239,-334.1"/>
+</g>
+<!-- 53->42 -->
+<g id="edge82" class="edge">
+<title>53->42</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M454.15,-724.91C496.67,-714.17 551.67,-700.28 595.95,-689.09"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="596.97,-692.44 605.81,-686.6 595.25,-685.66 596.97,-692.44"/>
+</g>
+<!-- 54 -->
+<g id="node55" class="node">
+<title>54</title>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M633,-540C633,-540 518,-540 518,-540 512,-540 506,-534 506,-528 506,-528 506,-516 506,-516 506,-510 512,-504 518,-504 518,-504 633,-504 633,-504 639,-504 645,-510 645,-516 645,-516 645,-528 645,-528 645,-534 639,-540 633,-540"/>
+<text text-anchor="middle" x="575.5" y="-525" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<text text-anchor="middle" x="575.5" y="-514" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 54->43 -->
+<g id="edge83" class="edge">
+<title>54->43</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M575.5,-503.87C575.5,-479.67 575.5,-435.21 575.5,-406.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="579,-406.19 575.5,-396.19 572,-406.19 579,-406.19"/>
+</g>
+<!-- 64 -->
+<g id="node65" class="node">
+<title>64</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M907.5,-468C907.5,-468 713.5,-468 713.5,-468 707.5,-468 701.5,-462 701.5,-456 701.5,-456 701.5,-444 701.5,-444 701.5,-438 707.5,-432 713.5,-432 713.5,-432 907.5,-432 907.5,-432 913.5,-432 919.5,-438 919.5,-444 919.5,-444 919.5,-456 919.5,-456 919.5,-462 913.5,-468 907.5,-468"/>
+<text text-anchor="middle" x="810.5" y="-447.5" font-family="sans" font-size="10.00">concatenate_transcriptome_and_genome</text>
+</g>
+<!-- 54->64 -->
+<g id="edge118" class="edge">
+<title>54->64</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M632.69,-503.97C666.09,-494.01 708.42,-481.41 743.4,-470.99"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="744.47,-474.32 753.06,-468.11 742.47,-467.61 744.47,-474.32"/>
+</g>
+<!-- 55->44 -->
+<g id="edge84" class="edge">
+<title>55->44</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1112.16,-724.82C1137.82,-714.48 1170.67,-701.25 1197.81,-690.32"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1199.18,-693.54 1207.15,-686.56 1196.57,-687.05 1199.18,-693.54"/>
</g>
<!-- 56 -->
<g id="node57" class="node">
<title>56</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M712.5,-468C712.5,-468 676.5,-468 676.5,-468 670.5,-468 664.5,-462 664.5,-456 664.5,-456 664.5,-444 664.5,-444 664.5,-438 670.5,-432 676.5,-432 676.5,-432 712.5,-432 712.5,-432 718.5,-432 724.5,-438 724.5,-444 724.5,-444 724.5,-456 724.5,-456 724.5,-462 718.5,-468 712.5,-468"/>
-<text text-anchor="middle" x="694.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M1161,-468C1161,-468 1066,-468 1066,-468 1060,-468 1054,-462 1054,-456 1054,-456 1054,-444 1054,-444 1054,-438 1060,-432 1066,-432 1066,-432 1161,-432 1161,-432 1167,-432 1173,-438 1173,-444 1173,-444 1173,-456 1173,-456 1173,-462 1167,-468 1161,-468"/>
+<text text-anchor="middle" x="1113.5" y="-447.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
-<!-- 56->42 -->
-<g id="edge77" class="edge">
-<title>56->42</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M724.6451,-438.3401C730.8393,-436.11 737.348,-433.8857 743.5,-432 787.5825,-418.4876 837.4538,-405.9367 878.3604,-396.342"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="879.3424,-399.7071 888.2879,-394.0301 877.7546,-392.8895 879.3424,-399.7071"/>
-</g>
-<!-- 56->43 -->
-<g id="edge78" class="edge">
-<title>56->43</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M724.7438,-437.648C730.8728,-435.4989 737.3315,-433.4817 743.5,-432 870.8879,-401.4011 909.2319,-417.5833 1042.0957,-396.1293"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1042.9576,-399.5343 1052.2509,-394.4466 1041.8133,-392.6285 1042.9576,-399.5343"/>
+<!-- 56->45 -->
+<g id="edge85" class="edge">
+<title>56->45</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1111.03,-431.7C1109.93,-423.98 1108.6,-414.71 1107.37,-406.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1110.82,-405.51 1105.94,-396.1 1103.89,-406.5 1110.82,-405.51"/>
</g>
<!-- 57 -->
<g id="node58" class="node">
<title>57</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M1827.5,-468C1827.5,-468 1791.5,-468 1791.5,-468 1785.5,-468 1779.5,-462 1779.5,-456 1779.5,-456 1779.5,-444 1779.5,-444 1779.5,-438 1785.5,-432 1791.5,-432 1791.5,-432 1827.5,-432 1827.5,-432 1833.5,-432 1839.5,-438 1839.5,-444 1839.5,-444 1839.5,-456 1839.5,-456 1839.5,-462 1833.5,-468 1827.5,-468"/>
-<text text-anchor="middle" x="1809.5" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
-</g>
-<!-- 57->44 -->
-<g id="edge79" class="edge">
-<title>57->44</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1814.7992,-431.8314C1817.0698,-424.0463 1819.7746,-414.7729 1822.294,-406.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1825.6894,-406.9933 1825.1295,-396.4133 1818.9694,-405.0332 1825.6894,-406.9933"/>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M1298,-468C1298,-468 1203,-468 1203,-468 1197,-468 1191,-462 1191,-456 1191,-456 1191,-444 1191,-444 1191,-438 1197,-432 1203,-432 1203,-432 1298,-432 1298,-432 1304,-432 1310,-438 1310,-444 1310,-444 1310,-456 1310,-456 1310,-462 1304,-468 1298,-468"/>
+<text text-anchor="middle" x="1250.5" y="-447.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 57->45 -->
-<g id="edge80" class="edge">
+<g id="edge86" class="edge">
<title>57->45</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1839.6352,-438.2717C1866.3801,-427.8629 1906.1449,-412.3869 1938.6831,-399.7234"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1940.0384,-402.9517 1948.0881,-396.063 1937.4996,-396.4283 1940.0384,-402.9517"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1214.54,-431.88C1194.62,-422.39 1169.68,-410.51 1148.48,-400.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1149.88,-397.21 1139.34,-396.07 1146.87,-403.53 1149.88,-397.21"/>
</g>
<!-- 58->46 -->
-<g id="edge81" class="edge">
+<g id="edge87" class="edge">
<title>58->46</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M674.0286,-287.9243C713.0381,-277.3255 762.2902,-263.9438 801.9712,-253.1626"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="803.1088,-256.4804 811.8413,-250.4809 801.2734,-249.7253 803.1088,-256.4804"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1586.73,-291.28C1589.65,-290.07 1592.61,-288.94 1595.5,-288 1672.97,-262.7 1698.04,-269.82 1781.53,-252.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1782.42,-255.5 1791.44,-249.95 1780.93,-248.66 1782.42,-255.5"/>
</g>
-<!-- 59->50 -->
-<g id="edge86" class="edge">
-<title>59->50</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M750.1542,-575.8878C767.9524,-567.6652 785.8109,-556.0701 797.5,-540 810.3897,-522.2794 813.427,-497.3723 813.5014,-478.2512"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="816.9956,-477.9509 813.2685,-468.0333 809.9974,-478.1105 816.9956,-477.9509"/>
-</g>
-<!-- 59->56 -->
-<g id="edge100" class="edge">
-<title>59->56</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M627.9397,-576.2456C610.5375,-568.1131 593.6429,-556.4803 583.5,-540 575.1137,-526.3739 575.0145,-517.5645 583.5,-504 599.0019,-479.2196 629.4944,-465.516 654.6033,-458.1202"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="655.5357,-461.4939 664.2702,-455.4973 653.7026,-454.7381 655.5357,-461.4939"/>
-</g>
-<!-- 60 -->
-<g id="node61" class="node">
-<title>60</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M776.5,-540C776.5,-540 604.5,-540 604.5,-540 598.5,-540 592.5,-534 592.5,-528 592.5,-528 592.5,-516 592.5,-516 592.5,-510 598.5,-504 604.5,-504 604.5,-504 776.5,-504 776.5,-504 782.5,-504 788.5,-510 788.5,-516 788.5,-516 788.5,-528 788.5,-528 788.5,-534 782.5,-540 776.5,-540"/>
-<text text-anchor="middle" x="690.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="690.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">seqmode: pe</text>
-</g>
-<!-- 59->60 -->
-<g id="edge107" class="edge">
-<title>59->60</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M690.5,-575.8314C690.5,-568.131 690.5,-558.9743 690.5,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="694.0001,-550.4132 690.5,-540.4133 687.0001,-550.4133 694.0001,-550.4132"/>
-</g>
-<!-- 60->50 -->
-<g id="edge87" class="edge">
-<title>60->50</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M721.0334,-503.8314C736.5101,-494.6221 755.4869,-483.3301 772.0563,-473.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="774.1724,-476.2843 780.9764,-468.1628 770.5929,-470.2687 774.1724,-476.2843"/>
+<!-- 59->46 -->
+<g id="edge88" class="edge">
+<title>59->46</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1968.38,-292C1947.54,-282.01 1918.31,-267.99 1894.05,-256.36"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1895.55,-253.2 1885.02,-252.03 1892.53,-259.51 1895.55,-253.2"/>
</g>
-<!-- 60->56 -->
-<g id="edge101" class="edge">
-<title>60->56</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M691.5094,-503.8314C691.9372,-496.131 692.4459,-486.9743 692.9213,-478.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="696.4169,-478.592 693.477,-468.4133 689.4276,-478.2037 696.4169,-478.592"/>
+<!-- 60->47 -->
+<g id="edge89" class="edge">
+<title>60->47</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1766.54,-297.24C1802.26,-287 1866.37,-268.6 1915.68,-254.46"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1916.68,-257.81 1925.33,-251.69 1914.75,-251.08 1916.68,-257.81"/>
</g>
-<!-- 61 -->
-<g id="node62" class="node">
-<title>61</title>
-<path fill="none" stroke="#d87556" stroke-width="2" d="M992.5,-540C992.5,-540 856.5,-540 856.5,-540 850.5,-540 844.5,-534 844.5,-528 844.5,-528 844.5,-516 844.5,-516 844.5,-510 850.5,-504 856.5,-504 856.5,-504 992.5,-504 992.5,-504 998.5,-504 1004.5,-510 1004.5,-516 1004.5,-516 1004.5,-528 1004.5,-528 1004.5,-534 998.5,-540 992.5,-540"/>
-<text text-anchor="middle" x="924.5" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<!-- 61->47 -->
+<g id="edge90" class="edge">
+<title>61->47</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M2046.74,-287.7C2036.26,-278.97 2023.39,-268.24 2012,-258.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2013.95,-255.82 2004.03,-252.1 2009.47,-261.19 2013.95,-255.82"/>
</g>
-<!-- 61->50 -->
-<g id="edge88" class="edge">
-<title>61->50</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M895.9853,-503.8314C881.6658,-494.7074 864.1376,-483.539 848.7662,-473.7449"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="850.3199,-470.5847 840.0055,-468.1628 846.5583,-476.4882 850.3199,-470.5847"/>
+<!-- 62 -->
+<g id="node63" class="node">
+<title>62</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M1023.5,-468C1023.5,-468 987.5,-468 987.5,-468 981.5,-468 975.5,-462 975.5,-456 975.5,-456 975.5,-444 975.5,-444 975.5,-438 981.5,-432 987.5,-432 987.5,-432 1023.5,-432 1023.5,-432 1029.5,-432 1035.5,-438 1035.5,-444 1035.5,-444 1035.5,-456 1035.5,-456 1035.5,-462 1029.5,-468 1023.5,-468"/>
+<text text-anchor="middle" x="1005.5" y="-447.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
-<!-- 61->51 -->
+<!-- 62->48 -->
<g id="edge91" class="edge">
-<title>61->51</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M935.3507,-503.8314C940.2023,-495.7079 946.0217,-485.9637 951.368,-477.0118"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="954.3806,-478.7933 956.5032,-468.4133 948.3708,-475.2041 954.3806,-478.7933"/>
+<title>62->48</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1035.78,-435.15C1039.02,-433.96 1042.3,-432.88 1045.5,-432 1052.84,-429.98 1239.29,-404.98 1351.35,-390.05"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1351.84,-393.51 1361.29,-388.73 1350.92,-386.58 1351.84,-393.51"/>
</g>
-<!-- 62->51 -->
-<g id="edge89" class="edge">
-<title>62->51</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1156.7605,-575.9145C1136.2294,-566.0828 1111.0337,-553.2464 1089.5,-540 1056.8123,-519.8922 1021.7828,-493.4935 997.6832,-474.493"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="999.6442,-471.581 989.6364,-468.1033 995.2912,-477.0629 999.6442,-471.581"/>
-</g>
-<!-- 62->57 -->
-<g id="edge102" class="edge">
-<title>62->57</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1250.0946,-581.4101C1370.9279,-553.0251 1662.3719,-484.5619 1769.2964,-459.4442"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1770.4165,-462.7765 1779.3511,-457.0823 1768.8157,-455.962 1770.4165,-462.7765"/>
+<!-- 62->49 -->
+<g id="edge92" class="edge">
+<title>62->49</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1035.72,-434.95C1038.98,-433.8 1042.27,-432.79 1045.5,-432 1246.29,-383.06 1306.74,-424.05 1515.22,-396.05"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1515.84,-399.5 1525.26,-394.67 1514.88,-392.57 1515.84,-399.5"/>
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<!-- 63 -->
<g id="node64" class="node">
<title>63</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M1282.5,-540C1282.5,-540 1110.5,-540 1110.5,-540 1104.5,-540 1098.5,-534 1098.5,-528 1098.5,-528 1098.5,-516 1098.5,-516 1098.5,-510 1104.5,-504 1110.5,-504 1110.5,-504 1282.5,-504 1282.5,-504 1288.5,-504 1294.5,-510 1294.5,-516 1294.5,-516 1294.5,-528 1294.5,-528 1294.5,-534 1288.5,-540 1282.5,-540"/>
-<text text-anchor="middle" x="1196.5" y="-525" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
-<text text-anchor="middle" x="1196.5" y="-514" font-family="sans" font-size="10.00" fill="#000000">seqmode: se</text>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M1984.5,-468C1984.5,-468 1948.5,-468 1948.5,-468 1942.5,-468 1936.5,-462 1936.5,-456 1936.5,-456 1936.5,-444 1936.5,-444 1936.5,-438 1942.5,-432 1948.5,-432 1948.5,-432 1984.5,-432 1984.5,-432 1990.5,-432 1996.5,-438 1996.5,-444 1996.5,-444 1996.5,-456 1996.5,-456 1996.5,-462 1990.5,-468 1984.5,-468"/>
+<text text-anchor="middle" x="1966.5" y="-447.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
-<!-- 62->63 -->
-<g id="edge110" class="edge">
-<title>62->63</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1196.5,-575.8314C1196.5,-568.131 1196.5,-558.9743 1196.5,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1200.0001,-550.4132 1196.5,-540.4133 1193.0001,-550.4133 1200.0001,-550.4132"/>
+<!-- 63->50 -->
+<g id="edge93" class="edge">
+<title>63->50</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1971.69,-431.7C1974.03,-423.9 1976.85,-414.51 1979.45,-405.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1982.85,-406.69 1982.37,-396.1 1976.14,-404.68 1982.85,-406.69"/>
</g>
<!-- 63->51 -->
-<g id="edge90" class="edge">
+<g id="edge94" class="edge">
<title>63->51</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1139.0092,-503.9243C1107.2952,-493.9531 1067.7473,-481.5188 1034.6225,-471.104"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1035.6038,-467.7437 1025.0144,-468.0831 1033.5042,-474.4214 1035.6038,-467.7437"/>
-</g>
-<!-- 63->57 -->
-<g id="edge103" class="edge">
-<title>63->57</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1294.6491,-510.4719C1431.573,-494.3895 1673.8386,-465.9341 1769.2647,-454.7258"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1769.8407,-458.1823 1779.3641,-453.5396 1769.0241,-451.2301 1769.8407,-458.1823"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M1996.57,-439.56C2029.44,-429.24 2083.07,-412.41 2125.45,-399.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2126.64,-402.4 2135.13,-396.07 2124.54,-395.72 2126.64,-402.4"/>
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<!-- 64->52 -->
-<g id="edge93" class="edge">
+<g id="edge95" class="edge">
<title>64->52</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1216.4605,-362.1284C1213.4351,-361.3884 1210.4346,-360.6742 1207.5,-360 1127.6633,-341.6577 1101.9806,-350.5534 1020.3743,-323.8133"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1021.2776,-320.4246 1010.6836,-320.5592 1019.0492,-327.0605 1021.2776,-320.4246"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M919.63,-435.45C987.76,-426.35 1077.44,-413.22 1165.14,-396.18"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1165.85,-399.61 1174.99,-394.25 1164.5,-392.74 1165.85,-399.61"/>
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-<!-- 64->53 -->
-<g id="edge95" class="edge">
-<title>64->53</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1332.6487,-367.1573C1374.6163,-358.5136 1432.5569,-344.8987 1490.5717,-323.9614"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1492.083,-327.1347 1500.2587,-320.3961 1489.6652,-320.5655 1492.083,-327.1347"/>
+<!-- 65->56 -->
+<g id="edge100" class="edge">
+<title>65->56</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1008.29,-575.94C1027.84,-567.42 1049.4,-555.55 1065.5,-540 1083.56,-522.55 1096.43,-496.81 1104.26,-477.49"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1107.57,-478.65 1107.9,-468.06 1101.04,-476.13 1107.57,-478.65"/>
+</g>
+<!-- 65->62 -->
+<g id="edge114" class="edge">
+<title>65->62</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M896.25,-575.95C878.75,-567.98 861.72,-556.47 851.5,-540 843.06,-526.41 842.21,-517.03 851.5,-504 864.97,-485.11 924.45,-468.66 965.42,-459.29"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="966.4,-462.65 975.39,-457.06 964.87,-455.82 966.4,-462.65"/>
+</g>
+<!-- 66 -->
+<g id="node67" class="node">
+<title>66</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1044.5,-540C1044.5,-540 872.5,-540 872.5,-540 866.5,-540 860.5,-534 860.5,-528 860.5,-528 860.5,-516 860.5,-516 860.5,-510 866.5,-504 872.5,-504 872.5,-504 1044.5,-504 1044.5,-504 1050.5,-504 1056.5,-510 1056.5,-516 1056.5,-516 1056.5,-528 1056.5,-528 1056.5,-534 1050.5,-540 1044.5,-540"/>
+<text text-anchor="middle" x="958.5" y="-525" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="958.5" y="-514" font-family="sans" font-size="10.00">seqmode: pe</text>
+</g>
+<!-- 65->66 -->
+<g id="edge121" class="edge">
+<title>65->66</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M958.5,-575.7C958.5,-567.98 958.5,-558.71 958.5,-550.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="962,-550.1 958.5,-540.1 955,-550.1 962,-550.1"/>
+</g>
+<!-- 66->56 -->
+<g id="edge101" class="edge">
+<title>66->56</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M996.42,-503.88C1017.51,-494.35 1043.96,-482.41 1066.37,-472.28"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1068.03,-475.37 1075.71,-468.07 1065.15,-468.99 1068.03,-475.37"/>
+</g>
+<!-- 66->62 -->
+<g id="edge115" class="edge">
+<title>66->62</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M970.12,-503.7C975.64,-495.47 982.35,-485.48 988.43,-476.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="991.35,-478.36 994.02,-468.1 985.54,-474.46 991.35,-478.36"/>
+</g>
+<!-- 67 -->
+<g id="node68" class="node">
+<title>67</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1298.5,-540C1298.5,-540 1162.5,-540 1162.5,-540 1156.5,-540 1150.5,-534 1150.5,-528 1150.5,-528 1150.5,-516 1150.5,-516 1150.5,-510 1156.5,-504 1162.5,-504 1162.5,-504 1298.5,-504 1298.5,-504 1304.5,-504 1310.5,-510 1310.5,-516 1310.5,-516 1310.5,-528 1310.5,-528 1310.5,-534 1304.5,-540 1298.5,-540"/>
+<text text-anchor="middle" x="1230.5" y="-519.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 67->56 -->
+<g id="edge102" class="edge">
+<title>67->56</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1201.88,-503.88C1186.58,-494.72 1167.56,-483.34 1151.08,-473.48"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1152.61,-470.32 1142.23,-468.19 1149.02,-476.33 1152.61,-470.32"/>
</g>
-<!-- 64->54 -->
-<g id="edge97" class="edge">
-<title>64->54</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1273.743,-359.8314C1273.4221,-352.131 1273.0406,-342.9743 1272.684,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1276.1806,-334.2589 1272.2672,-324.4133 1269.1867,-334.5503 1276.1806,-334.2589"/>
+<!-- 67->57 -->
+<g id="edge105" class="edge">
+<title>67->57</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1235.44,-503.7C1237.67,-495.9 1240.35,-486.51 1242.83,-477.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1246.23,-478.68 1245.61,-468.1 1239.5,-476.76 1246.23,-478.68"/>
</g>
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-<g id="edge99" class="edge">
-<title>64->55</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1332.7281,-371.9568C1389.7665,-364.9647 1478.925,-351.1687 1562.6653,-323.7981"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1563.9451,-327.0608 1572.321,-320.5726 1561.7272,-320.4214 1563.9451,-327.0608"/>
+<!-- 68->57 -->
+<g id="edge103" class="edge">
+<title>68->57</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1465.92,-575.9C1445.05,-565.89 1418.54,-552.74 1395.5,-540 1357.08,-518.75 1314.4,-492.18 1285.35,-473.62"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1287.1,-470.59 1276.8,-468.14 1283.33,-476.48 1287.1,-470.59"/>
+</g>
+<!-- 68->63 -->
+<g id="edge116" class="edge">
+<title>68->63</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1556.18,-576.57C1650.4,-547.74 1843.41,-488.67 1926.74,-463.17"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1927.81,-466.5 1936.34,-460.23 1925.76,-459.81 1927.81,-466.5"/>
+</g>
+<!-- 69 -->
+<g id="node70" class="node">
+<title>69</title>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1588.5,-540C1588.5,-540 1416.5,-540 1416.5,-540 1410.5,-540 1404.5,-534 1404.5,-528 1404.5,-528 1404.5,-516 1404.5,-516 1404.5,-510 1410.5,-504 1416.5,-504 1416.5,-504 1588.5,-504 1588.5,-504 1594.5,-504 1600.5,-510 1600.5,-516 1600.5,-516 1600.5,-528 1600.5,-528 1600.5,-534 1594.5,-540 1588.5,-540"/>
+<text text-anchor="middle" x="1502.5" y="-525" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1502.5" y="-514" font-family="sans" font-size="10.00">seqmode: se</text>
+</g>
+<!-- 68->69 -->
+<g id="edge124" class="edge">
+<title>68->69</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1502.5,-575.7C1502.5,-567.98 1502.5,-558.71 1502.5,-550.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1506,-550.1 1502.5,-540.1 1499,-550.1 1506,-550.1"/>
+</g>
+<!-- 69->57 -->
+<g id="edge104" class="edge">
+<title>69->57</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1441.18,-503.97C1404.67,-493.82 1358.22,-480.92 1320.3,-470.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1320.93,-466.93 1310.36,-467.63 1319.05,-473.68 1320.93,-466.93"/>
+</g>
+<!-- 69->63 -->
+<g id="edge117" class="edge">
+<title>69->63</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1600.62,-506.2C1701.76,-490.94 1854.51,-467.9 1926.4,-457.05"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1927.04,-460.49 1936.41,-455.54 1926,-453.57 1927.04,-460.49"/>
+</g>
+<!-- 70->58 -->
+<g id="edge107" class="edge">
+<title>70->58</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1694.23,-359.96C1667.13,-350.94 1633.57,-339.23 1596.41,-324.19"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1597.46,-320.84 1586.88,-320.3 1594.81,-327.32 1597.46,-320.84"/>
+</g>
+<!-- 70->59 -->
+<g id="edge109" class="edge">
+<title>70->59</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1805.54,-365.71C1846.39,-357.03 1902.32,-343.69 1958.78,-323.92"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1959.97,-327.21 1968.22,-320.56 1957.62,-320.62 1959.97,-327.21"/>
+</g>
+<!-- 70->60 -->
+<g id="edge111" class="edge">
+<title>70->60</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1745.52,-359.7C1744.64,-351.98 1743.58,-342.71 1742.6,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1746.07,-333.64 1741.45,-324.1 1739.11,-334.44 1746.07,-333.64"/>
+</g>
+<!-- 70->61 -->
+<g id="edge113" class="edge">
+<title>70->61</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1805.69,-370.58C1861.6,-363.43 1948.28,-349.74 2030.3,-323.95"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2031.83,-327.13 2040.28,-320.74 2029.69,-320.47 2031.83,-327.13"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 3cb5d62265295574e6b130bf12683c9e82cdd434..e18e021ca84ba00b8eff48a25e0c743a3816ce65 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,601 +1,649 @@
<?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 2.40.1 (20161225.0304)
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<svg width="1237pt" height="836pt"
- viewBox="0.00 0.00 1237.00 836.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1163pt" height="836pt"
+ viewBox="0.00 0.00 1163.00 836.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 832)">
<title>snakemake_dag</title>
-<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-832 1233,-832 1233,4 -4,4"/>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-832 1159,-832 1159,4 -4,4"/>
<!-- 0 -->
<g id="node1" class="node">
<title>0</title>
-<path fill="none" stroke="#ced856" stroke-width="2" d="M483,-36C483,-36 453,-36 453,-36 447,-36 441,-30 441,-24 441,-24 441,-12 441,-12 441,-6 447,0 453,0 453,0 483,0 483,0 489,0 495,-6 495,-12 495,-12 495,-24 495,-24 495,-30 489,-36 483,-36"/>
-<text text-anchor="middle" x="468" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
+<path fill="none" stroke="#9fd856" stroke-width="2" d="M681,-36C681,-36 651,-36 651,-36 645,-36 639,-30 639,-24 639,-24 639,-12 639,-12 639,-6 645,0 651,0 651,0 681,0 681,0 687,0 693,-6 693,-12 693,-12 693,-24 693,-24 693,-30 687,-36 681,-36"/>
+<text text-anchor="middle" x="666" 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="#d8ac56" stroke-width="2" d="M776,-108C776,-108 712,-108 712,-108 706,-108 700,-102 700,-96 700,-96 700,-84 700,-84 700,-78 706,-72 712,-72 712,-72 776,-72 776,-72 782,-72 788,-78 788,-84 788,-84 788,-96 788,-96 788,-102 782,-108 776,-108"/>
-<text text-anchor="middle" x="744" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">multiqc_report</text>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M475,-108C475,-108 411,-108 411,-108 405,-108 399,-102 399,-96 399,-96 399,-84 399,-84 399,-78 405,-72 411,-72 411,-72 475,-72 475,-72 481,-72 487,-78 487,-84 487,-84 487,-96 487,-96 487,-102 481,-108 475,-108"/>
+<text text-anchor="middle" x="443" y="-87.5" font-family="sans" font-size="10.00">multiqc_report</text>
</g>
<!-- 1->0 -->
-<g id="edge4" class="edge">
+<g id="edge2" class="edge">
<title>1->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M699.9618,-78.5118C645.9987,-64.4344 555.5307,-40.8341 504.9989,-27.6519"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="505.7083,-24.2199 495.1486,-25.0822 503.9413,-30.9932 505.7083,-24.2199"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M487.06,-75.17C528.54,-62.15 589.97,-42.87 628.98,-30.62"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="630.38,-33.85 638.87,-27.52 628.28,-27.17 630.38,-33.85"/>
</g>
<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1144.5,-252C1144.5,-252 1075.5,-252 1075.5,-252 1069.5,-252 1063.5,-246 1063.5,-240 1063.5,-240 1063.5,-228 1063.5,-228 1063.5,-222 1069.5,-216 1075.5,-216 1075.5,-216 1144.5,-216 1144.5,-216 1150.5,-216 1156.5,-222 1156.5,-228 1156.5,-228 1156.5,-240 1156.5,-240 1156.5,-246 1150.5,-252 1144.5,-252"/>
-<text text-anchor="middle" x="1110" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">prepare_bigWig</text>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1088.5,-252C1088.5,-252 1019.5,-252 1019.5,-252 1013.5,-252 1007.5,-246 1007.5,-240 1007.5,-240 1007.5,-228 1007.5,-228 1007.5,-222 1013.5,-216 1019.5,-216 1019.5,-216 1088.5,-216 1088.5,-216 1094.5,-216 1100.5,-222 1100.5,-228 1100.5,-228 1100.5,-240 1100.5,-240 1100.5,-246 1094.5,-252 1088.5,-252"/>
+<text text-anchor="middle" x="1054" y="-231.5" font-family="sans" font-size="10.00">prepare_bigWig</text>
</g>
<!-- 2->0 -->
-<g id="edge1" class="edge">
+<g id="edge6" class="edge">
<title>2->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1089.1753,-215.8325C1065.8056,-196.1369 1026.1528,-164.7459 988,-144 822.9295,-54.2416 594.0667,-27.662 505.2806,-20.4592"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M1045.74,-215.87C1028.64,-182.37 985.97,-108.29 927,-72 856.49,-28.61 756.92,-19.99 703.45,-18.73"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="703.44,-15.23 693.39,-18.56 703.33,-22.23 703.44,-15.23"/>
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<g id="node4" class="node">
<title>3</title>
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-<text text-anchor="middle" x="76" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M791,-252C791,-252 663,-252 663,-252 657,-252 651,-246 651,-240 651,-240 651,-228 651,-228 651,-222 657,-216 663,-216 663,-216 791,-216 791,-216 797,-216 803,-222 803,-228 803,-228 803,-240 803,-240 803,-246 797,-252 791,-252"/>
+<text text-anchor="middle" x="727" y="-231.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
<!-- 3->0 -->
-<g id="edge2" class="edge">
+<g id="edge5" class="edge">
<title>3->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M91.9791,-431.898C113.1909,-405.9361 148,-355.7525 148,-306 148,-306 148,-306 148,-162 148,-92.8193 212.5468,-101.7585 275,-72 326.433,-47.4925 391.0317,-32.2436 430.9109,-24.4358"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M803.42,-219.49C845.4,-210.34 891.45,-196.85 904,-180 932.66,-141.5 934.03,-109.45 904,-72 879.27,-41.16 763.93,-27.11 703.36,-21.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="703.34,-18.25 693.08,-20.89 702.75,-25.22 703.34,-18.25"/>
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+<!-- 12 -->
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M571.5,-180C571.5,-180 520.5,-180 520.5,-180 514.5,-180 508.5,-174 508.5,-168 508.5,-168 508.5,-156 508.5,-156 508.5,-150 514.5,-144 520.5,-144 520.5,-144 571.5,-144 571.5,-144 577.5,-144 583.5,-150 583.5,-156 583.5,-156 583.5,-168 583.5,-168 583.5,-174 577.5,-180 571.5,-180"/>
+<text text-anchor="middle" x="546" y="-159.5" font-family="sans" font-size="10.00">pca_salmon</text>
+</g>
+<!-- 3->12 -->
+<g id="edge33" class="edge">
+<title>3->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M682.72,-215.88C655.57,-205.38 620.84,-191.94 593.17,-181.24"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="594.29,-177.92 583.7,-177.58 591.77,-184.45 594.29,-177.92"/>
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<g id="node5" class="node">
<title>4</title>
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-<text text-anchor="middle" x="257" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_transcripts</text>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M621,-252C621,-252 471,-252 471,-252 465,-252 459,-246 459,-240 459,-240 459,-228 459,-228 459,-222 465,-216 471,-216 471,-216 621,-216 621,-216 627,-216 633,-222 633,-228 633,-228 633,-240 633,-240 633,-246 627,-252 621,-252"/>
+<text text-anchor="middle" x="546" y="-231.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
<!-- 4->0 -->
-<g id="edge3" class="edge">
+<g id="edge4" class="edge">
<title>4->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M257,-431.8146C257,-404.4983 257,-351.25 257,-306 257,-306 257,-306 257,-162 257,-78.7801 370.3638,-40.1916 430.9031,-25.5175"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M633.11,-217.5C636.11,-216.99 639.08,-216.49 642,-216 692.81,-207.51 837.52,-219.15 871,-180 928.86,-112.33 776.7,-53.58 703.16,-30.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="703.93,-26.58 693.34,-26.92 701.83,-33.26 703.93,-26.58"/>
+</g>
+<!-- 4->12 -->
+<g id="edge32" class="edge">
+<title>4->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M546,-215.7C546,-207.98 546,-198.71 546,-190.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="549.5,-190.1 546,-180.1 542.5,-190.1 549.5,-190.1"/>
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<g id="node6" class="node">
<title>5</title>
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-<text text-anchor="middle" x="545" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">kallisto_merge_transcripts</text>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M200,-252C200,-252 78,-252 78,-252 72,-252 66,-246 66,-240 66,-240 66,-228 66,-228 66,-222 72,-216 78,-216 78,-216 200,-216 200,-216 206,-216 212,-222 212,-228 212,-228 212,-240 212,-240 212,-246 206,-252 200,-252"/>
+<text text-anchor="middle" x="139" y="-231.5" font-family="sans" font-size="10.00">kallisto_merge_transcripts</text>
</g>
<!-- 5->0 -->
-<g id="edge5" class="edge">
+<g id="edge3" class="edge">
<title>5->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M525.5696,-71.8314C516.268,-63.1337 504.9796,-52.5783 494.8714,-43.1265"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M148.74,-215.79C168.99,-181.8 219.2,-106.38 284,-72 343.42,-40.48 544.85,-25.79 628.79,-20.93"/>
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+<title>13</title>
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+<text text-anchor="middle" x="302" y="-159.5" font-family="sans" font-size="10.00">pca_kallisto</text>
+</g>
+<!-- 5->13 -->
+<g id="edge35" class="edge">
+<title>5->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M178.87,-215.88C201.92,-205.98 231.04,-193.47 255.17,-183.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="256.69,-186.27 264.5,-179.11 253.93,-179.84 256.69,-186.27"/>
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<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
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-<text text-anchor="middle" x="392" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">kallisto_merge_genes</text>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M342,-252C342,-252 242,-252 242,-252 236,-252 230,-246 230,-240 230,-240 230,-228 230,-228 230,-222 236,-216 242,-216 242,-216 342,-216 342,-216 348,-216 354,-222 354,-228 354,-228 354,-240 354,-240 354,-246 348,-252 342,-252"/>
+<text text-anchor="middle" x="292" y="-231.5" font-family="sans" font-size="10.00">kallisto_merge_genes</text>
</g>
<!-- 6->0 -->
-<g id="edge6" class="edge">
+<g id="edge1" class="edge">
<title>6->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M411.178,-71.8314C420.3588,-63.1337 431.5006,-52.5783 441.4776,-43.1265"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="443.9757,-45.5811 448.8281,-36.1628 439.1615,-40.4995 443.9757,-45.5811"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M275.63,-215.9C260.04,-197.44 240.88,-167.53 255,-144 289.99,-85.69 325.89,-94.67 390,-72 472.37,-42.88 574.54,-28.56 628.52,-22.59"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="629.08,-26.05 638.65,-21.51 628.33,-19.09 629.08,-26.05"/>
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+<!-- 6->13 -->
+<g id="edge34" class="edge">
+<title>6->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M294.47,-215.7C295.57,-207.98 296.9,-198.71 298.13,-190.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="301.61,-190.5 299.56,-180.1 294.68,-189.51 301.61,-190.5"/>
</g>
<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M1217,-396C1217,-396 1187,-396 1187,-396 1181,-396 1175,-390 1175,-384 1175,-384 1175,-372 1175,-372 1175,-366 1181,-360 1187,-360 1187,-360 1217,-360 1217,-360 1223,-360 1229,-366 1229,-372 1229,-372 1229,-384 1229,-384 1229,-390 1223,-396 1217,-396"/>
-<text text-anchor="middle" x="1202" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M52,-756C52,-756 22,-756 22,-756 16,-756 10,-750 10,-744 10,-744 10,-732 10,-732 10,-726 16,-720 22,-720 22,-720 52,-720 52,-720 58,-720 64,-726 64,-732 64,-732 64,-744 64,-744 64,-750 58,-756 52,-756"/>
+<text text-anchor="middle" x="37" y="-735.5" font-family="sans" font-size="10.00">fastqc</text>
</g>
<!-- 7->1 -->
-<g id="edge10" class="edge">
+<g id="edge7" class="edge">
<title>7->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1203.1008,-359.8379C1204.0828,-327.1418 1201.4647,-257.8883 1166,-216 1118.1269,-159.4558 900.8972,-116.3139 798.1578,-98.6869"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M29.51,-719.89C18.7,-693.58 0,-641.37 0,-595 0,-595 0,-595 0,-233 0,-170.8 51.29,-169.54 108,-144 200.56,-102.32 320.38,-92.74 388.77,-90.93"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="388.96,-94.43 398.89,-90.71 388.81,-87.43 388.96,-94.43"/>
</g>
<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
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-<text text-anchor="middle" x="567" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M202.5,-324C202.5,-324 39.5,-324 39.5,-324 33.5,-324 27.5,-318 27.5,-312 27.5,-312 27.5,-300 27.5,-300 27.5,-294 33.5,-288 39.5,-288 39.5,-288 202.5,-288 202.5,-288 208.5,-288 214.5,-294 214.5,-300 214.5,-300 214.5,-312 214.5,-312 214.5,-318 208.5,-324 202.5,-324"/>
+<text text-anchor="middle" x="121" y="-303.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 8->1 -->
-<g id="edge8" class="edge">
+<g id="edge9" class="edge">
<title>8->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M611.6646,-143.8314C635.6385,-134.0792 665.354,-121.9916 690.5493,-111.7427"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="692.0187,-114.9235 699.9629,-107.9134 689.3811,-108.4394 692.0187,-114.9235"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M90.23,-287.91C77.46,-279.02 64,-266.88 57,-252 50.19,-237.52 47.82,-229.11 57,-216 95.64,-160.83 291.94,-118.33 388.8,-100.36"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="389.49,-103.79 398.7,-98.55 388.23,-96.91 389.49,-103.79"/>
</g>
<!-- 8->5 -->
-<g id="edge19" class="edge">
+<g id="edge21" class="edge">
<title>8->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M561.4485,-143.8314C559.0697,-136.0463 556.2362,-126.7729 553.5967,-118.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="556.8958,-116.954 550.6263,-108.4133 550.2013,-118.9996 556.8958,-116.954"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M125.45,-287.7C127.45,-279.9 129.87,-270.51 132.1,-261.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="135.5,-262.66 134.6,-252.1 128.72,-260.92 135.5,-262.66"/>
</g>
<!-- 8->6 -->
-<g id="edge21" class="edge">
+<g id="edge23" class="edge">
<title>8->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M522.8401,-143.8314C499.2268,-134.1162 469.9798,-122.0831 445.13,-111.8592"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="446.4219,-108.6061 435.8423,-108.038 443.7585,-115.0797 446.4219,-108.6061"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M162.83,-287.88C186.42,-278.22 216.06,-266.09 241,-255.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="242.38,-259.1 250.3,-252.07 239.72,-252.62 242.38,-259.1"/>
</g>
<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M443,-180C443,-180 297,-180 297,-180 291,-180 285,-174 285,-168 285,-168 285,-156 285,-156 285,-150 291,-144 297,-144 297,-144 443,-144 443,-144 449,-144 455,-150 455,-156 455,-156 455,-168 455,-168 455,-174 449,-180 443,-180"/>
-<text text-anchor="middle" x="370" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M391,-324C391,-324 245,-324 245,-324 239,-324 233,-318 233,-312 233,-312 233,-300 233,-300 233,-294 239,-288 245,-288 245,-288 391,-288 391,-288 397,-288 403,-294 403,-300 403,-300 403,-312 403,-312 403,-318 397,-324 391,-324"/>
+<text text-anchor="middle" x="318" y="-303.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 9->1 -->
-<g id="edge12" class="edge">
+<g id="edge10" class="edge">
<title>9->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M455.3344,-145.572C527.4246,-131.6937 628.4768,-112.2398 689.9122,-100.4126"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="690.6344,-103.838 699.7924,-98.5106 689.311,-96.9642 690.6344,-103.838"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M336.24,-287.95C345.57,-278.26 356.34,-265.4 363,-252 384.89,-207.97 362.75,-186.77 387,-144 393.19,-133.08 402.36,-123.05 411.49,-114.73"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="413.82,-117.34 419.09,-108.15 409.24,-112.05 413.82,-117.34"/>
</g>
<!-- 9->5 -->
-<g id="edge20" class="edge">
+<g id="edge22" class="edge">
<title>9->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M414.1599,-143.8314C437.7732,-134.1162 467.0202,-122.0831 491.87,-111.8592"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="493.2415,-115.0797 501.1577,-108.038 490.5781,-108.6061 493.2415,-115.0797"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M274.21,-287.88C249.42,-278.18 218.22,-265.98 192.04,-255.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="193.23,-252.45 182.65,-252.07 190.68,-258.97 193.23,-252.45"/>
</g>
<!-- 9->6 -->
-<g id="edge22" class="edge">
+<g id="edge24" class="edge">
<title>9->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M375.5515,-143.8314C377.9303,-136.0463 380.7638,-126.7729 383.4033,-118.1347"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="386.7987,-118.9996 386.3737,-108.4133 380.1042,-116.954 386.7987,-118.9996"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M311.57,-287.7C308.64,-279.81 305.11,-270.3 301.86,-261.55"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="305.12,-260.26 298.35,-252.1 298.55,-262.7 305.12,-260.26"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M835,-324C835,-324 765,-324 765,-324 759,-324 753,-318 753,-312 753,-312 753,-300 753,-300 753,-294 759,-288 765,-288 765,-288 835,-288 835,-288 841,-288 847,-294 847,-300 847,-300 847,-312 847,-312 847,-318 841,-324 835,-324"/>
-<text text-anchor="middle" x="800" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">plot_TIN_scores</text>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M478,-180C478,-180 408,-180 408,-180 402,-180 396,-174 396,-168 396,-168 396,-156 396,-156 396,-150 402,-144 408,-144 408,-144 478,-144 478,-144 484,-144 490,-150 490,-156 490,-156 490,-168 490,-168 490,-174 484,-180 478,-180"/>
+<text text-anchor="middle" x="443" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
</g>
<!-- 10->1 -->
-<g id="edge11" class="edge">
+<g id="edge14" class="edge">
<title>10->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M808.447,-287.8113C821.6472,-256.5398 843.2711,-191.3829 819,-144 812.763,-131.8238 802.3605,-121.7682 791.2593,-113.7713"/>
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+<path fill="none" stroke="grey" stroke-width="2" d="M443,-143.7C443,-135.98 443,-126.71 443,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="446.5,-118.1 443,-108.1 439.5,-118.1 446.5,-118.1"/>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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-<text text-anchor="middle" x="923" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">alfa_concat_results</text>
+<path fill="none" stroke="#5663d8" stroke-width="2" d="M849.5,-180C849.5,-180 762.5,-180 762.5,-180 756.5,-180 750.5,-174 750.5,-168 750.5,-168 750.5,-156 750.5,-156 750.5,-150 756.5,-144 762.5,-144 762.5,-144 849.5,-144 849.5,-144 855.5,-144 861.5,-150 861.5,-156 861.5,-156 861.5,-168 861.5,-168 861.5,-174 855.5,-180 849.5,-180"/>
+<text text-anchor="middle" x="806" y="-159.5" font-family="sans" font-size="10.00">alfa_concat_results</text>
</g>
<!-- 11->1 -->
-<g id="edge7" class="edge">
+<g id="edge11" class="edge">
<title>11->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M877.8307,-143.8314C853.4941,-134.0423 823.3069,-121.9 797.7653,-111.6263"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="798.8094,-108.2738 788.2257,-107.7891 796.1971,-114.7681 798.8094,-108.2738"/>
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-<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
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-<text text-anchor="middle" x="744" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">prepare_multiqc_config</text>
+<path fill="none" stroke="grey" stroke-width="2" d="M750.22,-145.89C747.45,-145.23 744.69,-144.6 742,-144 656.96,-125.2 557.17,-108.6 497.07,-99.18"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="497.47,-95.7 487.05,-97.62 496.4,-102.62 497.47,-95.7"/>
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<!-- 12->1 -->
-<g id="edge9" class="edge">
+<g id="edge13" class="edge">
<title>12->1</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M744,-143.8314C744,-136.131 744,-126.9743 744,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="747.5001,-118.4132 744,-108.4133 740.5001,-118.4133 747.5001,-118.4132"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M520.8,-143.88C507.59,-134.89 491.21,-123.76 476.89,-114.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="478.53,-110.92 468.29,-108.19 474.6,-116.71 478.53,-110.92"/>
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-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M1093,-324C1093,-324 1027,-324 1027,-324 1021,-324 1015,-318 1015,-312 1015,-312 1015,-300 1015,-300 1015,-294 1021,-288 1027,-288 1027,-288 1093,-288 1093,-288 1099,-288 1105,-294 1105,-300 1105,-300 1105,-312 1105,-312 1105,-318 1099,-324 1093,-324"/>
-<text text-anchor="middle" x="1060" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">sort_bed_4_big</text>
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-<g id="edge13" class="edge">
-<title>13->2</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1072.6171,-287.8314C1078.3172,-279.6232 1085.1663,-269.7606 1091.4359,-260.7323"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1094.3838,-262.6234 1097.213,-252.4133 1088.6342,-258.6306 1094.3838,-262.6234"/>
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+<g id="edge8" class="edge">
+<title>13->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M336.49,-143.88C355.44,-134.47 379.13,-122.71 399.36,-112.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="400.97,-115.77 408.37,-108.19 397.86,-109.5 400.97,-115.77"/>
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<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
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-<text text-anchor="middle" x="945" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M720.5,-180C720.5,-180 613.5,-180 613.5,-180 607.5,-180 601.5,-174 601.5,-168 601.5,-168 601.5,-156 601.5,-156 601.5,-150 607.5,-144 613.5,-144 613.5,-144 720.5,-144 720.5,-144 726.5,-144 732.5,-150 732.5,-156 732.5,-156 732.5,-168 732.5,-168 732.5,-174 726.5,-180 720.5,-180"/>
+<text text-anchor="middle" x="667" y="-159.5" font-family="sans" font-size="10.00">prepare_multiqc_config</text>
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-<!-- 14->2 -->
-<g id="edge14" class="edge">
-<title>14->2</title>
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-<g id="node25" class="node">
-<title>24</title>
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-<g id="edge42" class="edge">
-<title>14->24</title>
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-<!-- 32 -->
-<g id="node33" class="node">
-<title>32</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M995.5,-612C995.5,-612 894.5,-612 894.5,-612 888.5,-612 882.5,-606 882.5,-600 882.5,-600 882.5,-588 882.5,-588 882.5,-582 888.5,-576 894.5,-576 894.5,-576 995.5,-576 995.5,-576 1001.5,-576 1007.5,-582 1007.5,-588 1007.5,-588 1007.5,-600 1007.5,-600 1007.5,-606 1001.5,-612 995.5,-612"/>
-<text text-anchor="middle" x="945" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
-</g>
-<!-- 14->32 -->
-<g id="edge56" class="edge">
-<title>14->32</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M945,-647.8314C945,-640.131 945,-630.9743 945,-622.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="948.5001,-622.4132 945,-612.4133 941.5001,-622.4133 948.5001,-622.4132"/>
-</g>
-<!-- 35 -->
-<g id="node36" class="node">
-<title>35</title>
-<path fill="none" stroke="#56d8d0" stroke-width="2" d="M852.5,-612C852.5,-612 769.5,-612 769.5,-612 763.5,-612 757.5,-606 757.5,-600 757.5,-600 757.5,-588 757.5,-588 757.5,-582 763.5,-576 769.5,-576 769.5,-576 852.5,-576 852.5,-576 858.5,-576 864.5,-582 864.5,-588 864.5,-588 864.5,-600 864.5,-600 864.5,-606 858.5,-612 852.5,-612"/>
-<text text-anchor="middle" x="811" y="-591.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
-</g>
-<!-- 14->35 -->
-<g id="edge60" class="edge">
-<title>14->35</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M911.1861,-647.8314C893.7293,-638.4516 872.2513,-626.9112 853.6648,-616.9244"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="855.2686,-613.8129 844.803,-612.1628 851.9554,-619.9792 855.2686,-613.8129"/>
-</g>
-<!-- 36 -->
-<g id="node37" class="node">
-<title>36</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M943,-396C943,-396 851,-396 851,-396 845,-396 839,-390 839,-384 839,-384 839,-372 839,-372 839,-366 845,-360 851,-360 851,-360 943,-360 943,-360 949,-360 955,-366 955,-372 955,-372 955,-384 955,-384 955,-390 949,-396 943,-396"/>
-<text text-anchor="middle" x="897" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">generate_alfa_index</text>
-</g>
-<!-- 14->36 -->
-<g id="edge61" class="edge">
-<title>14->36</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M973.2988,-647.8492C987.2857,-638.1424 1003.9233,-625.4374 1017,-612 1054.0212,-573.9578 1079.6148,-555.7965 1068,-504 1060.2568,-469.469 1059.832,-456.1879 1034,-432 1023.1018,-421.7955 993.631,-409.6621 964.8031,-399.4839"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="965.6739,-396.0815 955.0791,-396.1128 963.381,-402.6953 965.6739,-396.0815"/>
+<!-- 14->1 -->
+<g id="edge12" class="edge">
+<title>14->1</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M612.49,-143.97C577.33,-132.98 531.81,-118.75 496.79,-107.81"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="497.8,-104.46 487.21,-104.82 495.71,-111.14 497.8,-104.46"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M324,-540C324,-540 206,-540 206,-540 200,-540 194,-534 194,-528 194,-528 194,-516 194,-516 194,-510 200,-504 206,-504 206,-504 324,-504 324,-504 330,-504 336,-510 336,-516 336,-516 336,-528 336,-528 336,-534 330,-540 324,-540"/>
-<text text-anchor="middle" x="265" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<path fill="none" stroke="#5673d8" stroke-width="2" d="M1087,-324C1087,-324 1021,-324 1021,-324 1015,-324 1009,-318 1009,-312 1009,-312 1009,-300 1009,-300 1009,-294 1015,-288 1021,-288 1021,-288 1087,-288 1087,-288 1093,-288 1099,-294 1099,-300 1099,-300 1099,-312 1099,-312 1099,-318 1093,-324 1087,-324"/>
+<text text-anchor="middle" x="1054" y="-303.5" font-family="sans" font-size="10.00">sort_bed_4_big</text>
</g>
-<!-- 15->3 -->
-<g id="edge15" class="edge">
-<title>15->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M217.3073,-503.8314C191.6927,-494.0734 159.9398,-481.977 133.026,-471.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="133.9406,-468.3273 123.3497,-468.038 131.4486,-474.8687 133.9406,-468.3273"/>
-</g>
-<!-- 15->4 -->
-<g id="edge17" class="edge">
-<title>15->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M262.9813,-503.8314C262.1257,-496.131 261.1083,-486.9743 260.1574,-478.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="263.6289,-477.9656 259.0459,-468.4133 256.6717,-478.7386 263.6289,-477.9656"/>
+<!-- 15->2 -->
+<g id="edge16" class="edge">
+<title>15->2</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1054,-287.7C1054,-279.98 1054,-270.71 1054,-262.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1057.5,-262.1 1054,-252.1 1050.5,-262.1 1057.5,-262.1"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M163.5,-540C163.5,-540 62.5,-540 62.5,-540 56.5,-540 50.5,-534 50.5,-528 50.5,-528 50.5,-516 50.5,-516 50.5,-510 56.5,-504 62.5,-504 62.5,-504 163.5,-504 163.5,-504 169.5,-504 175.5,-510 175.5,-516 175.5,-516 175.5,-528 175.5,-528 175.5,-534 169.5,-540 163.5,-540"/>
-<text text-anchor="middle" x="113" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
+<path fill="none" stroke="#56c1d8" stroke-width="2" d="M989,-684C989,-684 909,-684 909,-684 903,-684 897,-678 897,-672 897,-672 897,-660 897,-660 897,-654 903,-648 909,-648 909,-648 989,-648 989,-648 995,-648 1001,-654 1001,-660 1001,-660 1001,-672 1001,-672 1001,-678 995,-684 989,-684"/>
+<text text-anchor="middle" x="949" y="-663.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
-<!-- 16->3 -->
-<g id="edge16" class="edge">
-<title>16->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M103.6633,-503.8314C99.5757,-495.8771 94.6896,-486.369 90.1691,-477.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="93.1461,-475.7078 85.4624,-468.4133 86.9201,-478.9074 93.1461,-475.7078"/>
+<!-- 16->2 -->
+<g id="edge15" class="edge">
+<title>16->2</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1001.3,-656.32C1033.15,-648.9 1073.12,-635.52 1102,-612 1137.69,-582.92 1155,-569.04 1155,-523 1155,-523 1155,-523 1155,-377 1155,-328.19 1114.89,-284.51 1085.22,-258.87"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1087.09,-255.87 1077.17,-252.13 1082.59,-261.23 1087.09,-255.87"/>
</g>
-<!-- 16->4 -->
-<g id="edge18" class="edge">
-<title>16->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M149.3373,-503.8314C168.3396,-494.3302 191.7758,-482.6121 211.9252,-472.5374"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="213.545,-475.6407 220.924,-468.038 210.4145,-469.3797 213.545,-475.6407"/>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M591.5,-396C591.5,-396 494.5,-396 494.5,-396 488.5,-396 482.5,-390 482.5,-384 482.5,-384 482.5,-372 482.5,-372 482.5,-366 488.5,-360 494.5,-360 494.5,-360 591.5,-360 591.5,-360 597.5,-360 603.5,-366 603.5,-372 603.5,-372 603.5,-384 603.5,-384 603.5,-390 597.5,-396 591.5,-396"/>
+<text text-anchor="middle" x="543" y="-375.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+</g>
+<!-- 16->26 -->
+<g id="edge48" class="edge">
+<title>16->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M951.45,-647.88C956.59,-604.61 963.37,-490.23 902,-432 861.69,-393.75 706.5,-383.05 613.87,-380.09"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="613.83,-376.59 603.73,-379.79 613.62,-383.59 613.83,-376.59"/>
+</g>
+<!-- 34 -->
+<g id="node35" class="node">
+<title>34</title>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M759.5,-612C759.5,-612 658.5,-612 658.5,-612 652.5,-612 646.5,-606 646.5,-600 646.5,-600 646.5,-588 646.5,-588 646.5,-582 652.5,-576 658.5,-576 658.5,-576 759.5,-576 759.5,-576 765.5,-576 771.5,-582 771.5,-588 771.5,-588 771.5,-600 771.5,-600 771.5,-606 765.5,-612 759.5,-612"/>
+<text text-anchor="middle" x="709" y="-591.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+</g>
+<!-- 16->34 -->
+<g id="edge62" class="edge">
+<title>16->34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M896.92,-649.81C861.87,-639.59 815.28,-626 777.26,-614.91"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="777.87,-611.44 767.29,-612 775.91,-618.16 777.87,-611.44"/>
+</g>
+<!-- 37 -->
+<g id="node38" class="node">
+<title>37</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M908.5,-612C908.5,-612 825.5,-612 825.5,-612 819.5,-612 813.5,-606 813.5,-600 813.5,-600 813.5,-588 813.5,-588 813.5,-582 819.5,-576 825.5,-576 825.5,-576 908.5,-576 908.5,-576 914.5,-576 920.5,-582 920.5,-588 920.5,-588 920.5,-600 920.5,-600 920.5,-606 914.5,-612 908.5,-612"/>
+<text text-anchor="middle" x="867" y="-591.5" font-family="sans" font-size="10.00">map_genome_star</text>
+</g>
+<!-- 16->37 -->
+<g id="edge66" class="edge">
+<title>16->37</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M928.73,-647.7C918.5,-638.97 905.94,-628.24 894.82,-618.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="896.91,-615.94 887.04,-612.1 892.37,-621.26 896.91,-615.94"/>
+</g>
+<!-- 38 -->
+<g id="node39" class="node">
+<title>38</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M1081,-612C1081,-612 989,-612 989,-612 983,-612 977,-606 977,-600 977,-600 977,-588 977,-588 977,-582 983,-576 989,-576 989,-576 1081,-576 1081,-576 1087,-576 1093,-582 1093,-588 1093,-588 1093,-600 1093,-600 1093,-606 1087,-612 1081,-612"/>
+<text text-anchor="middle" x="1035" y="-591.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+</g>
+<!-- 16->38 -->
+<g id="edge67" class="edge">
+<title>16->38</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M970.26,-647.7C981.09,-638.88 994.42,-628.03 1006.16,-618.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1008.44,-621.13 1013.99,-612.1 1004.02,-615.7 1008.44,-621.13"/>
</g>
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
-<path fill="none" stroke="#97d856" stroke-width="2" d="M646,-828C646,-828 616,-828 616,-828 610,-828 604,-822 604,-816 604,-816 604,-804 604,-804 604,-798 610,-792 616,-792 616,-792 646,-792 646,-792 652,-792 658,-798 658,-804 658,-804 658,-816 658,-816 658,-822 652,-828 646,-828"/>
-<text text-anchor="middle" x="631" y="-807.5" font-family="sans" font-size="10.00" fill="#000000">start</text>
-</g>
-<!-- 17->7 -->
-<g id="edge23" class="edge">
-<title>17->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M658.1064,-808.9708C770.368,-803.9871 1193,-777.8007 1193,-666 1193,-666 1193,-666 1193,-522 1193,-481.7977 1196.5375,-435.4047 1199.1768,-406.385"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1202.6864,-406.4457 1200.1352,-396.1626 1195.717,-405.7923 1202.6864,-406.4457"/>
-</g>
-<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M702.5,-756C702.5,-756 559.5,-756 559.5,-756 553.5,-756 547.5,-750 547.5,-744 547.5,-744 547.5,-732 547.5,-732 547.5,-726 553.5,-720 559.5,-720 559.5,-720 702.5,-720 702.5,-720 708.5,-720 714.5,-726 714.5,-732 714.5,-732 714.5,-744 714.5,-744 714.5,-750 708.5,-756 702.5,-756"/>
-<text text-anchor="middle" x="631" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-</g>
-<!-- 17->25 -->
-<g id="edge43" class="edge">
-<title>17->25</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M631,-791.8314C631,-784.131 631,-774.9743 631,-766.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="634.5001,-766.4132 631,-756.4133 627.5001,-766.4133 634.5001,-766.4132"/>
+<path fill="none" stroke="#56d86b" stroke-width="2" d="M590,-324C590,-324 472,-324 472,-324 466,-324 460,-318 460,-312 460,-312 460,-300 460,-300 460,-294 466,-288 472,-288 472,-288 590,-288 590,-288 596,-288 602,-294 602,-300 602,-300 602,-312 602,-312 602,-318 596,-324 590,-324"/>
+<text text-anchor="middle" x="531" y="-303.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
-<!-- 27 -->
-<g id="node28" class="node">
-<title>27</title>
-<path fill="none" stroke="#56a9d8" stroke-width="2" d="M375,-756C375,-756 249,-756 249,-756 243,-756 237,-750 237,-744 237,-744 237,-732 237,-732 237,-726 243,-720 249,-720 249,-720 375,-720 375,-720 381,-720 387,-726 387,-732 387,-732 387,-744 387,-744 387,-750 381,-756 375,-756"/>
-<text text-anchor="middle" x="312" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
+<!-- 17->3 -->
+<g id="edge17" class="edge">
+<title>17->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M578.7,-287.97C606.08,-278.19 640.66,-265.84 669.53,-255.52"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="670.85,-258.77 679.09,-252.11 668.5,-252.18 670.85,-258.77"/>
</g>
-<!-- 17->27 -->
-<g id="edge44" class="edge">
-<title>17->27</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M603.8022,-803.8613C558.5659,-793.6512 466.0433,-772.7684 397.2464,-757.2406"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="397.8018,-753.778 387.2766,-754.9903 396.2606,-760.6062 397.8018,-753.778"/>
+<!-- 17->4 -->
+<g id="edge19" class="edge">
+<title>17->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M534.71,-287.7C536.36,-279.98 538.35,-270.71 540.19,-262.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="543.66,-262.62 542.33,-252.1 536.82,-261.15 543.66,-262.62"/>
</g>
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M665,-684C665,-684 537,-684 537,-684 531,-684 525,-678 525,-672 525,-672 525,-660 525,-660 525,-654 531,-648 537,-648 537,-648 665,-648 665,-648 671,-648 677,-654 677,-660 677,-660 677,-672 677,-672 677,-678 671,-684 665,-684"/>
-<text text-anchor="middle" x="601" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M733.5,-324C733.5,-324 632.5,-324 632.5,-324 626.5,-324 620.5,-318 620.5,-312 620.5,-312 620.5,-300 620.5,-300 620.5,-294 626.5,-288 632.5,-288 632.5,-288 733.5,-288 733.5,-288 739.5,-288 745.5,-294 745.5,-300 745.5,-300 745.5,-312 745.5,-312 745.5,-318 739.5,-324 733.5,-324"/>
+<text text-anchor="middle" x="683" y="-303.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 18->8 -->
-<g id="edge24" class="edge">
-<title>18->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M595.3306,-647.8704C588.0535,-623.5963 575.7953,-579.0581 571,-540 555.0812,-410.3404 561.499,-253.7868 565.1423,-190.5482"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="568.6583,-190.3842 565.7631,-180.1926 561.6709,-189.9652 568.6583,-190.3842"/>
-</g>
-<!-- 18->15 -->
-<g id="edge31" class="edge">
-<title>18->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M558.7856,-647.9081C497.2161,-621.5212 382.9067,-572.5315 316.4826,-544.064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="317.6119,-540.7401 307.0417,-540.0179 314.8544,-547.1741 317.6119,-540.7401"/>
+<!-- 18->3 -->
+<g id="edge18" class="edge">
+<title>18->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M693.88,-287.7C698.99,-279.56 705.2,-269.69 710.84,-260.7"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="713.89,-262.43 716.25,-252.1 707.96,-258.71 713.89,-262.43"/>
</g>
-<!-- 18->32 -->
-<g id="edge55" class="edge">
-<title>18->32</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M677.1308,-652.061C729.5514,-642.2029 801.0165,-628.2533 872.2723,-612.3398"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="873.3339,-615.6886 882.3234,-610.0815 871.7994,-608.8589 873.3339,-615.6886"/>
+<!-- 18->4 -->
+<g id="edge20" class="edge">
+<title>18->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M649.49,-287.88C631.16,-278.51 608.26,-266.81 588.67,-256.8"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="590.14,-253.62 579.64,-252.19 586.96,-259.86 590.14,-253.62"/>
</g>
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M509.5,-252C509.5,-252 412.5,-252 412.5,-252 406.5,-252 400.5,-246 400.5,-240 400.5,-240 400.5,-228 400.5,-228 400.5,-222 406.5,-216 412.5,-216 412.5,-216 509.5,-216 509.5,-216 515.5,-216 521.5,-222 521.5,-228 521.5,-228 521.5,-240 521.5,-240 521.5,-246 515.5,-252 509.5,-252"/>
-<text text-anchor="middle" x="461" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M206,-828C206,-828 176,-828 176,-828 170,-828 164,-822 164,-816 164,-816 164,-804 164,-804 164,-798 170,-792 176,-792 176,-792 206,-792 206,-792 212,-792 218,-798 218,-804 218,-804 218,-816 218,-816 218,-822 212,-828 206,-828"/>
+<text text-anchor="middle" x="191" y="-807.5" font-family="sans" font-size="10.00">start</text>
</g>
-<!-- 19->8 -->
+<!-- 19->7 -->
<g id="edge25" class="edge">
-<title>19->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M487.7483,-215.8314C501.0553,-206.7927 517.316,-195.7476 531.6375,-186.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="533.9547,-188.677 540.2603,-180.1628 530.0215,-182.8864 533.9547,-188.677"/>
+<title>19->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M163.82,-796.65C138.72,-785.24 101.23,-768.2 73.52,-755.6"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="74.72,-752.3 64.16,-751.35 71.82,-758.67 74.72,-752.3"/>
</g>
-<!-- 19->9 -->
-<g id="edge27" class="edge">
-<title>19->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M438.0369,-215.8314C426.8285,-206.9632 413.1791,-196.1637 401.0561,-186.5718"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="402.9697,-183.6229 392.9558,-180.1628 398.6263,-189.1125 402.9697,-183.6229"/>
+<!-- 27 -->
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M262.5,-756C262.5,-756 119.5,-756 119.5,-756 113.5,-756 107.5,-750 107.5,-744 107.5,-744 107.5,-732 107.5,-732 107.5,-726 113.5,-720 119.5,-720 119.5,-720 262.5,-720 262.5,-720 268.5,-720 274.5,-726 274.5,-732 274.5,-732 274.5,-744 274.5,-744 274.5,-750 268.5,-756 262.5,-756"/>
+<text text-anchor="middle" x="191" y="-735.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 19->27 -->
+<g id="edge49" class="edge">
+<title>19->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M191,-791.7C191,-783.98 191,-774.71 191,-766.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="194.5,-766.1 191,-756.1 187.5,-766.1 194.5,-766.1"/>
+</g>
+<!-- 29 -->
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M430,-756C430,-756 304,-756 304,-756 298,-756 292,-750 292,-744 292,-744 292,-732 292,-732 292,-726 298,-720 304,-720 304,-720 430,-720 430,-720 436,-720 442,-726 442,-732 442,-732 442,-744 442,-744 442,-750 436,-756 430,-756"/>
+<text text-anchor="middle" x="367" y="-735.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 19->29 -->
+<g id="edge50" class="edge">
+<title>19->29</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M218.11,-798.22C243.72,-788.03 282.81,-772.48 314.51,-759.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="316.09,-763.01 324.09,-756.07 313.51,-756.51 316.09,-763.01"/>
</g>
<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
-<path fill="none" stroke="#afd856" stroke-width="2" d="M427,-684C427,-684 317,-684 317,-684 311,-684 305,-678 305,-672 305,-672 305,-660 305,-660 305,-654 311,-648 317,-648 317,-648 427,-648 427,-648 433,-648 439,-654 439,-660 439,-660 439,-672 439,-672 439,-678 433,-684 427,-684"/>
-<text text-anchor="middle" x="372" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
+<path fill="none" stroke="#c6d856" stroke-width="2" d="M262,-684C262,-684 134,-684 134,-684 128,-684 122,-678 122,-672 122,-672 122,-660 122,-660 122,-654 128,-648 134,-648 134,-648 262,-648 262,-648 268,-648 274,-654 274,-660 274,-660 274,-672 274,-672 274,-678 268,-684 262,-684"/>
+<text text-anchor="middle" x="198" y="-663.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
-<!-- 20->9 -->
+<!-- 20->8 -->
<g id="edge26" class="edge">
-<title>20->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M372,-647.8146C372,-620.4983 372,-567.25 372,-522 372,-522 372,-522 372,-306 372,-265.8721 371.2139,-219.4602 370.6274,-190.416"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="374.1218,-190.1092 370.4144,-180.1843 367.1234,-190.255 374.1218,-190.1092"/>
+<title>20->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M178.25,-647.91C152.03,-623.21 109,-574.79 109,-523 109,-523 109,-523 109,-449 109,-408.85 113.82,-362.55 117.35,-334.02"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="120.84,-334.37 118.63,-324.01 113.89,-333.49 120.84,-334.37"/>
</g>
-<!-- 20->16 -->
-<g id="edge33" class="edge">
-<title>20->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M304.8785,-649.5161C253.503,-636.5164 189.6749,-619.3885 179,-612 155.8934,-596.007 137.7849,-569.2491 126.4275,-549.0565"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="129.3804,-547.1587 121.5465,-540.0256 123.2223,-550.4871 129.3804,-547.1587"/>
+<!-- 20->17 -->
+<g id="edge37" class="edge">
+<title>20->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M219.1,-647.68C246.54,-623.08 291,-575.16 291,-523 291,-523 291,-523 291,-449 291,-373.44 380.21,-337.23 449.85,-320.48"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="451.01,-323.8 459.97,-318.15 449.44,-316.98 451.01,-323.8"/>
</g>
-<!-- 20->35 -->
-<g id="edge59" class="edge">
-<title>20->35</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M439.1525,-654.9864C522.9656,-641.2403 665.2549,-617.9035 747.383,-604.4338"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="748.0352,-607.8736 757.3369,-602.8012 746.9022,-600.9659 748.0352,-607.8736"/>
+<!-- 20->34 -->
+<g id="edge61" class="edge">
+<title>20->34</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M274.07,-650.74C279.79,-649.78 285.49,-648.85 291,-648 411.58,-629.35 552.47,-612.5 636.03,-603.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="636.63,-606.48 646.18,-601.88 635.85,-599.53 636.63,-606.48"/>
</g>
<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
-<path fill="none" stroke="#56d8d8" stroke-width="2" d="M808.5,-396C808.5,-396 725.5,-396 725.5,-396 719.5,-396 713.5,-390 713.5,-384 713.5,-384 713.5,-372 713.5,-372 713.5,-366 719.5,-360 725.5,-360 725.5,-360 808.5,-360 808.5,-360 814.5,-360 820.5,-366 820.5,-372 820.5,-372 820.5,-384 820.5,-384 820.5,-390 814.5,-396 808.5,-396"/>
-<text text-anchor="middle" x="767" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">merge_TIN_scores</text>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M248.5,-396C248.5,-396 151.5,-396 151.5,-396 145.5,-396 139.5,-390 139.5,-384 139.5,-384 139.5,-372 139.5,-372 139.5,-366 145.5,-360 151.5,-360 151.5,-360 248.5,-360 248.5,-360 254.5,-360 260.5,-366 260.5,-372 260.5,-372 260.5,-384 260.5,-384 260.5,-390 254.5,-396 248.5,-396"/>
+<text text-anchor="middle" x="200" y="-375.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
-<!-- 21->10 -->
-<g id="edge28" class="edge">
-<title>21->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M775.3273,-359.8314C778.973,-351.8771 783.3309,-342.369 787.3627,-333.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="790.5757,-334.9622 791.5606,-324.4133 784.2123,-332.0456 790.5757,-334.9622"/>
+<!-- 21->8 -->
+<g id="edge27" class="edge">
+<title>21->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M180.47,-359.7C170.62,-350.97 158.51,-340.24 147.8,-330.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="150.11,-328.12 140.3,-324.1 145.47,-333.36 150.11,-328.12"/>
+</g>
+<!-- 21->9 -->
+<g id="edge29" class="edge">
+<title>21->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M228.87,-359.88C244.29,-350.72 263.48,-339.34 280.1,-329.48"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="282.21,-332.3 289.02,-324.19 278.64,-326.28 282.21,-332.3"/>
</g>
<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
-<path fill="none" stroke="#d87d56" stroke-width="2" d="M970,-252C970,-252 878,-252 878,-252 872,-252 866,-246 866,-240 866,-240 866,-228 866,-228 866,-222 872,-216 878,-216 878,-216 970,-216 970,-216 976,-216 982,-222 982,-228 982,-228 982,-240 982,-240 982,-246 976,-252 970,-252"/>
-<text text-anchor="middle" x="924" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc_all_samples</text>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M422,-684C422,-684 312,-684 312,-684 306,-684 300,-678 300,-672 300,-672 300,-660 300,-660 300,-654 306,-648 312,-648 312,-648 422,-648 422,-648 428,-648 434,-654 434,-660 434,-660 434,-672 434,-672 434,-678 428,-684 422,-684"/>
+<text text-anchor="middle" x="367" y="-663.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
-<!-- 22->11 -->
-<g id="edge29" class="edge">
-<title>22->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M923.7477,-215.8314C923.6407,-208.131 923.5135,-198.9743 923.3947,-190.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="926.8944,-190.3637 923.2557,-180.4133 919.8951,-190.4609 926.8944,-190.3637"/>
+<!-- 22->9 -->
+<g id="edge28" class="edge">
+<title>22->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M359.31,-647.91C348.21,-621.62 329,-569.45 329,-523 329,-523 329,-523 329,-449 329,-408.88 324.58,-362.57 321.34,-334.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="324.81,-333.54 320.17,-324.02 317.86,-334.36 324.81,-333.54"/>
+</g>
+<!-- 22->18 -->
+<g id="edge39" class="edge">
+<title>22->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M363.18,-647.99C356.94,-615.36 348.71,-543.69 386,-504 447.24,-438.81 510.16,-518.48 584,-468 632.16,-435.08 661.17,-370.23 674.41,-333.68"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="677.74,-334.77 677.73,-324.17 671.13,-332.46 677.74,-334.77"/>
+</g>
+<!-- 22->37 -->
+<g id="edge65" class="edge">
+<title>22->37</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M434.25,-657.81C516.32,-648.71 659.23,-631.81 781,-612 788.31,-610.81 795.95,-609.46 803.53,-608.05"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="804.25,-611.48 813.43,-606.17 802.95,-604.6 804.25,-611.48"/>
</g>
<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
-<path fill="none" stroke="#d86656" stroke-width="2" d="M1107,-396C1107,-396 985,-396 985,-396 979,-396 973,-390 973,-384 973,-384 973,-372 973,-372 973,-366 979,-360 985,-360 985,-360 1107,-360 1107,-360 1113,-360 1119,-366 1119,-372 1119,-372 1119,-384 1119,-384 1119,-390 1113,-396 1107,-396"/>
-<text text-anchor="middle" x="1046" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">rename_star_rpm_for_alfa</text>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M452.5,-396C452.5,-396 369.5,-396 369.5,-396 363.5,-396 357.5,-390 357.5,-384 357.5,-384 357.5,-372 357.5,-372 357.5,-366 363.5,-360 369.5,-360 369.5,-360 452.5,-360 452.5,-360 458.5,-360 464.5,-366 464.5,-372 464.5,-372 464.5,-384 464.5,-384 464.5,-390 458.5,-396 452.5,-396"/>
+<text text-anchor="middle" x="411" y="-375.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
</g>
-<!-- 23->13 -->
+<!-- 23->10 -->
<g id="edge30" class="edge">
-<title>23->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1049.5328,-359.8314C1051.0301,-352.131 1052.8105,-342.9743 1054.4745,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1057.9465,-334.8975 1056.4196,-324.4133 1051.0752,-333.5614 1057.9465,-334.8975"/>
-</g>
-<!-- 29 -->
-<g id="node30" class="node">
-<title>29</title>
-<path fill="none" stroke="#56d8a2" stroke-width="2" d="M939,-324C939,-324 909,-324 909,-324 903,-324 897,-318 897,-312 897,-312 897,-300 897,-300 897,-294 903,-288 909,-288 909,-288 939,-288 939,-288 945,-288 951,-294 951,-300 951,-300 951,-312 951,-312 951,-318 945,-324 939,-324"/>
-<text text-anchor="middle" x="924" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">alfa_qc</text>
-</g>
-<!-- 23->29 -->
-<g id="edge49" class="edge">
-<title>23->29</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1015.2142,-359.8314C998.3832,-349.8983 977.4465,-337.5422 959.8783,-327.1741"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="961.4289,-324.0251 951.0379,-321.9568 957.8711,-330.0536 961.4289,-324.0251"/>
+<title>23->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M413.56,-359.85C419.1,-322.83 432.21,-235.18 438.9,-190.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="442.41,-190.64 440.42,-180.23 435.48,-189.6 442.41,-190.64"/>
</g>
-<!-- 24->15 -->
-<g id="edge32" class="edge">
-<title>24->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M253.0375,-575.8314C254.7487,-568.131 256.7835,-558.9743 258.6852,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="262.1554,-550.9344 260.9082,-540.4133 255.3221,-549.4159 262.1554,-550.9344"/>
-</g>
-<!-- 24->16 -->
-<g id="edge34" class="edge">
-<title>24->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M214.6815,-575.8314C196.9641,-566.4516 175.1655,-554.9112 156.3016,-544.9244"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="157.7831,-541.7485 147.3076,-540.1628 154.5078,-547.935 157.7831,-541.7485"/>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#68d856" stroke-width="2" d="M974,-252C974,-252 882,-252 882,-252 876,-252 870,-246 870,-240 870,-240 870,-228 870,-228 870,-222 876,-216 882,-216 882,-216 974,-216 974,-216 980,-216 986,-222 986,-228 986,-228 986,-240 986,-240 986,-246 980,-252 974,-252"/>
+<text text-anchor="middle" x="928" y="-231.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
-<!-- 25->18 -->
-<g id="edge35" class="edge">
-<title>25->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M623.4297,-719.8314C620.1507,-711.9617 616.238,-702.5712 612.6055,-693.8533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="615.7492,-692.2979 608.6722,-684.4133 609.2876,-694.9902 615.7492,-692.2979"/>
+<!-- 24->11 -->
+<g id="edge31" class="edge">
+<title>24->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M898.16,-215.88C882.06,-206.64 862,-195.13 844.71,-185.21"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="846.37,-182.13 835.96,-180.19 842.89,-188.2 846.37,-182.13"/>
</g>
-<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#5673d8" stroke-width="2" d="M517.5,-756C517.5,-756 416.5,-756 416.5,-756 410.5,-756 404.5,-750 404.5,-744 404.5,-744 404.5,-732 404.5,-732 404.5,-726 410.5,-720 416.5,-720 416.5,-720 517.5,-720 517.5,-720 523.5,-720 529.5,-726 529.5,-732 529.5,-732 529.5,-744 529.5,-744 529.5,-750 523.5,-756 517.5,-756"/>
-<text text-anchor="middle" x="467" y="-735.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M1115,-396C1115,-396 993,-396 993,-396 987,-396 981,-390 981,-384 981,-384 981,-372 981,-372 981,-366 987,-360 993,-360 993,-360 1115,-360 1115,-360 1121,-360 1127,-366 1127,-372 1127,-372 1127,-384 1127,-384 1127,-390 1121,-396 1115,-396"/>
+<text text-anchor="middle" x="1054" y="-375.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
-<!-- 26->19 -->
+<!-- 25->15 -->
<g id="edge36" class="edge">
-<title>26->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M467,-719.8146C467,-692.4983 467,-639.25 467,-594 467,-594 467,-594 467,-378 467,-337.8412 464.6417,-291.4372 462.8821,-262.4031"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="466.3599,-261.9376 462.2432,-252.1753 459.3736,-262.3741 466.3599,-261.9376"/>
+<title>25->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1054,-359.7C1054,-351.98 1054,-342.71 1054,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1057.5,-334.1 1054,-324.1 1050.5,-334.1 1057.5,-334.1"/>
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<!-- 31 -->
<g id="node32" class="node">
<title>31</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M275,-684C275,-684 81,-684 81,-684 75,-684 69,-678 69,-672 69,-672 69,-660 69,-660 69,-654 75,-648 81,-648 81,-648 275,-648 275,-648 281,-648 287,-654 287,-660 287,-660 287,-672 287,-672 287,-678 281,-684 275,-684"/>
-<text text-anchor="middle" x="178" y="-663.5" font-family="sans" font-size="10.00" fill="#000000">concatenate_transcriptome_and_genome</text>
+<path fill="none" stroke="#56a9d8" stroke-width="2" d="M968,-324C968,-324 938,-324 938,-324 932,-324 926,-318 926,-312 926,-312 926,-300 926,-300 926,-294 932,-288 938,-288 938,-288 968,-288 968,-288 974,-288 980,-294 980,-300 980,-300 980,-312 980,-312 980,-318 974,-324 968,-324"/>
+<text text-anchor="middle" x="953" y="-303.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
-<!-- 26->31 -->
-<g id="edge54" class="edge">
-<title>26->31</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M404.2848,-722.0806C401.4853,-721.3762 398.7137,-720.6801 396,-720 351.4509,-708.8355 301.7459,-696.5129 261.0607,-686.4615"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="261.7363,-683.0233 251.1888,-684.0234 260.0579,-689.8191 261.7363,-683.0233"/>
+<!-- 25->31 -->
+<g id="edge55" class="edge">
+<title>25->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1029.29,-359.88C1016.33,-350.89 1000.27,-339.76 986.23,-330.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="988.02,-327.01 977.8,-324.19 984.03,-332.76 988.02,-327.01"/>
+</g>
+<!-- 26->17 -->
+<g id="edge38" class="edge">
+<title>26->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M540.03,-359.7C538.71,-351.98 537.12,-342.71 535.65,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="539.07,-333.37 533.93,-324.1 532.17,-334.55 539.07,-333.37"/>
+</g>
+<!-- 26->18 -->
+<g id="edge40" class="edge">
+<title>26->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M577.25,-359.88C596.06,-350.47 619.58,-338.71 639.67,-328.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="641.24,-331.79 648.62,-324.19 638.11,-325.53 641.24,-331.79"/>
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<!-- 27->20 -->
-<g id="edge37" class="edge">
+<g id="edge41" class="edge">
<title>27->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M327.1405,-719.8314C334.1217,-711.454 342.5391,-701.3531 350.1876,-692.1749"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="352.9425,-694.3362 356.6556,-684.4133 347.5649,-689.8548 352.9425,-694.3362"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M192.73,-719.7C193.5,-711.98 194.43,-702.71 195.29,-694.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="198.78,-694.4 196.29,-684.1 191.81,-693.71 198.78,-694.4"/>
</g>
<!-- 28 -->
<g id="node29" class="node">
<title>28</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M814.5,-468C814.5,-468 719.5,-468 719.5,-468 713.5,-468 707.5,-462 707.5,-456 707.5,-456 707.5,-444 707.5,-444 707.5,-438 713.5,-432 719.5,-432 719.5,-432 814.5,-432 814.5,-432 820.5,-432 826.5,-438 826.5,-444 826.5,-444 826.5,-456 826.5,-456 826.5,-462 820.5,-468 814.5,-468"/>
-<text text-anchor="middle" x="767" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M250.5,-540C250.5,-540 149.5,-540 149.5,-540 143.5,-540 137.5,-534 137.5,-528 137.5,-528 137.5,-516 137.5,-516 137.5,-510 143.5,-504 149.5,-504 149.5,-504 250.5,-504 250.5,-504 256.5,-504 262.5,-510 262.5,-516 262.5,-516 262.5,-528 262.5,-528 262.5,-534 256.5,-540 250.5,-540"/>
+<text text-anchor="middle" x="200" y="-519.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
<!-- 28->21 -->
-<g id="edge38" class="edge">
+<g id="edge42" class="edge">
<title>28->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M767,-431.8314C767,-424.131 767,-414.9743 767,-406.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="770.5001,-406.4132 767,-396.4133 763.5001,-406.4133 770.5001,-406.4132"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M200,-503.87C200,-479.67 200,-435.21 200,-406.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="203.5,-406.19 200,-396.19 196.5,-406.19 203.5,-406.19"/>
+</g>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M563,-468C563,-468 369,-468 369,-468 363,-468 357,-462 357,-456 357,-456 357,-444 357,-444 357,-438 363,-432 369,-432 369,-432 563,-432 563,-432 569,-432 575,-438 575,-444 575,-444 575,-456 575,-456 575,-462 569,-468 563,-468"/>
+<text text-anchor="middle" x="466" y="-447.5" font-family="sans" font-size="10.00">concatenate_transcriptome_and_genome</text>
+</g>
+<!-- 28->33 -->
+<g id="edge60" class="edge">
+<title>28->33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M262.7,-504.5C301.16,-494.38 350.61,-481.37 391.12,-470.71"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="392.16,-474.05 400.94,-468.12 390.38,-467.28 392.16,-474.05"/>
</g>
<!-- 29->22 -->
-<g id="edge39" class="edge">
+<g id="edge43" class="edge">
<title>29->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M924,-287.8314C924,-280.131 924,-270.9743 924,-262.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="927.5001,-262.4132 924,-252.4133 920.5001,-262.4133 927.5001,-262.4132"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M367,-719.7C367,-711.98 367,-702.71 367,-694.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="370.5,-694.1 367,-684.1 363.5,-694.1 370.5,-694.1"/>
</g>
<!-- 30 -->
<g id="node31" class="node">
<title>30</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M1013,-468C1013,-468 977,-468 977,-468 971,-468 965,-462 965,-456 965,-456 965,-444 965,-444 965,-438 971,-432 977,-432 977,-432 1013,-432 1013,-432 1019,-432 1025,-438 1025,-444 1025,-444 1025,-456 1025,-456 1025,-462 1019,-468 1013,-468"/>
-<text text-anchor="middle" x="995" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm</text>
+<path fill="none" stroke="#56d8d8" stroke-width="2" d="M738.5,-468C738.5,-468 643.5,-468 643.5,-468 637.5,-468 631.5,-462 631.5,-456 631.5,-456 631.5,-444 631.5,-444 631.5,-438 637.5,-432 643.5,-432 643.5,-432 738.5,-432 738.5,-432 744.5,-432 750.5,-438 750.5,-444 750.5,-444 750.5,-456 750.5,-456 750.5,-462 744.5,-468 738.5,-468"/>
+<text text-anchor="middle" x="691" y="-447.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 30->23 -->
-<g id="edge40" class="edge">
+<g id="edge44" class="edge">
<title>30->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1007.8695,-431.8314C1013.6835,-423.6232 1020.6696,-413.7606 1027.0646,-404.7323"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1030.0331,-406.5966 1032.9573,-396.4133 1024.321,-402.5505 1030.0331,-406.5966"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M631.5,-434.87C590.14,-424.96 533.5,-411.2 474.47,-396.09"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="475.15,-392.65 464.59,-393.56 473.41,-399.43 475.15,-392.65"/>
</g>
<!-- 31->24 -->
-<g id="edge41" class="edge">
+<g id="edge45" class="edge">
<title>31->24</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M195.9163,-647.8314C204.3442,-639.2848 214.541,-628.9443 223.736,-619.6198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="226.3131,-621.9912 230.8425,-612.4133 221.3289,-617.0761 226.3131,-621.9912"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M946.82,-287.7C944,-279.81 940.61,-270.3 937.48,-261.55"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="940.77,-260.34 934.11,-252.1 934.18,-262.7 940.77,-260.34"/>
</g>
-<!-- 32->28 -->
-<g id="edge48" class="edge">
-<title>32->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M898.6506,-575.9617C878.7822,-566.9259 856.046,-554.7466 838,-540 815.9494,-521.9809 796.3677,-495.9884 783.3837,-476.5649"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="786.2925,-474.6179 777.8971,-468.155 780.4298,-478.4427 786.2925,-474.6179"/>
-</g>
-<!-- 32->30 -->
-<g id="edge53" class="edge">
-<title>32->30</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1007.5603,-576.2456C1024.9625,-568.1131 1041.8571,-556.4803 1052,-540 1060.3863,-526.3739 1058.3221,-518.698 1052,-504 1047.2509,-492.9589 1039.0115,-483.1176 1030.2494,-474.9593"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1032.339,-472.1388 1022.4894,-468.2354 1027.755,-477.4291 1032.339,-472.1388"/>
-</g>
-<!-- 33 -->
-<g id="node34" class="node">
-<title>33</title>
-<path fill="none" stroke="#56d85b" stroke-width="2" d="M1031,-540C1031,-540 859,-540 859,-540 853,-540 847,-534 847,-528 847,-528 847,-516 847,-516 847,-510 853,-504 859,-504 859,-504 1031,-504 1031,-504 1037,-504 1043,-510 1043,-516 1043,-516 1043,-528 1043,-528 1043,-534 1037,-540 1031,-540"/>
-<text text-anchor="middle" x="945" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<!-- 32 -->
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M881,-468C881,-468 845,-468 845,-468 839,-468 833,-462 833,-456 833,-456 833,-444 833,-444 833,-438 839,-432 845,-432 845,-432 881,-432 881,-432 887,-432 893,-438 893,-444 893,-444 893,-456 893,-456 893,-462 887,-468 881,-468"/>
+<text text-anchor="middle" x="863" y="-447.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
-<!-- 32->33 -->
-<g id="edge58" class="edge">
-<title>32->33</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M945,-575.8314C945,-568.131 945,-558.9743 945,-550.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="948.5001,-550.4132 945,-540.4133 941.5001,-550.4133 948.5001,-550.4132"/>
+<!-- 32->25 -->
+<g id="edge46" class="edge">
+<title>32->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M893.26,-437.91C921.34,-427.62 963.82,-412.05 998.07,-399.5"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="999.3,-402.77 1007.49,-396.05 996.89,-396.2 999.3,-402.77"/>
</g>
-<!-- 33->28 -->
-<g id="edge45" class="edge">
-<title>33->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M900.0831,-503.8314C876.065,-494.1162 846.3166,-482.0831 821.0408,-471.8592"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="822.1767,-468.5432 811.5939,-468.038 819.5518,-475.0325 822.1767,-468.5432"/>
+<!-- 33->26 -->
+<g id="edge47" class="edge">
+<title>33->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M485.03,-431.7C494.54,-423.05 506.21,-412.45 516.57,-403.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="519.14,-405.42 524.19,-396.1 514.43,-400.24 519.14,-405.42"/>
</g>
-<!-- 33->30 -->
-<g id="edge51" class="edge">
-<title>33->30</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M957.6171,-503.8314C963.3172,-495.6232 970.1663,-485.7606 976.4359,-476.7323"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="979.3838,-478.6234 982.213,-468.4133 973.6342,-474.6306 979.3838,-478.6234"/>
+<!-- 34->30 -->
+<g id="edge52" class="edge">
+<title>34->30</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M646.75,-575.95C629.25,-567.98 612.22,-556.47 602,-540 593.56,-526.41 594.09,-517.91 602,-504 609.36,-491.04 621.29,-480.92 634.05,-473.16"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="635.96,-476.1 642.97,-468.15 632.53,-469.99 635.96,-476.1"/>
</g>
-<!-- 34 -->
-<g id="node35" class="node">
-<title>34</title>
-<path fill="none" stroke="#d88d56" stroke-width="2" d="M741,-540C741,-540 605,-540 605,-540 599,-540 593,-534 593,-528 593,-528 593,-516 593,-516 593,-510 599,-504 605,-504 605,-504 741,-504 741,-504 747,-504 753,-510 753,-516 753,-516 753,-528 753,-528 753,-534 747,-540 741,-540"/>
-<text text-anchor="middle" x="673" y="-519.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<!-- 34->32 -->
+<g id="edge57" class="edge">
+<title>34->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M759.13,-575.89C778.61,-567.39 800.04,-555.55 816,-540 833.9,-522.55 846.48,-496.81 854.08,-477.5"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="857.39,-478.65 857.61,-468.06 850.83,-476.2 857.39,-478.65"/>
</g>
-<!-- 34->28 -->
-<g id="edge47" class="edge">
-<title>34->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M696.7202,-503.8314C708.4094,-494.8779 722.6688,-483.9558 735.2809,-474.2955"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="737.4769,-477.0222 743.2874,-468.1628 733.2203,-471.4651 737.4769,-477.0222"/>
+<!-- 35 -->
+<g id="node36" class="node">
+<title>35</title>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M795,-540C795,-540 623,-540 623,-540 617,-540 611,-534 611,-528 611,-528 611,-516 611,-516 611,-510 617,-504 623,-504 623,-504 795,-504 795,-504 801,-504 807,-510 807,-516 807,-516 807,-528 807,-528 807,-534 801,-540 795,-540"/>
+<text text-anchor="middle" x="709" y="-519.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
-<!-- 35->28 -->
-<g id="edge46" class="edge">
-<title>35->28</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M757.2532,-588.8041C697.0784,-581.7456 605.1884,-566.8201 584,-540 548.3016,-494.8132 631.8376,-470.715 697.5067,-459.1486"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="698.1838,-462.5838 707.4602,-457.4652 697.0165,-455.6819 698.1838,-462.5838"/>
+<!-- 34->35 -->
+<g id="edge63" class="edge">
+<title>34->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M709,-575.7C709,-567.98 709,-558.71 709,-550.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="712.5,-550.1 709,-540.1 705.5,-550.1 712.5,-550.1"/>
</g>
<!-- 35->30 -->
-<g id="edge52" class="edge">
+<g id="edge54" class="edge">
<title>35->30</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M811.7077,-575.6902C813.4544,-555.5713 819.2369,-523.5255 838,-504 868.811,-471.937 919.5025,-458.9075 954.9243,-453.6152"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="955.4924,-457.0704 964.9339,-452.2633 954.5554,-450.1334 955.4924,-457.0704"/>
+<path fill="none" stroke="grey" stroke-width="2" d="M704.55,-503.7C702.55,-495.9 700.13,-486.51 697.9,-477.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="701.28,-476.92 695.4,-468.1 694.5,-478.66 701.28,-476.92"/>
</g>
-<!-- 35->33 -->
-<g id="edge57" class="edge">
-<title>35->33</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M844.8139,-575.8314C862.2707,-566.4516 883.7487,-554.9112 902.3352,-544.9244"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="904.0446,-547.9792 911.197,-540.1628 900.7314,-541.8129 904.0446,-547.9792"/>
+<!-- 35->32 -->
+<g id="edge59" class="edge">
+<title>35->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M746.67,-503.88C770,-493.27 799.9,-479.68 823.54,-468.93"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="825.27,-471.99 832.93,-464.67 822.38,-465.62 825.27,-471.99"/>
</g>
-<!-- 36->29 -->
-<g id="edge50" class="edge">
-<title>36->29</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M903.8132,-359.8314C906.7644,-351.9617 910.2858,-342.5712 913.555,-333.8533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="916.8609,-335.0055 917.095,-324.4133 910.3066,-332.5476 916.8609,-335.0055"/>
+<!-- 36 -->
+<g id="node37" class="node">
+<title>36</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M543,-540C543,-540 407,-540 407,-540 401,-540 395,-534 395,-528 395,-528 395,-516 395,-516 395,-510 401,-504 407,-504 407,-504 543,-504 543,-504 549,-504 555,-510 555,-516 555,-516 555,-528 555,-528 555,-534 549,-540 543,-540"/>
+<text text-anchor="middle" x="475" y="-519.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 36->30 -->
+<g id="edge51" class="edge">
+<title>36->30</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M527.56,-503.97C558.01,-494.1 596.51,-481.62 628.5,-471.25"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="629.77,-474.52 638.2,-468.11 627.61,-467.86 629.77,-474.52"/>
+</g>
+<!-- 37->30 -->
+<g id="edge53" class="edge">
+<title>37->30</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M861,-575.72C853.35,-555.98 838.38,-523.86 816,-504 800.01,-489.82 779.67,-479.03 760.07,-471.02"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="761.11,-467.67 750.52,-467.3 758.57,-474.19 761.11,-467.67"/>
+</g>
+<!-- 37->32 -->
+<g id="edge58" class="edge">
+<title>37->32</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M875.31,-575.79C879.74,-565.63 884.74,-552.38 887,-540 889.87,-524.26 890.38,-519.64 887,-504 885.04,-494.92 881.39,-485.52 877.51,-477.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="880.54,-475.42 872.95,-468.02 874.27,-478.53 880.54,-475.42"/>
+</g>
+<!-- 37->35 -->
+<g id="edge64" class="edge">
+<title>37->35</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M828.35,-575.88C806.75,-566.31 779.65,-554.3 756.73,-544.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="758.09,-540.92 747.53,-540.07 755.25,-547.32 758.09,-540.92"/>
+</g>
+<!-- 38->31 -->
+<g id="edge56" class="edge">
+<title>38->31</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1028.85,-575.78C1016.85,-541.74 989.9,-463.32 972,-396 966.55,-375.52 961.6,-352.06 958.11,-334.37"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="961.48,-333.34 956.14,-324.18 954.6,-334.66 961.48,-333.34"/>
</g>
</g>
</svg>
diff --git a/pipeline_documentation.md b/pipeline_documentation.md
index e9b582a05fb7774c7ff0d7ab4dcbb7a4e326ecdb..17decd1845b6a8c54bec126d401db7ac20ed2689 100644
--- a/pipeline_documentation.md
+++ b/pipeline_documentation.md
@@ -32,6 +32,8 @@ on installation and usage please see [here](README.md).
- [**salmon_quantmerge_transcripts**](#salmon_quantmerge_transcripts)
- [**kallisto_merge_genes**](#kallisto_merge_genes)
- [**kallisto_merge_transcripts**](#kallisto_merge_transcripts)
+ - [**pca_kallisto**](#pca_kallisto)
+ - [**pca_salmon**](#pca_salmon)
- [**generate_alfa_index**](#generate_alfa_index)
- [**alfa_qc**](#alfa_qc)
- [**alfa_qc_all_samples**](#alfa_qc_all_samples)
@@ -400,7 +402,7 @@ Merge gene-level expression estimates for all samples with
- Gene TPM table (custom `.tsv`); used in
[**multiqc_report**](#multiqc_report)
- Gene read count table (custom `.tsv`); used in
- [**multiqc_report**](#multiqc_report)
+ [**pca_salmon**](#pca_salmon) and [**pca_kallisto**](#pca_kallisto)
#### `salmon_quantmerge_transcripts`
@@ -416,7 +418,7 @@ Merge transcript-level expression estimates for all samples with
- Transcript TPM table (custom `.tsv`); used in
[**multiqc_report**](#multiqc_report)
- Transcript read count table (custom `.tsv`); used in
- [**multiqc_report**](#multiqc_report)
+ [**pca_salmon**](#pca_salmon) and [**pca_kallisto**](#pca_kallisto)
#### `kallisto_merge_genes`
@@ -448,6 +450,28 @@ Merge transcript-level expression estimates for all samples with
- Transcript TPM table (custom `.tsv`)
- Transcript read count table (custom `.tsv`)
+#### `pca_kallisto`
+
+Run PCA analysis on kallisto genes and transcripts with [custom script][custom-script-zpca].
+
+> Rule is run one time for transcript estimates and one time for genes estimates
+
+- **Input**
+ - Transcript/Genes TPM table (custom `.tsv`)
+- **Output**
+ - Directory with PCA plots, scree plot and top loading scores.
+
+#### `pca_salmon`
+
+Run PCA analysis on salmon genes and transcripts with [custom script][custom-script-zpca].
+
+> Rule is run one time for transcript estimates and one time for genes estimates
+
+- **Input**
+ - Transcript/Genes TPM table (custom `.tsv`)
+- **Output**
+ - Directory with PCA plots, scree plot and top loading scores.
+
#### `generate_alfa_index`
Create index for [**ALFA**](#third-party-software-used).
@@ -714,6 +738,7 @@ Generate pseudoalignments of reads to transcripts with
[custom-script-gtf-to-bed12]: <https://git.scicore.unibas.ch/zavolan_group/tools/gtf_transcript_type_to_bed12>
[custom-script-tin]: <https://git.scicore.unibas.ch/zavolan_group/tools/tin_score_calculation>
[custom-script-merge-kallisto]: <https://github.com/zavolanlab/merge_kallisto>
+[custom-script-zpca]: <https://github.com/zavolanlab/zpca>
[docs-alfa]: <https://github.com/biocompibens/ALFA#manual>
[docs-bedgraphtobigwig]: <http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/>
[docs-bedtools]: <https://bedtools.readthedocs.io/en/latest/>
diff --git a/scripts/fg_extract_transcripts.py b/scripts/fg_extract_transcripts.py
deleted file mode 100755
index 07e80a4ef4b8c830d3a69b4f6f29f5ad8319481c..0000000000000000000000000000000000000000
--- a/scripts/fg_extract_transcripts.py
+++ /dev/null
@@ -1,104 +0,0 @@
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# import needed (external) modules
-# -----------------------------------------------------------------------------
-
-try:
- import HTSeq
-except(Exception):
- raise("[ERROR] HTSeq was not imported properly. Exiting.")
- sys.exit(-1)
-
-try:
- from argparse import ArgumentParser, RawTextHelpFormatter, FileType
-except(Exception):
- raise("[ERROR] argparse was not imported properly. Exiting.")
- sys.exit(-1)
-
-try:
- import sys
-except(Exception):
- raise("[ERROR] sys was not imported properly. Exiting.")
- sys.exit(-1)
-
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# Main function
-# -----------------------------------------------------------------------------
-def main():
-
- """ Main function """
-
- __doc__ = "Filter gtf file based on the transcript biotype."
-
- parser = ArgumentParser(description=__doc__, formatter_class=RawTextHelpFormatter)
-
-
- parser.add_argument("--gtf",
- dest = "gtf",
- help = "Annotation file in GTF format with transcript support level information",
- required = True,
- metavar = "FILE")
-
- parser.add_argument("--out",
- dest = "out",
- help = "GTF output file",
- required = True,
- metavar="FILE")
-
- parser.add_argument("--transcript_biotype",
- dest = "transcript_biotype",
- help = "Transcript biotype or transcript type to include",
- required = True,
- default = "protein_coding,lincRNA")
-
- parser.add_argument("-v",
- "--verbose",
- action = "store_true",
- dest = "verbose",
- default = False,
- required = False,
- help = "Verbose")
-
- # _________________________________________________________________________
- # -------------------------------------------------------------------------
- # get the arguments
- # -------------------------------------------------------------------------
- try:
- options = parser.parse_args()
- except(Exception):
- parser.print_help()
-
- if len(sys.argv) == 1:
- parser.print_help()
- sys.exit(1)
-
- if options.verbose:
- sys.stdout.write("Parsing gtf file and keep %s transcripts\n" % (str(options.transcript_biotype)))
-
- list_of_transcript_types = str(options.transcript_biotype).split(",")
-
- # parse gtf file
- gtf = HTSeq.GFF_Reader(options.gtf)
- # open output file
- w = open(options.out, 'w')
- for gtf_line in gtf:
- if "transcript_biotype" in gtf_line.attr:
- if gtf_line.attr['transcript_biotype'] in list_of_transcript_types:
- w.write(gtf_line.get_gff_line())
- if "transcript_type" in gtf_line.attr:
- if gtf_line.attr['transcript_type'] in list_of_transcript_types:
- w.write(gtf_line.get_gff_line())
- w.close()
-
-
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# Call the Main function and catch Keyboard interrups
-# -----------------------------------------------------------------------------
-if __name__ == '__main__':
- try:
- main()
- except KeyboardInterrupt:
- sys.stderr.write("User interrupt!\n")
- sys.exit(0)
diff --git a/scripts/heatmap_and_clustermap.py b/scripts/heatmap_and_clustermap.py
deleted file mode 100755
index ae2a9f3fa1c96117ad37a870aa43bd64d56c5af3..0000000000000000000000000000000000000000
--- a/scripts/heatmap_and_clustermap.py
+++ /dev/null
@@ -1,112 +0,0 @@
-#!/usr/bin/env python
-
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# import needed (external) modules
-# -----------------------------------------------------------------------------
-
-import sys
-import os
-import pandas as pd
-import numpy as np
-import seaborn as sns
-import matplotlib.pyplot as plt
-from argparse import ArgumentParser, RawTextHelpFormatter
-
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# Main function
-# -----------------------------------------------------------------------------
-
-
-def main():
- """ Main function """
-
- __doc__ = "Create heatmap and clustermap based on a table (rows are genes/transcripts, columns are samples)."
-
- parser = ArgumentParser(
- description=__doc__,
- formatter_class=RawTextHelpFormatter
- )
-
- parser.add_argument(
- "--tpm",
- dest="tpm",
- help="TPM table (tsv)",
- required=True,
- metavar="FILE"
- )
-
- parser.add_argument(
- "--out",
- dest="out",
- help="Output directory",
- required=True,
- metavar="FILE"
- )
-
- parser.add_argument(
- "-v",
- "--verbose",
- action="store_true",
- dest="verbose",
- default=False,
- required=False,
- help="Verbose"
- )
-
- # _________________________________________________________________________
- # -------------------------------------------------------------------------
- # get the arguments
- # -------------------------------------------------------------------------
- try:
- options = parser.parse_args()
- except(Exception):
- parser.print_help()
-
- if len(sys.argv) == 1:
- parser.print_help()
- sys.exit(1)
-
- if options.verbose:
- sys.stdout.write(f"Creating output directory: {options.out} {os.linesep}")
-
- if not os.path.exists(options.out):
- os.makedirs(options.out)
-
- if options.verbose:
- sys.stdout.write(f"Reading: {options.tpm} {os.linesep}")
- df = pd.read_csv(options.tpm, header=0, sep="\t")
- df.set_index(["Name"], inplace=True)
- df = df + 1/32
- df = np.log2(df)
-
- if options.verbose:
- sys.stdout.write(f"Generating heatmap {os.linesep}")
-
- plt.rcParams["figure.figsize"] = (20,20)
- g = sns.heatmap(df.corr(method="pearson"))
- plt.savefig(os.path.join(options.out, "heatmap.pdf"))
-
- if options.verbose:
- sys.stdout.write(f"Generating clustermap {os.linesep}")
-
- plt.rcParams["figure.figsize"] = (20,20)
- g = sns.clustermap(df.corr(method="pearson"))
- plt.savefig(os.path.join(options.out, "clustermap.pdf"))
-
- if options.verbose:
- sys.stdout.write(f"Done {os.linesep}")
-
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# Call the Main function and catch Keyboard interrups
-# -----------------------------------------------------------------------------
-
-
-if __name__ == '__main__':
- try:
- main()
- except KeyboardInterrupt:
- sys.stderr.write("User interrupt!" + os.linesep)
- sys.exit(0)
diff --git a/scripts/perform_PCA.py b/scripts/perform_PCA.py
deleted file mode 100755
index 3150d4a2f7ccc1b77c6edec9f06562c9b00806e1..0000000000000000000000000000000000000000
--- a/scripts/perform_PCA.py
+++ /dev/null
@@ -1,210 +0,0 @@
-#!/usr/bin/env python
-
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# import needed (external) modules
-# -----------------------------------------------------------------------------
-
-
-import sys
-import os
-import pandas as pd
-import numpy as np
-import random as rd
-from sklearn.decomposition import PCA
-from sklearn import preprocessing
-import matplotlib
-import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
-from argparse import ArgumentParser, RawTextHelpFormatter
-
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# Main function
-# -----------------------------------------------------------------------------
-
-
-def main():
- """ Main function """
-
- __doc__ = "Perform PCA based on a table (rows are genes/transcripts, columns are samples)."
-
- parser = ArgumentParser(
- description=__doc__,
- formatter_class=RawTextHelpFormatter
- )
-
- parser.add_argument(
- "--tpm",
- dest="tpm",
- help="TPM table (tsv)",
- required=True,
- metavar="FILE"
- )
-
- parser.add_argument(
- "--out",
- dest="out",
- help="Output directory",
- required=True,
- metavar="FILE"
- )
-
- parser.add_argument(
- "-v",
- "--verbose",
- action="store_true",
- dest="verbose",
- default=False,
- required=False,
- help="Verbose"
- )
-
- # _________________________________________________________________________
- # -------------------------------------------------------------------------
- # get the arguments
- # -------------------------------------------------------------------------
- try:
- options = parser.parse_args()
- except(Exception):
- parser.print_help()
-
- if len(sys.argv) == 1:
- parser.print_help()
- sys.exit(1)
-
- if options.verbose:
- sys.stdout.write(f"Creating output directory: {options.out} {os.linesep}")
-
- if not os.path.exists(options.out):
- os.makedirs(options.out)
-
- if options.verbose:
- sys.stdout.write(f"Reading: {options.tpm} {os.linesep}")
- df = pd.read_csv(options.tpm, header=0, sep="\t")
- df.set_index(["Name"], inplace=True)
-
- if options.verbose:
- sys.stdout.write(f"Performing PCA {os.linesep}")
-
- scaled_data = preprocessing.scale(df.T)
-
- pca = PCA()
- pca.fit(scaled_data)
- pca_data = pca.transform(scaled_data)
-
- per_var = np.round(pca.explained_variance_ratio_* 100, decimals=1)
- labels = ['PC' + str(x) for x in range(1, len(per_var)+1)]
- plt.figure()
- plt.rcParams["figure.figsize"] = (20,20)
- plt.bar(x=range(1,len(per_var)+1), height=per_var, tick_label=labels)
- plt.ylabel('Percentage of Explained Variance')
- plt.xlabel('Principal Component')
- plt.title('Scree Plot')
- plt.xticks(rotation='vertical')
- plt.savefig(os.path.join(options.out, "scree_plot.pdf"))
- plt.close()
-
- pca_df = pd.DataFrame(pca_data, index=[*df], columns=labels)
-
- if options.verbose:
- sys.stdout.write(f"Generating plots in: {options.out} {os.linesep}")
-
- # -------------------------------------------------------------------------
- # PCA 1st and 2nd component
- # -------------------------------------------------------------------------
-
- plt.figure()
- plt.rcParams["figure.figsize"] = (20,20)
- plt.scatter(pca_df.PC1, pca_df.PC2)
- plt.xlabel('PC1 - {0}%'.format(per_var[0]), fontsize=22)
- plt.ylabel('PC2 - {0}%'.format(per_var[1]), fontsize=22)
- plt.title('PCA components 1 & 2', fontsize=22)
- for sample in pca_df.index:
- plt.annotate(sample, (pca_df.PC1.loc[sample], pca_df.PC2.loc[sample]))
- plt.savefig(os.path.join(options.out, "PCA_1_2.pdf"))
- plt.close()
-
- # -------------------------------------------------------------------------
- # PCA 2nd and 3rd component
- # -------------------------------------------------------------------------
-
- plt.figure()
- plt.rcParams["figure.figsize"] = (20,20)
- plt.scatter(pca_df.PC2, pca_df.PC3)
- plt.xlabel('PC2 - {0}%'.format(per_var[1]), fontsize=22)
- plt.ylabel('PC3 - {0}%'.format(per_var[2]), fontsize=22)
- plt.title('PCA components 2 & 3', fontsize=22)
- for sample in pca_df.index:
- plt.annotate(sample, (pca_df.PC2.loc[sample], pca_df.PC3.loc[sample]))
- plt.savefig(os.path.join(options.out, "PCA_2_3.pdf"))
- plt.close()
-
-
- # -------------------------------------------------------------------------
- # PCA 1st and 3rd component
- # -------------------------------------------------------------------------
-
- plt.figure()
- plt.rcParams["figure.figsize"] = (20,20)
- plt.scatter(pca_df.PC1, pca_df.PC3)
- plt.xlabel('PC1 - {0}%'.format(per_var[0]), fontsize=22)
- plt.ylabel('PC3 - {0}%'.format(per_var[2]), fontsize=22)
- plt.title('PCA components 1 & 3', fontsize=22)
- for sample in pca_df.index:
- plt.annotate(sample, (pca_df.PC1.loc[sample], pca_df.PC3.loc[sample]))
- plt.savefig(os.path.join(options.out, "PCA_1_3.pdf"))
- plt.close()
-
-
- # -------------------------------------------------------------------------
- # PCA 3D
- # -------------------------------------------------------------------------
-
- labels = []
- pc1 = []
- pc2 = []
- pc3 = []
- for i, row in pca_df.iterrows():
- labels.append(i)
- pc1.append(row["PC1"])
- pc2.append(row["PC2"])
- pc3.append(row["PC3"])
-
- fig = plt.figure(figsize=(20,20))
- ax = fig.add_subplot(111, projection='3d')
- ax.scatter(pc1, pc2, pc3)
-
- ax.set_xlabel('PC1 - {0}%'.format(per_var[0]))
- ax.set_ylabel('PC2 - {0}%'.format(per_var[1]))
- ax.set_zlabel('PC3 - {0}%'.format(per_var[2]))
- for label, x, y, z in zip(labels, pc1, pc2, pc3):
- ax.text(x, y, z, label)
- plt.savefig(os.path.join(options.out, "PCA_3D.pdf"))
-
- # -------------------------------------------------------------------------
- # Write loading scores
- # -------------------------------------------------------------------------
-
- if options.verbose:
- sys.stdout.write(f"Writing loading scores in: {options.out} {os.linesep}")
-
- loading_scores = pd.Series(pca.components_[0], index=list(df.index))
- sorted_loading_scores = loading_scores.abs().sort_values(ascending=False)
- sorted_loading_scores.to_csv(os.path.join(options.out, "loading_scores.tsv"), header=False, sep="\t")
-
- if options.verbose:
- sys.stdout.write(f"Done {os.linesep}")
-
-# _____________________________________________________________________________
-# -----------------------------------------------------------------------------
-# Call the Main function and catch Keyboard interrups
-# -----------------------------------------------------------------------------
-
-
-if __name__ == '__main__':
- try:
- main()
- except KeyboardInterrupt:
- sys.stderr.write("User interrupt!" + os.linesep)
- sys.exit(0)