diff --git a/Snakefile b/Snakefile
index 3f398bab13942fedefd8e8158fc3d03d72c57c4f..7c8185c2212afdec42f122dbe28c38644e105b34 100644
--- a/Snakefile
+++ b/Snakefile
@@ -53,17 +53,6 @@ rule finish:
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)]),
- salmon_gn_estimates = expand(
- os.path.join(
- config['output_dir'],
- "{seqmode}",
- "{sample}",
- "salmon_quant",
- "quant.genes.sf"),
- zip,
- sample=[i for i in list(samples_table.index.values)],
- seqmode=[samples_table.loc[i, 'seqmode']
- for i in list(samples_table.index.values)]),
pseudoalignment = expand(
os.path.join(
config['output_dir'],
@@ -329,11 +318,140 @@ rule extract_transcripts_as_bed12:
2> {log.stderr}"
+rule index_genomic_alignment_samtools:
+ '''
+ Index genome bamfile using samtools
+ '''
+ input:
+ bam = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam")
+
+ output:
+ bai = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam.bai")
+
+ singularity:
+ "docker://zavolab/samtools:1.10-slim"
+
+ threads: 1
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "{seqmode}",
+ "{sample}",
+ "index_genomic_alignment_samtools.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "{seqmode}",
+ "{sample}",
+ "index_genomic_alignment_samtools.stdout.log")
+
+ shell:
+ "(samtools index {input.bam} {output.bai};) \
+ 1> {log.stdout} 2> {log.stderr}"
+
+
+rule star_rpm:
+ ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
+ input:
+ bam = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam"),
+ bai = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam.bai")
+
+ output:
+ str1 = (os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str1.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str1.out.bg")),
+ str2 = (os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.Unique.str2.out.bg"),
+ os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str2.out.bg"))
+
+ params:
+ out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
+ prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
+ str(wildcards.sample) + "_"),
+ stranded = "Stranded"
+
+ singularity:
+ "docker://zavolab/star:2.7.3a-slim"
+
+ log:
+ stderr = os.path.join(
+ config["log_dir"],
+ "{seqmode}",
+ "{sample}",
+ "star_rpm_single_end.stderr.log"),
+ stdout = os.path.join(
+ config["log_dir"],
+ "{seqmode}",
+ "{sample}",
+ "star_rpm_single_end.stdout.log")
+
+ threads: 4
+
+ shell:
+ """
+ (mkdir -p {params.out_dir}; \
+ chmod -R 777 {params.out_dir}; \
+ STAR \
+ --runMode inputAlignmentsFromBAM \
+ --runThreadN {threads} \
+ --inputBAMfile {input.bam} \
+ --outWigType "bedGraph" \
+ --outWigStrand {params.stranded} \
+ --outWigNorm "RPM" \
+ --outFileNamePrefix {params.prefix}) \
+ 1> {log.stdout} 2> {log.stderr}
+ """
+
+
rule calculate_TIN_scores:
"""
Caluclate transcript integrity (TIN) score
"""
input:
+ bam = os.path.join(
+ config['output_dir'],
+ "{seqmode}",
+ "{sample}",
+ "map_genome",
+ "{sample}_Aligned.sortedByCoord.out.bam"),
bai = os.path.join(
config['output_dir'],
"{seqmode}",
@@ -353,12 +471,6 @@ rule calculate_TIN_scores:
"TIN_score.tsv")
params:
- bam = os.path.join(
- config['output_dir'],
- "{seqmode}",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam"),
sample = "{sample}"
log:
@@ -375,7 +487,7 @@ rule calculate_TIN_scores:
shell:
"(tin_score_calculation.py \
- -i {params.bam} \
+ -i {input.bam} \
-r {input.transcripts_bed12} \
-c 0 \
--names {params.sample} \
@@ -500,4 +612,4 @@ rule salmon_quantmerge_transcripts:
--names {params.sample_name_list} \
--column {params.salmon_merge_on} \
--output {output.salmon_out}) \
- 1> {log.stdout} 2> {log.stderr}"
+ 1> {log.stdout} 2> {log.stderr}"
\ No newline at end of file
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 5b222ac1b8de89838e844ccb08792b141a3d0888..0c0c25a7a513e3dd8c1fd0299cde5aada907fa4d 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,483 +1,407 @@
<?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 2.38.0 (20140413.2041)
-->
<!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 1949.50 409.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<svg width="1858pt" height="409pt"
+ viewBox="0.00 0.00 1857.85 409.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 405)">
<title>snakemake_dag</title>
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+<polygon fill="white" stroke="none" points="-4,4 -4,-405 1853.85,-405 1853.85,4 -4,4"/>
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-<text text-anchor="middle" x="1073" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
+<g id="node1" class="node"><title>0</title>
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+<text text-anchor="middle" x="1035" y="-15.5" font-family="sans" font-size="10.00">finish</text>
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-<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<g id="node2" class="node"><title>1</title>
+<path fill="none" stroke="#56d8a2" stroke-width="2" d="M280,-108C280,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 280,-72 280,-72 286,-72 292,-78 292,-84 292,-84 292,-96 292,-96 292,-102 286,-108 280,-108"/>
+<text text-anchor="middle" x="146" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
+<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
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-<title>1->0</title>
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+<g id="edge1" class="edge"><title>1->0</title>
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-<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+<g id="node3" class="node"><title>2</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M602,-108C602,-108 322,-108 322,-108 316,-108 310,-102 310,-96 310,-96 310,-84 310,-84 310,-78 316,-72 322,-72 322,-72 602,-72 602,-72 608,-72 614,-78 614,-84 614,-84 614,-96 614,-96 614,-102 608,-108 602,-108"/>
+<text text-anchor="middle" x="462" y="-93" font-family="sans" font-size="10.00">fastqc</text>
+<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g>
<!-- 2->0 -->
-<g id="edge2" class="edge">
-<title>2->0</title>
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+<g id="edge2" class="edge"><title>2->0</title>
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-<title>3</title>
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-<text text-anchor="middle" x="987" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
+<g id="node4" class="node"><title>3</title>
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+<text text-anchor="middle" x="642" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
</g>
<!-- 3->0 -->
-<g id="edge3" class="edge">
-<title>3->0</title>
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-<text text-anchor="middle" x="1324" y="-93" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
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-<title>3->9</title>
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-<!-- 3->10 -->
-<g id="edge29" class="edge">
-<title>3->10</title>
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-<title>4->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1116.3448,-143.8314C1093.1042,-134.159 1064.3432,-122.1891 1039.8477,-111.9944"/>
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-<title>4->12</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1163.5001,-118.4132 1160,-108.4133 1156.5001,-118.4133 1163.5001,-118.4132"/>
+<g id="edge4" class="edge"><title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M746.115,-143.919C728.035,-136.04 710.736,-124.592 700,-108 691.308,-94.567 689.608,-84.1656 700,-72 737.975,-27.5452 918.617,-20.167 997.736,-19.0937"/>
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-<g id="node6" class="node">
-<title>5</title>
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-<text text-anchor="middle" x="648" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
+<g id="node6" class="node"><title>5</title>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M1472,-108C1472,-108 1384,-108 1384,-108 1378,-108 1372,-102 1372,-96 1372,-96 1372,-84 1372,-84 1372,-78 1378,-72 1384,-72 1384,-72 1472,-72 1472,-72 1478,-72 1484,-78 1484,-84 1484,-84 1484,-96 1484,-96 1484,-102 1478,-108 1472,-108"/>
+<text text-anchor="middle" x="1428" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
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-<title>5->0</title>
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+<g id="edge5" class="edge"><title>5->0</title>
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-<g id="node7" class="node">
-<title>6</title>
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-<text text-anchor="middle" x="824" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
+<g id="node7" class="node"><title>6</title>
+<path fill="none" stroke="#8fd856" stroke-width="2" d="M1676,-108C1676,-108 1588,-108 1588,-108 1582,-108 1576,-102 1576,-96 1576,-96 1576,-84 1576,-84 1576,-78 1582,-72 1588,-72 1588,-72 1676,-72 1676,-72 1682,-72 1688,-78 1688,-84 1688,-84 1688,-96 1688,-96 1688,-102 1682,-108 1676,-108"/>
+<text text-anchor="middle" x="1632" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
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<!-- 6->0 -->
-<g id="edge6" class="edge">
-<title>6->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M764.8288,-143.88C748.0479,-135.7024 731.715,-124.1357 722,-108 713.7471,-94.2927 711.5819,-84.1434 722,-72 742.3046,-48.3328 949.7311,-28.3477 1035.8409,-21.0061"/>
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+<g id="edge6" class="edge"><title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1575.75,-73.7128C1572.8,-73.0916 1569.87,-72.515 1567,-72 1383.05,-38.991 1159.35,-25.1198 1072.23,-20.7018"/>
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<!-- 7 -->
-<g id="node8" class="node">
-<title>7</title>
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-<text text-anchor="middle" x="1630" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
-<text text-anchor="middle" x="1630" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: paired_end</text>
+<g id="node8" class="node"><title>7</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1342,-108C1342,-108 1230,-108 1230,-108 1224,-108 1218,-102 1218,-96 1218,-96 1218,-84 1218,-84 1218,-78 1224,-72 1230,-72 1230,-72 1342,-72 1342,-72 1348,-72 1354,-78 1354,-84 1354,-84 1354,-96 1354,-96 1354,-102 1348,-108 1342,-108"/>
+<text text-anchor="middle" x="1286" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1286" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
<!-- 7->0 -->
-<g id="edge7" class="edge">
-<title>7->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1573.7608,-73.8301C1570.808,-73.168 1567.8748,-72.5521 1565,-72 1397.0468,-39.7453 1192.867,-25.0044 1110.3037,-20.0406"/>
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+<g id="edge7" class="edge"><title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1224.92,-71.9656C1177.03,-58.6095 1111.97,-40.4647 1071.77,-29.2542"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.68,-25.8757 1062.11,-26.5606 1070.8,-32.6184 1072.68,-25.8757"/>
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<!-- 8 -->
-<g id="node9" class="node">
-<title>8</title>
-<path fill="none" stroke="#56d8a2" stroke-width="2" d="M1804,-108C1804,-108 1716,-108 1716,-108 1710,-108 1704,-102 1704,-96 1704,-96 1704,-84 1704,-84 1704,-78 1710,-72 1716,-72 1716,-72 1804,-72 1804,-72 1810,-72 1816,-78 1816,-84 1816,-84 1816,-96 1816,-96 1816,-102 1810,-108 1804,-108"/>
-<text text-anchor="middle" x="1760" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
-<text text-anchor="middle" x="1760" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: single_end</text>
+<g id="node9" class="node"><title>8</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M841.5,-108C841.5,-108 720.5,-108 720.5,-108 714.5,-108 708.5,-102 708.5,-96 708.5,-96 708.5,-84 708.5,-84 708.5,-78 714.5,-72 720.5,-72 720.5,-72 841.5,-72 841.5,-72 847.5,-72 853.5,-78 853.5,-84 853.5,-84 853.5,-96 853.5,-96 853.5,-102 847.5,-108 841.5,-108"/>
+<text text-anchor="middle" x="781" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="781" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
<!-- 8->0 -->
-<g id="edge8" class="edge">
-<title>8->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1703.7757,-73.7502C1700.819,-73.109 1697.8809,-72.5194 1695,-72 1475.7405,-32.4691 1207.5916,-21.6058 1110.4092,-18.8593"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1110.3032,-15.3553 1100.2122,-18.5836 1110.1139,-22.3527 1110.3032,-15.3553"/>
+<g id="edge8" class="edge"><title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M842.811,-71.9656C891.409,-58.5722 957.482,-40.3633 998.132,-29.1604"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="999.183,-32.5015 1007.89,-26.4704 997.323,-25.7531 999.183,-32.5015"/>
+</g>
+<!-- 9 -->
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1014.5,-108C1014.5,-108 883.5,-108 883.5,-108 877.5,-108 871.5,-102 871.5,-96 871.5,-96 871.5,-84 871.5,-84 871.5,-78 877.5,-72 883.5,-72 883.5,-72 1014.5,-72 1014.5,-72 1020.5,-72 1026.5,-78 1026.5,-84 1026.5,-84 1026.5,-96 1026.5,-96 1026.5,-102 1020.5,-108 1014.5,-108"/>
+<text text-anchor="middle" x="949" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="949" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g>
<!-- 9->0 -->
-<g id="edge9" class="edge">
-<title>9->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1260.9861,-71.9243C1213.2951,-58.244 1149.4414,-39.9274 1109.7811,-28.5508"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1110.578,-25.1383 1100.0006,-25.7452 1108.6478,-31.8669 1110.578,-25.1383"/>
+<g id="edge9" class="edge"><title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M970.258,-71.6966C981.089,-62.8807 994.418,-52.0321 1006.16,-42.4742"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1008.44,-45.1316 1013.99,-36.1043 1004.02,-39.7026 1008.44,-45.1316"/>
+</g>
+<!-- 10 -->
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M1187.5,-108C1187.5,-108 1056.5,-108 1056.5,-108 1050.5,-108 1044.5,-102 1044.5,-96 1044.5,-96 1044.5,-84 1044.5,-84 1044.5,-78 1050.5,-72 1056.5,-72 1056.5,-72 1187.5,-72 1187.5,-72 1193.5,-72 1199.5,-78 1199.5,-84 1199.5,-84 1199.5,-96 1199.5,-96 1199.5,-102 1193.5,-108 1187.5,-108"/>
+<text text-anchor="middle" x="1122" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1122" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g>
<!-- 10->0 -->
-<g id="edge10" class="edge">
-<title>10->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M882.7671,-71.9243C931.1305,-58.215 995.9194,-39.8496 1036.0346,-28.4784"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1037.0103,-31.8398 1045.6767,-25.7452 1035.1012,-25.1051 1037.0103,-31.8398"/>
+<g id="edge10" class="edge"><title>10->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1100.49,-71.6966C1089.54,-62.8807 1076.05,-52.0321 1064.18,-42.4742"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1066.24,-39.6462 1056.26,-36.1043 1061.86,-45.1001 1066.24,-39.6462"/>
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+<!-- 11 -->
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M1545.5,-108C1545.5,-108 1514.5,-108 1514.5,-108 1508.5,-108 1502.5,-102 1502.5,-96 1502.5,-96 1502.5,-84 1502.5,-84 1502.5,-78 1508.5,-72 1514.5,-72 1514.5,-72 1545.5,-72 1545.5,-72 1551.5,-72 1557.5,-78 1557.5,-84 1557.5,-84 1557.5,-96 1557.5,-96 1557.5,-102 1551.5,-108 1545.5,-108"/>
+<text text-anchor="middle" x="1530" y="-87.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 11->0 -->
-<g id="edge11" class="edge">
-<title>11->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1008.7014,-71.8314C1019.1921,-63.0485 1031.9455,-52.3712 1043.3194,-42.8489"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1045.8847,-45.2659 1051.3055,-36.1628 1041.3911,-39.8986 1045.8847,-45.2659"/>
+<g id="edge11" class="edge"><title>11->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1502.48,-75.2191C1499.33,-73.9871 1496.13,-72.8766 1493,-72 1341.16,-29.4948 1151.82,-21.0221 1072.59,-19.3746"/>
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+<!-- 12 -->
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M1762.5,-108C1762.5,-108 1731.5,-108 1731.5,-108 1725.5,-108 1719.5,-102 1719.5,-96 1719.5,-96 1719.5,-84 1719.5,-84 1719.5,-78 1725.5,-72 1731.5,-72 1731.5,-72 1762.5,-72 1762.5,-72 1768.5,-72 1774.5,-78 1774.5,-84 1774.5,-84 1774.5,-96 1774.5,-96 1774.5,-102 1768.5,-108 1762.5,-108"/>
+<text text-anchor="middle" x="1747" y="-87.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 12->0 -->
-<g id="edge12" class="edge">
-<title>12->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1138.0462,-71.8314C1127.3305,-62.9632 1114.2811,-52.1637 1102.691,-42.5718"/>
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+<g id="edge12" class="edge"><title>12->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1719.31,-78.2242C1712.14,-75.8128 1704.36,-73.5217 1697,-72 1462.81,-23.5966 1173.55,-18.8355 1072.18,-18.772"/>
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-<g id="node14" class="node">
-<title>13</title>
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-<text text-anchor="middle" x="1502" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_paired_end</text>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M910,-326.5C910,-326.5 798,-326.5 798,-326.5 792,-326.5 786,-320.5 786,-314.5 786,-314.5 786,-302.5 786,-302.5 786,-296.5 792,-290.5 798,-290.5 798,-290.5 910,-290.5 910,-290.5 916,-290.5 922,-296.5 922,-302.5 922,-302.5 922,-314.5 922,-314.5 922,-320.5 916,-326.5 910,-326.5"/>
+<text text-anchor="middle" x="854" y="-306" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+</g>
+<!-- 13->3 -->
+<g id="edge13" class="edge"><title>13->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M816.97,-290.282C796.361,-280.126 770.587,-266.455 749,-252 719.625,-232.331 688.877,-206.074 667.92,-187.184"/>
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-<title>13->0</title>
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+<!-- 16 -->
+<g id="node17" class="node"><title>16</title>
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+<text text-anchor="middle" x="1315" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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+<!-- 13->16 -->
+<g id="edge39" class="edge"><title>13->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M922.353,-290.735C926.962,-289.762 931.542,-288.84 936,-288 1044.5,-267.56 1171.85,-251.323 1247.85,-242.446"/>
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+<g id="node22" class="node"><title>21</title>
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+<text text-anchor="middle" x="976" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+</g>
+<!-- 13->21 -->
+<g id="edge44" class="edge"><title>13->21</title>
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<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#56d873" stroke-width="2" d="M1929.5,-108C1929.5,-108 1846.5,-108 1846.5,-108 1840.5,-108 1834.5,-102 1834.5,-96 1834.5,-96 1834.5,-84 1834.5,-84 1834.5,-78 1840.5,-72 1846.5,-72 1846.5,-72 1929.5,-72 1929.5,-72 1935.5,-72 1941.5,-78 1941.5,-84 1941.5,-84 1941.5,-96 1941.5,-96 1941.5,-102 1935.5,-108 1929.5,-108"/>
-<text text-anchor="middle" x="1888" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_single_end</text>
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M854,-252C854,-252 770,-252 770,-252 764,-252 758,-246 758,-240 758,-240 758,-228 758,-228 758,-222 764,-216 770,-216 770,-216 854,-216 854,-216 860,-216 866,-222 866,-228 866,-228 866,-240 866,-240 866,-246 860,-252 854,-252"/>
+<text text-anchor="middle" x="812" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+</g>
+<!-- 14->3 -->
+<g id="edge14" class="edge"><title>14->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M770.413,-215.876C746.967,-206.222 717.496,-194.087 692.703,-183.878"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="694.031,-180.639 683.452,-180.068 691.366,-187.112 694.031,-180.639"/>
</g>
-<!-- 14->0 -->
-<g id="edge14" class="edge">
-<title>14->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1834.2148,-73.8421C1831.1116,-73.1569 1828.0244,-72.5347 1825,-72 1685.2143,-47.2858 1242.4607,-25.6858 1110.482,-19.6645"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1110.25,-16.1505 1100.1017,-19.1939 1109.9329,-23.1433 1110.25,-16.1505"/>
+<!-- 14->4 -->
+<g id="edge16" class="edge"><title>14->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M813.483,-215.697C814.144,-207.983 814.939,-198.712 815.676,-190.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="819.167,-190.367 816.534,-180.104 812.193,-189.769 819.167,-190.367"/>
</g>
<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#56a9d8" stroke-width="2" d="M918,-326.5C918,-326.5 806,-326.5 806,-326.5 800,-326.5 794,-320.5 794,-314.5 794,-314.5 794,-302.5 794,-302.5 794,-296.5 800,-290.5 806,-290.5 806,-290.5 918,-290.5 918,-290.5 924,-290.5 930,-296.5 930,-302.5 930,-302.5 930,-314.5 930,-314.5 930,-320.5 924,-326.5 918,-326.5"/>
-<text text-anchor="middle" x="862" y="-306" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
-</g>
-<!-- 15->3 -->
-<g id="edge15" class="edge">
-<title>15->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M877.5786,-290.2419C899.5931,-264.4409 939.9104,-217.189 964.9793,-187.8083"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="967.7895,-189.907 971.6177,-180.028 962.4644,-185.3634 967.7895,-189.907"/>
-</g>
-<!-- 15->5 -->
-<g id="edge19" class="edge">
-<title>15->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M825.7098,-290.3394C805.8181,-279.9088 781.007,-266.1075 760,-252 729.9375,-231.8113 697.9539,-205.5778 675.8955,-186.6474"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="678.0935,-183.921 668.2397,-180.0282 673.5152,-189.2163 678.0935,-183.921"/>
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#56d87b" stroke-width="2" d="M1202,-326.5C1202,-326.5 1106,-326.5 1106,-326.5 1100,-326.5 1094,-320.5 1094,-314.5 1094,-314.5 1094,-302.5 1094,-302.5 1094,-296.5 1100,-290.5 1106,-290.5 1106,-290.5 1202,-290.5 1202,-290.5 1208,-290.5 1214,-296.5 1214,-302.5 1214,-302.5 1214,-314.5 1214,-314.5 1214,-320.5 1208,-326.5 1202,-326.5"/>
+<text text-anchor="middle" x="1154" y="-306" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+</g>
+<!-- 15->4 -->
+<g id="edge15" class="edge"><title>15->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1093.95,-291.497C1036.84,-276.202 958.661,-255.033 952,-252 913.239,-234.354 873.108,-206.15 846.993,-186.228"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="849.08,-183.417 839.026,-180.075 844.801,-188.957 849.08,-183.417"/>
+</g>
+<!-- 19 -->
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M1668.5,-252C1668.5,-252 1595.5,-252 1595.5,-252 1589.5,-252 1583.5,-246 1583.5,-240 1583.5,-240 1583.5,-228 1583.5,-228 1583.5,-222 1589.5,-216 1595.5,-216 1595.5,-216 1668.5,-216 1668.5,-216 1674.5,-216 1680.5,-222 1680.5,-228 1680.5,-228 1680.5,-240 1680.5,-240 1680.5,-246 1674.5,-252 1668.5,-252"/>
+<text text-anchor="middle" x="1632" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
+</g>
+<!-- 15->19 -->
+<g id="edge42" class="edge"><title>15->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1214.06,-298.391C1306.38,-284.388 1482.06,-257.742 1573.46,-243.879"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1574.01,-247.335 1583.38,-242.375 1572.96,-240.414 1574.01,-247.335"/>
</g>
<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1455.5,-252C1455.5,-252 1366.5,-252 1366.5,-252 1360.5,-252 1354.5,-246 1354.5,-240 1354.5,-240 1354.5,-228 1354.5,-228 1354.5,-222 1360.5,-216 1366.5,-216 1366.5,-216 1455.5,-216 1455.5,-216 1461.5,-216 1467.5,-222 1467.5,-228 1467.5,-228 1467.5,-240 1467.5,-240 1467.5,-246 1461.5,-252 1455.5,-252"/>
-<text text-anchor="middle" x="1411" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M1158.5,-180C1158.5,-180 1071.5,-180 1071.5,-180 1065.5,-180 1059.5,-174 1059.5,-168 1059.5,-168 1059.5,-156 1059.5,-156 1059.5,-150 1065.5,-144 1071.5,-144 1071.5,-144 1158.5,-144 1158.5,-144 1164.5,-144 1170.5,-150 1170.5,-156 1170.5,-156 1170.5,-168 1170.5,-168 1170.5,-174 1164.5,-180 1158.5,-180"/>
+<text text-anchor="middle" x="1115" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
<!-- 15->22 -->
-<g id="edge46" class="edge">
-<title>15->22</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M930.3123,-290.7169C934.9305,-289.7326 939.5245,-288.8146 944,-288 1085.2977,-262.2809 1252.997,-246.4049 1344.041,-238.9922"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1344.5331,-242.464 1354.22,-238.1727 1343.9713,-235.4865 1344.5331,-242.464"/>
-</g>
-<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M1068.5,-252C1068.5,-252 983.5,-252 983.5,-252 977.5,-252 971.5,-246 971.5,-240 971.5,-240 971.5,-228 971.5,-228 971.5,-222 977.5,-216 983.5,-216 983.5,-216 1068.5,-216 1068.5,-216 1074.5,-216 1080.5,-222 1080.5,-228 1080.5,-228 1080.5,-240 1080.5,-240 1080.5,-246 1074.5,-252 1068.5,-252"/>
-<text text-anchor="middle" x="1026" y="-237" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
-<text text-anchor="middle" x="1026" y="-226" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
-</g>
-<!-- 16->3 -->
-<g id="edge16" class="edge">
-<title>16->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1016.1587,-215.8314C1011.8043,-207.7925 1006.5902,-198.1666 1001.7831,-189.2918"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1004.8143,-187.5392 996.9739,-180.4133 998.6592,-190.8732 1004.8143,-187.5392"/>
-</g>
-<!-- 16->4 -->
-<g id="edge18" class="edge">
-<title>16->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1059.8139,-215.8314C1077.2707,-206.4516 1098.7487,-194.9112 1117.3352,-184.9244"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1119.0446,-187.9792 1126.197,-180.1628 1115.7314,-181.8129 1119.0446,-187.9792"/>
+<g id="edge46" class="edge"><title>15->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1149.37,-290.357C1142.69,-265.588 1130.26,-219.546 1122.32,-190.135"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1125.61,-188.864 1119.62,-180.121 1118.85,-190.688 1125.61,-188.864"/>
</g>
-<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M1210,-326.5C1210,-326.5 1114,-326.5 1114,-326.5 1108,-326.5 1102,-320.5 1102,-314.5 1102,-314.5 1102,-302.5 1102,-302.5 1102,-296.5 1108,-290.5 1114,-290.5 1114,-290.5 1210,-290.5 1210,-290.5 1216,-290.5 1222,-296.5 1222,-302.5 1222,-302.5 1222,-314.5 1222,-314.5 1222,-320.5 1216,-326.5 1210,-326.5"/>
-<text text-anchor="middle" x="1162" y="-306" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
-</g>
-<!-- 17->4 -->
-<g id="edge17" class="edge">
-<title>17->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1161.7507,-290.2419C1161.4075,-265.1025 1160.7863,-219.5981 1160.3837,-190.1029"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1163.8824,-189.9793 1160.2461,-180.028 1156.883,-190.0749 1163.8824,-189.9793"/>
-</g>
-<!-- 17->6 -->
-<g id="edge21" class="edge">
-<title>17->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1101.7546,-291.9557C1045.2913,-276.3765 968.5797,-254.9907 962,-252 922.9956,-234.2714 882.3898,-206.4771 855.4101,-186.4657"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="857.2474,-183.4685 847.1486,-180.2647 853.0452,-189.0669 857.2474,-183.4685"/>
+<!-- 16->5 -->
+<g id="edge17" class="edge"><title>16->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1261.78,-215.963C1245.11,-207.835 1228.58,-196.231 1219,-180 1210.87,-166.221 1209.15,-156.611 1219,-144 1257.7,-94.4397 1295.38,-121.499 1361.95,-107.991"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1363.03,-111.337 1371.99,-105.69 1361.46,-104.514 1363.03,-111.337"/>
</g>
-<!-- 23 -->
-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M1752.5,-252C1752.5,-252 1679.5,-252 1679.5,-252 1673.5,-252 1667.5,-246 1667.5,-240 1667.5,-240 1667.5,-228 1667.5,-228 1667.5,-222 1673.5,-216 1679.5,-216 1679.5,-216 1752.5,-216 1752.5,-216 1758.5,-216 1764.5,-222 1764.5,-228 1764.5,-228 1764.5,-240 1764.5,-240 1764.5,-246 1758.5,-252 1752.5,-252"/>
-<text text-anchor="middle" x="1716" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<!-- 16->11 -->
+<g id="edge31" class="edge"><title>16->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1350.89,-215.807C1369.48,-206.262 1392.16,-193.588 1411,-180 1430.13,-166.199 1431.44,-158.561 1450,-144 1463.79,-133.184 1479.75,-122.31 1493.77,-113.251"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1495.67,-116.192 1502.21,-107.861 1491.9,-110.292 1495.67,-116.192"/>
</g>
-<!-- 17->23 -->
-<g id="edge48" class="edge">
-<title>17->23</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1222.078,-300.4209C1329.0221,-286.0395 1551.1122,-256.1735 1657.1603,-241.9126"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1657.9155,-245.3426 1667.3598,-240.541 1656.9825,-238.405 1657.9155,-245.3426"/>
+<!-- 17 -->
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1390,-180C1390,-180 1240,-180 1240,-180 1234,-180 1228,-174 1228,-168 1228,-168 1228,-156 1228,-156 1228,-150 1234,-144 1240,-144 1240,-144 1390,-144 1390,-144 1396,-144 1402,-150 1402,-156 1402,-156 1402,-168 1402,-168 1402,-174 1396,-180 1390,-180"/>
+<text text-anchor="middle" x="1315" y="-165" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1315" y="-154" font-family="sans" font-size="10.00">seqmode: paired_end</text>
+</g>
+<!-- 16->17 -->
+<g id="edge40" class="edge"><title>16->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1315,-215.697C1315,-207.983 1315,-198.712 1315,-190.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1318.5,-190.104 1315,-180.104 1311.5,-190.104 1318.5,-190.104"/>
+</g>
+<!-- 17->5 -->
+<g id="edge18" class="edge"><title>17->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1342.64,-143.876C1357.42,-134.724 1375.79,-123.342 1391.7,-113.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1393.59,-116.431 1400.25,-108.19 1389.91,-110.481 1393.59,-116.431"/>
+</g>
+<!-- 17->11 -->
+<g id="edge32" class="edge"><title>17->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1380.41,-143.913C1414.38,-134.442 1456.34,-121.802 1493,-108 1493.1,-107.964 1493.19,-107.928 1493.29,-107.892"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1494.35,-111.239 1502.3,-104.238 1491.72,-104.752 1494.35,-111.239"/>
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<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M865,-252C865,-252 781,-252 781,-252 775,-252 769,-246 769,-240 769,-240 769,-228 769,-228 769,-222 775,-216 781,-216 781,-216 865,-216 865,-216 871,-216 877,-222 877,-228 877,-228 877,-240 877,-240 877,-246 871,-252 865,-252"/>
-<text text-anchor="middle" x="823" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M1591.5,-180C1591.5,-180 1470.5,-180 1470.5,-180 1464.5,-180 1458.5,-174 1458.5,-168 1458.5,-168 1458.5,-156 1458.5,-156 1458.5,-150 1464.5,-144 1470.5,-144 1470.5,-144 1591.5,-144 1591.5,-144 1597.5,-144 1603.5,-150 1603.5,-156 1603.5,-156 1603.5,-168 1603.5,-168 1603.5,-174 1597.5,-180 1591.5,-180"/>
+<text text-anchor="middle" x="1531" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 18->5 -->
-<g id="edge20" class="edge">
-<title>18->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M778.8401,-215.8314C755.2268,-206.1162 725.9798,-194.0831 701.13,-183.8592"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="702.4219,-180.6061 691.8423,-180.038 699.7585,-187.0797 702.4219,-180.6061"/>
+<g id="edge19" class="edge"><title>18->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1505.8,-143.876C1492.59,-134.893 1476.21,-123.763 1461.89,-114.034"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1463.53,-110.916 1453.29,-108.19 1459.6,-116.705 1463.53,-110.916"/>
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<!-- 18->6 -->
-<g id="edge22" class="edge">
-<title>18->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M823.2523,-215.8314C823.3593,-208.131 823.4865,-198.9743 823.6053,-190.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="827.1049,-190.4609 823.7443,-180.4133 820.1056,-190.3637 827.1049,-190.4609"/>
+<g id="edge22" class="edge"><title>18->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1555.71,-143.876C1568.67,-134.893 1584.73,-123.763 1598.77,-114.034"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1600.97,-116.763 1607.2,-108.19 1596.98,-111.009 1600.97,-116.763"/>
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-<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M1556,-180C1556,-180 1390,-180 1390,-180 1384,-180 1378,-174 1378,-168 1378,-168 1378,-156 1378,-156 1378,-150 1384,-144 1390,-144 1390,-144 1556,-144 1556,-144 1562,-144 1568,-150 1568,-156 1568,-156 1568,-168 1568,-168 1568,-174 1562,-180 1556,-180"/>
-<text text-anchor="middle" x="1473" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
-</g>
-<!-- 19->7 -->
-<g id="edge23" class="edge">
-<title>19->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1512.6177,-143.8314C1533.5222,-134.2446 1559.3483,-122.4008 1581.4488,-112.2655"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1583.0364,-115.388 1590.6672,-108.038 1580.1184,-109.0252 1583.0364,-115.388"/>
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-<!-- 19->13 -->
-<g id="edge36" class="edge">
-<title>19->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1480.3179,-143.8314C1483.4876,-135.9617 1487.27,-126.5712 1490.7813,-117.8533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1494.0939,-118.9968 1494.5835,-108.4133 1487.6008,-116.3815 1494.0939,-118.9968"/>
+<!-- 19->6 -->
+<g id="edge20" class="edge"><title>19->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1632,-215.871C1632,-191.67 1632,-147.211 1632,-118.393"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1635.5,-118.189 1632,-108.189 1628.5,-118.189 1635.5,-118.189"/>
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-<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M1719.5,-180C1719.5,-180 1598.5,-180 1598.5,-180 1592.5,-180 1586.5,-174 1586.5,-168 1586.5,-168 1586.5,-156 1586.5,-156 1586.5,-150 1592.5,-144 1598.5,-144 1598.5,-144 1719.5,-144 1719.5,-144 1725.5,-144 1731.5,-150 1731.5,-156 1731.5,-156 1731.5,-168 1731.5,-168 1731.5,-174 1725.5,-180 1719.5,-180"/>
-<text text-anchor="middle" x="1659" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
-</g>
-<!-- 20->7 -->
-<g id="edge24" class="edge">
-<title>20->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1651.6821,-143.8314C1648.5124,-135.9617 1644.73,-126.5712 1641.2187,-117.8533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1644.3992,-116.3815 1637.4165,-108.4133 1637.9061,-118.9968 1644.3992,-116.3815"/>
-</g>
-<!-- 20->8 -->
-<g id="edge26" class="edge">
-<title>20->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1684.4866,-143.8314C1697.1659,-134.7927 1712.6596,-123.7476 1726.3055,-114.0198"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1728.4105,-116.8176 1734.5216,-108.1628 1724.3471,-111.1176 1728.4105,-116.8176"/>
+<!-- 19->12 -->
+<g id="edge33" class="edge"><title>19->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1680.75,-227.646C1736.69,-220.381 1823.26,-205.316 1843,-180 1852.84,-167.383 1851.13,-157.779 1843,-144 1830.39,-122.628 1805.73,-109.279 1784.56,-101.324"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1785.42,-97.9183 1774.83,-97.9398 1783.12,-104.53 1785.42,-97.9183"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1912,-180C1912,-180 1762,-180 1762,-180 1756,-180 1750,-174 1750,-168 1750,-168 1750,-156 1750,-156 1750,-150 1756,-144 1762,-144 1762,-144 1912,-144 1912,-144 1918,-144 1924,-150 1924,-156 1924,-156 1924,-168 1924,-168 1924,-174 1918,-180 1912,-180"/>
-<text text-anchor="middle" x="1837" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
+<!-- 20 -->
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1822,-180C1822,-180 1672,-180 1672,-180 1666,-180 1660,-174 1660,-168 1660,-168 1660,-156 1660,-156 1660,-150 1666,-144 1672,-144 1672,-144 1822,-144 1822,-144 1828,-144 1834,-150 1834,-156 1834,-156 1834,-168 1834,-168 1834,-174 1828,-180 1822,-180"/>
+<text text-anchor="middle" x="1747" y="-165" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1747" y="-154" font-family="sans" font-size="10.00">seqmode: single_end</text>
+</g>
+<!-- 19->20 -->
+<g id="edge43" class="edge"><title>19->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1660.13,-215.876C1675.17,-206.724 1693.87,-195.342 1710.06,-185.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1712.04,-188.379 1718.76,-180.19 1708.4,-182.4 1712.04,-188.379"/>
+</g>
+<!-- 20->6 -->
+<g id="edge21" class="edge"><title>20->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1718.87,-143.876C1703.83,-134.724 1685.13,-123.342 1668.94,-113.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1670.6,-110.4 1660.24,-108.19 1666.96,-116.379 1670.6,-110.4"/>
+</g>
+<!-- 20->12 -->
+<g id="edge34" class="edge"><title>20->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1747,-143.697C1747,-135.983 1747,-126.712 1747,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1750.5,-118.104 1747,-108.104 1743.5,-118.104 1750.5,-118.104"/>
+</g>
+<!-- 21->7 -->
+<g id="edge23" class="edge"><title>21->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1039.83,-146.527C1043.61,-145.672 1047.35,-144.824 1051,-144 1103.35,-132.163 1162.27,-118.875 1208.02,-108.565"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1208.88,-111.958 1217.87,-106.345 1207.34,-105.13 1208.88,-111.958"/>
</g>
<!-- 21->8 -->
-<g id="edge25" class="edge">
-<title>21->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1817.5696,-143.8314C1808.268,-135.1337 1796.9796,-124.5783 1786.8714,-115.1265"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1789.1189,-112.4363 1779.4241,-108.1628 1784.3379,-117.5493 1789.1189,-112.4363"/>
-</g>
-<!-- 21->14 -->
-<g id="edge38" class="edge">
-<title>21->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1849.8695,-143.8314C1855.6835,-135.6232 1862.6696,-125.7606 1869.0646,-116.7323"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1872.0331,-118.5966 1874.9573,-108.4133 1866.321,-114.5505 1872.0331,-118.5966"/>
-</g>
-<!-- 22->13 -->
-<g id="edge35" class="edge">
-<title>22->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1391.8604,-215.8802C1374.3626,-197.0568 1353.3998,-167.1709 1369,-144 1377.5714,-131.269 1408.6828,-118.2882 1438.6606,-108.2451"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1439.903,-111.5213 1448.3238,-105.0916 1437.7313,-104.8667 1439.903,-111.5213"/>
-</g>
-<!-- 22->19 -->
-<g id="edge43" class="edge">
-<title>22->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1426.6452,-215.8314C1433.8591,-207.454 1442.557,-197.3531 1450.4605,-188.1749"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1453.2711,-190.2748 1457.1441,-180.4133 1447.9667,-185.7071 1453.2711,-190.2748"/>
-</g>
-<!-- 23->14 -->
-<g id="edge37" class="edge">
-<title>23->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1764.6187,-228.8067C1822.0772,-221.5499 1912.4985,-206.2285 1933,-180 1948.4125,-160.2821 1932.4822,-134.4478 1915.4622,-115.5178"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1917.8661,-112.9664 1908.4443,-108.1207 1912.7879,-117.7842 1917.8661,-112.9664"/>
-</g>
-<!-- 23->21 -->
-<g id="edge44" class="edge">
-<title>23->21</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1746.5334,-215.8314C1762.0101,-206.6221 1780.9869,-195.3301 1797.5563,-185.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1799.6724,-188.2843 1806.4764,-180.1628 1796.0929,-182.2687 1799.6724,-188.2843"/>
+<g id="edge25" class="edge"><title>21->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M928.298,-143.876C901.048,-134.094 866.703,-121.765 838.034,-111.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="839.142,-108.153 828.547,-108.068 836.777,-114.741 839.142,-108.153"/>
+</g>
+<!-- 21->9 -->
+<g id="edge27" class="edge"><title>21->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M969.326,-143.697C966.285,-135.813 962.617,-126.304 959.239,-117.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="962.462,-116.175 955.597,-108.104 955.931,-118.694 962.462,-116.175"/>
+</g>
+<!-- 21->10 -->
+<g id="edge29" class="edge"><title>21->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1011.72,-143.876C1031.5,-134.392 1056.27,-122.513 1077.33,-112.419"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1078.9,-115.548 1086.4,-108.068 1075.87,-109.236 1078.9,-115.548"/>
+</g>
+<!-- 22->7 -->
+<g id="edge24" class="edge"><title>22->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1156.83,-143.876C1180.42,-134.222 1210.06,-122.087 1235,-111.878"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1236.38,-115.096 1244.3,-108.068 1233.72,-108.618 1236.38,-115.096"/>
+</g>
+<!-- 22->8 -->
+<g id="edge26" class="edge"><title>22->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1059.24,-146.384C1055.78,-145.556 1052.35,-144.754 1049,-144 969.907,-126.177 947.224,-124.641 863.791,-108.136"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="864.358,-104.68 853.867,-106.159 862.991,-111.545 864.358,-104.68"/>
+</g>
+<!-- 22->9 -->
+<g id="edge28" class="edge"><title>22->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1074.39,-143.876C1051.6,-134.264 1022.97,-122.193 998.83,-112.013"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1000.05,-108.729 989.476,-108.068 997.331,-115.179 1000.05,-108.729"/>
+</g>
+<!-- 22->10 -->
+<g id="edge30" class="edge"><title>22->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1116.73,-143.697C1117.5,-135.983 1118.43,-126.712 1119.29,-118.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1122.78,-118.403 1120.29,-108.104 1115.81,-117.706 1122.78,-118.403"/>
+</g>
+<!-- 23 -->
+<g id="node24" class="node"><title>23</title>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M975,-401C975,-401 707,-401 707,-401 701,-401 695,-395 695,-389 695,-389 695,-377 695,-377 695,-371 701,-365 707,-365 707,-365 975,-365 975,-365 981,-365 987,-371 987,-377 987,-377 987,-389 987,-389 987,-395 981,-401 975,-401"/>
+<text text-anchor="middle" x="841" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="841" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 23->13 -->
+<g id="edge35" class="edge"><title>23->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M844.081,-364.819C845.586,-356.422 847.434,-346.116 849.125,-336.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="852.621,-337.019 850.941,-326.558 845.731,-335.783 852.621,-337.019"/>
</g>
<!-- 24 -->
-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M983,-401C983,-401 715,-401 715,-401 709,-401 703,-395 703,-389 703,-389 703,-377 703,-377 703,-371 709,-365 715,-365 715,-365 983,-365 983,-365 989,-365 995,-371 995,-377 995,-377 995,-389 995,-389 995,-395 989,-401 983,-401"/>
-<text text-anchor="middle" x="849" y="-386" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="849" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
-</g>
-<!-- 24->15 -->
-<g id="edge39" class="edge">
-<title>24->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M852.1469,-364.9656C853.6369,-356.427 855.4506,-346.0333 857.1138,-336.502"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="860.5658,-337.0793 858.837,-326.6265 853.67,-335.876 860.5658,-337.0793"/>
+<g id="node25" class="node"><title>24</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1057.5,-326.5C1057.5,-326.5 956.5,-326.5 956.5,-326.5 950.5,-326.5 944.5,-320.5 944.5,-314.5 944.5,-314.5 944.5,-302.5 944.5,-302.5 944.5,-296.5 950.5,-290.5 956.5,-290.5 956.5,-290.5 1057.5,-290.5 1057.5,-290.5 1063.5,-290.5 1069.5,-296.5 1069.5,-302.5 1069.5,-302.5 1069.5,-314.5 1069.5,-314.5 1069.5,-320.5 1063.5,-326.5 1057.5,-326.5"/>
+<text text-anchor="middle" x="1007" y="-311.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<text text-anchor="middle" x="1007" y="-300.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 24->14 -->
+<g id="edge36" class="edge"><title>24->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M960.788,-290.319C932.86,-279.935 897.084,-266.634 867.613,-255.677"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="868.473,-252.263 857.881,-252.058 866.034,-258.824 868.473,-252.263"/>
+</g>
+<!-- 27 -->
+<g id="node28" class="node"><title>27</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1057.5,-252C1057.5,-252 972.5,-252 972.5,-252 966.5,-252 960.5,-246 960.5,-240 960.5,-240 960.5,-228 960.5,-228 960.5,-222 966.5,-216 972.5,-216 972.5,-216 1057.5,-216 1057.5,-216 1063.5,-216 1069.5,-222 1069.5,-228 1069.5,-228 1069.5,-240 1069.5,-240 1069.5,-246 1063.5,-252 1057.5,-252"/>
+<text text-anchor="middle" x="1015" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="1015" y="-226" font-family="sans" font-size="10.00">kmer: 31</text>
+</g>
+<!-- 24->27 -->
+<g id="edge48" class="edge"><title>24->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1008.9,-290.319C1009.82,-281.922 1010.96,-271.616 1012,-262.186"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1015.5,-262.382 1013.12,-252.058 1008.54,-261.614 1015.5,-262.382"/>
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<!-- 25 -->
-<g id="node26" class="node">
-<title>25</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1066.5,-326.5C1066.5,-326.5 965.5,-326.5 965.5,-326.5 959.5,-326.5 953.5,-320.5 953.5,-314.5 953.5,-314.5 953.5,-302.5 953.5,-302.5 953.5,-296.5 959.5,-290.5 965.5,-290.5 965.5,-290.5 1066.5,-290.5 1066.5,-290.5 1072.5,-290.5 1078.5,-296.5 1078.5,-302.5 1078.5,-302.5 1078.5,-314.5 1078.5,-314.5 1078.5,-320.5 1072.5,-326.5 1066.5,-326.5"/>
-<text text-anchor="middle" x="1016" y="-311.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
-<text text-anchor="middle" x="1016" y="-300.5" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
-</g>
-<!-- 25->16 -->
-<g id="edge40" class="edge">
-<title>25->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1018.4207,-290.4656C1019.5547,-282.0178 1020.9323,-271.7542 1022.2005,-262.3064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1025.7054,-262.5033 1023.5669,-252.1265 1018.7676,-261.572 1025.7054,-262.5033"/>
-</g>
-<!-- 25->18 -->
-<g id="edge42" class="edge">
-<title>25->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M969.2801,-290.4656C942.218,-280.0194 907.9633,-266.7967 879.4062,-255.7734"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="880.5481,-252.4625 869.9586,-252.1265 878.0273,-258.9929 880.5481,-252.4625"/>
+<g id="node26" class="node"><title>25</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M1297,-401C1297,-401 1017,-401 1017,-401 1011,-401 1005,-395 1005,-389 1005,-389 1005,-377 1005,-377 1005,-371 1011,-365 1017,-365 1017,-365 1297,-365 1297,-365 1303,-365 1309,-371 1309,-377 1309,-377 1309,-389 1309,-389 1309,-395 1303,-401 1297,-401"/>
+<text text-anchor="middle" x="1157" y="-386" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1157" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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-<!-- 26 -->
-<g id="node27" class="node">
-<title>26</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M1305,-401C1305,-401 1025,-401 1025,-401 1019,-401 1013,-395 1013,-389 1013,-389 1013,-377 1013,-377 1013,-371 1019,-365 1025,-365 1025,-365 1305,-365 1305,-365 1311,-365 1317,-371 1317,-377 1317,-377 1317,-389 1317,-389 1317,-395 1311,-401 1305,-401"/>
-<text text-anchor="middle" x="1165" y="-386" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1165" y="-375" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
-</g>
-<!-- 26->17 -->
-<g id="edge41" class="edge">
-<title>26->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1164.2738,-364.9656C1163.9336,-356.5178 1163.5203,-346.2542 1163.1399,-336.8064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1166.6295,-336.4776 1162.7299,-326.6265 1159.6352,-336.7593 1166.6295,-336.4776"/>
+<!-- 25->15 -->
+<g id="edge37" class="edge"><title>25->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1156.29,-364.819C1155.94,-356.422 1155.52,-346.116 1155.12,-336.686"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1158.62,-336.405 1154.71,-326.558 1151.62,-336.694 1158.62,-336.405"/>
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-<!-- 27 -->
-<g id="node28" class="node">
-<title>27</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M1613.5,-329C1613.5,-329 1512.5,-329 1512.5,-329 1506.5,-329 1500.5,-323 1500.5,-317 1500.5,-317 1500.5,-300 1500.5,-300 1500.5,-294 1506.5,-288 1512.5,-288 1512.5,-288 1613.5,-288 1613.5,-288 1619.5,-288 1625.5,-294 1625.5,-300 1625.5,-300 1625.5,-317 1625.5,-317 1625.5,-323 1619.5,-329 1613.5,-329"/>
-<text text-anchor="middle" x="1563" y="-317" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
-<text text-anchor="middle" x="1563" y="-306" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
-<text text-anchor="middle" x="1563" y="-295" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
+<!-- 26 -->
+<g id="node27" class="node"><title>26</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M1523.5,-329C1523.5,-329 1422.5,-329 1422.5,-329 1416.5,-329 1410.5,-323 1410.5,-317 1410.5,-317 1410.5,-300 1410.5,-300 1410.5,-294 1416.5,-288 1422.5,-288 1422.5,-288 1523.5,-288 1523.5,-288 1529.5,-288 1535.5,-294 1535.5,-300 1535.5,-300 1535.5,-317 1535.5,-317 1535.5,-323 1529.5,-329 1523.5,-329"/>
+<text text-anchor="middle" x="1473" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1473" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1473" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 26->16 -->
+<g id="edge38" class="edge"><title>26->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1430.24,-287.88C1408.99,-278.127 1383.26,-266.323 1361.51,-256.343"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1362.7,-253.035 1352.15,-252.046 1359.78,-259.397 1362.7,-253.035"/>
+</g>
+<!-- 26->19 -->
+<g id="edge41" class="edge"><title>26->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1516.03,-287.88C1537.51,-278.083 1563.54,-266.217 1585.49,-256.209"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1586.97,-259.379 1594.62,-252.046 1584.07,-253.01 1586.97,-259.379"/>
+</g>
+<!-- 27->21 -->
+<g id="edge45" class="edge"><title>27->21</title>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 9ba29ef63af3646654959d2305a4f8db3cfc8a20..a2a0d009dcc914acf858cb6594e35f11f4f963cf 100644
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+<g id="edge3" class="edge"><title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M632.418,-83.7958C566.659,-71.3886 400.61,-40.0585 326.141,-26.0077"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="326.736,-22.5583 316.261,-24.1435 325.438,-29.437 326.736,-22.5583"/>
+</g>
+<!-- 9 -->
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M649,-324C649,-324 537,-324 537,-324 531,-324 525,-318 525,-312 525,-312 525,-300 525,-300 525,-294 531,-288 537,-288 537,-288 649,-288 649,-288 655,-288 661,-294 661,-300 661,-300 661,-312 661,-312 661,-318 655,-324 649,-324"/>
+<text text-anchor="middle" x="593" y="-303.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
+</g>
+<!-- 9->3 -->
+<g id="edge9" class="edge"><title>9->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M524.947,-290.684C520.566,-289.772 516.222,-288.872 512,-288 456.398,-276.52 394.088,-263.859 344.297,-253.792"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="344.686,-250.3 334.191,-251.749 343.299,-257.161 344.686,-250.3"/>
</g>
-<!-- 9->0 -->
-<g id="edge5" class="edge">
-<title>9->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M401,-71.8314C401,-64.131 401,-54.9743 401,-46.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="404.5001,-46.4132 401,-36.4133 397.5001,-46.4133 404.5001,-46.4132"/>
+<!-- 12 -->
+<g id="node13" class="node"><title>12</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M870.5,-252C870.5,-252 781.5,-252 781.5,-252 775.5,-252 769.5,-246 769.5,-240 769.5,-240 769.5,-228 769.5,-228 769.5,-222 775.5,-216 781.5,-216 781.5,-216 870.5,-216 870.5,-216 876.5,-216 882.5,-222 882.5,-228 882.5,-228 882.5,-240 882.5,-240 882.5,-246 876.5,-252 870.5,-252"/>
+<text text-anchor="middle" x="826" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+</g>
+<!-- 9->12 -->
+<g id="edge27" class="edge"><title>9->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M649.7,-287.966C682.945,-277.978 725.103,-265.312 759.857,-254.871"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="760.88,-258.219 769.45,-251.989 758.865,-251.515 760.88,-258.219"/>
+</g>
+<!-- 16 -->
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M596.5,-252C596.5,-252 493.5,-252 493.5,-252 487.5,-252 481.5,-246 481.5,-240 481.5,-240 481.5,-228 481.5,-228 481.5,-222 487.5,-216 493.5,-216 493.5,-216 596.5,-216 596.5,-216 602.5,-216 608.5,-222 608.5,-228 608.5,-228 608.5,-240 608.5,-240 608.5,-246 602.5,-252 596.5,-252"/>
+<text text-anchor="middle" x="545" y="-231.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+</g>
+<!-- 9->16 -->
+<g id="edge33" class="edge"><title>9->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M581.135,-287.697C575.497,-279.474 568.646,-269.483 562.431,-260.421"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="565.271,-258.372 556.729,-252.104 559.497,-262.331 565.271,-258.372"/>
</g>
<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M1157.5,-108C1157.5,-108 1074.5,-108 1074.5,-108 1068.5,-108 1062.5,-102 1062.5,-96 1062.5,-96 1062.5,-84 1062.5,-84 1062.5,-78 1068.5,-72 1074.5,-72 1074.5,-72 1157.5,-72 1157.5,-72 1163.5,-72 1169.5,-78 1169.5,-84 1169.5,-84 1169.5,-96 1169.5,-96 1169.5,-102 1163.5,-108 1157.5,-108"/>
-<text text-anchor="middle" x="1116" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_paired_end</text>
+<g id="node11" class="node"><title>10</title>
+<path fill="none" stroke="#d88556" stroke-width="2" d="M226,-324C226,-324 142,-324 142,-324 136,-324 130,-318 130,-312 130,-312 130,-300 130,-300 130,-294 136,-288 142,-288 142,-288 226,-288 226,-288 232,-288 238,-294 238,-300 238,-300 238,-312 238,-312 238,-318 232,-324 226,-324"/>
+<text text-anchor="middle" x="184" y="-303.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+</g>
+<!-- 10->3 -->
+<g id="edge10" class="edge"><title>10->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M200.562,-287.697C208.675,-279.22 218.588,-268.864 227.471,-259.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="230.243,-261.749 234.629,-252.104 225.186,-256.908 230.243,-261.749"/>
</g>
-<!-- 10->0 -->
-<g id="edge11" class="edge">
-<title>10->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1062.2179,-83.3888C1032.9042,-79.857 995.9769,-75.5237 963,-72 765.4177,-50.8876 528.3387,-29.3498 438.2183,-21.2997"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="438.4877,-17.8099 428.2163,-20.4078 437.8659,-24.7822 438.4877,-17.8099"/>
+<!-- 10->4 -->
+<g id="edge11" class="edge"><title>10->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M157.336,-287.876C143.216,-278.808 125.689,-267.552 110.439,-257.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="112.073,-254.648 101.767,-252.19 108.29,-260.538 112.073,-254.648"/>
</g>
<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M784.5,-108C784.5,-108 701.5,-108 701.5,-108 695.5,-108 689.5,-102 689.5,-96 689.5,-96 689.5,-84 689.5,-84 689.5,-78 695.5,-72 701.5,-72 701.5,-72 784.5,-72 784.5,-72 790.5,-72 796.5,-78 796.5,-84 796.5,-84 796.5,-96 796.5,-96 796.5,-102 790.5,-108 784.5,-108"/>
-<text text-anchor="middle" x="743" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">star_rpm_single_end</text>
+<g id="node12" class="node"><title>11</title>
+<path fill="none" stroke="#5682d8" stroke-width="2" d="M364,-324C364,-324 268,-324 268,-324 262,-324 256,-318 256,-312 256,-312 256,-300 256,-300 256,-294 262,-288 268,-288 268,-288 364,-288 364,-288 370,-288 376,-294 376,-300 376,-300 376,-312 376,-312 376,-318 370,-324 364,-324"/>
+<text text-anchor="middle" x="316" y="-303.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
-<!-- 11->0 -->
-<g id="edge6" class="edge">
-<title>11->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M689.2575,-75.4333C684.446,-74.2324 679.6409,-73.0704 675,-72 590.8464,-52.5906 491.1471,-34.0478 438.2775,-24.5626"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="438.8061,-21.1017 428.3464,-22.7887 437.5752,-27.9926 438.8061,-21.1017"/>
+<!-- 11->4 -->
+<g id="edge12" class="edge"><title>11->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M257.353,-287.966C223.094,-278.015 179.684,-265.406 143.814,-254.987"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="144.489,-251.539 133.91,-252.111 142.537,-258.261 144.489,-251.539"/>
</g>
-<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M602,-324C602,-324 490,-324 490,-324 484,-324 478,-318 478,-312 478,-312 478,-300 478,-300 478,-294 484,-288 490,-288 490,-288 602,-288 602,-288 608,-288 614,-294 614,-300 614,-300 614,-312 614,-312 614,-318 608,-324 602,-324"/>
-<text text-anchor="middle" x="546" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
+<!-- 15 -->
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#d86e56" stroke-width="2" d="M739.5,-252C739.5,-252 666.5,-252 666.5,-252 660.5,-252 654.5,-246 654.5,-240 654.5,-240 654.5,-228 654.5,-228 654.5,-222 660.5,-216 666.5,-216 666.5,-216 739.5,-216 739.5,-216 745.5,-216 751.5,-222 751.5,-228 751.5,-228 751.5,-240 751.5,-240 751.5,-246 745.5,-252 739.5,-252"/>
+<text text-anchor="middle" x="703" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
-<!-- 12->3 -->
-<g id="edge13" class="edge">
-<title>12->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M545.8733,-287.7623C545.7028,-263.201 545.3976,-219.2474 545.1969,-190.3541"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="548.6951,-190.065 545.1256,-180.0896 541.6952,-190.1137 548.6951,-190.065"/>
+<!-- 11->15 -->
+<g id="edge32" class="edge"><title>11->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M376.141,-289.854C379.131,-289.204 382.097,-288.582 385,-288 487.311,-267.499 514.24,-270.121 617,-252 625.916,-250.428 635.331,-248.668 644.533,-246.894"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="645.255,-250.319 654.401,-244.97 643.916,-243.448 645.255,-250.319"/>
</g>
-<!-- 12->5 -->
-<g id="edge17" class="edge">
-<title>12->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M489.0978,-287.9875C461.3893,-278.493 427.8994,-265.9316 399,-252 358.6163,-232.5322 315.0772,-205.2176 285.7526,-185.797"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="287.3881,-182.6806 277.1274,-180.0408 283.5023,-188.5031 287.3881,-182.6806"/>
+<!-- 17 -->
+<g id="node18" class="node"><title>17</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M451.5,-252C451.5,-252 364.5,-252 364.5,-252 358.5,-252 352.5,-246 352.5,-240 352.5,-240 352.5,-228 352.5,-228 352.5,-222 358.5,-216 364.5,-216 364.5,-216 451.5,-216 451.5,-216 457.5,-216 463.5,-222 463.5,-228 463.5,-228 463.5,-240 463.5,-240 463.5,-246 457.5,-252 451.5,-252"/>
+<text text-anchor="middle" x="408" y="-231.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M1039.5,-252C1039.5,-252 950.5,-252 950.5,-252 944.5,-252 938.5,-246 938.5,-240 938.5,-240 938.5,-228 938.5,-228 938.5,-222 944.5,-216 950.5,-216 950.5,-216 1039.5,-216 1039.5,-216 1045.5,-216 1051.5,-222 1051.5,-228 1051.5,-228 1051.5,-240 1051.5,-240 1051.5,-246 1045.5,-252 1039.5,-252"/>
-<text text-anchor="middle" x="995" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
+<!-- 11->17 -->
+<g id="edge36" class="edge"><title>11->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M338.742,-287.697C350.44,-278.796 364.861,-267.823 377.51,-258.199"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="379.681,-260.945 385.52,-252.104 375.442,-255.374 379.681,-260.945"/>
</g>
-<!-- 12->19 -->
-<g id="edge37" class="edge">
-<title>12->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M614.1934,-295.0647C699.2963,-281.418 843.8898,-258.2315 928.293,-244.6969"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="928.96,-248.1347 938.2796,-243.0955 927.8516,-241.223 928.96,-248.1347"/>
+<!-- 12->5 -->
+<g id="edge13" class="edge"><title>12->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M882.701,-227.711C942.874,-220.787 1032.12,-206.314 1053,-180 1097.93,-123.369 978.505,-102.581 898.196,-95.0901"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="898.392,-91.5938 888.123,-94.2002 897.776,-98.5667 898.392,-91.5938"/>
+</g>
+<!-- 12->8 -->
+<g id="edge21" class="edge"><title>12->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M828.376,-215.846C830.096,-196.225 829.723,-164.213 813,-144 784.703,-109.797 733.1,-97.6237 697.71,-93.3162"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="698.055,-89.8333 687.741,-92.257 697.316,-96.7942 698.055,-89.8333"/>
</g>
<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#d89556" stroke-width="2" d="M505.5,-252C505.5,-252 420.5,-252 420.5,-252 414.5,-252 408.5,-246 408.5,-240 408.5,-240 408.5,-228 408.5,-228 408.5,-222 414.5,-216 420.5,-216 420.5,-216 505.5,-216 505.5,-216 511.5,-216 517.5,-222 517.5,-228 517.5,-228 517.5,-240 517.5,-240 517.5,-246 511.5,-252 505.5,-252"/>
-<text text-anchor="middle" x="463" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
-</g>
-<!-- 13->3 -->
-<g id="edge12" class="edge">
-<title>13->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M483.6921,-215.8314C493.6948,-207.0485 505.855,-196.3712 516.6999,-186.8489"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="519.1094,-189.3909 524.3146,-180.1628 514.4908,-184.1308 519.1094,-189.3909"/>
-</g>
-<!-- 13->4 -->
-<g id="edge15" class="edge">
-<title>13->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M449.1212,-215.8314C442.7864,-207.5386 435.1616,-197.557 428.2074,-188.4533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="430.9175,-186.2353 422.0657,-180.4133 425.3548,-190.4847 430.9175,-186.2353"/>
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#569ad8" stroke-width="2" d="M792,-180C792,-180 642,-180 642,-180 636,-180 630,-174 630,-168 630,-168 630,-156 630,-156 630,-150 636,-144 642,-144 642,-144 792,-144 792,-144 798,-144 804,-150 804,-156 804,-156 804,-168 804,-168 804,-174 798,-180 792,-180"/>
+<text text-anchor="middle" x="717" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
-<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M431,-324C431,-324 335,-324 335,-324 329,-324 323,-318 323,-312 323,-312 323,-300 323,-300 323,-294 329,-288 335,-288 335,-288 431,-288 431,-288 437,-288 443,-294 443,-300 443,-300 443,-312 443,-312 443,-318 437,-324 431,-324"/>
-<text text-anchor="middle" x="383" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
-</g>
-<!-- 14->4 -->
-<g id="edge14" class="edge">
-<title>14->4</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M386.1663,-287.7623C390.4492,-263.0928 398.1285,-218.8598 403.1436,-189.9731"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="406.5973,-190.541 404.8594,-180.0896 399.7004,-189.3435 406.5973,-190.541"/>
-</g>
-<!-- 14->6 -->
-<g id="edge19" class="edge">
-<title>14->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M322.8075,-290.1425C267.2147,-275.3972 192.2896,-255.2299 186,-252 153.1752,-235.1432 121.024,-207.494 99.8437,-187.2831"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="102.1687,-184.6621 92.5559,-180.2072 97.2925,-189.6843 102.1687,-184.6621"/>
+<!-- 12->13 -->
+<g id="edge29" class="edge"><title>12->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M799.336,-215.876C785.216,-206.808 767.689,-195.552 752.439,-185.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="754.073,-182.648 743.767,-180.19 750.29,-188.538 754.073,-182.648"/>
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-<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#d87d56" stroke-width="2" d="M730.5,-252C730.5,-252 657.5,-252 657.5,-252 651.5,-252 645.5,-246 645.5,-240 645.5,-240 645.5,-228 645.5,-228 645.5,-222 651.5,-216 657.5,-216 657.5,-216 730.5,-216 730.5,-216 736.5,-216 742.5,-222 742.5,-228 742.5,-228 742.5,-240 742.5,-240 742.5,-246 736.5,-252 730.5,-252"/>
-<text text-anchor="middle" x="694" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
+<!-- 13->5 -->
+<g id="edge15" class="edge"><title>13->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M745.132,-143.876C760.168,-134.724 778.867,-123.342 795.06,-113.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="797.038,-116.379 803.76,-108.19 793.398,-110.4 797.038,-116.379"/>
</g>
-<!-- 14->20 -->
-<g id="edge39" class="edge">
-<title>14->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M443.3327,-292.0323C498.7078,-279.2123 580.245,-260.3356 635.1476,-247.625"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="636.124,-250.9916 645.0768,-245.3263 634.5451,-244.172 636.124,-250.9916"/>
+<!-- 13->8 -->
+<g id="edge23" class="edge"><title>13->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M702.91,-143.697C696.077,-135.305 687.743,-125.07 680.244,-115.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="682.956,-113.649 673.928,-108.104 677.528,-118.069 682.956,-113.649"/>
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-<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
-<path fill="none" stroke="#56c1d8" stroke-width="2" d="M291,-252C291,-252 207,-252 207,-252 201,-252 195,-246 195,-240 195,-240 195,-228 195,-228 195,-222 201,-216 207,-216 207,-216 291,-216 291,-216 297,-216 303,-222 303,-228 303,-228 303,-240 303,-240 303,-246 297,-252 291,-252"/>
-<text text-anchor="middle" x="249" y="-231.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
+<!-- 14 -->
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M1031.5,-180C1031.5,-180 910.5,-180 910.5,-180 904.5,-180 898.5,-174 898.5,-168 898.5,-168 898.5,-156 898.5,-156 898.5,-150 904.5,-144 910.5,-144 910.5,-144 1031.5,-144 1031.5,-144 1037.5,-144 1043.5,-150 1043.5,-156 1043.5,-156 1043.5,-168 1043.5,-168 1043.5,-174 1037.5,-180 1031.5,-180"/>
+<text text-anchor="middle" x="971" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 14->5 -->
+<g id="edge16" class="edge"><title>14->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M936.997,-143.876C918.402,-134.512 895.173,-122.814 875.294,-112.803"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="876.64,-109.562 866.134,-108.19 873.491,-115.814 876.64,-109.562"/>
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<!-- 15->5 -->
-<g id="edge16" class="edge">
-<title>15->5</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M249.5047,-215.8314C249.7186,-208.131 249.9729,-198.9743 250.2106,-190.4166"/>
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+<g id="edge14" class="edge"><title>15->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M748.156,-215.971C774.497,-205.165 804.224,-191.167 813,-180 826.692,-162.577 831.084,-137.531 832.257,-118.444"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="835.761,-118.387 832.619,-108.269 828.766,-118.138 835.761,-118.387"/>
</g>
-<!-- 15->6 -->
-<g id="edge18" class="edge">
-<title>15->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M205.0925,-215.8314C181.7176,-206.159 152.7903,-194.1891 128.1532,-183.9944"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="129.1702,-180.6275 118.5918,-180.038 126.4937,-187.0956 129.1702,-180.6275"/>
+<!-- 15->8 -->
+<g id="edge22" class="edge"><title>15->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M660.382,-215.989C645.126,-207.58 629.591,-195.781 621,-180 609.599,-159.056 622.679,-134.107 636.68,-115.961"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="639.458,-118.093 643.094,-108.141 634.046,-113.654 639.458,-118.093"/>
</g>
-<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M1199,-180C1199,-180 1033,-180 1033,-180 1027,-180 1021,-174 1021,-168 1021,-168 1021,-156 1021,-156 1021,-150 1027,-144 1033,-144 1033,-144 1199,-144 1199,-144 1205,-144 1211,-150 1211,-156 1211,-156 1211,-168 1211,-168 1211,-174 1205,-180 1199,-180"/>
-<text text-anchor="middle" x="1116" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
+<!-- 15->13 -->
+<g id="edge30" class="edge"><title>15->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M706.461,-215.697C708.003,-207.983 709.858,-198.712 711.578,-190.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="715.05,-190.597 713.579,-180.104 708.186,-189.224 715.05,-190.597"/>
</g>
-<!-- 16->7 -->
-<g id="edge21" class="edge">
-<title>16->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1061.2708,-143.9243C1031.2098,-133.9959 993.755,-121.6255 962.3046,-111.2382"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="963.3449,-107.8959 952.7517,-108.0831 961.1496,-114.5428 963.3449,-107.8959"/>
+<!-- 16->6 -->
+<g id="edge17" class="edge"><title>16->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M535.36,-215.697C530.873,-207.644 525.441,-197.894 520.476,-188.982"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="523.454,-187.137 515.53,-180.104 517.339,-190.544 523.454,-187.137"/>
</g>
-<!-- 16->10 -->
-<g id="edge28" class="edge">
-<title>16->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1116,-143.8314C1116,-136.131 1116,-126.9743 1116,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1119.5001,-118.4132 1116,-108.4133 1112.5001,-118.4133 1119.5001,-118.4132"/>
+<!-- 16->7 -->
+<g id="edge19" class="edge"><title>16->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M495.6,-215.966C467.113,-206.142 431.114,-193.729 401.129,-183.389"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="402.216,-180.062 391.621,-180.111 399.934,-186.68 402.216,-180.062"/>
</g>
-<!-- 17 -->
-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M990.5,-180C990.5,-180 869.5,-180 869.5,-180 863.5,-180 857.5,-174 857.5,-168 857.5,-168 857.5,-156 857.5,-156 857.5,-150 863.5,-144 869.5,-144 869.5,-144 990.5,-144 990.5,-144 996.5,-144 1002.5,-150 1002.5,-156 1002.5,-156 1002.5,-168 1002.5,-168 1002.5,-174 996.5,-180 990.5,-180"/>
-<text text-anchor="middle" x="930" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
+<!-- 17->6 -->
+<g id="edge18" class="edge"><title>17->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M431.973,-215.876C444.55,-206.893 460.132,-195.763 473.752,-186.034"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="475.831,-188.85 481.934,-180.19 471.763,-183.154 475.831,-188.85"/>
</g>
<!-- 17->7 -->
-<g id="edge22" class="edge">
-<title>17->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M921.925,-143.8314C918.3898,-135.8771 914.164,-126.369 910.2544,-117.5723"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="913.4435,-116.1299 906.1837,-108.4133 907.0468,-118.9729 913.4435,-116.1299"/>
+<g id="edge20" class="edge"><title>17->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M391.685,-215.697C383.693,-207.22 373.928,-196.864 365.178,-187.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="367.534,-184.979 358.127,-180.104 362.441,-189.781 367.534,-184.979"/>
</g>
<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#9fd856" stroke-width="2" d="M827,-180C827,-180 677,-180 677,-180 671,-180 665,-174 665,-168 665,-168 665,-156 665,-156 665,-150 671,-144 677,-144 677,-144 827,-144 827,-144 833,-144 839,-150 839,-156 839,-156 839,-168 839,-168 839,-174 833,-180 827,-180"/>
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-</g>
-<!-- 18->7 -->
-<g id="edge20" class="edge">
-<title>18->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M788.842,-143.8314C808.1082,-134.3302 831.8699,-122.6121 852.2992,-112.5374"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="854.0023,-115.6 861.423,-108.038 850.9062,-109.3219 854.0023,-115.6"/>
-</g>
-<!-- 18->11 -->
-<g id="edge29" class="edge">
-<title>18->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M749.7289,-143.8314C748.7664,-136.131 747.6218,-126.9743 746.5521,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="750.0151,-117.9019 745.3017,-108.4133 743.0691,-118.7702 750.0151,-117.9019"/>
+<g id="node19" class="node"><title>18</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M658,-396C658,-396 532,-396 532,-396 526,-396 520,-390 520,-384 520,-384 520,-372 520,-372 520,-366 526,-360 532,-360 532,-360 658,-360 658,-360 664,-360 670,-366 670,-372 670,-372 670,-384 670,-384 670,-390 664,-396 658,-396"/>
+<text text-anchor="middle" x="595" y="-375.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 18->9 -->
+<g id="edge24" class="edge"><title>18->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M594.506,-359.697C594.285,-351.983 594.02,-342.712 593.775,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="597.273,-334 593.489,-324.104 590.276,-334.2 597.273,-334"/>
+</g>
+<!-- 19 -->
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M490.5,-396C490.5,-396 403.5,-396 403.5,-396 397.5,-396 391.5,-390 391.5,-384 391.5,-384 391.5,-372 391.5,-372 391.5,-366 397.5,-360 403.5,-360 403.5,-360 490.5,-360 490.5,-360 496.5,-360 502.5,-366 502.5,-372 502.5,-372 502.5,-384 502.5,-384 502.5,-390 496.5,-396 490.5,-396"/>
+<text text-anchor="middle" x="447" y="-375.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
<!-- 19->10 -->
-<g id="edge27" class="edge">
-<title>19->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1051.7598,-228.313C1111.4117,-221.0258 1199.419,-206.1048 1220,-180 1229.906,-167.4353 1228.3076,-157.6742 1220,-144 1210.64,-128.5934 1195.2997,-117.3827 1179.2404,-109.3089"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1180.2866,-105.9364 1169.7416,-104.9097 1177.3448,-112.2882 1180.2866,-105.9364"/>
+<g id="edge25" class="edge"><title>19->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M391.375,-362.331C353.51,-352.33 301.991,-338.689 248.035,-324.272"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="248.857,-320.869 238.292,-321.667 247.049,-327.631 248.857,-320.869"/>
</g>
-<!-- 19->16 -->
-<g id="edge35" class="edge">
-<title>19->16</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1025.5334,-215.8314C1041.0101,-206.6221 1059.9869,-195.3301 1076.5563,-185.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1078.6724,-188.2843 1085.4764,-180.1628 1075.0929,-182.2687 1078.6724,-188.2843"/>
+<!-- 22 -->
+<g id="node23" class="node"><title>22</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M491.5,-324C491.5,-324 406.5,-324 406.5,-324 400.5,-324 394.5,-318 394.5,-312 394.5,-312 394.5,-300 394.5,-300 394.5,-294 400.5,-288 406.5,-288 406.5,-288 491.5,-288 491.5,-288 497.5,-288 503.5,-294 503.5,-300 503.5,-300 503.5,-312 503.5,-312 503.5,-318 497.5,-324 491.5,-324"/>
+<text text-anchor="middle" x="449" y="-303.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
-<!-- 20->11 -->
-<g id="edge30" class="edge">
-<title>20->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M676.7008,-215.8753C661.1777,-197.3079 642.7255,-167.863 656,-144 663.0918,-131.2514 674.5767,-121.1272 686.9096,-113.255"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="688.7077,-116.2579 695.5397,-108.1601 685.149,-110.23 688.7077,-116.2579"/>
+<!-- 19->22 -->
+<g id="edge37" class="edge"><title>19->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M447.494,-359.697C447.715,-351.983 447.98,-342.712 448.225,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="451.724,-334.2 448.511,-324.104 444.727,-334 451.724,-334.2"/>
</g>
-<!-- 20->18 -->
-<g id="edge36" class="edge">
-<title>20->18</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M708.6358,-215.8314C715.3161,-207.5386 723.3568,-197.557 730.6904,-188.4533"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="733.6194,-190.3965 737.1671,-180.4133 728.1681,-186.0052 733.6194,-190.3965"/>
+<!-- 20 -->
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M361,-396C361,-396 251,-396 251,-396 245,-396 239,-390 239,-384 239,-384 239,-372 239,-372 239,-366 245,-360 251,-360 251,-360 361,-360 361,-360 367,-360 373,-366 373,-372 373,-372 373,-384 373,-384 373,-390 367,-396 361,-396"/>
+<text text-anchor="middle" x="306" y="-375.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 20->11 -->
+<g id="edge26" class="edge"><title>20->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M308.472,-359.697C309.574,-351.983 310.898,-342.712 312.127,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="315.607,-334.499 313.557,-324.104 308.677,-333.509 315.607,-334.499"/>
</g>
<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M609,-396C609,-396 483,-396 483,-396 477,-396 471,-390 471,-384 471,-384 471,-372 471,-372 471,-366 477,-360 483,-360 483,-360 609,-360 609,-360 615,-360 621,-366 621,-372 621,-372 621,-384 621,-384 621,-390 615,-396 609,-396"/>
-<text text-anchor="middle" x="546" y="-375.5" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#78d856" stroke-width="2" d="M819,-324C819,-324 749,-324 749,-324 743,-324 737,-318 737,-312 737,-312 737,-300 737,-300 737,-294 743,-288 749,-288 749,-288 819,-288 819,-288 825,-288 831,-294 831,-300 831,-300 831,-312 831,-312 831,-318 825,-324 819,-324"/>
+<text text-anchor="middle" x="784" y="-303.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
<!-- 21->12 -->
-<g id="edge31" class="edge">
-<title>21->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M546,-359.8314C546,-352.131 546,-342.9743 546,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="549.5001,-334.4132 546,-324.4133 542.5001,-334.4133 549.5001,-334.4132"/>
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-<!-- 22 -->
-<g id="node23" class="node">
-<title>22</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M292.5,-324C292.5,-324 205.5,-324 205.5,-324 199.5,-324 193.5,-318 193.5,-312 193.5,-312 193.5,-300 193.5,-300 193.5,-294 199.5,-288 205.5,-288 205.5,-288 292.5,-288 292.5,-288 298.5,-288 304.5,-294 304.5,-300 304.5,-300 304.5,-312 304.5,-312 304.5,-318 298.5,-324 292.5,-324"/>
-<text text-anchor="middle" x="249" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcriptome</text>
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-<g id="edge32" class="edge">
-<title>22->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M302.725,-287.9243C332.1073,-278.0387 368.6852,-265.7321 399.4758,-255.3726"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="400.8911,-258.5893 409.2529,-252.0831 398.6588,-251.9548 400.8911,-258.5893"/>
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-<g id="edge34" class="edge">
-<title>22->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M249,-287.8314C249,-280.131 249,-270.9743 249,-262.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="252.5001,-262.4132 249,-252.4133 245.5001,-262.4133 252.5001,-262.4132"/>
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-<g id="node24" class="node">
-<title>23</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M438,-396C438,-396 328,-396 328,-396 322,-396 316,-390 316,-384 316,-384 316,-372 316,-372 316,-366 322,-360 328,-360 328,-360 438,-360 438,-360 444,-360 450,-366 450,-372 450,-372 450,-384 450,-384 450,-390 444,-396 438,-396"/>
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-<g id="edge33" class="edge">
-<title>23->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M383,-359.8314C383,-352.131 383,-342.9743 383,-334.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="386.5001,-334.4132 383,-324.4133 379.5001,-334.4133 386.5001,-334.4132"/>
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-<g id="node25" class="node">
-<title>24</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M844,-324C844,-324 774,-324 774,-324 768,-324 762,-318 762,-312 762,-312 762,-300 762,-300 762,-294 768,-288 774,-288 774,-288 844,-288 844,-288 850,-288 856,-294 856,-300 856,-300 856,-312 856,-312 856,-318 850,-324 844,-324"/>
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-<g id="edge38" class="edge">
-<title>24->19</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M855.9357,-287.8314C881.1437,-278.0734 912.3926,-265.977 938.8791,-255.7242"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="940.3397,-258.912 948.4019,-252.038 937.8127,-252.384 940.3397,-258.912"/>
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-<title>24->20</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M779.9806,-287.8314C765.2714,-278.6221 747.2356,-267.3301 731.4878,-257.4706"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="733.3433,-254.5029 723.0101,-252.1628 729.6286,-260.436 733.3433,-254.5029"/>
+<g id="edge28" class="edge"><title>21->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M794.382,-287.697C799.265,-279.559 805.187,-269.689 810.579,-260.701"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="813.594,-262.48 815.737,-252.104 807.591,-258.879 813.594,-262.48"/>
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+<!-- 21->15 -->
+<g id="edge31" class="edge"><title>21->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M763.978,-287.697C753.874,-278.965 741.464,-268.24 730.482,-258.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="732.647,-255.995 722.792,-252.104 728.07,-261.291 732.647,-255.995"/>
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+<!-- 22->16 -->
+<g id="edge34" class="edge"><title>22->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M472.73,-287.697C484.937,-278.796 499.985,-267.823 513.184,-258.199"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="515.525,-260.824 521.543,-252.104 511.4,-255.168 515.525,-260.824"/>
+</g>
+<!-- 22->17 -->
+<g id="edge35" class="edge"><title>22->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M438.865,-287.697C434.148,-279.644 428.438,-269.894 423.218,-260.982"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="426.092,-258.964 418.018,-252.104 420.052,-262.502 426.092,-258.964"/>
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diff --git a/images/workflow_dag.svg b/images/workflow_dag.svg
deleted file mode 100644
index aed67148fb0960c5d2a497db4fb730c2be2faaf1..0000000000000000000000000000000000000000
--- a/images/workflow_dag.svg
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-<text text-anchor="middle" x="85" y="-93" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
-<text text-anchor="middle" x="85" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired</text>
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-<g id="edge1" class="edge">
-<title>1->0</title>
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-<!-- 2 -->
-<g id="node3" class="node">
-<title>2</title>
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-<text text-anchor="middle" x="276" y="-93" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
-<text text-anchor="middle" x="276" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1</text>
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-<!-- 2->0 -->
-<g id="edge2" class="edge">
-<title>2->0</title>
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-<title>3</title>
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-<text text-anchor="middle" x="477" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
-</g>
-<!-- 3->0 -->
-<g id="edge3" class="edge">
-<title>3->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M572.1926,-73.3851C575.1613,-72.9115 578.1027,-72.4486 581,-72 712.0945,-51.7009 868.2982,-31.5289 938.5332,-22.6716"/>
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-<g id="node5" class="node">
-<title>4</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M752,-108C752,-108 602,-108 602,-108 596,-108 590,-102 590,-96 590,-96 590,-84 590,-84 590,-78 596,-72 602,-72 602,-72 752,-72 752,-72 758,-72 764,-78 764,-84 764,-84 764,-96 764,-96 764,-102 758,-108 752,-108"/>
-<text text-anchor="middle" x="677" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
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-<!-- 4->0 -->
-<g id="edge4" class="edge">
-<title>4->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M752.0644,-71.9243C811.5694,-57.5953 892.1971,-38.18 938.7061,-26.9805"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="939.7465,-30.3301 948.6492,-24.5861 938.1077,-23.5246 939.7465,-30.3301"/>
-</g>
-<!-- 5 -->
-<g id="node6" class="node">
-<title>5</title>
-<path fill="none" stroke="#70d856" stroke-width="2" d="M963.5,-180C963.5,-180 860.5,-180 860.5,-180 854.5,-180 848.5,-174 848.5,-168 848.5,-168 848.5,-156 848.5,-156 848.5,-150 854.5,-144 860.5,-144 860.5,-144 963.5,-144 963.5,-144 969.5,-144 975.5,-150 975.5,-156 975.5,-156 975.5,-168 975.5,-168 975.5,-174 969.5,-180 963.5,-180"/>
-<text text-anchor="middle" x="912" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
-</g>
-<!-- 5->0 -->
-<g id="edge5" class="edge">
-<title>5->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M853.6599,-143.8856C836.9498,-135.6937 820.6591,-124.1172 811,-108 802.7751,-94.2759 801.6092,-84.9543 811,-72 826.1492,-51.1023 894.8804,-33.9967 938.718,-24.9629"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="939.6268,-28.3503 948.7408,-22.9481 938.2471,-21.4876 939.6268,-28.3503"/>
-</g>
-<!-- 9 -->
-<g id="node10" class="node">
-<title>9</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M960,-108C960,-108 832,-108 832,-108 826,-108 820,-102 820,-96 820,-96 820,-84 820,-84 820,-78 826,-72 832,-72 832,-72 960,-72 960,-72 966,-72 972,-78 972,-84 972,-84 972,-96 972,-96 972,-102 966,-108 960,-108"/>
-<text text-anchor="middle" x="896" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">pe_salmon_quantmerge_genes</text>
-</g>
-<!-- 5->9 -->
-<g id="edge23" class="edge">
-<title>5->9</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M907.9625,-143.8314C906.2513,-136.131 904.2165,-126.9743 902.3148,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="905.6779,-117.4159 900.0918,-108.4133 898.8446,-118.9344 905.6779,-117.4159"/>
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-<!-- 11 -->
-<g id="node12" class="node">
-<title>11</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1109.5,-108C1109.5,-108 1002.5,-108 1002.5,-108 996.5,-108 990.5,-102 990.5,-96 990.5,-96 990.5,-84 990.5,-84 990.5,-78 996.5,-72 1002.5,-72 1002.5,-72 1109.5,-72 1109.5,-72 1115.5,-72 1121.5,-78 1121.5,-84 1121.5,-84 1121.5,-96 1121.5,-96 1121.5,-102 1115.5,-108 1109.5,-108"/>
-<text text-anchor="middle" x="1056" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">pe_salmon_quantmerge_tr</text>
-</g>
-<!-- 5->11 -->
-<g id="edge25" class="edge">
-<title>5->11</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M948.3373,-143.8314C967.3396,-134.3302 990.7758,-122.6121 1010.9252,-112.5374"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1012.545,-115.6407 1019.924,-108.038 1009.4145,-109.3797 1012.545,-115.6407"/>
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-<!-- 6 -->
-<g id="node7" class="node">
-<title>6</title>
-<path fill="none" stroke="#56d882" stroke-width="2" d="M1310.5,-180C1310.5,-180 1223.5,-180 1223.5,-180 1217.5,-180 1211.5,-174 1211.5,-168 1211.5,-168 1211.5,-156 1211.5,-156 1211.5,-150 1217.5,-144 1223.5,-144 1223.5,-144 1310.5,-144 1310.5,-144 1316.5,-144 1322.5,-150 1322.5,-156 1322.5,-156 1322.5,-168 1322.5,-168 1322.5,-174 1316.5,-180 1310.5,-180"/>
-<text text-anchor="middle" x="1267" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">quantification_salmon</text>
-</g>
-<!-- 6->0 -->
-<g id="edge6" class="edge">
-<title>6->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1247.3898,-143.7542C1224.9107,-123.6927 1186.2216,-91.6982 1148,-72 1104.0675,-49.3586 1048.8886,-34.1028 1013.054,-25.7361"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1013.564,-22.2628 1003.0369,-23.4593 1012.0125,-29.0887 1013.564,-22.2628"/>
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-<!-- 10 -->
-<g id="node11" class="node">
-<title>10</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1340,-108C1340,-108 1228,-108 1228,-108 1222,-108 1216,-102 1216,-96 1216,-96 1216,-84 1216,-84 1216,-78 1222,-72 1228,-72 1228,-72 1340,-72 1340,-72 1346,-72 1352,-78 1352,-84 1352,-84 1352,-96 1352,-96 1352,-102 1346,-108 1340,-108"/>
-<text text-anchor="middle" x="1284" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes</text>
-</g>
-<!-- 6->10 -->
-<g id="edge24" class="edge">
-<title>6->10</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1271.2898,-143.8314C1273.108,-136.131 1275.2699,-126.9743 1277.2905,-118.4166"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1280.7608,-118.95 1279.6524,-108.4133 1273.9481,-117.3414 1280.7608,-118.95"/>
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-<!-- 12 -->
-<g id="node13" class="node">
-<title>12</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M1474,-108C1474,-108 1382,-108 1382,-108 1376,-108 1370,-102 1370,-96 1370,-96 1370,-84 1370,-84 1370,-78 1376,-72 1382,-72 1382,-72 1474,-72 1474,-72 1480,-72 1486,-78 1486,-84 1486,-84 1486,-96 1486,-96 1486,-102 1480,-108 1474,-108"/>
-<text text-anchor="middle" x="1428" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_tr</text>
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-<!-- 6->12 -->
-<g id="edge26" class="edge">
-<title>6->12</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1307.6271,-143.8314C1329.1599,-134.2018 1355.7849,-122.295 1378.5152,-112.1299"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1379.9652,-115.3155 1387.665,-108.038 1377.1074,-108.9254 1379.9652,-115.3155"/>
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-<!-- 7 -->
-<g id="node8" class="node">
-<title>7</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M1181,-180C1181,-180 1039,-180 1039,-180 1033,-180 1027,-174 1027,-168 1027,-168 1027,-156 1027,-156 1027,-150 1033,-144 1039,-144 1039,-144 1181,-144 1181,-144 1187,-144 1193,-150 1193,-156 1193,-156 1193,-168 1193,-168 1193,-174 1187,-180 1181,-180"/>
-<text text-anchor="middle" x="1110" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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-<!-- 7->0 -->
-<g id="edge7" class="edge">
-<title>7->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1122.0924,-143.7945C1133.3363,-124.353 1146.2414,-93.4497 1131,-72 1117.1153,-52.4595 1054.535,-35.2799 1013.2611,-25.7978"/>
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-<!-- 8 -->
-<g id="node9" class="node">
-<title>8</title>
-<path fill="none" stroke="#88d856" stroke-width="2" d="M1479,-180C1479,-180 1353,-180 1353,-180 1347,-180 1341,-174 1341,-168 1341,-168 1341,-156 1341,-156 1341,-150 1347,-144 1353,-144 1353,-144 1479,-144 1479,-144 1485,-144 1491,-150 1491,-156 1491,-156 1491,-168 1491,-168 1491,-174 1485,-180 1479,-180"/>
-<text text-anchor="middle" x="1416" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
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-<!-- 8->0 -->
-<g id="edge8" class="edge">
-<title>8->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1457.534,-143.9032C1472.1053,-135.2837 1486.8583,-123.4273 1495,-108 1502.4678,-93.8497 1505.7123,-83.8847 1495,-72 1462.8307,-36.3099 1127.5307,-22.6878 1013.6242,-19.0686"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1013.4133,-15.5605 1003.3097,-18.7492 1013.1966,-22.5572 1013.4133,-15.5605"/>
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-<!-- 9->0 -->
-<g id="edge9" class="edge">
-<title>9->0</title>
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-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="950.7275,-45.454 955.8191,-36.1628 946.0447,-40.251 950.7275,-45.454"/>
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-<!-- 10->0 -->
-<g id="edge10" class="edge">
-<title>10->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1215.6448,-74.0209C1153.1373,-59.4087 1063.0275,-38.3441 1013.0065,-26.6509"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1013.7953,-23.241 1003.2611,-24.3727 1012.2019,-30.0572 1013.7953,-23.241"/>
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-<!-- 11->0 -->
-<g id="edge11" class="edge">
-<title>11->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1035.8126,-71.8314C1026.1486,-63.1337 1014.4204,-52.5783 1003.9184,-43.1265"/>
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-<!-- 12->0 -->
-<g id="edge12" class="edge">
-<title>12->0</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1369.9993,-73.9492C1366.9638,-73.2561 1363.9505,-72.6009 1361,-72 1234.5556,-46.2493 1082.2442,-28.843 1013.2245,-21.6797"/>
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-<!-- 13 -->
-<g id="node14" class="node">
-<title>13</title>
-<path fill="none" stroke="#d8cb56" stroke-width="2" d="M694.5,-180C694.5,-180 605.5,-180 605.5,-180 599.5,-180 593.5,-174 593.5,-168 593.5,-168 593.5,-156 593.5,-156 593.5,-150 599.5,-144 605.5,-144 605.5,-144 694.5,-144 694.5,-144 700.5,-144 706.5,-150 706.5,-156 706.5,-156 706.5,-168 706.5,-168 706.5,-174 700.5,-180 694.5,-180"/>
-<text text-anchor="middle" x="650" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
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-<!-- 13->3 -->
-<g id="edge13" class="edge">
-<title>13->3</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M606.3448,-143.8314C583.1042,-134.159 554.3432,-122.1891 529.8477,-111.9944"/>
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-<!-- 14 -->
-<g id="node15" class="node">
-<title>14</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M809.5,-180C809.5,-180 736.5,-180 736.5,-180 730.5,-180 724.5,-174 724.5,-168 724.5,-168 724.5,-156 724.5,-156 724.5,-150 730.5,-144 736.5,-144 736.5,-144 809.5,-144 809.5,-144 815.5,-144 821.5,-150 821.5,-156 821.5,-156 821.5,-168 821.5,-168 821.5,-174 815.5,-180 809.5,-180"/>
-<text text-anchor="middle" x="773" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
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-<!-- 14->4 -->
-<g id="edge14" class="edge">
-<title>14->4</title>
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-<!-- 15 -->
-<g id="node16" class="node">
-<title>15</title>
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-<text text-anchor="middle" x="912" y="-234" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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-<!-- 15->5 -->
-<g id="edge15" class="edge">
-<title>15->5</title>
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-<title>15->7</title>
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-<title>15->13</title>
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-<!-- 16 -->
-<g id="node17" class="node">
-<title>16</title>
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-<text text-anchor="middle" x="1094" y="-234" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
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-<g id="node18" class="node">
-<title>17</title>
-<path fill="none" stroke="#59d856" stroke-width="2" d="M1315,-254.5C1315,-254.5 1219,-254.5 1219,-254.5 1213,-254.5 1207,-248.5 1207,-242.5 1207,-242.5 1207,-230.5 1207,-230.5 1207,-224.5 1213,-218.5 1219,-218.5 1219,-218.5 1315,-218.5 1315,-218.5 1321,-218.5 1327,-224.5 1327,-230.5 1327,-230.5 1327,-242.5 1327,-242.5 1327,-248.5 1321,-254.5 1315,-254.5"/>
-<text text-anchor="middle" x="1267" y="-234" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
-</g>
-<!-- 17->6 -->
-<g id="edge17" class="edge">
-<title>17->6</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1267,-218.4656C1267,-210.0178 1267,-199.7542 1267,-190.3064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1270.5001,-190.1265 1267,-180.1265 1263.5001,-190.1265 1270.5001,-190.1265"/>
-</g>
-<!-- 17->8 -->
-<g id="edge21" class="edge">
-<title>17->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1303.0687,-218.4656C1323.4162,-208.2919 1349.0306,-195.4847 1370.7191,-184.6405"/>
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-</g>
-<!-- 17->14 -->
-<g id="edge30" class="edge">
-<title>17->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1206.7501,-223.4738C1193.065,-220.7709 1178.5647,-218.1079 1165,-216 1020.9591,-193.6169 982.198,-207.2604 839,-180 836.6374,-179.5502 834.2356,-179.059 831.8155,-178.5356"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="832.349,-175.0668 821.818,-176.2274 830.7743,-181.8874 832.349,-175.0668"/>
-</g>
-<!-- 18 -->
-<g id="node19" class="node">
-<title>18</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M1462.5,-254.5C1462.5,-254.5 1361.5,-254.5 1361.5,-254.5 1355.5,-254.5 1349.5,-248.5 1349.5,-242.5 1349.5,-242.5 1349.5,-230.5 1349.5,-230.5 1349.5,-224.5 1355.5,-218.5 1361.5,-218.5 1361.5,-218.5 1462.5,-218.5 1462.5,-218.5 1468.5,-218.5 1474.5,-224.5 1474.5,-230.5 1474.5,-230.5 1474.5,-242.5 1474.5,-242.5 1474.5,-248.5 1468.5,-254.5 1462.5,-254.5"/>
-<text text-anchor="middle" x="1412" y="-239.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
-<text text-anchor="middle" x="1412" y="-228.5" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
-</g>
-<!-- 18->7 -->
-<g id="edge20" class="edge">
-<title>18->7</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1349.4126,-219.4641C1344.8775,-218.2769 1340.3707,-217.1114 1336,-216 1290.4851,-204.4264 1239.6293,-192.2119 1197.7028,-182.3327"/>
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-</g>
-<!-- 18->8 -->
-<g id="edge22" class="edge">
-<title>18->8</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1412.9683,-218.4656C1413.4219,-210.0178 1413.9729,-199.7542 1414.4802,-190.3064"/>
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-</g>
-<!-- 19 -->
-<g id="node20" class="node">
-<title>19</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M757.5,-257C757.5,-257 656.5,-257 656.5,-257 650.5,-257 644.5,-251 644.5,-245 644.5,-245 644.5,-228 644.5,-228 644.5,-222 650.5,-216 656.5,-216 656.5,-216 757.5,-216 757.5,-216 763.5,-216 769.5,-222 769.5,-228 769.5,-228 769.5,-245 769.5,-245 769.5,-251 763.5,-257 757.5,-257"/>
-<text text-anchor="middle" x="707" y="-245" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
-<text text-anchor="middle" x="707" y="-234" font-family="sans" font-size="10.00" fill="#000000">index_size: 76</text>
-<text text-anchor="middle" x="707" y="-223" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
-</g>
-<!-- 19->13 -->
-<g id="edge27" class="edge">
-<title>19->13</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M691.1223,-215.7476C684.565,-207.177 676.8905,-197.1463 669.9587,-188.0864"/>
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-</g>
-<!-- 19->14 -->
-<g id="edge29" class="edge">
-<title>19->14</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M725.3847,-215.7476C733.0549,-207.0896 742.0451,-196.9415 750.1354,-187.8093"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="752.9461,-189.9148 756.9574,-180.1087 747.7064,-185.2729 752.9461,-189.9148"/>
-</g>
-<!-- 20 -->
-<g id="node21" class="node">
-<title>20</title>
-<path fill="none" stroke="#56d89a" stroke-width="2" d="M985,-329C985,-329 839,-329 839,-329 833,-329 827,-323 827,-317 827,-317 827,-305 827,-305 827,-299 833,-293 839,-293 839,-293 985,-293 985,-293 991,-293 997,-299 997,-305 997,-305 997,-317 997,-317 997,-323 991,-329 985,-329"/>
-<text text-anchor="middle" x="912" y="-314" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="912" y="-303" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired</text>
-</g>
-<!-- 20->15 -->
-<g id="edge31" class="edge">
-<title>20->15</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M912,-292.9656C912,-284.5178 912,-274.2542 912,-264.8064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="915.5001,-264.6265 912,-254.6265 908.5001,-264.6265 915.5001,-264.6265"/>
-</g>
-<!-- 21 -->
-<g id="node22" class="node">
-<title>21</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M1343,-329C1343,-329 1191,-329 1191,-329 1185,-329 1179,-323 1179,-317 1179,-317 1179,-305 1179,-305 1179,-299 1185,-293 1191,-293 1191,-293 1343,-293 1343,-293 1349,-293 1355,-299 1355,-305 1355,-305 1355,-317 1355,-317 1355,-323 1349,-329 1343,-329"/>
-<text text-anchor="middle" x="1267" y="-314" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="1267" y="-303" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1</text>
-</g>
-<!-- 21->17 -->
-<g id="edge32" class="edge">
-<title>21->17</title>
-<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1267,-292.9656C1267,-284.5178 1267,-274.2542 1267,-264.8064"/>
-<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1270.5001,-264.6265 1267,-254.6265 1263.5001,-264.6265 1270.5001,-264.6265"/>
-</g>
-</g>
-</svg>
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 89c4f7e6bc94d5eca659d8c88add19fc3c0b02b0..f4fb1bf86b4eb4aa44f4f03d66c8138864cc33e9 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -278,45 +278,6 @@ rule pe_map_genome_star:
2> {log.stderr}"
-rule pe_index_genomic_alignment_samtools:
- '''
- Index the genomic alignment
- '''
- input:
- bam = os.path.join(
- config["output_dir"],
- "paired_end",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam"),
- output:
- bai = os.path.join(
- config["output_dir"],
- "paired_end",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam.bai"),
-
- singularity:
- "docker://zavolab/samtools:1.10-slim"
-
- log:
- stderr = os.path.join(
- config["log_dir"],
- "paired_end",
- "{sample}",
- "index_genomic_alignment_samtools.stderr.log"),
- stdout = os.path.join(
- config["log_dir"],
- "paired_end",
- "{sample}",
- "index_genomic_alignment_samtools.stdout.log")
-
- shell:
- "(samtools index {input.bam} {output.bai};) \
- 1> {log.stdout} 2> {log.stderr}"
-
-
rule pe_quantification_salmon:
'''
Quantification at transcript and gene level using Salmon
@@ -452,78 +413,4 @@ rule pe_genome_quantification_kallisto:
--pseudobam \
{params.directionality} \
{input.reads1} {input.reads2} > {output.pseudoalignment}) \
- 2> {log.stderr}"
-
-rule star_rpm_paired_end:
- ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
- input:
- bam = os.path.join(
- config["output_dir"],
- "paired_end",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam"),
- bai = os.path.join(
- config["output_dir"],
- "paired_end",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam.bai")
- output:
- str1 = (os.path.join(
- config["output_dir"],
- "paired_end",
- "{sample}",
- "STAR_coverage",
- "{sample}_Signal.Unique.str1.out.bg"),
- os.path.join(
- config["output_dir"],
- "paired_end",
- "{sample}",
- "STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str1.out.bg")),
- str2 = (os.path.join(
- config["output_dir"],
- "paired_end",
- "{sample}",
- "STAR_coverage",
- "{sample}_Signal.Unique.str2.out.bg"),
- os.path.join(
- config["output_dir"],
- "paired_end",
- "{sample}",
- "STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str2.out.bg"))
- params:
- out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
- prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
- str(wildcards.sample) + "_"),
- stranded = "Stranded"
- singularity:
- "docker://zavolab/star:2.7.3a-slim"
- log:
- stderr = os.path.join(
- config["log_dir"],
- "paired_end",
- "{sample}",
- "star_rpm_paired_end.stderr.log"),
- stdout = os.path.join(
- config["log_dir"],
- "paired_end",
- "{sample}",
- "star_rpm_paired_end.stdout.log")
- threads: 4
- shell:
- """
- (mkdir -p {params.out_dir}; \
- chmod -R 777 {params.out_dir}; \
- STAR \
- --runMode inputAlignmentsFromBAM \
- --runThreadN {threads} \
- --inputBAMfile {input.bam} \
- --outWigType "bedGraph" \
- --outWigStrand "{params.stranded}" \
- --outWigNorm "RPM" \
- --outFileNamePrefix {params.prefix}) \
- 1> {log.stdout} 2> {log.stderr}
- """
+ 2> {log.stderr}"
\ No newline at end of file
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index cf4c7c4eb1611b8bc4f5c55dda56a20222592aed..f1b7d27e59ab0fad4dea4b7f531cbe114f1fbbfd 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -237,48 +237,6 @@ rule map_genome_star:
2> {log.stderr}"
-rule index_genomic_alignment_samtools:
- '''
- Index genome bamfile using samtools
- '''
- input:
- bam = os.path.join(
- config["output_dir"],
- "single_end",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam")
-
- output:
- bai = os.path.join(
- config["output_dir"],
- "single_end",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam.bai")
-
- singularity:
- "docker://zavolab/samtools:1.10-slim"
-
- threads: 1
-
- log:
- stderr = os.path.join(
- config["log_dir"],
- "single_end",
- "{sample}",
- "index_genomic_alignment_samtools.stderr.log"),
- stdout = os.path.join(
- config["log_dir"],
- "single_end",
- "{sample}",
- "index_genomic_alignment_samtools.stdout.log")
-
- shell:
- "(samtools index {input.bam} {output.bai};) \
- 1> {log.stdout} 2> {log.stderr}"
-
-
rule quantification_salmon:
'''
Quantification at transcript and gene level using Salmon
@@ -411,78 +369,4 @@ rule genome_quantification_kallisto:
--pseudobam \
{params.directionality} \
{input.reads} > {output.pseudoalignment};) \
- 2> {log.stderr}"
-
-rule star_rpm_single_end:
- ''' Create stranded bedgraph coverage with STARs RPM normalisation '''
- input:
- bam = os.path.join(
- config["output_dir"],
- "single_end",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam"),
- bai = os.path.join(
- config["output_dir"],
- "single_end",
- "{sample}",
- "map_genome",
- "{sample}_Aligned.sortedByCoord.out.bam.bai")
- output:
- str1 = (os.path.join(
- config["output_dir"],
- "single_end",
- "{sample}",
- "STAR_coverage",
- "{sample}_Signal.Unique.str1.out.bg"),
- os.path.join(
- config["output_dir"],
- "single_end",
- "{sample}",
- "STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str1.out.bg")),
- str2 = (os.path.join(
- config["output_dir"],
- "single_end",
- "{sample}",
- "STAR_coverage",
- "{sample}_Signal.Unique.str2.out.bg"),
- os.path.join(
- config["output_dir"],
- "single_end",
- "{sample}",
- "STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str2.out.bg"))
- params:
- out_dir = lambda wildcards, output: os.path.dirname(output.str1[0]),
- prefix = lambda wildcards, output: os.path.join(os.path.dirname(output.str1[0]),
- str(wildcards.sample) + "_"),
- stranded = "Stranded"
- singularity:
- "docker://zavolab/star:2.7.3a-slim"
- log:
- stderr = os.path.join(
- config["log_dir"],
- "single_end",
- "{sample}",
- "star_rpm_single_end.stderr.log"),
- stdout = os.path.join(
- config["log_dir"],
- "single_end",
- "{sample}",
- "star_rpm_single_end.stdout.log")
- threads: 4
- shell:
- """
- (mkdir -p {params.out_dir}; \
- chmod -R 777 {params.out_dir}; \
- STAR \
- --runMode inputAlignmentsFromBAM \
- --runThreadN {threads} \
- --inputBAMfile {input.bam} \
- --outWigType "bedGraph" \
- --outWigStrand {params.stranded} \
- --outWigNorm "RPM" \
- --outFileNamePrefix {params.prefix}) \
- 1> {log.stdout} 2> {log.stderr}
- """
+ 2> {log.stderr}"
\ No newline at end of file