diff --git a/.gitignore b/.gitignore
index 23841973d5f14bdf49ea357b1b6f9798d6c5215b..791e748595ec85cc58b9efd02395f392ea9bd031 100644
--- a/.gitignore
+++ b/.gitignore
@@ -332,4 +332,5 @@ runs/.*
.snakemake/
logs/
results/
+!tests/test_alfa/results/
.java/
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 91ff05f215165c41c6ae063a84ab0db58914bc59..0b9cc4172ba3f10aa20bffa4e5fdfde066309f42 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -14,6 +14,7 @@ test:
# add script tests here
- bash tests/test_scripts_labkey_to_snakemake_table/test.sh
- bash tests/test_scripts_labkey_to_snakemake_api/test.sh
+ - bash tests/test_alfa/test.sh
# add integration tests here
- bash tests/test_create_dag_image/test.sh
- bash tests/test_create_rule_graph/test.sh
diff --git a/Snakefile b/Snakefile
index 7c8185c2212afdec42f122dbe28c38644e105b34..5075e82e1ae2e8f35cc829efccdacc52ed25cb5c 100644
--- a/Snakefile
+++ b/Snakefile
@@ -4,6 +4,7 @@ import os
import sys
import pandas as pd
+import shutil
# Get sample table
samples_table = pd.read_csv(
@@ -16,7 +17,7 @@ samples_table = pd.read_csv(
)
# Global config
-localrules: finish
+localrules: finish, rename_star_rpm_for_alfa
# Create log directories
os.makedirs(
@@ -99,7 +100,23 @@ rule finish:
zip,
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
- for i in list(samples_table.index.values)])
+ for i in list(samples_table.index.values)]),
+ alfa_reports = expand(os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "ALFA_plots.Biotypes.pdf"),
+ 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)]),
+ alfa_all_samples = os.path.join(
+ config["output_dir"],
+ "ALFA",
+ "ALFA_plots.Categories.pdf")
+
@@ -441,6 +458,47 @@ rule star_rpm:
"""
+rule rename_star_rpm_for_alfa:
+ input:
+ str1 = 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.UniqueMultiple.str2.out.bg")
+
+ output:
+ plus = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "{sample}_Signal.UniqueMultiple.out.plus.bg"),
+ minus = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "{sample}_Signal.UniqueMultiple.out.minus.bg")
+
+ params:
+ orientation = lambda wildcards: samples_table.loc[wildcards.sample, "kallisto_directionality"]
+
+ run:
+ if params['orientation'] == "--fr":
+ shutil.copy2(input['str1'], output['plus'])
+ shutil.copy2(input['str2'], output['minus'])
+ elif params['orientation'] == "--rf":
+ shutil.copy2(input['str1'], output['minus'])
+ shutil.copy2(input['str2'], output['plus'])
+
+
rule calculate_TIN_scores:
"""
Caluclate transcript integrity (TIN) score
@@ -612,4 +670,162 @@ rule salmon_quantmerge_transcripts:
--names {params.sample_name_list} \
--column {params.salmon_merge_on} \
--output {output.salmon_out}) \
- 1> {log.stdout} 2> {log.stderr}"
\ No newline at end of file
+ 1> {log.stdout} 2> {log.stderr}"
+
+
+#################################################################################
+### ALFA: Annotation Landscape For Aligned reads
+#################################################################################
+
+directionality = {"--fr": "fr-firststrand", "--rf": "fr-secondstrand"}
+
+
+rule generate_alfa_index:
+ ''' Generate ALFA index files from sorted GTF file '''
+ input:
+ gtf = lambda wildcards: samples_table["gtf"][samples_table["organism"]==wildcards.organism][0],
+ chr_len = os.path.join(
+ config["star_indexes"],
+ "{organism}",
+ "{index_size}",
+ "STAR_index",
+ "chrNameLength.txt"),
+
+ output:
+ index_stranded = os.path.join(config["alfa_indexes"],
+ "{organism}",
+ "{index_size}",
+ "ALFA",
+ "sorted_genes.stranded.ALFA_index"),
+ index_unstranded = os.path.join(config["alfa_indexes"],
+ "{organism}",
+ "{index_size}",
+ "ALFA",
+ "sorted_genes.unstranded.ALFA_index")
+
+ params:
+ genome_index = "sorted_genes",
+ out_dir = lambda wildcards, output: os.path.dirname(output.index_stranded)
+
+ threads: 4
+
+ singularity:
+ "docker://zavolab/alfa:1.1.1"
+
+ log:
+ os.path.join(config["log_dir"], "{organism}_{index_size}_generate_alfa_index.log")
+
+ shell:
+ """
+ alfa -a {input.gtf} \
+ -g {params.genome_index} \
+ --chr_len {input.chr_len} \
+ -p {threads} \
+ -o {params.out_dir} &> {log}
+ """
+
+
+rule alfa_qc:
+ ''' Run ALFA from stranded bedgraph files '''
+ input:
+ plus = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "{sample}_Signal.UniqueMultiple.out.plus.bg"),
+ minus = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "{sample}_Signal.UniqueMultiple.out.minus.bg"),
+ gtf = lambda wildcards: os.path.join(config["alfa_indexes"],
+ samples_table.loc[wildcards.sample, "organism"],
+ str(samples_table.loc[wildcards.sample, "index_size"]),
+ "ALFA",
+ "sorted_genes.stranded.ALFA_index")
+
+ output:
+ biotypes = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "ALFA_plots.Biotypes.pdf"),
+ categories = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "ALFA_plots.Categories.pdf"),
+ table = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "{sample}.ALFA_feature_counts.tsv")
+
+ params:
+ out_dir = lambda wildcards, output: os.path.dirname(output.biotypes),
+ alfa_orientation = lambda wildcards: directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]],
+ in_file_plus = lambda wildcards, input: os.path.basename(input.plus),
+ in_file_minus = lambda wildcards, input: os.path.basename(input.minus),
+ genome_index = lambda wildcards, input: os.path.abspath(os.path.join(os.path.dirname(input.gtf), "sorted_genes")),
+ name = "{sample}"
+
+ singularity:
+ "docker://zavolab/alfa:1.1.1"
+
+ log:
+ os.path.abspath(os.path.join(
+ config["log_dir"],
+ "{seqmode}",
+ "{sample}",
+ "alfa_qc.log"))
+
+ shell:
+ """
+ cd {params.out_dir}; \
+ (alfa -g {params.genome_index} \
+ --bedgraph {params.in_file_plus} {params.in_file_minus} {params.name} \
+ -s {params.alfa_orientation}) &> {log}
+ """
+
+
+rule alfa_qc_all_samples:
+ ''' Run ALFA from stranded bedgraph files on all samples '''
+ input:
+ tables = [os.path.join(
+ config["output_dir"],
+ samples_table.loc[sample1, "seqmode"],
+ str(sample1),
+ "ALFA",
+ sample1 + ".ALFA_feature_counts.tsv")
+ for sample1 in list(samples_table.index.values)]
+
+ output:
+ biotypes = os.path.join(
+ config["output_dir"],
+ "ALFA",
+ "ALFA_plots.Biotypes.pdf"),
+ categories = os.path.join(
+ config["output_dir"],
+ "ALFA",
+ "ALFA_plots.Categories.pdf")
+
+ params:
+ out_dir = lambda wildcards, output: os.path.dirname(output.biotypes)
+
+ log:
+ os.path.abspath(
+ os.path.join(config["log_dir"],
+ "alfa_qc_all_samples.log"))
+
+ singularity:
+ "docker://zavolab/alfa:1.1.1"
+
+ shell:
+ """
+ (alfa -c {input.tables} -o {params.out_dir}) &> {log}
+ """
diff --git a/images/dag_test_workflow.svg b/images/dag_test_workflow.svg
index 0c0c25a7a513e3dd8c1fd0299cde5aada907fa4d..720c5f02a83574369148ce65600ce833d0b3a919 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,407 +1,591 @@
<?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 2.38.0 (20140413.2041)
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
-->
<!-- Title: snakemake_dag Pages: 1 -->
-<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)">
+<svg width="2113pt" height="625pt"
+ viewBox="0.00 0.00 2112.50 625.00" 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(4 621)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-405 1853.85,-405 1853.85,4 -4,4"/>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-621 2108.5,-621 2108.5,4 -4,4"/>
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-<text text-anchor="middle" x="1035" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
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-<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 id="node2" class="node">
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+<path fill="none" stroke="#d8b456" stroke-width="2" d="M1766,-324C1766,-324 1671,-324 1671,-324 1665,-324 1659,-318 1659,-312 1659,-312 1659,-300 1659,-300 1659,-294 1665,-288 1671,-288 1671,-288 1766,-288 1766,-288 1772,-288 1778,-294 1778,-300 1778,-300 1778,-312 1778,-312 1778,-318 1772,-324 1766,-324"/>
+<text text-anchor="middle" x="1718.5" y="-303.5" 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>
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+<g id="edge6" class="edge">
+<title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1673.96,-287.94C1655.28,-279.22 1634.27,-267.21 1618.5,-252 1551.98,-187.87 1562.57,-150.9 1514.5,-72 1509.01,-62.99 1502.83,-53.25 1497.26,-44.6"/>
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<!-- 7 -->
-<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 id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M1440.5,-108C1440.5,-108 1312.5,-108 1312.5,-108 1306.5,-108 1300.5,-102 1300.5,-96 1300.5,-96 1300.5,-84 1300.5,-84 1300.5,-78 1306.5,-72 1312.5,-72 1312.5,-72 1440.5,-72 1440.5,-72 1446.5,-72 1452.5,-78 1452.5,-84 1452.5,-84 1452.5,-96 1452.5,-96 1452.5,-102 1446.5,-108 1440.5,-108"/>
+<text text-anchor="middle" x="1376.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="1376.5" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 7->0 -->
-<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"/>
+<g id="edge7" class="edge">
+<title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1401.94,-71.88C1415.29,-62.89 1431.82,-51.76 1446.28,-42.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1448.62,-44.68 1454.96,-36.19 1444.71,-38.87 1448.62,-44.68"/>
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<!-- 8 -->
-<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 id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M886,-108C886,-108 749,-108 749,-108 743,-108 737,-102 737,-96 737,-96 737,-84 737,-84 737,-78 743,-72 749,-72 749,-72 886,-72 886,-72 892,-72 898,-78 898,-84 898,-84 898,-96 898,-96 898,-102 892,-108 886,-108"/>
+<text text-anchor="middle" x="817.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<text text-anchor="middle" x="817.5" 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="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 id="edge8" class="edge">
+<title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M898.39,-73.35C901.46,-72.87 904.51,-72.42 907.5,-72 1108.54,-43.78 1351.45,-26.97 1443.09,-21.23"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1443.49,-24.71 1453.25,-20.6 1443.06,-17.73 1443.49,-24.71"/>
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<!-- 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 id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1078.5,-108C1078.5,-108 928.5,-108 928.5,-108 922.5,-108 916.5,-102 916.5,-96 916.5,-96 916.5,-84 916.5,-84 916.5,-78 922.5,-72 928.5,-72 928.5,-72 1078.5,-72 1078.5,-72 1084.5,-72 1090.5,-78 1090.5,-84 1090.5,-84 1090.5,-96 1090.5,-96 1090.5,-102 1084.5,-108 1078.5,-108"/>
+<text text-anchor="middle" x="1003.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1003.5" 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="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 id="edge9" class="edge">
+<title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1090.6,-73.43C1093.6,-72.94 1096.57,-72.46 1099.5,-72 1225.04,-52.16 1374.5,-32.53 1442.92,-23.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1443.72,-27.19 1453.19,-22.45 1442.83,-20.24 1443.72,-27.19"/>
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<!-- 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 id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1270.5,-108C1270.5,-108 1120.5,-108 1120.5,-108 1114.5,-108 1108.5,-102 1108.5,-96 1108.5,-96 1108.5,-84 1108.5,-84 1108.5,-78 1114.5,-72 1120.5,-72 1120.5,-72 1270.5,-72 1270.5,-72 1276.5,-72 1282.5,-78 1282.5,-84 1282.5,-84 1282.5,-96 1282.5,-96 1282.5,-102 1276.5,-108 1270.5,-108"/>
+<text text-anchor="middle" x="1195.5" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<text text-anchor="middle" x="1195.5" 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="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"/>
+<g id="edge10" class="edge">
+<title>10->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1264.85,-71.97C1321.11,-58.15 1398.22,-39.21 1443.37,-28.12"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1444.43,-31.46 1453.31,-25.68 1442.76,-24.66 1444.43,-31.46"/>
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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 id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1574.5,-324C1574.5,-324 1538.5,-324 1538.5,-324 1532.5,-324 1526.5,-318 1526.5,-312 1526.5,-312 1526.5,-300 1526.5,-300 1526.5,-294 1532.5,-288 1538.5,-288 1538.5,-288 1574.5,-288 1574.5,-288 1580.5,-288 1586.5,-294 1586.5,-300 1586.5,-300 1586.5,-312 1586.5,-312 1586.5,-318 1580.5,-324 1574.5,-324"/>
+<text text-anchor="middle" x="1556.5" y="-303.5" 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="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"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1072.22,-15.8673 1062.16,-19.1846 1072.09,-22.8662 1072.22,-15.8673"/>
+<g id="edge11" class="edge">
+<title>11->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1552.37,-287.98C1542.96,-249.41 1518.99,-152.46 1496.5,-72 1494.11,-63.44 1491.36,-54.16 1488.82,-45.79"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1492.14,-44.67 1485.87,-36.13 1485.45,-46.72 1492.14,-44.67"/>
+</g>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M1794.5,-252C1794.5,-252 1672.5,-252 1672.5,-252 1666.5,-252 1660.5,-246 1660.5,-240 1660.5,-240 1660.5,-228 1660.5,-228 1660.5,-222 1666.5,-216 1672.5,-216 1672.5,-216 1794.5,-216 1794.5,-216 1800.5,-216 1806.5,-222 1806.5,-228 1806.5,-228 1806.5,-240 1806.5,-240 1806.5,-246 1800.5,-252 1794.5,-252"/>
+<text text-anchor="middle" x="1733.5" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+</g>
+<!-- 11->26 -->
+<g id="edge57" class="edge">
+<title>11->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1586.53,-293.13C1612.36,-282.91 1650.22,-267.94 1681.05,-255.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1682.35,-258.99 1690.37,-252.06 1679.78,-252.48 1682.35,-258.99"/>
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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 id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M1969.5,-324C1969.5,-324 1933.5,-324 1933.5,-324 1927.5,-324 1921.5,-318 1921.5,-312 1921.5,-312 1921.5,-300 1921.5,-300 1921.5,-294 1927.5,-288 1933.5,-288 1933.5,-288 1969.5,-288 1969.5,-288 1975.5,-288 1981.5,-294 1981.5,-300 1981.5,-300 1981.5,-312 1981.5,-312 1981.5,-318 1975.5,-324 1969.5,-324"/>
+<text text-anchor="middle" x="1951.5" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
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<!-- 12->0 -->
-<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="edge12" class="edge">
+<title>12->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1921.02,-302.73C1853.83,-297.23 1695.43,-281.45 1651.5,-252 1612.17,-225.64 1567.75,-108.42 1537.5,-72 1529.07,-61.85 1518.77,-51.73 1509.27,-43.1"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1511.33,-40.24 1501.52,-36.22 1506.68,-45.48 1511.33,-40.24"/>
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+<!-- 28 -->
+<g id="node29" class="node">
+<title>28</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M2092.5,-252C2092.5,-252 1970.5,-252 1970.5,-252 1964.5,-252 1958.5,-246 1958.5,-240 1958.5,-240 1958.5,-228 1958.5,-228 1958.5,-222 1964.5,-216 1970.5,-216 1970.5,-216 2092.5,-216 2092.5,-216 2098.5,-216 2104.5,-222 2104.5,-228 2104.5,-228 2104.5,-240 2104.5,-240 2104.5,-246 2098.5,-252 2092.5,-252"/>
+<text text-anchor="middle" x="2031.5" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
+</g>
+<!-- 12->28 -->
+<g id="edge59" class="edge">
+<title>12->28</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1971.28,-287.7C1981.25,-278.97 1993.51,-268.24 2004.36,-258.75"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="2006.73,-261.32 2011.95,-252.1 2002.12,-256.06 2006.73,-261.32"/>
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<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
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-<text text-anchor="middle" x="854" y="-306" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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-<!-- 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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+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1760.5,-180C1760.5,-180 1730.5,-180 1730.5,-180 1724.5,-180 1718.5,-174 1718.5,-168 1718.5,-168 1718.5,-156 1718.5,-156 1718.5,-150 1724.5,-144 1730.5,-144 1730.5,-144 1760.5,-144 1760.5,-144 1766.5,-144 1772.5,-150 1772.5,-156 1772.5,-156 1772.5,-168 1772.5,-168 1772.5,-174 1766.5,-180 1760.5,-180"/>
+<text text-anchor="middle" x="1745.5" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
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-<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
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-<!-- 13->16 -->
-<g id="edge39" class="edge"><title>13->16</title>
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+<g id="edge13" class="edge">
+<title>13->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1727.32,-143.9C1701.31,-119.54 1655.57,-77.2 1646.5,-72 1605.47,-48.47 1552.65,-33.92 1517.74,-26.15"/>
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-<!-- 21 -->
-<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>
+<!-- 15 -->
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M1802.5,-108C1802.5,-108 1710.5,-108 1710.5,-108 1704.5,-108 1698.5,-102 1698.5,-96 1698.5,-96 1698.5,-84 1698.5,-84 1698.5,-78 1704.5,-72 1710.5,-72 1710.5,-72 1802.5,-72 1802.5,-72 1808.5,-72 1814.5,-78 1814.5,-84 1814.5,-84 1814.5,-96 1814.5,-96 1814.5,-102 1808.5,-108 1802.5,-108"/>
+<text text-anchor="middle" x="1756.5" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
-<!-- 13->21 -->
-<g id="edge44" class="edge"><title>13->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M868.474,-290.357C889.936,-264.936 930.317,-217.108 955.021,-187.848"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="957.768,-190.02 961.545,-180.121 952.419,-185.504 957.768,-190.02"/>
+<!-- 13->15 -->
+<g id="edge42" class="edge">
+<title>13->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1748.22,-143.7C1749.43,-135.98 1750.89,-126.71 1752.24,-118.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1755.72,-118.53 1753.81,-108.1 1748.8,-117.44 1755.72,-118.53"/>
</g>
<!-- 14 -->
-<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 id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M1887.5,-180C1887.5,-180 1857.5,-180 1857.5,-180 1851.5,-180 1845.5,-174 1845.5,-168 1845.5,-168 1845.5,-156 1845.5,-156 1845.5,-150 1851.5,-144 1857.5,-144 1857.5,-144 1887.5,-144 1887.5,-144 1893.5,-144 1899.5,-150 1899.5,-156 1899.5,-156 1899.5,-168 1899.5,-168 1899.5,-174 1893.5,-180 1887.5,-180"/>
+<text text-anchor="middle" x="1872.5" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
+</g>
+<!-- 14->0 -->
+<g id="edge14" class="edge">
+<title>14->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1868.06,-143.8C1861.78,-123.19 1848.21,-89.29 1823.5,-72 1774.63,-37.82 1596.27,-24.81 1517.89,-20.67"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1517.68,-17.15 1507.51,-20.14 1517.32,-24.14 1517.68,-17.15"/>
+</g>
+<!-- 14->15 -->
+<g id="edge43" class="edge">
+<title>14->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1845.3,-144.59C1829.93,-135.31 1810.5,-123.59 1793.74,-113.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1795.11,-110.21 1784.74,-108.04 1791.49,-116.2 1795.11,-110.21"/>
+</g>
+<!-- 15->0 -->
+<g id="edge15" class="edge">
+<title>15->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1698.3,-74.24C1643.75,-60.41 1563.86,-40.14 1517.52,-28.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1518.16,-24.94 1507.61,-25.87 1516.44,-31.73 1518.16,-24.94"/>
</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->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="#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>
+<!-- 16 -->
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M975.5,-542.5C975.5,-542.5 847.5,-542.5 847.5,-542.5 841.5,-542.5 835.5,-536.5 835.5,-530.5 835.5,-530.5 835.5,-518.5 835.5,-518.5 835.5,-512.5 841.5,-506.5 847.5,-506.5 847.5,-506.5 975.5,-506.5 975.5,-506.5 981.5,-506.5 987.5,-512.5 987.5,-518.5 987.5,-518.5 987.5,-530.5 987.5,-530.5 987.5,-536.5 981.5,-542.5 975.5,-542.5"/>
+<text text-anchor="middle" x="911.5" y="-522" font-family="sans" font-size="10.00">pe_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"/>
+<!-- 16->3 -->
+<g id="edge16" class="edge">
+<title>16->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M902.6,-506.22C889.74,-479.63 867.5,-426.73 867.5,-379 867.5,-379 867.5,-379 867.5,-305 867.5,-264.5 856.77,-218.63 848.84,-190.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="852.1,-188.93 845.96,-180.29 845.37,-190.87 852.1,-188.93"/>
</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 id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#56b9d8" stroke-width="2" d="M1481,-468C1481,-468 1380,-468 1380,-468 1374,-468 1368,-462 1368,-456 1368,-456 1368,-444 1368,-444 1368,-438 1374,-432 1380,-432 1380,-432 1481,-432 1481,-432 1487,-432 1493,-438 1493,-444 1493,-444 1493,-456 1493,-456 1493,-462 1487,-468 1481,-468"/>
+<text text-anchor="middle" x="1430.5" y="-447.5" font-family="sans" font-size="10.00">pe_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"/>
+<!-- 16->19 -->
+<g id="edge48" class="edge">
+<title>16->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M987.52,-512.88C1086.91,-499 1259.83,-474.84 1357.63,-461.18"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1358.31,-464.62 1367.73,-459.77 1357.34,-457.69 1358.31,-464.62"/>
</g>
-<!-- 22 -->
-<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="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>
-<!-- 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"/>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M1082.5,-180C1082.5,-180 964.5,-180 964.5,-180 958.5,-180 952.5,-174 952.5,-168 952.5,-168 952.5,-156 952.5,-156 952.5,-150 958.5,-144 964.5,-144 964.5,-144 1082.5,-144 1082.5,-144 1088.5,-144 1094.5,-150 1094.5,-156 1094.5,-156 1094.5,-168 1094.5,-168 1094.5,-174 1088.5,-180 1082.5,-180"/>
+<text text-anchor="middle" x="1023.5" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
-<!-- 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"/>
+<!-- 16->24 -->
+<g id="edge53" class="edge">
+<title>16->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M911.5,-506.15C911.5,-479.02 911.5,-424.91 911.5,-379 911.5,-379 911.5,-379 911.5,-305 911.5,-264.55 906.62,-248.64 930.5,-216 939.95,-203.08 953.57,-192.86 967.48,-184.97"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="969.43,-187.9 976.63,-180.13 966.15,-181.72 969.43,-187.9"/>
</g>
<!-- 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"/>
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#56d8c1" stroke-width="2" d="M1049,-252C1049,-252 952,-252 952,-252 946,-252 940,-246 940,-240 940,-240 940,-228 940,-228 940,-222 946,-216 952,-216 952,-216 1049,-216 1049,-216 1055,-216 1061,-222 1061,-228 1061,-228 1061,-240 1061,-240 1061,-246 1055,-252 1049,-252"/>
+<text text-anchor="middle" x="1000.5" y="-231.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+</g>
+<!-- 17->3 -->
+<g id="edge17" class="edge">
+<title>17->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M961.36,-215.88C939.49,-206.31 912.04,-194.3 888.84,-184.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="890.08,-180.87 879.51,-180.07 887.27,-187.28 890.08,-180.87"/>
+</g>
+<!-- 17->4 -->
+<g id="edge19" class="edge">
+<title>17->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1061.04,-217.91C1063.9,-217.25 1066.73,-216.61 1069.5,-216 1128.09,-203.08 1194.15,-190.17 1246.49,-180.33"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1247.25,-183.75 1256.44,-178.46 1245.96,-176.87 1247.25,-183.75"/>
</g>
<!-- 18 -->
-<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="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"/>
-</g>
-<!-- 18->6 -->
-<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"/>
-</g>
-<!-- 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"/>
-</g>
-<!-- 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 id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M1321.5,-542.5C1321.5,-542.5 1211.5,-542.5 1211.5,-542.5 1205.5,-542.5 1199.5,-536.5 1199.5,-530.5 1199.5,-530.5 1199.5,-518.5 1199.5,-518.5 1199.5,-512.5 1205.5,-506.5 1211.5,-506.5 1211.5,-506.5 1321.5,-506.5 1321.5,-506.5 1327.5,-506.5 1333.5,-512.5 1333.5,-518.5 1333.5,-518.5 1333.5,-530.5 1333.5,-530.5 1333.5,-536.5 1327.5,-542.5 1321.5,-542.5"/>
+<text text-anchor="middle" x="1266.5" y="-522" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
-<!-- 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"/>
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-<!-- 21->8 -->
-<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"/>
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-<!-- 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"/>
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-<!-- 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>
+<!-- 18->4 -->
+<g id="edge18" class="edge">
+<title>18->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1266.5,-506.15C1266.5,-479.02 1266.5,-424.91 1266.5,-379 1266.5,-379 1266.5,-379 1266.5,-305 1266.5,-259.77 1296.62,-214.85 1318.68,-188"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1321.44,-190.16 1325.23,-180.27 1316.09,-185.64 1321.44,-190.16"/>
</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"/>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M1877,-468C1877,-468 1794,-468 1794,-468 1788,-468 1782,-462 1782,-456 1782,-456 1782,-444 1782,-444 1782,-438 1788,-432 1794,-432 1794,-432 1877,-432 1877,-432 1883,-432 1889,-438 1889,-444 1889,-444 1889,-456 1889,-456 1889,-462 1883,-468 1877,-468"/>
+<text text-anchor="middle" x="1835.5" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
-<!-- 24 -->
-<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>
+<!-- 18->22 -->
+<g id="edge51" class="edge">
+<title>18->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1333.73,-514.93C1444.4,-500.83 1663.5,-472.92 1771.81,-459.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1772.46,-462.56 1781.94,-457.82 1771.58,-455.62 1772.46,-462.56"/>
</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"/>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M1226,-180C1226,-180 1125,-180 1125,-180 1119,-180 1113,-174 1113,-168 1113,-168 1113,-156 1113,-156 1113,-150 1119,-144 1125,-144 1125,-144 1226,-144 1226,-144 1232,-144 1238,-150 1238,-156 1238,-156 1238,-168 1238,-168 1238,-174 1232,-180 1226,-180"/>
+<text text-anchor="middle" x="1175.5" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+</g>
+<!-- 18->25 -->
+<g id="edge55" class="edge">
+<title>18->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1258.81,-506.09C1247.71,-479.33 1228.5,-426.21 1228.5,-379 1228.5,-379 1228.5,-379 1228.5,-305 1228.5,-264.46 1223.88,-253.51 1208.5,-216 1204.7,-206.72 1199.33,-197.22 1194.03,-188.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1196.82,-186.75 1188.38,-180.34 1190.98,-190.62 1196.82,-186.75"/>
+</g>
+<!-- 19->5 -->
+<g id="edge20" class="edge">
+<title>19->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1368.25,-431.95C1350.75,-423.98 1333.72,-412.47 1323.5,-396 1315.06,-382.41 1314.85,-373.46 1323.5,-360 1334.35,-343.11 1352.07,-331.53 1370.43,-323.63"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1371.76,-326.87 1379.76,-319.93 1369.18,-320.36 1371.76,-326.87"/>
+</g>
+<!-- 19->11 -->
+<g id="edge34" class="edge">
+<title>19->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1487.66,-431.93C1506.05,-423.8 1524.91,-412.21 1537.5,-396 1551.1,-378.5 1555.5,-353.46 1556.7,-334.4"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1560.2,-334.36 1557.08,-324.24 1553.21,-334.1 1560.2,-334.36"/>
</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>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M1516.5,-396C1516.5,-396 1344.5,-396 1344.5,-396 1338.5,-396 1332.5,-390 1332.5,-384 1332.5,-384 1332.5,-372 1332.5,-372 1332.5,-366 1338.5,-360 1344.5,-360 1344.5,-360 1516.5,-360 1516.5,-360 1522.5,-360 1528.5,-366 1528.5,-372 1528.5,-372 1528.5,-384 1528.5,-384 1528.5,-390 1522.5,-396 1516.5,-396"/>
+<text text-anchor="middle" x="1430.5" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1430.5" y="-370" font-family="sans" font-size="10.00">seqmode: paired_end</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"/>
+<!-- 19->20 -->
+<g id="edge49" class="edge">
+<title>19->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1430.5,-431.7C1430.5,-423.98 1430.5,-414.71 1430.5,-406.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1434,-406.1 1430.5,-396.1 1427,-406.1 1434,-406.1"/>
+</g>
+<!-- 20->5 -->
+<g id="edge21" class="edge">
+<title>20->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1432.72,-359.7C1433.72,-351.98 1434.91,-342.71 1436.01,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1439.5,-334.47 1437.3,-324.1 1432.55,-333.58 1439.5,-334.47"/>
+</g>
+<!-- 20->11 -->
+<g id="edge35" class="edge">
+<title>20->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1461.32,-359.88C1478.2,-350.5 1499.28,-338.79 1517.32,-328.77"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1519.39,-331.62 1526.43,-323.71 1515.99,-325.5 1519.39,-331.62"/>
</g>
-<!-- 25 -->
-<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>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M1732.5,-396C1732.5,-396 1596.5,-396 1596.5,-396 1590.5,-396 1584.5,-390 1584.5,-384 1584.5,-384 1584.5,-372 1584.5,-372 1584.5,-366 1590.5,-360 1596.5,-360 1596.5,-360 1732.5,-360 1732.5,-360 1738.5,-360 1744.5,-366 1744.5,-372 1744.5,-372 1744.5,-384 1744.5,-384 1744.5,-390 1738.5,-396 1732.5,-396"/>
+<text text-anchor="middle" x="1664.5" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 21->5 -->
+<g id="edge22" class="edge">
+<title>21->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1609.75,-359.97C1577.9,-350.06 1537.58,-337.51 1504.17,-327.12"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1505.09,-323.74 1494.5,-324.11 1503.01,-330.42 1505.09,-323.74"/>
+</g>
+<!-- 21->6 -->
+<g id="edge25" class="edge">
+<title>21->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1677.85,-359.7C1684.26,-351.39 1692.06,-341.28 1699.11,-332.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1701.97,-334.16 1705.31,-324.1 1696.43,-329.88 1701.97,-334.16"/>
+</g>
+<!-- 22->6 -->
+<g id="edge23" class="edge">
+<title>22->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1821.21,-431.84C1812.59,-421.47 1801.4,-407.99 1791.5,-396 1773.79,-374.54 1753.76,-350.1 1739.16,-332.27"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1741.51,-329.61 1732.46,-324.09 1736.09,-334.04 1741.51,-329.61"/>
+</g>
+<!-- 22->12 -->
+<g id="edge36" class="edge">
+<title>22->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1889.09,-448.07C1928.28,-444.23 1979.03,-431.98 2005.5,-396 2020.98,-374.96 2001.77,-349.31 1982.1,-330.96"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1984.41,-328.33 1974.61,-324.31 1979.77,-333.57 1984.41,-328.33"/>
</g>
-<!-- 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"/>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M1984.5,-396C1984.5,-396 1812.5,-396 1812.5,-396 1806.5,-396 1800.5,-390 1800.5,-384 1800.5,-384 1800.5,-372 1800.5,-372 1800.5,-366 1806.5,-360 1812.5,-360 1812.5,-360 1984.5,-360 1984.5,-360 1990.5,-360 1996.5,-366 1996.5,-372 1996.5,-372 1996.5,-384 1996.5,-384 1996.5,-390 1990.5,-396 1984.5,-396"/>
+<text text-anchor="middle" x="1898.5" y="-381" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<text text-anchor="middle" x="1898.5" y="-370" font-family="sans" font-size="10.00">seqmode: single_end</text>
+</g>
+<!-- 22->23 -->
+<g id="edge52" class="edge">
+<title>22->23</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1851.07,-431.7C1858.7,-423.22 1868.02,-412.86 1876.38,-403.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1879.02,-405.88 1883.11,-396.1 1873.81,-401.2 1879.02,-405.88"/>
+</g>
+<!-- 23->6 -->
+<g id="edge24" class="edge">
+<title>23->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1854.47,-359.88C1829.53,-350.18 1798.16,-337.98 1771.84,-327.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1772.98,-324.43 1762.39,-324.07 1770.44,-330.95 1772.98,-324.43"/>
+</g>
+<!-- 23->12 -->
+<g id="edge37" class="edge">
+<title>23->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1911.6,-359.7C1917.89,-351.39 1925.55,-341.28 1932.46,-332.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1935.3,-334.19 1938.55,-324.1 1929.72,-329.96 1935.3,-334.19"/>
+</g>
+<!-- 24->7 -->
+<g id="edge26" class="edge">
+<title>24->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1094.58,-145.82C1097.6,-145.2 1100.58,-144.59 1103.5,-144 1183.8,-127.78 1206.36,-124.57 1290.09,-108.27"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1290.91,-111.67 1300.05,-106.32 1289.56,-104.8 1290.91,-111.67"/>
+</g>
+<!-- 24->8 -->
+<g id="edge28" class="edge">
+<title>24->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M973.37,-143.97C944.46,-134.14 907.93,-121.73 877.5,-111.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="878.45,-108.01 867.85,-108.11 876.2,-114.64 878.45,-108.01"/>
+</g>
+<!-- 24->9 -->
+<g id="edge30" class="edge">
+<title>24->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1018.56,-143.7C1016.33,-135.9 1013.65,-126.51 1011.17,-117.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1014.5,-116.76 1008.39,-108.1 1007.77,-118.68 1014.5,-116.76"/>
+</g>
+<!-- 24->10 -->
+<g id="edge32" class="edge">
+<title>24->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1065.58,-143.88C1089.3,-134.22 1119.12,-122.09 1144.2,-111.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1145.62,-115.08 1153.56,-108.07 1142.98,-108.6 1145.62,-115.08"/>
+</g>
+<!-- 25->7 -->
+<g id="edge27" class="edge">
+<title>25->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1224.41,-143.97C1252.5,-134.19 1287.96,-121.84 1317.57,-111.52"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1319.07,-114.71 1327.37,-108.11 1316.77,-108.09 1319.07,-114.71"/>
+</g>
+<!-- 25->8 -->
+<g id="edge29" class="edge">
+<title>25->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1112.71,-145.98C1109.6,-145.3 1106.52,-144.63 1103.5,-144 1019.87,-126.46 996.21,-124.35 908.32,-108.14"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="908.92,-104.69 898.45,-106.31 907.64,-111.57 908.92,-104.69"/>
+</g>
+<!-- 25->9 -->
+<g id="edge31" class="edge">
+<title>25->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1133.42,-143.88C1109.7,-134.22 1079.88,-122.09 1054.8,-111.88"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1056.02,-108.6 1045.44,-108.07 1053.38,-115.08 1056.02,-108.6"/>
+</g>
+<!-- 25->10 -->
+<g id="edge33" class="edge">
+<title>25->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1180.44,-143.7C1182.67,-135.9 1185.35,-126.51 1187.83,-117.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1191.23,-118.68 1190.61,-108.1 1184.5,-116.76 1191.23,-118.68"/>
+</g>
+<!-- 26->13 -->
+<g id="edge38" class="edge">
+<title>26->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1736.47,-215.7C1737.79,-207.98 1739.38,-198.71 1740.85,-190.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1744.33,-190.55 1742.57,-180.1 1737.43,-189.37 1744.33,-190.55"/>
</g>
-<!-- 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>
-<path fill="none" stroke="grey" stroke-width="2" d="M1005.36,-215.697C1000.87,-207.644 995.441,-197.894 990.476,-188.982"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="993.454,-187.137 985.53,-180.104 987.339,-190.544 993.454,-187.137"/>
-</g>
-<!-- 27->22 -->
-<g id="edge47" class="edge"><title>27->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1039.46,-215.876C1052.3,-206.893 1068.2,-195.763 1082.09,-186.034"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1084.26,-188.792 1090.44,-180.19 1080.24,-183.057 1084.26,-188.792"/>
+<!-- 27 -->
+<g id="node28" class="node">
+<title>27</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M1928.5,-252C1928.5,-252 1836.5,-252 1836.5,-252 1830.5,-252 1824.5,-246 1824.5,-240 1824.5,-240 1824.5,-228 1824.5,-228 1824.5,-222 1830.5,-216 1836.5,-216 1836.5,-216 1928.5,-216 1928.5,-216 1934.5,-216 1940.5,-222 1940.5,-228 1940.5,-228 1940.5,-240 1940.5,-240 1940.5,-246 1934.5,-252 1928.5,-252"/>
+<text text-anchor="middle" x="1882.5" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
+</g>
+<!-- 27->13 -->
+<g id="edge39" class="edge">
+<title>27->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1848.99,-215.88C1828.65,-205.49 1802.7,-192.22 1781.87,-181.58"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1783.19,-178.33 1772.69,-176.9 1780.01,-184.56 1783.19,-178.33"/>
+</g>
+<!-- 27->14 -->
+<g id="edge41" class="edge">
+<title>27->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1880.03,-215.7C1878.93,-207.98 1877.6,-198.71 1876.37,-190.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1879.82,-189.51 1874.94,-180.1 1872.89,-190.5 1879.82,-189.51"/>
+</g>
+<!-- 28->14 -->
+<g id="edge40" class="edge">
+<title>28->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1992.6,-215.88C1967.01,-204.61 1933.73,-189.96 1908.7,-178.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1910.1,-175.73 1899.54,-174.9 1907.28,-182.14 1910.1,-175.73"/>
+</g>
+<!-- 29 -->
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M1062,-617C1062,-617 761,-617 761,-617 755,-617 749,-611 749,-605 749,-605 749,-593 749,-593 749,-587 755,-581 761,-581 761,-581 1062,-581 1062,-581 1068,-581 1074,-587 1074,-593 1074,-593 1074,-605 1074,-605 1074,-611 1068,-617 1062,-617"/>
+<text text-anchor="middle" x="911.5" y="-602" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="911.5" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+</g>
+<!-- 29->16 -->
+<g id="edge44" class="edge">
+<title>29->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M911.5,-580.82C911.5,-572.42 911.5,-562.12 911.5,-552.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="915,-552.56 911.5,-542.56 908,-552.56 915,-552.56"/>
+</g>
+<!-- 30 -->
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M1128,-324C1128,-324 1013,-324 1013,-324 1007,-324 1001,-318 1001,-312 1001,-312 1001,-300 1001,-300 1001,-294 1007,-288 1013,-288 1013,-288 1128,-288 1128,-288 1134,-288 1140,-294 1140,-300 1140,-300 1140,-312 1140,-312 1140,-318 1134,-324 1128,-324"/>
+<text text-anchor="middle" x="1070.5" y="-309" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<text text-anchor="middle" x="1070.5" y="-298" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 30->17 -->
+<g id="edge45" class="edge">
+<title>30->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1053.2,-287.7C1044.64,-279.14 1034.16,-268.66 1024.8,-259.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1027.15,-256.7 1017.6,-252.1 1022.2,-261.65 1027.15,-256.7"/>
+</g>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M1188,-252C1188,-252 1091,-252 1091,-252 1085,-252 1079,-246 1079,-240 1079,-240 1079,-228 1079,-228 1079,-222 1085,-216 1091,-216 1091,-216 1188,-216 1188,-216 1194,-216 1200,-222 1200,-228 1200,-228 1200,-240 1200,-240 1200,-246 1194,-252 1188,-252"/>
+<text text-anchor="middle" x="1139.5" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text>
+<text text-anchor="middle" x="1139.5" y="-226" font-family="sans" font-size="10.00">kmer: 31</text>
+</g>
+<!-- 30->33 -->
+<g id="edge60" class="edge">
+<title>30->33</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1087.56,-287.7C1096,-279.14 1106.32,-268.66 1115.54,-259.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.11,-261.68 1122.64,-252.1 1113.13,-256.77 1118.11,-261.68"/>
+</g>
+<!-- 31 -->
+<g id="node32" class="node">
+<title>31</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M1423,-617C1423,-617 1110,-617 1110,-617 1104,-617 1098,-611 1098,-605 1098,-605 1098,-593 1098,-593 1098,-587 1104,-581 1110,-581 1110,-581 1423,-581 1423,-581 1429,-581 1435,-587 1435,-593 1435,-593 1435,-605 1435,-605 1435,-611 1429,-617 1423,-617"/>
+<text text-anchor="middle" x="1266.5" y="-602" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<text text-anchor="middle" x="1266.5" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
+</g>
+<!-- 31->18 -->
+<g id="edge46" class="edge">
+<title>31->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1266.5,-580.82C1266.5,-572.42 1266.5,-562.12 1266.5,-552.69"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1270,-552.56 1266.5,-542.56 1263,-552.56 1270,-552.56"/>
+</g>
+<!-- 32 -->
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M1893,-545C1893,-545 1778,-545 1778,-545 1772,-545 1766,-539 1766,-533 1766,-533 1766,-516 1766,-516 1766,-510 1772,-504 1778,-504 1778,-504 1893,-504 1893,-504 1899,-504 1905,-510 1905,-516 1905,-516 1905,-533 1905,-533 1905,-539 1899,-545 1893,-545"/>
+<text text-anchor="middle" x="1835.5" y="-533" font-family="sans" font-size="10.00">create_index_star</text>
+<text text-anchor="middle" x="1835.5" y="-522" font-family="sans" font-size="10.00">index_size: 75</text>
+<text text-anchor="middle" x="1835.5" y="-511" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
+</g>
+<!-- 32->19 -->
+<g id="edge47" class="edge">
+<title>32->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1765.88,-511.04C1692.65,-497.93 1577.92,-477.39 1503.47,-464.06"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.69,-460.55 1493.23,-462.23 1502.46,-467.44 1503.69,-460.55"/>
+</g>
+<!-- 32->22 -->
+<g id="edge50" class="edge">
+<title>32->22</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1835.5,-503.69C1835.5,-495.91 1835.5,-486.84 1835.5,-478.45"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1839,-478.32 1835.5,-468.32 1832,-478.32 1839,-478.32"/>
+</g>
+<!-- 32->27 -->
+<g id="edge58" class="edge">
+<title>32->27</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1888.04,-503.93C1932.59,-484.19 1993.58,-448.99 2021.5,-396 2044.78,-351.82 2024.92,-324.18 1990.5,-288 1977.81,-274.66 1961.04,-264.22 1944.52,-256.27"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1945.95,-253.07 1935.4,-252.1 1943.04,-259.44 1945.95,-253.07"/>
+</g>
+<!-- 33->24 -->
+<g id="edge54" class="edge">
+<title>33->24</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1111.12,-215.88C1095.96,-206.72 1077.09,-195.34 1060.76,-185.48"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1062.36,-182.36 1051.99,-180.19 1058.74,-188.35 1062.36,-182.36"/>
+</g>
+<!-- 33->25 -->
+<g id="edge56" class="edge">
+<title>33->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M1148.4,-215.7C1152.5,-207.73 1157.45,-198.1 1161.99,-189.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1165.24,-190.6 1166.7,-180.1 1159.02,-187.4 1165.24,-190.6"/>
</g>
</g>
</svg>
diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index a2a0d009dcc914acf858cb6594e35f11f4f963cf..2cd57eb5e4559967bd92fae1fbe82566094a064c 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,313 +1,439 @@
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<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.38.0 (20140413.2041)
+<!-- Generated by graphviz version 2.42.3 (20191010.1750)
-->
<!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 1070.98 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 400)">
+<svg width="987pt" height="620pt"
+ viewBox="0.00 0.00 987.00 620.00" 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(4 616)">
<title>snakemake_dag</title>
-<polygon fill="white" stroke="none" points="-4,4 -4,-400 1066.98,-400 1066.98,4 -4,4"/>
+<polygon fill="white" stroke="transparent" points="-4,4 -4,-616 983,-616 983,4 -4,4"/>
<!-- 0 -->
-<g id="node1" class="node"><title>0</title>
-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M304,-36C304,-36 274,-36 274,-36 268,-36 262,-30 262,-24 262,-24 262,-12 262,-12 262,-6 268,-0 274,-0 274,-0 304,-0 304,-0 310,-0 316,-6 316,-12 316,-12 316,-24 316,-24 316,-30 310,-36 304,-36"/>
-<text text-anchor="middle" x="289" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
+<title>0</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M506,-36C506,-36 476,-36 476,-36 470,-36 464,-30 464,-24 464,-24 464,-12 464,-12 464,-6 470,0 476,0 476,0 506,0 506,0 512,0 518,-6 518,-12 518,-12 518,-24 518,-24 518,-30 512,-36 506,-36"/>
+<text text-anchor="middle" x="491" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
<!-- 1 -->
-<g id="node2" class="node"><title>1</title>
-<path fill="none" stroke="#56d892" stroke-width="2" d="M85.5,-108C85.5,-108 50.5,-108 50.5,-108 44.5,-108 38.5,-102 38.5,-96 38.5,-96 38.5,-84 38.5,-84 38.5,-78 44.5,-72 50.5,-72 50.5,-72 85.5,-72 85.5,-72 91.5,-72 97.5,-78 97.5,-84 97.5,-84 97.5,-96 97.5,-96 97.5,-102 91.5,-108 85.5,-108"/>
-<text text-anchor="middle" x="68" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
+<g id="node2" class="node">
+<title>1</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M188,-108C188,-108 148,-108 148,-108 142,-108 136,-102 136,-96 136,-96 136,-84 136,-84 136,-78 142,-72 148,-72 148,-72 188,-72 188,-72 194,-72 200,-78 200,-84 200,-84 200,-96 200,-96 200,-102 194,-108 188,-108"/>
+<text text-anchor="middle" x="168" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
</g>
<!-- 1->0 -->
-<g id="edge8" class="edge"><title>1->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M97.6525,-75.6092C100.786,-74.3338 103.944,-73.1059 107,-72 156.36,-54.1377 214.865,-37.9591 251.957,-28.3004"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="253.018,-31.6413 261.826,-25.753 251.268,-24.8635 253.018,-31.6413"/>
+<g id="edge4" class="edge">
+<title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M200,-74.99C203.01,-73.9 206.05,-72.88 209,-72 294.71,-46.48 398.9,-30.69 453.49,-23.53"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="454.26,-26.96 463.73,-22.21 453.36,-20.02 454.26,-26.96"/>
</g>
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-<g id="node3" class="node"><title>2</title>
-<path fill="none" stroke="#d8b456" stroke-width="2" d="M158,-108C158,-108 128,-108 128,-108 122,-108 116,-102 116,-96 116,-96 116,-84 116,-84 116,-78 122,-72 128,-72 128,-72 158,-72 158,-72 164,-72 170,-78 170,-84 170,-84 170,-96 170,-96 170,-102 164,-108 158,-108"/>
-<text text-anchor="middle" x="143" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
+<g id="node3" class="node">
+<title>2</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M260,-108C260,-108 230,-108 230,-108 224,-108 218,-102 218,-96 218,-96 218,-84 218,-84 218,-78 224,-72 230,-72 230,-72 260,-72 260,-72 266,-72 272,-78 272,-84 272,-84 272,-96 272,-96 272,-102 266,-108 260,-108"/>
+<text text-anchor="middle" x="245" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
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<!-- 2->0 -->
-<g id="edge7" class="edge"><title>2->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="254.026,-39.6497 261.53,-32.1703 251,-33.3377 254.026,-39.6497"/>
+<g id="edge2" class="edge">
+<title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M272.15,-77.12C276.73,-75.3 281.47,-73.52 286,-72 343.68,-52.69 412.45,-36.2 453.87,-26.95"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="454.78,-30.33 463.79,-24.76 453.27,-23.5 454.78,-30.33"/>
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-<g id="node4" class="node"><title>3</title>
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-<text text-anchor="middle" x="251" y="-231.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
+<g id="node4" class="node">
+<title>3</title>
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+<text text-anchor="middle" x="390" y="-447.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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-<g id="edge1" class="edge"><title>3->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="283.24,-46.7217 283.043,-36.1287 276.591,-44.5326 283.24,-46.7217"/>
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+<title>3->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M450.25,-431.97C470.89,-423.78 492.82,-412.12 509,-396 539.72,-365.39 549,-350.37 549,-307 549,-307 549,-307 549,-161 549,-117.7 525.6,-72.11 508.52,-44.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="511.36,-42.55 503.02,-36.01 505.46,-46.32 511.36,-42.55"/>
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-<path fill="none" stroke="#8fd856" stroke-width="2" d="M138,-252C138,-252 12,-252 12,-252 6,-252 1.42109e-14,-246 1.42109e-14,-240 1.42109e-14,-240 1.42109e-14,-228 1.42109e-14,-228 1.42109e-14,-222 6,-216 12,-216 12,-216 138,-216 138,-216 144,-216 150,-222 150,-228 150,-228 150,-240 150,-240 150,-246 144,-252 138,-252"/>
-<text text-anchor="middle" x="75" y="-231.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node5" class="node">
+<title>4</title>
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+<text text-anchor="middle" x="587" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 4->0 -->
-<g id="edge6" class="edge"><title>4->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M92.1508,-215.849C130.029,-177.971 220.923,-87.0767 264.668,-43.3318"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="267.171,-45.7784 271.768,-36.2325 262.222,-40.8287 267.171,-45.7784"/>
+<g id="edge8" class="edge">
+<title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M587,-431.95C587,-405.29 587,-352.11 587,-307 587,-307 587,-307 587,-161 587,-120.03 586.13,-105.82 563,-72 553.82,-58.57 540.08,-47.25 527.07,-38.57"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="528.56,-35.37 518.23,-32.99 524.82,-41.29 528.56,-35.37"/>
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-<path fill="none" stroke="#a7d856" stroke-width="2" d="M876,-108C876,-108 788,-108 788,-108 782,-108 776,-102 776,-96 776,-96 776,-84 776,-84 776,-78 782,-72 788,-72 788,-72 876,-72 876,-72 882,-72 888,-78 888,-84 888,-84 888,-96 888,-96 888,-102 882,-108 876,-108"/>
-<text text-anchor="middle" x="832" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<g id="node6" class="node">
+<title>5</title>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M450.5,-324C450.5,-324 355.5,-324 355.5,-324 349.5,-324 343.5,-318 343.5,-312 343.5,-312 343.5,-300 343.5,-300 343.5,-294 349.5,-288 355.5,-288 355.5,-288 450.5,-288 450.5,-288 456.5,-288 462.5,-294 462.5,-300 462.5,-300 462.5,-312 462.5,-312 462.5,-318 456.5,-324 450.5,-324"/>
+<text text-anchor="middle" x="403" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 5->0 -->
-<g id="edge5" class="edge"><title>5->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M775.935,-81.7724C664.916,-67.4607 419.77,-35.8579 326.247,-23.8017"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="326.492,-20.3043 316.126,-22.4969 325.597,-27.2469 326.492,-20.3043"/>
+<g id="edge7" class="edge">
+<title>5->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M446.39,-287.77C461.66,-279.38 477.21,-267.65 486,-252 523.15,-185.9 508.59,-91.71 498.12,-45.99"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="501.51,-45.12 495.77,-36.22 494.7,-46.76 501.51,-45.12"/>
</g>
<!-- 6 -->
-<g id="node7" class="node"><title>6</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M562,-180C562,-180 450,-180 450,-180 444,-180 438,-174 438,-168 438,-168 438,-156 438,-156 438,-150 444,-144 450,-144 450,-144 562,-144 562,-144 568,-144 574,-150 574,-156 574,-156 574,-168 574,-168 574,-174 568,-180 562,-180"/>
-<text text-anchor="middle" x="506" y="-159.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#5692d8" stroke-width="2" d="M775,-396C775,-396 647,-396 647,-396 641,-396 635,-390 635,-384 635,-384 635,-372 635,-372 635,-366 641,-360 647,-360 647,-360 775,-360 775,-360 781,-360 787,-366 787,-372 787,-372 787,-384 787,-384 787,-390 781,-396 775,-396"/>
+<text text-anchor="middle" x="711" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
<!-- 6->0 -->
-<g id="edge2" class="edge"><title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M479.825,-143.871C440.805,-118.338 367.323,-70.253 323.813,-41.7808"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="325.552,-38.7362 315.268,-36.1893 321.719,-44.5936 325.552,-38.7362"/>
+<g id="edge5" class="edge">
+<title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M700.02,-359.84C684.49,-333.89 658,-282.63 658,-235 658,-235 658,-235 658,-161 658,-93.03 576.72,-50.79 527.57,-31.45"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="528.79,-28.17 518.2,-27.89 526.31,-34.72 528.79,-28.17"/>
</g>
<!-- 7 -->
-<g id="node8" class="node"><title>7</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M407.5,-180C407.5,-180 276.5,-180 276.5,-180 270.5,-180 264.5,-174 264.5,-168 264.5,-168 264.5,-156 264.5,-156 264.5,-150 270.5,-144 276.5,-144 276.5,-144 407.5,-144 407.5,-144 413.5,-144 419.5,-150 419.5,-156 419.5,-156 419.5,-168 419.5,-168 419.5,-174 413.5,-180 407.5,-180"/>
-<text text-anchor="middle" x="342" y="-159.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#d6d856" stroke-width="2" d="M967,-396C967,-396 817,-396 817,-396 811,-396 805,-390 805,-384 805,-384 805,-372 805,-372 805,-366 811,-360 817,-360 817,-360 967,-360 967,-360 973,-360 979,-366 979,-372 979,-372 979,-384 979,-384 979,-390 973,-396 967,-396"/>
+<text text-anchor="middle" x="892" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
<!-- 7->0 -->
-<g id="edge4" class="edge"><title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M335.607,-143.871C326.495,-119.457 309.687,-74.4258 298.941,-45.6351"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="302.192,-44.3341 295.416,-36.1893 295.633,-46.7819 302.192,-44.3341"/>
+<g id="edge3" class="edge">
+<title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M871.12,-359.63C843.98,-334.97 800,-286.99 800,-235 800,-235 800,-235 800,-161 800,-42.65 610.53,-22.58 528.32,-19.44"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="528.26,-15.94 518.15,-19.12 528.04,-22.93 528.26,-15.94"/>
</g>
<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M675.5,-108C675.5,-108 644.5,-108 644.5,-108 638.5,-108 632.5,-102 632.5,-96 632.5,-96 632.5,-84 632.5,-84 632.5,-78 638.5,-72 644.5,-72 644.5,-72 675.5,-72 675.5,-72 681.5,-72 687.5,-78 687.5,-84 687.5,-84 687.5,-96 687.5,-96 687.5,-102 681.5,-108 675.5,-108"/>
-<text text-anchor="middle" x="660" y="-87.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M313,-324C313,-324 277,-324 277,-324 271,-324 265,-318 265,-312 265,-312 265,-300 265,-300 265,-294 271,-288 277,-288 277,-288 313,-288 313,-288 319,-288 325,-294 325,-300 325,-300 325,-312 325,-312 325,-318 319,-324 313,-324"/>
+<text text-anchor="middle" x="295" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 8->0 -->
-<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 id="edge1" class="edge">
+<title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M325.02,-290.82C342.15,-281.6 363.11,-268.27 378,-252 435.3,-189.42 469.53,-92.48 483.56,-45.85"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="486.94,-46.75 486.4,-36.17 480.23,-44.78 486.94,-46.75"/>
</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>
-<!-- 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>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M357,-252C357,-252 235,-252 235,-252 229,-252 223,-246 223,-240 223,-240 223,-228 223,-228 223,-222 229,-216 235,-216 235,-216 357,-216 357,-216 363,-216 369,-222 369,-228 369,-228 369,-240 369,-240 369,-246 363,-252 357,-252"/>
+<text text-anchor="middle" x="296" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</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"/>
+<!-- 8->20 -->
+<g id="edge42" class="edge">
+<title>8->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M295.25,-287.7C295.36,-279.98 295.49,-270.71 295.61,-262.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="299.11,-262.15 295.76,-252.1 292.11,-262.05 299.11,-262.15"/>
</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>
+<!-- 9 -->
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M314,-180C314,-180 284,-180 284,-180 278,-180 272,-174 272,-168 272,-168 272,-156 272,-156 272,-150 278,-144 284,-144 284,-144 314,-144 314,-144 320,-144 326,-150 326,-156 326,-156 326,-168 326,-168 326,-174 320,-180 314,-180"/>
+<text text-anchor="middle" x="299" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</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"/>
+<!-- 9->0 -->
+<g id="edge9" class="edge">
+<title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M298.06,-143.96C297.93,-124.14 300.83,-91.65 319,-72 353.79,-34.39 414.57,-23.22 453.78,-20.04"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="454.24,-23.52 463.99,-19.36 453.77,-16.53 454.24,-23.52"/>
</g>
<!-- 10 -->
-<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->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 id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M432,-108C432,-108 340,-108 340,-108 334,-108 328,-102 328,-96 328,-96 328,-84 328,-84 328,-78 334,-72 340,-72 340,-72 432,-72 432,-72 438,-72 444,-78 444,-84 444,-84 444,-96 444,-96 444,-102 438,-108 432,-108"/>
+<text text-anchor="middle" x="386" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+</g>
+<!-- 9->10 -->
+<g id="edge28" class="edge">
+<title>9->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M320.51,-143.7C331.46,-134.88 344.95,-124.03 356.82,-114.47"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="359.14,-117.1 364.74,-108.1 354.76,-111.65 359.14,-117.1"/>
+</g>
+<!-- 10->0 -->
+<g id="edge10" class="edge">
+<title>10->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M411.69,-71.88C425.29,-62.81 442.17,-51.55 456.86,-41.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="458.84,-44.65 465.22,-36.19 454.95,-38.82 458.84,-44.65"/>
</g>
<!-- 11 -->
-<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 id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M413,-540C413,-540 285,-540 285,-540 279,-540 273,-534 273,-528 273,-528 273,-516 273,-516 273,-510 279,-504 285,-504 285,-504 413,-504 413,-504 419,-504 425,-510 425,-516 425,-516 425,-528 425,-528 425,-534 419,-540 413,-540"/>
+<text text-anchor="middle" x="349" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
-<!-- 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"/>
+<!-- 11->3 -->
+<g id="edge11" class="edge">
+<title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M359.13,-503.7C363.85,-495.64 369.56,-485.89 374.78,-476.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="377.95,-478.5 379.98,-468.1 371.91,-474.96 377.95,-478.5"/>
</g>
-<!-- 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>
-<!-- 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"/>
+<!-- 14 -->
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#56b9d8" stroke-width="2" d="M141.5,-468C141.5,-468 40.5,-468 40.5,-468 34.5,-468 28.5,-462 28.5,-456 28.5,-456 28.5,-444 28.5,-444 28.5,-438 34.5,-432 40.5,-432 40.5,-432 141.5,-432 141.5,-432 147.5,-432 153.5,-438 153.5,-444 153.5,-444 153.5,-456 153.5,-456 153.5,-462 147.5,-468 141.5,-468"/>
+<text text-anchor="middle" x="91" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
-<!-- 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>
+<!-- 11->14 -->
+<g id="edge33" class="edge">
+<title>11->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M286.22,-503.97C249.25,-493.94 202.32,-481.2 163.75,-470.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="164.19,-467.23 153.62,-467.99 162.35,-473.99 164.19,-467.23"/>
</g>
-<!-- 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"/>
+<!-- 18 -->
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M820,-468C820,-468 702,-468 702,-468 696,-468 690,-462 690,-456 690,-456 690,-444 690,-444 690,-438 696,-432 702,-432 702,-432 820,-432 820,-432 826,-432 832,-438 832,-444 832,-444 832,-456 832,-456 832,-462 826,-468 820,-468"/>
+<text text-anchor="middle" x="761" y="-447.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
-<!-- 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"/>
+<!-- 11->18 -->
+<g id="edge38" class="edge">
+<title>11->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M425.27,-506.7C430.59,-505.77 435.87,-504.86 441,-504 544.26,-486.72 573.19,-487.17 680.05,-468.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="680.72,-471.55 689.94,-466.33 679.48,-464.66 680.72,-471.55"/>
</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"/>
+<!-- 12 -->
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M711.5,-540C711.5,-540 614.5,-540 614.5,-540 608.5,-540 602.5,-534 602.5,-528 602.5,-528 602.5,-516 602.5,-516 602.5,-510 608.5,-504 614.5,-504 614.5,-504 711.5,-504 711.5,-504 717.5,-504 723.5,-510 723.5,-516 723.5,-516 723.5,-528 723.5,-528 723.5,-534 717.5,-540 711.5,-540"/>
+<text text-anchor="middle" x="663" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+</g>
+<!-- 12->3 -->
+<g id="edge12" class="edge">
+<title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M602.41,-505.46C562.34,-495.19 509.46,-481.63 466.49,-470.61"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="467.19,-467.18 456.64,-468.09 465.45,-473.96 467.19,-467.18"/>
+</g>
+<!-- 12->4 -->
+<g id="edge13" class="edge">
+<title>12->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M644.21,-503.7C634.83,-495.05 623.32,-484.45 613.09,-475.03"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="615.3,-472.3 605.57,-468.1 610.55,-477.45 615.3,-472.3"/>
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<!-- 13 -->
-<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 id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M572,-540C572,-540 462,-540 462,-540 456,-540 450,-534 450,-528 450,-528 450,-516 450,-516 450,-510 456,-504 462,-504 462,-504 572,-504 572,-504 578,-504 584,-510 584,-516 584,-516 584,-528 584,-528 584,-534 578,-540 572,-540"/>
+<text text-anchor="middle" x="517" y="-519.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
-<!-- 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"/>
+<!-- 13->4 -->
+<g id="edge14" class="edge">
+<title>13->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M534.3,-503.7C542.86,-495.14 553.34,-484.66 562.7,-475.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="565.3,-477.65 569.9,-468.1 560.35,-472.7 565.3,-477.65"/>
</g>
-<!-- 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>
-<!-- 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"/>
+<!-- 17 -->
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M266.5,-468C266.5,-468 183.5,-468 183.5,-468 177.5,-468 171.5,-462 171.5,-456 171.5,-456 171.5,-444 171.5,-444 171.5,-438 177.5,-432 183.5,-432 183.5,-432 266.5,-432 266.5,-432 272.5,-432 278.5,-438 278.5,-444 278.5,-444 278.5,-456 278.5,-456 278.5,-462 272.5,-468 266.5,-468"/>
+<text text-anchor="middle" x="225" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
-<!-- 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>
+<!-- 13->17 -->
+<g id="edge37" class="edge">
+<title>13->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M449.71,-506.1C406.41,-496.35 348.7,-483.08 288.63,-468.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="289.13,-464.63 278.58,-465.6 287.43,-471.42 289.13,-464.63"/>
</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"/>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M963.5,-468C963.5,-468 862.5,-468 862.5,-468 856.5,-468 850.5,-462 850.5,-456 850.5,-456 850.5,-444 850.5,-444 850.5,-438 856.5,-432 862.5,-432 862.5,-432 963.5,-432 963.5,-432 969.5,-432 975.5,-438 975.5,-444 975.5,-444 975.5,-456 975.5,-456 975.5,-462 969.5,-468 963.5,-468"/>
+<text text-anchor="middle" x="913" y="-447.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 15->5 -->
-<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"/>
+<!-- 13->19 -->
+<g id="edge41" class="edge">
+<title>13->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M584.13,-505.88C587.47,-505.22 590.77,-504.59 594,-504 700.03,-484.59 730.32,-488.52 840.41,-468.01"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="841.06,-471.45 850.24,-466.16 839.76,-464.57 841.06,-471.45"/>
</g>
-<!-- 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>
-<!-- 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->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->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->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="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"/>
+<!-- 14->5 -->
+<g id="edge17" class="edge">
+<title>14->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M144.14,-431.97C172.41,-422.38 207.54,-409.62 238,-396 283.09,-375.85 332.69,-348.32 365.62,-329.24"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="367.57,-332.15 374.45,-324.09 364.05,-326.1 367.57,-332.15"/>
</g>
-<!-- 18 -->
-<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>
+<!-- 14->8 -->
+<g id="edge25" class="edge">
+<title>14->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M58.47,-431.98C45.21,-423.18 31.3,-411.09 24,-396 17.03,-381.6 13.83,-372.35 24,-360 52.71,-325.13 185.96,-312.88 254.32,-308.84"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="254.91,-312.31 264.7,-308.26 254.52,-305.32 254.91,-312.31"/>
</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"/>
+<!-- 15 -->
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#56d8c1" stroke-width="2" d="M217,-396C217,-396 45,-396 45,-396 39,-396 33,-390 33,-384 33,-384 33,-372 33,-372 33,-366 39,-360 45,-360 45,-360 217,-360 217,-360 223,-360 229,-366 229,-372 229,-372 229,-384 229,-384 229,-390 223,-396 217,-396"/>
+<text text-anchor="middle" x="131" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</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>
+<!-- 14->15 -->
+<g id="edge35" class="edge">
+<title>14->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M100.89,-431.7C105.49,-423.64 111.06,-413.89 116.15,-404.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="119.3,-406.52 121.23,-396.1 113.23,-403.05 119.3,-406.52"/>
</g>
-<!-- 19->10 -->
-<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"/>
+<!-- 15->5 -->
+<g id="edge15" class="edge">
+<title>15->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M197.19,-359.97C238.54,-349.33 291.69,-335.65 333.62,-324.85"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="334.67,-328.2 343.48,-322.32 332.92,-321.42 334.67,-328.2"/>
</g>
-<!-- 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>
+<!-- 15->8 -->
+<g id="edge23" class="edge">
+<title>15->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M171.12,-359.88C196.77,-348.93 229.88,-334.79 255.42,-323.89"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="256.99,-327.03 264.81,-319.89 254.24,-320.59 256.99,-327.03"/>
</g>
-<!-- 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"/>
+<!-- 16 -->
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M471,-396C471,-396 335,-396 335,-396 329,-396 323,-390 323,-384 323,-384 323,-372 323,-372 323,-366 329,-360 335,-360 335,-360 471,-360 471,-360 477,-360 483,-366 483,-372 483,-372 483,-384 483,-384 483,-390 477,-396 471,-396"/>
+<text text-anchor="middle" x="403" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 16->5 -->
+<g id="edge18" class="edge">
+<title>16->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M403,-359.7C403,-351.98 403,-342.71 403,-334.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="406.5,-334.1 403,-324.1 399.5,-334.1 406.5,-334.1"/>
+</g>
+<!-- 17->5 -->
+<g id="edge16" class="edge">
+<title>17->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M278.54,-434.21C281.73,-433.43 284.9,-432.69 288,-432 332.93,-421.99 462.41,-431.27 492,-396 502.28,-383.74 499.91,-373.91 492,-360 484.64,-347.04 472.71,-336.92 459.95,-329.16"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="461.47,-325.99 451.03,-324.15 458.04,-332.1 461.47,-325.99"/>
+</g>
+<!-- 17->8 -->
+<g id="edge24" class="edge">
+<title>17->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M233.44,-431.87C245.53,-407.35 267.87,-362.03 282.06,-333.26"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="285.24,-334.71 286.53,-324.19 278.97,-331.61 285.24,-334.71"/>
+</g>
+<!-- 17->15 -->
+<g id="edge34" class="edge">
+<title>17->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M201.76,-431.7C189.81,-422.8 175.08,-411.82 162.15,-402.2"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="164.08,-399.27 153.97,-396.1 159.9,-404.88 164.08,-399.27"/>
+</g>
+<!-- 18->6 -->
+<g id="edge19" class="edge">
+<title>18->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M748.64,-431.7C742.77,-423.47 735.63,-413.48 729.16,-404.42"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="731.88,-402.21 723.22,-396.1 726.18,-406.28 731.88,-402.21"/>
+</g>
+<!-- 18->7 -->
+<g id="edge21" class="edge">
+<title>18->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M793.05,-431.88C810.49,-422.55 832.27,-410.92 850.94,-400.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="852.66,-403.99 859.83,-396.19 849.36,-397.82 852.66,-403.99"/>
+</g>
+<!-- 19->6 -->
+<g id="edge20" class="edge">
+<title>19->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M863.84,-431.97C835.5,-422.14 799.68,-409.73 769.84,-399.39"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="770.97,-396.08 760.38,-396.11 768.68,-402.69 770.97,-396.08"/>
+</g>
+<!-- 19->7 -->
+<g id="edge22" class="edge">
+<title>19->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M907.81,-431.7C905.47,-423.9 902.65,-414.51 900.05,-405.83"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="903.36,-404.68 897.13,-396.1 896.65,-406.69 903.36,-404.68"/>
+</g>
+<!-- 20->9 -->
+<g id="edge26" class="edge">
+<title>20->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M296.74,-215.7C297.07,-207.98 297.47,-198.71 297.84,-190.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="301.34,-190.25 298.27,-180.1 294.34,-189.95 301.34,-190.25"/>
</g>
-<!-- 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>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M104,-252C104,-252 12,-252 12,-252 6,-252 0,-246 0,-240 0,-240 0,-228 0,-228 0,-222 6,-216 12,-216 12,-216 104,-216 104,-216 110,-216 116,-222 116,-228 116,-228 116,-240 116,-240 116,-246 110,-252 104,-252"/>
+<text text-anchor="middle" x="58" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</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"/>
+<!-- 21->9 -->
+<g id="edge27" class="edge">
+<title>21->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M116.03,-216.14C161.42,-202.96 223.15,-185.03 262.04,-173.74"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="263.26,-177.03 271.89,-170.88 261.31,-170.3 263.26,-177.03"/>
</g>
-<!-- 21 -->
-<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="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"/>
-</g>
-<!-- 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"/>
-</g>
-<!-- 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"/>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M416.5,-612C416.5,-612 273.5,-612 273.5,-612 267.5,-612 261.5,-606 261.5,-600 261.5,-600 261.5,-588 261.5,-588 261.5,-582 267.5,-576 273.5,-576 273.5,-576 416.5,-576 416.5,-576 422.5,-576 428.5,-582 428.5,-588 428.5,-588 428.5,-600 428.5,-600 428.5,-606 422.5,-612 416.5,-612"/>
+<text text-anchor="middle" x="345" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 22->11 -->
+<g id="edge29" class="edge">
+<title>22->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M345.99,-575.7C346.43,-567.98 346.96,-558.71 347.45,-550.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="350.95,-550.29 348.02,-540.1 343.96,-549.89 350.95,-550.29"/>
+</g>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M783.5,-612C783.5,-612 682.5,-612 682.5,-612 676.5,-612 670.5,-606 670.5,-600 670.5,-600 670.5,-588 670.5,-588 670.5,-582 676.5,-576 682.5,-576 682.5,-576 783.5,-576 783.5,-576 789.5,-576 795.5,-582 795.5,-588 795.5,-588 795.5,-600 795.5,-600 795.5,-606 789.5,-612 783.5,-612"/>
+<text text-anchor="middle" x="733" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+</g>
+<!-- 23->12 -->
+<g id="edge30" class="edge">
+<title>23->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M715.7,-575.7C707.14,-567.14 696.66,-556.66 687.3,-547.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="689.65,-544.7 680.1,-540.1 684.7,-549.65 689.65,-544.7"/>
+</g>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M850.5,-540C850.5,-540 753.5,-540 753.5,-540 747.5,-540 741.5,-534 741.5,-528 741.5,-528 741.5,-516 741.5,-516 741.5,-510 747.5,-504 753.5,-504 753.5,-504 850.5,-504 850.5,-504 856.5,-504 862.5,-510 862.5,-516 862.5,-516 862.5,-528 862.5,-528 862.5,-534 856.5,-540 850.5,-540"/>
+<text text-anchor="middle" x="802" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+</g>
+<!-- 23->26 -->
+<g id="edge44" class="edge">
+<title>23->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M750.06,-575.7C758.5,-567.14 768.82,-556.66 778.04,-547.3"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="780.61,-549.68 785.14,-540.1 775.63,-544.77 780.61,-549.68"/>
+</g>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M584,-612C584,-612 458,-612 458,-612 452,-612 446,-606 446,-600 446,-600 446,-588 446,-588 446,-582 452,-576 458,-576 458,-576 584,-576 584,-576 590,-576 596,-582 596,-588 596,-588 596,-600 596,-600 596,-606 590,-612 584,-612"/>
+<text text-anchor="middle" x="521" y="-591.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 24->13 -->
+<g id="edge31" class="edge">
+<title>24->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M520.01,-575.7C519.57,-567.98 519.04,-558.71 518.55,-550.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="522.04,-549.89 517.98,-540.1 515.05,-550.29 522.04,-549.89"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M131,-540C131,-540 51,-540 51,-540 45,-540 39,-534 39,-528 39,-528 39,-516 39,-516 39,-510 45,-504 51,-504 51,-504 131,-504 131,-504 137,-504 143,-510 143,-516 143,-516 143,-528 143,-528 143,-534 137,-540 131,-540"/>
+<text text-anchor="middle" x="91" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text>
+</g>
+<!-- 25->14 -->
+<g id="edge32" class="edge">
+<title>25->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M91,-503.7C91,-495.98 91,-486.71 91,-478.11"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="94.5,-478.1 91,-468.1 87.5,-478.1 94.5,-478.1"/>
+</g>
+<!-- 25->17 -->
+<g id="edge36" class="edge">
+<title>25->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M123.78,-503.88C141.63,-494.55 163.9,-482.92 183,-472.94"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="184.85,-475.92 192.09,-468.19 181.61,-469.72 184.85,-475.92"/>
+</g>
+<!-- 25->21 -->
+<g id="edge43" class="edge">
+<title>25->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M55.86,-503.78C41.94,-495.07 27.3,-483.1 19,-468 -18.19,-400.37 20.37,-306.26 43.41,-261.15"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="46.65,-262.52 48.2,-252.04 40.45,-259.26 46.65,-262.52"/>
+</g>
+<!-- 26->18 -->
+<g id="edge39" class="edge">
+<title>26->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M791.87,-503.7C787.15,-495.64 781.44,-485.89 776.22,-476.98"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="779.09,-474.96 771.02,-468.1 773.05,-478.5 779.09,-474.96"/>
+</g>
+<!-- 26->19 -->
+<g id="edge40" class="edge">
+<title>26->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M829.15,-503.88C843.53,-494.81 861.38,-483.55 876.91,-473.76"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="879.15,-476.48 885.74,-468.19 875.42,-470.56 879.15,-476.48"/>
</g>
</g>
</svg>
diff --git a/scripts/labkey_to_snakemake.py b/scripts/labkey_to_snakemake.py
index 4456e0089d4aba1b3fc3407a767dd9a0a648fedb..defefe3d57d86fd7dc2c96f0bb2002b1031127b7 100755
--- a/scripts/labkey_to_snakemake.py
+++ b/scripts/labkey_to_snakemake.py
@@ -275,6 +275,7 @@ def main():
kallisto_indexes: "results/kallisto_indexes/"
salmon_indexes: "results/salmon_indexes/"
star_indexes: "results/star_indexes/"
+ alfa_indexes: "results/alfa_indexes/"
...''')
sys.stdout.write('Create snakemake table finished successfully...\n')
diff --git a/tests/input_files/config.yaml b/tests/input_files/config.yaml
index b0a3f41c4216d08e4528f30cc82be02f0bb045db..0d879677d10cf46a0185779cb6a1d16a841c82bc 100644
--- a/tests/input_files/config.yaml
+++ b/tests/input_files/config.yaml
@@ -5,4 +5,5 @@
kallisto_indexes: "results/kallisto_indexes/"
salmon_indexes: "results/salmon_indexes/"
star_indexes: "results/star_indexes/"
+ alfa_indexes: "results/alfa_indexes/"
...
diff --git a/tests/input_files/config_alfa.yaml b/tests/input_files/config_alfa.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..33f97d5c6a5769a728b294479651d7cf1be67925
--- /dev/null
+++ b/tests/input_files/config_alfa.yaml
@@ -0,0 +1,9 @@
+---
+ samples: "../input_files/samples_alfa.tsv"
+ output_dir: "results/"
+ log_dir: "logs/"
+ kallisto_indexes: "results/kallisto_indexes/"
+ salmon_indexes: "results/salmon_indexes/"
+ star_indexes: "results/star_indexes/"
+ alfa_indexes: "results/alfa_indexes/"
+...
diff --git a/tests/input_files/homo_sapiens/annotation.gtf b/tests/input_files/homo_sapiens/annotation.gtf
index e41d542766ef72a2df834e9e634a62ab061b459c..b40ab99def551f041f0b74919df9d791cd8b0026 100644
--- a/tests/input_files/homo_sapiens/annotation.gtf
+++ b/tests/input_files/homo_sapiens/annotation.gtf
@@ -15,8 +15,8 @@
1-10000-20000 havana exon 2976 3053 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
1-10000-20000 havana exon 3222 3375 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
1-10000-20000 havana exon 3454 3671 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "6"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001863096"; exon_version "1"; tag "basic"; transcript_support_level "NA";
-1-10000-20000 havana gene 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
-1-10000-20000 havana transcript 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1-10000-20000 havana gene 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1-10000-20000 havana transcript 4405 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
1-10000-20000 havana exon 8269 8367 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "3"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003477500"; exon_version "1"; tag "basic"; transcript_support_level "NA";
1-10000-20000 havana exon 7916 8062 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "4"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003565697"; exon_version "1"; tag "basic"; transcript_support_level "NA";
1-10000-20000 havana exon 7607 7743 . - . gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003475637"; exon_version "1"; tag "basic"; transcript_support_level "NA";
diff --git a/tests/input_files/homo_sapiens/quick_start.gtf b/tests/input_files/homo_sapiens/quick_start.gtf
new file mode 100644
index 0000000000000000000000000000000000000000..4e9c0b9f22782ac948d160a68770bfe15e65ebdf
--- /dev/null
+++ b/tests/input_files/homo_sapiens/quick_start.gtf
@@ -0,0 +1,6 @@
+Chr1 ensembl_havana gene 251 1250 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana transcript 251 1250 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana exon 376 1000 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana CDS 376 1000 . + 0 gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana five_prime_utr 251 375 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1 ensembl_havana three_prime_utr 1001 1250 . + . gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
diff --git a/tests/input_files/samples_alfa.tsv b/tests/input_files/samples_alfa.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..df032482a4a8a10e75dfeca0ef4cbc5bbe188b28
--- /dev/null
+++ b/tests/input_files/samples_alfa.tsv
@@ -0,0 +1,5 @@
+sample seqmode fq1 index_size kmer fq2 fq1_3p fq1_5p fq2_3p fq2_5p organism gtf gtf_filtered genome tr_fasta_filtered sd mean multimappers soft_clip pass_mode libtype kallisto_directionality fq1_polya fq2_polya
+paired_end_R1_on_plus_sense paired_end XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX GATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
+paired_end_R1_on_plus_antisense paired_end XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
+paired_end_R1_on_minus_sense paired_end XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --fr AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
+paired_end_R1_on_minus_antisense paired_end XXXXXXXXXXXXX 75 31 XXXXXXXXXXXXX AGATCGGAAGAGCACA XXXXXXXXXXXXX AGATCGGAAGAGCGT XXXXXXXXXXXXX homo_sapiens ../input_files/homo_sapiens/quick_start.gtf ../input_files/homo_sapiens/quick_start.gtf XXXXXXXXXXXXX XXXXXXXXXXXXX 100 250 10 EndToEnd None A --rf AAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTT
diff --git a/tests/test_alfa/expected_output.md5 b/tests/test_alfa/expected_output.md5
new file mode 100644
index 0000000000000000000000000000000000000000..57f9dfd2d4e7ff3257de2171ea5c5ceef9f78303
--- /dev/null
+++ b/tests/test_alfa/expected_output.md5
@@ -0,0 +1,30 @@
+90e42aa46890e9cd0a47800428699fbf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
+ccc3cf5a57fddb0d469e597d4376b1bf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str1.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str2.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.Unique.str1.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.Unique.str2.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.str1.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.str2.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.Unique.str1.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/STAR_coverage/paired_end_R1_on_minus_sense_Signal.Unique.str2.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.str1.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.str2.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.Unique.str1.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/STAR_coverage/paired_end_R1_on_plus_antisense_Signal.Unique.str2.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.str1.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.str2.out.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str1.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str2.out.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.plus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.plus.bg
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam
new file mode 100644
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Binary files /dev/null and b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam differ
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam.bai
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Binary files /dev/null and b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam.bai differ
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam
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Binary files /dev/null and b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam differ
diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/paired_end/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam.bai
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diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam
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diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam.bai
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diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam
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diff --git a/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam.bai b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..f4e7b055bba5939ace1f1baac5ef5c2f99a9edb2
Binary files /dev/null and b/tests/test_alfa/results/paired_end/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam.bai differ
diff --git a/tests/test_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt b/tests/test_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
new file mode 100644
index 0000000000000000000000000000000000000000..81ed9d3b328231f3316a5dbb2afa57156356b9f4
--- /dev/null
+++ b/tests/test_alfa/results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
@@ -0,0 +1 @@
+Chr1 1500
diff --git a/tests/test_alfa/test.sh b/tests/test_alfa/test.sh
new file mode 100755
index 0000000000000000000000000000000000000000..280749cde715c6bc58b2b56a7cbb13560589a8e1
--- /dev/null
+++ b/tests/test_alfa/test.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+# Tear down test environment
+cleanup () {
+ rc=$?
+ rm -rf .java/
+ rm -rf .snakemake/
+ rm -rf logs/
+ rm -rfv results/alfa_indexes/
+ rm -rfv results/*/*/ALFA/
+ rm -rfv results/*/*/STAR_coverage/
+ rm -rfv results/ALFA/
+ cd $user_dir
+ echo "Exit status: $rc"
+}
+trap cleanup EXIT
+
+# Set up test environment
+set -eo pipefail # ensures that script exits at first command that exits with non-zero status
+set -u # ensures that script exits when unset variables are used
+set -x # facilitates debugging by printing out executed commands
+user_dir=$PWD
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)"
+cd $script_dir
+
+# Run tests
+snakemake \
+ --snakefile="../../Snakefile" \
+ --configfile="../input_files/config_alfa.yaml" \
+ --cores=4 \
+ --printshellcmds \
+ --rerun-incomplete \
+ --use-singularity \
+ --singularity-args="--bind ${PWD}/../input_files" \
+ --verbose \
+ results/ALFA/ALFA_plots.Categories.pdf
+
+# Check md5 sum of some output files
+find results/ -type f -name \*\.gz -exec gunzip '{}' \;
+find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
+md5sum --check "expected_output.md5"
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index f4909963da52d740b87c4c5b0689bb0c5a56fc91..4feedc098f227fb781ebf52e4e6fcfe546eff322 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -87,3 +87,11 @@ ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_s
ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
+6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
+2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
+c1254a0bae19ac3ffc39f73099ffcf2b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
+a9fdb9b135132dda339b85346525c9c5 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+ede14ac41c10067838f375106fce4852 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
+ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
\ No newline at end of file
diff --git a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
index 77083973160842bd6f8e523e8b88040b902c9729..569a4a8d598d09e9a978283e03c2992d16fe42e0 100644
--- a/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake_api/expected_output.md5
@@ -1,2 +1,2 @@
-ba5ae0649d1fb82d94f8d19481498ffd config.yaml
-cb58e046242c2702038e6e21dbd0bdb4 samples.tsv
\ No newline at end of file
+b163e7b06bd9e0a71f2fd1fc4935fea9 config.yaml
+cb58e046242c2702038e6e21dbd0bdb4 samples.tsv
diff --git a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5 b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
index c24f6019ddacafb5bd6334f1f6dcfcc50f74b689..569a4a8d598d09e9a978283e03c2992d16fe42e0 100644
--- a/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
+++ b/tests/test_scripts_labkey_to_snakemake_table/expected_output.md5
@@ -1,2 +1,2 @@
-ba5ae0649d1fb82d94f8d19481498ffd config.yaml
+b163e7b06bd9e0a71f2fd1fc4935fea9 config.yaml
cb58e046242c2702038e6e21dbd0bdb4 samples.tsv
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index f4fb1bf86b4eb4aa44f4f03d66c8138864cc33e9..c444f461b08af8aa28b5e74ef2bbe315eaefea27 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -413,4 +413,5 @@ rule pe_genome_quantification_kallisto:
--pseudobam \
{params.directionality} \
{input.reads1} {input.reads2} > {output.pseudoalignment}) \
- 2> {log.stderr}"
\ No newline at end of file
+ 2> {log.stderr}"
+
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index f1b7d27e59ab0fad4dea4b7f531cbe114f1fbbfd..d2df8889152c15402d21b8d0dd9f67ce8bd39cda 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -369,4 +369,5 @@ rule genome_quantification_kallisto:
--pseudobam \
{params.directionality} \
{input.reads} > {output.pseudoalignment};) \
- 2> {log.stderr}"
\ No newline at end of file
+ 2> {log.stderr}"
+