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 62b72781ddfe177810eb6699d7f73b98e3a89a13..97db0e37a7318235ecc8c990e8e94662a3d89e3b 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(
@@ -94,7 +95,23 @@ 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")
+
@@ -436,6 +453,47 @@ 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
@@ -704,4 +762,162 @@ 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>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index 4fed3d21f332937831860cd37e7b22b15f3c3ba9..aecdde5d80bc8aef876b61698ca2ea6529950019 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -4,330 +4,385 @@
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-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 544)">
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<title>snakemake_dag</title>
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+<polygon fill="white" stroke="none" points="-4,4 -4,-616 1070,-616 1070,4 -4,4"/>
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<g id="node1" class="node"><title>0</title>
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-<text text-anchor="middle" x="319" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<path fill="none" stroke="#a7d856" stroke-width="2" d="M339,-36C339,-36 309,-36 309,-36 303,-36 297,-30 297,-24 297,-24 297,-12 297,-12 297,-6 303,-0 309,-0 309,-0 339,-0 339,-0 345,-0 351,-6 351,-12 351,-12 351,-24 351,-24 351,-30 345,-36 339,-36"/>
+<text text-anchor="middle" x="324" y="-15.5" font-family="sans" font-size="10.00">finish</text>
</g>
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<g id="node2" class="node"><title>1</title>
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+<text text-anchor="middle" x="39" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
</g>
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-<g id="edge2" class="edge"><title>1->0</title>
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+<g id="edge1" class="edge"><title>1->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M68.5755,-75.3841C71.7245,-74.1526 74.9066,-72.9965 78,-72 150.446,-48.6629 238.217,-32.5434 286.903,-24.626"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="287.646,-28.0518 296.968,-23.016 286.54,-21.1396 287.646,-28.0518"/>
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<g id="node3" class="node"><title>2</title>
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-<text text-anchor="middle" x="207" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M129,-108C129,-108 99,-108 99,-108 93,-108 87,-102 87,-96 87,-96 87,-84 87,-84 87,-78 93,-72 99,-72 99,-72 129,-72 129,-72 135,-72 141,-78 141,-84 141,-84 141,-96 141,-96 141,-102 135,-108 129,-108"/>
+<text text-anchor="middle" x="114" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
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-<g id="edge1" class="edge"><title>2->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="285.124,-44.2997 291.749,-36.0316 281.414,-38.3637 285.124,-44.2997"/>
+<g id="edge9" class="edge"><title>2->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M141.214,-77.319C145.789,-75.4697 150.51,-73.6314 155,-72 199.981,-55.6584 252.733,-39.5974 287.182,-29.5158"/>
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<g id="node4" class="node"><title>3</title>
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-<text text-anchor="middle" x="363" y="-375.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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+<text text-anchor="middle" x="83" y="-447.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M322,-468C322,-468 196,-468 196,-468 190,-468 184,-462 184,-456 184,-456 184,-444 184,-444 184,-438 190,-432 196,-432 196,-432 322,-432 322,-432 328,-432 334,-438 334,-444 334,-444 334,-456 334,-456 334,-462 328,-468 322,-468"/>
+<text text-anchor="middle" x="259" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="339.093,-42.6485 330.81,-36.0417 333.165,-46.3716 339.093,-42.6485"/>
+<g id="edge7" class="edge"><title>4->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M246.068,-431.677C239.186,-421.702 231.112,-408.665 226,-396 210.862,-358.493 207,-347.447 207,-307 207,-307 207,-307 207,-161 207,-109.172 253.998,-66.0006 288.42,-41.3312"/>
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-<text text-anchor="middle" x="467" y="-87.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
+<path fill="none" stroke="#56d8b9" stroke-width="2" d="M510.5,-180C510.5,-180 445.5,-180 445.5,-180 439.5,-180 433.5,-174 433.5,-168 433.5,-168 433.5,-156 433.5,-156 433.5,-150 439.5,-144 445.5,-144 445.5,-144 510.5,-144 510.5,-144 516.5,-144 522.5,-150 522.5,-156 522.5,-156 522.5,-168 522.5,-168 522.5,-174 516.5,-180 510.5,-180"/>
+<text text-anchor="middle" x="478" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="356.549,-32.8878 346.012,-31.7761 353.556,-39.2157 356.549,-32.8878"/>
+<g id="edge2" class="edge"><title>5->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M459.424,-143.871C432.137,-118.711 381.103,-71.6535 350.073,-43.0415"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="352.366,-40.395 342.642,-36.1893 347.621,-45.5412 352.366,-40.395"/>
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-<text text-anchor="middle" x="68" y="-303.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<path fill="none" stroke="#56d882" stroke-width="2" d="M359,-396C359,-396 247,-396 247,-396 241,-396 235,-390 235,-384 235,-384 235,-372 235,-372 235,-366 241,-360 247,-360 247,-360 359,-360 359,-360 365,-360 371,-366 371,-372 371,-372 371,-384 371,-384 371,-390 365,-396 359,-396"/>
+<text text-anchor="middle" x="303" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
<!-- 6->0 -->
-<g id="edge4" class="edge"><title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M83.3284,-287.971C113.904,-253.955 184.56,-175.096 243,-108 261.747,-86.4755 282.806,-61.7729 297.993,-43.8623"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="300.736,-46.0396 304.529,-36.1469 295.395,-41.5151 300.736,-46.0396"/>
+<g id="edge3" class="edge"><title>6->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M303.198,-359.951C303.489,-333.292 304,-280.116 304,-235 304,-235 304,-235 304,-161 304,-120.822 311.948,-74.8689 317.823,-46.3889"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="321.296,-46.887 319.953,-36.3777 314.449,-45.4307 321.296,-46.887"/>
</g>
<!-- 7 -->
<g id="node8" class="node"><title>7</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M297.5,-324C297.5,-324 166.5,-324 166.5,-324 160.5,-324 154.5,-318 154.5,-312 154.5,-312 154.5,-300 154.5,-300 154.5,-294 160.5,-288 166.5,-288 166.5,-288 297.5,-288 297.5,-288 303.5,-288 309.5,-294 309.5,-300 309.5,-300 309.5,-312 309.5,-312 309.5,-318 303.5,-324 297.5,-324"/>
-<text text-anchor="middle" x="232" y="-303.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<path fill="none" stroke="#56d892" stroke-width="2" d="M532.5,-396C532.5,-396 401.5,-396 401.5,-396 395.5,-396 389.5,-390 389.5,-384 389.5,-384 389.5,-372 389.5,-372 389.5,-366 395.5,-360 401.5,-360 401.5,-360 532.5,-360 532.5,-360 538.5,-360 544.5,-366 544.5,-372 544.5,-372 544.5,-384 544.5,-384 544.5,-390 538.5,-396 532.5,-396"/>
+<text text-anchor="middle" x="467" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
<!-- 7->0 -->
-<g id="edge5" class="edge"><title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M250.018,-287.971C259.195,-278.286 269.715,-265.431 276,-252 308.374,-182.818 316.407,-91.4095 318.377,-46.4173"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="321.88,-46.3955 318.751,-36.2734 314.885,-46.1376 321.88,-46.3955"/>
+<g id="edge4" class="edge"><title>7->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M436.911,-359.894C400.497,-336.696 344,-291.588 344,-235 344,-235 344,-235 344,-161 344,-120.822 336.052,-74.8689 330.177,-46.3889"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="333.551,-45.4307 328.047,-36.3777 326.704,-46.887 333.551,-45.4307"/>
</g>
<!-- 8 -->
<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#c6d856" stroke-width="2" d="M765.5,-252C765.5,-252 734.5,-252 734.5,-252 728.5,-252 722.5,-246 722.5,-240 722.5,-240 722.5,-228 722.5,-228 722.5,-222 728.5,-216 734.5,-216 734.5,-216 765.5,-216 765.5,-216 771.5,-216 777.5,-222 777.5,-228 777.5,-228 777.5,-240 777.5,-240 777.5,-246 771.5,-252 765.5,-252"/>
-<text text-anchor="middle" x="750" y="-231.5" font-family="sans" font-size="10.00">star_rpm</text>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M866.5,-324C866.5,-324 835.5,-324 835.5,-324 829.5,-324 823.5,-318 823.5,-312 823.5,-312 823.5,-300 823.5,-300 823.5,-294 829.5,-288 835.5,-288 835.5,-288 866.5,-288 866.5,-288 872.5,-288 878.5,-294 878.5,-300 878.5,-300 878.5,-312 878.5,-312 878.5,-318 872.5,-324 866.5,-324"/>
+<text text-anchor="middle" x="851" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 8->0 -->
-<g id="edge7" class="edge"><title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M730.968,-215.978C693.481,-183.32 606.294,-111.602 521,-72 466.432,-46.6639 397.734,-31.905 356.151,-24.6562"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="356.632,-21.1879 346.188,-22.9733 355.466,-28.0901 356.632,-21.1879"/>
+<g id="edge10" class="edge"><title>8->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M823.408,-290.026C735.084,-242.093 459.299,-92.4259 360.045,-38.5615"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="361.462,-35.3482 351.003,-33.6545 358.123,-41.5006 361.462,-35.3482"/>
</g>
-<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M362,-468C362,-468 250,-468 250,-468 244,-468 238,-462 238,-456 238,-456 238,-444 238,-444 238,-438 244,-432 250,-432 250,-432 362,-432 362,-432 368,-432 374,-438 374,-444 374,-444 374,-456 374,-456 374,-462 368,-468 362,-468"/>
-<text text-anchor="middle" x="306" y="-447.5" 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="M320.09,-431.697C326.923,-423.305 335.257,-413.07 342.756,-403.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="345.472,-406.069 349.072,-396.104 340.044,-401.649 345.472,-406.069"/>
-</g>
-<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#d8ac56" stroke-width="2" d="M120.5,-396C120.5,-396 17.5,-396 17.5,-396 11.5,-396 5.5,-390 5.5,-384 5.5,-384 5.5,-372 5.5,-372 5.5,-366 11.5,-360 17.5,-360 17.5,-360 120.5,-360 120.5,-360 126.5,-360 132.5,-366 132.5,-372 132.5,-372 132.5,-384 132.5,-384 132.5,-390 126.5,-396 120.5,-396"/>
-<text text-anchor="middle" x="69" y="-375.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<!-- 20 -->
+<g id="node21" class="node"><title>20</title>
+<path fill="none" stroke="#d87d56" stroke-width="2" d="M903,-252C903,-252 797,-252 797,-252 791,-252 785,-246 785,-240 785,-240 785,-228 785,-228 785,-222 791,-216 797,-216 797,-216 903,-216 903,-216 909,-216 915,-222 915,-228 915,-228 915,-240 915,-240 915,-246 909,-252 903,-252"/>
+<text text-anchor="middle" x="850" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
-<!-- 9->13 -->
-<g id="edge26" class="edge"><title>9->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M248.326,-431.966C214.636,-422.015 171.947,-409.406 136.671,-398.987"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="137.514,-395.587 126.932,-396.111 135.531,-402.3 137.514,-395.587"/>
+<!-- 8->20 -->
+<g id="edge40" class="edge"><title>8->20</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M850.753,-287.697C850.643,-279.983 850.51,-270.712 850.387,-262.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="853.887,-262.053 850.244,-252.104 846.888,-262.153 853.887,-262.053"/>
</g>
-<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#56d8b1" stroke-width="2" d="M735.5,-396C735.5,-396 646.5,-396 646.5,-396 640.5,-396 634.5,-390 634.5,-384 634.5,-384 634.5,-372 634.5,-372 634.5,-366 640.5,-360 646.5,-360 646.5,-360 735.5,-360 735.5,-360 741.5,-360 747.5,-366 747.5,-372 747.5,-372 747.5,-384 747.5,-384 747.5,-390 741.5,-396 735.5,-396"/>
-<text text-anchor="middle" x="691" y="-375.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 9 -->
+<g id="node10" class="node"><title>9</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M850,-180C850,-180 820,-180 820,-180 814,-180 808,-174 808,-168 808,-168 808,-156 808,-156 808,-150 814,-144 820,-144 820,-144 850,-144 850,-144 856,-144 862,-150 862,-156 862,-156 862,-168 862,-168 862,-174 856,-180 850,-180"/>
+<text text-anchor="middle" x="835" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
-<!-- 9->15 -->
-<g id="edge30" class="edge"><title>9->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M374.384,-433.648C377.292,-433.075 380.173,-432.523 383,-432 489.057,-412.362 517.225,-417.104 623,-396 623.462,-395.908 623.926,-395.814 624.392,-395.72"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="625.273,-399.111 634.323,-393.602 623.813,-392.265 625.273,-399.111"/>
+<!-- 9->0 -->
+<g id="edge6" class="edge"><title>9->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M807.667,-145.655C789.461,-135.295 765.097,-121.159 744,-108 719.526,-92.7346 716.935,-82.3204 690,-72 575.896,-28.28 429.165,-20.273 361.382,-19.0424"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="361.247,-15.5402 351.199,-18.8986 361.148,-22.5395 361.247,-15.5402"/>
</g>
<!-- 10 -->
<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#b6d856" stroke-width="2" d="M488,-468C488,-468 404,-468 404,-468 398,-468 392,-462 392,-456 392,-456 392,-444 392,-444 392,-438 398,-432 404,-432 404,-432 488,-432 488,-432 494,-432 500,-438 500,-444 500,-444 500,-456 500,-456 500,-462 494,-468 488,-468"/>
-<text text-anchor="middle" x="446" y="-447.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+<path fill="none" stroke="#97d856" stroke-width="2" d="M846.5,-108C846.5,-108 765.5,-108 765.5,-108 759.5,-108 753.5,-102 753.5,-96 753.5,-96 753.5,-84 753.5,-84 753.5,-78 759.5,-72 765.5,-72 765.5,-72 846.5,-72 846.5,-72 852.5,-72 858.5,-78 858.5,-84 858.5,-84 858.5,-96 858.5,-96 858.5,-102 852.5,-108 846.5,-108"/>
+<text text-anchor="middle" x="806" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
</g>
-<!-- 10->3 -->
-<g id="edge10" class="edge"><title>10->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M425.483,-431.697C415.131,-422.965 402.414,-412.24 391.161,-402.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="393.182,-399.876 383.281,-396.104 388.669,-405.227 393.182,-399.876"/>
+<!-- 9->10 -->
+<g id="edge25" class="edge"><title>9->10</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M827.831,-143.697C824.565,-135.813 820.626,-126.304 816.998,-117.546"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="820.147,-116.003 813.086,-108.104 813.68,-118.683 820.147,-116.003"/>
</g>
-<!-- 10->4 -->
-<g id="edge12" class="edge"><title>10->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M468.989,-431.697C480.814,-422.796 495.392,-411.823 508.179,-402.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="510.391,-404.915 516.276,-396.104 506.181,-399.322 510.391,-404.915"/>
+<!-- 10->0 -->
+<g id="edge8" class="edge"><title>10->0</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M753.403,-75.7453C747.22,-74.3834 740.984,-73.0989 735,-72 598.087,-46.8556 433.355,-29.4441 361.065,-22.4398"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="361.372,-18.9533 351.084,-21.4822 360.704,-25.9213 361.372,-18.9533"/>
</g>
<!-- 11 -->
<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M629,-468C629,-468 533,-468 533,-468 527,-468 521,-462 521,-456 521,-456 521,-444 521,-444 521,-438 527,-432 533,-432 533,-432 629,-432 629,-432 635,-432 641,-438 641,-444 641,-444 641,-456 641,-456 641,-462 635,-468 629,-468"/>
-<text text-anchor="middle" x="581" y="-447.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M395,-540C395,-540 283,-540 283,-540 277,-540 271,-534 271,-528 271,-528 271,-516 271,-516 271,-510 277,-504 283,-504 283,-504 395,-504 395,-504 401,-504 407,-510 407,-516 407,-516 407,-528 407,-528 407,-534 401,-540 395,-540"/>
+<text text-anchor="middle" x="339" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
-<!-- 11->4 -->
-<g id="edge11" class="edge"><title>11->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M570.618,-431.697C565.735,-423.559 559.813,-413.689 554.421,-404.701"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="557.409,-402.879 549.263,-396.104 551.406,-406.48 557.409,-402.879"/>
+<!-- 11->3 -->
+<g id="edge11" class="edge"><title>11->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M276.703,-503.966C240.156,-493.972 193.806,-481.298 155.609,-470.854"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="156.146,-467.372 145.577,-468.111 154.299,-474.124 156.146,-467.372"/>
</g>
-<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#56d8c9" stroke-width="2" d="M249.5,-396C249.5,-396 162.5,-396 162.5,-396 156.5,-396 150.5,-390 150.5,-384 150.5,-384 150.5,-372 150.5,-372 150.5,-366 156.5,-360 162.5,-360 162.5,-360 249.5,-360 249.5,-360 255.5,-360 261.5,-366 261.5,-372 261.5,-372 261.5,-384 261.5,-384 261.5,-390 255.5,-396 249.5,-396"/>
-<text text-anchor="middle" x="206" y="-375.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<!-- 15 -->
+<g id="node16" class="node"><title>15</title>
+<path fill="none" stroke="#d8d356" stroke-width="2" d="M467.5,-468C467.5,-468 364.5,-468 364.5,-468 358.5,-468 352.5,-462 352.5,-456 352.5,-456 352.5,-444 352.5,-444 352.5,-438 358.5,-432 364.5,-432 364.5,-432 467.5,-432 467.5,-432 473.5,-432 479.5,-438 479.5,-444 479.5,-444 479.5,-456 479.5,-456 479.5,-462 473.5,-468 467.5,-468"/>
+<text text-anchor="middle" x="416" y="-447.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
-<!-- 11->14 -->
-<g id="edge27" class="edge"><title>11->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M520.971,-434.439C516.927,-433.578 512.909,-432.756 509,-432 407.042,-412.286 377.502,-417.243 271.399,-395.95"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="272.076,-392.516 261.578,-393.949 270.678,-399.375 272.076,-392.516"/>
+<!-- 11->15 -->
+<g id="edge30" class="edge"><title>11->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M358.034,-503.697C367.545,-495.05 379.207,-484.449 389.57,-475.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="392.14,-477.421 397.185,-468.104 387.431,-472.241 392.14,-477.421"/>
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<!-- 17 -->
<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#d8d356" stroke-width="2" d="M850.5,-396C850.5,-396 777.5,-396 777.5,-396 771.5,-396 765.5,-390 765.5,-384 765.5,-384 765.5,-372 765.5,-372 765.5,-366 771.5,-360 777.5,-360 777.5,-360 850.5,-360 850.5,-360 856.5,-360 862.5,-366 862.5,-372 862.5,-372 862.5,-384 862.5,-384 862.5,-390 856.5,-396 850.5,-396"/>
-<text text-anchor="middle" x="814" y="-375.5" font-family="sans" font-size="10.00">map_genome_star</text>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M887.5,-468C887.5,-468 798.5,-468 798.5,-468 792.5,-468 786.5,-462 786.5,-456 786.5,-456 786.5,-444 786.5,-444 786.5,-438 792.5,-432 798.5,-432 798.5,-432 887.5,-432 887.5,-432 893.5,-432 899.5,-438 899.5,-444 899.5,-444 899.5,-456 899.5,-456 899.5,-462 893.5,-468 887.5,-468"/>
+<text text-anchor="middle" x="843" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 11->17 -->
-<g id="edge33" class="edge"><title>11->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M637.7,-431.966C673.407,-421.238 719.397,-407.421 755.452,-396.59"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="756.771,-399.848 765.341,-393.619 754.756,-393.144 756.771,-399.848"/>
+<g id="edge35" class="edge"><title>11->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M407.368,-505.557C410.28,-505.009 413.167,-504.487 416,-504 542.678,-482.204 691.979,-465.763 776.257,-457.326"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="776.852,-460.784 786.456,-456.312 776.159,-453.819 776.852,-460.784"/>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
-<path fill="none" stroke="#d8bc56" stroke-width="2" d="M522,-180C522,-180 446,-180 446,-180 440,-180 434,-174 434,-168 434,-168 434,-156 434,-156 434,-150 440,-144 446,-144 446,-144 522,-144 522,-144 528,-144 534,-150 534,-156 534,-156 534,-168 534,-168 534,-174 528,-180 522,-180"/>
-<text text-anchor="middle" x="484" y="-159.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
-</g>
-<!-- 12->5 -->
-<g id="edge13" class="edge"><title>12->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M479.798,-143.697C477.904,-135.898 475.623,-126.509 473.516,-117.829"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="476.915,-116.996 471.154,-108.104 470.113,-118.648 476.915,-116.996"/>
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-<!-- 13->6 -->
-<g id="edge15" class="edge"><title>13->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M68.7528,-359.697C68.6426,-351.983 68.5102,-342.712 68.3873,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="71.8869,-334.053 68.2443,-324.104 64.8876,-334.153 71.8869,-334.053"/>
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-<!-- 13->7 -->
-<g id="edge17" class="edge"><title>13->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M108.874,-359.876C131.157,-350.307 159.115,-338.3 182.756,-328.148"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="184.448,-331.23 192.255,-324.068 181.686,-324.798 184.448,-331.23"/>
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-<!-- 14->6 -->
-<g id="edge14" class="edge"><title>14->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M172.241,-359.876C153.78,-350.512 130.718,-338.814 110.983,-328.803"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="112.39,-325.592 101.888,-324.19 109.223,-331.835 112.39,-325.592"/>
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-<!-- 14->7 -->
-<g id="edge16" class="edge"><title>14->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M212.427,-359.697C215.355,-351.813 218.887,-342.304 222.14,-333.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="225.446,-334.697 225.647,-324.104 218.884,-332.26 225.446,-334.697"/>
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-<!-- 15->8 -->
-<g id="edge20" class="edge"><title>15->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M745.82,-359.961C762.658,-351.866 779.295,-340.283 789,-324 801.284,-303.391 787.883,-278.213 773.544,-259.902"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="776.066,-257.461 766.979,-252.014 770.686,-261.939 776.066,-257.461"/>
+<path fill="none" stroke="#d88d56" stroke-width="2" d="M237,-540C237,-540 153,-540 153,-540 147,-540 141,-534 141,-528 141,-528 141,-516 141,-516 141,-510 147,-504 153,-504 153,-504 237,-504 237,-504 243,-504 249,-510 249,-516 249,-516 249,-528 249,-528 249,-534 243,-540 237,-540"/>
+<text text-anchor="middle" x="195" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
</g>
-<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#56d88a" stroke-width="2" d="M768,-324C768,-324 618,-324 618,-324 612,-324 606,-318 606,-312 606,-312 606,-300 606,-300 606,-294 612,-288 618,-288 618,-288 768,-288 768,-288 774,-288 780,-294 780,-300 780,-300 780,-312 780,-312 780,-318 774,-324 768,-324"/>
-<text text-anchor="middle" x="693" y="-303.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<!-- 12->3 -->
+<g id="edge12" class="edge"><title>12->3</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M167.602,-503.876C153.093,-494.808 135.084,-483.552 119.415,-473.759"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="120.839,-470.522 110.504,-468.19 117.129,-476.458 120.839,-470.522"/>
</g>
-<!-- 15->16 -->
-<g id="edge32" class="edge"><title>15->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M691.494,-359.697C691.715,-351.983 691.98,-342.712 692.225,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="695.724,-334.2 692.511,-324.104 688.727,-334 695.724,-334.2"/>
+<!-- 12->4 -->
+<g id="edge13" class="edge"><title>12->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M210.82,-503.697C218.57,-495.22 228.039,-484.864 236.524,-475.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="239.197,-477.846 243.362,-468.104 234.031,-473.123 239.197,-477.846"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#56d8a2" stroke-width="2" d="M559,-252C559,-252 471,-252 471,-252 465,-252 459,-246 459,-240 459,-240 459,-228 459,-228 459,-222 465,-216 471,-216 471,-216 559,-216 559,-216 565,-216 571,-222 571,-228 571,-228 571,-240 571,-240 571,-246 565,-252 559,-252"/>
-<text text-anchor="middle" x="515" y="-231.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<!-- 13 -->
+<g id="node14" class="node"><title>13</title>
+<path fill="none" stroke="#568ad8" stroke-width="2" d="M661,-540C661,-540 565,-540 565,-540 559,-540 553,-534 553,-528 553,-528 553,-516 553,-516 553,-510 559,-504 565,-504 565,-504 661,-504 661,-504 667,-504 673,-510 673,-516 673,-516 673,-528 673,-528 673,-534 667,-540 661,-540"/>
+<text text-anchor="middle" x="613" y="-519.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
-<!-- 15->21 -->
-<g id="edge38" class="edge"><title>15->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M634.288,-362.566C630.473,-361.674 626.684,-360.811 623,-360 581.244,-350.811 461.258,-356.94 434,-324 423.8,-311.673 426.39,-302.074 434,-288 440.818,-275.391 452.085,-265.3 464.079,-257.45"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="466.141,-260.294 472.888,-252.126 462.52,-254.303 466.141,-260.294"/>
+<!-- 13->4 -->
+<g id="edge14" class="edge"><title>13->4</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M552.723,-506.118C549.439,-505.383 546.181,-504.672 543,-504 457.739,-485.99 433.404,-485.008 344.115,-468.184"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="344.567,-464.707 334.09,-466.28 343.261,-471.585 344.567,-464.707"/>
</g>
-<!-- 16->8 -->
-<g id="edge18" class="edge"><title>16->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M707.09,-287.697C713.923,-279.305 722.257,-269.07 729.756,-259.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="732.472,-262.069 736.072,-252.104 727.044,-257.649 732.472,-262.069"/>
+<!-- 16 -->
+<g id="node17" class="node"><title>16</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M596.5,-468C596.5,-468 509.5,-468 509.5,-468 503.5,-468 497.5,-462 497.5,-456 497.5,-456 497.5,-444 497.5,-444 497.5,-438 503.5,-432 509.5,-432 509.5,-432 596.5,-432 596.5,-432 602.5,-432 608.5,-438 608.5,-444 608.5,-444 608.5,-456 608.5,-456 608.5,-462 602.5,-468 596.5,-468"/>
+<text text-anchor="middle" x="553" y="-447.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 16->21 -->
-<g id="edge35" class="edge"><title>16->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M649.456,-287.876C624.798,-278.179 593.777,-265.98 567.746,-255.743"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="568.989,-252.471 558.402,-252.068 566.428,-258.985 568.989,-252.471"/>
+<!-- 13->16 -->
+<g id="edge32" class="edge"><title>13->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M598.169,-503.697C590.975,-495.305 582.203,-485.07 574.31,-475.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="576.826,-473.419 567.661,-468.104 571.511,-477.975 576.826,-473.419"/>
</g>
-<!-- 17->8 -->
-<g id="edge19" class="edge"><title>17->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M833.772,-359.802C852.309,-341.524 875.081,-312.007 860,-288 844.242,-262.915 812.909,-249.424 787.701,-242.343"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="788.244,-238.869 777.688,-239.768 786.501,-245.649 788.244,-238.869"/>
+<!-- 19 -->
+<g id="node20" class="node"><title>19</title>
+<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1002.5,-468C1002.5,-468 929.5,-468 929.5,-468 923.5,-468 917.5,-462 917.5,-456 917.5,-456 917.5,-444 917.5,-444 917.5,-438 923.5,-432 929.5,-432 929.5,-432 1002.5,-432 1002.5,-432 1008.5,-432 1014.5,-438 1014.5,-444 1014.5,-444 1014.5,-456 1014.5,-456 1014.5,-462 1008.5,-468 1002.5,-468"/>
+<text text-anchor="middle" x="966" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
-<!-- 17->16 -->
-<g id="edge31" class="edge"><title>17->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M784.4,-359.876C768.433,-350.639 748.54,-339.131 731.394,-329.212"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="733.122,-326.168 722.714,-324.19 729.617,-332.227 733.122,-326.168"/>
+<!-- 13->19 -->
+<g id="edge39" class="edge"><title>13->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M673.279,-512.113C731.011,-503.162 820.701,-488.115 907.607,-467.955"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="908.43,-471.357 917.367,-465.666 906.832,-464.542 908.43,-471.357"/>
</g>
-<!-- 17->21 -->
-<g id="edge37" class="edge"><title>17->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M814.228,-359.872C813.512,-339.662 809.074,-306.478 789,-288 759.355,-260.712 652.576,-246.511 581.402,-239.909"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="581.446,-236.399 571.173,-238.99 580.819,-243.371 581.446,-236.399"/>
+<!-- 14 -->
+<g id="node15" class="node"><title>14</title>
+<path fill="none" stroke="#d8ac56" stroke-width="2" d="M577,-252C577,-252 501,-252 501,-252 495,-252 489,-246 489,-240 489,-240 489,-228 489,-228 489,-222 495,-216 501,-216 501,-216 577,-216 577,-216 583,-216 589,-222 589,-228 589,-228 589,-240 589,-240 589,-246 583,-252 577,-252"/>
+<text text-anchor="middle" x="539" y="-231.5" font-family="sans" font-size="10.00">merge_TIN_scores</text>
+</g>
+<!-- 14->5 -->
+<g id="edge15" class="edge"><title>14->5</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M523.921,-215.697C516.608,-207.305 507.69,-197.07 499.665,-187.861"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="502.114,-185.344 492.905,-180.104 496.836,-189.943 502.114,-185.344"/>
+</g>
+<!-- 15->6 -->
+<g id="edge17" class="edge"><title>15->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M388.357,-431.876C373.582,-422.724 355.209,-411.342 339.297,-401.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="341.093,-398.481 330.749,-396.19 337.407,-404.431 341.093,-398.481"/>
+</g>
+<!-- 15->7 -->
+<g id="edge19" class="edge"><title>15->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M428.607,-431.697C434.597,-423.474 441.876,-413.483 448.479,-404.421"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="451.478,-406.248 454.538,-396.104 445.821,-402.126 451.478,-406.248"/>
+</g>
+<!-- 16->6 -->
+<g id="edge16" class="edge"><title>16->6</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M497.206,-433.378C460.723,-423.163 412.756,-409.732 373.621,-398.774"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="374.447,-395.371 363.874,-396.045 372.56,-402.111 374.447,-395.371"/>
+</g>
+<!-- 16->7 -->
+<g id="edge18" class="edge"><title>16->7</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M531.742,-431.697C520.911,-422.881 507.582,-412.032 495.84,-402.474"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="497.979,-399.703 488.014,-396.104 493.56,-405.132 497.979,-399.703"/>
+</g>
+<!-- 17->8 -->
+<g id="edge22" class="edge"><title>17->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M899.722,-433.313C918.045,-425.265 936.359,-413.365 947,-396 955.359,-382.357 955.132,-373.779 947,-360 934.386,-338.628 909.727,-325.279 888.56,-317.324"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.422,-313.918 878.828,-313.94 887.123,-320.53 889.422,-313.918"/>
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<!-- 18 -->
<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#d87d56" stroke-width="2" d="M358,-540C358,-540 232,-540 232,-540 226,-540 220,-534 220,-528 220,-528 220,-516 220,-516 220,-510 226,-504 232,-504 232,-504 358,-504 358,-504 364,-504 370,-510 370,-516 370,-516 370,-528 370,-528 370,-534 364,-540 358,-540"/>
-<text text-anchor="middle" x="295" y="-519.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-</g>
-<!-- 18->9 -->
-<g id="edge21" class="edge"><title>18->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M297.719,-503.697C298.931,-495.983 300.388,-486.712 301.739,-478.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="305.217,-478.526 303.312,-468.104 298.302,-477.44 305.217,-478.526"/>
+<path fill="none" stroke="#b6d856" stroke-width="2" d="M926,-396C926,-396 776,-396 776,-396 770,-396 764,-390 764,-384 764,-384 764,-372 764,-372 764,-366 770,-360 776,-360 776,-360 926,-360 926,-360 932,-360 938,-366 938,-372 938,-372 938,-384 938,-384 938,-390 932,-396 926,-396"/>
+<text text-anchor="middle" x="851" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+</g>
+<!-- 17->18 -->
+<g id="edge37" class="edge"><title>17->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M844.978,-431.697C845.859,-423.983 846.919,-414.712 847.901,-406.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="851.387,-406.437 849.045,-396.104 844.432,-405.642 851.387,-406.437"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node"><title>25</title>
+<path fill="none" stroke="#56d0d8" stroke-width="2" d="M780,-324C780,-324 692,-324 692,-324 686,-324 680,-318 680,-312 680,-312 680,-300 680,-300 680,-294 686,-288 692,-288 692,-288 780,-288 780,-288 786,-288 792,-294 792,-300 792,-300 792,-312 792,-312 792,-318 786,-324 780,-324"/>
+<text text-anchor="middle" x="736" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+</g>
+<!-- 17->25 -->
+<g id="edge45" class="edge"><title>17->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M799.53,-431.827C783.272,-423.345 766.08,-411.537 755,-396 742.133,-377.959 737.662,-352.972 736.249,-334.065"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="739.741,-333.812 735.737,-324.002 732.75,-334.167 739.741,-333.812"/>
+</g>
+<!-- 18->8 -->
+<g id="edge20" class="edge"><title>18->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M851,-359.697C851,-351.983 851,-342.712 851,-334.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="854.5,-334.104 851,-324.104 847.5,-334.104 854.5,-334.104"/>
+</g>
+<!-- 18->25 -->
+<g id="edge42" class="edge"><title>18->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M822.868,-359.876C807.832,-350.724 789.133,-339.342 772.94,-329.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="774.602,-326.4 764.24,-324.19 770.962,-332.379 774.602,-326.4"/>
+</g>
+<!-- 19->8 -->
+<g id="edge21" class="edge"><title>19->8</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M970.876,-431.724C975.205,-412.573 978.916,-381.548 965,-360 948.17,-333.94 914.888,-320.48 888.609,-313.662"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.107,-310.183 878.57,-311.284 887.494,-316.994 889.107,-310.183"/>
+</g>
+<!-- 19->18 -->
+<g id="edge36" class="edge"><title>19->18</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M937.868,-431.876C922.832,-422.724 904.133,-411.342 887.94,-401.485"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="889.602,-398.4 879.24,-396.19 885.962,-404.379 889.602,-398.4"/>
+</g>
+<!-- 19->25 -->
+<g id="edge44" class="edge"><title>19->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M967.332,-431.807C967.882,-411.847 965.54,-379.215 947,-360 941.799,-354.609 861.991,-335.541 802.055,-321.821"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="802.775,-318.395 792.247,-319.582 801.217,-325.22 802.775,-318.395"/>
+</g>
+<!-- 20->9 -->
+<g id="edge23" class="edge"><title>20->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M846.292,-215.697C844.639,-207.983 842.653,-198.712 840.81,-190.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="844.183,-189.149 838.665,-180.104 837.338,-190.616 844.183,-189.149"/>
</g>
-<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#56d0d8" stroke-width="2" d="M487.5,-540C487.5,-540 400.5,-540 400.5,-540 394.5,-540 388.5,-534 388.5,-528 388.5,-528 388.5,-516 388.5,-516 388.5,-510 394.5,-504 400.5,-504 400.5,-504 487.5,-504 487.5,-504 493.5,-504 499.5,-510 499.5,-516 499.5,-516 499.5,-528 499.5,-528 499.5,-534 493.5,-540 487.5,-540"/>
-<text text-anchor="middle" x="444" y="-519.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<!-- 21 -->
+<g id="node22" class="node"><title>21</title>
+<path fill="none" stroke="#ced856" stroke-width="2" d="M1054,-324C1054,-324 974,-324 974,-324 968,-324 962,-318 962,-312 962,-312 962,-300 962,-300 962,-294 968,-288 974,-288 974,-288 1054,-288 1054,-288 1060,-288 1066,-294 1066,-300 1066,-300 1066,-312 1066,-312 1066,-318 1060,-324 1054,-324"/>
+<text text-anchor="middle" x="1014" y="-303.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
-<!-- 19->10 -->
-<g id="edge22" class="edge"><title>19->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M444.494,-503.697C444.715,-495.983 444.98,-486.712 445.225,-478.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="448.724,-478.2 445.511,-468.104 441.727,-478 448.724,-478.2"/>
+<!-- 21->9 -->
+<g id="edge24" class="edge"><title>21->9</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M998.839,-287.668C981.776,-268.746 952.678,-238.186 924,-216 907.558,-203.28 887.819,-191.241 871.112,-181.862"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="872.629,-178.702 862.182,-176.937 869.249,-184.831 872.629,-178.702"/>
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<!-- 22 -->
<g id="node23" class="node"><title>22</title>
-<path fill="none" stroke="#5692d8" stroke-width="2" d="M207.5,-468C207.5,-468 122.5,-468 122.5,-468 116.5,-468 110.5,-462 110.5,-456 110.5,-456 110.5,-444 110.5,-444 110.5,-438 116.5,-432 122.5,-432 122.5,-432 207.5,-432 207.5,-432 213.5,-432 219.5,-438 219.5,-444 219.5,-444 219.5,-456 219.5,-456 219.5,-462 213.5,-468 207.5,-468"/>
-<text text-anchor="middle" x="165" y="-447.5" font-family="sans" font-size="10.00">create_index_salmon</text>
-</g>
-<!-- 19->22 -->
-<g id="edge39" class="edge"><title>19->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M388.35,-506.366C385.188,-505.559 382.055,-504.766 379,-504 315.486,-488.074 297.099,-485.057 229.644,-468.13"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="230.342,-464.697 219.79,-465.646 228.632,-471.484 230.342,-464.697"/>
-</g>
-<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M640,-540C640,-540 530,-540 530,-540 524,-540 518,-534 518,-528 518,-528 518,-516 518,-516 518,-510 524,-504 530,-504 530,-504 640,-504 640,-504 646,-504 652,-510 652,-516 652,-516 652,-528 652,-528 652,-534 646,-540 640,-540"/>
-<text text-anchor="middle" x="585" y="-519.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<path fill="none" stroke="#80d856" stroke-width="2" d="M407,-612C407,-612 281,-612 281,-612 275,-612 269,-606 269,-600 269,-600 269,-588 269,-588 269,-582 275,-576 281,-576 281,-576 407,-576 407,-576 413,-576 419,-582 419,-588 419,-588 419,-600 419,-600 419,-606 413,-612 407,-612"/>
+<text text-anchor="middle" x="344" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
-<!-- 20->11 -->
-<g id="edge23" class="edge"><title>20->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M584.011,-503.697C583.57,-495.983 583.041,-486.712 582.549,-478.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="586.042,-477.888 581.977,-468.104 579.054,-478.288 586.042,-477.888"/>
-</g>
-<!-- 21->12 -->
-<g id="edge24" class="edge"><title>21->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M507.337,-215.697C503.808,-207.728 499.544,-198.1 495.631,-189.264"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="498.824,-187.831 491.575,-180.104 492.424,-190.665 498.824,-187.831"/>
-</g>
-<!-- 22->13 -->
-<g id="edge25" class="edge"><title>22->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M141.27,-431.697C129.063,-422.796 114.015,-411.823 100.816,-402.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="102.6,-399.168 92.4574,-396.104 98.4753,-404.824 102.6,-399.168"/>
-</g>
-<!-- 22->14 -->
-<g id="edge28" class="edge"><title>22->14</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M175.135,-431.697C179.852,-423.644 185.562,-413.894 190.782,-404.982"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="193.948,-406.502 195.982,-396.104 187.908,-402.964 193.948,-406.502"/>
+<!-- 22->11 -->
+<g id="edge26" class="edge"><title>22->11</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M342.764,-575.697C342.213,-567.983 341.551,-558.712 340.937,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="344.425,-549.83 340.222,-540.104 337.443,-550.328 344.425,-549.83"/>
</g>
<!-- 23 -->
<g id="node24" class="node"><title>23</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M787,-468C787,-468 717,-468 717,-468 711,-468 705,-462 705,-456 705,-456 705,-444 705,-444 705,-438 711,-432 717,-432 717,-432 787,-432 787,-432 793,-432 799,-438 799,-444 799,-444 799,-456 799,-456 799,-462 793,-468 787,-468"/>
-<text text-anchor="middle" x="752" y="-447.5" font-family="sans" font-size="10.00">create_index_star</text>
+<path fill="none" stroke="#56d8c9" stroke-width="2" d="M238.5,-612C238.5,-612 151.5,-612 151.5,-612 145.5,-612 139.5,-606 139.5,-600 139.5,-600 139.5,-588 139.5,-588 139.5,-582 145.5,-576 151.5,-576 151.5,-576 238.5,-576 238.5,-576 244.5,-576 250.5,-582 250.5,-588 250.5,-588 250.5,-600 250.5,-600 250.5,-606 244.5,-612 238.5,-612"/>
+<text text-anchor="middle" x="195" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
-<!-- 23->15 -->
-<g id="edge29" class="edge"><title>23->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M736.921,-431.697C729.608,-423.305 720.69,-413.07 712.665,-403.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="715.114,-401.344 705.905,-396.104 709.836,-405.943 715.114,-401.344"/>
+<!-- 23->12 -->
+<g id="edge27" class="edge"><title>23->12</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M195,-575.697C195,-567.983 195,-558.712 195,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="198.5,-550.104 195,-540.104 191.5,-550.104 198.5,-550.104"/>
</g>
-<!-- 23->17 -->
-<g id="edge34" class="edge"><title>23->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M767.326,-431.697C774.759,-423.305 783.823,-413.07 791.98,-403.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="794.84,-405.911 798.85,-396.104 789.6,-401.27 794.84,-405.911"/>
+<!-- 26 -->
+<g id="node27" class="node"><title>26</title>
+<path fill="none" stroke="#d89c56" stroke-width="2" d="M522.5,-540C522.5,-540 437.5,-540 437.5,-540 431.5,-540 425.5,-534 425.5,-528 425.5,-528 425.5,-516 425.5,-516 425.5,-510 431.5,-504 437.5,-504 437.5,-504 522.5,-504 522.5,-504 528.5,-504 534.5,-510 534.5,-516 534.5,-516 534.5,-528 534.5,-528 534.5,-534 528.5,-540 522.5,-540"/>
+<text text-anchor="middle" x="480" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+</g>
+<!-- 23->26 -->
+<g id="edge46" class="edge"><title>23->26</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M250.642,-578.334C253.806,-577.536 256.942,-576.753 260,-576 326.125,-559.727 345.31,-557.324 415.453,-540.091"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="416.35,-543.475 425.218,-537.678 414.67,-536.68 416.35,-543.475"/>
</g>
<!-- 24 -->
<g id="node25" class="node"><title>24</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M575.5,-324C575.5,-324 454.5,-324 454.5,-324 448.5,-324 442.5,-318 442.5,-312 442.5,-312 442.5,-300 442.5,-300 442.5,-294 448.5,-288 454.5,-288 454.5,-288 575.5,-288 575.5,-288 581.5,-288 587.5,-294 587.5,-300 587.5,-300 587.5,-312 587.5,-312 587.5,-318 581.5,-324 575.5,-324"/>
-<text text-anchor="middle" x="515" y="-303.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
-</g>
-<!-- 24->21 -->
-<g id="edge36" class="edge"><title>24->21</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M515,-287.697C515,-279.983 515,-270.712 515,-262.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="518.5,-262.104 515,-252.104 511.5,-262.104 518.5,-262.104"/>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M668,-612C668,-612 558,-612 558,-612 552,-612 546,-606 546,-600 546,-600 546,-588 546,-588 546,-582 552,-576 558,-576 558,-576 668,-576 668,-576 674,-576 680,-582 680,-588 680,-588 680,-600 680,-600 680,-606 674,-612 668,-612"/>
+<text text-anchor="middle" x="613" y="-591.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 24->13 -->
+<g id="edge28" class="edge"><title>24->13</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M613,-575.697C613,-567.983 613,-558.712 613,-550.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="616.5,-550.104 613,-540.104 609.5,-550.104 616.5,-550.104"/>
+</g>
+<!-- 25->14 -->
+<g id="edge29" class="edge"><title>25->14</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M688.06,-287.966C660.535,-278.185 625.783,-265.836 596.759,-255.524"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="597.749,-252.161 587.155,-252.111 595.406,-258.757 597.749,-252.161"/>
+</g>
+<!-- 26->15 -->
+<g id="edge31" class="edge"><title>26->15</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M464.18,-503.697C456.43,-495.22 446.961,-484.864 438.476,-475.583"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="440.969,-473.123 431.638,-468.104 435.803,-477.846 440.969,-473.123"/>
+</g>
+<!-- 26->16 -->
+<g id="edge33" class="edge"><title>26->16</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M498.045,-503.697C507.062,-495.05 518.118,-484.449 527.943,-475.027"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="530.367,-477.552 535.163,-468.104 525.522,-472.499 530.367,-477.552"/>
+</g>
+<!-- 27 -->
+<g id="node28" class="node"><title>27</title>
+<path fill="none" stroke="#d8c356" stroke-width="2" d="M1001,-540C1001,-540 931,-540 931,-540 925,-540 919,-534 919,-528 919,-528 919,-516 919,-516 919,-510 925,-504 931,-504 931,-504 1001,-504 1001,-504 1007,-504 1013,-510 1013,-516 1013,-516 1013,-528 1013,-528 1013,-534 1007,-540 1001,-540"/>
+<text text-anchor="middle" x="966" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text>
+</g>
+<!-- 27->17 -->
+<g id="edge34" class="edge"><title>27->17</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M935.911,-503.876C919.68,-494.639 899.458,-483.131 882.029,-473.212"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="883.627,-470.094 873.205,-468.19 880.165,-476.178 883.627,-470.094"/>
+</g>
+<!-- 27->19 -->
+<g id="edge38" class="edge"><title>27->19</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M966,-503.697C966,-495.983 966,-486.712 966,-478.112"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="969.5,-478.104 966,-468.104 962.5,-478.104 969.5,-478.104"/>
+</g>
+<!-- 27->21 -->
+<g id="edge41" class="edge"><title>27->21</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M993.34,-503.775C1005.11,-494.718 1017.62,-482.478 1024,-468 1043.27,-424.297 1032.42,-367.371 1023.04,-334.235"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="1026.3,-332.935 1020.08,-324.359 1019.6,-334.943 1026.3,-332.935"/>
+</g>
+<!-- 28 -->
+<g id="node29" class="node"><title>28</title>
+<path fill="none" stroke="#56d85b" stroke-width="2" d="M695.5,-396C695.5,-396 574.5,-396 574.5,-396 568.5,-396 562.5,-390 562.5,-384 562.5,-384 562.5,-372 562.5,-372 562.5,-366 568.5,-360 574.5,-360 574.5,-360 695.5,-360 695.5,-360 701.5,-360 707.5,-366 707.5,-372 707.5,-372 707.5,-384 707.5,-384 707.5,-390 701.5,-396 695.5,-396"/>
+<text text-anchor="middle" x="635" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 28->25 -->
+<g id="edge43" class="edge"><title>28->25</title>
+<path fill="none" stroke="grey" stroke-width="2" d="M659.707,-359.876C672.669,-350.893 688.728,-339.763 702.765,-330.034"/>
+<polygon fill="grey" stroke="grey" stroke-width="2" points="704.972,-332.763 711.198,-324.19 700.985,-327.009 704.972,-332.763"/>
</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
index 0000000000000000000000000000000000000000..5aabbdab18d2fde5d02988776ef0c7083fe7e072
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
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.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
new file mode 100644
index 0000000000000000000000000000000000000000..5aabbdab18d2fde5d02988776ef0c7083fe7e072
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
new file mode 100644
index 0000000000000000000000000000000000000000..95b615abec731d3dfd080ff2d6067edbaa051806
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.bai differ
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
new file mode 100644
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Binary files /dev/null and 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 differ
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
new file mode 100644
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Binary files /dev/null and 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 differ
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
new file mode 100644
index 0000000000000000000000000000000000000000..e4b8cb341acae604db9eba2f3eb23d9510ca783c
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 differ
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}"
+