diff --git a/Snakefile b/Snakefile
index 7c8185c2212afdec42f122dbe28c38644e105b34..a51dcf19c09c3e18cd991f6e7927934f06146081 100644
--- a/Snakefile
+++ b/Snakefile
@@ -4,6 +4,7 @@ import os
import sys
import pandas as pd
+import shutil
# Get sample table
samples_table = pd.read_csv(
@@ -16,7 +17,7 @@ samples_table = pd.read_csv(
)
# Global config
-localrules: finish
+localrules: finish, rename_star_rpm_for_alfa
# Create log directories
os.makedirs(
@@ -99,7 +100,23 @@ rule finish:
zip,
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
- for i in list(samples_table.index.values)])
+ for i in list(samples_table.index.values)]),
+ alfa_reports = expand(os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "ALFA_plots.Biotypes.pdf"),
+ zip,
+ sample= [i for i in list(samples_table.index.values)],
+ seqmode= [
+ samples_table.loc[i,"seqmode"]
+ for i in list(samples_table.index.values)]),
+ alfa_all_samples = os.path.join(
+ config["output_dir"],
+ "ALFA",
+ "ALFA_plots.Categories.pdf")
+
@@ -441,6 +458,47 @@ rule star_rpm:
"""
+rule rename_star_rpm_for_alfa:
+ input:
+ str1 = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str1.out.bg"),
+ str2 = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "STAR_coverage",
+ "{sample}_Signal.UniqueMultiple.str2.out.bg")
+
+ output:
+ plus = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "{sample}_Signal.UniqueMultiple.out.plus.bg"),
+ minus = os.path.join(
+ config["output_dir"],
+ "{seqmode}",
+ "{sample}",
+ "ALFA",
+ "{sample}_Signal.UniqueMultiple.out.minus.bg")
+
+ params:
+ orientation = lambda wildcards: samples_table.loc[wildcards.sample, "kallisto_directionality"]
+
+ run:
+ if params['orientation'] == "--fr":
+ shutil.copy2(input['str1'], output['plus'])
+ shutil.copy2(input['str2'], output['minus'])
+ elif params['orientation'] == "--rf":
+ shutil.copy2(input['str1'], output['minus'])
+ shutil.copy2(input['str2'], output['plus'])
+
+
rule calculate_TIN_scores:
"""
Caluclate transcript integrity (TIN) score
@@ -612,4 +670,166 @@ 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"}
+rename_files = {"fr-firststrand": ("Signal.UniqueMultiple.out.plus.bg",
+ "Signal.UniqueMultiple.out.minus.bg"),
+ "fr-secondstrand": ("Signal.UniqueMultiple.out.minus.bg",
+ "Signal.UniqueMultiple.out.plus.bg")}
+
+
+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..d3450b87b4a8e8a46daa3975c55391d0402b4520 100644
--- a/images/dag_test_workflow.svg
+++ b/images/dag_test_workflow.svg
@@ -1,407 +1,591 @@
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"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<!-- Generated by graphviz version 2.38.0 (20140413.2041)
+<!-- Generated by graphviz version 2.40.1 (20161225.0304)
-->
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+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 621)">
<title>snakemake_dag</title>
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+<title>6->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1565.2947,-287.934C1548.0535,-278.8932 1528.617,-266.7175 1514,-252 1448.8925,-186.4447 1457.7339,-151.1073 1410,-72 1404.6476,-63.1296 1398.6686,-53.534 1393.235,-44.9268"/>
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<!-- 7 -->
-<g id="node8" class="node"><title>7</title>
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-<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="#5692d8" 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>
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-<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="#c0c0c0" stroke-width="2" d="M1302.7295,-71.8314C1314.9162,-62.8779 1329.7823,-51.9558 1342.9312,-42.2955"/>
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<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
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-<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="#5692d8" 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>
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<!-- 8->0 -->
-<g id="edge8" class="edge"><title>8->0</title>
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-<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="#c0c0c0" stroke-width="2" d="M835.582,-73.4116C838.4198,-72.912 841.2331,-72.439 844,-72 1028.3968,-42.7416 1251.3991,-26.1272 1338.5488,-20.3477"/>
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<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
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-<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="#d8cb56" 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>
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<!-- 9->0 -->
-<g id="edge9" class="edge"><title>9->0</title>
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-<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="#c0c0c0" stroke-width="2" d="M1012.5906,-73.5314C1015.4267,-73.0047 1018.2366,-72.4925 1021,-72 1136.4028,-51.434 1273.7982,-31.947 1338.6202,-23.0491"/>
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<!-- 10 -->
-<g id="node11" class="node"><title>10</title>
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-<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="#d8cb56" 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>
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<!-- 10->0 -->
-<g id="edge10" class="edge"><title>10->0</title>
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-<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="#c0c0c0" stroke-width="2" d="M1176.7797,-71.9243C1228.104,-58.032 1297.092,-39.3585 1338.9564,-28.0268"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1339.9954,-31.3716 1348.7335,-25.3804 1338.1664,-24.6148 1339.9954,-31.3716"/>
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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="#d8a456" 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>
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<!-- 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"/>
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+<g id="edge11" class="edge">
+<title>11->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1447.561,-287.7343C1437.9116,-248.249 1414.1116,-152.0416 1392,-72 1389.6677,-63.5574 1387.0086,-54.4114 1384.5369,-46.088"/>
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+</g>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#56d88a" 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="#c0c0c0" stroke-width="2" d="M1480.2372,-294.1107C1504.718,-283.803 1540.7903,-268.6146 1570.5493,-256.0845"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1572.1086,-259.2256 1579.9668,-252.1193 1569.3922,-252.7742 1572.1086,-259.2256"/>
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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="#d8a456" 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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+<title>12->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1793.5802,-303.2749C1731.6888,-296.8917 1587.0545,-279.4064 1547,-252 1507.9241,-225.2632 1463.0834,-108.5619 1433,-72 1424.6772,-61.8849 1414.5713,-51.7549 1405.1936,-43.0465"/>
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+<!-- 28 -->
+<g id="node29" class="node">
+<title>28</title>
+<path fill="none" stroke="#56d88a" 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="#c0c0c0" stroke-width="2" d="M1841.935,-287.8314C1851.4783,-279.1337 1863.0599,-268.5783 1873.4306,-259.1265"/>
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<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
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-<g id="edge13" class="edge"><title>13->3</title>
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+<path fill="none" stroke="#56d8d0" 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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-<g id="node17" class="node"><title>16</title>
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+<g id="edge13" class="edge">
+<title>13->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1618.8187,-143.7193C1596.6623,-120.4792 1558.9656,-82.1486 1542,-72 1501.167,-47.5743 1447.9824,-32.798 1412.9546,-25.0224"/>
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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="#d85656" 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="#c0c0c0" stroke-width="2" d="M1639.0281,-143.8314C1640.3115,-136.131 1641.8376,-126.9743 1643.2639,-118.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1646.7394,-118.8526 1644.9311,-108.4133 1639.8347,-117.7018 1646.7394,-118.8526"/>
</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="#56d8d0" 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="#c0c0c0" stroke-width="2" d="M1750.5951,-143.9571C1745.6652,-123.1406 1734.4307,-89.5346 1711,-72 1664.433,-37.151 1490.3916,-23.9348 1413.233,-19.7128"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1413.1819,-16.2054 1403.0119,-19.1754 1412.8143,-23.1957 1413.1819,-16.2054"/>
+</g>
+<!-- 14->15 -->
+<g id="edge43" class="edge">
+<title>14->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1727.2517,-143.8314C1713.9447,-134.7927 1697.684,-123.7476 1683.3625,-114.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1684.9785,-110.8864 1674.7397,-108.1628 1681.0453,-116.677 1684.9785,-110.8864"/>
+</g>
+<!-- 15->0 -->
+<g id="edge15" class="edge">
+<title>15->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1594.2616,-75.7751C1540.6047,-61.5718 1459.5833,-40.125 1412.8282,-27.7486"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1413.6767,-24.3528 1403.114,-25.1772 1411.8854,-31.1197 1413.6767,-24.3528"/>
</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="#61d856" 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="#c0c0c0" stroke-width="2" d="M837.5048,-506.4544C825.4956,-479.2448 805,-425.8044 805,-378 805,-378 805,-378 805,-306 805,-265.2729 796.673,-218.7384 790.5061,-189.8595"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="793.9177,-189.0768 788.3512,-180.0621 787.0811,-190.5806 793.9177,-189.0768"/>
</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="#d8b456" 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="#c0c0c0" stroke-width="2" d="M916.0618,-513.826C1009.3527,-499.6129 1173.3413,-474.629 1266.0609,-460.503"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1266.8217,-463.9276 1276.1804,-458.9613 1265.7673,-457.0074 1266.8217,-463.9276"/>
</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="#566bd8" 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="#c0c0c0" stroke-width="2" d="M846,-506.4571C846,-478.8072 846,-424.2899 846,-378 846,-378 846,-378 846,-306 846,-265.1184 841.524,-249.4692 865,-216 873.792,-203.4655 886.5151,-193.253 899.5292,-185.2188"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="901.6392,-188.0416 908.5408,-180.003 898.1326,-181.9832 901.6392,-188.0416"/>
</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="#d88d56" 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="#c0c0c0" stroke-width="2" d="M892.4104,-215.8314C873.2761,-206.3302 849.6771,-194.6121 829.3878,-184.5374"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="830.8397,-181.3506 820.3265,-180.038 827.7265,-187.6203 830.8397,-181.3506"/>
+</g>
+<!-- 17->4 -->
+<g id="edge19" class="edge">
+<title>17->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M984.1009,-218.271C987.1065,-217.4855 990.0875,-216.7234 993,-216 1009.0118,-212.0231 1090.6917,-194.4637 1156.3959,-180.4329"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1157.3283,-183.8128 1166.3773,-178.3023 1155.867,-176.967 1157.3283,-183.8128"/>
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<!-- 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"/>
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-<!-- 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"/>
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-<!-- 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="#56c9d8" 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"/>
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-<!-- 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"/>
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-<!-- 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"/>
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-<!-- 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"/>
-</g>
-<!-- 21->9 -->
-<g id="edge27" class="edge"><title>21->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M969.326,-143.697C966.285,-135.813 962.617,-126.304 959.239,-117.546"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="962.462,-116.175 955.597,-108.104 955.931,-118.694 962.462,-116.175"/>
-</g>
-<!-- 21->10 -->
-<g id="edge29" class="edge"><title>21->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1011.72,-143.876C1031.5,-134.392 1056.27,-122.513 1077.33,-112.419"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1078.9,-115.548 1086.4,-108.068 1075.87,-109.236 1078.9,-115.548"/>
-</g>
-<!-- 22->7 -->
-<g id="edge24" class="edge"><title>22->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1156.83,-143.876C1180.42,-134.222 1210.06,-122.087 1235,-111.878"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1236.38,-115.096 1244.3,-108.068 1233.72,-108.618 1236.38,-115.096"/>
-</g>
-<!-- 22->8 -->
-<g id="edge26" class="edge"><title>22->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1059.24,-146.384C1055.78,-145.556 1052.35,-144.754 1049,-144 969.907,-126.177 947.224,-124.641 863.791,-108.136"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="864.358,-104.68 853.867,-106.159 862.991,-111.545 864.358,-104.68"/>
-</g>
-<!-- 22->9 -->
-<g id="edge28" class="edge"><title>22->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1074.39,-143.876C1051.6,-134.264 1022.97,-122.193 998.83,-112.013"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1000.05,-108.729 989.476,-108.068 997.331,-115.179 1000.05,-108.729"/>
-</g>
-<!-- 22->10 -->
-<g id="edge30" class="edge"><title>22->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M1116.73,-143.697C1117.5,-135.983 1118.43,-126.712 1119.29,-118.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="1122.78,-118.403 1120.29,-108.104 1115.81,-117.706 1122.78,-118.403"/>
-</g>
-<!-- 23 -->
-<g id="node24" class="node"><title>23</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M975,-401C975,-401 707,-401 707,-401 701,-401 695,-395 695,-389 695,-389 695,-377 695,-377 695,-371 701,-365 707,-365 707,-365 975,-365 975,-365 981,-365 987,-371 987,-377 987,-377 987,-389 987,-389 987,-395 981,-401 975,-401"/>
-<text text-anchor="middle" x="841" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
-<text text-anchor="middle" x="841" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
+<!-- 18->4 -->
+<g id="edge18" class="edge">
+<title>18->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1180,-506.4571C1180,-478.8072 1180,-424.2899 1180,-378 1180,-378 1180,-378 1180,-306 1180,-262.171 1204.7996,-216.6548 1223.2797,-188.8215"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1226.2621,-190.6608 1229.0183,-180.4307 1220.4841,-186.7091 1226.2621,-190.6608"/>
</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="#d88d56" stroke-width="2" d="M1752,-468C1752,-468 1676,-468 1676,-468 1670,-468 1664,-462 1664,-456 1664,-456 1664,-444 1664,-444 1664,-438 1670,-432 1676,-432 1676,-432 1752,-432 1752,-432 1758,-432 1764,-438 1764,-444 1764,-444 1764,-456 1764,-456 1764,-462 1758,-468 1752,-468"/>
+<text text-anchor="middle" x="1714" y="-447.5" font-family="sans" font-size="10.00" fill="#000000">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="#c0c0c0" stroke-width="2" d="M1241.5172,-515.9175C1344.6577,-501.5281 1551.2037,-472.7122 1653.5953,-458.4273"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1654.3473,-461.8563 1663.7677,-457.0081 1653.38,-454.9235 1654.3473,-461.8563"/>
</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="#56d873" 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="#c0c0c0" stroke-width="2" d="M1172.1264,-506.3912C1160.9959,-479.101 1142,-425.559 1142,-378 1142,-378 1142,-378 1142,-306 1142,-265.1184 1137.5773,-254.1944 1123,-216 1119.4899,-206.8032 1114.5546,-197.3165 1109.652,-188.9099"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1112.5935,-187.0106 1104.414,-180.2765 1106.6088,-190.6416 1112.5935,-187.0106"/>
+</g>
+<!-- 19->5 -->
+<g id="edge20" class="edge">
+<title>19->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1279.1233,-431.902C1262.6378,-423.6643 1246.4852,-412.0564 1237,-396 1228.862,-382.2242 1228.6658,-373.658 1237,-360 1246.0596,-345.1533 1260.6481,-334.2161 1276.1053,-326.2279"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1277.751,-329.3208 1285.2715,-321.8581 1274.7386,-323.0022 1277.751,-329.3208"/>
+</g>
+<!-- 19->11 -->
+<g id="edge34" class="edge">
+<title>19->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1386.4292,-431.9219C1403.6028,-423.4959 1421.3206,-411.7651 1433,-396 1446.1732,-378.2186 1450.6522,-353.3165 1451.9895,-334.2128"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1455.4956,-334.1536 1452.4503,-324.0059 1448.5028,-333.8378 1455.4956,-334.1536"/>
</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="#56d89a" 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="#c0c0c0" stroke-width="2" d="M1335,-431.8314C1335,-424.131 1335,-414.9743 1335,-406.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1338.5001,-406.4132 1335,-396.4133 1331.5001,-406.4133 1338.5001,-406.4132"/>
+</g>
+<!-- 20->5 -->
+<g id="edge21" class="edge">
+<title>20->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1336.7664,-359.8314C1337.515,-352.131 1338.4053,-342.9743 1339.2373,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1342.7256,-334.7051 1340.2098,-324.4133 1335.7585,-334.0276 1342.7256,-334.7051"/>
+</g>
+<!-- 20->11 -->
+<g id="edge35" class="edge">
+<title>20->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1364.524,-359.8314C1379.8318,-350.4112 1398.6808,-338.8118 1414.9572,-328.7955"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1417.014,-331.6395 1423.6962,-323.4177 1413.3453,-325.6779 1417.014,-331.6395"/>
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-<!-- 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="#56d8a9" 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="#c0c0c0" stroke-width="2" d="M1500.7771,-359.9243C1471.6694,-350.0387 1435.4334,-337.7321 1404.9306,-327.3726"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1405.8392,-323.9849 1395.2448,-324.0831 1403.5881,-330.6131 1405.8392,-323.9849"/>
+</g>
+<!-- 21->6 -->
+<g id="edge25" class="edge">
+<title>21->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1567.1218,-359.8314C1573.0499,-351.6232 1580.1729,-341.7606 1586.6933,-332.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1589.684,-334.5693 1592.7015,-324.4133 1584.0092,-330.4708 1589.684,-334.5693"/>
+</g>
+<!-- 22->6 -->
+<g id="edge23" class="edge">
+<title>22->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1700.3217,-431.7623C1681.4139,-406.5518 1647.1827,-360.9103 1625.5714,-332.0952"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1628.3673,-329.9896 1619.5672,-324.0896 1622.7672,-334.1897 1628.3673,-329.9896"/>
+</g>
+<!-- 22->12 -->
+<g id="edge36" class="edge">
+<title>22->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1764.3807,-439.3338C1805.313,-429.5257 1858.2759,-413.8321 1871,-396 1885.6478,-375.4719 1869.0511,-350.0834 1851.3198,-331.5109"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1853.307,-328.5529 1843.739,-324.0026 1848.381,-333.5264 1853.307,-328.5529"/>
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-<!-- 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="#56d89a" 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="#c0c0c0" stroke-width="2" d="M1728.8882,-431.8314C1735.753,-423.454 1744.0301,-413.3531 1751.5511,-404.1749"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1754.2803,-406.3665 1757.9114,-396.4133 1748.8659,-401.9297 1754.2803,-406.3665"/>
+</g>
+<!-- 23->6 -->
+<g id="edge24" class="edge">
+<title>23->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1730.8588,-359.8314C1708.5236,-350.2018 1680.9064,-338.295 1657.329,-328.1299"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1658.4067,-324.7831 1647.8381,-324.038 1655.6353,-331.2112 1658.4067,-324.7831"/>
+</g>
+<!-- 23->12 -->
+<g id="edge37" class="edge">
+<title>23->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1785.3648,-359.8314C1790.9509,-351.6232 1797.663,-341.7606 1803.8072,-332.7323"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1806.736,-334.6496 1809.4687,-324.4133 1800.949,-330.7112 1806.736,-334.6496"/>
+</g>
+<!-- 24->7 -->
+<g id="edge26" class="edge">
+<title>24->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1017.3431,-145.9846C1020.2669,-145.3062 1023.1629,-144.6418 1026,-144 1102.1762,-126.7681 1121.6776,-124.5725 1198,-108 1198.1,-107.9783 1198.2001,-107.9566 1198.3002,-107.9348"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1198.7515,-111.4189 1207.7731,-105.8636 1197.2562,-104.5805 1198.7515,-111.4189"/>
+</g>
+<!-- 24->8 -->
+<g id="edge28" class="edge">
+<title>24->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M903.8026,-143.8314C877.8034,-134.0306 845.5464,-121.8709 818.2719,-111.5894"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="819.4426,-108.2904 808.8508,-108.038 816.9734,-114.8404 819.4426,-108.2904"/>
+</g>
+<!-- 24->9 -->
+<g id="edge30" class="edge">
+<title>24->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M947.2055,-143.8314C945.1511,-136.0463 942.704,-126.7729 940.4244,-118.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="943.7948,-117.1892 937.8591,-108.4133 937.0265,-118.9753 943.7948,-117.1892"/>
+</g>
+<!-- 24->10 -->
+<g id="edge32" class="edge">
+<title>24->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M991.8701,-143.8314C1012.9077,-134.2446 1038.8983,-122.4008 1061.1396,-112.2655"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1062.7683,-115.3697 1070.4166,-108.038 1059.8655,-108.9999 1062.7683,-115.3697"/>
+</g>
+<!-- 25->7 -->
+<g id="edge27" class="edge">
+<title>25->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1138.9357,-143.8314C1164.1437,-134.0734 1195.3926,-121.977 1221.8791,-111.7242"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1223.3397,-114.912 1231.4019,-108.038 1220.8127,-108.384 1223.3397,-114.912"/>
+</g>
+<!-- 25->8 -->
+<g id="edge29" class="edge">
+<title>25->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1035.1836,-146.2296C1032.0824,-145.4548 1029.0061,-144.7063 1026,-144 948.8652,-125.877 926.4696,-124.7982 845.7798,-108.3405"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="846.1432,-104.842 835.643,-106.255 844.7326,-111.6984 846.1432,-104.842"/>
+</g>
+<!-- 25->9 -->
+<g id="edge31" class="edge">
+<title>25->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1051.8776,-143.8314C1030.7068,-134.2446 1004.5517,-122.4008 982.1697,-112.2655"/>
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+</g>
+<!-- 25->10 -->
+<g id="edge33" class="edge">
+<title>25->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1096.5422,-143.8314C1098.4884,-136.0463 1100.8068,-126.7729 1102.9663,-118.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1106.3668,-118.9636 1105.3967,-108.4133 1099.5758,-117.2658 1106.3668,-118.9636"/>
+</g>
+<!-- 26->13 -->
+<g id="edge38" class="edge">
+<title>26->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1626.2804,-215.8314C1627.6708,-208.131 1629.3241,-198.9743 1630.8692,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1634.3428,-190.8761 1632.6754,-180.4133 1627.4542,-189.6322 1634.3428,-190.8761"/>
</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>
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-<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"/>
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-<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"/>
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-<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"/>
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-<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="#afd856" 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="#c0c0c0" stroke-width="2" d="M1730.2049,-215.8314C1712.4119,-205.664 1690.1762,-192.9578 1671.7764,-182.4437"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1673.5071,-179.4016 1663.0882,-177.479 1670.0341,-185.4793 1673.5071,-179.4016"/>
+</g>
+<!-- 27->14 -->
+<g id="edge41" class="edge">
+<title>27->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1759.9813,-215.8314C1759.1257,-208.131 1758.1083,-198.9743 1757.1574,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1760.6289,-189.9656 1756.0459,-180.4133 1753.6717,-190.7386 1760.6289,-189.9656"/>
+</g>
+<!-- 28->14 -->
+<g id="edge40" class="edge">
+<title>28->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1863.9057,-215.8314C1841.4302,-204.823 1812.8786,-190.8385 1790.5097,-179.8823"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1791.8575,-176.6452 1781.3373,-175.3897 1788.7784,-182.9316 1791.8575,-176.6452"/>
+</g>
+<!-- 29 -->
+<g id="node30" class="node">
+<title>29</title>
+<path fill="none" stroke="#567bd8" 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="#c0c0c0" stroke-width="2" d="M846,-580.9656C846,-572.5178 846,-562.2542 846,-552.8064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="849.5001,-552.6265 846,-542.6265 842.5001,-552.6265 849.5001,-552.6265"/>
+</g>
+<!-- 30 -->
+<g id="node31" class="node">
+<title>30</title>
+<path fill="none" stroke="#88d856" 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="#c0c0c0" stroke-width="2" d="M977.5978,-287.8314C969.9585,-279.3694 960.7317,-269.1489 952.3793,-259.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="954.9221,-257.4906 945.6231,-252.4133 949.7262,-262.1813 954.9221,-257.4906"/>
+</g>
+<!-- 33 -->
+<g id="node34" class="node">
+<title>33</title>
+<path fill="none" stroke="#56d8c1" 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="#c0c0c0" stroke-width="2" d="M1010.1499,-287.8314C1017.6717,-279.3694 1026.7565,-269.1489 1034.9804,-259.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1037.6049,-262.2127 1041.6327,-252.4133 1032.373,-257.5621 1037.6049,-262.2127"/>
+</g>
+<!-- 31 -->
+<g id="node32" class="node">
+<title>31</title>
+<path fill="none" stroke="#d87d56" 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="#c0c0c0" stroke-width="2" d="M1180,-580.9656C1180,-572.5178 1180,-562.2542 1180,-552.8064"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1183.5001,-552.6265 1180,-542.6265 1176.5001,-552.6265 1183.5001,-552.6265"/>
+</g>
+<!-- 32 -->
+<g id="node33" class="node">
+<title>32</title>
+<path fill="none" stroke="#d6d856" 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="#c0c0c0" stroke-width="2" d="M1649.7078,-511.8621C1581.369,-498.4287 1473.7076,-477.2657 1403.7242,-463.5091"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1404.1686,-460.0296 1393.6813,-461.535 1402.8184,-466.8981 1404.1686,-460.0296"/>
+</g>
+<!-- 32->22 -->
+<g id="edge50" class="edge">
+<title>32->22</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1714,-503.7476C1714,-495.8767 1714,-486.7743 1714,-478.3232"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1717.5001,-478.1086 1714,-468.1087 1710.5001,-478.1087 1717.5001,-478.1086"/>
+</g>
+<!-- 32->27 -->
+<g id="edge58" class="edge">
+<title>32->27</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1762.5839,-503.8712C1804.1389,-483.2856 1861.1975,-447.3071 1887,-396 1909.2788,-351.6997 1891.5795,-325.3823 1859,-288 1847.884,-275.2453 1832.9862,-264.8884 1818.2072,-256.7847"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1819.5427,-253.5344 1809.0554,-252.0289 1816.3148,-259.7458 1819.5427,-253.5344"/>
+</g>
+<!-- 33->24 -->
+<g id="edge54" class="edge">
+<title>33->24</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1031.2517,-215.8314C1017.9447,-206.7927 1001.684,-195.7476 987.3625,-186.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="988.9785,-182.8864 978.7397,-180.1628 985.0453,-188.677 988.9785,-182.8864"/>
+</g>
+<!-- 33->25 -->
+<g id="edge56" class="edge">
+<title>33->25</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1066.5796,-215.8314C1070.3358,-207.8771 1074.8257,-198.369 1078.9798,-189.5723"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1082.1996,-190.9503 1083.3048,-180.4133 1075.8699,-187.9612 1082.1996,-190.9503"/>
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diff --git a/images/rule_graph.svg b/images/rule_graph.svg
index a2a0d009dcc914acf858cb6594e35f11f4f963cf..dcfb1f093607086b2cb837e182f20d9ff3285ef0 100644
--- a/images/rule_graph.svg
+++ b/images/rule_graph.svg
@@ -1,313 +1,439 @@
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+<!-- Generated by graphviz version 2.40.1 (20161225.0304)
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<!-- Title: snakemake_dag Pages: 1 -->
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- viewBox="0.00 0.00 1070.98 404.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 400)">
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<title>snakemake_dag</title>
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+<polygon fill="#ffffff" stroke="transparent" points="-4,4 -4,-616 924,-616 924,4 -4,4"/>
<!-- 0 -->
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-<path fill="none" stroke="#56c9d8" stroke-width="2" d="M304,-36C304,-36 274,-36 274,-36 268,-36 262,-30 262,-24 262,-24 262,-12 262,-12 262,-6 268,-0 274,-0 274,-0 304,-0 304,-0 310,-0 316,-6 316,-12 316,-12 316,-24 316,-24 316,-30 310,-36 304,-36"/>
-<text text-anchor="middle" x="289" y="-15.5" font-family="sans" font-size="10.00">finish</text>
+<g id="node1" class="node">
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+<text text-anchor="middle" x="491" 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="68" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
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+<text text-anchor="middle" x="168" y="-87.5" font-family="sans" font-size="10.00">pe_fastqc</text>
</g>
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-<g id="edge8" class="edge"><title>1->0</title>
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="253.018,-31.6413 261.826,-25.753 251.268,-24.8635 253.018,-31.6413"/>
+<g id="edge5" class="edge">
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+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M178.8809,-75.1457C181.7596,-73.9918 184.6625,-72.9199 187.5,-72 269.8699,-45.2967 370.6652,-29.5703 424.089,-22.5013"/>
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-<text text-anchor="middle" x="143" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
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+<text text-anchor="middle" x="245" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
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<!-- 2->0 -->
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-<polygon fill="grey" stroke="grey" stroke-width="2" points="254.026,-39.6497 261.53,-32.1703 251,-33.3377 254.026,-39.6497"/>
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+<title>3->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M426.8518,-431.9753C445.2157,-423.339 465.0745,-411.4518 479.5,-396 509.3711,-364.0037 519.5,-349.7727 519.5,-306 519.5,-306 519.5,-306 519.5,-162 519.5,-118.6562 496.6108,-72.9417 479.5907,-44.9402"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="482.3602,-42.7684 474.0851,-36.1522 476.4281,-46.4847 482.3602,-42.7684"/>
</g>
<!-- 4 -->
-<g id="node5" class="node"><title>4</title>
-<path fill="none" stroke="#8fd856" stroke-width="2" d="M138,-252C138,-252 12,-252 12,-252 6,-252 1.42109e-14,-246 1.42109e-14,-240 1.42109e-14,-240 1.42109e-14,-228 1.42109e-14,-228 1.42109e-14,-222 6,-216 12,-216 12,-216 138,-216 138,-216 144,-216 150,-222 150,-228 150,-228 150,-240 150,-240 150,-246 144,-252 138,-252"/>
-<text text-anchor="middle" x="75" y="-231.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
+<g id="node5" class="node">
+<title>4</title>
+<path fill="none" stroke="#567bd8" stroke-width="2" d="M660,-468C660,-468 514,-468 514,-468 508,-468 502,-462 502,-456 502,-456 502,-444 502,-444 502,-438 508,-432 514,-432 514,-432 660,-432 660,-432 666,-432 672,-438 672,-444 672,-444 672,-456 672,-456 672,-462 666,-468 660,-468"/>
+<text text-anchor="middle" x="587" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
</g>
<!-- 4->0 -->
-<g id="edge6" class="edge"><title>4->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M92.1508,-215.849C130.029,-177.971 220.923,-87.0767 264.668,-43.3318"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="267.171,-45.7784 271.768,-36.2325 262.222,-40.8287 267.171,-45.7784"/>
+<g id="edge7" class="edge">
+<title>4->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M557.5,-431.8146C557.5,-404.4983 557.5,-351.25 557.5,-306 557.5,-306 557.5,-306 557.5,-162 557.5,-113.9377 520.0183,-69.7161 491.8956,-43.3006"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="493.9995,-40.4826 484.2507,-36.3339 489.2845,-45.6565 493.9995,-40.4826"/>
</g>
<!-- 5 -->
-<g id="node6" class="node"><title>5</title>
-<path fill="none" stroke="#a7d856" stroke-width="2" d="M876,-108C876,-108 788,-108 788,-108 782,-108 776,-102 776,-96 776,-96 776,-84 776,-84 776,-78 782,-72 788,-72 788,-72 876,-72 876,-72 882,-72 888,-78 888,-84 888,-84 888,-96 888,-96 888,-102 882,-108 876,-108"/>
-<text text-anchor="middle" x="832" y="-87.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
+<g id="node6" class="node">
+<title>5</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M424,-324C424,-324 335,-324 335,-324 329,-324 323,-318 323,-312 323,-312 323,-300 323,-300 323,-294 329,-288 335,-288 335,-288 424,-288 424,-288 430,-288 436,-294 436,-300 436,-300 436,-312 436,-312 436,-318 430,-324 424,-324"/>
+<text text-anchor="middle" x="379.5" y="-303.5" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
</g>
<!-- 5->0 -->
-<g id="edge5" class="edge"><title>5->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M775.935,-81.7724C664.916,-67.4607 419.77,-35.8579 326.247,-23.8017"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="326.492,-20.3043 316.126,-22.4969 325.597,-27.2469 326.492,-20.3043"/>
+<g id="edge3" class="edge">
+<title>5->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M419.4342,-287.8338C433.7482,-279.1511 448.3504,-267.2686 456.5,-252 492.0906,-185.3197 478.6004,-91.9985 468.5639,-45.9554"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="471.9491,-45.0584 466.3062,-36.0914 465.1256,-46.6202 471.9491,-45.0584"/>
</g>
<!-- 6 -->
-<g id="node7" class="node"><title>6</title>
-<path fill="none" stroke="#56d8b9" stroke-width="2" d="M562,-180C562,-180 450,-180 450,-180 444,-180 438,-174 438,-168 438,-168 438,-156 438,-156 438,-150 444,-144 450,-144 450,-144 562,-144 562,-144 568,-144 574,-150 574,-156 574,-156 574,-168 574,-168 574,-174 568,-180 562,-180"/>
-<text text-anchor="middle" x="506" y="-159.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
+<g id="node7" class="node">
+<title>6</title>
+<path fill="none" stroke="#56a2d8" stroke-width="2" d="M775,-396C775,-396 647,-396 647,-396 641,-396 635,-390 635,-384 635,-384 635,-372 635,-372 635,-366 641,-360 647,-360 647,-360 775,-360 775,-360 781,-360 787,-366 787,-372 787,-372 787,-384 787,-384 787,-390 781,-396 775,-396"/>
+<text text-anchor="middle" x="711" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
</g>
<!-- 6->0 -->
-<g id="edge2" class="edge"><title>6->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M479.825,-143.871C440.805,-118.338 367.323,-70.253 323.813,-41.7808"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="325.552,-38.7362 315.268,-36.1893 321.719,-44.5936 325.552,-38.7362"/>
+<g id="edge2" class="edge">
+<title>6->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M666.1378,-359.615C657.3315,-332.4838 642.5,-279.9662 642.5,-234 642.5,-234 642.5,-234 642.5,-162 642.5,-89.0041 551.2336,-47.0665 498.3164,-28.8855"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="499.1909,-25.4882 488.5975,-25.6643 496.9886,-32.1327 499.1909,-25.4882"/>
</g>
<!-- 7 -->
-<g id="node8" class="node"><title>7</title>
-<path fill="none" stroke="#56d87b" stroke-width="2" d="M407.5,-180C407.5,-180 276.5,-180 276.5,-180 270.5,-180 264.5,-174 264.5,-168 264.5,-168 264.5,-156 264.5,-156 264.5,-150 270.5,-144 276.5,-144 276.5,-144 407.5,-144 407.5,-144 413.5,-144 419.5,-150 419.5,-156 419.5,-156 419.5,-168 419.5,-168 419.5,-174 413.5,-180 407.5,-180"/>
-<text text-anchor="middle" x="342" y="-159.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
+<g id="node8" class="node">
+<title>7</title>
+<path fill="none" stroke="#56d863" stroke-width="2" d="M967,-396C967,-396 817,-396 817,-396 811,-396 805,-390 805,-384 805,-384 805,-372 805,-372 805,-366 811,-360 817,-360 817,-360 967,-360 967,-360 973,-360 979,-366 979,-372 979,-372 979,-384 979,-384 979,-390 973,-396 967,-396"/>
+<text text-anchor="middle" x="892" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
</g>
<!-- 7->0 -->
-<g id="edge4" class="edge"><title>7->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M335.607,-143.871C326.495,-119.457 309.687,-74.4258 298.941,-45.6351"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="302.192,-44.3341 295.416,-36.1893 295.633,-46.7819 302.192,-44.3341"/>
+<g id="edge9" class="edge">
+<title>7->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M830.0847,-359.5566C815.9675,-332.7787 792.5,-281.1706 792.5,-234 792.5,-234 792.5,-234 792.5,-162 792.5,-98.468 584.8637,-45.2424 498.4964,-25.851"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="499.1075,-22.4016 488.5871,-23.6555 497.5932,-29.2358 499.1075,-22.4016"/>
</g>
<!-- 8 -->
-<g id="node9" class="node"><title>8</title>
-<path fill="none" stroke="#d85656" stroke-width="2" d="M675.5,-108C675.5,-108 644.5,-108 644.5,-108 638.5,-108 632.5,-102 632.5,-96 632.5,-96 632.5,-84 632.5,-84 632.5,-78 638.5,-72 644.5,-72 644.5,-72 675.5,-72 675.5,-72 681.5,-72 687.5,-78 687.5,-84 687.5,-84 687.5,-96 687.5,-96 687.5,-102 681.5,-108 675.5,-108"/>
-<text text-anchor="middle" x="660" y="-87.5" font-family="sans" font-size="10.00">star_rpm</text>
+<g id="node9" class="node">
+<title>8</title>
+<path fill="none" stroke="#56d88a" stroke-width="2" d="M313,-324C313,-324 277,-324 277,-324 271,-324 265,-318 265,-312 265,-312 265,-300 265,-300 265,-294 271,-288 277,-288 277,-288 313,-288 313,-288 319,-288 325,-294 325,-300 325,-300 325,-312 325,-312 325,-318 319,-324 313,-324"/>
+<text text-anchor="middle" x="295" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 8->0 -->
-<g id="edge3" class="edge"><title>8->0</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M632.418,-83.7958C566.659,-71.3886 400.61,-40.0585 326.141,-26.0077"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="326.736,-22.5583 316.261,-24.1435 325.438,-29.437 326.736,-22.5583"/>
+<g id="edge4" class="edge">
+<title>8->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M304.8323,-290.9295C320.6931,-281.406 339.9431,-267.906 353.5,-252 407.7356,-188.3668 440.338,-92.9502 453.9913,-46.0563"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="457.4015,-46.8595 456.7651,-36.2838 450.6675,-44.9481 457.4015,-46.8595"/>
</g>
-<!-- 9 -->
-<g id="node10" class="node"><title>9</title>
-<path fill="none" stroke="#56b1d8" stroke-width="2" d="M649,-324C649,-324 537,-324 537,-324 531,-324 525,-318 525,-312 525,-312 525,-300 525,-300 525,-294 531,-288 537,-288 537,-288 649,-288 649,-288 655,-288 661,-294 661,-300 661,-300 661,-312 661,-312 661,-318 655,-324 649,-324"/>
-<text text-anchor="middle" x="593" y="-303.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
-</g>
-<!-- 9->3 -->
-<g id="edge9" class="edge"><title>9->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M524.947,-290.684C520.566,-289.772 516.222,-288.872 512,-288 456.398,-276.52 394.088,-263.859 344.297,-253.792"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="344.686,-250.3 334.191,-251.749 343.299,-257.161 344.686,-250.3"/>
-</g>
-<!-- 12 -->
-<g id="node13" class="node"><title>12</title>
-<path fill="none" stroke="#56d863" stroke-width="2" d="M870.5,-252C870.5,-252 781.5,-252 781.5,-252 775.5,-252 769.5,-246 769.5,-240 769.5,-240 769.5,-228 769.5,-228 769.5,-222 775.5,-216 781.5,-216 781.5,-216 870.5,-216 870.5,-216 876.5,-216 882.5,-222 882.5,-228 882.5,-228 882.5,-240 882.5,-240 882.5,-246 876.5,-252 870.5,-252"/>
-<text text-anchor="middle" x="826" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
+<!-- 20 -->
+<g id="node21" class="node">
+<title>20</title>
+<path fill="none" stroke="#d8b456" stroke-width="2" d="M357,-252C357,-252 235,-252 235,-252 229,-252 223,-246 223,-240 223,-240 223,-228 223,-228 223,-222 229,-216 235,-216 235,-216 357,-216 357,-216 363,-216 369,-222 369,-228 369,-228 369,-240 369,-240 369,-246 363,-252 357,-252"/>
+<text text-anchor="middle" x="296" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
-<!-- 9->12 -->
-<g id="edge27" class="edge"><title>9->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M649.7,-287.966C682.945,-277.978 725.103,-265.312 759.857,-254.871"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="760.88,-258.219 769.45,-251.989 758.865,-251.515 760.88,-258.219"/>
+<!-- 8->20 -->
+<g id="edge42" class="edge">
+<title>8->20</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M276.7523,-287.8314C276.8593,-280.131 276.9865,-270.9743 277.1053,-262.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="280.6049,-262.4609 277.2443,-252.4133 273.6056,-262.3637 280.6049,-262.4609"/>
</g>
-<!-- 16 -->
-<g id="node17" class="node"><title>16</title>
-<path fill="none" stroke="#566bd8" stroke-width="2" d="M596.5,-252C596.5,-252 493.5,-252 493.5,-252 487.5,-252 481.5,-246 481.5,-240 481.5,-240 481.5,-228 481.5,-228 481.5,-222 487.5,-216 493.5,-216 493.5,-216 596.5,-216 596.5,-216 602.5,-216 608.5,-222 608.5,-228 608.5,-228 608.5,-240 608.5,-240 608.5,-246 602.5,-252 596.5,-252"/>
-<text text-anchor="middle" x="545" y="-231.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
+<!-- 9 -->
+<g id="node10" class="node">
+<title>9</title>
+<path fill="none" stroke="#56d89a" stroke-width="2" d="M314,-180C314,-180 284,-180 284,-180 278,-180 272,-174 272,-168 272,-168 272,-156 272,-156 272,-150 278,-144 284,-144 284,-144 314,-144 314,-144 320,-144 326,-150 326,-156 326,-156 326,-168 326,-168 326,-174 320,-180 314,-180"/>
+<text text-anchor="middle" x="299" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
</g>
-<!-- 9->16 -->
-<g id="edge33" class="edge"><title>9->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M581.135,-287.697C575.497,-279.474 568.646,-269.483 562.431,-260.421"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="565.271,-258.372 556.729,-252.104 559.497,-262.331 565.271,-258.372"/>
+<!-- 9->0 -->
+<g id="edge4" class="edge">
+<title>9->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M277.3361,-143.7724C277.0758,-123.7272 279.8143,-91.7472 297.5,-72 314.5332,-52.9814 381.5117,-35.3637 424.4262,-25.7033"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="425.2343,-29.1093 434.2453,-23.5367 423.726,-22.2737 425.2343,-29.1093"/>
</g>
<!-- 10 -->
-<g id="node11" class="node"><title>10</title>
-<path fill="none" stroke="#d88556" stroke-width="2" d="M226,-324C226,-324 142,-324 142,-324 136,-324 130,-318 130,-312 130,-312 130,-300 130,-300 130,-294 136,-288 142,-288 142,-288 226,-288 226,-288 232,-288 238,-294 238,-300 238,-300 238,-312 238,-312 238,-318 232,-324 226,-324"/>
-<text text-anchor="middle" x="184" y="-303.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
-</g>
-<!-- 10->3 -->
-<g id="edge10" class="edge"><title>10->3</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M200.562,-287.697C208.675,-279.22 218.588,-268.864 227.471,-259.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="230.243,-261.749 234.629,-252.104 225.186,-256.908 230.243,-261.749"/>
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-<!-- 10->4 -->
-<g id="edge11" class="edge"><title>10->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M157.336,-287.876C143.216,-278.808 125.689,-267.552 110.439,-257.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="112.073,-254.648 101.767,-252.19 108.29,-260.538 112.073,-254.648"/>
+<g id="node11" class="node">
+<title>10</title>
+<path fill="none" stroke="#bed856" stroke-width="2" d="M432,-108C432,-108 340,-108 340,-108 334,-108 328,-102 328,-96 328,-96 328,-84 328,-84 328,-78 334,-72 340,-72 340,-72 432,-72 432,-72 438,-72 444,-78 444,-84 444,-84 444,-96 444,-96 444,-102 438,-108 432,-108"/>
+<text text-anchor="middle" x="386" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
+</g>
+<!-- 9->10 -->
+<g id="edge28" class="edge">
+<title>9->10</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M299.1921,-143.8314C309.1948,-135.0485 321.355,-124.3712 332.1999,-114.8489"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="334.6094,-117.3909 339.8146,-108.1628 329.9908,-112.1308 334.6094,-117.3909"/>
+</g>
+<!-- 10->0 -->
+<g id="edge6" class="edge">
+<title>10->0</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M385.9866,-71.8314C398.6659,-62.7927 414.1596,-51.7476 427.8055,-42.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="429.9105,-44.8176 436.0216,-36.1628 425.8471,-39.1176 429.9105,-44.8176"/>
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<!-- 11 -->
-<g id="node12" class="node"><title>11</title>
-<path fill="none" stroke="#5682d8" stroke-width="2" d="M364,-324C364,-324 268,-324 268,-324 262,-324 256,-318 256,-312 256,-312 256,-300 256,-300 256,-294 262,-288 268,-288 268,-288 364,-288 364,-288 370,-288 376,-294 376,-300 376,-300 376,-312 376,-312 376,-318 370,-324 364,-324"/>
-<text text-anchor="middle" x="316" y="-303.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
+<g id="node12" class="node">
+<title>11</title>
+<path fill="none" stroke="#afd856" stroke-width="2" d="M413,-540C413,-540 285,-540 285,-540 279,-540 273,-534 273,-528 273,-528 273,-516 273,-516 273,-510 279,-504 285,-504 285,-504 413,-504 413,-504 419,-504 425,-510 425,-516 425,-516 425,-528 425,-528 425,-534 419,-540 413,-540"/>
+<text text-anchor="middle" x="349" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
</g>
-<!-- 11->4 -->
-<g id="edge12" class="edge"><title>11->4</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M257.353,-287.966C223.094,-278.015 179.684,-265.406 143.814,-254.987"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="144.489,-251.539 133.91,-252.111 142.537,-258.261 144.489,-251.539"/>
+<!-- 11->3 -->
+<g id="edge12" class="edge">
+<title>11->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M346.846,-503.8314C351.4237,-495.7925 356.9052,-486.1666 361.9588,-477.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="365.1077,-478.8351 367.0147,-468.4133 359.0248,-475.3712 365.1077,-478.8351"/>
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-<!-- 15 -->
-<g id="node16" class="node"><title>15</title>
-<path fill="none" stroke="#d86e56" stroke-width="2" d="M739.5,-252C739.5,-252 666.5,-252 666.5,-252 660.5,-252 654.5,-246 654.5,-240 654.5,-240 654.5,-228 654.5,-228 654.5,-222 660.5,-216 666.5,-216 666.5,-216 739.5,-216 739.5,-216 745.5,-216 751.5,-222 751.5,-228 751.5,-228 751.5,-240 751.5,-240 751.5,-246 745.5,-252 739.5,-252"/>
-<text text-anchor="middle" x="703" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
-</g>
-<!-- 11->15 -->
-<g id="edge32" class="edge"><title>11->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M376.141,-289.854C379.131,-289.204 382.097,-288.582 385,-288 487.311,-267.499 514.24,-270.121 617,-252 625.916,-250.428 635.331,-248.668 644.533,-246.894"/>
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+<!-- 14 -->
+<g id="node15" class="node">
+<title>14</title>
+<path fill="none" stroke="#d8cb56" stroke-width="2" d="M141.5,-468C141.5,-468 40.5,-468 40.5,-468 34.5,-468 28.5,-462 28.5,-456 28.5,-456 28.5,-444 28.5,-444 28.5,-438 34.5,-432 40.5,-432 40.5,-432 141.5,-432 141.5,-432 147.5,-432 153.5,-438 153.5,-444 153.5,-444 153.5,-456 153.5,-456 153.5,-462 147.5,-468 141.5,-468"/>
+<text text-anchor="middle" x="91" y="-447.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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-<!-- 17 -->
-<g id="node18" class="node"><title>17</title>
-<path fill="none" stroke="#56d8d0" stroke-width="2" d="M451.5,-252C451.5,-252 364.5,-252 364.5,-252 358.5,-252 352.5,-246 352.5,-240 352.5,-240 352.5,-228 352.5,-228 352.5,-222 358.5,-216 364.5,-216 364.5,-216 451.5,-216 451.5,-216 457.5,-216 463.5,-222 463.5,-228 463.5,-228 463.5,-240 463.5,-240 463.5,-246 457.5,-252 451.5,-252"/>
-<text text-anchor="middle" x="408" y="-231.5" font-family="sans" font-size="10.00">quantification_salmon</text>
+<!-- 11->14 -->
+<g id="edge33" class="edge">
+<title>11->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M276.4987,-503.9243C242.8786,-493.7961 200.8229,-481.1266 165.9254,-470.6135"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="166.8698,-467.2427 156.2852,-467.7094 164.8506,-473.9452 166.8698,-467.2427"/>
</g>
-<!-- 11->17 -->
-<g id="edge36" class="edge"><title>11->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M338.742,-287.697C350.44,-278.796 364.861,-267.823 377.51,-258.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="379.681,-260.945 385.52,-252.104 375.442,-255.374 379.681,-260.945"/>
+<!-- 18 -->
+<g id="node19" class="node">
+<title>18</title>
+<path fill="none" stroke="#d86656" stroke-width="2" d="M820,-468C820,-468 702,-468 702,-468 696,-468 690,-462 690,-456 690,-456 690,-444 690,-444 690,-438 696,-432 702,-432 702,-432 820,-432 820,-432 826,-432 832,-438 832,-444 832,-444 832,-456 832,-456 832,-462 826,-468 820,-468"/>
+<text text-anchor="middle" x="761" y="-447.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
</g>
-<!-- 12->5 -->
-<g id="edge13" class="edge"><title>12->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M882.701,-227.711C942.874,-220.787 1032.12,-206.314 1053,-180 1097.93,-123.369 978.505,-102.581 898.196,-95.0901"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="898.392,-91.5938 888.123,-94.2002 897.776,-98.5667 898.392,-91.5938"/>
+<!-- 11->18 -->
+<g id="edge39" class="edge">
+<title>11->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M406.7258,-507.2079C412.3955,-506.0937 418.0402,-505.0111 423.5,-504 517.7823,-486.5405 544.6875,-487.6299 642.2084,-468.1849"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="643.0795,-471.5798 652.1907,-466.1727 641.6962,-464.7179 643.0795,-471.5798"/>
</g>
-<!-- 12->8 -->
-<g id="edge21" class="edge"><title>12->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M828.376,-215.846C830.096,-196.225 829.723,-164.213 813,-144 784.703,-109.797 733.1,-97.6237 697.71,-93.3162"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="698.055,-89.8333 687.741,-92.257 697.316,-96.7942 698.055,-89.8333"/>
+<!-- 12 -->
+<g id="node13" class="node">
+<title>12</title>
+<path fill="none" stroke="#61d856" stroke-width="2" d="M711.5,-540C711.5,-540 614.5,-540 614.5,-540 608.5,-540 602.5,-534 602.5,-528 602.5,-528 602.5,-516 602.5,-516 602.5,-510 608.5,-504 614.5,-504 614.5,-504 711.5,-504 711.5,-504 717.5,-504 723.5,-510 723.5,-516 723.5,-516 723.5,-528 723.5,-528 723.5,-534 717.5,-540 711.5,-540"/>
+<text text-anchor="middle" x="663" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
+</g>
+<!-- 12->3 -->
+<g id="edge11" class="edge">
+<title>12->3</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M573.417,-506.1993C537.2316,-495.8194 489.4986,-482.1271 450.2079,-470.8564"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="450.9902,-467.4398 440.4128,-468.0467 449.06,-474.1684 450.9902,-467.4398"/>
+</g>
+<!-- 12->4 -->
+<g id="edge14" class="edge">
+<title>12->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M610.5837,-503.8314C602.1558,-495.2848 591.959,-484.9443 582.764,-475.6198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="585.1711,-473.0761 575.6575,-468.4133 580.1869,-477.9912 585.1711,-473.0761"/>
</g>
<!-- 13 -->
-<g id="node14" class="node"><title>13</title>
-<path fill="none" stroke="#569ad8" stroke-width="2" d="M792,-180C792,-180 642,-180 642,-180 636,-180 630,-174 630,-168 630,-168 630,-156 630,-156 630,-150 636,-144 642,-144 642,-144 792,-144 792,-144 798,-144 804,-150 804,-156 804,-156 804,-168 804,-168 804,-174 798,-180 792,-180"/>
-<text text-anchor="middle" x="717" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
+<g id="node14" class="node">
+<title>13</title>
+<path fill="none" stroke="#88d856" stroke-width="2" d="M572,-540C572,-540 462,-540 462,-540 456,-540 450,-534 450,-528 450,-528 450,-516 450,-516 450,-510 456,-504 462,-504 462,-504 572,-504 572,-504 578,-504 584,-510 584,-516 584,-516 584,-528 584,-528 584,-534 578,-540 572,-540"/>
+<text text-anchor="middle" x="517" y="-519.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
-<!-- 12->13 -->
-<g id="edge29" class="edge"><title>12->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M799.336,-215.876C785.216,-206.808 767.689,-195.552 752.439,-185.759"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="754.073,-182.648 743.767,-180.19 750.29,-188.538 754.073,-182.648"/>
+<!-- 13->4 -->
+<g id="edge13" class="edge">
+<title>13->4</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M509.6499,-503.8314C517.1717,-495.3694 526.2565,-485.1489 534.4804,-475.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="537.1049,-478.2127 541.1327,-468.4133 531.873,-473.5621 537.1049,-478.2127"/>
</g>
-<!-- 13->5 -->
-<g id="edge15" class="edge"><title>13->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M745.132,-143.876C760.168,-134.724 778.867,-123.342 795.06,-113.485"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="797.038,-116.379 803.76,-108.19 793.398,-110.4 797.038,-116.379"/>
-</g>
-<!-- 13->8 -->
-<g id="edge23" class="edge"><title>13->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M702.91,-143.697C696.077,-135.305 687.743,-125.07 680.244,-115.861"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="682.956,-113.649 673.928,-108.104 677.528,-118.069 682.956,-113.649"/>
+<!-- 17 -->
+<g id="node18" class="node">
+<title>17</title>
+<path fill="none" stroke="#56d8d0" stroke-width="2" d="M266.5,-468C266.5,-468 183.5,-468 183.5,-468 177.5,-468 171.5,-462 171.5,-456 171.5,-456 171.5,-444 171.5,-444 171.5,-438 177.5,-432 183.5,-432 183.5,-432 266.5,-432 266.5,-432 272.5,-432 278.5,-438 278.5,-444 278.5,-444 278.5,-456 278.5,-456 278.5,-462 272.5,-468 266.5,-468"/>
+<text text-anchor="middle" x="225" y="-447.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
-<!-- 14 -->
-<g id="node15" class="node"><title>14</title>
-<path fill="none" stroke="#d89c56" stroke-width="2" d="M1031.5,-180C1031.5,-180 910.5,-180 910.5,-180 904.5,-180 898.5,-174 898.5,-168 898.5,-168 898.5,-156 898.5,-156 898.5,-150 904.5,-144 910.5,-144 910.5,-144 1031.5,-144 1031.5,-144 1037.5,-144 1043.5,-150 1043.5,-156 1043.5,-156 1043.5,-168 1043.5,-168 1043.5,-174 1037.5,-180 1031.5,-180"/>
-<text text-anchor="middle" x="971" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+<!-- 13->17 -->
+<g id="edge37" class="edge">
+<title>13->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M431.7413,-506.8859C392.1771,-497.0263 339.5207,-483.5778 284.585,-468.2516"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="285.2411,-464.8006 274.6675,-465.471 283.3513,-471.5407 285.2411,-464.8006"/>
</g>
-<!-- 14->5 -->
-<g id="edge16" class="edge"><title>14->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M936.997,-143.876C918.402,-134.512 895.173,-122.814 875.294,-112.803"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="876.64,-109.562 866.134,-108.19 873.491,-115.814 876.64,-109.562"/>
+<!-- 19 -->
+<g id="node20" class="node">
+<title>19</title>
+<path fill="none" stroke="#70d856" stroke-width="2" d="M963.5,-468C963.5,-468 862.5,-468 862.5,-468 856.5,-468 850.5,-462 850.5,-456 850.5,-456 850.5,-444 850.5,-444 850.5,-438 856.5,-432 862.5,-432 862.5,-432 963.5,-432 963.5,-432 969.5,-432 975.5,-438 975.5,-444 975.5,-444 975.5,-456 975.5,-456 975.5,-462 969.5,-468 963.5,-468"/>
+<text text-anchor="middle" x="913" y="-447.5" font-family="sans" font-size="10.00">quantification_salmon</text>
</g>
-<!-- 15->5 -->
-<g id="edge14" class="edge"><title>15->5</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M748.156,-215.971C774.497,-205.165 804.224,-191.167 813,-180 826.692,-162.577 831.084,-137.531 832.257,-118.444"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="835.761,-118.387 832.619,-108.269 828.766,-118.138 835.761,-118.387"/>
+<!-- 13->19 -->
+<g id="edge41" class="edge">
+<title>13->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M555.3795,-505.9594C558.4577,-505.2723 561.5106,-504.6147 564.5,-504 661.4299,-484.0701 689.8687,-489.1188 790.7238,-468.0329"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="791.6611,-471.4119 800.7148,-465.909 790.2056,-464.5649 791.6611,-471.4119"/>
</g>
-<!-- 15->8 -->
-<g id="edge22" class="edge"><title>15->8</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M660.382,-215.989C645.126,-207.58 629.591,-195.781 621,-180 609.599,-159.056 622.679,-134.107 636.68,-115.961"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="639.458,-118.093 643.094,-108.141 634.046,-113.654 639.458,-118.093"/>
-</g>
-<!-- 15->13 -->
-<g id="edge30" class="edge"><title>15->13</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M706.461,-215.697C708.003,-207.983 709.858,-198.712 711.578,-190.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="715.05,-190.597 713.579,-180.104 708.186,-189.224 715.05,-190.597"/>
-</g>
-<!-- 16->6 -->
-<g id="edge17" class="edge"><title>16->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M535.36,-215.697C530.873,-207.644 525.441,-197.894 520.476,-188.982"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="523.454,-187.137 515.53,-180.104 517.339,-190.544 523.454,-187.137"/>
-</g>
-<!-- 16->7 -->
-<g id="edge19" class="edge"><title>16->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M495.6,-215.966C467.113,-206.142 431.114,-193.729 401.129,-183.389"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="402.216,-180.062 391.621,-180.111 399.934,-186.68 402.216,-180.062"/>
-</g>
-<!-- 17->6 -->
-<g id="edge18" class="edge"><title>17->6</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M431.973,-215.876C444.55,-206.893 460.132,-195.763 473.752,-186.034"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="475.831,-188.85 481.934,-180.19 471.763,-183.154 475.831,-188.85"/>
-</g>
-<!-- 17->7 -->
-<g id="edge20" class="edge"><title>17->7</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M391.685,-215.697C383.693,-207.22 373.928,-196.864 365.178,-187.583"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="367.534,-184.979 358.127,-180.104 362.441,-189.781 367.534,-184.979"/>
+<!-- 14->5 -->
+<g id="edge15" class="edge">
+<title>14->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M141.5461,-431.9436C165.2169,-421.9205 194.7481,-408.8995 220.5,-396 262.4452,-374.9889 308.9947,-348.2155 340.828,-329.351"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="343.0021,-332.1301 349.8062,-324.0088 339.4227,-326.1144 343.0021,-332.1301"/>
</g>
-<!-- 18 -->
-<g id="node19" class="node"><title>18</title>
-<path fill="none" stroke="#d6d856" stroke-width="2" d="M658,-396C658,-396 532,-396 532,-396 526,-396 520,-390 520,-384 520,-384 520,-372 520,-372 520,-366 526,-360 532,-360 532,-360 658,-360 658,-360 664,-360 670,-366 670,-372 670,-372 670,-384 670,-384 670,-390 664,-396 658,-396"/>
-<text text-anchor="middle" x="595" y="-375.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+<!-- 14->8 -->
+<g id="edge23" class="edge">
+<title>14->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M60.1998,-431.9669C46.3542,-423.189 32.1642,-411.2027 24.5,-396 17.2973,-381.7129 14.4412,-372.4427 24.5,-360 50.9458,-327.2868 174.4946,-313.4968 238.2346,-308.4803"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="238.5879,-311.9637 248.2966,-307.7223 238.062,-304.9835 238.5879,-311.9637"/>
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-<!-- 18->9 -->
-<g id="edge24" class="edge"><title>18->9</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M594.506,-359.697C594.285,-351.983 594.02,-342.712 593.775,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="597.273,-334 593.489,-324.104 590.276,-334.2 597.273,-334"/>
+<!-- 15 -->
+<g id="node16" class="node">
+<title>15</title>
+<path fill="none" stroke="#566bd8" stroke-width="2" d="M217,-396C217,-396 45,-396 45,-396 39,-396 33,-390 33,-384 33,-384 33,-372 33,-372 33,-366 39,-360 45,-360 45,-360 217,-360 217,-360 223,-360 229,-366 229,-372 229,-372 229,-384 229,-384 229,-390 223,-396 217,-396"/>
+<text text-anchor="middle" x="131" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
-<!-- 19 -->
-<g id="node20" class="node"><title>19</title>
-<path fill="none" stroke="#d8c356" stroke-width="2" d="M490.5,-396C490.5,-396 403.5,-396 403.5,-396 397.5,-396 391.5,-390 391.5,-384 391.5,-384 391.5,-372 391.5,-372 391.5,-366 397.5,-360 403.5,-360 403.5,-360 490.5,-360 490.5,-360 496.5,-360 502.5,-366 502.5,-372 502.5,-372 502.5,-384 502.5,-384 502.5,-390 496.5,-396 490.5,-396"/>
-<text text-anchor="middle" x="447" y="-375.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+<!-- 14->15 -->
+<g id="edge34" class="edge">
+<title>14->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M103.8086,-431.8314C106.5117,-424.0463 109.7316,-414.7729 112.731,-406.1347"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="116.1327,-407.0081 116.1065,-396.4133 109.52,-404.7119 116.1327,-407.0081"/>
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-<!-- 19->10 -->
-<g id="edge25" class="edge"><title>19->10</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M391.375,-362.331C353.51,-352.33 301.991,-338.689 248.035,-324.272"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="248.857,-320.869 238.292,-321.667 247.049,-327.631 248.857,-320.869"/>
+<!-- 15->5 -->
+<g id="edge16" class="edge">
+<title>15->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M187.0202,-359.9243C225.5374,-349.1335 274.3512,-335.458 313.1825,-324.5792"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="314.1425,-327.9451 322.8275,-321.8771 312.254,-321.2046 314.1425,-327.9451"/>
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-<!-- 22 -->
-<g id="node23" class="node"><title>22</title>
-<path fill="none" stroke="#61d856" stroke-width="2" d="M491.5,-324C491.5,-324 406.5,-324 406.5,-324 400.5,-324 394.5,-318 394.5,-312 394.5,-312 394.5,-300 394.5,-300 394.5,-294 400.5,-288 406.5,-288 406.5,-288 491.5,-288 491.5,-288 497.5,-288 503.5,-294 503.5,-300 503.5,-300 503.5,-312 503.5,-312 503.5,-318 497.5,-324 491.5,-324"/>
-<text text-anchor="middle" x="449" y="-303.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+<!-- 15->8 -->
+<g id="edge24" class="edge">
+<title>15->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M161.3607,-359.8314C185.1682,-348.7006 215.4834,-334.5272 239.0308,-323.5181"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="240.7672,-326.57 248.3436,-319.164 237.8024,-320.2288 240.7672,-326.57"/>
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-<!-- 19->22 -->
-<g id="edge37" class="edge"><title>19->22</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M447.494,-359.697C447.715,-351.983 447.98,-342.712 448.225,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="451.724,-334.2 448.511,-324.104 444.727,-334 451.724,-334.2"/>
+<!-- 16 -->
+<g id="node17" class="node">
+<title>16</title>
+<path fill="none" stroke="#d8a456" stroke-width="2" d="M471,-396C471,-396 335,-396 335,-396 329,-396 323,-390 323,-384 323,-384 323,-372 323,-372 323,-366 329,-360 335,-360 335,-360 471,-360 471,-360 477,-360 483,-366 483,-372 483,-372 483,-384 483,-384 483,-390 477,-396 471,-396"/>
+<text text-anchor="middle" x="403" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
+</g>
+<!-- 16->5 -->
+<g id="edge16" class="edge">
+<title>16->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M379.5,-359.8314C379.5,-352.131 379.5,-342.9743 379.5,-334.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="383.0001,-334.4132 379.5,-324.4133 376.0001,-334.4133 383.0001,-334.4132"/>
+</g>
+<!-- 17->5 -->
+<g id="edge17" class="edge">
+<title>17->5</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M274.6185,-434.3455C277.6155,-433.5227 280.5927,-432.734 283.5,-432 362.1799,-412.1365 411.0864,-458.7832 462.5,-396 472.6372,-383.6211 470.1286,-374.0643 462.5,-360 455.7065,-347.4754 444.6118,-337.4004 432.7131,-329.5017"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="434.3112,-326.376 423.9569,-324.1309 430.6512,-332.343 434.3112,-326.376"/>
+</g>
+<!-- 17->8 -->
+<g id="edge25" class="edge">
+<title>17->8</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M231.0858,-431.7623C240.0333,-406.9846 256.1076,-362.4714 266.5355,-333.5939"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="269.8631,-334.6839 269.9676,-324.0896 263.2792,-332.3064 269.8631,-334.6839"/>
+</g>
+<!-- 17->15 -->
+<g id="edge35" class="edge">
+<title>17->15</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M198.7611,-431.8314C185.9563,-422.7927 170.3091,-411.7476 156.5281,-402.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="158.4188,-399.0703 148.2307,-396.1628 154.382,-404.7891 158.4188,-399.0703"/>
+</g>
+<!-- 18->6 -->
+<g id="edge19" class="edge">
+<title>18->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M706.1446,-431.8314C701.0674,-423.7079 694.9773,-413.9637 689.3824,-405.0118"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="692.2763,-403.0383 684.0083,-396.4133 686.3403,-406.7483 692.2763,-403.0383"/>
+</g>
+<!-- 18->7 -->
+<g id="edge21" class="edge">
+<title>18->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M748.5381,-431.8314C764.2705,-422.6221 783.5611,-411.3301 800.4044,-401.4706"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="802.6098,-404.2352 809.4718,-396.1628 799.0735,-398.1941 802.6098,-404.2352"/>
+</g>
+<!-- 19->6 -->
+<g id="edge20" class="edge">
+<title>19->6</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M810.8167,-431.8314C785.7441,-422.0734 754.6633,-409.977 728.3191,-399.7242"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="729.4362,-396.4033 718.8476,-396.038 726.8973,-402.9266 729.4362,-396.4033"/>
+</g>
+<!-- 19->7 -->
+<g id="edge22" class="edge">
+<title>19->7</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M853.2102,-431.8314C851.392,-424.131 849.2301,-414.9743 847.2095,-406.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="850.5519,-405.3414 844.8476,-396.4133 843.7392,-406.95 850.5519,-405.3414"/>
+</g>
+<!-- 20->9 -->
+<g id="edge27" class="edge">
+<title>20->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M277.7523,-215.8314C277.8593,-208.131 277.9865,-198.9743 278.1053,-190.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="281.6049,-190.4609 278.2443,-180.4133 274.6056,-190.3637 281.6049,-190.4609"/>
</g>
-<!-- 20 -->
-<g id="node21" class="node"><title>20</title>
-<path fill="none" stroke="#bed856" stroke-width="2" d="M361,-396C361,-396 251,-396 251,-396 245,-396 239,-390 239,-384 239,-384 239,-372 239,-372 239,-366 245,-360 251,-360 251,-360 361,-360 361,-360 367,-360 373,-366 373,-372 373,-372 373,-384 373,-384 373,-390 367,-396 361,-396"/>
-<text text-anchor="middle" x="306" y="-375.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+<!-- 21 -->
+<g id="node22" class="node">
+<title>21</title>
+<path fill="none" stroke="#56c9d8" stroke-width="2" d="M104,-252C104,-252 12,-252 12,-252 6,-252 0,-246 0,-240 0,-240 0,-228 0,-228 0,-222 6,-216 12,-216 12,-216 104,-216 104,-216 110,-216 116,-222 116,-228 116,-228 116,-240 116,-240 116,-246 110,-252 104,-252"/>
+<text text-anchor="middle" x="58" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
-<!-- 20->11 -->
-<g id="edge26" class="edge"><title>20->11</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M308.472,-359.697C309.574,-351.983 310.898,-342.712 312.127,-334.112"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="315.607,-334.499 313.557,-324.104 308.677,-333.509 315.607,-334.499"/>
+<!-- 21->9 -->
+<g id="edge26" class="edge">
+<title>21->9</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M107.1072,-216.8457C148.5723,-203.5769 204.9025,-185.5512 241.477,-173.8474"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="242.7828,-177.1044 251.2403,-170.7231 240.6493,-170.4374 242.7828,-177.1044"/>
</g>
-<!-- 21 -->
-<g id="node22" class="node"><title>21</title>
-<path fill="none" stroke="#78d856" stroke-width="2" d="M819,-324C819,-324 749,-324 749,-324 743,-324 737,-318 737,-312 737,-312 737,-300 737,-300 737,-294 743,-288 749,-288 749,-288 819,-288 819,-288 825,-288 831,-294 831,-300 831,-300 831,-312 831,-312 831,-318 825,-324 819,-324"/>
-<text text-anchor="middle" x="784" y="-303.5" font-family="sans" font-size="10.00">create_index_star</text>
-</g>
-<!-- 21->12 -->
-<g id="edge28" class="edge"><title>21->12</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M794.382,-287.697C799.265,-279.559 805.187,-269.689 810.579,-260.701"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="813.594,-262.48 815.737,-252.104 807.591,-258.879 813.594,-262.48"/>
-</g>
-<!-- 21->15 -->
-<g id="edge31" class="edge"><title>21->15</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M763.978,-287.697C753.874,-278.965 741.464,-268.24 730.482,-258.75"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="732.647,-255.995 722.792,-252.104 728.07,-261.291 732.647,-255.995"/>
-</g>
-<!-- 22->16 -->
-<g id="edge34" class="edge"><title>22->16</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M472.73,-287.697C484.937,-278.796 499.985,-267.823 513.184,-258.199"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="515.525,-260.824 521.543,-252.104 511.4,-255.168 515.525,-260.824"/>
-</g>
-<!-- 22->17 -->
-<g id="edge35" class="edge"><title>22->17</title>
-<path fill="none" stroke="grey" stroke-width="2" d="M438.865,-287.697C434.148,-279.644 428.438,-269.894 423.218,-260.982"/>
-<polygon fill="grey" stroke="grey" stroke-width="2" points="426.092,-258.964 418.018,-252.104 420.052,-262.502 426.092,-258.964"/>
+<!-- 22 -->
+<g id="node23" class="node">
+<title>22</title>
+<path fill="none" stroke="#56d8a9" stroke-width="2" d="M416.5,-612C416.5,-612 273.5,-612 273.5,-612 267.5,-612 261.5,-606 261.5,-600 261.5,-600 261.5,-588 261.5,-588 261.5,-582 267.5,-576 273.5,-576 273.5,-576 416.5,-576 416.5,-576 422.5,-576 428.5,-582 428.5,-588 428.5,-588 428.5,-600 428.5,-600 428.5,-606 422.5,-612 416.5,-612"/>
+<text text-anchor="middle" x="345" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
+</g>
+<!-- 22->11 -->
+<g id="edge29" class="edge">
+<title>22->11</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M333.5094,-575.8314C333.9372,-568.131 334.4459,-558.9743 334.9213,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="338.4169,-550.592 335.477,-540.4133 331.4276,-550.2037 338.4169,-550.592"/>
+</g>
+<!-- 23 -->
+<g id="node24" class="node">
+<title>23</title>
+<path fill="none" stroke="#56d8c1" stroke-width="2" d="M783.5,-612C783.5,-612 682.5,-612 682.5,-612 676.5,-612 670.5,-606 670.5,-600 670.5,-600 670.5,-588 670.5,-588 670.5,-582 676.5,-576 682.5,-576 682.5,-576 783.5,-576 783.5,-576 789.5,-576 795.5,-582 795.5,-588 795.5,-588 795.5,-600 795.5,-600 795.5,-606 789.5,-612 783.5,-612"/>
+<text text-anchor="middle" x="733" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
+</g>
+<!-- 23->12 -->
+<g id="edge30" class="edge">
+<title>23->12</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M677.0978,-575.8314C669.4585,-567.3694 660.2317,-557.1489 651.8793,-547.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="654.4221,-545.4906 645.1231,-540.4133 649.2262,-550.1813 654.4221,-545.4906"/>
+</g>
+<!-- 26 -->
+<g id="node27" class="node">
+<title>26</title>
+<path fill="none" stroke="#d85656" stroke-width="2" d="M850.5,-540C850.5,-540 753.5,-540 753.5,-540 747.5,-540 741.5,-534 741.5,-528 741.5,-528 741.5,-516 741.5,-516 741.5,-510 747.5,-504 753.5,-504 753.5,-504 850.5,-504 850.5,-504 856.5,-504 862.5,-510 862.5,-516 862.5,-516 862.5,-528 862.5,-528 862.5,-534 856.5,-540 850.5,-540"/>
+<text text-anchor="middle" x="802" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text>
+</g>
+<!-- 23->26 -->
+<g id="edge44" class="edge">
+<title>23->26</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M709.6499,-575.8314C717.1717,-567.3694 726.2565,-557.1489 734.4804,-547.8971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="737.1049,-550.2127 741.1327,-540.4133 731.873,-545.5621 737.1049,-550.2127"/>
+</g>
+<!-- 24 -->
+<g id="node25" class="node">
+<title>24</title>
+<path fill="none" stroke="#56d873" stroke-width="2" d="M584,-612C584,-612 458,-612 458,-612 452,-612 446,-606 446,-600 446,-600 446,-588 446,-588 446,-582 452,-576 458,-576 458,-576 584,-576 584,-576 590,-576 596,-582 596,-588 596,-588 596,-600 596,-600 596,-606 590,-612 584,-612"/>
+<text text-anchor="middle" x="521" y="-591.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
+</g>
+<!-- 24->13 -->
+<g id="edge31" class="edge">
+<title>24->13</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M496.4906,-575.8314C496.0628,-568.131 495.5541,-558.9743 495.0787,-550.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="498.5724,-550.2037 494.523,-540.4133 491.5831,-550.592 498.5724,-550.2037"/>
+</g>
+<!-- 25 -->
+<g id="node26" class="node">
+<title>25</title>
+<path fill="none" stroke="#56b9d8" stroke-width="2" d="M131,-540C131,-540 51,-540 51,-540 45,-540 39,-534 39,-528 39,-528 39,-516 39,-516 39,-510 45,-504 51,-504 51,-504 131,-504 131,-504 137,-504 143,-510 143,-516 143,-516 143,-528 143,-528 143,-534 137,-540 131,-540"/>
+<text text-anchor="middle" x="91" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text>
+</g>
+<!-- 25->14 -->
+<g id="edge32" class="edge">
+<title>25->14</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M97.5,-503.8314C97.5,-496.131 97.5,-486.9743 97.5,-478.4166"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="101.0001,-478.4132 97.5,-468.4133 94.0001,-478.4133 101.0001,-478.4132"/>
+</g>
+<!-- 25->17 -->
+<g id="edge36" class="edge">
+<title>25->17</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M129.5475,-503.8314C145.942,-494.5368 166.0786,-483.1208 183.5829,-473.1971"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="185.4897,-476.1395 192.4628,-468.1628 182.0374,-470.05 185.4897,-476.1395"/>
+</g>
+<!-- 25->21 -->
+<g id="edge43" class="edge">
+<title>25->21</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M65.9199,-503.849C52.7374,-494.7208 38.4406,-482.5002 29.5,-468 12.3446,-440.1767 17.851,-428.5148 14.5,-396 12.8597,-380.0843 12.1076,-375.8201 14.5,-360 19.7362,-325.3745 32.6341,-287.1533 42.1712,-261.989"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="45.5467,-262.9641 45.8929,-252.3749 39.0188,-260.437 45.5467,-262.9641"/>
+</g>
+<!-- 26->18 -->
+<g id="edge38" class="edge">
+<title>26->18</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M747.4063,-503.8314C742.9403,-495.7925 737.5925,-486.1666 732.6621,-477.2918"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="735.6456,-475.4551 727.7296,-468.4133 729.5265,-478.8546 735.6456,-475.4551"/>
+</g>
+<!-- 26->19 -->
+<g id="edge40" class="edge">
+<title>26->19</title>
+<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M782.7342,-503.8314C795.288,-494.7927 810.6283,-483.7476 824.1391,-474.0198"/>
+<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="826.2036,-476.8463 832.2739,-468.1628 822.1134,-471.1655 826.2036,-476.8463"/>
</g>
</g>
</svg>
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/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/test_alfa/test.sh b/tests/test_alfa/test.sh
new file mode 100755
index 0000000000000000000000000000000000000000..6e7f39f0407a189aa124084170154a3f243a2714
--- /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.yaml" \
+ --cores=4 \
+ --printshellcmds \
+ --rerun-incomplete \
+ --use-singularity \
+ --singularity-args="--bind ${PWD}" \
+ --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/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}"
+