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.gitlab-ci.yml
View file @ 27f4fa5b
...@@ -4,7 +4,7 @@ before_script: ...@@ -4,7 +4,7 @@ before_script:
- apt update && apt install -y gcc - apt update && apt install -y gcc
- conda init bash && source ~/.bashrc && echo $CONDA_DEFAULT_ENV - conda init bash && source ~/.bashrc && echo $CONDA_DEFAULT_ENV
- conda env create -f install/environment.root.yml - conda env create -f install/environment.root.yml
- conda activate rnaseq_pipeline && echo $CONDA_DEFAULT_ENV - conda activate rhea && echo $CONDA_DEFAULT_ENV
- conda env update -f install/environment.dev.yml - conda env update -f install/environment.dev.yml
test: test:
......
README.md
View file @ 27f4fa5b
# RNA-Seq pipeline # Rhea pipeline
[Snakemake][snakemake] workflow for general purpose RNA-Seq library annotation [Snakemake][snakemake] workflow for general purpose RNA-Seq library annotation
developed by the [Zavolan lab][zavolan-lab]. developed by the [Zavolan lab][zavolan-lab].
...@@ -29,8 +29,8 @@ Traverse to the desired path on your file system, then clone the repository and ...@@ -29,8 +29,8 @@ Traverse to the desired path on your file system, then clone the repository and
move into it with: move into it with:
```bash ```bash
git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rnaseqpipeline.git git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rhea.git
cd rnaseqpipeline cd rhea
``` ```
### Installing Conda ### Installing Conda
...@@ -87,7 +87,7 @@ conda env create -f install/environment.root.yml ...@@ -87,7 +87,7 @@ conda env create -f install/environment.root.yml
Activate the Conda environment with: Activate the Conda environment with:
```bash ```bash
conda activate rnaseq_pipeline conda activate rhea
``` ```
### Installing non-essential dependencies ### Installing non-essential dependencies
......
Snakefile
View file @ 27f4fa5b
...@@ -5,6 +5,8 @@ import sys ...@@ -5,6 +5,8 @@ import sys
import pandas as pd import pandas as pd
import shutil import shutil
import glob
from zipfile import ZipFile
# Get sample table # Get sample table
samples_table = pd.read_csv( samples_table = pd.read_csv(
...@@ -17,7 +19,8 @@ samples_table = pd.read_csv( ...@@ -17,7 +19,8 @@ samples_table = pd.read_csv(
) )
# Global config # Global config
localrules: finish, rename_star_rpm_for_alfa localrules: finish, rename_star_rpm_for_alfa, prepare_files_for_report, \
prepare_MultiQC_config
# Create log directories # Create log directories
os.makedirs( os.makedirs(
...@@ -44,76 +47,11 @@ rule finish: ...@@ -44,76 +47,11 @@ rule finish:
Rule for collecting outputs Rule for collecting outputs
""" """
input: input:
outdir1 = expand( MultiQC_report = expand(
os.path.join(
config['output_dir'],
"{seqmode}",
"{sample}",
"mate1_fastqc"),
zip,
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)]),
pseudoalignment = expand(
os.path.join( os.path.join(
config['output_dir'], config['output_dir'],
"{seqmode}", "multiqc_summary"),
"{sample}", output_dir=config["output_dir"])
"quant_kallisto",
"{sample}.kallisto.pseudo.sam"),
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)]),
TIN_boxplot_PNG = os.path.join(
config['output_dir'],
"TIN_scores_boxplot.png"),
TIN_boxplot_PDF = os.path.join(
config['output_dir'],
"TIN_scores_boxplot.pdf"),
salmon_merge_genes = expand(
os.path.join(
config["output_dir"],
"summary_salmon",
"quantmerge",
"genes_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"]),
salmon_merge_transcripts = expand(
os.path.join(
config["output_dir"],
"summary_salmon",
"quantmerge",
"transcripts_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"]),
star_rpm = expand(
os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str1.out.bg"),
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_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")
rule create_index_star: rule create_index_star:
""" """
...@@ -921,3 +859,377 @@ rule alfa_qc_all_samples: ...@@ -921,3 +859,377 @@ rule alfa_qc_all_samples:
""" """
(alfa -c {input.tables} -o {params.out_dir}) &> {log} (alfa -c {input.tables} -o {params.out_dir}) &> {log}
""" """
rule prepare_files_for_report:
'''
Re-structure the results and add comments for MultiQC parsing
'''
input:
outdir1 = expand(
os.path.join(
config['output_dir'],
"{seqmode}",
"{sample}",
"mate1_fastqc"),
zip,
sample=[i for i in list(samples_table.index.values)],
seqmode=[samples_table.loc[i, 'seqmode']
for i in list(samples_table.index.values)]),
pseudoalignment = expand(
os.path.join(
config['output_dir'],
"{seqmode}",
"{sample}",
"quant_kallisto",
"{sample}.kallisto.pseudo.sam"),
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)]),
TIN_boxplot_PNG = os.path.join(
config['output_dir'],
"TIN_scores_boxplot.png"),
TIN_boxplot_PDF = os.path.join(
config['output_dir'],
"TIN_scores_boxplot.pdf"),
salmon_merge_genes = expand(
os.path.join(
config["output_dir"],
"summary_salmon",
"quantmerge",
"genes_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"]),
salmon_merge_transcripts = expand(
os.path.join(
config["output_dir"],
"summary_salmon",
"quantmerge",
"transcripts_{salmon_merge_on}.tsv"),
salmon_merge_on=["tpm", "numreads"]),
star_rpm = expand(
os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"STAR_coverage",
"{sample}_Signal.UniqueMultiple.str1.out.bg"),
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_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")
output:
samples_dir = directory(os.path.join(
"{output_dir}",
"samples"))
params:
results_dir = config["output_dir"],
log_dir = config["log_dir"],
log_samples_dir = os.path.join(
config["log_dir"],
"samples")
log:
LOG_local_log = \
os.path.join("{output_dir}", "local_log", \
"prepare_files_for_report.log")
run:
# remove "single/paired end" from the results directories
os.mkdir(output.samples_dir)
# move paired end results
paired_end_dir = glob.glob(
os.path.join(
params.results_dir,
"paired_end",
"*"))
for s in paired_end_dir:
sample_name = s.split("/")[-1]
shutil.copytree(
s, \
os.path.join(
params.results_dir,
"samples",
sample_name))
shutil.rmtree(
os.path.join(
params.results_dir,
"paired_end"),
ignore_errors=False,
onerror=None)
# move single end results
single_end_dir = glob.glob(
os.path.join(
params.results_dir,
"single_end",
"*"))
for s in single_end_dir:
sample_name = s.split("/")[-1]
shutil.copytree(
s, \
os.path.join(
params.results_dir,
"samples",
sample_name))
shutil.rmtree(
os.path.join(
params.results_dir,
"single_end"),
ignore_errors=False,
onerror=None)
# remove "single/paired end" from the logs directories
os.mkdir(params.log_samples_dir)
# move paired end results
paired_end_dir = glob.glob(
os.path.join(
params.log_dir,
"paired_end",
"*"))
for s in paired_end_dir:
sample_name = s.split("/")[-1]
shutil.copytree(
s, \
os.path.join(
params.log_dir,
"samples",
sample_name))
shutil.rmtree(
os.path.join(
params.log_dir,
"paired_end"),
ignore_errors=False,
onerror=None)
# move single end results
single_end_dir = glob.glob(
os.path.join(
params.log_dir,
"single_end",
"*"))
for s in single_end_dir:
sample_name = s.split("/")[-1]
shutil.copytree(
s, \
os.path.join(
params.log_dir,
"samples",
sample_name))
shutil.rmtree(
os.path.join(
params.log_dir,
"single_end"),
ignore_errors=False,
onerror=None)
# encapsulate salmon quantification results
all_samples_dirs = glob.glob(
os.path.join(
params.results_dir,
"samples",
"*"))
for s in all_samples_dirs:
sample_name = s.split("/")[-1]
shutil.move(
os.path.join(
s,
"salmon_quant"),
os.path.join(
s,
sample_name)
)
os.mkdir(os.path.join(
s,
"salmon_quant"))
shutil.move(
os.path.join(
s,
sample_name),
os.path.join(
s,
"salmon_quant",
sample_name)
)
# adjust FastQC results 'Filename' field:
fastq_zip_list = glob.glob(
os.path.join(
params.results_dir,
"samples",
"*",
"*_fastqc",
"*_fastqc.zip"))
for zipfile in fastq_zip_list:
sample_name = zipfile.split("/")[-3]
zipfile_path_chunks = zipfile.split("/")
new_path = os.path.join(*(zipfile_path_chunks[:-1]))
with ZipFile(zipfile, 'r') as zip_f:
zip_f.extractall(new_path)
fastqc_data_f = os.path.join(
zipfile[:-4],
"fastqc_data.txt")
with open(fastqc_data_f) as f:
log_lines = f.read().splitlines()
log_lines[3] = "Filename\t" + sample_name+"|"+log_lines[3].split("\t")[1]
with open(fastqc_data_f, "w") as f:
for i in log_lines: f.write(i+"\n")
os.remove(zipfile)
# adjust Kallisto quantification logs
kallisto_logs = glob.glob(
os.path.join(
params.log_dir,
"samples",
"*",
"genome_quantification_kallisto.stderr.log"))
for kallisto_log in kallisto_logs:
with open(kallisto_log) as f:
log_lines = f.read().splitlines()
temp = log_lines[8].split(".")
log_lines[8] = temp[0] + "." + temp[2] + "." + temp[3]
with open(kallisto_log+".MODIFIED", "w") as f:
for i in log_lines: f.write(i+"\n")
# add #-comment to all cutadapt logs:
cutadapt_logs = glob.glob(
os.path.join(
params.log_dir,
"samples",
"*",
"remove_*_cutadapt.stdout.log"))
for cutadapt_log in cutadapt_logs:
sample_name = cutadapt_log.split("/")[-2]
with open(cutadapt_log) as f:
log_lines = f.read().splitlines()
log_lines[1] = log_lines[1] + " # " + sample_name
with open(cutadapt_log, "w") as f:
for i in log_lines: f.write(i+"\n")
# adjust TIN boxplots filenames for MutliQC recognition
os.rename(
input.TIN_boxplot_PNG,
os.path.join(
params.results_dir,
"TIN scores_mqc.png"))
os.rename(
input.TIN_boxplot_PDF,
os.path.join(
params.results_dir,
"TIN scores_mqc.pdf"))
rule prepare_MultiQC_config:
'''
Prepare config for the MultiQC
'''
input:
multiqc_input_dir = os.path.join(
"{output_dir}",
"samples")
output:
multiqc_config = os.path.join(
"{output_dir}",
"MultiQC_config.yaml")
params:
logo_path = os.path.join(
"..",
"..",
"images",
"logo.128px.png"),
results_dir = config["output_dir"]
log:
LOG_local_log = \
os.path.join("{output_dir}", "local_log", \
"prepare_MultiQC_config.log")
run:
with open(output.multiqc_config, "w") as YAML:
YAML.write("---\n\n")
YAML.write("title: \"Rhea\"\n")
YAML.write("subtitle: \"RNA-Seq processing pipeline developed by the members of Zavolan Lab\"\n")
YAML.write("intro_text: \"Short analysis title from config[analysis_title]\"\n")
YAML.write("custom_logo: \""+params.logo_path+"\"\n")
YAML.write("custom_logo_url: \"https://www.biozentrum.unibas.ch/research/researchgroups/overview/unit/zavolan/research-group-mihaela-zavolan/\"\n")
YAML.write("custom_logo_title: \"ZavoLab\"\n\n")
YAML.write("report_header_info:\n")
YAML.write(" - Project Type: \"Snakemake workflow\"\n")
YAML.write(" - Analysis Type: \"RNA-seq\"\n")
YAML.write(" - Analysis Author: \"config[author_name]\"\n")
YAML.write(" - Contact E-mail: \"config[author_email]\"\n\n")
YAML.write("top_modules:\n\n")
YAML.write(" - fastqc:\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/mate1_fastqc/*\"\n")
YAML.write(" - \"*/mate2_fastqc/*\"\n")
YAML.write("\n")
YAML.write(" - cutadapt:\n")
YAML.write(" name: \"Cutadapt: adapter removal\"\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/remove_adapters_cutadapt.stdout.log\"\n")
YAML.write("\n")
YAML.write(" - cutadapt:\n")
YAML.write(" name: \"Cutadapt: polyA tails removal\"\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/remove_polya_cutadapt.stdout.log\"\n")
YAML.write("\n")
YAML.write(" - star:\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/map_genome/*\"\n")
YAML.write("\n")
YAML.write(" - TIN_scores:\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/TIN scores_mqc.png\"\n")
YAML.write("\n")
YAML.write(" - salmon:\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/salmon_quant/*\"\n")
YAML.write("\n")
YAML.write(" - kallisto:\n")
YAML.write(" path_filters:\n")
YAML.write(" - \"*/genome_quantification_kallisto.stderr.log.MODIFIED\"\n")
YAML.write("\n")
YAML.write("...")
rule MULTIQC_report:
'''
Create report with MultiQC
'''
input:
multiqc_config = os.path.join(
config["output_dir"],
"MultiQC_config.yaml")
output:
MultiQC_report = \
directory(os.path.join("{output_dir}", "multiqc_summary"))
params:
results_dir = config["output_dir"],
log_dir = config["log_dir"]
log:
LOG_local_log = \
os.path.join("{output_dir}", "local_log", \
"MULTIQC_report.log")
singularity:
"docker://ewels/multiqc:1.7"
shell:
"""
multiqc \
--outdir {output.MultiQC_report} \
--config {input.multiqc_config} \
{params.results_dir} \
{params.log_dir} \
&> {log.LOG_local_log};
"""
\ No newline at end of file
images/dag_test_workflow.svg
View file @ 27f4fa5b
...@@ -4,514 +4,545 @@ ...@@ -4,514 +4,545 @@
<!-- Generated by graphviz version 2.38.0 (20140413.2041) <!-- Generated by graphviz version 2.38.0 (20140413.2041)
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<g id="node4" class="node"><title>3</title> <g id="node4" class="node"><title>3</title>
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<text text-anchor="middle" x="759" y="-159.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text> <text text-anchor="middle" x="1294" y="-237" font-family="sans" font-size="10.00">prepare_files_for_report</text>
<text text-anchor="middle" x="1294" y="-226" font-family="sans" font-size="10.00">output_dir: results</text>
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<!-- 3&#45;&gt;0 --> <!-- 3&#45;&gt;2 -->
<g id="edge3" class="edge"><title>3&#45;&gt;0</title> <g id="edge3" class="edge"><title>3&#45;&gt;2</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1256.92,-22.7581 1266.89,-19.1659 1256.85,-15.7584 1256.92,-22.7581"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1297.5,-190.104 1294,-180.104 1290.5,-190.104 1297.5,-190.104"/>
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<!-- 4 --> <!-- 4 -->
<g id="node5" class="node"><title>4</title> <g id="node5" class="node"><title>4</title>
<path fill="none" stroke="#566bd8" stroke-width="2" d="M1273,-180C1273,-180 1147,-180 1147,-180 1141,-180 1135,-174 1135,-168 1135,-168 1135,-156 1135,-156 1135,-150 1141,-144 1147,-144 1147,-144 1273,-144 1273,-144 1279,-144 1285,-150 1285,-156 1285,-156 1285,-168 1285,-168 1285,-174 1279,-180 1273,-180"/> <path fill="none" stroke="#d85656" stroke-width="2" d="M280,-324C280,-324 12,-324 12,-324 6,-324 0,-318 0,-312 0,-312 0,-300 0,-300 0,-294 6,-288 12,-288 12,-288 280,-288 280,-288 286,-288 292,-294 292,-300 292,-300 292,-312 292,-312 292,-318 286,-324 280,-324"/>
<text text-anchor="middle" x="1210" y="-159.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text> <text text-anchor="middle" x="146" y="-309" font-family="sans" font-size="10.00">pe_fastqc</text>
<text text-anchor="middle" x="146" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<!-- 4&#45;&gt;0 --> <!-- 4&#45;&gt;3 -->
<g id="edge4" class="edge"><title>4&#45;&gt;0</title> <g id="edge4" class="edge"><title>4&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1280.09,-143.929C1298.08,-136.036 1315.35,-124.579 1326,-108 1338.64,-88.3232 1327.31,-62.9893 1314.77,-44.3855"/> <path fill="none" stroke="grey" stroke-width="2" d="M292.011,-288.756C295.033,-288.494 298.032,-288.242 301,-288 646.799,-259.831 1061.61,-243.227 1223.99,-237.39"/>
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<!-- 5 --> <!-- 5 -->
<g id="node6" class="node"><title>5</title> <g id="node6" class="node"><title>5</title>
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<text text-anchor="middle" x="1430" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text> <text text-anchor="middle" x="462" y="-309" font-family="sans" font-size="10.00">fastqc</text>
<text text-anchor="middle" x="462" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<!-- 5&#45;&gt;0 --> <!-- 5&#45;&gt;3 -->
<g id="edge5" class="edge"><title>5&#45;&gt;0</title> <g id="edge5" class="edge"><title>5&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1427.43,-143.676C1423.74,-124.193 1415.26,-92.5933 1397,-72 1379.42,-52.1643 1352.63,-38.7041 1330.79,-30.3127"/> <path fill="none" stroke="grey" stroke-width="2" d="M614.408,-289.257C618.989,-288.827 623.528,-288.407 628,-288 845.188,-268.24 1102.6,-248.916 1224,-240.047"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1331.74,-26.9356 1321.15,-26.8091 1329.35,-33.5145 1331.74,-26.9356"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1224.54,-243.516 1234.26,-239.298 1224.03,-236.535 1224.54,-243.516"/>
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<!-- 6 --> <!-- 6 -->
<g id="node7" class="node"><title>6</title> <g id="node7" class="node"><title>6</title>
<path fill="none" stroke="#56d882" stroke-width="2" d="M1141,-108C1141,-108 1029,-108 1029,-108 1023,-108 1017,-102 1017,-96 1017,-96 1017,-84 1017,-84 1017,-78 1023,-72 1029,-72 1029,-72 1141,-72 1141,-72 1147,-72 1153,-78 1153,-84 1153,-84 1153,-96 1153,-96 1153,-102 1147,-108 1141,-108"/> <path fill="none" stroke="#d86656" stroke-width="2" d="M830,-396C830,-396 688,-396 688,-396 682,-396 676,-390 676,-384 676,-384 676,-372 676,-372 676,-366 682,-360 688,-360 688,-360 830,-360 830,-360 836,-360 842,-366 842,-372 842,-372 842,-384 842,-384 842,-390 836,-396 830,-396"/>
<text text-anchor="middle" x="1085" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text> <text text-anchor="middle" x="759" y="-375.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
<text text-anchor="middle" x="1085" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 6&#45;&gt;0 --> <!-- 6&#45;&gt;3 -->
<g id="edge6" class="edge"><title>6&#45;&gt;0</title> <g id="edge6" class="edge"><title>6&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1135.86,-71.9656C1173.31,-59.4227 1223.37,-42.6564 1257.05,-31.3763"/> <path fill="none" stroke="grey" stroke-width="2" d="M704.98,-359.962C688.226,-351.851 671.643,-340.258 662,-324 653.838,-310.239 651.169,-299.777 662,-288 699.432,-247.298 1067.28,-237.839 1223.94,-235.652"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1258.57,-34.5572 1266.94,-28.0624 1256.35,-27.9196 1258.57,-34.5572"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1224.44,-239.146 1234.39,-235.513 1224.35,-232.147 1224.44,-239.146"/>
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<!-- 7 --> <!-- 7 -->
<g id="node8" class="node"><title>7</title> <g id="node8" class="node"><title>7</title>
<path fill="none" stroke="#56d882" stroke-width="2" d="M1304.5,-108C1304.5,-108 1183.5,-108 1183.5,-108 1177.5,-108 1171.5,-102 1171.5,-96 1171.5,-96 1171.5,-84 1171.5,-84 1171.5,-78 1177.5,-72 1183.5,-72 1183.5,-72 1304.5,-72 1304.5,-72 1310.5,-72 1316.5,-78 1316.5,-84 1316.5,-84 1316.5,-96 1316.5,-96 1316.5,-102 1310.5,-108 1304.5,-108"/> <path fill="none" stroke="#5663d8" stroke-width="2" d="M1273,-396C1273,-396 1147,-396 1147,-396 1141,-396 1135,-390 1135,-384 1135,-384 1135,-372 1135,-372 1135,-366 1141,-360 1147,-360 1147,-360 1273,-360 1273,-360 1279,-360 1285,-366 1285,-372 1285,-372 1285,-384 1285,-384 1285,-390 1279,-396 1273,-396"/>
<text text-anchor="middle" x="1244" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text> <text text-anchor="middle" x="1210" y="-375.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
<text text-anchor="middle" x="1244" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<!-- 7&#45;&gt;0 --> <!-- 7&#45;&gt;3 -->
<g id="edge7" class="edge"><title>7&#45;&gt;0</title> <g id="edge7" class="edge"><title>7&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1256.36,-71.6966C1262.23,-63.4741 1269.37,-53.4832 1275.84,-44.4207"/> <path fill="none" stroke="grey" stroke-width="2" d="M1280.09,-359.929C1298.08,-352.036 1315.35,-340.579 1326,-324 1338.64,-304.323 1327.31,-278.989 1314.77,-260.386"/>
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<!-- 8 --> <!-- 8 -->
<g id="node9" class="node"><title>8</title> <g id="node9" class="node"><title>8</title>
<path fill="none" stroke="#56b1d8" stroke-width="2" d="M813.5,-108C813.5,-108 682.5,-108 682.5,-108 676.5,-108 670.5,-102 670.5,-96 670.5,-96 670.5,-84 670.5,-84 670.5,-78 676.5,-72 682.5,-72 682.5,-72 813.5,-72 813.5,-72 819.5,-72 825.5,-78 825.5,-84 825.5,-84 825.5,-96 825.5,-96 825.5,-102 819.5,-108 813.5,-108"/> <path fill="none" stroke="#56d8a9" stroke-width="2" d="M1462.5,-396C1462.5,-396 1397.5,-396 1397.5,-396 1391.5,-396 1385.5,-390 1385.5,-384 1385.5,-384 1385.5,-372 1385.5,-372 1385.5,-366 1391.5,-360 1397.5,-360 1397.5,-360 1462.5,-360 1462.5,-360 1468.5,-360 1474.5,-366 1474.5,-372 1474.5,-372 1474.5,-384 1474.5,-384 1474.5,-390 1468.5,-396 1462.5,-396"/>
<text text-anchor="middle" x="748" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text> <text text-anchor="middle" x="1430" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
<text text-anchor="middle" x="748" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g> </g>
<!-- 8&#45;&gt;0 --> <!-- 8&#45;&gt;3 -->
<g id="edge8" class="edge"><title>8&#45;&gt;0</title> <g id="edge8" class="edge"><title>8&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M825.735,-73.4985C828.861,-72.9741 831.958,-72.472 835,-72 990.957,-47.7965 1178.31,-29.4911 1256.68,-22.3138"/> <path fill="none" stroke="grey" stroke-width="2" d="M1427.43,-359.676C1423.74,-340.193 1415.26,-308.593 1397,-288 1385.29,-274.792 1369.5,-264.41 1353.81,-256.47"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.36,-25.7666 1267,-21.3755 1256.72,-18.7954 1257.36,-25.7666"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1355.14,-253.228 1344.61,-252.074 1352.12,-259.544 1355.14,-253.228"/>
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<!-- 9 --> <!-- 9 -->
<g id="node10" class="node"><title>9</title> <g id="node10" class="node"><title>9</title>
<path fill="none" stroke="#56b1d8" stroke-width="2" d="M986.5,-108C986.5,-108 855.5,-108 855.5,-108 849.5,-108 843.5,-102 843.5,-96 843.5,-96 843.5,-84 843.5,-84 843.5,-78 849.5,-72 855.5,-72 855.5,-72 986.5,-72 986.5,-72 992.5,-72 998.5,-78 998.5,-84 998.5,-84 998.5,-96 998.5,-96 998.5,-102 992.5,-108 986.5,-108"/> <path fill="none" stroke="#568ad8" stroke-width="2" d="M1141,-324C1141,-324 1029,-324 1029,-324 1023,-324 1017,-318 1017,-312 1017,-312 1017,-300 1017,-300 1017,-294 1023,-288 1029,-288 1029,-288 1141,-288 1141,-288 1147,-288 1153,-294 1153,-300 1153,-300 1153,-312 1153,-312 1153,-318 1147,-324 1141,-324"/>
<text text-anchor="middle" x="921" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text> <text text-anchor="middle" x="1085" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="921" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text> <text text-anchor="middle" x="1085" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g> </g>
<!-- 9&#45;&gt;0 --> <!-- 9&#45;&gt;3 -->
<g id="edge9" class="edge"><title>9&#45;&gt;0</title> <g id="edge9" class="edge"><title>9&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M998.781,-73.7625C1001.89,-73.165 1004.98,-72.5756 1008,-72 1097.25,-55.0116 1202.3,-35.7258 1256.87,-25.7615"/> <path fill="none" stroke="grey" stroke-width="2" d="M1135.86,-287.966C1165.19,-278.142 1202.25,-265.729 1233.12,-255.389"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1257.56,-29.1926 1266.77,-23.9542 1256.31,-22.3063 1257.56,-29.1926"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1234.54,-258.606 1242.91,-252.111 1232.32,-251.968 1234.54,-258.606"/>
</g> </g>
<!-- 10 --> <!-- 10 -->
<g id="node11" class="node"><title>10</title> <g id="node11" class="node"><title>10</title>
<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1358.5,-324C1358.5,-324 1327.5,-324 1327.5,-324 1321.5,-324 1315.5,-318 1315.5,-312 1315.5,-312 1315.5,-300 1315.5,-300 1315.5,-294 1321.5,-288 1327.5,-288 1327.5,-288 1358.5,-288 1358.5,-288 1364.5,-288 1370.5,-294 1370.5,-300 1370.5,-300 1370.5,-312 1370.5,-312 1370.5,-318 1364.5,-324 1358.5,-324"/> <path fill="none" stroke="#568ad8" stroke-width="2" d="M1304.5,-324C1304.5,-324 1183.5,-324 1183.5,-324 1177.5,-324 1171.5,-318 1171.5,-312 1171.5,-312 1171.5,-300 1171.5,-300 1171.5,-294 1177.5,-288 1183.5,-288 1183.5,-288 1304.5,-288 1304.5,-288 1310.5,-288 1316.5,-294 1316.5,-300 1316.5,-300 1316.5,-312 1316.5,-312 1316.5,-318 1310.5,-324 1304.5,-324"/>
<text text-anchor="middle" x="1343" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text> <text text-anchor="middle" x="1244" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="1244" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
</g> </g>
<!-- 10&#45;&gt;0 --> <!-- 10&#45;&gt;3 -->
<g id="edge10" class="edge"><title>10&#45;&gt;0</title> <g id="edge10" class="edge"><title>10&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1346.95,-287.853C1355.25,-248.209 1371.41,-147.802 1342,-72 1337.87,-61.3668 1330.53,-51.5395 1322.8,-43.3091"/> <path fill="none" stroke="grey" stroke-width="2" d="M1256.36,-287.697C1262.23,-279.474 1269.37,-269.483 1275.84,-260.421"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1325.24,-40.7972 1315.68,-36.2223 1320.3,-45.758 1325.24,-40.7972"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1278.82,-262.276 1281.78,-252.104 1273.12,-258.207 1278.82,-262.276"/>
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<!-- 25 -->
<g id="node26" class="node"><title>25</title>
<path fill="none" stroke="#d87d56" stroke-width="2" d="M1489,-252C1489,-252 1383,-252 1383,-252 1377,-252 1371,-246 1371,-240 1371,-240 1371,-228 1371,-228 1371,-222 1377,-216 1383,-216 1383,-216 1489,-216 1489,-216 1495,-216 1501,-222 1501,-228 1501,-228 1501,-240 1501,-240 1501,-246 1495,-252 1489,-252"/>
<text text-anchor="middle" x="1436" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
<!-- 10&#45;&gt;25 -->
<g id="edge53" class="edge"><title>10&#45;&gt;25</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1365.99,-287.697C1377.81,-278.796 1392.39,-267.823 1405.18,-258.199"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1407.39,-260.915 1413.28,-252.104 1403.18,-255.322 1407.39,-260.915"/>
</g> </g>
<!-- 11 --> <!-- 11 -->
<g id="node12" class="node"><title>11</title> <g id="node12" class="node"><title>11</title>
<path fill="none" stroke="#56d8b9" stroke-width="2" d="M1863.5,-324C1863.5,-324 1832.5,-324 1832.5,-324 1826.5,-324 1820.5,-318 1820.5,-312 1820.5,-312 1820.5,-300 1820.5,-300 1820.5,-294 1826.5,-288 1832.5,-288 1832.5,-288 1863.5,-288 1863.5,-288 1869.5,-288 1875.5,-294 1875.5,-300 1875.5,-300 1875.5,-312 1875.5,-312 1875.5,-318 1869.5,-324 1863.5,-324"/> <path fill="none" stroke="#567bd8" stroke-width="2" d="M813.5,-324C813.5,-324 682.5,-324 682.5,-324 676.5,-324 670.5,-318 670.5,-312 670.5,-312 670.5,-300 670.5,-300 670.5,-294 676.5,-288 682.5,-288 682.5,-288 813.5,-288 813.5,-288 819.5,-288 825.5,-294 825.5,-300 825.5,-300 825.5,-312 825.5,-312 825.5,-318 819.5,-324 813.5,-324"/>
<text text-anchor="middle" x="1848" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text> <text text-anchor="middle" x="748" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="748" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
</g> </g>
<!-- 11&#45;&gt;0 --> <!-- 11&#45;&gt;3 -->
<g id="edge11" class="edge"><title>11&#45;&gt;0</title> <g id="edge11" class="edge"><title>11&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1870.6,-287.963C1881.06,-278.635 1892.4,-266.107 1898,-252 1903.91,-237.13 1906.17,-229.758 1898,-216 1829.77,-101.072 1760.57,-114.929 1634,-72 1528.11,-36.0846 1395.31,-24.3556 1331.55,-20.6448"/> <path fill="none" stroke="grey" stroke-width="2" d="M825.735,-289.499C828.861,-288.974 831.958,-288.472 835,-288 972.388,-266.678 1134.14,-249.934 1224.29,-241.342"/>
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<!-- 27 -->
<g id="node28" class="node"><title>27</title>
<path fill="none" stroke="#d87d56" stroke-width="2" d="M1877,-252C1877,-252 1771,-252 1771,-252 1765,-252 1759,-246 1759,-240 1759,-240 1759,-228 1759,-228 1759,-222 1765,-216 1771,-216 1771,-216 1877,-216 1877,-216 1883,-216 1889,-222 1889,-228 1889,-228 1889,-240 1889,-240 1889,-246 1883,-252 1877,-252"/>
<text text-anchor="middle" x="1824" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
</g>
<!-- 11&#45;&gt;27 -->
<g id="edge55" class="edge"><title>11&#45;&gt;27</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1842.07,-287.697C1839.39,-279.898 1836.17,-270.509 1833.2,-261.829"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1836.42,-260.429 1829.86,-252.104 1829.8,-262.699 1836.42,-260.429"/>
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<!-- 12 --> <!-- 12 -->
<g id="node13" class="node"><title>12</title> <g id="node13" class="node"><title>12</title>
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<!-- 12&#45;&gt;0 -->
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<!-- 14 -->
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<!-- 12&#45;&gt;14 --> <!-- 12&#45;&gt;3 -->
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<!-- 13 --> <!-- 13 -->
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<!-- 13&#45;&gt;3 -->
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<!-- 13&#45;&gt;0 --> <!-- 28 -->
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<!-- 13&#45;&gt;14 --> <!-- 13&#45;&gt;28 -->
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<!-- 14&#45;&gt;0 --> <!-- 14 -->
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<!-- 14&#45;&gt;3 -->
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<!-- 30 -->
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<!-- 14&#45;&gt;30 -->
<g id="edge58" class="edge"><title>14&#45;&gt;30</title>
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<!-- 15 --> <!-- 15 -->
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<!-- 15&#45;&gt;3 --> <!-- 15&#45;&gt;3 -->
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<!-- 19 -->
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<!-- 15&#45;&gt;19 -->
<g id="edge43" class="edge"><title>15&#45;&gt;19</title>
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<!-- 21 --> <!-- 17 -->
<g id="node22" class="node"><title>21</title> <g id="node18" class="node"><title>17</title>
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<!-- 15&#45;&gt;21 --> <!-- 15&#45;&gt;17 -->
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<!-- 16 --> <!-- 16 -->
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<!-- 16&#45;&gt;3 --> <!-- 16&#45;&gt;3 -->
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<!-- 17 --> <!-- 17&#45;&gt;3 -->
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<!-- 17&#45;&gt;4 --> <!-- 18 -->
<g id="edge17" class="edge"><title>17&#45;&gt;4</title> <g id="node19" class="node"><title>18</title>
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<!-- 20 --> <!-- 18&#45;&gt;6 -->
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<!-- 17&#45;&gt;20 --> <!-- 22 -->
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<!-- 23 --> <!-- 18&#45;&gt;22 -->
<g id="node24" class="node"><title>23</title> <g id="edge46" class="edge"><title>18&#45;&gt;22</title>
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<!-- 17&#45;&gt;23 --> <!-- 24 -->
<g id="edge51" class="edge"><title>17&#45;&gt;23</title> <g id="node25" class="node"><title>24</title>
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<!-- 18 --> <!-- 18&#45;&gt;24 -->
<g id="node19" class="node"><title>18</title> <g id="edge51" class="edge"><title>18&#45;&gt;24</title>
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<!-- 18&#45;&gt;5 --> <!-- 19 -->
<g id="edge19" class="edge"><title>18&#45;&gt;5</title> <g id="node20" class="node"><title>19</title>
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<!-- 19&#45;&gt;6 --> <!-- 19&#45;&gt;6 -->
<g id="edge20" class="edge"><title>19&#45;&gt;6</title> <g id="edge19" class="edge"><title>19&#45;&gt;6</title>
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<!-- 19&#45;&gt;7 --> <!-- 19&#45;&gt;7 -->
<g id="edge22" class="edge"><title>19&#45;&gt;7</title> <g id="edge21" class="edge"><title>19&#45;&gt;7</title>
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<!-- 19&#45;&gt;8 -->
<g id="edge24" class="edge"><title>19&#45;&gt;8</title>
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<!-- 19&#45;&gt;9 -->
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<!-- 20&#45;&gt;6 --> <!-- 20 -->
<g id="edge21" class="edge"><title>20&#45;&gt;6</title> <g id="node21" class="node"><title>20</title>
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<!-- 20&#45;&gt;7 --> <!-- 20&#45;&gt;7 -->
<g id="edge23" class="edge"><title>20&#45;&gt;7</title> <g id="edge20" class="edge"><title>20&#45;&gt;7</title>
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<!-- 20&#45;&gt;8 --> <!-- 23 -->
<g id="edge25" class="edge"><title>20&#45;&gt;8</title> <g id="node24" class="node"><title>23</title>
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<!-- 20&#45;&gt;9 --> <!-- 20&#45;&gt;23 -->
<g id="edge27" class="edge"><title>20&#45;&gt;9</title> <g id="edge48" class="edge"><title>20&#45;&gt;23</title>
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<!-- 21&#45;&gt;10 --> <!-- 26 -->
<g id="edge28" class="edge"><title>21&#45;&gt;10</title> <g id="node27" class="node"><title>26</title>
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<!-- 22 --> <!-- 20&#45;&gt;26 -->
<g id="node23" class="node"><title>22</title> <g id="edge54" class="edge"><title>20&#45;&gt;26</title>
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<text text-anchor="middle" x="1343" y="-370" font-family="sans" font-size="10.00">seqmode: paired_end</text>
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<!-- 21&#45;&gt;22 --> <!-- 21 -->
<g id="edge49" class="edge"><title>21&#45;&gt;22</title> <g id="node22" class="node"><title>21</title>
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<!-- 31 --> <!-- 21&#45;&gt;8 -->
<g id="node32" class="node"><title>31</title> <g id="edge22" class="edge"><title>21&#45;&gt;8</title>
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<!-- 21&#45;&gt;31 --> <!-- 22&#45;&gt;9 -->
<g id="edge56" class="edge"><title>21&#45;&gt;31</title> <g id="edge23" class="edge"><title>22&#45;&gt;9</title>
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<!-- 22&#45;&gt;10 --> <!-- 22&#45;&gt;10 -->
<g id="edge29" class="edge"><title>22&#45;&gt;10</title> <g id="edge25" class="edge"><title>22&#45;&gt;10</title>
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<!-- 22&#45;&gt;31 --> <!-- 22&#45;&gt;11 -->
<g id="edge57" class="edge"><title>22&#45;&gt;31</title> <g id="edge27" class="edge"><title>22&#45;&gt;11</title>
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<!-- 22&#45;&gt;12 -->
<g id="edge29" class="edge"><title>22&#45;&gt;12</title>
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<!-- 23&#45;&gt;9 -->
<g id="edge24" class="edge"><title>23&#45;&gt;9</title>
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<!-- 23&#45;&gt;10 -->
<g id="edge26" class="edge"><title>23&#45;&gt;10</title>
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<!-- 23&#45;&gt;11 --> <!-- 23&#45;&gt;11 -->
<g id="edge30" class="edge"><title>23&#45;&gt;11</title> <g id="edge28" class="edge"><title>23&#45;&gt;11</title>
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<!-- 24 --> <!-- 23&#45;&gt;12 -->
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<!-- 23&#45;&gt;24 --> <!-- 24&#45;&gt;13 -->
<g id="edge52" class="edge"><title>23&#45;&gt;24</title> <g id="edge31" class="edge"><title>24&#45;&gt;13</title>
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<!-- 32 --> <!-- 25 -->
<g id="node33" class="node"><title>32</title> <g id="node26" class="node"><title>25</title>
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<text text-anchor="middle" x="1343" y="-586" font-family="sans" font-size="10.00">seqmode: paired_end</text>
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<!-- 23&#45;&gt;32 --> <!-- 24&#45;&gt;25 -->
<g id="edge59" class="edge"><title>23&#45;&gt;32</title> <g id="edge52" class="edge"><title>24&#45;&gt;25</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1704.03,-431.545C1696.54,-421.31 1687.04,-408.06 1679,-396 1665.11,-375.148 1650.21,-350.925 1639.44,-333.019"/> <path fill="none" stroke="grey" stroke-width="2" d="M1343,-647.697C1343,-639.983 1343,-630.712 1343,-622.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1642.34,-331.061 1634.2,-324.282 1636.34,-334.659 1642.34,-331.061"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-622.104 1343,-612.104 1339.5,-622.104 1346.5,-622.104"/>
</g> </g>
<!-- 24&#45;&gt;11 --> <!-- 34 -->
<g id="edge31" class="edge"><title>24&#45;&gt;11</title> <g id="node35" class="node"><title>34</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1793.04,-359.697C1802.06,-351.05 1813.12,-340.449 1822.94,-331.027"/> <path fill="none" stroke="#d88556" stroke-width="2" d="M1520,-540C1520,-540 1432,-540 1432,-540 1426,-540 1420,-534 1420,-528 1420,-528 1420,-516 1420,-516 1420,-510 1426,-504 1432,-504 1432,-504 1520,-504 1520,-504 1526,-504 1532,-510 1532,-516 1532,-516 1532,-528 1532,-528 1532,-534 1526,-540 1520,-540"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1825.37,-333.552 1830.16,-324.104 1820.52,-328.499 1825.37,-333.552"/> <text text-anchor="middle" x="1476" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g> </g>
<!-- 24&#45;&gt;32 --> <!-- 24&#45;&gt;34 -->
<g id="edge60" class="edge"><title>24&#45;&gt;32</title> <g id="edge59" class="edge"><title>24&#45;&gt;34</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1738.06,-359.876C1717.51,-350.349 1691.75,-338.407 1669.91,-328.283"/> <path fill="none" stroke="grey" stroke-width="2" d="M1387.92,-647.937C1405.7,-639.364 1425.16,-627.461 1439,-612 1454.73,-594.433 1464.35,-569.241 1469.82,-550.14"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1671.36,-325.099 1660.82,-324.068 1668.42,-331.45 1671.36,-325.099"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1473.27,-550.805 1472.45,-540.242 1466.5,-549.01 1473.27,-550.805"/>
</g> </g>
<!-- 25&#45;&gt;12 --> <!-- 25&#45;&gt;13 -->
<g id="edge32" class="edge"><title>25&#45;&gt;12</title> <g id="edge32" class="edge"><title>25&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1459.97,-215.876C1472.55,-206.893 1488.13,-195.763 1501.75,-186.034"/> <path fill="none" stroke="grey" stroke-width="2" d="M1343,-575.697C1343,-567.983 1343,-558.712 1343,-550.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.83,-188.85 1509.93,-180.19 1499.76,-183.154 1503.83,-188.85"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1346.5,-550.104 1343,-540.104 1339.5,-550.104 1346.5,-550.104"/>
</g> </g>
<!-- 26 --> <!-- 25&#45;&gt;34 -->
<g id="node27" class="node"><title>26</title> <g id="edge60" class="edge"><title>25&#45;&gt;34</title>
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<text text-anchor="middle" x="1689" y="-231.5" font-family="sans" font-size="10.00">generate_alfa_index</text> <polygon fill="grey" stroke="grey" stroke-width="2" points="1436.12,-547.944 1443.34,-540.19 1432.86,-541.75 1436.12,-547.944"/>
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<!-- 26&#45;&gt;12 --> <!-- 26&#45;&gt;14 -->
<g id="edge33" class="edge"><title>26&#45;&gt;12</title> <g id="edge33" class="edge"><title>26&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1651.08,-215.876C1626.56,-204.799 1594.8,-190.457 1570.55,-179.504"/> <path fill="none" stroke="grey" stroke-width="2" d="M1765.69,-662.525C1801.26,-657.86 1847.27,-645.261 1871,-612 1884.22,-593.466 1875.57,-567.952 1865.31,-548.991"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1571.87,-176.264 1561.32,-175.338 1568.99,-182.643 1571.87,-176.264"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1868.29,-547.152 1860.23,-540.269 1862.24,-550.673 1868.29,-547.152"/>
</g> </g>
<!-- 26&#45;&gt;13 --> <!-- 27 -->
<g id="edge35" class="edge"><title>26&#45;&gt;13</title> <g id="node28" class="node"><title>27</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1684.06,-215.697C1681.83,-207.898 1679.15,-198.509 1676.67,-189.829"/> <path fill="none" stroke="#d8b456" stroke-width="2" d="M1850,-612C1850,-612 1700,-612 1700,-612 1694,-612 1688,-606 1688,-600 1688,-600 1688,-588 1688,-588 1688,-582 1694,-576 1700,-576 1700,-576 1850,-576 1850,-576 1856,-576 1862,-582 1862,-588 1862,-588 1862,-600 1862,-600 1862,-606 1856,-612 1850,-612"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1680,-188.758 1673.89,-180.104 1673.27,-190.681 1680,-188.758"/> <text text-anchor="middle" x="1775" y="-597" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
<text text-anchor="middle" x="1775" y="-586" font-family="sans" font-size="10.00">seqmode: single_end</text>
</g> </g>
<!-- 27&#45;&gt;13 --> <!-- 26&#45;&gt;27 -->
<g id="edge34" class="edge"><title>27&#45;&gt;13</title> <g id="edge55" class="edge"><title>26&#45;&gt;27</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1786.08,-215.876C1761.56,-204.799 1729.8,-190.457 1705.55,-179.504"/> <path fill="none" stroke="grey" stroke-width="2" d="M1731.34,-647.697C1738.29,-639.305 1746.77,-629.07 1754.4,-619.861"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1706.87,-176.264 1696.32,-175.338 1703.99,-182.643 1706.87,-176.264"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1757.14,-622.038 1760.83,-612.104 1751.75,-617.571 1757.14,-622.038"/>
</g> </g>
<!-- 28 --> <!-- 35 -->
<g id="node29" class="node"><title>28</title> <g id="node36" class="node"><title>35</title>
<path fill="none" stroke="#70d856" stroke-width="2" d="M994,-617C994,-617 726,-617 726,-617 720,-617 714,-611 714,-605 714,-605 714,-593 714,-593 714,-587 720,-581 726,-581 726,-581 994,-581 994,-581 1000,-581 1006,-587 1006,-593 1006,-593 1006,-605 1006,-605 1006,-611 1000,-617 994,-617"/> <path fill="none" stroke="#d88556" stroke-width="2" d="M1668,-540C1668,-540 1580,-540 1580,-540 1574,-540 1568,-534 1568,-528 1568,-528 1568,-516 1568,-516 1568,-510 1574,-504 1580,-504 1580,-504 1668,-504 1668,-504 1674,-504 1680,-510 1680,-516 1680,-516 1680,-528 1680,-528 1680,-534 1674,-540 1668,-540"/>
<text text-anchor="middle" x="860" y="-602" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text> <text text-anchor="middle" x="1624" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="860" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text> </g>
<!-- 26&#45;&gt;35 -->
<g id="edge62" class="edge"><title>26&#45;&gt;35</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1704.03,-647.545C1696.54,-637.31 1687.04,-624.06 1679,-612 1665.11,-591.148 1650.21,-566.925 1639.44,-549.019"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1642.34,-547.061 1634.2,-540.282 1636.34,-550.659 1642.34,-547.061"/>
</g>
<!-- 27&#45;&gt;14 -->
<g id="edge34" class="edge"><title>27&#45;&gt;14</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1793.04,-575.697C1802.06,-567.05 1813.12,-556.449 1822.94,-547.027"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1825.37,-549.552 1830.16,-540.104 1820.52,-544.499 1825.37,-549.552"/>
</g>
<!-- 27&#45;&gt;35 -->
<g id="edge63" class="edge"><title>27&#45;&gt;35</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1738.06,-575.876C1717.51,-566.349 1691.75,-554.407 1669.91,-544.283"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1671.36,-541.099 1660.82,-540.068 1668.42,-547.45 1671.36,-541.099"/>
</g> </g>
<!-- 28&#45;&gt;15 --> <!-- 28&#45;&gt;15 -->
<g id="edge38" class="edge"><title>28&#45;&gt;15</title> <g id="edge35" class="edge"><title>28&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M860,-580.819C860,-572.422 860,-562.116 860,-552.686"/> <path fill="none" stroke="grey" stroke-width="2" d="M1459.97,-431.876C1472.55,-422.893 1488.13,-411.763 1501.75,-402.034"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="863.5,-552.558 860,-542.558 856.5,-552.558 863.5,-552.558"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1503.83,-404.85 1509.93,-396.19 1499.76,-399.154 1503.83,-404.85"/>
</g> </g>
<!-- 29 --> <!-- 29 -->
<g id="node30" class="node"><title>29</title> <g id="node30" class="node"><title>29</title>
<path fill="none" stroke="#d85656" stroke-width="2" d="M1056.5,-324C1056.5,-324 955.5,-324 955.5,-324 949.5,-324 943.5,-318 943.5,-312 943.5,-312 943.5,-300 943.5,-300 943.5,-294 949.5,-288 955.5,-288 955.5,-288 1056.5,-288 1056.5,-288 1062.5,-288 1068.5,-294 1068.5,-300 1068.5,-300 1068.5,-312 1068.5,-312 1068.5,-318 1062.5,-324 1056.5,-324"/> <path fill="none" stroke="#a7d856" stroke-width="2" d="M1729,-468C1729,-468 1649,-468 1649,-468 1643,-468 1637,-462 1637,-456 1637,-456 1637,-444 1637,-444 1637,-438 1643,-432 1649,-432 1649,-432 1729,-432 1729,-432 1735,-432 1741,-438 1741,-444 1741,-444 1741,-456 1741,-456 1741,-462 1735,-468 1729,-468"/>
<text text-anchor="middle" x="1006" y="-309" font-family="sans" font-size="10.00">extract_transcriptome</text> <text text-anchor="middle" x="1689" y="-447.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
<text text-anchor="middle" x="1006" y="-298" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g> </g>
<!-- 29&#45;&gt;16 --> <!-- 29&#45;&gt;15 -->
<g id="edge39" class="edge"><title>29&#45;&gt;16</title> <g id="edge36" class="edge"><title>29&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1021.82,-287.697C1029.57,-279.22 1039.04,-268.864 1047.52,-259.583"/> <path fill="none" stroke="grey" stroke-width="2" d="M1651.08,-431.876C1626.56,-420.799 1594.8,-406.457 1570.55,-395.504"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1050.2,-261.846 1054.36,-252.104 1045.03,-257.123 1050.2,-261.846"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1571.87,-392.264 1561.32,-391.338 1568.99,-398.643 1571.87,-392.264"/>
</g> </g>
<!-- 33 --> <!-- 29&#45;&gt;16 -->
<g id="node34" class="node"><title>33</title> <g id="edge38" class="edge"><title>29&#45;&gt;16</title>
<path fill="none" stroke="#56d892" stroke-width="2" d="M985.5,-252C985.5,-252 900.5,-252 900.5,-252 894.5,-252 888.5,-246 888.5,-240 888.5,-240 888.5,-228 888.5,-228 888.5,-222 894.5,-216 900.5,-216 900.5,-216 985.5,-216 985.5,-216 991.5,-216 997.5,-222 997.5,-228 997.5,-228 997.5,-240 997.5,-240 997.5,-246 991.5,-252 985.5,-252"/> <path fill="none" stroke="grey" stroke-width="2" d="M1684.06,-431.697C1681.83,-423.898 1679.15,-414.509 1676.67,-405.829"/>
<text text-anchor="middle" x="943" y="-237" font-family="sans" font-size="10.00">create_index_salmon</text> <polygon fill="grey" stroke="grey" stroke-width="2" points="1680,-404.758 1673.89,-396.104 1673.27,-406.681 1680,-404.758"/>
<text text-anchor="middle" x="943" y="-226" font-family="sans" font-size="10.00">kmer: 31</text>
</g>
<!-- 29&#45;&gt;33 -->
<g id="edge62" class="edge"><title>29&#45;&gt;33</title>
<path fill="none" stroke="grey" stroke-width="2" d="M990.427,-287.697C982.798,-279.22 973.477,-268.864 965.124,-259.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="967.685,-257.196 958.394,-252.104 962.482,-261.879 967.685,-257.196"/>
</g> </g>
<!-- 30 --> <!-- 30&#45;&gt;16 -->
<g id="node31" class="node"><title>30</title> <g id="edge37" class="edge"><title>30&#45;&gt;16</title>
<path fill="none" stroke="#56d8a9" stroke-width="2" d="M1330,-617C1330,-617 1050,-617 1050,-617 1044,-617 1038,-611 1038,-605 1038,-605 1038,-593 1038,-593 1038,-587 1044,-581 1050,-581 1050,-581 1330,-581 1330,-581 1336,-581 1342,-587 1342,-593 1342,-593 1342,-605 1342,-605 1342,-611 1336,-617 1330,-617"/> <path fill="none" stroke="grey" stroke-width="2" d="M1786.08,-431.876C1761.56,-420.799 1729.8,-406.457 1705.55,-395.504"/>
<text text-anchor="middle" x="1190" y="-602" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text> <polygon fill="grey" stroke="grey" stroke-width="2" points="1706.87,-392.264 1696.32,-391.338 1703.99,-398.643 1706.87,-392.264"/>
<text text-anchor="middle" x="1190" y="-591" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g> </g>
<!-- 30&#45;&gt;17 --> <!-- 31 -->
<g id="edge40" class="edge"><title>30&#45;&gt;17</title> <g id="node32" class="node"><title>31</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1190,-580.819C1190,-572.422 1190,-562.116 1190,-552.686"/> <path fill="none" stroke="#88d856" stroke-width="2" d="M994,-833C994,-833 726,-833 726,-833 720,-833 714,-827 714,-821 714,-821 714,-809 714,-809 714,-803 720,-797 726,-797 726,-797 994,-797 994,-797 1000,-797 1006,-803 1006,-809 1006,-809 1006,-821 1006,-821 1006,-827 1000,-833 994,-833"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.5,-552.558 1190,-542.558 1186.5,-552.558 1193.5,-552.558"/> <text text-anchor="middle" x="860" y="-818" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="860" y="-807" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g> </g>
<!-- 31&#45;&gt;18 --> <!-- 31&#45;&gt;18 -->
<g id="edge41" class="edge"><title>31&#45;&gt;18</title> <g id="edge41" class="edge"><title>31&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1498.99,-287.697C1510.81,-278.796 1525.39,-267.823 1538.18,-258.199"/> <path fill="none" stroke="grey" stroke-width="2" d="M860,-796.819C860,-788.422 860,-778.116 860,-768.686"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1540.39,-260.915 1546.28,-252.104 1536.18,-255.322 1540.39,-260.915"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="863.5,-768.558 860,-758.558 856.5,-768.558 863.5,-768.558"/>
</g> </g>
<!-- 32&#45;&gt;18 --> <!-- 32 -->
<g id="edge42" class="edge"><title>32&#45;&gt;18</title> <g id="node33" class="node"><title>32</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1610.4,-287.697C1603.88,-279.389 1595.93,-269.277 1588.75,-260.141"/> <path fill="none" stroke="#78d856" stroke-width="2" d="M1056.5,-540C1056.5,-540 955.5,-540 955.5,-540 949.5,-540 943.5,-534 943.5,-528 943.5,-528 943.5,-516 943.5,-516 943.5,-510 949.5,-504 955.5,-504 955.5,-504 1056.5,-504 1056.5,-504 1062.5,-504 1068.5,-510 1068.5,-516 1068.5,-516 1068.5,-528 1068.5,-528 1068.5,-534 1062.5,-540 1056.5,-540"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1591.37,-257.805 1582.44,-252.104 1585.87,-262.13 1591.37,-257.805"/> <text text-anchor="middle" x="1006" y="-525" font-family="sans" font-size="10.00">extract_transcriptome</text>
<text text-anchor="middle" x="1006" y="-514" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 32&#45;&gt;19 -->
<g id="edge42" class="edge"><title>32&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1021.82,-503.697C1029.57,-495.22 1039.04,-484.864 1047.52,-475.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1050.2,-477.846 1054.36,-468.104 1045.03,-473.123 1050.2,-477.846"/>
</g>
<!-- 36 -->
<g id="node37" class="node"><title>36</title>
<path fill="none" stroke="#59d856" stroke-width="2" d="M985.5,-468C985.5,-468 900.5,-468 900.5,-468 894.5,-468 888.5,-462 888.5,-456 888.5,-456 888.5,-444 888.5,-444 888.5,-438 894.5,-432 900.5,-432 900.5,-432 985.5,-432 985.5,-432 991.5,-432 997.5,-438 997.5,-444 997.5,-444 997.5,-456 997.5,-456 997.5,-462 991.5,-468 985.5,-468"/>
<text text-anchor="middle" x="943" y="-453" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="943" y="-442" font-family="sans" font-size="10.00">kmer: 31</text>
</g>
<!-- 32&#45;&gt;36 -->
<g id="edge65" class="edge"><title>32&#45;&gt;36</title>
<path fill="none" stroke="grey" stroke-width="2" d="M990.427,-503.697C982.798,-495.22 973.477,-484.864 965.124,-475.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="967.685,-473.196 958.394,-468.104 962.482,-477.879 967.685,-473.196"/>
</g> </g>
<!-- 33&#45;&gt;19 --> <!-- 33 -->
<g id="edge44" class="edge"><title>33&#45;&gt;19</title> <g id="node34" class="node"><title>33</title>
<path fill="none" stroke="grey" stroke-width="2" d="M938.303,-215.697C936.187,-207.898 933.638,-198.509 931.282,-189.829"/> <path fill="none" stroke="#56b9d8" stroke-width="2" d="M1330,-833C1330,-833 1050,-833 1050,-833 1044,-833 1038,-827 1038,-821 1038,-821 1038,-809 1038,-809 1038,-803 1044,-797 1050,-797 1050,-797 1330,-797 1330,-797 1336,-797 1342,-803 1342,-809 1342,-809 1342,-821 1342,-821 1342,-827 1336,-833 1330,-833"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="934.64,-188.838 928.643,-180.104 927.884,-190.672 934.64,-188.838"/> <text text-anchor="middle" x="1190" y="-818" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1190" y="-807" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
</g> </g>
<!-- 33&#45;&gt;20 --> <!-- 33&#45;&gt;20 -->
<g id="edge46" class="edge"><title>33&#45;&gt;20</title> <g id="edge43" class="edge"><title>33&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M971.866,-215.876C987.295,-206.724 1006.48,-195.342 1023.1,-185.485"/> <path fill="none" stroke="grey" stroke-width="2" d="M1190,-796.819C1190,-788.422 1190,-778.116 1190,-768.686"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.21,-188.302 1032.02,-180.19 1021.64,-182.282 1025.21,-188.302"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="1193.5,-768.558 1190,-758.558 1186.5,-768.558 1193.5,-768.558"/>
</g>
<!-- 34 -->
<g id="node35" class="node"><title>34</title>
<path fill="none" stroke="#56d0d8" stroke-width="2" d="M1767.5,-545C1767.5,-545 1666.5,-545 1666.5,-545 1660.5,-545 1654.5,-539 1654.5,-533 1654.5,-533 1654.5,-516 1654.5,-516 1654.5,-510 1660.5,-504 1666.5,-504 1666.5,-504 1767.5,-504 1767.5,-504 1773.5,-504 1779.5,-510 1779.5,-516 1779.5,-516 1779.5,-533 1779.5,-533 1779.5,-539 1773.5,-545 1767.5,-545"/>
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<text text-anchor="middle" x="1717" y="-522" font-family="sans" font-size="10.00">index_size: 75</text>
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images/logo.128px.png

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images/rule_graph.svg
View file @ 27f4fa5b
...@@ -4,11 +4,11 @@ ...@@ -4,11 +4,11 @@
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<!-- 7 --> <!-- 7 -->
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<text text-anchor="middle" x="467" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text> <text text-anchor="middle" x="259" y="-663.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 7&#45;&gt;0 --> <!-- 7&#45;&gt;3 -->
<g id="edge1" class="edge"><title>7&#45;&gt;0</title> <g id="edge5" class="edge"><title>7&#45;&gt;3</title>
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<!-- 8 --> <!-- 8 -->
<g id="node9" class="node"><title>8</title> <g id="node9" class="node"><title>8</title>
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<text text-anchor="middle" x="851" y="-303.5" font-family="sans" font-size="10.00">star_rpm</text> <text text-anchor="middle" x="478" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
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<!-- 8&#45;&gt;0 --> <!-- 8&#45;&gt;3 -->
<g id="edge10" class="edge"><title>8&#45;&gt;0</title> <g id="edge8" class="edge"><title>8&#45;&gt;3</title>
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<!-- 20 -->
<g id="node21" class="node"><title>20</title>
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<!-- 8&#45;&gt;20 -->
<g id="edge40" class="edge"><title>8&#45;&gt;20</title>
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<!-- 9 --> <!-- 9 -->
<g id="node10" class="node"><title>9</title> <g id="node10" class="node"><title>9</title>
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<text text-anchor="middle" x="835" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text> <text text-anchor="middle" x="303" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
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<!-- 9&#45;&gt;0 --> <!-- 9&#45;&gt;3 -->
<g id="edge5" class="edge"><title>9&#45;&gt;0</title> <g id="edge9" class="edge"><title>9&#45;&gt;3</title>
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<!-- 10 --> <!-- 10 -->
<g id="node11" class="node"><title>10</title> <g id="node11" class="node"><title>10</title>
<path fill="none" stroke="#56c1d8" stroke-width="2" d="M846.5,-108C846.5,-108 765.5,-108 765.5,-108 759.5,-108 753.5,-102 753.5,-96 753.5,-96 753.5,-84 753.5,-84 753.5,-78 759.5,-72 765.5,-72 765.5,-72 846.5,-72 846.5,-72 852.5,-72 858.5,-78 858.5,-84 858.5,-84 858.5,-96 858.5,-96 858.5,-102 852.5,-108 846.5,-108"/> <path fill="none" stroke="#56d8c9" stroke-width="2" d="M532.5,-612C532.5,-612 401.5,-612 401.5,-612 395.5,-612 389.5,-606 389.5,-600 389.5,-600 389.5,-588 389.5,-588 389.5,-582 395.5,-576 401.5,-576 401.5,-576 532.5,-576 532.5,-576 538.5,-576 544.5,-582 544.5,-588 544.5,-588 544.5,-600 544.5,-600 544.5,-606 538.5,-612 532.5,-612"/>
<text text-anchor="middle" x="806" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text> <text text-anchor="middle" x="467" y="-591.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
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<!-- 9&#45;&gt;10 -->
<g id="edge25" class="edge"><title>9&#45;&gt;10</title>
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<!-- 10&#45;&gt;0 --> <!-- 10&#45;&gt;3 -->
<g id="edge2" class="edge"><title>10&#45;&gt;0</title> <g id="edge4" class="edge"><title>10&#45;&gt;3</title>
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<!-- 11 --> <!-- 11 -->
<g id="node12" class="node"><title>11</title> <g id="node12" class="node"><title>11</title>
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<!-- 11&#45;&gt;3 --> <!-- 11&#45;&gt;3 -->
<g id="edge11" class="edge"><title>11&#45;&gt;3</title> <g id="edge11" class="edge"><title>11&#45;&gt;3</title>
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<!-- 15 --> <!-- 23 -->
<g id="node16" class="node"><title>15</title> <g id="node24" class="node"><title>23</title>
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<!-- 11&#45;&gt;15 -->
<g id="edge31" class="edge"><title>11&#45;&gt;15</title>
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<!-- 17 -->
<g id="node18" class="node"><title>17</title>
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<!-- 11&#45;&gt;17 --> <!-- 11&#45;&gt;23 -->
<g id="edge35" class="edge"><title>11&#45;&gt;17</title> <g id="edge43" class="edge"><title>11&#45;&gt;23</title>
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<!-- 12 --> <!-- 12 -->
<g id="node13" class="node"><title>12</title> <g id="node13" class="node"><title>12</title>
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<text text-anchor="middle" x="195" y="-519.5" font-family="sans" font-size="10.00">create_index_kallisto</text> <text text-anchor="middle" x="835" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
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<!-- 12&#45;&gt;3 --> <!-- 12&#45;&gt;3 -->
<g id="edge12" class="edge"><title>12&#45;&gt;3</title> <g id="edge12" class="edge"><title>12&#45;&gt;3</title>
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<!-- 12&#45;&gt;4 -->
<g id="edge14" class="edge"><title>12&#45;&gt;4</title>
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<!-- 13 --> <!-- 13 -->
<g id="node14" class="node"><title>13</title> <g id="node14" class="node"><title>13</title>
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<!-- 13&#45;&gt;4 --> <!-- 12&#45;&gt;13 -->
<g id="edge13" class="edge"><title>13&#45;&gt;4</title> <g id="edge28" class="edge"><title>12&#45;&gt;13</title>
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<!-- 16 --> <!-- 13&#45;&gt;3 -->
<g id="node17" class="node"><title>16</title> <g id="edge6" class="edge"><title>13&#45;&gt;3</title>
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<!-- 13&#45;&gt;16 --> <!-- 14 -->
<g id="edge33" class="edge"><title>13&#45;&gt;16</title> <g id="node15" class="node"><title>14</title>
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<!-- 19 --> <!-- 14&#45;&gt;6 -->
<g id="node20" class="node"><title>19</title> <g id="edge15" class="edge"><title>14&#45;&gt;6</title>
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<!-- 13&#45;&gt;19 --> <!-- 18 -->
<g id="edge39" class="edge"><title>13&#45;&gt;19</title> <g id="node19" class="node"><title>18</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="908.43,-471.357 917.367,-465.666 906.832,-464.542 908.43,-471.357"/> <text text-anchor="middle" x="416" y="-663.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<!-- 14 --> <!-- 14&#45;&gt;18 -->
<g id="node15" class="node"><title>14</title> <g id="edge34" class="edge"><title>14&#45;&gt;18</title>
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<text text-anchor="middle" x="539" y="-231.5" font-family="sans" font-size="10.00">merge_TIN_scores</text> <polygon fill="grey" stroke="grey" stroke-width="2" points="392.14,-693.421 397.185,-684.104 387.431,-688.241 392.14,-693.421"/>
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<!-- 20 -->
<g id="node21" class="node"><title>20</title>
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<text text-anchor="middle" x="843" y="-663.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
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<!-- 14&#45;&gt;20 -->
<g id="edge38" class="edge"><title>14&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M407.368,-721.557C410.28,-721.009 413.167,-720.487 416,-720 542.678,-698.204 691.979,-681.763 776.257,-673.326"/>
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<!-- 14&#45;&gt;5 --> <!-- 15 -->
<g id="edge15" class="edge"><title>14&#45;&gt;5</title> <g id="node16" class="node"><title>15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M523.921,-215.697C516.608,-207.305 507.69,-197.07 499.665,-187.861"/> <path fill="none" stroke="#56a9d8" stroke-width="2" d="M237,-756C237,-756 153,-756 153,-756 147,-756 141,-750 141,-744 141,-744 141,-732 141,-732 141,-726 147,-720 153,-720 153,-720 237,-720 237,-720 243,-720 249,-726 249,-732 249,-732 249,-744 249,-744 249,-750 243,-756 237,-756"/>
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<!-- 15&#45;&gt;6 --> <!-- 15&#45;&gt;6 -->
<g id="edge16" class="edge"><title>15&#45;&gt;6</title> <g id="edge14" class="edge"><title>15&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M388.357,-431.876C373.582,-422.724 355.209,-411.342 339.297,-401.485"/> <path fill="none" stroke="grey" stroke-width="2" d="M167.602,-719.876C153.093,-710.808 135.084,-699.552 119.415,-689.759"/>
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<!-- 15&#45;&gt;7 --> <!-- 15&#45;&gt;7 -->
<g id="edge18" class="edge"><title>15&#45;&gt;7</title> <g id="edge16" class="edge"><title>15&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M428.607,-431.697C434.597,-423.474 441.876,-413.483 448.479,-404.421"/> <path fill="none" stroke="grey" stroke-width="2" d="M210.82,-719.697C218.57,-711.22 228.039,-700.864 236.524,-691.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="451.478,-406.248 454.538,-396.104 445.821,-402.126 451.478,-406.248"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="239.197,-693.846 243.362,-684.104 234.031,-689.123 239.197,-693.846"/>
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<!-- 16&#45;&gt;6 --> <!-- 16 -->
<g id="edge17" class="edge"><title>16&#45;&gt;6</title> <g id="node17" class="node"><title>16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M497.206,-433.378C460.723,-423.163 412.756,-409.732 373.621,-398.774"/> <path fill="none" stroke="#d89556" stroke-width="2" d="M661,-756C661,-756 565,-756 565,-756 559,-756 553,-750 553,-744 553,-744 553,-732 553,-732 553,-726 559,-720 565,-720 565,-720 661,-720 661,-720 667,-720 673,-726 673,-732 673,-732 673,-744 673,-744 673,-750 667,-756 661,-756"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="374.447,-395.371 363.874,-396.045 372.56,-402.111 374.447,-395.371"/> <text text-anchor="middle" x="613" y="-735.5" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
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<!-- 16&#45;&gt;7 --> <!-- 16&#45;&gt;7 -->
<g id="edge19" class="edge"><title>16&#45;&gt;7</title> <g id="edge17" class="edge"><title>16&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M531.742,-431.697C520.911,-422.881 507.582,-412.032 495.84,-402.474"/> <path fill="none" stroke="grey" stroke-width="2" d="M552.723,-722.118C549.439,-721.383 546.181,-720.672 543,-720 457.739,-701.99 433.404,-701.008 344.115,-684.184"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="497.979,-399.703 488.014,-396.104 493.56,-405.132 497.979,-399.703"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="344.567,-680.707 334.09,-682.28 343.261,-687.585 344.567,-680.707"/>
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<!-- 17&#45;&gt;8 --> <!-- 19 -->
<g id="edge20" class="edge"><title>17&#45;&gt;8</title> <g id="node20" class="node"><title>19</title>
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<!-- 18 --> <!-- 16&#45;&gt;19 -->
<g id="node19" class="node"><title>18</title> <g id="edge36" class="edge"><title>16&#45;&gt;19</title>
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<text text-anchor="middle" x="851" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text> <polygon fill="grey" stroke="grey" stroke-width="2" points="576.826,-689.419 567.661,-684.104 571.511,-693.975 576.826,-689.419"/>
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<!-- 17&#45;&gt;18 --> <!-- 22 -->
<g id="edge36" class="edge"><title>17&#45;&gt;18</title> <g id="node23" class="node"><title>22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M844.978,-431.697C845.859,-423.983 846.919,-414.712 847.901,-406.112"/> <path fill="none" stroke="#56d8a9" stroke-width="2" d="M1002.5,-684C1002.5,-684 929.5,-684 929.5,-684 923.5,-684 917.5,-678 917.5,-672 917.5,-672 917.5,-660 917.5,-660 917.5,-654 923.5,-648 929.5,-648 929.5,-648 1002.5,-648 1002.5,-648 1008.5,-648 1014.5,-654 1014.5,-660 1014.5,-660 1014.5,-672 1014.5,-672 1014.5,-678 1008.5,-684 1002.5,-684"/>
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<!-- 25 --> <!-- 16&#45;&gt;22 -->
<g id="node26" class="node"><title>25</title> <g id="edge42" class="edge"><title>16&#45;&gt;22</title>
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<text text-anchor="middle" x="736" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text> <polygon fill="grey" stroke="grey" stroke-width="2" points="908.43,-687.357 917.367,-681.666 906.832,-680.542 908.43,-687.357"/>
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<!-- 17&#45;&gt;25 --> <!-- 17 -->
<g id="edge42" class="edge"><title>17&#45;&gt;25</title> <g id="node18" class="node"><title>17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M799.53,-431.827C783.272,-423.345 766.08,-411.537 755,-396 742.133,-377.959 737.662,-352.972 736.249,-334.065"/> <path fill="none" stroke="#56c9d8" stroke-width="2" d="M577,-468C577,-468 501,-468 501,-468 495,-468 489,-462 489,-456 489,-456 489,-444 489,-444 489,-438 495,-432 501,-432 501,-432 577,-432 577,-432 583,-432 589,-438 589,-444 589,-444 589,-456 589,-456 589,-462 583,-468 577,-468"/>
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<!-- 18&#45;&gt;8 --> <!-- 17&#45;&gt;8 -->
<g id="edge21" class="edge"><title>18&#45;&gt;8</title> <g id="edge18" class="edge"><title>17&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M851,-359.697C851,-351.983 851,-342.712 851,-334.112"/> <path fill="none" stroke="grey" stroke-width="2" d="M523.921,-431.697C516.608,-423.305 507.69,-413.07 499.665,-403.861"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="854.5,-334.104 851,-324.104 847.5,-334.104 854.5,-334.104"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="502.114,-401.344 492.905,-396.104 496.836,-405.943 502.114,-401.344"/>
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<!-- 18&#45;&gt;25 --> <!-- 18&#45;&gt;9 -->
<g id="edge44" class="edge"><title>18&#45;&gt;25</title> <g id="edge20" class="edge"><title>18&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M822.868,-359.876C807.832,-350.724 789.133,-339.342 772.94,-329.485"/> <path fill="none" stroke="grey" stroke-width="2" d="M388.357,-647.876C373.582,-638.724 355.209,-627.342 339.297,-617.485"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="774.602,-326.4 764.24,-324.19 770.962,-332.379 774.602,-326.4"/> <polygon fill="grey" stroke="grey" stroke-width="2" points="341.093,-614.481 330.749,-612.19 337.407,-620.431 341.093,-614.481"/>
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<!-- 19&#45;&gt;8 --> <!-- 18&#45;&gt;10 -->
<g id="edge22" class="edge"><title>19&#45;&gt;8</title> <g id="edge22" class="edge"><title>18&#45;&gt;10</title>
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<!-- 19&#45;&gt;18 --> <!-- 19&#45;&gt;9 -->
<g id="edge37" class="edge"><title>19&#45;&gt;18</title> <g id="edge19" class="edge"><title>19&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M937.868,-431.876C922.832,-422.724 904.133,-411.342 887.94,-401.485"/> <path fill="none" stroke="grey" stroke-width="2" d="M497.206,-649.378C460.723,-639.163 412.756,-625.732 373.621,-614.774"/>
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<!-- 19&#45;&gt;25 --> <!-- 19&#45;&gt;10 -->
<g id="edge45" class="edge"><title>19&#45;&gt;25</title> <g id="edge21" class="edge"><title>19&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M967.332,-431.807C967.882,-411.847 965.54,-379.215 947,-360 941.799,-354.609 861.991,-335.541 802.055,-321.821"/> <path fill="none" stroke="grey" stroke-width="2" d="M531.742,-647.697C520.911,-638.881 507.582,-628.032 495.84,-618.474"/>
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<!-- 20&#45;&gt;9 --> <!-- 20&#45;&gt;11 -->
<g id="edge23" class="edge"><title>20&#45;&gt;9</title> <g id="edge24" class="edge"><title>20&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M846.292,-215.697C844.639,-207.983 842.653,-198.712 840.81,-190.112"/> <path fill="none" stroke="grey" stroke-width="2" d="M899.722,-649.313C918.045,-641.265 936.359,-629.365 947,-612 955.359,-598.357 955.132,-589.779 947,-576 934.386,-554.628 909.727,-541.279 888.56,-533.324"/>
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<!-- 21 --> <!-- 21 -->
<g id="node22" class="node"><title>21</title> <g id="node22" class="node"><title>21</title>
<path fill="none" stroke="#80d856" stroke-width="2" d="M1054,-324C1054,-324 974,-324 974,-324 968,-324 962,-318 962,-312 962,-312 962,-300 962,-300 962,-294 968,-288 974,-288 974,-288 1054,-288 1054,-288 1060,-288 1066,-294 1066,-300 1066,-300 1066,-312 1066,-312 1066,-318 1060,-324 1054,-324"/> <path fill="none" stroke="#56b9d8" stroke-width="2" d="M926,-612C926,-612 776,-612 776,-612 770,-612 764,-606 764,-600 764,-600 764,-588 764,-588 764,-582 770,-576 776,-576 776,-576 926,-576 926,-576 932,-576 938,-582 938,-588 938,-588 938,-600 938,-600 938,-606 932,-612 926,-612"/>
<text text-anchor="middle" x="1014" y="-303.5" font-family="sans" font-size="10.00">generate_alfa_index</text> <text text-anchor="middle" x="851" y="-591.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
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<!-- 21&#45;&gt;9 --> <!-- 20&#45;&gt;21 -->
<g id="edge24" class="edge"><title>21&#45;&gt;9</title> <g id="edge40" class="edge"><title>20&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M998.839,-287.668C981.776,-268.746 952.678,-238.186 924,-216 907.558,-203.28 887.819,-191.241 871.112,-181.862"/> <path fill="none" stroke="grey" stroke-width="2" d="M844.978,-647.697C845.859,-639.983 846.919,-630.712 847.901,-622.112"/>
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<!-- 22 --> <!-- 28 -->
<g id="node23" class="node"><title>22</title> <g id="node29" class="node"><title>28</title>
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<text text-anchor="middle" x="344" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text> <text text-anchor="middle" x="736" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
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<!-- 20&#45;&gt;28 -->
<g id="edge46" class="edge"><title>20&#45;&gt;28</title>
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<!-- 21&#45;&gt;11 -->
<g id="edge23" class="edge"><title>21&#45;&gt;11</title>
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<!-- 21&#45;&gt;28 -->
<g id="edge45" class="edge"><title>21&#45;&gt;28</title>
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<!-- 22&#45;&gt;11 --> <!-- 22&#45;&gt;11 -->
<g id="edge26" class="edge"><title>22&#45;&gt;11</title> <g id="edge25" class="edge"><title>22&#45;&gt;11</title>
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<!-- 23 --> <!-- 22&#45;&gt;21 -->
<g id="node24" class="node"><title>23</title> <g id="edge39" class="edge"><title>22&#45;&gt;21</title>
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<!-- 23&#45;&gt;26 -->
<g id="edge46" class="edge"><title>23&#45;&gt;26</title>
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<!-- 24 --> <!-- 24 -->
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<!-- 24&#45;&gt;13 --> <!-- 24&#45;&gt;12 -->
<g id="edge28" class="edge"><title>24&#45;&gt;13</title> <g id="edge26" class="edge"><title>24&#45;&gt;12</title>
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<!-- 25&#45;&gt;14 --> <!-- 25&#45;&gt;14 -->
<g id="edge29" class="edge"><title>25&#45;&gt;14</title> <g id="edge29" class="edge"><title>25&#45;&gt;14</title>
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<!-- 26&#45;&gt;15 --> <!-- 26&#45;&gt;15 -->
<g id="edge30" class="edge"><title>26&#45;&gt;15</title> <g id="edge30" class="edge"><title>26&#45;&gt;15</title>
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<g id="node30" class="node"><title>29</title>
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<!-- 26&#45;&gt;16 --> <!-- 26&#45;&gt;29 -->
<g id="edge32" class="edge"><title>26&#45;&gt;16</title> <g id="edge49" class="edge"><title>26&#45;&gt;29</title>
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<!-- 27 --> <!-- 27 -->
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<!-- 27&#45;&gt;17 --> <!-- 27&#45;&gt;16 -->
<g id="edge34" class="edge"><title>27&#45;&gt;17</title> <g id="edge31" class="edge"><title>27&#45;&gt;16</title>
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<!-- 27&#45;&gt;19 --> <!-- 28&#45;&gt;17 -->
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<!-- 27&#45;&gt;21 --> <!-- 29&#45;&gt;18 -->
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<!-- 28 --> <!-- 29&#45;&gt;19 -->
<g id="node29" class="node"><title>28</title> <g id="edge35" class="edge"><title>29&#45;&gt;19</title>
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<!-- 28&#45;&gt;25 --> <!-- 30 -->
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install/environment.dev.yml
View file @ 27f4fa5b
name: rnaseq_pipeline name: rhea
channels: channels:
- bioconda - bioconda
- conda-forge - conda-forge
......
install/environment.root.yml
View file @ 27f4fa5b
name: rnaseq_pipeline name: rhea
channels: channels:
- conda-forge - conda-forge
- defaults - defaults
......
install/environment.yml
View file @ 27f4fa5b
name: rnaseq_pipeline name: rhea
channels: channels:
- defaults - defaults
dependencies: dependencies:
......
pipeline_documentation.md
View file @ 27f4fa5b
# RNAseq pipeline documentation # Rhea workflow documentation
This document describes the individual rules of the pipeline for information purposes. For instructions on installation and usage please refer to the [README](README.md). This document describes the individual rules of the pipeline for information purposes. For instructions on installation and usage please refer to the [README](README.md).
## Overview ## Overview
...@@ -14,11 +14,16 @@ This document describes the individual rules of the pipeline for information pur ...@@ -14,11 +14,16 @@ This document describes the individual rules of the pipeline for information pur
* **star_rpm** * **star_rpm**
* **rename_star_rpm_for_alfa** * **rename_star_rpm_for_alfa**
* **calculate_TIN_scores** * **calculate_TIN_scores**
* **merge_TIN_scores**
* **plot_TIN_scores**
* **salmon_quantmerge_genes** * **salmon_quantmerge_genes**
* **salmon_quantmerge_transcripts** * **salmon_quantmerge_transcripts**
* **generate_alfa_index** * **generate_alfa_index**
* **alfa_qc** * **alfa_qc**
* **alfa_qc_all_samples** * **alfa_qc_all_samples**
* **prepare_files_for_report**
* **prepare_MultiQC_config**
* **MULTIQC_report**
### Sequencing mode specific ### Sequencing mode specific
* **(pe_)fastqc** * **(pe_)fastqc**
...@@ -160,6 +165,22 @@ Given a set of BAM files and a gene annotation BED file, calculates the Transcri ...@@ -160,6 +165,22 @@ Given a set of BAM files and a gene annotation BED file, calculates the Transcri
#### merge_TIN_scores
Concatenates the tsv files of all samples into one wider table.
**Input:** TIN score tsv files per sample
**Output:** TIN score tsv file for all samples
#### plot_TIN_scores
Generates sample-wise [boxplots](https://en.wikipedia.org/wiki/Box_plot) of TIN scores.
**Input:** TIN score tsv file for all samples
**Output:** .pdf and .png files with boxplots
#### salmon_quantmerge_genes #### salmon_quantmerge_genes
Merge the salmon quantification *gene* results for all samples of same sequencing mode into a single file. Do this for tpm and number of reads separately. Merge the salmon quantification *gene* results for all samples of same sequencing mode into a single file. Do this for tpm and number of reads separately.
...@@ -197,7 +218,29 @@ The main output of ALFA are two plots, `ALFA_Biotypes.pdf` and `ALFA_Categories. ...@@ -197,7 +218,29 @@ The main output of ALFA are two plots, `ALFA_Biotypes.pdf` and `ALFA_Categories.
Combine the output of all samples into one plot generated by [ALFA](https://github.com/biocompibens/ALFA). Combine the output of all samples into one plot generated by [ALFA](https://github.com/biocompibens/ALFA).
**Input:** ALFA_feature_counts.tsv from each sample in `samples.tsv` **Input:** ALFA_feature_counts.tsv from each sample in `samples.tsv`
**Output:** ALFA_Biotypes.pdf and ALFA_Categories.pdf for all samples together **Output:** ALFA_Biotypes.pdf and ALFA_Categories.pdf for all samples together
#### prepare_files_for_report
This is an internal rule with `run` directive. It gathers all the output files, restructures the `log` and `results` directories and modifies some `stdout` and `stderr` streams of previous rules for proper parsing of sample names in the final report.
#### prepare_MultiQC_config
Prepares a dedicated config file for [MultiQC](https://multiqc.info/).
**Input:** Currently directories created during `prepare_files_for_report` serve as input.
**Output:** Config file in .yaml format
#### MULTIQC_report
Creates an interactive report after the pipeline is finished. [MultiQC](https://multiqc.info/) gathers results and logs after distinct bioinformatics tools, parses them and presents the output graphically in an HTML file.
**Input:** Config file fort MultiQC in .yaml format
**Output:** Directory with automatically generated HTML report
### Sequencing mode specific rules ### Sequencing mode specific rules
...@@ -315,3 +358,4 @@ Spliced Transcripts Alignment to a Reference; Read the [Publication](https://www ...@@ -315,3 +358,4 @@ Spliced Transcripts Alignment to a Reference; Read the [Publication](https://www
* -l: fragment length, user specified as `mean` * -l: fragment length, user specified as `mean`
* -s: fragment length SD, user specified as `sd` * -s: fragment length SD, user specified as `sd`
tests/test_alfa/test.sh
View file @ 27f4fa5b
...@@ -31,7 +31,7 @@ snakemake \ ...@@ -31,7 +31,7 @@ snakemake \
--printshellcmds \ --printshellcmds \
--rerun-incomplete \ --rerun-incomplete \
--use-singularity \ --use-singularity \
--singularity-args="--bind ${PWD}/../input_files" \ --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose \ --verbose \
results/ALFA/ALFA_plots.Categories.pdf results/ALFA/ALFA_plots.Categories.pdf
......
tests/test_integration_workflow/expected_output.files
View file @ 27f4fa5b
...@@ -16,66 +16,66 @@ results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt ...@@ -16,66 +16,66 @@ results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate1.fastq results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate1.fastq
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bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg
ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa 3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index 6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index 2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
c1254a0bae19ac3ffc39f73099ffcf2b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg c266d31e0a2ad84975cb9de335891e64 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg 0139e75ddbfe6eb081c2c2d9b9108ab4 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
c1254a0bae19ac3ffc39f73099ffcf2b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv c1254a0bae19ac3ffc39f73099ffcf2b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg bcccf679a8c083d01527514c9f5680a0 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg ea91b4f85622561158bff2f7c9c312b3 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
\ No newline at end of file \ No newline at end of file
tests/test_integration_workflow/test.local.sh
View file @ 27f4fa5b
...@@ -29,7 +29,7 @@ snakemake \ ...@@ -29,7 +29,7 @@ snakemake \
--printshellcmds \ --printshellcmds \
--rerun-incomplete \ --rerun-incomplete \
--use-singularity \ --use-singularity \
--singularity-args="--bind ${PWD}/../input_files" \ --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose --verbose
# Check md5 sum of some output files # Check md5 sum of some output files
...@@ -55,7 +55,7 @@ md5sum --check "expected_output.md5" ...@@ -55,7 +55,7 @@ md5sum --check "expected_output.md5"
echo "Verifying STAR output" echo "Verifying STAR output"
result=$(bedtools intersect -F 1 -v -bed \ result=$(bedtools intersect -F 1 -v -bed \
-a ../input_files/synthetic.mate_1.bed \ -a ../input_files/synthetic.mate_1.bed \
-b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \ -b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
| wc -l) | wc -l)
if [ $result != "0" ]; then if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth" echo "Alignments for mate 1 reads are not consistent with ground truth"
...@@ -63,7 +63,7 @@ if [ $result != "0" ]; then ...@@ -63,7 +63,7 @@ if [ $result != "0" ]; then
fi fi
result=$(bedtools intersect -F 1 -v -bed \ result=$(bedtools intersect -F 1 -v -bed \
-a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
-b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \ -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
| wc -l) | wc -l)
if [ $result != "0" ]; then if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth" echo "Alignments for mate 1 reads are not consistent with ground truth"
...@@ -73,9 +73,9 @@ fi ...@@ -73,9 +73,9 @@ fi
# Check whether Salmon assigns reads to expected genes # Check whether Salmon assigns reads to expected genes
echo "Verifying Salmon output" echo "Verifying Salmon output"
diff \ diff \
<(cat results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
<(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff \ diff \
<(cat results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/synthetic_10_reads_paired_synthetic_10_reads_paired/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
<(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
tests/test_integration_workflow/test.slurm.sh
View file @ 27f4fa5b
...@@ -31,7 +31,7 @@ snakemake \ ...@@ -31,7 +31,7 @@ snakemake \
--printshellcmds \ --printshellcmds \
--rerun-incomplete \ --rerun-incomplete \
--use-singularity \ --use-singularity \
--singularity-args="--bind ${PWD}/../input_files" \ --singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose --verbose
# Check md5 sum of some output files # Check md5 sum of some output files
...@@ -57,7 +57,7 @@ md5sum --check "expected_output.md5" ...@@ -57,7 +57,7 @@ md5sum --check "expected_output.md5"
echo "Verifying STAR output" echo "Verifying STAR output"
result=$(bedtools intersect -F 1 -v -bed \ result=$(bedtools intersect -F 1 -v -bed \
-a ../input_files/synthetic.mate_1.bed \ -a ../input_files/synthetic.mate_1.bed \
-b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \ -b results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Aligned.sortedByCoord.out.bam \
| wc -l) | wc -l)
if [ $result != "0" ]; then if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth" echo "Alignments for mate 1 reads are not consistent with ground truth"
...@@ -65,7 +65,7 @@ if [ $result != "0" ]; then ...@@ -65,7 +65,7 @@ if [ $result != "0" ]; then
fi fi
result=$(bedtools intersect -F 1 -v -bed \ result=$(bedtools intersect -F 1 -v -bed \
-a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \
-b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \ -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_Aligned.sortedByCoord.out.bam \
| wc -l) | wc -l)
if [ $result != "0" ]; then if [ $result != "0" ]; then
echo "Alignments for mate 1 reads are not consistent with ground truth" echo "Alignments for mate 1 reads are not consistent with ground truth"
...@@ -75,9 +75,9 @@ fi ...@@ -75,9 +75,9 @@ fi
# Check whether Salmon assigns reads to expected genes # Check whether Salmon assigns reads to expected genes
echo "Verifying Salmon output" echo "Verifying Salmon output"
diff \ diff \
<(cat results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
<(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
diff \ diff \
<(cat results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/salmon_quant/synthetic_10_reads_paired_synthetic_10_reads_paired/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \
<(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}')
workflow/rules/paired_end.snakefile.smk
View file @ 27f4fa5b
...@@ -177,7 +177,7 @@ rule pe_remove_polya_cutadapt: ...@@ -177,7 +177,7 @@ rule pe_remove_polya_cutadapt:
-o {output.reads1} \ -o {output.reads1} \
-p {output.reads2} \ -p {output.reads2} \
{input.reads1} \ {input.reads1} \
{input.reads2};) \ {input.reads2}) \
1> {log.stdout} 2>{log.stderr}" 1> {log.stdout} 2>{log.stderr}"
......
workflow/rules/single_end.snakefile.smk
View file @ 27f4fa5b
...@@ -84,7 +84,7 @@ rule remove_adapters_cutadapt: ...@@ -84,7 +84,7 @@ rule remove_adapters_cutadapt:
-a {params.adapters_3} \ -a {params.adapters_3} \
-g {params.adapters_5} \ -g {params.adapters_5} \
-o {output.reads} \ -o {output.reads} \
{input.reads};) \ {input.reads}) \
1> {log.stdout} 2> {log.stderr}" 1> {log.stdout} 2> {log.stderr}"
......