Commit 6991a125 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Remove pigz version

parent fd0dc2a9
......@@ -38,7 +38,7 @@ fastqcScript = Channel.fromPath("$baseDir/scripts/fastqc.sh")
versionsScript = Channel.fromPath("$baseDir/scripts/generate_versions.py")
referencesScript = Channel.fromPath("$baseDir/scripts/generate_references.py")
versions_pythonScript = Channel.fromPath("$baseDir/scripts/versions_python.sh")
versions_pigzScript = Channel.fromPath("$baseDir/scripts/versions_pigz.sh")
#versions_pigzScript = Channel.fromPath("$baseDir/scripts/versions_pigz.sh")
versions_cellrangerScript = Channel.fromPath("$baseDir/scripts/versions_cellranger.sh")
versions_bcl2fastqScript = Channel.fromPath("$baseDir/scripts/versions_bcl2fastq.sh")
versions_fastqcScript = Channel.fromPath("$baseDir/scripts/versions_fastqc.sh")
......@@ -90,12 +90,12 @@ process untarBCL {
input:
file untarBCLScript
file versions_pigzScript
#file versions_pigzScript
each file(tar) from tarList
output:
file("*[!version_pigz.txt]") into bclPaths mode flatten
file("version_pigz.txt") into version_pigz
#file("version_pigz.txt") into version_pigz
script:
"""
......@@ -103,7 +103,7 @@ process untarBCL {
ulimit -u 16384
ulimit -a
bash untarBCL.sh -t ${tar}
bash versions_pigz.sh > version_pigz.txt
#bash versions_pigz.sh > version_pigz.txt
"""
}
......
......@@ -29,7 +29,7 @@ SOFTWARE_REGEX = {
'Pipeline': ['version_pipeline.txt', r"(\S+)"],
'Nextflow': ['version_nextflow.txt', r"(\S+)"],
'python': ['version_python.txt', r"(\S+)"],
'pigz': ['version_pigz.txt', r"(\S+)"],
#'pigz': ['version_pigz.txt', r"(\S+)"],
'cellranger': ['version_cellranger.txt', r"(\S+)"],
'bcl2fastq': ['version_bcl2fastq.txt', r"(\S+)"],
'fastqc': ['version_fastqc.txt', r"(\S+)"],
......@@ -78,10 +78,10 @@ def main():
out_filename = output + '_mqc.yaml'
results = OrderedDict()
#results['Pipeline'] = '<span style="color:#999999;\">N/A</span>'
#results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
results['Pipeline'] = '<span style="color:#999999;\">N/A</span>'
results['Nextflow'] = '<span style="color:#999999;\">N/A</span>'
results['python'] = '<span style="color:#999999;\">N/A</span>'
results['pigz'] = '<span style="color:#999999;\">N/A</span>'
#results['pigz'] = '<span style="color:#999999;\">N/A</span>'
results['cellranger'] = '<span style="color:#999999;\">N/A</span>'
results['bcl2fastq'] = '<span style="color:#999999;\">N/A</span>'
results['fastqc'] = '<span style="color:#999999;\">N/A</span>'
......
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