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

Remove pigz version

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