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BICF
Astrocyte
cellranger_mkfastq
Commits
6991a125
Commit
6991a125
authored
Jun 20, 2020
by
Gervaise Henry
🤠
Browse files
Remove pigz version
parent
fd0dc2a9
Changes
2
Hide whitespace changes
Inline
Side-by-side
workflow/main.nf
View file @
6991a125
...
...
@@ -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
"""
}
...
...
workflow/scripts/generate_versions.py
View file @
6991a125
...
...
@@ -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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