Commit 4ca2deb0 authored by Jeremy Mathews's avatar Jeremy Mathews
Browse files

Update versions to run correctly

parent b4b389fc
Pipeline #8351 failed with stages
in 5 minutes and 3 seconds
......@@ -189,7 +189,7 @@ process cellranger_mkfastq {
val "${bcl.simpleName}" into bclNameCell
file("**/outs/**/*.fastq.gz") into cellrangerCount mode flatten
file("**/outs/fastq_path/Stats/*") into bqcPathsCell
file("version_ranger.txt") into version_cellranger
file("version_Cellranger.txt") into version_cellranger
file("version_bcl2fastq.txt") into version_bcl2fastqCell
when:
......@@ -204,7 +204,7 @@ process cellranger_mkfastq {
mkdir fq
mkdir "fq/${bcl.simpleName}"
find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
bash versions_cellranger.sh > version_ranger.txt
bash versions_cellranger.sh > version_Cellranger.txt
bash versions_bcl2fastq.sh > version_bcl2fastq.txt
"""
}
......@@ -227,7 +227,7 @@ process spaceranger_mkfastq {
val "${bcl.simpleName}" into bclNameSpace
file("**/outs/**/*.fastq.gz") into spacerangerCount mode flatten
file("**/outs/fastq_path/Stats/*") into bqcPathsSpace
file("version_ranger.txt") into version_spaceranger
file("version_Spaceranger.txt") into version_spaceranger
file("version_bcl2fastq.txt") into version_bcl2fastqSpace
when:
......@@ -242,7 +242,7 @@ process spaceranger_mkfastq {
mkdir fq
mkdir "fq/${bcl.simpleName}"
find . -name "*.fastq.gz" -exec cp {} fq/${bcl.simpleName}/ \\;
bash versions_spaceranger.sh > version_ranger.txt
bash versions_spaceranger.sh > version_Spaceranger.txt
bash versions_bcl2fastq.sh > version_bcl2fastq.txt
"""
}
......
......@@ -25,12 +25,12 @@ logger.addHandler(logging.NullHandler())
logger.propagate = False
logger.setLevel(logging.INFO)
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+)"],
'10x-ranger': ['version_ranger.txt', r"(\S+)"],
'bcl2fastq': ['version_bcl2fastq.txt', r"(\S+)"],
'fastqc': ['version_fastqc.txt', r"(\S+)"],
}
......@@ -56,6 +56,18 @@ def get_args():
return args
def rangerType(files):
'''Determine Type of Ranger being used'''
for fname in files:
ranger = re.findall("version_(.*)ranger.txt", fname)
if not ranger: continue
ranger_type = ranger[0]+"ranger"
SOFTWARE_REGEX[ranger_type] = [fname, r"(\S+)"]
return ranger_type
def check_files(files):
'''Check if version files are found.'''
......@@ -77,12 +89,14 @@ def main():
out_filename = output + '_mqc.yaml'
ranger_type = rangerType(files)
results = OrderedDict()
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['10x-ranger'] = '<span style="color:#999999;\">N/A</span>'
results[ranger_type] = '<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>'
......
......@@ -6,4 +6,4 @@
#* --------------------------------------------------------------------------
#*
cellranger mkfastq --version | grep 'cellranger mkfastq ' | sed 's/.*(\(.*\))/\1/'
\ No newline at end of file
cellranger mkfastq --version | grep 'cellranger mkfastq ' | sed 's/.*-\(.*\))/\1/'
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