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Buzz lightyear

Merged Jeremy Mathews requested to merge Buzz_Lightyear into develop
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@@ -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>'
@@ -95,7+109,7 @@
versions = x.read()
match = re.search(v[1], versions)
if match:
results[k] = "v{}".format(match.group(1))
# Dump to YAML
print(