If there are samples in the samples.json file that didn't get run through the qc generation workflow, the general_parse_stats.py file will exit due to these lines:
https://github.com/msk-access/access_utils/blob/multiqc-utils/multiqc_prep/general_stats_parse.py#L322-L327
It may be better to change sys.exit(1) to a continue, so that this script can handle parsing just the subset of samples that overlap
Similarly, a return could be used here to make the module more flexible
if not os.path.exists(args.samples_json):
print('could not find file: {}!'.format(args.samples_json))
sys.exit(1)
If there are samples in the
samples.jsonfile that didn't get run through the qc generation workflow, thegeneral_parse_stats.pyfile will exit due to these lines:https://github.com/msk-access/access_utils/blob/multiqc-utils/multiqc_prep/general_stats_parse.py#L322-L327
It may be better to change
sys.exit(1)to acontinue, so that this script can handle parsing just the subset of samples that overlapSimilarly, a return could be used here to make the module more flexible