def _get_pipeline(item): from bcbio.log import logger SUPPORTED_PIPELINES = {x.name.lower(): x for x in utils.itersubclasses(AbstractPipeline)} analysis_type = item.get("analysis", "").lower() if analysis_type not in SUPPORTED_PIPELINES: logger.error("Cannot determine which type of analysis to run, " "set in the run_info under details.") sys.exit(1) else: return SUPPORTED_PIPELINES[analysis_type]
def _get_pipeline(item): from bcbio.log import logger SUPPORTED_PIPELINES = {x.name.lower(): x for x in utils.itersubclasses(AbstractPipeline)} analysis_type = item.get("analysis", "").lower() if analysis_type not in SUPPORTED_PIPELINES: logger.error("Cannot determine which type of analysis to run, " "set in the run_info under details.") sys.exit(1) else: return SUPPORTED_PIPELINES[analysis_type]