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]