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Disabled TSO500 ctDNA BAM somalier extract step #519

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Oct 23, 2022
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Disabled TSO500 ctDNA BAM somalier extract step #519

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33 changes: 18 additions & 15 deletions data_processors/pipeline/lambdas/orchestrator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -245,21 +245,24 @@ def next_step(this_workflow: Workflow, skip: dict, context=None):

return results

elif this_workflow.type_name.lower() == WorkflowType.DRAGEN_TSO_CTDNA.value.lower() and \
this_workflow.end_status.lower() == WorkflowStatus.SUCCEEDED.value.lower():
logger.info("Received DRAGEN_TSO_CTDNA workflow notification")

WorkflowRule(this_workflow).must_have_output()

results = list()

if "SOMALIER_EXTRACT_STEP" in skiplist:
logger.info("Skip performing SOMALIER_EXTRACT_STEP")
else:
logger.info("Performing SOMALIER_EXTRACT_STEP")
results.append(somalier_extract_step.perform(this_workflow))

return results
# FIXME TSO500 ctDNA RUO bundle reference genome hg19
# https://github.com/umccr/data-portal-apis/issues/509
# https://github.com/umccr/cwl-ica/issues/153
# elif this_workflow.type_name.lower() == WorkflowType.DRAGEN_TSO_CTDNA.value.lower() and \
# this_workflow.end_status.lower() == WorkflowStatus.SUCCEEDED.value.lower():
# logger.info("Received DRAGEN_TSO_CTDNA workflow notification")
#
# WorkflowRule(this_workflow).must_have_output()
#
# results = list()
#
# if "SOMALIER_EXTRACT_STEP" in skiplist:
# logger.info("Skip performing SOMALIER_EXTRACT_STEP")
# else:
# logger.info("Performing SOMALIER_EXTRACT_STEP")
# results.append(somalier_extract_step.perform(this_workflow))
#
# return results

elif this_workflow.type_name.lower() == WorkflowType.TUMOR_NORMAL.value.lower() and \
this_workflow.end_status.lower() == WorkflowStatus.SUCCEEDED.value.lower():
Expand Down