From dca29aeb1a0c9d17473587fb6c20c0ac1df3774e Mon Sep 17 00:00:00 2001 From: Alexis Lucattini Date: Thu, 7 Nov 2024 18:05:23 +1100 Subject: [PATCH] Update dragen somatic pipeline id Dragen somatic with germline pipeline didn't have the enable_cnv_somatic flag available in the workflow (and in the past we have just used enable_cnv), since we do not need the cnv on the germline calls we use just enable_cnv_somatic instead. --- config/constants.ts | 2 +- .../get_boolean_parameters_from_event_input.py | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/config/constants.ts b/config/constants.ts index 46a47363e..d791f6ecf 100644 --- a/config/constants.ts +++ b/config/constants.ts @@ -334,7 +334,7 @@ TN Stateless stack */ // Deployed under dev/stg/prod -export const tnIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/tumor_normal_4.2.4_pipeline_id'; // 0f5575bc-6cf8-4a90-a80e-05088aae8ed7 +export const tnIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/tumor_normal_4.2.4_pipeline_id'; // 6ce2b636-ba2f-4004-8065-f3557f286c98 export const tnIcav2PipelineWorkflowType = 'tumor-normal'; export const tnIcav2PipelineWorkflowTypeVersion = '4.2.4'; export const tnIcav2ServiceVersion = '2024.07.01'; diff --git a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/get_boolean_parameters_from_event_input_py/get_boolean_parameters_from_event_input.py b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/get_boolean_parameters_from_event_input_py/get_boolean_parameters_from_event_input.py index 6a7a43507..b09c87b26 100644 --- a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/get_boolean_parameters_from_event_input_py/get_boolean_parameters_from_event_input.py +++ b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/get_boolean_parameters_from_event_input_py/get_boolean_parameters_from_event_input.py @@ -19,12 +19,15 @@ def handler(event, context) -> Dict[str, Dict]: # Get the boolean parameters from the event input cwl_parameter_dict: Dict = { + # Write normal bam in somatic workflow + # But take the vcf from the germline workflow "enable_map_align_somatic": True, "enable_map_align_output_somatic": event_data_input.get('enableMapAlignOutput', True), "enable_map_align_germline": True, "enable_map_align_output_germline": False, "enable_duplicate_marking": event_data_input.get('enableDuplicateMarking', True), "enable_cnv_somatic": event_data_input.get('enableCnvSomatic', None), + # HRD is somatic Only "enable_hrd": event_data_input.get('enableHrdSomatic', None), "enable_sv_somatic": event_data_input.get('enableSvSomatic', None), "cnv_use_somatic_vc_baf": event_data_input.get('cnvUseSomaticVcBaf', None)