From c74540337f627e9e4199c0a8d12cd62f3d58127d Mon Sep 17 00:00:00 2001 From: Benjamin Capodanno Date: Tue, 11 Aug 2026 14:16:14 -0700 Subject: [PATCH] fix(workflow): stop scheduling VEP annotation in the pipeline VEP consequences were sourced from the top-level most_severe_consequence, which reports the worst call across all overlapping transcripts instead of the transcript the variant was actually mapped to, producing misleading annotations. The job definition is left commented out rather than deleted so it can be restored once VEP annotates Allele rows directly. Refs #772 --- src/mavedb/lib/workflow/definitions.py | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/src/mavedb/lib/workflow/definitions.py b/src/mavedb/lib/workflow/definitions.py index 056ff530..f23da015 100644 --- a/src/mavedb/lib/workflow/definitions.py +++ b/src/mavedb/lib/workflow/definitions.py @@ -96,16 +96,20 @@ def annotation_pipeline_job_definitions( }, "dependencies": [("warm_clingen_cache", DependencyType.SUCCESS_REQUIRED)], }, - { - "key": "populate_vep_for_score_set", - "function": "populate_vep_for_score_set", - "type": JobType.MAPPED_VARIANT_ANNOTATION, - "params": { - "correlation_id": None, # Required param to be filled in at runtime - "score_set_id": None, # Required param to be filled in at runtime - }, - "dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)], - }, + # VEP annotation is intentionally not scheduled: its consequences came from VEP's top-level + # most_severe_consequence, the worst call across all overlapping transcripts rather than the + # one the variant was mapped to. + # TODO(#772): Re-enable once VEP annotates Allele rows directly. + # { + # "key": "populate_vep_for_score_set", + # "function": "populate_vep_for_score_set", + # "type": JobType.MAPPED_VARIANT_ANNOTATION, + # "params": { + # "correlation_id": None, # Required param to be filled in at runtime + # "score_set_id": None, # Required param to be filled in at runtime + # }, + # "dependencies": [("submit_score_set_mappings_to_car", DependencyType.SUCCESS_REQUIRED)], + # }, { "key": "populate_variant_translations_for_score_set", "function": "populate_variant_translations_for_score_set",