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fix(workflow): stop scheduling VEP annotation in the pipeline #840

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Merged
bencap merged 1 commit into from
Aug 12, 2026
Merged

fix(workflow): stop scheduling VEP annotation in the pipeline #840

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24 changes: 14 additions & 10 deletions src/mavedb/lib/workflow/definitions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
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