feat(pipeline): VEP database mode, and a pipeline-specific database URL

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Makes a real annotation runnable locally without the 25 GB VEP cache, which is what
the demo needs and what a reviewer can reproduce in minutes.

- params.vep_database (VEP_DATABASE=true) queries Ensembl's public database instead of
  a local cache. Slower per variant and fewer fields, so --everything is swapped for the
  flags the loader actually stores. Its cache placeholder is NO_CACHE, not NO_FILE:
  Nextflow rejects two staged inputs sharing a filename.
- PIPELINE_DATABASE_URL is handed to the pipeline when set. The loader runs inside a
  container, where the API's own localhost URL would point at the container itself.
- README: how to run the UI's annotate button locally against host Nextflow + Docker.

Verified end to end on pipeline/tests/data/tiny.vcf: bcftools norm split the multiallelic
record, VEP 113 annotated 4 variants live, the loader wrote them and marked the job
succeeded, and the UI shows them. The deletion came back as 22:42126611 CT>C with exact
VCF alleles, which is the case the audit's ID-tagging fix exists for.

Tests: api 51, loader 16, stub run 3/3; ruff, mypy clean.

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This commit is contained in:

Kemal Yaylali

2026-09-12 07:39:19 +01:00

parent 11fb6b3d73

commit ae58e33fe2

8 changed files with 64 additions and 4 deletions

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pipeline/assets/NO_CACHE