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BLAST Options Reference (mkdocs)

Motivation

BLAST execution options were documented across several pages without a single reference: docs/user-guide/new-search.md listed only a handful of flag names, docs/user-guide/api-reference.md showed example payloads, and the canonical mapping rules (e.g. low_complexity_filter ↔ dust) lived inside research notes. There was no end-user-facing catalogue of "every option, its default, its CLI flag, and what blocks submit".

User-facing change

  • New page BLAST Options Reference under User Guide, listing every option exposed by the submit form / OpenAPI / Celery backend with its default, allowed values, CLI mapping, and validation rule.
  • Sections cover: program & query, search set, taxonomy filter, task profile, execution profile (cluster + sharding + warmup), algorithm parameters, preflight gates, and OpenAPI-only fields.
  • docs/user-guide/new-search.md now links to the new reference at the end of the Algorithm parameters paragraph.

API / IaC diff summary

None — documentation only. No code, schema, or infra changes.

Validation evidence

  • uv run mkdocs build --strict — builds clean (only unrelated MkDocs 2.0 promo banner + the expected "new file has no git history" warning for the new page).
  • All source-of-truth links in the new page (api/_http_utils.py, api/services/blast/config.py, api/services/blast/submit_payload.py, api/services/blast/task_config.py, api/services/sharding_precision.py, api/routes/blast/preflight.py, api/routes/blast/submit.py, web/src/api/blast.ts, web/src/pages/blastSubmitModel.ts, web/src/pages/blastSubmit/useSubmitMutation.ts, web/src/pages/blastSubmit/AlgorithmParametersSection.tsx, web/src/pages/blastSubmit/shardingAvailability.ts, web/src/pages/blastSubmit/computeEnvironment.ts) verified to exist via [[ -f $f ]] audit.