galaxyproject / galaxyproject/brc-analytics
Pangenome: re-run the analysis as a reproducible Galaxy workflow
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Description
Parent epic: #1322
Re-run the Pv4 pangenome analysis (currently a standalone pipeline at `nekrut/Pv4-pangenome`) as a **Galaxy workflow**, to get:
- a **reproducible artifact** — the v0 bundle regenerated from a defined workflow, and
- a **linkable Galaxy workflow/invocation** users can open to see how the bundle was created.
During the rerun, **resolve the assembly accession (GCA/GCF) mismatch** so the analysis references only accessions BRC already carries — avoiding the GCA→GCF seqname-conversion gymnastics otherwise needed for UCSC track deployment. Two ways:
- **Reuse the accession BRC/UCSC already has** (e.g. Sal-I → `GCF_000002415.2`), or
- **Import the alternative assembly** into BRC so everything is consistent.
**Concrete instance — Sal-I:** the pangenome was built on `GCA_000002415.2`, but BRC and UCSC have `GCF_000002415.2` (the GCA GenArk hub 404s), so it's the member that needs conversion.
## Acceptance criteria
- The pangenome analysis runs as a Galaxy workflow producing the v0 bundle artifacts.
- A public, linkable Galaxy workflow (and/or invocation) showing how the bundle was created.
- The rerun uses accessions consistent with BRC's catalog (no downstream GCA↔GCF conversion), via reuse or import.
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