feat(cluster)(zarr3): species-parameterize CORUM + MSigDB benchmark generation (#238) - #241
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…eneration (#238) Port of the brieflow-main cluster benchmark species fix onto the zarr3 line. - get_corum_data / generate_corum_group_benchmark: accept species_id; human keeps its native export unchanged, other species are filtered out of the CORUM complete export by organism. - generate_msigdb_group_benchmark: accept species_id and resolve the MSigDB collection per species (human=KEGG MEDICUS; mouse=native Reactome). - STRING and UniProt generators were already species-aware; no change. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FRP7UVsNz6igHrJE72nVfT
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Summary
zarr3-line port of the cluster benchmark species fix (companion to #240 on
main). Closes #238 on the zarr3 line.workflow/lib/cluster/scrape_benchmarks.pyhardwired human sources, blocking mouse/non-human cluster benchmarks.get_corum_data/generate_corum_group_benchmark): acceptspecies_id. Human keeps its nativefile_id=humanexport unchanged; other species are filtered out of the CORUMcompleteexport byorganism.generate_msigdb_group_benchmark): acceptspecies_id; human = KEGG MEDICUS, mouse = native Reactome (MSigDB has no native mouse KEGG). Expliciturlstill overrides.species_id-aware — no change.The file is identical on
mainandzarr3, so this is a clean cherry-pick of themaincommit (verifiedruff check+ruff format --check). No zarr3-specific divergence in this module.See #240 for the full verification notes and the mouse "KEGG"→Reactome naming rationale.