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Introduces SYMPHONY_INTEGRATE module and wires it into INTEGRATE as integration_methods symphony, with nf-test coverage and docs. Requires symphonypy 0.2.3 for harmonypy 0.2 compatibility (symphonypy#9).
Update symphonypy to 0.2.4 with a rebuilt Wave image, and use importlib.metadata for package versions since symphonypy does not expose __version__. Co-authored-by: Cursor <cursoragent@cursor.com>
Align the process name with symphonypy's harmony_integrate entry point and update references and nf-test snapshots. Co-authored-by: Cursor <cursoragent@cursor.com>
Route the harmony integration method through SYMPHONY_HARMONYINTEGRATE, remove the duplicate symphony option, and delete the old scanpy/harmony module. Co-authored-by: Cursor <cursoragent@cursor.com>
The extension_base artifacts now live in nf-core/test-datasets, so the temporary build and collection scripts are no longer needed in this repo.
Users now select symphony in integration_methods and pass symphony_reference for query mapping, with outputs published under combine/integrate/symphony.
Use the upstream extension_base commit for reference mapping, extension, and sub-atlas tests instead of branch URLs or the temporary fork.
Regenerated module, subworkflow, and pipeline snapshots with real H5AD outputs from the new official test datasets.
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Point pipeline nf-tests back at the forked fixtures needed by existing tests and align the COMBINE test inputs with the current workflow signature.
Support gene_ids and gene_id in filtered matrices and fall back to var index when neither is present, fixing AMBIENT_CORRECTION tests on symbol-only h5ad inputs.
Add bioconductor-glmgampoi and bump r-seurat so SCTransform uses the supported v2 backend in the Wave image.
Run SCANPY_FILTER on raw counts before HVG selection and refresh integration and combat snapshots.
Surface actionable context when mygene.info returns server or network errors instead of a raw httpx traceback.
Pass species from the pipeline into unify and quality control so gene ID conversion respects the configured organism, and update tests and parameter docs accordingly.
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