scanpy-related local modules use harmonized Seqera image#271

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kim-fehl wants to merge 16 commits intonf-core:devfrom

kim-fehl:containers

Commits on Mar 16, 2026

refactor(singler): switch to seqera bioc container and trim deps
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Revert "refactor(singler): switch to seqera bioc container and trim deps"
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refactor(containers): harmonize containers of local scanpy/anndata modules
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refactor(containers): pin numpy=2.3.5 since 2.4 breaks upsetplot for now
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refactor(containers): upgrade python=3.13.12 because of read_pickle/Categorical issue, exclude bbknn requiring py3.12
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fix(harmony): account for harmonypy>=0.2.0 Z_corr breaking change
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test(containers): refresh nf-test snapshots
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refactor(collectsizes): use harmonized container with pandas and pyyaml
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test(containers): refresh nf-test snapshots for collectsizes
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refactor(scvi): align local scvi modules to use nf-core/modules scvi-tools 1.3.3 image
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test(containers): refresh nf-test scvitools snapshots
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