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Enable opt-in tensor factorisation of donor-level LIANA scores with loadings plots, MultiQC embedding, and PROGENy enrichment. Generated by Cursor Grok 4.5
Resolve --interesting_genes with file() so DE modules receive a path, and interpolate factor names into Cell2cell MultiQC section headings. Generated by Cursor Grok 4.5
AnnData 0.12 rejects pandas StringDtype indexes/columns unless allow_write_nullable_strings is enabled; cast obs and opt in before write. Generated by Cursor Grok 4.5
Label at most the top 10 significant interesting genes when a list is provided, otherwise the top 10 significant genes, and use adjustText. For Scanpy comparisons with exactly two groups, show a single A vs B volcano instead of mirrored vs-rest panels. Generated by Cursor Grok 4.5
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.0.3. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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Use container= in containers_conda_lock_files configs so nf-core pipelines lint container_configs passes. Generated by Cursor Grok 4.5
Merged AnnData can carry pandas StringDtype indexes from scanpy rank_genes_groups pts tables; opt in before writing cellxgene h5ad. Generated by Cursor Grok 4.5
Rewrite string indexes as CategoricalIndex in rankgenesgroups and cytetype so newer anndata encodings remain readable by nft-anndata, and keep allow_write_nullable_strings as a write safety net in extend/prepcellxgene. Generated by Cursor Grok 4.5
Regenerate module, subworkflow, and pipeline snapshots via nftu to match CategoricalIndex sanitisation and package versions. Generated by Cursor Grok 4.5
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Summary
liana/bysample) then tensor factorisation and sender-receiver loadings-product heatmaps (cell2cell/tensor), wired throughPER_GROUPwhen--cell2cell true.adjustText, and collapse two-group Scanpy one-vs-rest panels into a single{A} vs {B}volcano.ADATA_EXTENDh5ad writes failing on pandas nullable string dtypes with AnnData 0.12.interesting_genespath staging and Cell2cell MultiQC factor titles.Test plan
nf-testformodules/local/liana/bysample,modules/local/cell2cell/tensor, andsubworkflows/local/per_group(cell2cell path)--cell2cell trueand--interesting_genesGenerated by Cursor Grok 4.5
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).