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fix: handle annotation availability and external labels, reporting only available cell annotations - #12
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Sergio-ote
added this pull request to stack #10
September 9, 2026 11:17
…ly available cell annotations
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What & why
Improved annotation handling so annotation-dependent plots, composition outputs, and report panels are generated only for annotation sources containing meaningful labels. Previously, when no manual cluster-to-cell-type TSV mapping was provided, an all
Unannotatedcell_type_tsvplaceholder could be treated as a valid annotation. The placeholder is still retained in the h5ad for compatibility but is excluded from annotation outputs.External annotations now support arbitrary source-column names from metadata TSVs or decoupled h5ad objects, with consistent handling of retained unannotated cells.
Validation
.test/.test/dry-run builds the CoreBlock DAGworkflow/schemas/config.schema.yamlmkdocs build --strictpasses, if documentation was changed.smkrules and scripts; documentation was updated if behaviour changed