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fix: handle annotation availability and external labels, reporting only available cell annotations - #12

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Sergio-ote merged 1 commit into
plot_point_sizesfrom
report_annotation_selection
Sep 9, 2026
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Sergio-ote merged 1 commit into
plot_point_sizesfrom
report_annotation_selection

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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 Unannotated cell_type_tsv placeholder 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

  • Workflow lint passes against .test/
  • Decoupled .test/ dry-run builds the CoreBlock DAG
  • Affected HeadBlock mode was dry-run with a complete mode-specific config and representative inputs, if applicable
  • Config validates against workflow/schemas/config.schema.yaml
  • mkdocs build --strict passes, if documentation was changed
  • Catalogue rule graph was generated before a release, if applicable
  • Parameter names match between .smk rules and scripts; documentation was updated if behaviour changed

@Sergio-ote
Sergio-ote added this pull request to stack #10 September 9, 2026 11:17
@Sergio-ote
Sergio-ote force-pushed the report_annotation_selection branch from 0429898 to c87e91b Compare September 9, 2026 20:27
@Sergio-ote
Sergio-ote merged commit 9bf65a7 into dev Sep 9, 2026
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@Sergio-ote
Sergio-ote deleted the report_annotation_selection branch September 9, 2026 20:35
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