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feature: pseudobulk support for common alternative experimental designs - #9

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Sergio-ote merged 4 commits into
devfrom
pseudobulk_improvement
Sep 9, 2026
Merged

Sergio-ote merged 4 commits into
devfrom
pseudobulk_improvement

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What & why

Included pseudobulk support for common experimental designs propagated from sample metadata, fixing current support for contrasts between region levels only. Former behavior prevented from performing comparisons when samples belonged entirely to a specific phenotype or region type.

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 changed the title Pseudobulk support for common alternative experimental designs feature: pseudobulk support for common alternative experimental designs Sep 9, 2026
@dgruano
dgruano force-pushed the pseudobulk_improvement branch from 7e82de9 to 8949244 Compare September 9, 2026 18:50
Base automatically changed from style/linting-bug to dev September 9, 2026 19:02
@dgruano
dgruano force-pushed the pseudobulk_improvement branch from 8949244 to ac214bd Compare September 9, 2026 19:02
@Sergio-ote
Sergio-ote merged commit 9bf65a7 into dev Sep 9, 2026
3 checks passed
@Sergio-ote
Sergio-ote deleted the pseudobulk_improvement branch September 9, 2026 20:35
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