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Add per-label integration for sub mode#294

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per-group-integration
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Add per-label integration for sub mode#294
nictru wants to merge 1 commit into
devfrom
per-group-integration

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@nictru

@nictru nictru commented Jun 7, 2026

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Summary

  • Add --integrate_per_label for base-adata-only sub mode to split by base_label_col and reuse the existing INTEGRATE subworkflow per label.
  • Preserve per-label metadata through integration and clustering so outputs can be merged back into a single finalized AnnData.
  • Add focused nf-test coverage for the new subworkflow and an end-to-end pipeline case using nft-anndata.

Test plan

  • nftu subworkflows/local/sub_integrate/tests/main.nf.test
  • nft subworkflows/local/sub_integrate/tests/main.nf.test
  • nft tests/main_pipeline_sub_integrate_per_label.nf.test

@nictru
Add per-label integration for sub mode
ba38533 
Reuse the existing integration workflow after splitting base AnnData labels so sub-mode runs can create per-label embeddings in the combined output.
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github-actions Bot commented Jun 7, 2026

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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit ba38533

+| ✅ 293 tests passed       |+
#| ❔   1 tests had warnings |#
!| ❗  15 tests had warnings |!
-| ❌   1 tests failed       |-
Details

❌ Test failures:

  • nf_test_content - 'tests/main_pipeline_sub_integrate_per_label.nf.test' does not snapshot a 'versions.yml' file

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-07 10:38:32

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