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Warn when reference models are used with per-label integration#299

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sub-reference-warning
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Warn when reference models are used with per-label integration#299
nictru wants to merge 1 commit into
devfrom
sub-reference-warning

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@nictru

@nictru nictru commented Jun 26, 2026

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Summary

  • Log a warning in SUB_INTEGRATE when integrate_per_label is enabled together with a reference model (scvi_model, scanvi_model, scimilarity_model, or symphony_reference), since query mapping bypasses per-group training and can yield identical embeddings across label groups.
  • Validate integrate_per_label_whitelist against obs[split_col] via nf-anndata before SPLITCOL, instead of relying on post-split subset filenames.

Test plan

  • nf-test test --profile +apptainer subworkflows/local/sub_integrate/tests/main.nf.test

@nictru
Warn on reference models during per-label integration and validate wh…
4f516f7 
…itelist upfront.

Reference mapping bypasses per-group training, so log a warning when model checkpoints are provided alongside integrate_per_label. Validate integrate_per_label_whitelist against obs before SPLITCOL using nf-anndata.
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github-actions Bot commented Jun 26, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4f516f7

+| ✅ 298 tests passed       |+
#| ❔   1 tests had warnings |#
!| ❗  15 tests had warnings |!
Details

❗ 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • 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
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-26 14:26:45

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