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Centralize pipeline nf-test analysis plans and enable LIANA#293

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nictru merged 1 commit into
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test-analysis-plans
Jun 6, 2026
Merged

Centralize pipeline nf-test analysis plans and enable LIANA#293
nictru merged 1 commit into
devfrom
test-analysis-plans

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@nictru

@nictru nictru commented Jun 6, 2026 •
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Summary

  • Rename tests/analysis_plan_extension.csv to tests/analysis_plan.csv and enable LIANA (paga,liana,de) for the shared scvi/global/0.5 plan row
  • Wire the shared plan into tests/nextflow.config so relevant pipeline nf-tests use it by default
  • Add tests/analysis_plan_sub.csv and switch the subclustering test to scvi with a per-label plan so Leiden/Entropy still run
  • Regenerate affected pipeline test snapshots

Test plan

  • nftu on tests/default.nf.test, tests/main_pipeline_build.nf.test, tests/main_pipeline_extend.nf.test, tests/main_pipeline_reference_mapping.nf.test, tests/main_pipeline_sub.nf.test
  • CI nf-test pipeline checks pass

@nictru
Centralize pipeline nf-test analysis plans and enable LIANA.
fb019af 
Use a shared analysis_plan.csv for pipeline tests to limit downstream work to scvi/global/0.5 with paga, liana, and de, and add a subclustering-specific plan for the scvi per-label test.
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github-actions Bot commented Jun 6, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fb019af

+| ✅ 291 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 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 2026-06-06 13:36:00

@nictru nictru merged commit bcb4c67 into dev Jun 6, 2026
56 checks passed
@nictru nictru deleted the test-analysis-plans branch June 6, 2026 14:37
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