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Allow zero-intercept models in contrasts schema #513

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@grst grst commented Sep 25, 2025 •
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These are valid formulae (0 intercept models) that are not matched by
the current regex:

~ 0 + category

~ category - 1

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@grst
Fix formula regex in contrast schema
e47d96a 
These are valid formulae (0 intercept models) that are not matched by
the current regex:

`~ 0 + category`

`~ category - 1`
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@grst grst changed the base branch from master to dev September 25, 2025 08:50
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grst commented Sep 25, 2025

@nf-core-bot fix linting

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github-actions bot commented Sep 25, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e8d109c

+| ✅ 363 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)
  • schema_description - No description provided in schema for parameter: deseq2_seed

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • nextflow_config - Config default ignored: params.report_file
  • nextflow_config - Config default ignored: params.logo_file
  • nextflow_config - Config default ignored: params.css_file
  • nextflow_config - Config default ignored: params.citations_file
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_dark.png
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-09-25 08:52:55

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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit e47d96a

+| ✅ 364 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   7 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)
  • schema_description - No description provided in schema for parameter: deseq2_seed

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • nextflow_config - Config default ignored: params.report_file
  • nextflow_config - Config default ignored: params.logo_file
  • nextflow_config - Config default ignored: params.css_file
  • nextflow_config - Config default ignored: params.citations_file
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-differentialabundance_logo_dark.png
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-09-25 08:51:02

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@grst @nf-core-bot