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update nf-schema#22

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di-hardt merged 1 commit into
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fix-cli
Jun 9, 2026
Merged

update nf-schema#22
di-hardt merged 1 commit into
devfrom
fix-cli

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@di-hardt

@di-hardt di-hardt commented May 21, 2026

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fix CLI parameter validation

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/mspepid branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

@di-hardt di-hardt requested a review from julianu May 21, 2026 15:08
@github-actions

github-actions Bot commented May 21, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8537bd1

+| ✅ 195 tests passed       |+
#| ❔   6 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  23 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • 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 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 README.md: If applicable, make list of people who have also contributed
  • 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 CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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 meta.yml: # Add a description of the module and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as input
  • pipeline_todos - TODO string in meta.yml: ##Add a description of all of the variables used as output
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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!

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-05-21 15:09:28

@julianu

julianu commented May 21, 2026

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Fine for me

@di-hardt di-hardt merged commit 6b5c623 into dev Jun 9, 2026
9 checks passed
@julianu julianu deleted the fix-cli branch June 9, 2026 11:35
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@julianu julianu julianu approved these changes

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@di-hardt @julianu