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Update utils_nfschema_pipeline to allow --help#967

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jfy133 merged 1 commit intodevfrom
update-utils-subworkflow
Jan 25, 2026
Merged

Update utils_nfschema_pipeline to allow --help#967
jfy133 merged 1 commit intodevfrom
update-utils-subworkflow

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@jfy133 jfy133 commented Jan 25, 2026

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/mag 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).

@jfy133 jfy133 marked this pull request as ready for review January 25, 2026 13:27
@jfy133 jfy133 changed the title Update utils_nfcore_pipeline for strict purposes syntax Update utils_nfschema_pipeline to allow --help Jan 25, 2026
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github-actions Bot commented Jan 25, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 63468a1

+| ✅ 382 tests passed       |+
#| ❔   1 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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 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 nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-25 13:30:16

@jfy133 jfy133 merged commit 3cbc2a6 into dev Jan 25, 2026
22 checks passed
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@dialvarezs dialvarezs dialvarezs approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

@prototaxites prototaxites Awaiting requested review from prototaxites prototaxites is a code owner

@muabnezor muabnezor Awaiting requested review from muabnezor muabnezor is a code owner

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