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Update help_text formatting for spades and megahit options#994

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jfy133 merged 1 commit intodevfrom
improve-spades-options-docs
Mar 10, 2026
Merged

Update help_text formatting for spades and megahit options#994
jfy133 merged 1 commit intodevfrom
improve-spades-options-docs

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@jfy133 jfy133 commented Mar 10, 2026

Improve *_options docs

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 March 10, 2026 08:52
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github-actions Bot commented Mar 10, 2026 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 07e3634

+| ✅ 382 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 5.4.1
  • 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 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:

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

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-03-10 08:55:01

@jfy133 jfy133 merged commit 220e272 into dev Mar 10, 2026
9 checks passed
@jfy133 jfy133 deleted the improve-spades-options-docs branch March 10, 2026 13:29
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jfy133 commented Mar 10, 2026

Thanks @prototaxites !

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@prototaxites prototaxites prototaxites approved these changes

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

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

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

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