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Implement review suggestions 2 - #89

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delfiterradas merged 6 commits into
nf-core:devfrom
delfiterradas:review_dev
Sep 9, 2026
Merged

Implement review suggestions 2#89
delfiterradas merged 6 commits into
nf-core:devfrom
delfiterradas:review_dev

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@delfiterradas

@delfiterradas delfiterradas commented Sep 8, 2026 •
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Implement suggestions from #88 for first release. These changes include:

  • Clean code, delete unused files
  • Update metro plot using nf-metro
  • Modify CHANGELOG.md to mention implemented features
  • Improve samplesheet.csv
  • Add --help text
  • Modify icons for params in schema file

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/datasync branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core 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).

@delfiterradas delfiterradas self-assigned this Sep 8, 2026
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github-actions Bot commented Sep 8, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 89905cb

+| ✅ 204 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • 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.

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-09-09 13:52:12

@delfiterradas delfiterradas mentioned this pull request Sep 8, 2026
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@delfiterradas
delfiterradas marked this pull request as ready for review September 9, 2026 12:01
atrigila
atrigila approved these changes Sep 9, 2026
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Remember to add in the PR body issue why these changes are happening or link which is the review suggestion.

Comment thread CHANGELOG.md Outdated
@delfiterradas
delfiterradas merged commit d2afa32 into nf-core:dev Sep 9, 2026
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@delfiterradas delfiterradas changed the title Implement review suggestions Implement review suggestions 2 Sep 9, 2026
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