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Prerelease 3.19.0 fixes#1567

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pinin4fjords merged 2 commits into
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prerelease_3.19.0_fixes
Jun 10, 2025
Merged

Prerelease 3.19.0 fixes#1567
pinin4fjords merged 2 commits into
devfrom
prerelease_3.19.0_fixes

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@pinin4fjords pinin4fjords commented Jun 10, 2025

Fixes from PR review of #1564

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/rnaseq 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).

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github-actions Bot commented Jun 10, 2025

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@pinin4fjords pinin4fjords requested a review from mashehu June 10, 2025 09:09
@pinin4fjords pinin4fjords changed the base branch from master to dev June 10, 2025 09:09
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github-actions Bot commented Jun 10, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 79ce41a

+| ✅ 277 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  10 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 3.19.0
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 base.config: Check the defaults for all processes
  • pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-10 09:13:21

@pinin4fjords pinin4fjords enabled auto-merge June 10, 2025 09:13
@pinin4fjords pinin4fjords merged commit 3ea471b into dev Jun 10, 2025
34 checks passed
@pinin4fjords pinin4fjords deleted the prerelease_3.19.0_fixes branch June 10, 2025 09:33
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@maxulysse maxulysse maxulysse approved these changes

@mashehu mashehu mashehu approved these changes

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