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Final adjustments to 3.1.0 Release #426

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Merged
jonasscheid merged 2 commits into from
Dec 18, 2025
Merged

Final adjustments to 3.1.0 Release #426

jonasscheid merged 2 commits into from
Dec 18, 2025

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@jonasscheid
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@jonasscheid jonasscheid commented Dec 17, 2025

Dropping testing for conda temporarily since conda env building is unstable currently. Need to wait for conda lock file support

Remove epicore tests due to the tool being under active development and therefore we should reduce this testing overhead.

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/mhcquant 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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nf-core-bot commented Dec 17, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Dec 17, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7487e49

+| ✅ 297 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.1.0
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-12-17 15:10:26

@jonasscheid
Update CHANGELOG with CI testing changes
7487e49 
Temporarily drop conda and epicore testing due to unstable CI tests.
@jonasscheid jonasscheid merged commit f29a8d9 into dev Dec 18, 2025
7 checks passed
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@axelwalter axelwalter axelwalter approved these changes

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

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@jonasscheid @nf-core-bot @axelwalter