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Merged
merged 6 commits into from
Oct 1, 2025
Merged

Skip conda tests that cannot be run due to lacking dependencies #2008

merged 6 commits into from
Oct 1, 2025

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maxulysse
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@maxulysse maxulysse commented Sep 30, 2025 •
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Should only run the tests that are compatible with conda, (using the conda tag) when on conda.

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/sarek 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 Sep 30, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 384bfc4

+| ✅ 225 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-09-30 18:04:40

@maxulysse maxulysse changed the base branch from dev to master September 30, 2025 17:05
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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 @maxulysse,

It looks like this pull-request is has been made against the nf-core/sarek 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/sarek 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!

@maxulysse maxulysse changed the base branch from master to dev September 30, 2025 18:00
matthdsm
matthdsm approved these changes Oct 1, 2025
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🚀

@maxulysse maxulysse merged commit c3ba7da into dev Oct 1, 2025
42 of 44 checks passed
@matthdsm matthdsm deleted the conda_tests_disable branch October 1, 2025 07:12
famosab
famosab reviewed Oct 1, 2025
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I don't see how that would skip the conda tests 🤔

@maxulysse maxulysse mentioned this pull request Oct 1, 2025
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maxulysse added a commit that referenced this pull request Oct 1, 2025
@maxulysse
Conda tests disable again (#2010)
d0316ca 
Continuing on #2008

<!--
# nf-core/sarek pull request

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not
relevant).
These are the most common things requested on pull requests (PRs).

Remember that PRs should be made against the dev branch, unless you're
preparing a pipeline release.

Learn more about contributing:
[CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
-->

## 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](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/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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@famosab famosab famosab left review comments

@matthdsm matthdsm matthdsm approved these changes

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

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3 participants

@maxulysse @matthdsm @famosab