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avoid empty ch_versions in trimagalore subworkflow #171

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Merged
danilodileo merged 6 commits into from
Nov 12, 2025
Merged

avoid empty ch_versions in trimagalore subworkflow #171

danilodileo merged 6 commits into from
Nov 12, 2025

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@danilodileo danilodileo commented Nov 12, 2025

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/magmap 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).
  • 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).

with the combination of parameters

´skip_qc´, ´skip_fastqc´and/or ´skip_trimming` the pipeline failed because the ch_versions gets empty.

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github-actions bot commented Nov 12, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ff58c77

+| ✅ 244 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • 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.
  • pipeline_todos - TODO string in README.md: If you use nf-core/magmap for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX Add bibliography of tools and data used in your pipeline
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-12 14:34:51

erikrikarddaniel
erikrikarddaniel reviewed Nov 12, 2025
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No test case!

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erikrikarddaniel commented Nov 12, 2025

The tests are failing. It looks funny, because the first test diff is missing TRIMGALORE among the versions and that should not have changed.

erikrikarddaniel
erikrikarddaniel approved these changes Nov 12, 2025
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👍

@danilodileo @erikrikarddaniel
Update workflows/magmap.nf
ff58c77 
Co-authored-by: Daniel Lundin <[email protected]>
@danilodileo danilodileo merged commit d82edf9 into nf-core:dev Nov 12, 2025
16 of 18 checks passed
@danilodileo danilodileo mentioned this pull request Nov 12, 2025
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