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Merged
erikrikarddaniel merged 1 commit into from
Oct 21, 2025
Merged

Update snapshots #162

erikrikarddaniel merged 1 commit into from
Oct 21, 2025

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@erikrikarddaniel erikrikarddaniel commented Oct 20, 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).

I don't know what you're doing, @danilodileo

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github-actions bot commented Oct 20, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9e04d7c

+| ✅ 244 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 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
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/magmap/magmap/subworkflows/local/fastqc_trimgalore/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • 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 2025-10-20 18:23:27

danilodileo
danilodileo approved these changes Oct 21, 2025
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Tests work now! Only one is failing though. Certainly I am not updating my snapshots correctly.

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erikrikarddaniel commented Oct 21, 2025 •
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Tests work now! Only one is failing though. Certainly I am not updating my snapshots correctly.

The one that failed was cancelled, so I think all are safe. Let's hope this happens also for the main PR.

@erikrikarddaniel erikrikarddaniel merged commit cf368c6 into nf-core:nf-core-template-merge-3.4.1 Oct 21, 2025
16 of 18 checks passed
@erikrikarddaniel erikrikarddaniel deleted the nf-core-template-merge-3.4.1 branch October 21, 2025 06:42
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