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samplesheet schema pattern fix, and end-to-end snapshot updated#58

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vagkaratzas merged 1 commit into
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bug-fix-shcema-pattern
Dec 1, 2025
Merged

samplesheet schema pattern fix, and end-to-end snapshot updated#58
vagkaratzas merged 1 commit into
devfrom
bug-fix-shcema-pattern

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@vagkaratzas

@vagkaratzas vagkaratzas commented Dec 1, 2025

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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/proteinannotator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (e.g. nf-test test */local --profile=~test,docker for all new local tests).
  • Check for unexpected warnings in debug mode (nf-test test */local --profile=~test,docker,debug).
  • 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).
    • docs/images/proteinannotator-metromap.light.excalidraw.png and docs/images/proteinannotator-metromap.light.excalidraw.png (edit the light version only, then export and turn on dark mode) are both updated (use the excalidraw website or VS Code plugin to edit)

@github-actions

github-actions Bot commented Dec 1, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ce0e0bc

+| ✅ 195 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/ci.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-proteinannotator_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-12-01 13:34:33

mirpedrol
mirpedrol approved these changes Dec 1, 2025
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@mirpedrol mirpedrol left a comment

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LGTM :)

@vagkaratzas vagkaratzas merged commit 850b37b into dev Dec 1, 2025
7 checks passed
@vagkaratzas vagkaratzas deleted the bug-fix-shcema-pattern branch December 1, 2025 13:42
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@mirpedrol mirpedrol mirpedrol approved these changes

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@vagkaratzas @mirpedrol