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Linting of patched subworkflows #3755

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Merged
Parent: dev -> main for 3.4.1
merged 7 commits into from
Sep 30, 2025
Merged

Linting of patched subworkflows #3755

merged 7 commits into from
Sep 30, 2025

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@muffato
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@muffato muffato commented Sep 13, 2025 •
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Hello,

One of our pipelines had a faulty subworkflow patch and I investigated why it wasn't reported by nf-core pipelines lint.

The main problem is that the LookupError was ignored. I don't know what "This error is already reported by subworkflow_patch" is referring to. It certainly wasn't working ! So here I propose to directly log an error.

The other problem is I think unrelated, but I found that while debugging. As far as I can tell, self.meta cannot be False. It can be None, though.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@muffato muffato self-assigned this Sep 13, 2025
@muffato muffato added bug Something isn't working subworkflows labels Sep 13, 2025
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codecov bot commented Sep 13, 2025 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.33%. Comparing base (26b7b10) to head (b682f79).
⚠️ Report is 29 commits behind head on dev.

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@muffato muffato changed the title Subworkflow patch Linting of patched subworkflows Sep 13, 2025
@muffato muffato marked this pull request as ready for review September 13, 2025 23:42
@muffato muffato mentioned this pull request Sep 14, 2025
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mashehu
mashehu approved these changes Sep 30, 2025
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nice work!

@muffato muffato merged commit 7ba3e5e into dev Sep 30, 2025
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@muffato muffato deleted the subworkflow_patch branch September 30, 2025 08:58
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