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Add linting for meta and ext keys#4127

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mashehu merged 15 commits into
nf-core:devfrom
mahesh-panchal:feat/ext-linting
Mar 25, 2026
Merged

Add linting for meta and ext keys#4127
mashehu merged 15 commits into
nf-core:devfrom
mahesh-panchal:feat/ext-linting

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@mahesh-panchal

@mahesh-panchal mahesh-panchal commented Mar 20, 2026 •
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Description

Adds linting checks for meta and ext maps in the script section.

Closes #2537
Closes #4112

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

@codecov

codecov Bot commented Mar 20, 2026 •
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Codecov Report

❌ Patch coverage is 90.90909% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 78.48%. Comparing base (aa3c3d0) to head (2f769dc).
⚠️ Report is 1 commits behind head on dev.

Files with missing lines Patch % Lines
nf_core/modules/lint/main_nf.py 90.90% 1 Missing ⚠️

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@mahesh-panchal

mahesh-panchal commented Mar 20, 2026

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@nf-core-bot changelog

@mahesh-panchal mahesh-panchal marked this pull request as ready for review March 20, 2026 14:45
@mahesh-panchal mahesh-panchal mentioned this pull request Mar 20, 2026
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@mahesh-panchal mahesh-panchal requested a review from mashehu March 20, 2026 15:21
@mahesh-panchal mahesh-panchal marked this pull request as draft March 21, 2026 07:29
@mahesh-panchal

mahesh-panchal commented Mar 21, 2026 •
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I don't see where I am supposed to write tests. ( and sorry for the commit spam ...)

And need to know what's permitted with meta. Is meta\d* enough, or do I need meta\w*

@mahesh-panchal mahesh-panchal marked this pull request as ready for review March 21, 2026 07:36
@jfy133

jfy133 commented Mar 22, 2026 •
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Answer is here: https://nfcore.slack.com/archives/C043UU89KKQ/p1774078044671669

Only allow meta, meta2, meta3 etc.

Related docs PR: https://github.com/nf-core/website/pull/4080/changes

@mahesh-panchal

mahesh-panchal commented Mar 24, 2026

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Tests added

@mashehu

mashehu commented Mar 24, 2026

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simplified the code a bit. Hope that was okay 🙂

@mahesh-panchal

mahesh-panchal commented Mar 25, 2026

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It's fine by me. I wouldn't call it simpler, just shorter, but then I'm not so experienced in Python.

@mashehu mashehu enabled auto-merge (squash) March 25, 2026 11:34
@mashehu mashehu merged commit 635784c into nf-core:dev Mar 25, 2026
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This was referenced Mar 27, 2026
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@mahesh-panchal @jfy133 @mashehu @nf-core-bot