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dev -> main for 4.0.1#4247

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mashehu merged 21 commits intomainfrom
dev
Apr 29, 2026
Merged

dev -> main for 4.0.1#4247
mashehu merged 21 commits intomainfrom
dev

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@mashehu mashehu commented Apr 29, 2026

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SPPearce and others added 20 commits April 28, 2026 10:29
@SPPearce
Allow task.ext.prefix2
2196f07
@SPPearce
Update Changelog
e7cc0c6
@SPPearce
Only allow prefix2, and check prefix1 doesn't pass
6b39258
@SPPearce
Implement Mahesh's comments
dc9808a
@mashehu
bump to 4.0.1
dd99571
@mashehu
Merge pull request #4237 from mashehu/bump-to-4.0.1
33d9944
@mashehu @nf-core-bot
fix failing api doc generation script (#4239)
a6f5d77 
Co-authored-by: nf-core-bot <core@nf-co.re>
@mashehu @nf-core-bot
use non-strict-syntax nextflow version for sync (#4236)
38e896a 
Co-authored-by: nf-core-bot <core@nf-co.re>
@renovate
Update dawidd6/action-download-artifact action to v21 (#4240)
ac6d1fe 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@mashehu @nf-core-bot
handle prek not being exposed to $PATH (#4238)
1d3bdda 
Co-authored-by: nf-core-bot <core@nf-co.re>
@SPPearce
Add invalid keys into the test
8eb4913
@SPPearce
Merge remote-tracking branch 'origin/dev' into prefix2
b7c639d
@SPPearce
Merge in dev and fix Changelog
b0af01e
@renovate @nf-core-bot @mashehu
Update j178/prek-action digest to 6ad8027 (#4244)
93221e4 
* Update j178/prek-action digest to 6ad8027

* [automated] Update CHANGELOG.md

* Apply suggestion from @mashehu

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@nf-core-bot
[automated] Update CHANGELOG.md
1660c42
@SPPearce
Merge branch 'dev' into prefix2
8a653c3
@SPPearce
Merge pull request #4234 from nf-core/prefix2
7071315 
Allow task.ext.prefix2 in modules linting
@mashehu @nf-core-bot
switch changelog bot trigger only on comments (#4241)
6e00316 
Co-authored-by: nf-core-bot <core@nf-co.re>
@mashehu @nf-core-bot
fix indentation in generated api docs (#4245)
9aaec84 
Co-authored-by: nf-core-bot <core@nf-co.re>
@mashehu
bump to 4.0.1 (#4246)
0783bbf
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codecov Bot commented Apr 29, 2026 •
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Codecov Report

❌ Patch coverage is 87.50000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 77.80%. Comparing base (37394a9) to head (9cf0b98).
⚠️ Report is 24 commits behind head on main.

Files with missing lines Patch % Lines
nf_core/pipelines/lint_utils.py 85.71% 1 Missing ⚠️

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@mashehu mashehu merged commit d61f919 into main Apr 29, 2026
199 of 209 checks passed
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@JulianFlesch JulianFlesch JulianFlesch approved these changes

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@mashehu @JulianFlesch @SPPearce @nf-core-bot