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Linting: Addressing more cases than can happen when processing input and output values #3541

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Merged
merged 9 commits into from
May 8, 2025
Merged

Linting: Addressing more cases than can happen when processing input and output values #3541

merged 9 commits into from
May 8, 2025

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toniher
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@toniher toniher commented Apr 23, 2025

Coming from #3530

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All modified and coverable lines are covered by tests ✅

Project coverage is 76.36%. Comparing base (742897d) to head (622ace0).
Report is 31 commits behind head on dev.

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@toniher toniher requested a review from mirpedrol April 23, 2025 14:45
mashehu
mashehu reviewed Apr 24, 2025
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please add test cases for this changes, so we don't run into this again 🙂

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toniher commented Apr 24, 2025

please add test cases for this changes, so we don't run into this again 🙂

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Testing for inputs existing modules such as trinity https://github.com/nf-core/modules/blob/d802effd844103fcc5e233184f95c84026ed44d6/modules/nf-core/trinity/main.nf#L12 and for output ones such as trimgalore https://github.com/nf-core/modules/blob/d802effd844103fcc5e233184f95c84026ed44d6/modules/nf-core/trimgalore/main.nf#L14 I think could be enough. Actually, thanks to the trimgalore already present

tools/tests/modules/test_lint.py

Line 181 in 52e8109

def test_modules_lint_trimgalore(self):
I noticed that something was wrong. Can you point me if simply adding in test/modules/test_lint.py a function for trinity could be enough for triggering the test? Should anything else be added as well somewhere else? (This is my first time adding a nf-core tool test). Thx!

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toniher commented May 5, 2025

@nf-core-bot update changelog

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toniher commented May 5, 2025

@mashehu @mirpedrol I added a trinity module test for linting. I suspect it went through, but I am not fully sure from Github actions outcomes. Let me know!

@toniher toniher requested a review from mashehu May 5, 2025 16:21
mirpedrol
mirpedrol approved these changes May 7, 2025
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Hello @toniher, sorry for the late reply. The test you added looks good 🙂 I think it is ready to merge 👍

@mirpedrol mirpedrol changed the title Addressing more cases than can happen when processing input and output values Linting: Addressing more cases than can happen when processing input and output values May 7, 2025
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@nf-core-bot changelog

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merging this now! I hope it's ok 😄

@mirpedrol mirpedrol merged commit e5ec63b into nf-core:dev May 8, 2025
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@mirpedrol mirpedrol mirpedrol approved these changes

@mashehu mashehu Awaiting requested review from mashehu

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@toniher @mirpedrol @mashehu @nf-core-bot
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