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Fix modules meta.yml file structure #3532

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Merged
merged 21 commits into from
Jul 7, 2025

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mirpedrol
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@mirpedrol mirpedrol commented Apr 7, 2025

Close: #3248

Code to fix/update:

@mirpedrol mirpedrol marked this pull request as ready for review April 17, 2025 09:29
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The modules from GitLab, which we use for the CI tests, need to be fixed. But fixing this will break all other tools' tests. So I will mark the PR for review and fix the tests right before merging.
This should be a coordinated merge together with the PR on the website and the modules repo + an additional PR updating all modules to avoid linting errors there (the modules repo uses the dev version). And I would do all this before the release, to prevent people contributing to modules from having to use the dev version of tools.

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didn't we want to do this with pydantic?

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didn't we want to do this with pydantic?

Yes! I have been trying, but I can't find a way to use the ruamel.yaml.comments.CommentedMap type, which we need to add and maintain comments in the template.
I have followed the Pydantic docs on handling third-party types, but this will validate the CommentedMap and always return a dict, and we can't add comments to a dict. Do you know of a way to use CommentedMap?

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mashehu commented May 6, 2025

can you make a new branch with the pydantic approach, so that I can have a look?

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@nf-core-bot fix linting please!

mirpedrol and others added 3 commits June 30, 2025 16:14
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
@mirpedrol mirpedrol merged commit 47e667d into nf-core:dev Jul 7, 2025
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