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.

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?

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

@nf-core-bot fix linting please!