Fix modules meta.yml file structure

[mirpedrol]

Close: #3248

Code to fix/update:

• The module template
• Running nf-core modules create
• When running nf-core modules lint with the --fix argument
• In the website, when showing the inputs and outputs of modules (Handle new meta yaml structure website#3304)
• The JSON schema from nf-core/modules must be updated (Update modules meta-schema.json modules#8226)
• All modules meta.yml must be fixed (can be done with a bulk PR by running nf-core modules lint --fix --all)
• Add tests

[mirpedrol]

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.

[mashehu]

Suggested change

	elif len(channel_elements) > 0:
	elif len(channel_elements) == 0:

[mirpedrol]

Would be == 1 if we want to use the equal 😄

Suggested change

	elif len(channel_elements) > 0:
	elif len(channel_elements) == 1:

[mashehu]

didn't we want to do this with pydantic?

[mashehu]

wrong path

[mirpedrol]

oops thanks! I was testing and missed that I pushed it