Fix linting for modules.json to add support for only installing subworkflows from a repository

[beatrizsavinhas]

Improve linting for modules.json:

• Add support for repositories from where only subworkflows have been installed since this was currently not allowed.
• Add explicit linting error message for when there are either no modules or subworkflows installed for a repository.
• Add explicit linting error messages for repository links that don't start with "http" - this was an existing check that only returned a general error message.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

❌ Patch coverage is 62.50000% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.35%. Comparing base (4c78254) to head (2c305f9).

Files with missing lines	Patch %	Lines
nf_core/pipelines/lint/modules_json.py	62.50%	6 Missing ⚠️

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[beatrizsavinhas]

This change is arguably out of scope for the PR however I thought it simplified the logic.

[mashehu]

@nf-core-bot fix linting

[github-actions]

⚠️ Cannot proceed with deployment

• reviewDecision: REVIEW_REQUIRED
• commitStatus: null

Your pull request is missing required approvals

[mashehu]

Thanks for the contribution, looks good!
Could you please also add a test case for a modules_json with only subworkflow entries (and one completely empty ones) to tests/modules/test_modules_json.py?

[beatrizsavinhas]

Thanks for the contribution, looks good! Could you please also add a test case for a modules_json with only subworkflow entries (and one completely empty ones) to tests/modules/test_modules_json.py?

Very fair to request tests! We were trying to quickly patch the bug to move on with development. But I'll spend some extra time adding tests as I do agree it would make the codebase better.