I can see some CI failures when the YAML schema can't be found. Would I check whether Path(subworkflow.base_dir, "subworkflows/yaml-schema.json") exists and fallback to Path(subworkflow_lint_object.modules_repo.local_repo_dir, "subworkflows/yaml-schema.json") ?

Hi again, I could do some tests, the issue is that you have to provide the git remote in the linting command, like nf-core subworkflows --git-remote https://github.com/<custom_org>/modules.git lint, that way module_lint_object.modules_repo.local_repo_dir will point to the right path

Hi again, I could do some tests, the issue is that you have to provide the git remote in the linting command, like nf-core subworkflows --git-remote https://github.com/<custom_org>/modules.git lint, that way module_lint_object.modules_repo.local_repo_dir will point to the right path

I can confirm it works for subworkflows (I still need to check modules). But I'm still wondering: why is nf-core making a git clone of the remote of the current repository instead of simply using the existing checkout that the user is trying to lint ?

If i understand it correctly, we use this setup to handle multiple remote repositories correctly, so it always compares against the correct one

Alright. I've now removed that part of the change.

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.10%. Comparing base (5081480) to head (ae7ca23).
⚠️ Report is 41 commits behind head on dev.

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