Preserve the value of self.modules_repo across nested calls

[muffato]

Fixes #3876

I think this is all that is needed to fix #3876. I ran the four commands listed in the issue and pipelines lint now works.

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

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.41%. Comparing base (c9d3b76) to head (eae5c97).
⚠️ Report is 14 commits behind head on dev.

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[prototaxites]

I have tested it, and it does seem to work correctly. The modules.json file is correct and subworkflow installation and linting work without failure.

[mashehu]

nice, could we have a test for this, so we don't run into the same thing in the future?

[mirpedrol]

LGTM, thanks!
I agree with @mashehu that we should add a test for this before merging 🙂

[muffato]

Test added and passing.

Requires nf-core-test/modules#4 to be merged and the last commit to be removed before merging

[prototaxites]

Hi all, wondering if we would be able to squeeze this one into 3.5.0 as well? I am encountering this bug working on my pipeline and it would be good to be able to install the required subworkflows correctly!

[muffato]

Thanks. nf-core-test/modules#4 should probably be approved too (although technically main isn't protected there, and I could merge it without a review)

[muffato]

Thank you !