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Configure the default module repository, branch, and path from environment variables. #3481

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edanielson-ginkgo
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@edanielson-ginkgo edanielson-ginkgo commented Mar 5, 2025

Add the ability to configure the default modules repo, branch, and name as environment variables.

Context:
Within our org, we're looking to build an nf-core-style module repository in Gitlab - this is possible with the command line flags, but it's a hassle to set --git-branch every time we run a module command.

This PR adds the ability to set NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, and NF_CORE_MODULES_DEFAULT_BRANCH as environment variables, defaulting to the existing constants for those values if the variables are not set.

I took a quick look for other similar constants, but didn't see any, nor did I find an existing config file or object - if I missed something, let me know and I'll be happy to update this.

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

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codecov bot commented Mar 6, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.50%. Comparing base (67146de) to head (b221780).
Report is 23 commits behind head on dev.

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@mirpedrol mirpedrol left a comment

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LGTM, thanks!

We should also update the documentation here

@edanielson-ginkgo
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Thanks! Looks like docs for that are here:
https://github.com/nf-core/website/blob/main/sites/docs/src/content/docs/nf-core-tools/custom_remotes.md
I'm happy to contribute verbiage, but what's the preferred flow for that? Doesn't look like there's a dev branch or similar concept on that repo.

@edanielson-ginkgo edanielson-ginkgo merged commit f7207a5 into nf-core:dev Mar 6, 2025
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3 participants