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

[edanielson-ginkgo]

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

[codecov]

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]

LGTM, thanks!

We should also update the documentation here

[edanielson-ginkgo]

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.

[mashehu]

Sorry just saw this PR now. We use click for our CLI, which automatically conversats environment variables to parameters, eg. NFCORE_GIT_BRANCH in your case https://click.palletsprojects.com/en/stable/options/

[edanielson-ginkgo]

Oh, interesting - can you point me to that in the code? The docs on Click suggest that's an option you can set, but it doesn't seem to be working for me by default - IOW, setting NFCORE_GIT_REMOTE (to match the --git-remote flag) doesn't affect the CLI's behavior.

I'm happy to open a new PR to switch to defaulting the behavior on Click, if that's the preferred method.