Skip pre-commit in component directories other than local in template

[prototaxites]

Tools supports installing modules and subworkflows from other remotes than just nf-core, but these components are not excluded from changes when running pre-commit.

I recently ran into a problem where pre-commit was fixing a git diff created by patching a subworkflow, causing a linting failure as the patch was no longer applicable.

This PR excludes all directories inside modules/ and subworkflows/ except local/ from pre-commit in the pipeline template, allowing files from other remotes to remain unchanged.

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

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @prototaxites,

It looks like this pull-request is has been made against the prototaxites/tools main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the prototaxites/tools dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.46%. Comparing base (8a27fac) to head (6bf9ba6).

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