…an flag

Co-authored-by: Júlia Mir Pedrol <[email protected]>

utils.get_wf_files has logic for parsing .gitignore files and using the
patterns there as an ignore list, but it doesn't implement the full semantics
of gitignore patterns. This change adds support for trailing slash which should
ignore an entire directory, which is important as such patterns are included in
the pipeline TEMPLATE .gitignore.

Also, relative path handling is implemented in the ignore pattern checking.
This means ignore patterns still work correctly when the -d option is given to
lint a directory other than the current one.

Finally, .git/* is added as an implicit ignore pattern that is always in
effect.

Co-authored-by: Júlia Mir Pedrol <[email protected]>

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <[email protected]>

…bworkflows

Preserve the value of self.modules_repo across nested calls

Co-authored-by: nf-core-bot <[email protected]>

Linting: Add linting of topics

Co-authored-by: Matthias Zepper <[email protected]>

* chore(deps): update actions/checkout digest to 93cb6ef

* [automated] Update CHANGELOG.md

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: nf-core-bot <[email protected]>

Co-authored-by: nf-core-bot <[email protected]>

Co-authored-by: Júlia Mir Pedrol <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>

Improve file ignores in workflow file enumeration

Co-authored-by: Júlia Mir Pedrol <[email protected]>
Co-authored-by: nf-core-bot <[email protected]>

Enable CI tests for pipelines/download

Co-authored-by: nf-core-bot <[email protected]>

Update pipeline creation information page to be more exclusive as to what should use the full nf-core pipeline template