Modules fail linting on pipeline integration

[nikhil]

When we load modules into a pipeline we fail the linting pr-commit checks even though it passed all the linting checks on the module level.

See this for an example: https://github.com/mskcc/NeoAntigen-Pipeline/actions/runs/8622226575/job/23632903027

This is probably because nf-core pipelines ship with a default .editorconfig and we don't have that check on module integration

Probably related to, and possibly fixed by #87

[buehlere]

I had this issue as well.

[anoronh4]

i think you should be able to merge changes from #88 into your dev branch, fix the resulting linting errors and then re-install the modules in your pipeline. you may have to manually run the linting in your branch as i don't think the repo is set up to automatically trigger linting when you're not making a PR to develop or main.

[anoronh4]

i am unfortunately STILL getting some issues with editorconfig in my pipeline, although most are cleaned up. i am making the following modification to my pipeline to make sure installed modules don't cause issues:

https://github.com/mskcc/forte/blob/e826931ad188b33e58febc2a8539bd6757e20399/.editorconfig#L15

i think it makes more sense to just filter these files from the editorconfig check anyways because it's not the responsibility of my pipeline to lint installed modules -- it should be linted in the modules repo.