We should consider the ability to include or exclude specific files via the .nf-core.yml here. Not clear how we should do this yet but it could be a specific key for the .nf-core.yml:

exclude:
  - .github/workflows/fix-linting.yml
  - .github/workflows/clean-up.yml
include:
  - .github/workflows/ci.yml

This would override the broad categories by the wizard. It could be bypassed when using the TUI for now, consider it an advanced feature.

Originally posted by @adamrtalbot in #3084 (comment)