[Feature Request] Configuration file to enable/disable a set of linting rules or skip individual files/directories

[kgalens]

It would be very useful to be able to configure a set of linting rules which should be applied via a configuration file. The nf-core lint has something similar with a .nf-core.yml and python projects are configured via pyproject.toml files. This should allow users/organizations to customize the rules they see as important or ignore any linting rules which they need. Keeping them in a configuration file allows these to be shared across an organization, keeping local development consistent.

Having a dedicated configuration file can be helpful when setting up linting for the first time in CI and gradually updating Nextflow files to adhere to the linting rules. This allows a user to activate a single rule at a time, update the Nextflow files to pass these rules and then require that any future commits meet these requirements. It also allows organizations to ignore linting rules they may not care about.

It would also be great to see a list of rules checked by nextflow lint command (similar to this page for nf-core lint or even better, a set of rules, with description and suggested fixes, such as this page from ruff,

[bentsherman]

Duplicate of nextflow-io/nextflow#5934

Feel free to join the discussion there!