modules.json - inconsistent formatting across functions

[CormacKinsella]

Description of the bug

Currently nf-core modules update runs prettier on modules.json, but for example modules patch does not.

For git history this leads to problems with actually viewing the diffs, as git sees it as the entire file being rewritten. Is there a reason for the inconsistent usage of prettier, or could it just be made the default?

Currently dump has a false default:

    def dump(self, run_prettier: bool = False) -> None:

And prettier is selectively run sporadically elsewhere in the code.

[mashehu]

the main problem is that we sometimes write the file multiple times (e.g. when installing dependencies of a subworkflow) and applying prettier on it slows this down by quite a bit. But thanks for pointing out the specific case of inconsistency, it should always run at the end and we probably missed that for the patch command

[CormacKinsella]

Gotcha, that makes sense. Cheers for the reply!