Codecov Report

Merging #1125 (22de883) into dev (4c5720d) will decrease coverage by 0.73%.
The diff coverage is 91.48%.

@@            Coverage Diff             @@
##              dev    #1125      +/-   ##
==========================================
- Coverage   70.57%   69.83%   -0.74%     
==========================================
  Files          48       49       +1     
  Lines        4849     4883      +34     
==========================================
- Hits         3422     3410      -12     
- Misses       1427     1473      +46     

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 4c5720d...22de883. Read the comment docs.

I think maybe don't prompt to create the meta if it's not there? Just fail. As this command is primarily used by automated CI I'm a bit wary of adding user interactivity.

Could potentially create it with --fix testname if we want? To be consistent with the other linting. But to be honest, we already have a commands to create the file so I think a flat fail is fine.

Sorry, for consistency with other tests I think the pattern is to ignore the test if the file isn't there. But then the files_exist test can warn / fail if it's not there.

Maybe we can have a hard fail if there are module files there and no JSON though? That's a bit of a special case.

Okay, leaving the prompt out 👍
Yes we need to somehow annoy the users so that they just go ahead and create the file (which just means running nf-core modules install).

The files_exist test only runs when using nf-core lint, not when running nf-core modules lint, so maybe we still check for the file and then just fail telling the user to create the modules.json file first.

Okay so now it just fails when no modules.json is available, and I actually think that's good because this is an essential file.

And nf-core modules lint should only be run on DSL2 pipelines, which again should have the file.

Thanks for the review @ErikDanielsson !
Yes the lint should fail in these cases. The meta.yml is actually an essential part of every module (not really used, but every module should have it). The modules that don't have meta.yml files are due to us being to lazy to actually add them 👀
So it's good that the linter reminds us to update them.

Alright I also added the load_lint_config() function to the ModulesCommand, who knows maybe it's useful to some other command in the future. Really liking this new code structure! 👍