Bad check on pipelines `modules.json`

[AlexVCaron]

I removed the multiqc module from nf-core from my pipeline to install my own for development purposes. Now, I get this error for no valid reason :

The error disappear once I reinstall the multiqc module from nf-core.

I believe this behavior from the lint test is not the one expected, nor wanted. It is caused by this line in the modules.json lint test, that checks that all repositories listed install modules, which is now not the case for my nf-core after uninstalling multiqc (only subworkflows). I also don't think it's a requirement that makes sense to be enforced.

I'll try to propose a quick PR to fix this if I end up having some time.

[awgymer]

Have you tried just adding multiqc to the skip_features section of your .nf-core.yml?

Alternatively that error does not appear to actually care about multiqc at all? When you say you "removed" it, did you just delete the files for it, or did you actually run nf-core modules remove? If you didn't use that command then the modules.json will still contain the entry for multiqc and cause this error to appear.

Either remove the entry manually, or uninstall modules using the command.