`nf-core pipelines lint` silently suppresses all module linting on error.

[awgymer]

Description of the bug

If you run nf-core pipelines lint on a pipeline which has anything in its module directory which causes module linting to fail then the module linting is totally suppressed from the output with no obvious indication it failed or why.

An easy example to trigger this is to remove the meta.yml from one of the nf-core modules in the pipeline.

• pipelines lint: suppresses error
• modules lint: FileNotFoundError: meta.yml not found at modules/nf-core/repeatmodeler/repeatmodeler/meta.yml

Other examples that can cause this:

• failed patch application
• error in any local module

Command used and terminal output

System information

No response

[JulianFlesch]

Thanks for writing the issue!
I am working on it here: #4450

... causes module linting to fail then the module linting is totally suppressed

I could only find one instance so far where an issue with a module blocks the linting and it is exactly the one you describe and I addressed in the PR: If a module has no meta.yml the linter surfaced an exception instead of trying to proceed gracefully.

Do you have other examples?

[awgymer]

Did you try breaking a local module?

For example split an output tuple across two lines and then run pipelines lint.

For the patch failure you need to make a patch that is outdated for the module and then try running the linting. This will cause the module to fail I believe.