nf-core / nf-core/tools

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

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#4,447 4 comments 0 reactions 1 assignee View on GitHub

@JulianFlesch is already working on this.

Since Aug 20, 2026.

bug
Dominant language
Python
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Description

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

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