error_retry label not recognized as standard label for certain module structures

[Felix-Kummer]

Description of the bug

Running nf-core lint on certain pipelines returns Non-standard labels found: error_retry even though the error_retry label is defined in conf/base.conf.
This behaviour only appears when the modules that have the error_retry label are structured as single .nf file in the modules directory (e.g. modules/local/force-mosaic.nf).
The warning does not appear for modules that are structured using a directory that contains a main.nf file (e.g. modules/local/force-mosaic/main.nf).
An example where this behaviour appears is the rangeland pipeline.

Command used and terminal output

$ nf-core lint

│ force-higher_level              │ modules/local/force-higher_level.nf             │ Non-standard labels found: error_retry                                             │
│ force-preprocess                │ modules/local/force-preprocess.nf               │ Non-standard labels found: error_retry                                             │
│ higher_level_force_config       │ modules/local/higher_level_force_config.nf      │ Non-standard labels found: error_retry                                             │
│ merge                           │ modules/local/merge.nf                          │ Non-standard labels found: error_retry                                             │
│ preprocess_force_config         │ modules/local/preprocess_force_config.nf        │ Non-standard labels found: error_retry

System information

nextflow version 24.04.4.5917
nf-core/tools version 2.14.1
Local executor on Ubuntu Linux

[mirpedrol]

Hi @Felix-Kummer, thanks for reporting. This linting test checks the nf-core standard labels. We should skip the tests for local modules, as you can add custom labels as in your case.

[Felix-Kummer]

But error_retry is defined in the templates conf/base.conf. Shouldn't that be a standard label?
The bug/issue is likely related to the structure of local modules.
If they have a separate directory under modules/local (e.g. modules/local/force-mosaic/main.nf instead of modules/local/force-mosaic.nf) the warning does not appear.
The warning only appearing for local modules that don't have this structure suggest that the linter evaluates linting tests differently for different directory structures.

I get that having a separate directory and a main.nf file is the preferred structure but its not strictly enforced anywhere.
The question is whether structures like modules/local/force-mosaic/main.nf should still be allowed.