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nf-core / tools

Python package with helper tools for the nf-core community.
https://nf-co.re
MIT License
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error_retry label not recognized as standard label for certain module structures #3160

Open Felix-Kummer opened 1 week ago

Felix-Kummer commented 1 week ago

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 commented 5 days ago

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.