Felix Kummer
08/29/2024, 8:54 AMerror_retry label to some of my modules. The heads of these modules look like this now:
process FORCE_HIGHER_LEVEL {
tag { tile }
label 'process_medium'
label 'error_retry'
When linting the pipeline, every module that has the error_retry label produces this warning:
force-higher_level │ modules/local/force-higher_level.nf │ Non-standard labels found: error_retry
The error_retry is defined in the template's base.config file, so I assumed that it would be a standard label.
Am I misunderstanding the usage of error_retry or is that a bug in nf-core lint?Sateesh_Peri
09/06/2024, 9:42 AMSateesh_Peri
09/06/2024, 9:42 AMFelix Kummer
09/06/2024, 9:49 AMnf-core/tools version 2.14.1
Just pushed the changes to our fork: https://github.com/CRC-FONDA/nf-core-rangelandSateesh_Peri
09/06/2024, 10:10 AMSateesh_Peri
09/06/2024, 10:23 AMFelix Kummer
09/06/2024, 10:34 AMerror_retry label.
Adding a local module with the label to methylseq produces the same warning for me.
Adding the label to a nf-core module does not produce the warning (but rather the error: "Local copy of module does not match remote")
Seems to be related to local modules?Sateesh_Peri
09/06/2024, 10:35 AMSateesh_Peri
09/06/2024, 10:36 AMSateesh_Peri
09/06/2024, 10:36 AMSateesh_Peri
09/06/2024, 10:39 AMFelix Kummer
09/06/2024, 10:40 AMFelix Kummer
09/06/2024, 10:55 AM.nf file, e.g. modules/local/force-mosaic.nf
It seems to be a standard that the modules are organized like this: modules/local/force-mosaic/main.nf
Is the latter enforced by nf-core? The guidelines appear vague on that.Felix Kummer
09/06/2024, 11:02 AMFelix Kummer
09/06/2024, 11:21 AMSateesh_Peri
09/06/2024, 11:23 AMmodules/local/force-mosaic/main.nf as soon you will be expected to have a tests/ sub-folder along with the main of each module