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I've just come across an issue which I'm 100% what's going on, but I think its related to the new JSON schema validation in nf-core/tools 1.13.
Command: nextflow run nf-core/eager -r dev -profile shh,singularity The error: N E X T F L O W ~ version 20.10.0 Launching `nf-core/eager` [Eager2_Gubbio_Iron_Italy_20210326] - revision: c0cb097fa2 [dev] ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/eager v2.3.3dev ------------------------------------------------------ ERROR: Validation of pipeline parameters failed! * --max_time: string [24d 20h 31m 24s] does not match pattern ^[\d\.]+\.*(s|m|h|d)$ (24d 20h 31m 24s)
--max_time is defined in the nf-core/configs under https://github.com/nf-core/configs/blob/26b5904df15ab28edcd4447cfe8e290e7da85a4f/conf/shh.config#L8 as max_time = 720.h
--max_time
max_time = 720.h
However, nextflow on load is resolving this as max_time = '24d 20h 31m 24s'
I can confirm this if I run: nextflow config nf-core/eager -profile shh,singularity
config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs' config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_url = 'https://shh.mpg.de' max_memory = '2 TB' max_cpus = 128 max_time = '24d 20h 31m 24s' }
Maybe the validation check of this values doesn't work if loaded via a config rather than supplied at the CLI/JSON?
Try loading an nf-core/config profile, where --max_time is defined as e.g. 720.h.
The schema REGEX to account for Nextflow-resolved duration objects
The text was updated successfully, but these errors were encountered:
Note, this was originally reported by GitHub newcomer @mrgvanni
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Description of the bug
I've just come across an issue which I'm 100% what's going on, but I think its related to the new JSON schema validation in nf-core/tools 1.13.
--max_time
is defined in the nf-core/configs under https://github.com/nf-core/configs/blob/26b5904df15ab28edcd4447cfe8e290e7da85a4f/conf/shh.config#L8 asmax_time = 720.h
However, nextflow on load is resolving this as max_time = '24d 20h 31m 24s'
I can confirm this if I run: nextflow config nf-core/eager -profile shh,singularity
Maybe the validation check of this values doesn't work if loaded via a config rather than supplied at the CLI/JSON?
Steps to reproduce
Try loading an nf-core/config profile, where
--max_time
is defined as e.g. 720.h.Expected behaviour
The schema REGEX to account for Nextflow-resolved duration objects
System
Nextflow Installation
Additional context
The text was updated successfully, but these errors were encountered: