Schema validation of time resources doesn't work when param loaded from config #973
Description
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.
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
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?
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
- Hardware: HPC
- Executor: SLURM
- OS: Ubuntu 18.04
- Version of nf-core/tools:
Nextflow Installation
- Version: 20.10.0