https://nf-co.re logo
Join Slack
Powered by
Is there a way to overwrite a label of a module in...
# configs
t
Is there a way to overwrite a label of a module in a config? Like overwriting the default label of process in 
modules.config
or something? Any example?
p
Yes, it's possible but doesn't do what most people expect and is almost always the wrong thing to do. What do you want to do?
t
FASTP by default (of the nf-core process) is a medium size job
However, 6 threads break the CI runner.
So I'd like to downsize the resources.
process {
withName: 'FASTP' {
resourceLimits = [
cpus: 4
]
}
}
doesn't work 😕
p
In most cases, 
resourceLimits
would be a "site" configuration and it makes more sense to put it in 
process
without qualifiers.
Not that I see why that shouldn't work, but you should equally be able to set the resource directly.
But is it really the CPU resources and not the memory limit that is the problem?
But also good to check that the match really works.
t
yes
Copy code
> Caused by:
    >   Process requirement exceeds available CPUs -- req: 6; avail: 4
p
But as for the "set a label"; any new label you set won't lead to those resources being applied. Set the resources explicitly.
t
good pont about the process directly
works. Thanks!
NOW the memory is the problem 🙂 Is that known issue with CI and FASTP?
🤷 1
a
I thought the test profile (used in CI) limited all processes to 1/2 CPU and 8 GB or something small for mem 🤔
👍 1
Where is the failing CI job? An nf-core pipeline repo?
3 Views
Open in Slack
PreviousNext
Powered by