I'm trying to override some of the configuration settings in an nf-core pipeline through the supply of a custom.config file. I wrote the custom.config as shown:

process {
    executor = 'slurm'
    queue = 'myqueue'
    clusterOptions = '--account=myaccount --qos=myqos'
    cpus = 10
    memory = 30.GB
    time = '8h'
}
trace.overwrite = true
executor.queueSize = 5

I provide the custom.config to the nextflow command as:

nextflow run nf-core/taxprofiler -params-file ~/params.yaml -profile apptainer -c custom.config

But my specifications in the custom.config are being ignored and those supplied from the pipeline (in this case, taxprofiler) are used, instead. How do I override an nf-core pipelines' default configuration settings correctly?

Which ones? Note that process specificity is still important, so if you have a process

withLabel

selector in the pipeline that'll still win

Well, I need to override all processes with these defaults - for potentially all nf-core pipelines. Is

withLabel

required?

yes: https://docs.seqera.io/nextflow/config#selector-priority

Ah, that makes sense

Nope, those are just config profiles, same hierarchy applies however the config is loaded

Where the pipeline config takes highest priority?

Not pipeline, selector

Yeah I'd just try to do something like this:

process {
    withName: '.*' {
        executor = 'slurm'
        queue = 'myqueue'
        clusterOptions = '--account=myaccount --qos=myqos'
        cpus = 10
        memory = 30.GB
        time = '8h'
    }
}

Thank you both! I didn't know wildcards could be used like that - it is working as intended!

Glad you got it working!