process.clusterOptions incompatible with slurm

[nick-youngblut]

The nextflow.config includes: process.clusterOptions = '-S /bin/bash', but this throws the following error when run with -process.executor slurm:

sbatch: error: Invalid numeric value "/bin/bash" for --core-spec.

[nick-youngblut]

More generally, I don't see the point of setting params.max_memory and parmas.max_cpus lower than process.memory and process.cpus, since the latter values will be used for setting the cluster job resources.

Also, resources are globally applied to processes, but steps like STEP4b_matrix don't set CPUs (or memory). Why not use the nf-core approach:

def check_max(obj, type){
    if(type == 'memory'){
        if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1){
            return params.max_memory as nextflow.util.MemoryUnit
        }
    } else if(type == 'time'){
        if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1){
            return params.max_time as nextflow.util.Duration
        }
    } else if(type == 'cpus'){
        if (obj > params.max_cpus as int){
            return params.max_cpus as int
        }
    }
    return obj
}

process {
    cpus = { check_max( 8, "cpus" ) }
    memory = { check_max( 32.GB, "memory" ) }
    time = { check_max( 48.h, "time" ) }

    withLabel:process_low {
        cpus = { check_max( 1, "cpus" ) }
        memory = { check_max( 8.GB, "memory" ) }
        time = { check_max( 8.h, "time" ) }
    }
}