imperial.config

//Profile config names for nf-core/configs

params {
    // Config Params
    config_profile_description = 'Imperial College London - HPC Profile -- provided by nf-core/configs.'
    config_profile_contact     = 'Nurun Fancy (@nfancy)'
    config_profile_url         = 'https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/'

    // Resources
    max_memory                 = 920.GB
    max_cpus                   = 256
    max_time                   = 1000.h
}

process {
    resourceLimits = [
        memory: 920.GB,
        cpus: 256,
        time: 1000.h
    ]
}

profiles {
    imperial {
        process {
            executor      = 'pbspro'

            // Update amount of max retries and set "retry" as the error strategy for all error codes
            errorStrategy = 'retry'
            maxRetries    = 5
            maxErrors     = '-1'


            // General resource requirements
            cpus          = { 1 * task.attempt }
            memory        = { 6.GB * task.attempt }
            time          = { 4.h * task.attempt }

            // Process-specific resource requirements
            withLabel: process_single {
                cpus   = 1
                memory = { 6.GB * task.attempt }
                time   = { 4.h * task.attempt }
            }

            withLabel: process_low {
                cpus   = { 2 * task.attempt }
                memory = { 48.GB * task.attempt }
                time   = { 8.h * task.attempt }
            }

            withLabel: process_medium {
                cpus   = { 8 * task.attempt }
                memory = { 64.GB * task.attempt }
                time   = { 12.h * task.attempt }
            }

            withLabel: process_high {
                cpus   = { 12 * task.attempt }
                memory = { 120.GB * task.attempt }
                time   = { 12.h * task.attempt }
            }

            withLabel: process_long {
                cpus   = 9
                memory = 100.GB
                time   = { 24.h * task.attempt }
            }

            withLabel: process_high_memory {
                cpus   = { 10 * task.attempt }
                memory = { 200.GB * task.attempt }
                time   = { 24.h * task.attempt }
            }
            withLabel: with_gpus {
                time             = 24.h
                clusterOptions   = '-l select=1:ncpus=4:mem=24gb:ngpus=1:gpu_type=RTX6000'
                maxForks         = 1
                containerOptions = {
                    workflow.containerEngine == "singularity"
                        ? '--nv --env CUDA_VISIBLE_DEVICES=$CUDA_VISIBLE_DEVICES'
                        : (workflow.containerEngine == "docker" ? '--gpus all' : null)
                }
                beforeScript     = 'module load tools/prod'
            }
        }
    }
    medbio {
        process {
            executor = 'pbspro'
        }
    }
}

executor {
    '$pbspro' {
        queueSize       = 49
        submitRateLimit = '10 sec'
        maxForks        = 49
    }

    '$local' {
        cpus      = 2
        queueSize = 1
        memory    = '6 GB'
    }
}

singularity {
    enabled    = true
    autoMounts = true
    runOptions = "-B /rds/,/rds/general/user/${USER}/ephemeral/tmp/:/tmp,/rds/general/user/${USER}/ephemeral/tmp/:/var/tmp"
}