haplotyper-battle-royale/nextflow.config

params {
    reference = null

    // Config options
    config_profile_name = null
    config_profile_description = null
    custom_config_version = 'master'
    custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_contact = null
    config_profile_url = null

    // Max resource options
    // Defaults only, expecting to be overwritten
    max_memory = '128.GB'
    max_cpus = 16
    max_time = '240.h'
}

process {
    cpus = { check_max(1 * task.attempt, 'cpus') }
    memory = { check_max(6.GB * task.attempt, 'memory') }
    time = { check_max(4.h * task.attempt, 'time') }

    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
    maxRetries = 1
    maxErrors = '-1'

    withLabel:process_single {
        cpus = { check_max(1, 'cpus') }
        memory = { check_max( 6.GB * task.attempt, 'memory') }
        time = { check_max( 4.h * task.attempt, 'time') }
    }
    withLabel:process_low {
        cpus = { check_max( 2 * task.attempt, 'cpus') }
        memory = { check_max( 12.GB * task.attempt, 'memory') }
        time = { check_max( 4.h * task.attempt, 'time') }
    }
    withLabel:process_medium {
        cpus = { check_max( 6 * task.attempt, 'cpus') }
        memory = { check_max( 36.GB * task.attempt, 'memory') }
        time = { check_max( 8.h * task.attempt, 'time') }
    }
    withLabel:process_high {
        cpus = { check_max( 12 * task.attempt, 'cpus') }
        memory = { check_max( 72.GB * task.attempt, 'memory') }
        time = { check_max( 16.h  * task.attempt, 'time') }
    }

    withName: 'HAPLINK_ML_HAPLOTYPES' {
        ext.ml_args = """
        --simulated-reads \\
        --overlap-min 20 \\
        --overlap-max 8000 \\
        """
    }
}

try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

profiles {
    docker {
        docker.enabled = true
        docker.userEmulation = true
        conda.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
    }
    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
        conda.enabled = false
        docker.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
    }
    podman {
        podman.enabled = true
        conda.enabled = false
        docker.enabled = false
        singularity.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
    }
    shifter {
        shifter.enabled = true
        conda.enabled = false
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        charliecloud.enabled = false
        apptainer.enabled = false
    }
    charliecloud {
        charliecloud.enabled = true
        conda.enabled = false
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        apptainer.enabled = false
    }
    apptainer {
        apptainer.enabled = true
        apptainer.autoMounts = true
        conda.enabled = false
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
    }
}

env {
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}

def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}