cfc.config

// Profile config names for nf-core/configs

validation.ignoreParams = ['sarek_cfc_check_resource_func']

params {
    // Specific nf-core/configs params
    config_profile_contact = 'Friederike Hanssen (@FriederikeHanssen)'
    config_profile_description = 'nf-core/sarek CFC profile provided by nf-core/configs'
}

// Specific nf-core/sarek process configuration
process {
    withName:'StrelkaSingle|Strelka|StrelkaBP|MantaSingle|Manta' {
        cpus = { params.sarek_cfc_check_resource_func( 20 * task.attempt) }
        memory = { params.sarek_cfc_check_resource_func( 59.GB * task.attempt) }
    }
    withName:'MSIsensor_scan|MSIsensor_msi' {
        memory = { params.sarek_cfc_check_resource_func( 55.GB * task.attempt ) }

    }
    withName:BamQC {
        memory = { params.sarek_cfc_check_resource_func( 372.GB * task.attempt) }
    }

    withName:MapReads{
        cpus = { params.sarek_cfc_check_resource_func( 20 * task.attempt ) }
        memory = { params.sarek_cfc_check_resource_func( 59.GB * task.attempt) }
    }
}

params.sarek_cfc_check_resource_func = { obj ->
    try {
        if (obj.getClass() == nextflow.util.MemoryUnit && obj.compareTo(params.max_memory as MemoryUnit) == 1)
            return params.max_memory as MemoryUnit
        else if (obj.getClass() == nextflow.util.Duration && obj.compareTo(params.max_time as Duration) == 1)
            return params.max_time as Duration
        else if (obj.getClass() == java.lang.Integer)
            return Math.min(obj, params.max_cpus as int)
        else
            return obj
    } catch (_) {
        println "   ### ERROR ###   Max params max_memory:'${params.max_memory}', max_time:'${params.max_time}' or max_cpus:'${params.max_cpus}'  is not valid! Using default value: $obj"
    }
}