uge.config

/*
* ----------------------------------------------
*       nf-core/configs: Univa Grid Engine
* ----------------------------------------------
*/


// Basic params of config file
params {
    config_profile_description = 'Univa Grid Engine config file'
    config_profile_contact = 'Gregory Sprenger (@gregorysprenger)'
}

// Use Singularity
singularity {
    enabled = true
    autoMounts = true
}

// Submit up to 100 jobs at once with 15 secs between to avoid spamming the cluster
executor {
    queueSize = 100
    pollInterval = '15 sec'
}

// Process specific resource requirements
process {
    // Error and retry handling
    errorStrategy = { task.exitStatus in [143,137,104,134,139,71,255] ? 'retry' : 'finish' }
    maxRetries    = 3
    
    // Executor and queue information
    executor = 'sge'
    penv = 'smp'
    queue = { task.time <= 4.h ? 'short.q' : task.time > 5.h ? 'all.q' : 'short.q' }
}

// Function to ensure that resource requirements don't go beyond limit
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
        }
    }
}