nextflow.config

workDir =    "${projectDir}/../../work"
tmpDir =     "${projectDir}/../../tmp"

params {
  outdir =    "${projectDir}/../../results"
  reportdir = "${projectDir}/../../reports"
}

timeline {
  enabled = true
  file = "${params.reportdir}/timeline.html"
}

trace {
  enabled = true
  file = "${params.reportdir}/trace.txt"
}

profiles {
  lsf {
    includeConfig './confs/lsf.conf'
    includeConfig './confs/lsf_tasks.conf'
  }
  fce {
    includeConfig './confs/fce.conf'
    includeConfig './confs/fce_tasks.conf'
  }
}


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