base.config

/*
 * -------------------------------------------------
 *  Nextflow base config file
 * -------------------------------------------------
 * A 'blank slate' config file, appropriate for general
 * use on most high performace compute environments.
 * Assumes that all software is installed and available
 * on the PATH. Runs in `local` mode - all jobs will be
 * run on the logged in environment.
 */

params {
	// Defaults only, expecting to be overwritten
	//max_memory = 32.GB
	//max_cpus = 8
	//max_time = 240.h
}

//executor{
	//cpus = 12
	//memory = 200.GB
//}

process{
  cpus = { check_max( 1 * task.attempt, 'cpus' ) }
  memory = { check_max( 7.GB * task.attempt, 'memory' ) }
  time = { check_max( 4.h * task.attempt, 'time' ) }

  errorStrategy = { task.exitStatus in [140,143,137,104,134,139,138] ? 'retry' : 'finish'; task.exitStatus in [1,2,255] ? 'ignore' : 'finish' }

  maxRetries = 2
  maxErrors = '-1'

  withLabel:process_low {
    cpus = { check_max( 2, 'cpus' ) }
    memory = { check_max( 1.GB * task.attempt, 'memory' ) }
    time = { check_max( 1.h * task.attempt, 'time' ) }
  }
  withLabel:process_medium {
    cpus = { check_max( 4, 'cpus' ) }
    memory = { check_max( 12.GB * task.attempt, 'memory' ) }
    time = { check_max( 7.h * task.attempt, 'time' ) }
  }
  withLabel:process_high {
    cpus = { check_max( 20, 'cpus' ) }
    memory = { check_max( 32.GB * task.attempt, 'memory' ) }
    time = { check_max( 30.h * task.attempt, 'time' ) }
  }
  withLabel:process_long {
    time = { check_max( 20.h * task.attempt, 'time' ) }
  }
}

env {
     _JAVA_OPTIONS = '-Xmx2G'
     //JAVA_OPTS = "-Xms512M"
     PILON_PATH = "/opt/pilon/pilon-1.22/pilon-1.22.jar"
     TRIMMOMATIC_PATH = "/opt/Trimmomatic-0.33"
     LC_ALL="en_US.utf-8"
     LANG="en_US.utf-8"
  	 CLASSPATH='/scif/apps/varscan/varscan-2.3.9/varscan-2.3.9.tar:/scif/apps/picard/bin/picard.jar:/scif/apps/gatk/gatk-3.8/GenomeAnalysisTK.jar'
     SRST2_SAMTOOLS='/scif/apps/srst2/samtools-0.1.18/samtools'
}