eager/conf/base.config at 7518f3268dbf92932b471c26134e3f61c9e56a52 · maxibor/eager · GitHub

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/*
 * -------------------------------------------------
 *  nf-core/eager 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.
 */

process {
  cpus = { check_max( 1 * task.attempt, 'cpus' ) }
  memory = { check_max( 4.GB * task.attempt, 'memory' ) }
  time = { check_max( 2.h * task.attempt, 'time' ) }

  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
  maxRetries = 3
  maxErrors = '-1'

  // Generic resource requirements - s(ingle)c(ore)/m(ulti)c(ore)

  withLabel:'sc_tiny'{
      cpus = { check_max( 1, 'cpus' ) }
      memory = { check_max( 1.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
  }

  withLabel:'sc_small'{
      cpus = { check_max( 1, 'cpus' ) }
      memory = { check_max( 4.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
  }

  withLabel:'sc_medium'{
      cpus = { check_max( 1, 'cpus' ) }
      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
  }

  withLabel:'mc_small'{
      cpus = { check_max( 2, 'cpus' ) }
      memory = { check_max( 4.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
  }

  withLabel:'mc_medium' {
      cpus = { check_max( 4, 'cpus' ) }
      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
  }

  withLabel:'mc_large'{
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
  }

  withLabel:'mc_huge'{
      cpus = { check_max( 32, 'cpus' ) }
      memory = { check_max( 256.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
  }

  // Process-specific resource requirements (others leave at default, e.g. Fastqc)
  withName:get_software_versions {
    memory = { check_max( 2.GB, 'memory' ) }
    cache = false
  }


  withName:qualimap{
    errorStrategy = 'ignore'
  }

  withName:preseq {
    errorStrategy = 'ignore'
  }

  // Add 141 ignore due to unclean pipe closing by pmdtools https://github.com/pontussk/PMDtools/issues/7
  withName: pmdtools {
    errorStrategy = { task.exitStatus in [141] ? 'ignore' : 'retry' }
  }

  withName: multiqc {
    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
  }
}

params {
  // Defaults only, expecting to be overwritten
  max_memory = 128.GB
  max_cpus = 16
  max_time = 240.h
  igenomes_base = 's3://ngi-igenomes/igenomes/'
}