eager/conf/base.config at 8d26b3391f7a513bb450758f8836490c4aceca2e · apeltzer/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 {

  container = params.container

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

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

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

  withName:convertBam {
    cpus = { check_max(8 * task.attempt, 'cpus') }
  }
  withName:makeSeqDict {
    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
  }

  withName:bwa {
    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
    cpus = { check_max(8 * task.attempt, 'cpus') }
    time = { check_max(8.h * task.attempt, 'time') }
  }
  withName:bwamem{
    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
    cpus = { check_max(8 * task.attempt, 'cpus') }
    time = { check_max(8.h * task.attempt, 'time') }
  }
  withName:qualimap{
    cpus = { check_max(8 * task.attempt, 'cpus') }
  }
  withName:bam_trim{
    cpus = { check_max(4 * task.attempt, 'cpus') }
  }
  withName:markDup{
    cpus = { check_max(8 * task.attempt, 'cpus') }
  }
  withName:preseq {
    errorStrategy = 'ignore'
  }
  withName: fastqc {
    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
  }
  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/'
}