base.config

/*
 * -------------------------------------------------
 * h3achipimputation 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( 8.GB * task.attempt, 'memory' ) }
  time = { check_max( 2.h * task.attempt, 'time' ) }

  stageOutMode = 'rsync'

  errorStrategy = { (task.exitStatus in [143,137,255]) || (task.attempt < 3) ? 'retry' : 'finish' }
  maxRetries = 3
  maxErrors = '-1'

  // Process-specific resource requirements
  withLabel: 'medium'{
    errorStrategy = { (task.exitStatus in [143,137,255]) || (task.attempt < 2) ? 'retry' : 'ignore' }
  }
  withLabel: 'bigmem' {
    errorStrategy = { (task.exitStatus in [143,137,255]) || (task.attempt < 2) ? 'retry' : 'ignore' }
  }
}

params {
  // Defaults only, expecting to be overwritten
  max_memory = 128.GB
  max_cpus = 16
  max_time = 240.h
}