base.config

/*
 * -------------------------------------------------
 *  ICGC-FeatureCounts 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
  //Different container provided from ICGC/TCGA directly
  withName:fetch_encrypted_s3_url {
    container = 'overture/score'
  }

  withName:workflow_summary_mqc{
    memory = 800.MB
    cpus = 1
  }



}

params {
  // Defaults only, expecting to be overwritten
  max_memory = 8.GB
  max_cpus = 2
  max_time = 240.h
  igenomes_base = 's3://ngi-igenomes/igenomes/'
}