base.config

/*
vim: syntax=groovy
-*- mode: groovy;-*-
 * -------------------------------------------------
 *  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 = { "nf-core/exoseq:${workflow.revision ? workflow.revision : 'latest'}" }
  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 = 2
  maxErrors = '-1'

  // Process-specific resource requirements
  $fastqc {
    time = { check_max( 12.h * task.attempt, 'time' ) } 
  }

  $trim_galore {
    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
    time = { check_max( 16.h * task.attempt, 'time' ) }
  }

  $bwamem {
    cpus = { check_max( 14 * task.attempt, 'cpus' ) }
    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
    time = { check_max( 16.h * task.attempt, 'time' ) }
  }

  $makeBWAIndex{
    time = { check_max( 8.h * task.attempt, 'time' ) }
  }

  $sortSam {
    cpus = { check_max( 14 * task.attempt, 'cpus' ) }
    time = { check_max( 8.h * task.attempt, 'time' ) }
  }

  $makeFastaIndex {
    container = 'shub://qbicsoftware/qbic-singularity-samtools'
    time = { check_max( 8.h * task.attempt, 'time' ) }
  }

  $markDuplicates {
    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
    cpus = { check_max( 7 * task.attempt, 'cpus' ) }
    time = 8.h
  }

  $recal_bam_files {
    cpus = { check_max( 14 * task.attempt, 'cpus' ) }
    time = { check_max( 20.h * task.attempt, 'time' ) }
  }

  $applyBQSR{
    cpus = { check_max( 1 * task.attempt, 'cpus' ) }
    time = { check_max( 20.h * task.attempt, 'time' ) }
  }

  $realign {
    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
    time = { check_max( 16.h * task.attempt, 'time' ) }
  }

  $qualiMap {
    container = 'shub://qbicsoftware/qbic-singularity-qualimap2'
    cpus = { check_max( 14 * task.attempt, 'cpus' ) }
    time = { check_max( 4.h * task.attempt, 'time' ) }
  }

  $variantCall {
    cpus = { check_max( 14 * task.attempt, 'cpus' ) }
    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
    time = { check_max( 8.h * task.attempt, 'time' ) }
  }
}