mapping_paired.config

profiles {
  docker {
    docker.temp = 'auto'
    docker.enabled = true
    process {
      withname: mapping_fastq {
        container = "bowtie2:2.3.4.1"
      }
    }
  }
  psmn {
    process{
      withname: mapping_fastq {
        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
        module = "Bowtie2/2.3.4.1:SAMtools/1.7"
        executor = "sge"
        cpus = 16
        memory = "30GB"
        time = "24h"
        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
        penv = 'openmp16'
      }
    }
  }
}