mapping_paired.config

profiles {
  docker {
    docker.temp = 'auto'
    docker.enabled = true
    process {
      withName: mapping_fastq {
        container = "bwa:0.7.17"
        cpus = 4
      }
    }
  }
  singularity {
    singularity.enabled = true
    process {
      withName: mapping_fastq {
        container = "file://bin/bwa:0.7.17.img"
        cpus = 4
      }
    }
  }
  psmn {
    process{
      withName: mapping_fastq {
        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
        module = "bwa/0.7.17"
        executor = "sge"
        clusterOptions = "-cwd -V"
        cpus = 16
        memory = "30GB"
        time = "24h"
        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
        penv = 'openmp16'
      }
    }
  }
  ccin2p3_conda {
    process{
      withName: mapping_fastq {
        beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
        conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"
        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
        -o ~/logs/ -e ~/logs/"
        cpus = 1
        queue = 'huge'
      }
    }
  }
  ccin2p3 {
    singularity.enabled = true
    singularity.runOptions = "--bind /pbs,/sps,/scratch"
    process{
      withName: mapping_fastq {
        container = "/sps/lbmc/common/singularity/bwa:0.7.17.img"
        scratch = true
        stageInMode = "copy"
        stageOutMode = "rsync"
        executor = "sge"
        clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
        -o ~/logs/ -e ~/logs/"
        cpus = 1
        queue = 'huge'
      }
    }
  }
}