NGSCheckmate_pipeline/tasks/fastq_ncm.wdl

task fastq_ncm {
  
  File fastq_smp
  String out_id
  String subsampling_rate
  String docker
  String cluster_config
  String disk_size

  command <<<
    set -o pipefail
    set -e
    nt=$(nproc)
    python /NGSCheckMate/ncm_fastq.py -l ${fastq_smp} -O ${out_id} -p $nt -pt /NGSCheckMate/SNP/SNP.pt 
    #-s ${subsampling_rate}
    #-N ChIP_batch
    tar cvf ${out_id}.tar ${out_id}
  >>>

  runtime {
    docker:docker
      cluster:cluster_config
      systemDisk:"cloud_ssd 40"
      dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
  }
  output {
    File result="${out_id}.tar"
  }
}