NGSCheckMate_parallel/tasks/ngscheckmate_fastq.wdl

task ngscheckmate_fastq {
  
  File fq1
  File fq2
  String output_id=basename(fq1, "_R1.fastq.gz")
  String subsampling_rate
  String docker
  String cluster_config
  String disk_size

  command <<<
    set -o pipefail
    set -e
    nt=$(nproc)
    export NCM_HOME=/opt/NGSCheckMate
    python /opt/NGSCheckMate/ncm_fastq.py -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${output_id}.vaf
  >>>

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