arcasHLA/tasks/hisat2.wdl

task hisat2 {
   File idx
   File read_1P
   File read_2P
   String idx_prefix
   String base = sub(basename(read_1P),"\\.\\S+$", "")
   String docker
   String cluster

   command {
   	 nt=$(nproc)
     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${base}.sam  --un-conc-gz ${base}_un.fq.gz
   }
   
   runtime { 
		docker: docker 
		cluster: cluster
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd 200 /cromwell_root/"
   }

   output {
      File sam = base + ".sam"
      File unmapread_1p = base + "_un.fq.1.gz"
      File unmapread_2p = base + "_un.fq.2.gz"
   }
}