task hisat2 {
   File idx
   File Trim_R1
   File Trim_R2
   String idx_prefix
   String sample_id
   String docker
   String cluster
   String disk_size
   String pen_intronlen
   Int pen_cansplice
   Int pen_noncansplice
   Int min_intronlen
   Int max_intronlen
   Int maxins
   Int minins
   
   command <<<
      nt=$(nproc)
      hisat2 -t -p $nt \
                -x ${idx}/${idx_prefix} \
                --pen-cansplice ${pen_cansplice} \
                --pen-noncansplice ${pen_noncansplice} \
                --pen-canintronlen ${pen_intronlen} \
                --min-intronlen ${min_intronlen} \
                --max-intronlen ${max_intronlen} \
                --maxins ${maxins} --minins ${minins} \
                --rna-strandness RF \
                --un-conc-gz ${sample_id}_un.fq.gz \
                -1 ${Trim_R1} \
                -2 ${Trim_R2} \
                -S ${sample_id}.sam 
   >>>
   
   runtime { 
		docker: docker 
		cluster: cluster
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }

   output {
      File sam = "${sample_id}.sam"
      File unmapread_1p = "${sample_id}_un.fq.1.gz"
      File unmapread_2p = "${sample_id}_un.fq.2.gz"
   }
}