rnaseq_for_se/tasks/hisat2.wdl

task hisat2 {
   File idx
   File Trim
   String idx_prefix
   String sample_id=basename(Trim, ".fastq.gz")
   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-intronlen ${pen_intronlen} --min-intronlen ${min_intronlen} --max-intronlen ${max_intronlen} --maxins ${maxins} --minins ${minins} --un-conc-gz ${sample_id}_un.fq.gz -1 ${Trim}  -S ${sample_id}.sam 
   >>>
   
   runtime { 
		docker: docker 
		cluster: cluster
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
   }

   output {
      File sam = "${sample_id}.sam"
      File unmapreads = "${sample_id}_un.fq.gz"
   }
}