rna-seq-tophat/tasks/tophat2.wdl

task tophat2 {
   File gtf
   File genome_directory
   String idx_prefix
	File read1
	File read2
   String base = basename(read1, ".fq.gz")
   String baseout
   String docker
   String cluster

   command <<<
      tophat2 -p 8 -G ${gtf} -o ${base} --library-type fr-unstranded --solexa-quals ${genome_directory}/${idx_prefix} ${read1} ${read2}
   >>>
   
   runtime { 
      docker: docker 
		cluster: cluster
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd 200 /cromwell_root/"
   }

   output {
      File accepted_hits = "${base}/${base}_accepted_hits.bam"
      File unmapped_bam = "${base}/${base}_unmapped.bam"
   }
}