rna-seq-tophat/tasks/tophat2.wdl

task tophat2 {
   File gtf
   File genome_directory
   String base = sub(basename(read),"\\.\\S+$", "")
   String idx_prefix
   File read_1P
   File read_2P
   String baseout
   String docker

   command {
      tophat2 -p 24 -o ${base} -G ${gtf} --library-type fr-unstranded --solexa-quals ${genome_directory}/${idx_prefix} ${read_1P} ${read_2P}
   }
   
   runtime { 
      dockerTag: docker 
   }

   output {
      File accepted_hits = "${baseout}/accepted_hits.bam"
      File unmapped_bam = "${baseout}/unmapped.bam"
   }
}