bioruby-ngs tophat task with sorting and indexing

gistfile1.rb

  desc "tophat DIST INDEX OUTPUTDIR FASTQS", "run tophat as from command line, default 6 processors and then create a sorted bam indexed."
  method_option :paired, :type => :boolean, :default => false, :desc => 'Are reads paired? If you chose this option pass just the basename of the file without forward/reverse and .fastq'
  Bio::Ngs::Tophat.new.thor_task(self, :tophat) do |wrapper, task, dist, index, outputdir, fastqs|
      wrapper.params = task.options #merge passed options to the wrapper.
      wrapper.params = {"mate-inner-dist"=>dist, "output-dir"=>outputdir, "num-threads"=>6, "solexa1.3-quals"=>true}
      fastq_files = task.options[:paired] ? ["#{fastqs}_forward.fastq","#{fastqs}_reverse.fastq"]  : ["#{fastqs}"]
      wrapper.run :arguments=>[index, fastq_files ].flatten, :separator=>"="


      accepted_hits_bam_fn = File.join(outputdir, "accepted_hit.bam")
      if File.exists?(accepted_hits_bam_fn)
        #bam sort
        Bio::DB::SAM::Tools.bam_sort(accepted_hits_bam_fn, "accepted_hist_sort")
        #bam index sorted file
        Bio::DB::SAM::Tools.bam_index_build(File.join(outputdir,"accepted_hits_sort.bam"))
      else
        warn "[#{Time.now}] There was an error, tophat did not create any accepted_hit file "
      end
      #you tasks here
  end