code: def index_transcriptome(gtf_file, ref_file, data):
      
      gtf_fasta = gtf.gtf_to_fasta(gtf_file, ref_file)
      bowtie2_index = os.path.splitext(gtf_fasta)[0]
      bowtie2_build = config_utils.get_program("bowtie2", data["config"]) + "-build"
      cmd = "{bowtie2_build} --offrate 1 {gtf_fasta} {bowtie2_index}".format(**locals())
      message = "Creating transcriptome index of %s with bowtie2." % (gtf_fasta)
      do.run(cmd, message)
      return bowtie2_index
docs: use a GTF file and a reference FASTA file to index the transcriptome