code: def create_combined_fasta(data):
      
      out_dir = os.path.join(dd.get_work_dir(data), "inputs", "transcriptome")
      items = disambiguate.split([data])
      fasta_files = []
      for i in items:
          odata = i[0]
          gtf_file = dd.get_gtf_file(odata)
          ref_file = dd.get_ref_file(odata)
          out_file = os.path.join(out_dir, dd.get_genome_build(odata) + ".fa")
          if file_exists(out_file):
              fasta_files.append(out_file)
          else:
              out_file = gtf.gtf_to_fasta(gtf_file, ref_file, out_file=out_file)
              fasta_files.append(out_file)
      out_stem = os.path.join(out_dir, dd.get_genome_build(data))
      if dd.get_disambiguate(data):
          out_stem = "-".join([out_stem] + (dd.get_disambiguate(data) or []))
      combined_file = out_stem + ".fa"
      if file_exists(combined_file):
          return combined_file
  
      fasta_file_string = " ".join(fasta_files)
      cmd = "cat {fasta_file_string} > {tx_out_file}"
      with file_transaction(data, combined_file) as tx_out_file:
          do.run(cmd.format(**locals()), "Combining transcriptome FASTA files.")
      return combined_file
docs: if there are genomes to be disambiguated, create a FASTA file of
      all of the transcripts for all genomes