code: def _setup_reference_files(data, tx_out_dir):
      
      aligner = dd.get_aligner(data) or "bwa"
      out_dir = utils.safe_makedir(os.path.join(tx_out_dir, aligner))
      ref_fasta = dd.get_ref_file(data)
      ref_files = ["%s%s" % (utils.splitext_plus(ref_fasta)[0], ext) for ext in [".fa", ".fa.fai", ".dict"]]
      for orig_file in ref_files + tz.get_in(("reference", aligner, "indexes"), data):
          utils.symlink_plus(orig_file, os.path.join(out_dir, os.path.basename(orig_file)))
      return os.path.join(out_dir, os.path.basename(ref_fasta))
docs: Create a reference directory with fasta and bwa indices.
  
      GRIDSS requires all files in a single directory, so setup with symlinks.
      This needs bwa aligner indices available, which we ensure with `get_aligner_with_aliases`
      during YAML sample setup.