code: def close(args):
      
      p = OptionParser(close.__doc__)
      p.set_home("gapfiller")
      p.set_cpus()
      opts, args = p.parse_args(args)
  
      if len(args) < 1:
          sys.exit(not p.print_help())
  
      scaffolds = args[0]
      libtxt = write_libraries(args[1:], aligner="bwa")
  
      cmd = "perl " + op.join(opts.gapfiller_home, "GapFiller.pl")
      cmd += " -l {0} -s {1} -T {2}".format(libtxt, scaffolds, opts.cpus)
      runsh = "run.sh"
      write_file(runsh, cmd)
docs: %prog close scaffolds.fasta PE*.fastq
  
      Run GapFiller to fill gaps.