docs: def run_flag_hw(in_prefix, in_type, out_prefix, base_dir, options):
      """Runs step12 (flag HW).
  
      :param in_prefix: the prefix of the input files.
      :param in_type: the type of the input files.
      :param out_prefix: the output prefix.
      :param base_dir: the output directory.
      :param options: the options needed.
  
      :type in_prefix: str
      :type in_type: str
      :type out_prefix: str
      :type base_dir: str
      :type options: list
  
      :returns: a tuple containing the prefix of the output files (the input
                prefix for the next script) and the type of the output files
                (``bfile``).
  
      This function calls the :py:mod:`pyGenClean.FlagHW.flag_hw` module. The
      required file type for this module is ``bfile``, hence the need to use the
      :py:func:`check_input_files` to check if the file input file type is the
      good one, or to create it if needed.
  
      .. note::
          The :py:mod:`pyGenClean.FlagHW.flag_hw` module doesn't return usable
          output files. Hence, this function returns the input file prefix and
          its type.
  
      """
      # Creating the output directory
      os.mkdir(out_prefix)
  
      # We know we need bfile
      required_type = "bfile"
      check_input_files(in_prefix, in_type, required_type)
  
      # We need to inject the name of the input file and the name of the output
      # prefix
      script_prefix = os.path.join(out_prefix, "flag_hw")
      options += ["--{}".format(required_type), in_prefix,
                  "--out", script_prefix]
  
      # We run the script
      try:
          flag_hw.main(options)
      except flag_hw.ProgramError as e:
          msg = "flag_hw: {}".format(e)
          raise ProgramError(msg)
  
      # Finding the two files containing the list of flagged markers
      filenames = glob(script_prefix + ".snp_flag_threshold_[0-9]*")
      thresholds = {}
      for filename in filenames:
          # Finding the threshold of the file
          threshold = re.sub(
              r"^flag_hw.snp_flag_threshold_",
              "",
              os.path.basename(filename),
          )
  
          # Counting the number of markers in the file
          nb_markers = None
          with open(filename, "r") as i_file:
              nb_markers = len(i_file.read().splitlines())
  
          # Saving the values
          thresholds[threshold] = (nb_markers, filename)
  
      # We create the LaTeX summary
      latex_file = os.path.join(script_prefix + ".summary.tex")
      try:
          with open(latex_file, "w") as o_file:
              print >>o_file, latex_template.subsection(
                  flag_hw.pretty_name
              )
  
              # Data to write
              sorted_keys = sorted(thresholds.keys(), key=float)
  
              text = (
                  "Markers which failed Hardy-Weinberg equilibrium test (using "
                  "Plink) were flagged. A total of {:,d} marker{} failed with a "
                  "threshold of {}. A total of {:,d} marker{} failed with a "
                  "threshold of {}. For a total list, check the files {} and "
                  "{}, respectively.".format(
                      thresholds[sorted_keys[0]][0],
                      "s" if thresholds[sorted_keys[0]][0] - 1 > 1 else "",
                      latex_template.format_numbers(sorted_keys[0]),
                      thresholds[sorted_keys[1]][0],
                      "s" if thresholds[sorted_keys[1]][0] - 1 > 1 else "",
                      latex_template.format_numbers(sorted_keys[1]),
                      latex_template.texttt(
                          latex_template.sanitize_tex(os.path.basename(
                              thresholds[sorted_keys[0]][1],
                          )),
                      ),
                      latex_template.texttt(
                          latex_template.sanitize_tex(os.path.basename(
                              thresholds[sorted_keys[1]][1],
                          )),
                      ),
                  )
              )
              print >>o_file, latex_template.wrap_lines(text)
  
      except IOError:
          msg = "{}: cannot write LaTeX summary".format(latex_file)
          raise ProgramError(msg)
  
      # Writing the summary results
      with open(os.path.join(base_dir, "results_summary.txt"), "a") as o_file:
          print >>o_file, "# {}".format(script_prefix)
          print >>o_file, "Number of markers flagged for HW"
          print >>o_file, "  - {}\t{:,d}".format(
                              sorted_keys[0],
                              thresholds[sorted_keys[0]][0],
                          )
          print >>o_file, "  - {}\t{:,d}".format(
                              sorted_keys[1],
                              thresholds[sorted_keys[1]][0],
                          )
          print >>o_file, "---"
  
      # We know this step doesn't produce an new data set, so we return the old
      # prefix and the old in_type
      return _StepResult(
          next_file=in_prefix,
          next_file_type=required_type,
          latex_summary=latex_file,
          description=flag_hw.desc,
          long_description=flag_hw.long_desc,
          graph_path=None,
      )