def run_command(self, input_file, output_dir=None):
        """Return the command for running bfconvert as a list.
        
        :param input_file: path to microscopy image to be converted
        :param ouput_dir: directory to write output tiff files to
        :returns: list
        """
        base_name = os.path.basename(input_file)
        name, suffix = base_name.split('.', 1)
        output_file = '{}{}.tif'.format(name, self.split_pattern)
        if output_dir:
            output_file = os.path.join(output_dir, output_file)
        return ['bfconvert', input_file, output_file]