def update_args(self, override_args):
        """Update the argument used to invoke the application

        Note that this will also update the dictionary of input
        and output files.

        Parameters
        -----------
        override_args : dict
            dictionary passed to the links

        """
        self.args = extract_arguments(override_args, self.args)
        self._map_arguments(self.args)

        scratch_dir = self.args.get('scratch', None)
        if is_not_null(scratch_dir):
            self._file_stage = FileStageManager(scratch_dir, '.')
        for link in self._links.values():
            link._set_file_stage(self._file_stage)
        self._latch_file_info()