36fd4b4079113f9aa9a5c31b544ad222d2c0d507,anvio/workflows/metagenomics/__init__.py,MetagenomicsWorkflow,sanity_check_for_kraken,#MetagenomicsWorkflow#,327

Before Change

                                   the krakenhll database using the --db parameter in the config file.")

            // if a kraken_txt was supplied then let"s run kraken by default
            self.config["krakenhll"]["run"] = True

            kraken_annotation_dict = u.get_TAB_delimited_file_as_dictionary(kraken_txt)
            if next(iter(next(iter(kraken_annotation_dict.values())).keys())) != "path":

After Change

        self.run_krakenhll = self.get_param_value_from_config(["krakenhll", "run"]) == True

        if kraken_txt:
            if self.get_param_value_from_config(["krakenhll", "run"]) == True:
                raise ConfigError("You supplied a kraken_txt file (\"%s\") but you set krakenhll \
                                   to run in the config file. anvi"o is confused and \
                                   is officially going on a strike. Ok, let"s clarify, \

Instances