75ec13dea174377dce7da44610cd940f81b2a327,anvio/migrations/config/v0_to_v1.py,,migrate,#Any#,19

Before Change

        // if the param belongs to special params then we skip it
            continue
        elif type(default_config[param]) == dict:
            if "run" in default_config[param].keys() and not w.A(["param", "run"], config):
            // if this is a rule that has a "run" parameter then
            // if run is not set to true in the config then skip this rule
                continue
            else:
            // otherwise update config rule parameters
                new_config[param] = default_config[param].update(config.get(param,""))
        else:
            // if it"s not a dict then it"s a general parameter
            // update the general parameter
            new_config[param] = config.get(param, default_config[param])

After Change

    config = workflow_object.config

    default_config = workflow_object.default_config
    new_config = config.copy()
    new_config["config_version"] = "1"

    //// Deal with special cases
    special_params = ["fasta_txt", "references_for_removal", "references_mode"]

Instances