30fbe7d024c86566a2178d03f4e8bbf388b868fa,anvio/workflows/phylogenomics/__init__.py,PhylogenomicsWorkflow,sanity_checks,#PhylogenomicsWorkflow#,82

Before Change

    def sanity_checks(self):
        if not self.get_rule_param("anvi_get_sequences_for_hmm_hits", "--gene-names"):
            raise ConfigError("You must provide a list of genes to use for the phylogenomics. \
                         To do so, please use the "--gene-names" parameter of rule anvi_get_sequences_for_hmm_hits.")

        if not self.get_rule_param("anvi_get_sequences_for_hmm_hits", "--return-best-hit"):
            run.warning("You changed the value for --return-best-hit for the rule anvi_get_sequences_for_hmm_hits \
                         to something other than the default value, which is "true", while we allow you to do it \

After Change

    def sanity_checks(self):
        if not self.get_rule_param("anvi_get_sequences_for_hmm_hits", "--gene-names"):
            run.warning("You did not provide a list of genes to use for phylogenomics. This is ok and things might work \
                        but we wanted to make sure this is intended. If you change your mind, you can provide a list of genes \
                        by using the "--gene-names" parameter of rule anvi_get_sequences_for_hmm_hits.")

        if not self.get_rule_param("anvi_get_sequences_for_hmm_hits", "--return-best-hit"):
            run.warning("You changed the value for --return-best-hit for the rule anvi_get_sequences_for_hmm_hits \
                         to something other than the default value, which is "true", while we allow you to do it \

Instances