EcoPhylo modify anvi_profile --min-percent-identity

merenlab · Sep 13, 2023 · e264bf6 · e264bf6
1 parent a28088d
commit e264bf6
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/anvio/workflows/ecophylo/__init__.py b/anvio/workflows/ecophylo/__init__.py
@@ -84,7 +84,7 @@ def __init__(self, args=None, run=terminal.Run(), progress=terminal.Progress()):
         rule_acceptable_params_dict['remove_sequences_with_X_percent_gaps'] = ['--max-percentage-gaps']
         rule_acceptable_params_dict['fasttree'] = ['run']
         rule_acceptable_params_dict['iqtree'] = ['run', '-m', 'additional_params']
-        rule_acceptable_params_dict['run_metagenomics_workflow'] = ['clusterize', 'clusterize_submission_params', 'HPC_string', 'snakemake_additional_params', 'bowtie2_additional_params']
+        rule_acceptable_params_dict['run_metagenomics_workflow'] = ['clusterize', 'clusterize_submission_params', 'HPC_string', 'snakemake_additional_params', 'bowtie2_additional_params', 'anvi_profile_min_percent_identity']
 
         self.rule_acceptable_params_dict.update(rule_acceptable_params_dict)
 
@@ -293,6 +293,7 @@ def init(self):
         self.metagenomics_workflow_snakemake_additional_params = self.get_param_value_from_config(['run_metagenomics_workflow', 'snakemake_additional_params'])
 
         self.bowtie2_additional_params = self.get_param_value_from_config(['run_metagenomics_workflow','bowtie2_additional_params'])
+        self.anvi_profile_min_percent_identity = self.get_param_value_from_config(['run_metagenomics_workflow','anvi_profile_min_percent_identity'])
 
         metagenomics_workflow_snakemake_additional_params_list = self.metagenomics_workflow_snakemake_additional_params.split(' ')
 

diff --git a/anvio/workflows/ecophylo/rules/profile_mode.smk b/anvio/workflows/ecophylo/rules/profile_mode.smk
@@ -44,6 +44,9 @@ rule make_metagenomics_config_file:
         if M.bowtie2_additional_params:
             config_dict['bowtie']['additional_params'] = " ".join(["--no-unal", M.bowtie2_additional_params]) 
 
+        if M.anvi_profile_min_percent_identity:
+            config_dict['anvi_profile']['--min-percent-identity'] = M.anvi_profile_min_percent_identity
+
         with open(output.config, "w") as outfile:
             json.dump(config_dict, outfile, indent=4)