Specify phylophlan params for trimming

biobakery · Sep 27, 2023 · d4f1cff · d4f1cff
1 parent 39c927d
commit d4f1cff
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/metaphlan/utils/phylophlan_controller.py b/metaphlan/utils/phylophlan_controller.py
@@ -90,7 +90,8 @@ def execute_phylophlan(self, samples_markers_dir, tmp_dir):
         cmd = f'phylophlan' \
               f' -i {samples_markers_dir} -o . --output_folder {self.output_dir} --nproc {self.nprocs}' \
               f' --strainphlan --{self.phylophlan_mode} --data_folder {tmp_dir} -f {self.phylophlan_configuration}' \
-              f' -t n --diversity low --genome_extension fna --min_num_entries 1 --min_num_markers 1'
+              f' -t n --diversity low --genome_extension fna --min_num_entries 1 --min_num_markers 1' \
+              f' --fragmentary_threshold 1.0 --not_variant_threshold 1.0 --gap_perc_threshold 0.8'
 
         if self.phylophlan_params is not None:
             cmd += " " + self.phylophlan_params