fixed bug on iter mode (iqtree)

Author: y3tseng

workflow/config.yaml

@@ -35,3 +35,10 @@ matrix: ""
 
 # Iterative Mode
 mask_gappy: 0.995                         # Minimum proportion of gappy sites that would be mask before proceed to tree inference step
+
+
+# IQ-TREE Model Selection
+# Automatically determine the best model without specifying one, though this may take some time.
+# If you would like to speed up the process, please specify a model (e.g., "-m GTR"). 
+# See "https://iqtree.github.io/doc/Substitution-Models" for more details on available models.
+iqtree_model: ""

workflow/rules/iqtree.smk

@@ -5,15 +5,15 @@ rule iqtree:
     params:
         iqtree_exe=config["iqtree"],
         temp=config["work_dir"],
-        model="",
+        model=config["iqtree_model"],
         threshold=config["mask_gappy"],
         tempFile=config["work_dir"]+"/msa.mask.fa"
     threads: config["num_threads"]
     shell:
         '''
         python3 scripts/reduceLen.py {input.msa} {params.tempFile} {params.threshold}
         {params.iqtree_exe} -s {params.tempFile} {params.model} --threads-max {threads}
-        mv {params.temp}/msa_iter1.mask.fa.treefile {output}
-        rm {params.temp}/msa_iter1.mask.fa.*
+        mv {params.temp}/msa.mask.fa.treefile {output}
+        rm {params.temp}/msa.mask.fa.*
         rm {params.tempFile}
         '''