submodules pb

Author: gregdenay

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "scripts/--force"]
+	path = scripts/--force
+	url = https://github.com/CVUA-RRW/taxidTools
+[submodule "taxidTools"]
+	path = taxidTools
+	url = https://github.com/CVUA-RRW/taxidTools

README.md

@@ -18,7 +18,7 @@ or using 'git clone':
 
 ```bash
 cd path/to/repo/
-git clone https://github.com/CVUA-RRW/BAnalyzer.git
+git clone --recurse-submodules https://github.com/CVUA-RRW/BAnalyzer.git
 ```
 
 Set up a conda environment containing snakemake, python and the pandas library and activate it:

Snakefile

@@ -309,6 +309,16 @@ rule db_stats:
         
         echo $(( $(grep -c "^>" {input.unfiltered}) - $(grep -c "^>" {input.seq}) )) > {output.highN}
         """
+        
+rule get_consensus_level:
+    input:
+        distance_table = "reports/distances.tsv",
+    output:
+        cons = "reports/consensus.tsv"
+    message:
+        "Determining consensus ranks"
+    script:
+        "../scripts/consensus_levels.py"
 
 rule write_report:
     input: