add mapping on ribosomal RNA

Snakefile

@@ -125,13 +125,15 @@ ref = [ config["genome"]["name"] ]
 if config["genome"]["host_mapping"]:
     ref += [ config["genome"]["host_name"] ]
 elif config["genome"]["rRNA_mapping"]:
-    ref += [ config["genome"]["ribo_fasta_file"] ]
+    ref += [ "Ribo" ]
 
 def mapping_index(wildcards):
     if (wildcards.REF == config["genome"]["name"]):
         input = config["genome"]["fasta_file"]
     elif (wildcards.REF == config["genome"]["host_name"]):
         input = config["genome"]["host_fasta_file"]
+    elif (wildcards.REF == "Ribo" ):
+        input = config["genome"]["ribo_fasta_file"]    
     return(input)
     
 def annot_index(wildcards):
@@ -139,6 +141,8 @@ def annot_index(wildcards):
         input = config["genome"]["gff_file"]
     elif (wildcards.REF == config["genome"]["host_name"]):
         input = config["genome"]["host_gff_file"]
+    elif (wildcards.REF == "Ribo" ):
+        input = ""
     return(input)
 
 
@@ -233,6 +237,9 @@ def counting_index(wildcards):
 
 
 if config["feature_counts"]["do"]: 
+    #if mapping on ribosomal RNA done, do not perform counting
+    if "Ribo" in ref:
+        ref.pop()
 
     feature_counts_input = counting_index
     feature_counts_output_count = "03-Counting/{MAP}/{REF}/{SAMPLE}_{REF}_feature.out"

config/config.yaml

@@ -63,7 +63,7 @@ genome:
     host_name: hg38
     host_fasta_file: /home/rlegendre/Documents/RNAflow/genome/hg38.fa
     host_gff_file: /home/rlegendre/Documents/RNAflow/genome/hg38.gff
-    rRNA_mapping: false
+    rRNA_mapping: true
     ribo_fasta_file: /home/rlegendre/Documents/RNAflow/genome/hg38.fa    
 
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