Paired- or single-end mode for StrandPhasR

Snake.config.json

@@ -23,7 +23,9 @@
         "medium"    : 0.33,
         "many"      : 0.9
     },
-    
+
+    "paired_end"    : false,
+
     "simulation_min_vaf" : 0.01,
     "simulation_max_vaf" : 1.0,
     "simulation_neg_binom_p" : {

Snakefile

@@ -398,7 +398,10 @@ rule prepare_strandphaser_config_per_chrom:
             print("[General]",                    file = f)
             print("numCPU           = 1",         file = f)
             print("chromosomes      = '" + wildcards.chrom + "'", file = f)
-            print("pairedEndReads   = TRUE",      file = f)
+            if (config["paired_end"]):
+                print("pairedEndReads   = TRUE",  file = f)
+            else:
+                print("pairedEndReads   = FALSE", file = f)
             print("min.mapq         = 10",        file = f)
             print("",                             file = f)
             print("[StrandPhaseR]",               file = f)