removed dup

cluster.json

@@ -26,13 +26,6 @@
         "out"       : "{rule}_{wildcards.sample}.out"
     },
 
-    "merge_bams" :
-    {
-        "time"      : "12:00:00",
-        "cores"     : 10,
-        "mem"       : "16g"
-    },
-
     "freebayes" :
     {
         "jobname"   : "{rule}",
@@ -66,15 +59,6 @@
         "out"       : "{rule}_{wildcards.sample}.out"
     },
 
-    "trim_and_merge_pe"  :
-    {
-        "jobname"   : "{rule}_{wildcards.sample}",
-        "time"      : "08:00:00",
-        "cores"     : 4,
-        "mem"       : "16g",
-        "out"       : "{rule}_{wildcards.sample}.out"
-    },
-
     "cutadapt_pe"  :
     {
         "jobname"   : "{rule}_{wildcards.sample}",
@@ -314,6 +298,26 @@
         "mem"       : "2g"
     },
 
+
+    "MarkDuplicates" :
+    {
+        "jobname"   : "{rule}_{wildcards.sample}",
+        "time"      : "36:00:00",
+        "cores"     : 1,
+        "mem"       : "7g",
+        "out"       : "{rule}_{wildcards.sample}.out"
+    },
+
+    "SplitNCigarReads" :
+    {
+        "jobname"   : "{rule}_{wildcards.sample}",
+        "time"      : "36:00:00",
+        "cores"     : 1,
+        "mem"       : "7g",
+        "out"       : "{rule}_{wildcards.sample}.out"
+    },
+
+
     "gatk4_hc" :
     {
         "jobname"   : "{rule}_{wildcards.sample}-{wildcards.mychr}",