Merge pull request #883 from chriswyatt1/cs_cluster_1cpu

Added scratch location

Author: chriswyatt1

conf/ucl_cscluster.config

@@ -12,10 +12,14 @@ executor {
 singularity.runOptions = "-B ${HOME},${PWD}"
 
 process {
-
-    //NEED TO SET PARALLEL ENVIRONMENT TO SMP SO MULTIPLE CPUS CAN BE SUBMITTED
-    penv           = 'smp'
-
-    //ADD MEMORY TO CLUSTEROPTIONS
-    clusterOptions = { "-S /bin/bash -l tmem=${task.memory.mega}M,h_vmem=${task.memory.mega}M" }
+    scratch = "/scratch0/${USER}/"
+    executor = 'sge'
+    penv = { task.cpus > 1 ? 'smp' : '' }
+    clusterOptions = {
+        def mem = task.memory.mega
+        def cpus = task.cpus
+        def baseOpts = "-S /bin/bash -l tmem=${mem}M,h_vmem=${mem}M "
+        def peOpts = cpus > 1 ? " -R y " : ""
+        return baseOpts + peOpts
+    }
 }