jobtimelimit in core

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -58,6 +58,11 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
    */
   var jobDelayTime: Option[Int] = config("job_delay_time")
 
+  /**
+    * wall clock time limit in seconds for a job
+    */
+  var jobWallClockTimeLimit: Option[Int] = config("job_wall_time_limit")
+
   // This overrides the default "sh" from queue. For Biopet the default is "bash"
   updateJobRun = {
     case jt: JobTemplate =>
@@ -99,6 +104,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
     _pipesJobs.foreach(_.beforeGraph())
     _pipesJobs.foreach(_.internalBeforeGraph())
+    jobWallClockTimeLimit.foreach(x => jobNativeArgs = jobNativeArgs.toList ::: List(s"-l h_rt=$x"))
 
   }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala

@@ -128,9 +128,7 @@ class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Refer
   override def defaultCoreMemory = 50
 
   // wallclock time limit in seconds
-  var wallClockTimeLimit: Int = config("wall_time_limit", namespace = "freec", default = 7200)
-
-  jobNativeArgs = jobNativeArgs.toList ::: List(s"-l h_rt=$wallClockTimeLimit")
+  jobWallClockTimeLimit = config("job_wall_time_limit", namespace = "freec", default = 7200)
 
   private var configFile: File = _