use correct location for time limit

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

@@ -58,11 +58,6 @@ 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 =>
@@ -104,7 +99,6 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
 
     _pipesJobs.foreach(_.beforeGraph())
     _pipesJobs.foreach(_.internalBeforeGraph())
-    jobWallClockTimeLimit.foreach(x => jobNativeArgs = jobNativeArgs.toList ::: List(s"-l h_rt=$x"))
 
   }
 

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

@@ -18,7 +18,7 @@ import java.io.File
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
-import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
 import nl.lumc.sasc.biopet.utils.{ ConfigUtils, FastaUtils, Logging }
 
 import scala.collection.JavaConversions._

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

@@ -22,6 +22,8 @@ import org.broadinstitute.gatk.utils.commandline._
 
 class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
 
+  override def defaults = Map("max_walltime_limit" -> 7200)
+
   @Input(doc = "BAMfile", required = true)
   var input: File = _
 
@@ -127,9 +129,6 @@ class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Refer
   override def defaultThreads = 4
   override def defaultCoreMemory = 50
 
-  // wallclock time limit in seconds
-  jobWallClockTimeLimit = config("job_wall_time_limit", namespace = "freec", default = 7200)
-
   private var configFile: File = _
 
   override def beforeGraph {

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnmopsMethod.scala

 package nl.lumc.sasc.biopet.pipelines.kopisu.methods
 
-import htsjdk.samtools.{SAMSequenceDictionary, SamReaderFactory}
+import htsjdk.samtools.{ SAMSequenceDictionary, SamReaderFactory }
 import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.extensions.Cnmops
 import nl.lumc.sasc.biopet.utils.config.Configurable