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/Cnmops.scala

@@ -55,8 +55,8 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
    */
   def versionCheck: Boolean = {
     getVersion.flatMap(getSemanticVersion(_)) match {
-      case Some(version) =>  (version.major == 1 && version.minor >= 18) || version.major >= 2
-      case _ => false
+      case Some(version) => (version.major == 1 && version.minor >= 18) || version.major >= 2
+      case _             => false
     }
   }
 
@@ -74,7 +74,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
   lazy val outputCnv: File = {
     outputDir match {
       case Some(dir) => new File(dir, "cnv.txt")
-      case _                       => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNV output")
+      case _         => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNV output")
     }
   }
 
@@ -82,15 +82,15 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
   lazy val outputCnr: File = {
     outputDir match {
       case Some(dir) => new File(dir, "cnr.txt")
-      case _                       => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNR output")
+      case _         => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNR output")
     }
   }
 
   @Output(doc = "Raw output")
   lazy val rawOutput: File = {
     outputDir match {
-      case Some(dir)  => new File(dir, "rawoutput.txt")
-      case _                       => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS raw output")
+      case Some(dir) => new File(dir, "rawoutput.txt")
+      case _         => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS raw output")
     }
   }
 

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