Switch gatk parts to new memory limits

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -9,9 +9,6 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {
-  memoryLimit = Option(4)
-  override val defaultVmem = "8G"
-
   if (config.contains("scattercount")) scatterCount = config("scattercount", default = 1)
   if (config.contains("dbsnp")) knownSites :+= new File(config("dbsnp").asString)
   if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").asString)

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -15,7 +15,7 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
 
   jarFile = config("gatk_jar")
 
-  override val defaultVmem = "7G"
+  override val defaultCoreMemory = 4.0
 
   if (config.contains("intervals")) intervals = config("intervals").asFileList
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -9,10 +9,6 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
-  memoryLimit = Option(4)
-
-  override val defaultVmem = "8G"
-
   if (config.contains("scattercount")) scatterCount = config("scattercount")
 }
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -9,9 +9,6 @@ import java.io.File
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
-  override val defaultVmem = "6G"
-  memoryLimit = Some(2.5)
-
   if (config.contains("scattercount")) scatterCount = config("scattercount")
 
   if (config.contains("known")) known ++= config("known").asFileList