GC options can now be set through the config

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

@@ -5,6 +5,10 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
   executable = "java"
 
+  javaGCThreads = config("java_gc_threads")
+  javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
+  javaGCTimeLimit = config("java_gc_timelimit")
+
   override def afterGraph {
     memoryLimit = config("memory_limit")
   }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala

@@ -6,7 +6,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 class SamToFastq(val root: Configurable) extends Picard {
   javaMainClass = "picard.sam.SamToFastq"
-  javaGCThreads = config("gcthreads", default = 2)
 
   @Input(doc = "The input SAM or BAM files to analyze.", required = true)
   var input: File = _