Fix threads / memlimit

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

@@ -41,7 +41,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
       threads = 1
       logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
     }
-    nct = Some(threads)
+    nct = Some(getThreads(1))
     memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
   }
 

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

@@ -15,7 +15,7 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
     if (config.contains("scattercount")) scatterCount = config("scattercount")
     if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
     this.sample_ploidy = config("ploidy")
-    nct = config("threads", default = 1)
+    nct = Some(getThreads(1))
     memoryLimit = Option(nct.getOrElse(1) * 2)
     if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
     if (config.contains("output_mode")) {