refactor memorylimit

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala

@@ -28,7 +28,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
   var residentFactor: Double = config("resident_factor", default = 1.2)
 
   private var _coreMemory: Double = 2.0
-  def coreMemeory = _coreMemory
+  def coreMemory = _coreMemory
 
   var retry = 0
 
@@ -89,7 +89,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
     commands.foreach(_.setResources())
     nCoresRequest = Some(commands.map(_.threads).sum)
 
-    _coreMemory = commands.map(cmd => cmd.coreMemeory * (cmd.threads.toDouble / threads.toDouble)).sum
+    _coreMemory = commands.map(cmd => cmd.coreMemory * (cmd.threads.toDouble / threads.toDouble)).sum
     memoryLimit = Some(_coreMemory * threads)
     residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor)
     vmem = Some((_coreMemory * (vmemFactor + (0.5 * retry))) + "G")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

@@ -29,6 +29,8 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input wig file")
   var inputWigFile: File = _
 
+  override def defaultCoreMemory = 3.0
+
   @Input(doc = "Input chrom sizes file", required = true)
   var inputChromSizesFile: File = _
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala

@@ -27,7 +27,7 @@ class SamtoolsSort(val root: Configurable) extends Samtools {
   }
 
   def cmdLine = required(executable) + required("sort") +
-    optional("-m", (coreMemeory + "G")) +
+    optional("-m", (coreMemory + "G")) +
     optional("-@", threads) +
     optional("-O", outputFormat) +
     required("-T", prefix) +