Style updates

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -95,7 +95,7 @@ class Gentrap(val root: Configurable) extends QScript
       case otherwise   => throw new IllegalStateException(otherwise.toString)
     })) ++ (ribosomalRefFlat match {
       case Some(rbs) => Map("ribosomal_intervals" -> rbs.toString)
-      case None => Map()
+      case None      => Map()
     })
 
   /** Default pipeline config */

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -377,7 +377,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     sorter.sortOrder = "coordinate"
     sorter.isIntermediate = true
     add(sorter)
-    
+
     // merge with mapped file
     val mergeSamFile = MergeSamFiles(this, List(tophat.outputAcceptedHits, sorter.output),
       tophat.output_dir, "coordinate")

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala

@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Wrapper for the tophat-recondition.py script.
- * 
+ *
  * NOTE: we are modifying the input and output to be the BAM files directly so the wrapper works nice with Queue.
  */
 class TophatRecondition(val root: Configurable) extends PythonCommandLineFunction {
@@ -45,6 +45,6 @@ class TophatRecondition(val root: Configurable) extends PythonCommandLineFunctio
     require(inputBam != null, "Input must be defined.")
     require(outputSam != null, "Output must be defined.")
   }
-  
+
   def cmdLine = getPythonCommand + required(inputDir) + required(outputDir)
 }