Code style fix

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 

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

@@ -19,7 +19,7 @@ import java.io.File
 
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
-import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 /**

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 

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

@@ -45,9 +45,9 @@ import nl.lumc.sasc.biopet.tools.{ MergeTables, WipeReads }
  * @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
  */
 class Gentrap(val root: Configurable) extends QScript
-    with MultiSampleQScript
-    with SummaryQScript
-    with Reference { qscript =>
+  with MultiSampleQScript
+  with SummaryQScript
+  with Reference { qscript =>
 
   import Gentrap._
   import Gentrap.ExpMeasures._

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -109,9 +109,9 @@ class MappingTest extends TestNGSuite with Matchers {
 
     // Sort sam or replace readgroup
     val sort = aligner match {
-      case "bwa" | "bwa-aln" | "stampy"     => "sortsam"
+      case "bwa" | "bwa-aln" | "stampy" => "sortsam"
       case "star" | "star-2pass" | "bowtie" | "gsnap" | "tophat" => "replacereadgroups"
-      case _                                => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
+      case _ => throw new IllegalArgumentException("aligner: " + aligner + " does not exist")
     }
 
     mapping.functions.count(_.isInstanceOf[SortSam]) shouldBe ((if (sort == "sortsam") 1 else 0) * chunks)