Move Bowtie2 to package bowtie

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie2.scala → public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala

-package nl.lumc.sasc.biopet.extensions
+package nl.lumc.sasc.biopet.extensions.bowtie
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
+import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
 /**
  * Extension for bowtie 2

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

@@ -20,7 +20,7 @@ import java.util.Date
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.bowtie.Bowtie
+import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie2, Bowtie}
 import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }