Sync with develop

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

@@ -18,8 +18,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
-
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class CatVariants(val root: Configurable) extends Gatk {
   val analysisType = "CatVariants"
@@ -32,7 +31,7 @@ class CatVariants(val root: Configurable) extends Gatk {
 
   override def cmdLine = super.cmdLine +
     (for (file <- inputFiles) yield {
-        required("-V", file)
+      required("-V", file)
     }).mkString +
     required("-o", outputFile)
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Delly.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
 import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
@@ -66,7 +66,6 @@ class Delly(val root: Configurable) extends QScript with Reference with SummaryQ
     )
   }
 
-
   def biopetScript() {
     // write the pipeline here
     logger.info("Configuring Delly pipeline")

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 
 import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, SampleLibraryTag}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
 import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
 import nl.lumc.sasc.biopet.utils.Logging