style changes

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

@@ -239,7 +239,7 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
         p.commands.last._outputAsStdout = true
         new BiopetPipe(p.commands ::: that :: Nil)
       }
-      case _             => new BiopetPipe(List(this, that))
+      case _ => new BiopetPipe(List(this, that))
     }
   }
 

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

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
  * This class can pipe multiple BiopetCommandFunctions to 1 job
@@ -33,7 +33,6 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
     stdoutFile = stdoutFile.map(_.getAbsoluteFile)
     stdinFile = stdinFile.map(_.getAbsoluteFile)
 
-
     if (stdoutFile.isDefined) {
       commands.last.stdoutFile = None
       commands.last._outputAsStdout = true

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.tools.{SeqStat, FastqSync}
+import nl.lumc.sasc.biopet.tools.{ SeqStat, FastqSync }
 import org.broadinstitute.gatk.queue.QScript
 
 class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.{Cat, Ln}
+import nl.lumc.sasc.biopet.extensions.{ Cat, Ln }
 
 class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq(root) {
   var fastqc: Fastqc = _
@@ -51,7 +51,7 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
       analysisName = getClass.getSimpleName + "-skip"
       (inputAsStdin, outputAsStsout) match {
         case (true, true) => super.cmdLine
-        case _ => Ln(this, input, output).cmd
+        case _            => Ln(this, input, output).cmd
       }
     }
   }