Optimize imports

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

@@ -19,7 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Created by pjvan_thof on 1/29/15.

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

@@ -15,10 +15,11 @@
  */
 package nl.lumc.sasc.biopet.extensions
 
+import java.io.File
+
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 /** Extension for zcat */
 class Zcat(val root: Configurable) extends BiopetCommandLineFunction {

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

@@ -15,10 +15,11 @@
  */
 package nl.lumc.sasc.biopet.extensions.bedtools
 
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
 /** Extension for bedtools coverage */
 class BedtoolsCoverage(val root: Configurable) extends Bedtools {
 

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

@@ -15,10 +15,11 @@
  */
 package nl.lumc.sasc.biopet.extensions.bedtools
 
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
 /**
  * Wrapper for the bedtools groupby tool
  * Written based on bedtools v2.21.0 (md5: b5a9a64bad721d96f6cbf2b3805b0fbe)

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

@@ -15,10 +15,11 @@
  */
 package nl.lumc.sasc.biopet.extensions.bedtools
 
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
 /** Extension for bedtools intersect */
 class BedtoolsIntersect(val root: Configurable) extends Bedtools {
 

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

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

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

@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.extensions.bwa
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

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

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

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

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

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

@@ -15,7 +15,6 @@
  */
 package nl.lumc.sasc.biopet.extensions.conifer
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
 
 abstract class Conifer extends PythonCommandLineFunction {

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

@@ -18,7 +18,6 @@ package nl.lumc.sasc.biopet.extensions.conifer
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.Ln
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 class ConiferAnalyze(val root: Configurable) extends Conifer {

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class ConiferCall(val root: Configurable) extends Conifer {
 

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.conifer
 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.{ Input, Output }
 
 class ConiferRPKM(val root: Configurable) extends Conifer {
 

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

@@ -2,14 +2,11 @@ package nl.lumc.sasc.biopet.extensions.delly
 
 import java.io.File
 
-import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
-import nl.lumc.sasc.biopet.core.BiopetQScript
-import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.Ln
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
 
 class Delly(val root: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)

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

@@ -2,10 +2,9 @@ package nl.lumc.sasc.biopet.extensions.delly
 
 import java.io.File
 
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction {
   executable = config("exe", default = "delly")

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
 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.{ Input, Output }
 
 /**
  * Created by pjvan_thof on 2/26/15.

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

@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
 import org.broadinstitute.gatk.utils.commandline.Input
 
 /**

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

@@ -16,9 +16,10 @@
 
 package nl.lumc.sasc.biopet.extensions.igvtools
 
+import java.io.{ File, FileNotFoundException }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
-import java.io.{ FileNotFoundException, File }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * IGVTools `count` wrapper

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

@@ -22,8 +22,6 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.util.matching.Regex
-
 /** Extension for Kraken */
 class Kraken(val root: Configurable) extends BiopetCommandLineFunction {
 

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.macs2
 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.{ Input, Output }
 
 /** Extension for macs2*/
 class Macs2CallPeak(val root: Configurable) extends Macs2 {