Optimize imports

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.ApplyRecalibration with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.BaseRecalibrator with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class CombineGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineGVCFs with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class CombineVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.CombineVariants with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
 trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class SelectVariants(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.SelectVariants with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class VariantAnnotator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantAnnotator with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -6,6 +6,7 @@
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala

@@ -5,10 +5,10 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+
 import scala.util.Random
 
 class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with BiopetQScript {

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

@@ -5,11 +5,10 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{ SelectVariants, GenotypeGVCFs }
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ GenotypeGVCFs, SelectVariants }
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
 class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -5,20 +5,18 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.MultiSampleQScript
-import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.core.config.Configurable
 import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineVariants, CombineGVCFs }
-import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
-import scala.collection.JavaConversions._
-import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
-import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ CombineGVCFs, CombineVariants }
+import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, SamToFastq }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
+import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Argument }
+
+import scala.collection.JavaConversions._
 
 class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript {
   qscript =>

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala

@@ -5,8 +5,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-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.gatk.broad.{ ApplyRecalibration, VariantAnnotator, VariantRecalibrator }
 import org.broadinstitute.gatk.queue.QScript

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -5,17 +5,18 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.tools.{ VcfStats, MpileupToVcf, VcfFilter, MergeAlleles }
-import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
+import nl.lumc.sasc.biopet.tools.{ MergeAlleles, MpileupToVcf, VcfFilter, VcfStats }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
-import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+
 import scala.collection.SortedMap
 import scala.language.reflectiveCalls
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaVariantcallingTrait, ShivaTrait }
+import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, ShivaVariantcallingTrait }
 import org.broadinstitute.gatk.queue.QScript
 
 /**

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import java.io.{ FileOutputStream, File }
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
@@ -17,7 +17,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ Test, DataProvider }
+import org.testng.annotations.{ DataProvider, Test }
 
 /**
  * Created by pjvan_thof on 3/2/15.

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

@@ -5,19 +5,19 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import java.io.{ FileOutputStream, File }
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{ UnifiedGenotyper, HaplotypeCaller }
-import nl.lumc.sasc.biopet.tools.{ VcfStats, MpileupToVcf, VcfFilter }
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ HaplotypeCaller, UnifiedGenotyper }
+import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter, VcfStats }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test, AfterClass }
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 import scala.collection.mutable.ListBuffer
 

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -22,7 +22,6 @@ import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions.WigToBigWig
 import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
  * Created by pjvan_thof on 1/29/15.

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala

@@ -15,12 +15,13 @@
  */
 package nl.lumc.sasc.biopet.pipelines.bamtobigwig
 
-import java.io.{ PrintWriter, File }
+import java.io.{ File, PrintWriter }
 
 import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.queue.function.InProcessFunction
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import scala.collection.JavaConversions._
 
 /**

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -15,16 +15,17 @@
  */
 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
-import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.scripts.CoverageStats
-import org.broadinstitute.gatk.queue.QScript
-import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, PipelineCommand }
 import java.io.File
-import nl.lumc.sasc.biopet.tools.BiopetFlagstat
+
 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.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
+import nl.lumc.sasc.biopet.scripts.CoverageStats
+import nl.lumc.sasc.biopet.tools.BiopetFlagstat
+import org.broadinstitute.gatk.queue.QScript
 
 class BamMetrics(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
   def this() = this(null)

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
-import java.io.{ PrintWriter, File }
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportPage, ReportSection }
-import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
-import nl.lumc.sasc.biopet.extensions.rscript.{ XYPlot, StackedBarPlot }
+import nl.lumc.sasc.biopet.core.summary.{ Summary, SummaryValue }
+import nl.lumc.sasc.biopet.extensions.rscript.{ StackedBarPlot, XYPlot }
 
 /**
  * Created by pjvan_thof on 3/30/15.

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
-import java.io.{ FileOutputStream, File }
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
@@ -14,7 +14,7 @@ import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ Test, DataProvider, AfterClass }
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 /**
  * Created by pjvan_thof on 4/30/15.

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

@@ -21,10 +21,10 @@
 package nl.lumc.sasc.biopet.pipelines.basty
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.core.MultiSampleQScript
-import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.extensions.{ RunGubbins, Cat, Raxml }
-import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, Shiva }
+import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
+import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
 import nl.lumc.sasc.biopet.tools.BastyGenerateFasta
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 

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

@@ -15,15 +15,16 @@
  */
 package nl.lumc.sasc.biopet.core
 
-import java.io.File
+import java.io.{ File, FileInputStream }
+import java.security.MessageDigest
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.queue.function.CommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.Input
+
 import scala.collection.mutable
 import scala.sys.process.{ Process, ProcessLogger }
 import scala.util.matching.Regex
-import java.io.FileInputStream
-import java.security.MessageDigest
 
 /** Biopet command line trait to auto check executable and cluster values */
 trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {

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

@@ -16,12 +16,12 @@
 package nl.lumc.sasc.biopet.core
 
 import java.io.{ PrintWriter, StringWriter }
-import scala.io.Source
 
+import nl.lumc.sasc.biopet.core.BiopetExecutable._
+import nl.lumc.sasc.biopet.{ FullVersion, LastCommitHash }
 import org.apache.log4j.Logger
 
-import nl.lumc.sasc.biopet.{ FullVersion, LastCommitHash }
-import nl.lumc.sasc.biopet.core.BiopetExecutable._
+import scala.io.Source
 
 /**
  * This is the main trait for the biopet executable

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

@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import org.broadinstitute.gatk.queue.QSettings
 import org.broadinstitute.gatk.queue.function.QFunction
 import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
-import org.broadinstitute.gatk.queue.util.{Logging => GatkLogging}
+import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 import org.broadinstitute.gatk.utils.commandline.Argument
 
 import scala.collection.mutable.ListBuffer

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
+import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.Argument
 

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

@@ -15,12 +15,12 @@
  */
 package nl.lumc.sasc.biopet.core
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
-import org.apache.log4j.{PatternLayout, WriterAppender}
-import org.broadinstitute.gatk.queue.util.{Logging => GatkLogging}
+import org.apache.log4j.{ PatternLayout, WriterAppender }
+import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 
 /** Wrapper around executable from Queue */
 trait PipelineCommand extends MainCommand with GatkLogging {

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

@@ -4,6 +4,7 @@ import java.io.File
 
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import nl.lumc.sasc.biopet.core.config.Configurable
+
 import scala.collection.JavaConversions._
 
 /**

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

@@ -38,7 +38,7 @@ trait ToolCommand extends MainCommand with Logging {
       }
     } text "Log level" validate {
       case "debug" | "info" | "warn" | "error" => success
-      case _ => failure("Log level must be <debug/info/warn/error>")
+      case _                                   => failure("Log level must be <debug/info/warn/error>")
     }
     opt[Unit]('h', "help") foreach { _ =>
       System.err.println(this.usage)

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

@@ -15,7 +15,8 @@
  */
 package nl.lumc.sasc.biopet.core.config
 
-import java.io.{ PrintWriter, File }
+import java.io.{ File, PrintWriter }
+
 import nl.lumc.sasc.biopet.core.Logging
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.ConfigUtils._

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

@@ -16,6 +16,7 @@
 package nl.lumc.sasc.biopet.core.config
 
 import java.io.File
+
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 
 class ConfigValue(val requestIndex: ConfigValueIndex, val foundIndex: ConfigValueIndex, val value: Any, val default: Boolean) {

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

@@ -2,11 +2,11 @@ package nl.lumc.sasc.biopet.core.report
 
 import java.io._
 
-import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.summary.Summary
-import org.broadinstitute.gatk.utils.commandline.Input
-import org.fusesource.scalate.{ TemplateSource, TemplateEngine }
+import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
 import nl.lumc.sasc.biopet.utils.IoUtils
+import org.broadinstitute.gatk.utils.commandline.Input
+import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
 
 /**
  * Created by pjvan_thof on 3/27/15.

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

@@ -15,7 +15,7 @@ class Summary(file: File) {
   lazy val samples: Set[String] = {
     ConfigUtils.getValueFromPath(map, List("samples")) match {
       case Some(s) => ConfigUtils.any2map(s).keySet
-      case _             => Set()
+      case _       => Set()
     }
   }
 

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

@@ -16,16 +16,16 @@
 package nl.lumc.sasc.biopet.core.summary
 
 import java.io.{ File, PrintWriter }
-import scala.collection.mutable
-import scala.io.Source
 
-import org.broadinstitute.gatk.queue.function.{ QFunction, InProcessFunction }
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
-
-import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, BiopetCommandLineFunction, BiopetCommandLineFunctionTrait, SampleLibraryTag }
 import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetCommandLineFunctionTrait, BiopetJavaCommandLineFunction, SampleLibraryTag }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
+import org.broadinstitute.gatk.queue.function.{ InProcessFunction, QFunction }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import scala.collection.mutable
+import scala.io.Source
 
 /**
  * Created by pjvan_thof on 2/14/15.

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

@@ -45,24 +45,21 @@
 
 package nl.lumc.sasc.biopet.core.workaround
 
-import collection.JavaConversions._
 import java.io.{ File, FileOutputStream }
-import java.net.URL
-import java.util.{ ResourceBundle, Arrays }
+import java.util.{ Arrays, ResourceBundle }
 
-import org.apache.commons.io.FilenameUtils
-import org.broadinstitute.gatk.utils.commandline._
-import org.broadinstitute.gatk.queue.util._
+import nl.lumc.sasc.biopet.FullVersion
+import nl.lumc.sasc.biopet.core.Logging
+import org.broadinstitute.gatk.queue.engine.{ QGraph, QGraphSettings }
+import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging, ScalaCompoundArgumentTypeDescriptor, ClassFieldCache }
 import org.broadinstitute.gatk.queue.{ QCommandPlugin, QScript, QScriptManager }
-import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
-import org.broadinstitute.gatk.queue.engine.{ QStatusMessenger, QGraphSettings, QGraph }
 import org.broadinstitute.gatk.utils.classloader.PluginManager
-import org.broadinstitute.gatk.utils.exceptions.UserException
-import org.broadinstitute.gatk.utils.io.IOUtils
+import org.broadinstitute.gatk.utils.commandline._
 import org.broadinstitute.gatk.utils.help.ApplicationDetails
+import org.broadinstitute.gatk.utils.io.IOUtils
 import org.broadinstitute.gatk.utils.text.TextFormattingUtils
 
-import nl.lumc.sasc.biopet.FullVersion
+import scala.collection.JavaConversions._
 
 /**
  * Entry point of Queue.  Compiles and runs QScripts passed in to the command line.