Style fixes

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

@@ -5,8 +5,8 @@ import java.io.File
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /**
-  * Created by pjvan_thof on 11/20/15.
-  */
+ * Created by pjvan_thof on 11/20/15.
+ */
 trait TargetRegions extends Configurable {
   /** Bed files for region of interests */
   var roiBedFiles: List[File] = config("regions_of_interest", Nil)

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

@@ -135,7 +135,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
         that.biopetScript()
         this match {
           case s: SummaryQScript => s.addSummaryQScript(that)
-          case _ =>
+          case _                 =>
         }
       case that: BiopetQScript =>
         that.init()

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala

 /**
-  * Biopet is built on top of GATK Queue for building bioinformatic
-  * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
-  * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
-  * should also be able to execute Biopet tools and pipelines.
-  *
-  * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-  *
-  * Contact us at: sasc@lumc.nl
-  *
-  * A dual licensing mode is applied. The source code within this project that are
-  * not part of GATK Queue is freely available for non-commercial use under an AGPL
-  * license; For commercial users or users who do not want to follow the AGPL
-  * license, please contact us to obtain a separate license.
-  */
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
 package nl.lumc.sasc.biopet.extensions.vt
 
 import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 
 /**
-  * General bwa extension
-  *
-  * Created by pjvan_thof on 1/16/15.
-  */
+ * General bwa extension
+ *
+ * Created by pjvan_thof on 1/16/15.
+ */
 abstract class Vt extends BiopetCommandLineFunction {
   override def subPath = "vt" :: super.subPath
   executable = config("exe", default = "vt")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala

@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.vt
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, Version}
+import nl.lumc.sasc.biopet.core.{ Reference, Version }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
-  * Created by pjvanthof on 20/11/15.
-  */
+ * Created by pjvanthof on 20/11/15.
+ */
 class VtDecompose(val root: Configurable) extends Vt with Version with Reference {
   def versionRegex = """decompose (.*)""".r
   override def versionExitcode = List(0, 1)

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala

@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.vt
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, Version}
+import nl.lumc.sasc.biopet.core.{ Reference, Version }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
-  * Created by pjvanthof on 20/11/15.
-  */
+ * Created by pjvanthof on 20/11/15.
+ */
 class VtNormalize(val root: Configurable) extends Vt with Version with Reference {
   def versionRegex = """normalize (.*)""".r
   override def versionExitcode = List(0, 1)

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

@@ -116,7 +116,8 @@ object ShivaReport extends MultisampleReportBuilder {
       )).toList.sortBy(_._1),
       List(),
       Map())
-    ) else None
+    )
+    else None
   }
 
   /** Files page, can be used general or at sample level */
@@ -192,7 +193,7 @@ object ShivaReport extends MultisampleReportBuilder {
     def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
       val path = target match {
         case Some(t) => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller-$t", "genotype")
-        case _ => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "genotype")
+        case _       => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "genotype")
       }
       val homVar = new SummaryValue(path :+ "HomVar", summary, Some(sample), lib).value.getOrElse(0).toString.toLong
       val homRef = new SummaryValue(path :+ "HomRef", summary, Some(sample), lib).value.getOrElse(0).toString.toLong

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 nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{Delly, Breakdancer, Clever, SvCaller}
+import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Delly, Breakdancer, Clever, SvCaller }
 import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript

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

@@ -19,7 +19,7 @@ import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, Reference }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, SamToFastq }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.{TargetRegions, BamMetrics}
+import nl.lumc.sasc.biopet.pipelines.bammetrics.{ TargetRegions, BamMetrics }
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
 import nl.lumc.sasc.biopet.utils.Logging

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

@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
 import nl.lumc.sasc.biopet.extensions.tools.VcfStats
-import nl.lumc.sasc.biopet.extensions.vt.{VtDecompose, VtNormalize}
+import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
 import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers._
 import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }

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

 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerVCF, BreakdancerCaller, BreakdancerConfig}
+import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerVCF, BreakdancerCaller, BreakdancerConfig }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caler Breakdancer */

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

 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.core.{Reference, BiopetQScript}
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetQScript }
 import org.broadinstitute.gatk.queue.QScript
 
 /**
-  * Created by pjvanthof on 23/11/15.
-  */
+ * Created by pjvanthof on 23/11/15.
+ */
 trait SvCaller extends QScript with BiopetQScript with Reference {
 
   /** Name of mode, this should also be used in the config */