Style fixes

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala

@@ -19,7 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Wrapper for the Cnmops command line tool.

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala

@@ -15,9 +15,9 @@
  */
 package nl.lumc.sasc.biopet.extensions.freec
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline._
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCAssessSignificancePlot.scala

@@ -4,7 +4,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
 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 FreeCAssessSignificancePlot(val root: Configurable) extends RscriptCommandLineFunction {
   protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/freec/freec_assess_significance.R")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala

@@ -4,7 +4,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
 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 FreeCBAFPlot(val root: Configurable) extends RscriptCommandLineFunction {
   protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/freec/freec_BAFPlot.R")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala

@@ -4,7 +4,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
 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 FreeCCNVPlot(val root: Configurable) extends RscriptCommandLineFunction {
   protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.R")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
 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 SambambaMpileup(val root: Configurable) extends Sambamba {
   override val defaultThreads = 4

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala

@@ -5,8 +5,8 @@ import nl.lumc.sasc.biopet.core.Reference
 import org.broadinstitute.gatk.queue.QScript
 
 /**
-  * Created by pjvanthof on 10/05/16.
-  */
+ * Created by pjvanthof on 10/05/16.
+ */
 trait CnvMethod extends QScript with SummaryQScript with Reference {
 
   /** Name of mode, this should also be used in the config */

kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala

@@ -2,51 +2,52 @@ package nl.lumc.sasc.biopet.pipelines.kopisu.methods
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.extensions.freec.{FreeC, FreeCAssessSignificancePlot, FreeCBAFPlot, FreeCCNVPlot}
+import nl.lumc.sasc.biopet.extensions.freec.{ FreeC, FreeCAssessSignificancePlot, FreeCBAFPlot, FreeCCNVPlot }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /**
-  * Created by pjvanthof on 10/05/16.
-  */
+ * Created by pjvanthof on 10/05/16.
+ */
 class FreecMethod(val root: Configurable) extends CnvMethod {
   def name = "freec"
 
   var snpFile: Option[File] = config("snp_file", freeVar = false)
 
   def biopetScript: Unit = {
-    inputBams.foreach { case (sampleName, bamFile) =>
+    inputBams.foreach {
+      case (sampleName, bamFile) =>
 
-      val sampleOutput = new File(outputDir, sampleName)
+        val sampleOutput = new File(outputDir, sampleName)
 
-      val freec = new FreeC(this)
-      freec.input = bamFile
-      freec.inputFormat = Some("BAM")
-      freec.outputPath = sampleOutput
-      freec.snpFile = snpFile
-      add(freec)
+        val freec = new FreeC(this)
+        freec.input = bamFile
+        freec.inputFormat = Some("BAM")
+        freec.outputPath = sampleOutput
+        freec.snpFile = snpFile
+        add(freec)
 
-      /*
+        /*
       * These scripts will wait for FreeC to Finish
       *
       * R-scripts to plot FreeC results
       * */
-      val fcAssessSignificancePlot = new FreeCAssessSignificancePlot(this)
-      fcAssessSignificancePlot.cnv = freec.cnvOutput
-      fcAssessSignificancePlot.ratios = freec.ratioOutput
-      fcAssessSignificancePlot.output = new File(sampleOutput, sampleName + ".freec_significant_calls.txt")
-      add(fcAssessSignificancePlot)
-
-      val fcCnvPlot = new FreeCCNVPlot(this)
-      fcCnvPlot.input = freec.ratioOutput
-      fcCnvPlot.output = new File(sampleOutput, sampleName + ".freec_cnv")
-      add(fcCnvPlot)
-
-      snpFile.foreach { _ =>
-        val fcBAFPlot = new FreeCBAFPlot(this)
-        fcBAFPlot.input = freec.bafOutput
-        fcBAFPlot.output = new File(sampleOutput, sampleName + ".freec_baf")
-        add(fcBAFPlot)
-      }
+        val fcAssessSignificancePlot = new FreeCAssessSignificancePlot(this)
+        fcAssessSignificancePlot.cnv = freec.cnvOutput
+        fcAssessSignificancePlot.ratios = freec.ratioOutput
+        fcAssessSignificancePlot.output = new File(sampleOutput, sampleName + ".freec_significant_calls.txt")
+        add(fcAssessSignificancePlot)
+
+        val fcCnvPlot = new FreeCCNVPlot(this)
+        fcCnvPlot.input = freec.ratioOutput
+        fcCnvPlot.output = new File(sampleOutput, sampleName + ".freec_cnv")
+        add(fcCnvPlot)
+
+        snpFile.foreach { _ =>
+          val fcBAFPlot = new FreeCBAFPlot(this)
+          fcBAFPlot.input = freec.bafOutput
+          fcBAFPlot.output = new File(sampleOutput, sampleName + ".freec_baf")
+          add(fcBAFPlot)
+        }
     }
   }