autostyle fixes

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala

@@ -20,11 +20,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
 
   private var _summaryFile: File = _
   private var _statisticsFile: File = _
-  private var _intervalSummaryFile: File =  _
+  private var _intervalSummaryFile: File = _
   private var _intervalStatisticsFile: File = _
   private var _geneSummaryFile: File = _
   private var _geneStatisticsFile: File = _
-  private var _cumulativeCoverageCountsFile: File =  _
+  private var _cumulativeCoverageCountsFile: File = _
   private var _cumulativeCoverageProportionsFile: File = _
 
   @Output
@@ -84,7 +84,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
 
   var includeRefNSites: Boolean = config("include_ref_n_sites", namespace = "depth_of_coverage", default = false)
 
-  var printBinEndpointsAndExit: Boolean = config("print_bin_endpoint_and_exit", namespace = "depth_of_coverage" , default = false)
+  var printBinEndpointsAndExit: Boolean = config("print_bin_endpoint_and_exit", namespace = "depth_of_coverage", default = false)
 
   override def beforeGraph() = {
     super.beforeGraph()
@@ -93,11 +93,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
     }
     _summaryFile = new File(out + ".sample_summary")
     _statisticsFile = new File(out + ".sample_statistics")
-    _intervalSummaryFile =  new File(out + ".sample_interval_summary")
+    _intervalSummaryFile = new File(out + ".sample_interval_summary")
     _intervalStatisticsFile = new File(out + ".sample_interval_statistics")
     _geneSummaryFile = new File(out + ".sample_gene_summary")
     _geneStatisticsFile = new File(out + ".sample_gene_statistics")
-    _cumulativeCoverageCountsFile =  new File(out + ".sample_cumulative_coverage_counts")
+    _cumulativeCoverageCountsFile = new File(out + ".sample_cumulative_coverage_counts")
     _cumulativeCoverageProportionsFile = new File(out + ".sample_cumulative_coverage_proportions")
   }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions.xhmm
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
 
 /**
  * Created by Sander Bollen on 23-11-16.

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala

 package nl.lumc.sasc.biopet.tools
 
-import java.io.{BufferedWriter, File, FileWriter, PrintWriter}
+import java.io.{ BufferedWriter, File, FileWriter, PrintWriter }
 
 import nl.lumc.sasc.biopet.tools.VepNormalizer.Args
 import nl.lumc.sasc.biopet.utils.ToolCommand

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

@@ -30,7 +30,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
         "n_bins" -> 200,
         "include_ref_n_sites" -> true,
         "count_type" -> "COUNT_FRAGMENTS"
-        )
+      )
     )
   }