Fixed summary file name

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

@@ -18,9 +18,9 @@ package nl.lumc.sasc.biopet.extensions.kraken
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, 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 }
 
 /** Extension for Kraken */
 class Kraken(val root: Configurable) extends BiopetCommandLineFunction with Version {

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

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.extensions.sambamba
 
-import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
 
 /** General Sambamba extension */
 abstract class Sambamba extends BiopetCommandLineFunction with Version {

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala

@@ -9,7 +9,7 @@ import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
  * KrakenReportToJson function class for usage in Biopet pipelines

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala

@@ -19,7 +19,7 @@ package nl.lumc.sasc.biopet.tools
  * Created by wyleung on 25-9-15.
  */
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 import nl.lumc.sasc.biopet.utils.ToolCommand

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala

@@ -16,11 +16,11 @@
 package nl.lumc.sasc.biopet.pipelines.gears
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{PipelineCommand, SampleLibraryTag}
-import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
-import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, KrakenReportToJson}
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, KrakenReportToJson }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -158,7 +158,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
   }
 
   /** Location of summary file */
-  def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".gears.summary.json")
+  def summaryFile = new File(outputDir, sampleId.getOrElse("sampleName_unknown") + ".gears.summary.json")
 
   /** Pipeline settings shown in the summary file */
   def summarySettings: Map[String, Any] = Map.empty

public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala

@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import java.io.File
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
+import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
-import nl.lumc.sasc.biopet.extensions.tools.{FastqSync, KrakenReportToJson}
+import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, KrakenReportToJson }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils