diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
index 6e0905e9fd84a4d7b60a68f197d716acb017df46..86df5c4151d114fcb2b654cbf7b0c28bb78b9bcf 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+++ b/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 {
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
index 6da7c3ed11c0c589adc3863be9e15cb671056b55..b12ff9584da1090aa90970dbbd137c0bb6b792e9 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
+++ b/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 {
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
index df97f7bb1413a7d4b8cbd8c4a98cd37b6e5f3b36..475d0b0b2e1f4d5837d77d0785cad6a0158fbbdb 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
+++ b/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
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
index 3fa672cfa05c8a1ce96414d695b2c80b5ca37257..ee59a22aaab5a1b21ad8565a74f41d432cde096b 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala
+++ b/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
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index aabbedb8629246b1695387125ae508d66bd12252..53dcb1df34bf772e120fb652533bc216d52ef51f 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/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
diff --git a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
index 9091635548b5a9124409ce61b80868ba5a5c2a08..64add19081cf4647ccfa9539a44f4af8358f43be 100644
--- a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
+++ b/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