diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
index cd14d23234de1fd370ab52ceec2676325e705c06..40b40c1419e3bde5e44af8585a4896bdadf6a384 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
@@ -2,23 +2,23 @@ package nl.lumc.sasc.biopet.pipelines.gears
 
 import nl.lumc.sasc.biopet.core.SampleLibraryTag
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.{Cutadapt, Flash}
+import nl.lumc.sasc.biopet.extensions.{ Cutadapt, Flash }
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 /**
-  * Created by pjvanthof on 29/12/15.
-  */
+ * Created by pjvanthof on 29/12/15.
+ */
 class CombineReads(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
   @Input(doc = "R1 reads in FastQ format", shortName = "R1", required = false)
   var fastqR1: File = _
 
   @Input(doc = "R2 reads in FastQ format", shortName = "R2", required = false)
   var fastqR2: File = _
-  
+
   override def fixedValues = Map("flash" -> Map("compress" -> true))
-  
+
   /** Init for pipeline */
   def init(): Unit = {
   }
@@ -27,7 +27,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
 
   private lazy val forwardPrimers: List[String] = config("forward_primers")
   private lazy val reversePrimers: List[String] = config("reverse_primers")
-  
+
   def combinedFastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty)
     swapExt(outputDir, flash.combinedFastq, ".fastq.gz", ".clip.fastq.gz")
   else flash.combinedFastq
@@ -57,7 +57,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
       add(cutadapt)
       addSummarizable(cutadapt, "cutadapt")
     }
-    
+
     val combinedFastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "combined_fastqc"))
     add(combinedFastqc)
     addSummarizable(combinedFastqc, "fastqc_combined")
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 ac38cb34c2852a3ded6fdd4dcd1683deeaed8513..ba29af9d5de5383588405b2e23a63368d0702f2c 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
@@ -156,9 +156,9 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
 
   /** File to put in the summary for thie pipeline */
   def summaryFiles: Map[String, File] = (
-      qiimeClosedOtuTable.map("qiime_closed_otu_table" -> _) ++
-      qiimeClosedOtuMap.map("qiime_closed_otu_map" -> _)
-    ).toMap
+    qiimeClosedOtuTable.map("qiime_closed_otu_table" -> _) ++
+    qiimeClosedOtuMap.map("qiime_closed_otu_map" -> _)
+  ).toMap
 }
 
 object Gears extends PipelineCommand
\ No newline at end of file
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
index 3c7b0d0f5f7aa8cb1c381eee1deab693b110f4a4..d1eda017425529f4732e166836500abda153958c 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
@@ -127,11 +127,11 @@ object GearsKraken {
             if (k == "root") {
               val unclassified = summaries(sample)("unclassified").asInstanceOf[Map[String, Any]]("size").asInstanceOf[Long]
               <val>
-                {getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0).toString.toLong + unclassified}
+                { getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0).toString.toLong + unclassified }
               </val>
             } else {
               <val>
-                {getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0)}
+                { getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0) }
               </val>
             }
           }
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
index f78a7f20718d1dbdd635879a3c3955d170b36a31..cad3657534ecfa21da9c63532008c44e29c264b3 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
@@ -59,7 +59,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
   def summarySettings: Map[String, Any] = Map()
 
   /** File to put in the summary for thie pipeline */
-  def summaryFiles: Map[String, File] = Map("otu_table" -> otuTable,"otu_map" -> otuMap)
+  def summaryFiles: Map[String, File] = Map("otu_table" -> otuTable, "otu_map" -> otuMap)
 
   /** Name of summary output file */
   def summaryFile: File = new File(outputDir, "summary.closed_reference.json")
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index 8c8dcc6a84a4c2af8a34c7b05b6132564d205bf0..aa819f08c3ddd78d96853e88c4f660417f89ae8f 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
@@ -80,7 +80,7 @@ object GearsReport extends MultisampleReportBuilder {
 
     ReportPage(
       (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
-        ) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
+      ) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
         "Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
         )), Map()))
       else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
index 94968849c2a24cab358b8cce01df9609adfa98ca..70b850ce1ae85d8f9dcf70cab4484e126b6eb589 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
@@ -1,14 +1,14 @@
 package nl.lumc.sasc.biopet.pipelines.gears
 
-import nl.lumc.sasc.biopet.core.{BiopetQScript, SampleLibraryTag}
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, SampleLibraryTag }
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.tools.SageCountFastq
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 /**
-  * Created by pjvan_thof on 12/29/15.
-  */
+ * Created by pjvan_thof on 12/29/15.
+ */
 class GearsSeqCount(val root: Configurable) extends QScript with BiopetQScript with SampleLibraryTag {
 
   var fastqInput: File = _