Style update by IDEA

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

@@ -32,9 +32,9 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFuntion with
   override def defaultCoreMemory = 1.0
 
   override def cmdLine = super.cmdLine +
-                      required("-i", inputReport) +
-                      required("-o", output) +
-                      conditional(skipNames, "--skipnames")
+    required("-i", inputReport) +
+    required("-o", output) +
+    conditional(skipNames, "--skipnames")
 
   def summaryStats: Map[String, Any] = {
     val map = ConfigUtils.fileToConfigMap(output)

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
-import nl.lumc.sasc.biopet.extensions.picard.{SortSam, SamToFastq}
+import nl.lumc.sasc.biopet.extensions.picard.{ SortSam, SamToFastq }
 import nl.lumc.sasc.biopet.extensions.sambamba.SambambaView
 import nl.lumc.sasc.biopet.extensions.tools.{ KrakenReportToJson, FastqSync }
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -76,7 +76,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
 
       // start bam to fastq (only on unaligned reads) also extract the matesam
       val samToFastq = new SamToFastq(qscript)
-      samToFastq.input= samFilterUnmapped.output
+      samToFastq.input = samFilterUnmapped.output
       samToFastq.stringency = Some("LENIENT")
       samToFastq.fastqR1 = new File(outputDir, s"$outputName.unmapped.R1.fq.gz")
       samToFastq.fastqR2 = new File(outputDir, s"$outputName.unmapped.R2.fq.gz")