Fix format

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala

 package nl.lumc.sasc.biopet.core
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
-import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.utils.summary.Summary
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Question, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Question, ToolCommand }
 
 import scala.io.Source
 
@@ -58,7 +57,7 @@ trait TemplateTool extends ToolCommand {
       case Some(f) => f
       case _ => sys.env.get("BIOPET_SCRIPT_TEMPLATE") match {
         case Some(file) => new File(file)
-        case _ => throw new IllegalArgumentException("No template found on argument or 'BIOPET_SCRIPT_TEMPLATE'")
+        case _          => throw new IllegalArgumentException("No template found on argument or 'BIOPET_SCRIPT_TEMPLATE'")
       }
     }
 

biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala

@@ -46,6 +46,7 @@ object BiopetExecutableMain extends BiopetExecutable {
 
   def templates: List[MainCommand] = List(
     nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping,
-    nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva
+    nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva,
+    nl.lumc.sasc.biopet.pipelines.gentrap.template.Gentrap
   )
 }

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala

@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.template
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.TemplateTool
-import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.{ExpMeasures, StrandProtocol}
+import nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.{ ExpMeasures, StrandProtocol }
 import nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping
 import nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva
 import nl.lumc.sasc.biopet.utils._
@@ -43,10 +43,10 @@ object Gentrap extends TemplateTool {
       "strand_protocol" -> strandProtocol,
       "annotation_refflat" -> annotationRefFlat
     ) ++ (if (Question.boolean("Call variants")) {
-      val variantCallers = Question.list("Variantcallers", posibleValues = Shiva.possibleVariantcallers,
-        default = Some(List("varscan_cns_singlesample")))
+        val variantCallers = Question.list("Variantcallers", posibleValues = Shiva.possibleVariantcallers,
+          default = Some(List("varscan_cns_singlesample")))
 
-      Map("call_variants" -> true, "variantcallers" -> variantCallers)
-    } else Map("call_variants" -> false))
+        Map("call_variants" -> true, "variantcallers" -> variantCallers)
+      } else Map("call_variants" -> false))
   }
 }