Style fixes

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/Stringtie.scala

@@ -54,7 +54,8 @@ class Stringtie(val parent: Configurable)
   /** Regex to get version from version command output */
   def versionRegex: Regex = ".*".r
 
-  def cmdLine: String = required(executable) +
+  def cmdLine: String =
+    required(executable) +
       required(inputBam) +
       conditional(v, "-v") +
       required("-p", threads) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/StringtieMerge.scala

@@ -39,7 +39,8 @@ class StringtieMerge(val parent: Configurable)
   /** Regex to get version from version command output */
   def versionRegex: Regex = ".*".r
 
-    def cmdLine: String = required(executable) +
+  def cmdLine: String =
+    required(executable) +
       required("--merge")
   conditional(v, "-v") +
     required("-p", threads) +
@@ -53,4 +54,4 @@ class StringtieMerge(val parent: Configurable)
     (if (outputAsStdout) "" else required("-o", outputGtf)) +
     repeat(inputGtfs)
 
-  }
+}

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

@@ -305,7 +305,8 @@ object Gentrap extends PipelineCommand {
 
   /** Enumeration of available expression measures */
   object ExpMeasures extends Enumeration {
-    val FragmentsPerGene, BaseCounts, CufflinksStrict, CufflinksGuided, CufflinksBlind, Stringtie = Value
+    val FragmentsPerGene, BaseCounts, CufflinksStrict, CufflinksGuided, CufflinksBlind, Stringtie =
+      Value
   }
 
   /** Enumeration of available strandedness */

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Stringtie.scala

@@ -22,10 +22,7 @@ import org.broadinstitute.gatk.queue.QScript
 /**
   * Created by pjvan_thof on 1/12/16.
   */
-class Stringtie(val parent: Configurable)
-    extends QScript
-    with Measurement
-    with AnnotationGtf {
+class Stringtie(val parent: Configurable) extends QScript with Measurement with AnnotationGtf {
   def mergeArgs = MergeArgs(idCols = List(1), valCol = 2, fallback = "0")
 
   /** Pipeline itself */