Style fixes

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

@@ -9,7 +9,7 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 import scala.util.matching.Regex
 
 class Stringtie(val parent: Configurable)
-  extends BiopetCommandLineFunction
+    extends BiopetCommandLineFunction
     with Reference
     with Version {
 
@@ -54,28 +54,29 @@ class Stringtie(val parent: Configurable)
   /** Regex to get version from version command output */
   def versionRegex: Regex = ".*".r
 
-  def cmdLine: String = required(executable) +
-    required(inputBam) +
-    conditional(v, "-v") +
-    required("-p", threads) +
-    conditional(rf, "--rf") +
-    conditional(fr, "--fr") +
-    optional("-l", l) +
-    optional("-f", f) +
-    optional("-m", m) +
-    optional("-A", geneAbundances) +
-    optional("-C", referenceCoverage) +
-    optional("-a", a) +
-    optional("-j", j) +
-    conditional(t, "-t") +
-    optional("-c", c) +
-    optional("-g", g) +
-    conditional(B, "-B") +
-    optional("-b", b) +
-    conditional(e, "-e") +
-    optional("-M", M) +
-    optional("-G", referenceGtf) +
-    (if (x.nonEmpty) optional("-x", x.mkString(",")) else "") +
-    (if (outputAsStdout) "" else required("-o", outputGtf))
+  def cmdLine: String =
+    required(executable) +
+      required(inputBam) +
+      conditional(v, "-v") +
+      required("-p", threads) +
+      conditional(rf, "--rf") +
+      conditional(fr, "--fr") +
+      optional("-l", l) +
+      optional("-f", f) +
+      optional("-m", m) +
+      optional("-A", geneAbundances) +
+      optional("-C", referenceCoverage) +
+      optional("-a", a) +
+      optional("-j", j) +
+      conditional(t, "-t") +
+      optional("-c", c) +
+      optional("-g", g) +
+      conditional(B, "-B") +
+      optional("-b", b) +
+      conditional(e, "-e") +
+      optional("-M", M) +
+      optional("-G", referenceGtf) +
+      (if (x.nonEmpty) optional("-x", x.mkString(",")) else "") +
+      (if (outputAsStdout) "" else required("-o", outputGtf))
 
 }

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

@@ -9,48 +9,49 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 import scala.util.matching.Regex
 
 class StringtieMerge(val parent: Configurable)
-  extends BiopetCommandLineFunction
-      with Reference
-      with Version {
+    extends BiopetCommandLineFunction
+    with Reference
+    with Version {
 
-    executable = config("exe", "stringtie")
+  executable = config("exe", "stringtie")
 
-    @Input(required = true)
-    var inputGtfs: List[File] = Nil
+  @Input(required = true)
+  var inputGtfs: List[File] = Nil
 
-    @Input(required = false)
-    var referenceGtf: Option[File] = None
+  @Input(required = false)
+  var referenceGtf: Option[File] = None
 
-    @Output
-    var outputGtf: File = _
+  @Output
+  var outputGtf: File = _
 
-    var v: Boolean = config("v", default = logger.isDebugEnabled)
-    var l: Option[String] = None
-    var f: Option[Double] = config("f")
-    var m: Option[Int] = config("m")
-    var c: Option[Float] = config("c")
-    var F: Option[Double] = config("F")
-    var T: Option[Double] = config("T")
-    var i: Boolean = config("i", default = false)
+  var v: Boolean = config("v", default = logger.isDebugEnabled)
+  var l: Option[String] = None
+  var f: Option[Double] = config("f")
+  var m: Option[Int] = config("m")
+  var c: Option[Float] = config("c")
+  var F: Option[Double] = config("F")
+  var T: Option[Double] = config("T")
+  var i: Boolean = config("i", default = false)
 
-    /** Command to get version of executable */
-    def versionCommand: String = executable + " --version"
+  /** Command to get version of executable */
+  def versionCommand: String = executable + " --version"
 
-    /** Regex to get version from version command output */
-    def versionRegex: Regex = ".*".r
+  /** 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) +
-      optional("-l", l) +
-      optional("-f", f) +
-      optional("-m", m) +
-      optional("-c", c) +
-      optional("-F", F) +
-      conditional(i, "-i") +
-      optional("-G", referenceGtf) +
-      (if (outputAsStdout) "" else required("-o", outputGtf)) +
-      repeat(inputGtfs)
-
-  }
+  conditional(v, "-v") +
+    required("-p", threads) +
+    optional("-l", l) +
+    optional("-f", f) +
+    optional("-m", m) +
+    optional("-c", c) +
+    optional("-F", F) +
+    conditional(i, "-i") +
+    optional("-G", referenceGtf) +
+    (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 */