Style fixes

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorCount.scala

@@ -13,11 +13,10 @@ class WisecondorCount(val root: Configurable) extends Wisecondor {
   @Input
   var inputBam: File = _
 
-  def cmdLine = {
-    executable + required("count") +
-      required("-I", inputBam) +
-      required("-O", output) +
-      required("-R", referenceFasta()) +
-      binCommand
-  }
+  def cmdLine = executable +
+    required("count") +
+    required("-I", inputBam) +
+    required("-O", output) +
+    required("-R", referenceFasta()) +
+    binCommand
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala

@@ -18,16 +18,14 @@ class WisecondorGcCorrect(val root: Configurable) extends Wisecondor {
   var nIter: Option[Int] = config("iter", namespace = "wisecondor", default = None)
   var fracLowess: Option[Float] = config("frac_lowess", namespace = "wisecondor", default = None)
 
-  def cmdLine = {
-    executable + required("gc-correct") +
-      required("-I", inputBed) +
-      required("-R", referenceFasta()) +
-      required("-O", output) +
-      binCommand +
-      optional("-n", fracN) +
-      optional("-r", fracR) +
-      optional("-t", nIter) +
-      optional("-l", fracLowess)
-
-  }
+  def cmdLine = executable +
+    required("gc-correct") +
+    required("-I", inputBed) +
+    required("-R", referenceFasta()) +
+    required("-O", output) +
+    binCommand +
+    optional("-n", fracN) +
+    optional("-r", fracR) +
+    optional("-t", nIter) +
+    optional("-l", fracLowess)
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorNewRef.scala

@@ -6,8 +6,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 
 /**
-  * Created by Sander Bollen on 22-3-17.
-  */
+ * Created by Sander Bollen on 22-3-17.
+ */
 class WisecondorNewRef(val root: Configurable) extends Wisecondor {
 
   @Input
@@ -15,13 +15,12 @@ class WisecondorNewRef(val root: Configurable) extends Wisecondor {
 
   var nNeighbourBins: Option[Int] = config("n_neighbour_bins", namespace = "wisecondor", default = None)
 
-  def cmdLine = {
-    executable + required("newref") +
-      repeat("-I", inputBeds) +
-      required("-O", output) +
-      required("-R", referenceFasta()) +
-      binCommand +
-      optional("-n", nNeighbourBins)
-  }
+  def cmdLine = executable +
+    required("newref") +
+    repeat("-I", inputBeds) +
+    required("-O", output) +
+    required("-R", referenceFasta()) +
+    binCommand +
+    optional("-n", nNeighbourBins)
 
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorZscore.scala

@@ -16,12 +16,11 @@ class WisecondorZscore(val root: Configurable) extends Wisecondor {
   @Input
   var referenceDictionary: File = config("reference_dictionary", namespace = "wisecondor")
 
-  def cmdLine = {
-    executable + required("zscore") +
-      required("-I", inputBed) +
-      required("-O", output) +
-      required("-R", referenceFasta()) +
-      required("-D", referenceDictionary) +
-      binCommand
-  }
+  def cmdLine = executable +
+    required("zscore") +
+    required("-I", inputBed) +
+    required("-O", output) +
+    required("-R", referenceFasta()) +
+    required("-D", referenceDictionary) +
+    binCommand
 }