Code style fix

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

@@ -101,22 +101,22 @@ class Gentrap(val root: Configurable) extends QScript
 
   /** Default pipeline config */
   override def defaults = Map(
-      "gsnap" -> Map(
-        "novelsplicing" -> 1,
-        "batch" -> 4,
-        "format" -> "sam"
-      ),
-      "cutadapt" -> Map("minimum_length" -> 20),
-      // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
-      "picard" -> Map(
-        "programrecordid" -> "null"
-      ),
-      // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
-      "mapping" -> Map(
-        "skip_markduplicates" -> true,
-        "skip_metrics" -> true
-      )
+    "gsnap" -> Map(
+      "novelsplicing" -> 1,
+      "batch" -> 4,
+      "format" -> "sam"
+    ),
+    "cutadapt" -> Map("minimum_length" -> 20),
+    // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
+    "picard" -> Map(
+      "programrecordid" -> "null"
+    ),
+    // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
+    "mapping" -> Map(
+      "skip_markduplicates" -> true,
+      "skip_metrics" -> true
     )
+  )
 
   /** Adds output merge jobs for the given expression mode */
   // TODO: can we combine the enum with the file extension (to reduce duplication and potential errors)

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -98,11 +98,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
   def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".summary.json")
 
   override def defaults = Map(
-      "gsnap" -> Map(
-        "batch" -> 4,
-        "format" -> "sam"
-      )
+    "gsnap" -> Map(
+      "batch" -> 4,
+      "format" -> "sam"
     )
+  )
 
   /** File to add to the summary */
   def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1,

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -38,19 +38,19 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
 
   override def defaults = Map(
     "bowtie" -> Map(
-    "m" -> 1,
-    "k" -> 1,
-    "best" -> true,
-    "strata" -> true,
-    "seedmms" -> 1
-  ), "mapping" -> Map(
-    "aligner" -> "bowtie",
-    "skip_flexiprep" -> true,
-    "skip_markduplicates" -> true
-  ), "flexiprep" -> Map(
-    "skip_clip" -> true,
-    "skip_trim" -> true
-  ), "strandSensitive" -> true
+      "m" -> 1,
+      "k" -> 1,
+      "best" -> true,
+      "strata" -> true,
+      "seedmms" -> 1
+    ), "mapping" -> Map(
+      "aligner" -> "bowtie",
+      "skip_flexiprep" -> true,
+      "skip_markduplicates" -> true
+    ), "flexiprep" -> Map(
+      "skip_clip" -> true,
+      "skip_trim" -> true
+    ), "strandSensitive" -> true
   )
 
   def summaryFile: File = new File(outputDir, "Sage.summary.json")