Added a merge step

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -20,7 +20,7 @@ import java.io.{ File, PrintWriter }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.utils.ConfigUtils
-import nl.lumc.sasc.biopet.{ LastCommitHash, Version }
+import nl.lumc.sasc.biopet.LastCommitHash
 import org.broadinstitute.gatk.queue.function.{ InProcessFunction, QFunction }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -90,7 +90,7 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
         }
 
         (
-          qscript.functions.flatMap(fetchVersion(_)) ++
+          qscript.functions.flatMap(fetchVersion) ++
           qscript.functions
           .flatMap {
             case f: BiopetCommandLineFunction => f.pipesJobs
@@ -99,28 +99,28 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
         ).toMap
       }
 
-      val map = Map(qscript.summaryName -> (Map(
+      val map = Map(qscript.summaryName -> Map(
         "settings" -> settings,
         "files" -> Map("pipeline" -> files),
-        "executables" -> executables.toMap))
+        "executables" -> executables.toMap)
       )
 
       qscript match {
         case tag: SampleLibraryTag => prefixSampleLibrary(map, tag.sampleId, tag.libId)
-        case q: MultiSampleQScript => {
-          Map("samples" -> q.samples.map {
-            case (sampleName, sample) =>
-              sampleName -> Map(
-                qscript.summaryName -> Map("settings" -> sample.summarySettings),
-                "libraries" -> sample.libraries.map {
-                  case (libName, lib) =>
-                    sampleName -> Map(
-                      qscript.summaryName -> Map("settings" -> lib)
-                    )
-                }
-              )
-          }) ++ map
-        }
+        case q: MultiSampleQScript =>
+          ConfigUtils.mergeMaps(
+            Map("samples" -> q.samples.map {
+              case (sampleName, sample) =>
+                sampleName -> Map(
+                  qscript.summaryName -> Map("settings" -> sample.summarySettings),
+                  "libraries" -> sample.libraries.map {
+                    case (libName, lib) =>
+                      sampleName -> Map(
+                        qscript.summaryName -> Map("settings" -> lib.summarySettings)
+                      )
+                  }
+                )
+            }), map)
         case _ => map
       }
     }