Convert mapping to sortsam for pipes

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

@@ -337,10 +337,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     val sortSam = new SortSam(this)
     sortSam.output = output
     if (config("use_pipes", default = true).asBoolean) {
-      val samtoolsSort = new SamtoolsSort(this)
-      samtoolsSort.outputFormat = Some("bam")
-      samtoolsSort.output = output
-      add(bwaCommand | samtoolsSort, chunking || !skipMarkduplicates)
+      //val samtoolsSort = new SamtoolsSort(this)
+      //samtoolsSort.outputFormat = Some("bam")
+      //samtoolsSort.output = output
+      add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
     } else {
       bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
       add(bwaCommand)