Convert pipe to SortSam again

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala

@@ -31,31 +31,32 @@ class SortSam(val root: Configurable) extends Picard {
   var output: File = _
 
   @Argument(doc = "Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} ", required = true)
-  var sortOrder: String = _
+  var sortOrder: String = config("sort_order", default = "coordinate")
 
   @Output(doc = "Bam Index", required = true)
   private var outputIndex: File = _
 
   override def beforeGraph() {
     super.beforeGraph()
+    if (outputAsStsout) createIndex = false
     if (createIndex) outputIndex = new File(output.getAbsolutePath.stripSuffix(".bam") + ".bai")
   }
 
   /** Returns command to execute */
   override def cmdLine = super.cmdLine +
-    required("INPUT=", input, spaceSeparated = false) +
-    required("OUTPUT=", output, spaceSeparated = false) +
+    (if (inputAsStdin) required("INPUT=", new File("/dev/stdin"), spaceSeparated = false)
+    else required("INPUT=", input, spaceSeparated = false)) +
+    (if (outputAsStsout) required("OUTPUT=", new File("/dev/stdout"), spaceSeparated = false)
+    else required("OUTPUT=", output, spaceSeparated = false)) +
     required("SORT_ORDER=", sortOrder, spaceSeparated = false)
 }
 
 object SortSam {
   /** Returns default SortSam */
-  def apply(root: Configurable, input: File, output: File, sortOrder: String = null): SortSam = {
+  def apply(root: Configurable, input: File, output: File): SortSam = {
     val sortSam = new SortSam(root)
     sortSam.input = input
     sortSam.output = output
-    if (sortOrder == null) sortSam.sortOrder = "coordinate"
-    else sortSam.sortOrder = sortOrder
     sortSam
   }
 }
\ No newline at end of file

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

@@ -334,16 +334,18 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     bwaCommand.deps = deps
     bwaCommand.R = Some(getReadGroupBwa)
     bwaCommand.isIntermediate = true
+    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)
+      add(bwaCommand | samtoolsSort, chunking || !skipMarkduplicates)
     } else {
       bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
       add(bwaCommand)
-      val sortSam = SortSam(this, bwaCommand.output, output)
-      if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
+      sortSam.input = bwaCommand.output
+      sortSam.isIntermediate = chunking || !skipMarkduplicates
       add(sortSam)
     }
     output