Fix errors caused by merging

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

@@ -29,7 +29,7 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
 
   // mpileup, varscan, fix_mpileup.py, binom_test.py, bgzip, tabix
   private def mpileup = new SamtoolsMpileup(wrapper.root) {
-    this.input = wrapper.input
+    this.input = List(wrapper.input)
     disableBaq = true
     reference = config("reference")
     depth = Option(1000000)

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -156,7 +156,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
                 add(baiLn)
 
                 val bamLn = Ln(qscript, oldBamFile, bamFile.get)
-                bamLn.deps :+= baiLn.out
+                bamLn.deps :+= baiLn.output
                 add(bamLn)
               }
 
@@ -197,7 +197,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
         add(baiLn)
 
         val bamLn = Ln(qscript, input.head, bamFile)
-        bamLn.deps :+= baiLn.out
+        bamLn.deps :+= baiLn.output
         add(bamLn)
         Some(bamFile)
       } else {