Fix symlinking of the final bai file

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

@@ -720,12 +720,12 @@ class Gentrap(val root: Configurable) extends QScript
       if (inFiles.size == 1) {
 
         val jobBam = new Ln(qscript)
-        jobBam.input = inFiles.head
+        jobBam.input = inFiles.head.getAbsoluteFile
         jobBam.output = outFile
 
         val jobIdx = new Ln(qscript)
-        jobIdx.input = swapExt(jobBam.input, ".bam", ".bai")
-        jobIdx.output = swapExt(jobBam.output, ".bam", ".bai")
+        jobIdx.input = swapExt(libraries.values.head.libDir, jobBam.input, ".bam", ".bai")
+        jobIdx.output = swapExt(sampleDir, jobBam.output, ".bam", ".bai")
 
         CombineFileJobSet(jobBam, Some(jobIdx))
       } else {

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

@@ -268,7 +268,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
 
     add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, finalBamFile, ".bam", ".bai")))
     add(Ln(this, bamFile, finalBamFile))
-    outputFiles += ("finalBamFile" -> bamFile)
+    outputFiles += ("finalBamFile" -> finalBamFile.getAbsoluteFile)
 
     if (config("generate_wig", default = false).asBoolean)
       addAll(Bam2Wig(this, finalBamFile).functions)