Add merge jobs for cufflinks outputs

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

@@ -132,21 +132,34 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
     /** Adds output merge jobs for the given expression mode */
     // TODO: can we combine the enum with the file extension (to reduce duplication and potential errors)
     def addMergeTableJob(expMode: ExpMeasures.Value, inFunc: (Sample => Option[File]), ext: String,
-                         idCols: List[Int], valCol: Int, outName: String): Unit =
+                         idCols: List[Int], valCol: Int, outBaseName: String = "all_samples"): Unit =
       if (expMeasures.contains(expMode)) {
         val job = new MergeTables(qscript)
         job.inputTables = samples.values.map { inFunc }.toList.flatten
-        job.output = new File(outputDir, outName)
+        job.output = new File(outputDir, outBaseName + ext)
         job.idColumnIndices = idCols.map(_.toString)
         job.valueColumnIndex = valCol
         job.fileExtension = Option(ext)
         add(job)
       }
 
-    addMergeTableJob(FragmentsPerGene, (s: Sample) => s.geneFragmentsCount, ".fragments_per_gene", List(1), 2,
-      "all_samples.fragments_per_gene")
-    addMergeTableJob(FragmentsPerExon, (s: Sample) => s.exonFragmentsCount, ".fragments_per_exon", List(1), 2,
-      "all_samples.fragments_per_exon")
+    // merge htseq outputs
+    addMergeTableJob(FragmentsPerGene, (s: Sample) => s.geneFragmentsCount, ".fragments_per_gene", List(1), 2)
+    addMergeTableJob(FragmentsPerExon, (s: Sample) => s.exonFragmentsCount, ".fragments_per_exon", List(1), 2)
+
+    // merge cufflinks outputs
+    addMergeTableJob(CufflinksStrict, (s: Sample) => s.geneFpkmCufflinksStrict, ".genes_fpkm_cufflinks_strict",
+      List(1, 7), 10)
+    addMergeTableJob(CufflinksStrict, (s: Sample) => s.isoformFpkmCufflinksStrict, ".isoforms_fpkm_cufflinks_strict",
+      List(1, 7), 10)
+    addMergeTableJob(CufflinksGuided, (s: Sample) => s.geneFpkmCufflinksGuided, ".genes_fpkm_cufflinks_guided",
+      List(1, 7), 10)
+    addMergeTableJob(CufflinksGuided, (s: Sample) => s.isoformFpkmCufflinksGuided, ".isoforms_fpkm_cufflinks_guided",
+      List(1, 7), 10)
+    addMergeTableJob(CufflinksBlind, (s: Sample) => s.geneFpkmCufflinksBlind, ".genes_fpkm_cufflinks_blind",
+      List(1, 7), 10)
+    addMergeTableJob(CufflinksBlind, (s: Sample) => s.isoformFpkmCufflinksBlind, ".isoforms_fpkm_cufflinks_blind",
+      List(1, 7), 10)
 
     // TODO: use proper notation
     addSummaryJobs