Fixed bammetrics tests

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -50,22 +50,22 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   @DataProvider(name = "bammetricsOptions")
   def bammetricsOptions = {
     val rois = Array(0, 1, 2, 3)
-    val amplicon = Array(true, false)
-    val rna = Array(true, false)
+    val bool = Array(true, false)
 
     for (
       rois <- rois;
-      amplicon <- amplicon;
-      rna <- rna
-    ) yield Array(rois, amplicon, rna)
+      amplicon <- bool;
+      rna <- bool;
+      wgs <- bool
+    ) yield Array(rois, amplicon, rna, wgs)
   }
 
   @Test(dataProvider = "bammetricsOptions")
-  def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean) = {
-    val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir),
+  def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean) = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir, "rna_metrics" -> rna, "wgs_metrics" -> wgs),
       Map(BamMetricsTest.executables.toSeq: _*)) ++
       (if (amplicon) Map("amplicon_bed" -> "amplicon.bed") else Map()) ++
-      (if (rna) Map("transcript_refflat" -> "transcripts.refFlat") else Map()) ++
+      (if (rna) Map("annotation_refflat" -> "transcripts.refFlat") else Map()) ++
       Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
     val bammetrics: BamMetrics = initPipeline(map)
 
@@ -77,7 +77,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
     var regions: Int = rois + (if (amplicon) 1 else 0)
 
     bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0)
-    bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe (if (rna) 0 else 1)
+    bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe (if (wgs) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
     bammetrics.functions.count(_.isInstanceOf[CalculateHsMetrics]) shouldBe (if (amplicon) 1 else 0)
     bammetrics.functions.count(_.isInstanceOf[CollectTargetedPcrMetrics]) shouldBe (if (amplicon) 1 else 0)