Added cnv to summary settings

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala

@@ -209,6 +209,7 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
     "annotation" -> annotation.isDefined,
     "multisample_variantcalling" -> multisampleVariantCalling.isDefined,
     "sv_calling" -> svCalling.isDefined,
+    "cnv_calling" -> cnvCalling.isDefined,
     "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
     "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
   )

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -104,6 +104,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
 
       pipeline.summarySettings.get("annotation") shouldBe Some(annotation)
       pipeline.summarySettings.get("sv_calling") shouldBe Some(svCalling)
+      pipeline.summarySettings.get("cnv_calling") shouldBe Some(cnvCalling)
 
       pipeline.samples foreach {
         case (sampleId, sample) =>