add varscan test to shiva variantcalling test

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala

@@ -53,28 +53,31 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
       bams <- 0 to 3;
       raw <- bool;
       bcftools <- bool;
-      bcftools_singlesample <- bool;
-      freebayes <- bool
-    ) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray
+      bcftoolsSinglesample <- bool;
+      freebayes <- bool;
+      varscanCnsSinglesample <- bool
+    ) yield Array(bams, raw, bcftools, bcftoolsSinglesample, freebayes, varscanCnsSinglesample)).toArray
   }
 
   @Test(dataProvider = "shivaVariantcallingOptions")
   def testShivaVariantcalling(bams: Int,
                               raw: Boolean,
                               bcftools: Boolean,
-                              bcftools_singlesample: Boolean,
-                              freebayes: Boolean) = {
+                              bcftoolsSinglesample: Boolean,
+                              freebayes: Boolean, 
+                              varscanCnsSinglesample: Boolean) = {
     val callers: ListBuffer[String] = ListBuffer()
     if (raw) callers.append("raw")
     if (bcftools) callers.append("bcftools")
-    if (bcftools_singlesample) callers.append("bcftools_singlesample")
+    if (bcftoolsSinglesample) callers.append("bcftools_singlesample")
     if (freebayes) callers.append("freebayes")
+    if (varscanCnsSinglesample) callers.append("varscan_cns_singlesample")
     val map = Map("variantcallers" -> callers.toList)
     val pipeline = initPipeline(map)
 
     pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
 
-    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftools_singlesample && !freebayes)
+    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftoolsSinglesample && !freebayes)
 
     if (illegalArgumentException) intercept[IllegalArgumentException] {
       pipeline.script()