added bcftools singlesample to the test

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

@@ -44,12 +44,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
       bams <- 0 to 2;
       raw <- bool;
       bcftools <- bool;
+      bcftools_singlesample <- bool;
       haplotypeCallerGvcf <- bool;
       haplotypeCallerAllele <- bool;
       unifiedGenotyperAllele <- bool;
       unifiedGenotyper <- bool;
       haplotypeCaller <- bool
-    ) yield Array[Any](bams, raw, bcftools, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
+    ) yield Array[Any](bams, raw, bcftools, bcftools_singlesample, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
     ).toArray
   }
 
@@ -57,6 +58,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
   def testShivaVariantcalling(bams: Int,
                               raw: Boolean,
                               bcftools: Boolean,
+                              bcftools_singlesample: Boolean,
                               unifiedGenotyper: Boolean,
                               haplotypeCaller: Boolean,
                               haplotypeCallerGvcf: Boolean,
@@ -65,6 +67,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
     val callers: ListBuffer[String] = ListBuffer()
     if (raw) callers.append("raw")
     if (bcftools) callers.append("bcftools")
+    if (bcftools_singlesample) callers.append("bcftools_singlesample")
     if (unifiedGenotyper) callers.append("unifiedgenotyper")
     if (haplotypeCallerGvcf) callers.append("haplotypecaller_gvcf")
     if (haplotypeCallerAllele) callers.append("haplotypecaller_allele")
@@ -78,7 +81,8 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
     val illegalArgumentException = pipeline.inputBams.isEmpty ||
       (!raw && !bcftools &&
         !haplotypeCaller && !unifiedGenotyper &&
-        !haplotypeCallerGvcf && !haplotypeCallerAllele && !unifiedGenotyperAllele)
+        !haplotypeCallerGvcf && !haplotypeCallerAllele && !unifiedGenotyperAllele &&
+        !bcftools_singlesample)
 
     if (illegalArgumentException) intercept[IllegalArgumentException] {
       pipeline.script()