changed imports

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -18,12 +18,12 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{Reference, SampleLibraryTag}
-import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge}
+import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
-import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
-import nl.lumc.sasc.biopet.extensions.{Bgzip, Tabix}
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
+import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
 import nl.lumc.sasc.biopet.utils.Logging
 import org.broadinstitute.gatk.utils.commandline.Input
 

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

@@ -49,11 +49,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
   @DataProvider(name = "shivaVariantcallingOptions")
   def shivaVariantcallingOptions = {
     val bool = Array(true, false)
-    (for (bams <- 0 to 3;
-          raw <- bool;
-          bcftools <- bool;
-          bcftools_singlesample <- bool;
-          freebayes <- bool) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray
+    (for (
+      bams <- 0 to 3;
+      raw <- bool;
+      bcftools <- bool;
+      bcftools_singlesample <- bool;
+      freebayes <- bool
+    ) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray
   }
 
   @Test(dataProvider = "shivaVariantcallingOptions")
@@ -72,7 +74,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
 
     pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
 
-    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !freebayes)
+    val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftools_singlesample && !freebayes)
 
     if (illegalArgumentException) intercept[IllegalArgumentException] {
       pipeline.script()