Style fixes

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

@@ -15,20 +15,20 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 import java.nio.file.Paths
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerCaller, BreakdancerConfig, BreakdancerVCF}
+import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
 import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
 import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
-import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelConfig, PindelVCF}
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelConfig, PindelVCF }
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{DataProvider, Test}
+import org.testng.annotations.{ DataProvider, Test }
 
 import scala.collection.mutable.ListBuffer
 

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

@@ -39,16 +39,16 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
     }
   }
 
-  def raw  : Boolean = false
-  def bcftools  : Boolean = false
-  def bcftools_singlesample  : Boolean = false
-  def haplotypeCallerGvcf  : Boolean = false
-  def haplotypeCallerAllele  : Boolean = false
-  def unifiedGenotyperAllele  : Boolean = false
-  def unifiedGenotyper  : Boolean = false
-  def haplotypeCaller  : Boolean = false
-  def freebayes  : Boolean = false
-  def varscanCnsSinglesample  : Boolean = false
+  def raw: Boolean = false
+  def bcftools: Boolean = false
+  def bcftools_singlesample: Boolean = false
+  def haplotypeCallerGvcf: Boolean = false
+  def haplotypeCallerAllele: Boolean = false
+  def unifiedGenotyperAllele: Boolean = false
+  def unifiedGenotyper: Boolean = false
+  def haplotypeCaller: Boolean = false
+  def freebayes: Boolean = false
+  def varscanCnsSinglesample: Boolean = false
 
   @DataProvider(name = "shivaVariantcallingOptions")
   def shivaVariantcallingOptions = {
@@ -114,46 +114,46 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
 
 class ShivaVariantcallingNoVariantcallersTest extends ShivaVariantcallingTestTrait
 class ShivaVariantcallingAllTest extends ShivaVariantcallingTestTrait {
-  override def raw  : Boolean = true
-  override def bcftools  : Boolean = true
-  override def bcftools_singlesample  : Boolean = true
-  override def haplotypeCallerGvcf  : Boolean = true
-  override def haplotypeCallerAllele  : Boolean = true
-  override def unifiedGenotyperAllele  : Boolean = true
-  override def unifiedGenotyper  : Boolean = true
-  override def haplotypeCaller  : Boolean = true
-  override def freebayes  : Boolean = true
-  override def varscanCnsSinglesample  : Boolean = true
+  override def raw: Boolean = true
+  override def bcftools: Boolean = true
+  override def bcftools_singlesample: Boolean = true
+  override def haplotypeCallerGvcf: Boolean = true
+  override def haplotypeCallerAllele: Boolean = true
+  override def unifiedGenotyperAllele: Boolean = true
+  override def unifiedGenotyper: Boolean = true
+  override def haplotypeCaller: Boolean = true
+  override def freebayes: Boolean = true
+  override def varscanCnsSinglesample: Boolean = true
 }
 class ShivaVariantcallingRawTest extends ShivaVariantcallingTestTrait {
-  override def raw  : Boolean = true
+  override def raw: Boolean = true
 }
 class ShivaVariantcallingBcftoolsTest extends ShivaVariantcallingTestTrait {
-  override def bcftools  : Boolean = true
+  override def bcftools: Boolean = true
 }
 class ShivaVariantcallingBcftoolsSinglesampleTest extends ShivaVariantcallingTestTrait {
-  override def bcftools_singlesample  : Boolean = true
+  override def bcftools_singlesample: Boolean = true
 }
 class ShivaVariantcallingHaplotypeCallerGvcfTest extends ShivaVariantcallingTestTrait {
-  override def haplotypeCallerGvcf  : Boolean = true
+  override def haplotypeCallerGvcf: Boolean = true
 }
 class ShivaVariantcallingHaplotypeCallerAlleleTest extends ShivaVariantcallingTestTrait {
-  override def haplotypeCallerAllele  : Boolean = true
+  override def haplotypeCallerAllele: Boolean = true
 }
 class ShivaVariantcallingUnifiedGenotyperAlleleTest extends ShivaVariantcallingTestTrait {
-  override def unifiedGenotyperAllele  : Boolean = true
+  override def unifiedGenotyperAllele: Boolean = true
 }
 class ShivaVariantcallingUnifiedGenotyperTest extends ShivaVariantcallingTestTrait {
-  override def unifiedGenotyper  : Boolean = true
+  override def unifiedGenotyper: Boolean = true
 }
 class ShivaVariantcallingHaplotypeCallerTest extends ShivaVariantcallingTestTrait {
-  override def haplotypeCaller  : Boolean = true
+  override def haplotypeCaller: Boolean = true
 }
 class ShivaVariantcallingFreebayesTest extends ShivaVariantcallingTestTrait {
-  override def freebayes  : Boolean = true
+  override def freebayes: Boolean = true
 }
 class ShivaVariantcallingVarscanCnsSinglesampleTest extends ShivaVariantcallingTestTrait {
-  override def varscanCnsSinglesample  : Boolean = true
+  override def varscanCnsSinglesample: Boolean = true
 }
 
 object ShivaVariantcallingTest {