Style fixes

basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

@@ -14,20 +14,20 @@
  */
 package nl.lumc.sasc.biopet.pipelines.basty
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.{Raxml, RunGubbins}
-import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator}
+import nl.lumc.sasc.biopet.extensions.{ Raxml, RunGubbins }
+import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
-import nl.lumc.sasc.biopet.extensions.tools.{BastyGenerateFasta, VcfStats}
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.extensions.tools.{ BastyGenerateFasta, VcfStats }
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 /**
  * Created by pjvanthof on 27/09/16.

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala

@@ -61,7 +61,6 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers {
 
     }
 
-
     val tempDir = Files.createTempDir()
     tempDir.deleteOnExit()
     val args = Array("-s", dbFile.getAbsolutePath, "-o", tempDir.getAbsolutePath)

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala

@@ -21,7 +21,7 @@ import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{DataProvider, Test}
+import org.testng.annotations.{ DataProvider, Test }
 
 import scala.concurrent.Await
 import scala.concurrent.duration.Duration

biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala

@@ -14,20 +14,20 @@
  */
 package nl.lumc.sasc.biopet.core.summary
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
+import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
 import nl.lumc.sasc.biopet.utils.summary.Summary
 import org.broadinstitute.gatk.queue.function.CommandLineFunction
-import org.broadinstitute.gatk.queue.{QScript, QSettings}
+import org.broadinstitute.gatk.queue.{ QScript, QSettings }
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import WriteSummaryTest._
 import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
 import org.apache.commons.io.FileUtils
-import org.testng.annotations.{AfterClass, Test}
+import org.testng.annotations.{ AfterClass, Test }
 
 import scala.concurrent.Await
 import scala.concurrent.duration.Duration
@@ -98,7 +98,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
 
     val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
     basicSummaryTest(summary, qscript.summaryRunId, dir)
-    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), keyValues = Map("key" ->  List("key"))) shouldBe Map("key" -> Some("value"))
+    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
     Await.result(summary.getFile(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
   }
 
@@ -119,7 +119,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
 
     val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
     basicSummaryTest(summary, qscript.summaryRunId, dir)
-    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), keyValues = Map("key" ->  List("key"))) shouldBe Map("key" -> Some("value"))
+    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
     Await.result(summary.getFile(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
   }
 
@@ -140,7 +140,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
 
     val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
     basicSummaryTest(summary, qscript.summaryRunId, dir)
-    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), keyValues = Map("key" ->  List("key"))) shouldBe Map("key" -> Some("value"))
+    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
     Await.result(summary.getFile(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
   }
 
@@ -161,7 +161,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
 
     val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
     basicSummaryTest(summary, qscript.summaryRunId, dir)
-    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), Some(Right("sampleName")), Some(Right("libName")), keyValues = Map("key" ->  List("key"))) shouldBe Map("key" -> Some("value"))
+    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), Some(Right("sampleName")), Some(Right("libName")), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
     Await.result(summary.getFile(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), Some(Right("sampleName")), Some(Right("libName")), key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
   }
 
@@ -202,7 +202,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
 
     val summary = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
     basicSummaryTest(summary, qscript.summaryRunId, dir)
-    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), keyValues = Map("key" ->  List("key"))) shouldBe Map("key" -> Some("value"))
+    summary.getStatKeys(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), keyValues = Map("key" -> List("key"))) shouldBe Map("key" -> Some("value"))
     Await.result(summary.getFile(qscript.summaryRunId, Right("test"), Some(Right("tool_1")), None, None, key = "file_1"), Duration.Inf).map(_.md5) shouldBe Some("checksum")
   }
 

biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDbTest.scala

@@ -72,7 +72,6 @@ class SummaryDbTest extends TestNGSuite with Matchers {
     Await.result(db.getLibraries(), Duration.Inf) shouldBe empty
     val libraryId = Await.result(db.createLibrary("test_lib", runId, sampleId), Duration.Inf)
 
-
     Await.result(db.getLibraries(), Duration.Inf) shouldBe Seq(Schema.Library(libraryId, "test_lib", runId, sampleId, None))
     Await.result(db.getLibraryName(libraryId), Duration.Inf) shouldBe Some("test_lib")
     Await.result(db.getLibraryId(runId, sampleId, "test_lib"), Duration.Inf) shouldBe Some(libraryId)
@@ -328,21 +327,20 @@ class SummaryDbTest extends TestNGSuite with Matchers {
     val libraryId = Await.result(db.createLibrary("test_library", runId, sampleId), Duration.Inf)
 
     Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path", "md5", link = false, 1), Duration.Inf)
-    Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,None,None,None,"key","path","md5",link = false,1))
-    Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path","md5",link = false,1))
+    Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, None, None, None, "key", "path", "md5", link = false, 1))
+    Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0, 0, None, None, None, "key", "path", "md5", link = false, 1))
     Await.result(db.createOrUpdateFile(runId, pipelineId, None, None, None, "key", "path2", "md5", link = false, 1), Duration.Inf)
-    Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1))
-    Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1))
+    Await.result(db.getFile(runId, Left(pipelineId), None, None, None, "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, None, None, None, "key", "path2", "md5", link = false, 1))
+    Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0, 0, None, None, None, "key", "path2", "md5", link = false, 1))
 
     // Test join queries
     Await.result(db.createOrUpdateFile(runId, pipelineId, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", link = false, 1), Duration.Inf)
-    Await.result(db.getFile(runId, Right("test_pipeline"), Some(Right("test_module")), Some(Right("test_sample")), Some(Right("test_library")), "key"), Duration.Inf) shouldBe Some(Schema.File(0,0,Some(moduleId), Some(sampleId), Some(libraryId),"key","path3","md5",link = false,1))
-    Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0,0,None,None,None,"key","path2","md5",link = false,1), Schema.File(0,0,Some(moduleId), Some(sampleId), Some(libraryId),"key","path3","md5",link = false,1))
+    Await.result(db.getFile(runId, Right("test_pipeline"), Some(Right("test_module")), Some(Right("test_sample")), Some(Right("test_library")), "key"), Duration.Inf) shouldBe Some(Schema.File(0, 0, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", link = false, 1))
+    Await.result(db.getFiles(), Duration.Inf) shouldBe Seq(Schema.File(0, 0, None, None, None, "key", "path2", "md5", link = false, 1), Schema.File(0, 0, Some(moduleId), Some(sampleId), Some(libraryId), "key", "path3", "md5", link = false, 1))
 
     db.close()
   }
 
-
   @Test
   def testExecutable(): Unit = {
     val dbFile = File.createTempFile("summary.", ".db")

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -18,12 +18,12 @@ import java.io.File
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.extensions.centrifuge.{Centrifuge, CentrifugeKreport}
-import nl.lumc.sasc.biopet.extensions.kraken.{Kraken, KrakenReport}
+import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
+import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
 import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala

@@ -17,13 +17,13 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import java.io.File
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 /**
  * Created by pjvanthof on 04/02/16.

generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala

@@ -23,7 +23,7 @@ import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, Test}
+import org.testng.annotations.{ AfterClass, Test }
 
 /**
  * Created by pjvan_thof on 13-5-16.

gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -14,22 +14,22 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, BiopetPipe}
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
-import nl.lumc.sasc.biopet.extensions.tools.{BaseCounter, WipeReads}
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.extensions.tools.{ BaseCounter, WipeReads }
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.utils.camelize
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends TestNGSuite with Matchers {
 

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala

@@ -24,7 +24,7 @@ import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, Test}
+import org.testng.annotations.{ AfterClass, Test }
 
 /**
  * Created by pjvan_thof on 4/11/16.

gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala

@@ -23,7 +23,7 @@ import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, Test}
+import org.testng.annotations.{ AfterClass, Test }
 
 /**
  * Created by pjvan_thof on 31-5-16.

kopisu/src/test/scala/nl/lumc/sasc/biopet/pipelines/kopisu/KopisuTest.scala

@@ -14,17 +14,17 @@
  */
 package nl.lumc.sasc.biopet.pipelines.kopisu
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.freec.{FreeC, FreeCAssessSignificancePlot, FreeCCNVPlot}
+import nl.lumc.sasc.biopet.extensions.freec.{ FreeC, FreeCAssessSignificancePlot, FreeCCNVPlot }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 import scala.collection.mutable.ListBuffer
 

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

@@ -14,19 +14,19 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
-import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, MergeSamFiles}
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles }
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 /**
  * Created by pjvanthof on 15/05/16.

sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala

@@ -14,16 +14,16 @@
  */
 package nl.lumc.sasc.biopet.pipelines.sage
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 /**
  * Created by pjvanthof on 28/09/16.

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

@@ -14,21 +14,21 @@
  */
 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.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 import scala.collection.mutable.ListBuffer
 

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

@@ -14,19 +14,19 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator}
+import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
 import nl.lumc.sasc.biopet.extensions.tools.VcfStats
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 /**
  * Class for testing shiva

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

@@ -19,22 +19,22 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{File, FileOutputStream}
+import java.io.{ File, FileOutputStream }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.BiopetPipe
 import nl.lumc.sasc.biopet.extensions.Freebayes
-import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge}
-import nl.lumc.sasc.biopet.extensions.gatk.{CombineVariants, GenotypeConcordance, HaplotypeCaller, UnifiedGenotyper}
+import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
+import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance, HaplotypeCaller, UnifiedGenotyper }
 import nl.lumc.sasc.biopet.utils.config.Config
-import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
-import nl.lumc.sasc.biopet.extensions.vt.{VtDecompose, VtNormalize}
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
+import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, DataProvider, Test}
+import org.testng.annotations.{ AfterClass, DataProvider, Test }
 
 import scala.collection.mutable.ListBuffer
 

toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala

@@ -25,7 +25,7 @@ import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{AfterClass, Test}
+import org.testng.annotations.{ AfterClass, Test }
 
 /**
  * Created by pjvan_thof on 4/11/16.