Fix compile errors

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -98,7 +98,7 @@ object BammetricsReport extends ReportBuilder {
 
   /**
    * Generate a stackbar plot for alignment stats
- *
+   *
    * @param outputDir OutputDir for the tsv and png file
    * @param prefix Prefix of the tsv and png file
    * @param summary Summary class
@@ -162,7 +162,7 @@ object BammetricsReport extends ReportBuilder {
 
   /**
    * Generate a line plot for insertsize
- *
+   *
    * @param outputDir OutputDir for the tsv and png file
    * @param prefix Prefix of the tsv and png file
    * @param summary Summary class
@@ -251,7 +251,7 @@ object BammetricsReport extends ReportBuilder {
 
   /**
    * Generate a line plot for wgs coverage
- *
+   *
    * @param outputDir OutputDir for the tsv and png file
    * @param prefix Prefix of the tsv and png file
    * @param summary Summary class
@@ -342,7 +342,7 @@ object BammetricsReport extends ReportBuilder {
 
   /**
    * Generate a line plot for rna coverage
- *
+   *
    * @param outputDir OutputDir for the tsv and png file
    * @param prefix Prefix of the tsv and png file
    * @param summary Summary class

basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -24,7 +24,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
-import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
+import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
 import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -44,7 +44,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
     "variantcallers" -> variantcallers
   )
 
-  lazy val shiva: ShivaTrait = new Shiva(qscript)
+  lazy val shiva = new Shiva(qscript)
 
   def summaryFile: File = new File(outputDir, "Basty.summary.json")
 

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -205,11 +205,12 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     logger.info(s"Starting script for ${samples.size} samples")
     var count = 0
     if (onlySamples.isEmpty || samples.forall(x => onlySamples.contains(x._1))) {
-      samples.foreach { case (sampleId, sample) =>
-        logger.info(s"Starting script sample '$sampleId'")
-        sample.addAndTrackJobs()
-        count += 1
-        logger.info(s"Finish script for '$sampleId', samples done: $count / ${samples.size}")
+      samples.foreach {
+        case (sampleId, sample) =>
+          logger.info(s"Starting script sample '$sampleId'")
+          sample.addAndTrackJobs()
+          count += 1
+          logger.info(s"Finish script for '$sampleId', samples done: $count / ${samples.size}")
       }
       logger.info("Starting script for multisample jobs")
       addMultiSampleJobs()

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -189,7 +189,7 @@ trait ReportBuilder extends ToolCommand {
 
   /**
    * This method will render the page and the subpages recursivly
- *
+   *
    * @param summary The summary object
    * @param page Page to render
    * @param outputDir Root output dir of the report

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala

@@ -120,7 +120,7 @@ object ShivaReport extends MultisampleMappingReportTrait {
 
   /**
    * Generate a stackbar plot for found variants
- *
+   *
    * @param outputDir OutputDir for the tsv and png file
    * @param prefix Prefix of the tsv and png file
    * @param summary Summary class

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

@@ -22,7 +22,6 @@ import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordanc
 import nl.lumc.sasc.biopet.extensions.tools.VcfStats
 import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
-import nl.lumc.sasc.biopet.pipelines.gatk.variantcallers._
 import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.{ VarscanCnsSingleSample, _ }
 import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Configurable

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

@@ -15,7 +15,7 @@
  */
 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.broad._
@@ -26,13 +26,13 @@ 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 }
 
 /**
-  * Class for testing shiva
-  *
-  * Created by pjvan_thof on 3/2/15.
-  */
+ * Class for testing shiva
+ *
+ * Created by pjvan_thof on 3/2/15.
+ */
 class ShivaTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): Shiva = {
     new Shiva() {

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

 /**
-  * Due to the license issue with GATK, this part of Biopet can only be used inside the
-  * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
-  * on how to use this protected part of biopet or contact us at sasc@lumc.nl
-  */
+ * Due to the license issue with GATK, this part of Biopet can only be used inside the
+ * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+ * on how to use this protected part of biopet or contact us at sasc@lumc.nl
+ */
 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.bcftools.{ BcftoolsCall, BcftoolsMerge }
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
-import nl.lumc.sasc.biopet.extensions.gatk.broad.{HaplotypeCaller, UnifiedGenotyper}
-import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats}
+import nl.lumc.sasc.biopet.extensions.gatk.broad.{ HaplotypeCaller, UnifiedGenotyper }
+import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
 import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
 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
 
 /**
-  * Class for testing ShivaVariantcalling
-  *
-  * Created by pjvan_thof on 3/2/15.
-  */
+ * Class for testing ShivaVariantcalling
+ *
+ * Created by pjvan_thof on 3/2/15.
+ */
 class ShivaVariantcallingTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): ShivaVariantcalling = {
     new ShivaVariantcalling() {
@@ -55,7 +55,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
       unifiedGenotyper <- bool;
       haplotypeCaller <- bool
     ) yield Array[Any](bams, raw, bcftools, bcftools_singlesample, unifiedGenotyper, haplotypeCaller, haplotypeCallerGvcf, haplotypeCallerAllele, unifiedGenotyperAllele)
-      ).toArray
+    ).toArray
   }
 
   @Test(dataProvider = "shivaVariantcallingOptions")