Fixes style

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala

 /**
-  * Biopet is built on top of GATK Queue for building bioinformatic
-  * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
-  * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
-  * should also be able to execute Biopet tools and pipelines.
-  *
-  * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
-  *
-  * Contact us at: sasc@lumc.nl
-  *
-  * A dual licensing mode is applied. The source code within this project that are
-  * not part of GATK Queue is freely available for non-commercial use under an AGPL
-  * license; For commercial users or users who do not want to follow the AGPL
-  * license, please contact us to obtain a separate license.
-  */
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
 package nl.lumc.sasc.biopet.extensions.gatk
 
 import java.io.File
@@ -21,10 +21,10 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
-  * Extension for CombineVariants from GATK
-  *
-  * Created by pjvan_thof on 2/26/15.
-  */
+ * Extension for CombineVariants from GATK
+ *
+ * Created by pjvan_thof on 2/26/15.
+ */
 class SelectVariants(val root: Configurable) extends Gatk {
   val analysisType = "SelectVariants"
 

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -20,11 +20,11 @@ import java.io.File
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
-import nl.lumc.sasc.biopet.extensions.bedtools.{BedtoolsIntersect, BedtoolsMerge}
-import nl.lumc.sasc.biopet.extensions.gatk.{CatVariants, SelectVariants}
-import nl.lumc.sasc.biopet.extensions.manwe.{ManweAnnotateVcf, ManweSamplesImport}
-import nl.lumc.sasc.biopet.extensions.tools.{GvcfToBed, VcfWithVcf, VepNormalizer}
-import nl.lumc.sasc.biopet.extensions.{Bgzip, Ln, VariantEffectPredictor}
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsIntersect, BedtoolsMerge }
+import nl.lumc.sasc.biopet.extensions.gatk.{ CatVariants, SelectVariants }
+import nl.lumc.sasc.biopet.extensions.manwe.{ ManweAnnotateVcf, ManweSamplesImport }
+import nl.lumc.sasc.biopet.extensions.tools.{ GvcfToBed, VcfWithVcf, VepNormalizer }
+import nl.lumc.sasc.biopet.extensions.{ Bgzip, Ln, VariantEffectPredictor }
 import nl.lumc.sasc.biopet.utils.VcfUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
@@ -75,62 +75,62 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
       .scatter(config("bin_size", default = 50000000))
       .allRecords.map { region =>
 
-      val chunkName = s"${region.chr}-${region.start}-${region.end}"
-      val chunkDir = new File(outputDir, "chunk" + File.separator + chunkName)
-      val sv = new SelectVariants(this)
-      sv.inputFiles :+= useVcf
-      sv.outputFile = new File(chunkDir, chunkName + ".vcf.gz")
-      sv.isIntermediate = true
-      add(sv)
-
-      val vep = new VariantEffectPredictor(this)
-      vep.input = sv.outputFile
-      vep.output = new File(chunkDir, chunkName + ".vep.vcf")
-      vep.isIntermediate = true
-      add(vep)
-      addSummarizable(vep, "variant_effect_predictor")
-
-      val normalizer = new VepNormalizer(this)
-      normalizer.inputVCF = vep.output
-      normalizer.outputVcf = new File(chunkDir, chunkName + ".normalized.vcf.gz")
-      add(normalizer)
-
-      var outputFile = normalizer.outputVcf
-
-      gonlVcfFile match {
-        case Some(gonlFile) =>
-          val vcfWithVcf = new VcfWithVcf(this)
-          vcfWithVcf.input = outputFile
-          vcfWithVcf.secondaryVcf = gonlFile
-          vcfWithVcf.output = swapExt(chunkDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
-          vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
-          add(vcfWithVcf)
-          outputFile = vcfWithVcf.output
-        case _ =>
+        val chunkName = s"${region.chr}-${region.start}-${region.end}"
+        val chunkDir = new File(outputDir, "chunk" + File.separator + chunkName)
+        val sv = new SelectVariants(this)
+        sv.inputFiles :+= useVcf
+        sv.outputFile = new File(chunkDir, chunkName + ".vcf.gz")
+        sv.isIntermediate = true
+        add(sv)
+
+        val vep = new VariantEffectPredictor(this)
+        vep.input = sv.outputFile
+        vep.output = new File(chunkDir, chunkName + ".vep.vcf")
+        vep.isIntermediate = true
+        add(vep)
+        addSummarizable(vep, "variant_effect_predictor")
+
+        val normalizer = new VepNormalizer(this)
+        normalizer.inputVCF = vep.output
+        normalizer.outputVcf = new File(chunkDir, chunkName + ".normalized.vcf.gz")
+        add(normalizer)
+
+        var outputFile = normalizer.outputVcf
+
+        gonlVcfFile match {
+          case Some(gonlFile) =>
+            val vcfWithVcf = new VcfWithVcf(this)
+            vcfWithVcf.input = outputFile
+            vcfWithVcf.secondaryVcf = gonlFile
+            vcfWithVcf.output = swapExt(chunkDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
+            vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
+            add(vcfWithVcf)
+            outputFile = vcfWithVcf.output
+          case _ =>
+        }
+
+        exacVcfFile match {
+          case Some(exacFile) =>
+            val vcfWithVcf = new VcfWithVcf(this)
+            vcfWithVcf.input = outputFile
+            vcfWithVcf.secondaryVcf = exacFile
+            vcfWithVcf.output = swapExt(chunkDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
+            vcfWithVcf.fields ::= ("AF", "AF_exac", None)
+            add(vcfWithVcf)
+            outputFile = vcfWithVcf.output
+          case _ =>
+        }
+
+        outputFile
       }
 
-      exacVcfFile match {
-        case Some(exacFile) =>
-          val vcfWithVcf = new VcfWithVcf(this)
-          vcfWithVcf.input = outputFile
-          vcfWithVcf.secondaryVcf = exacFile
-          vcfWithVcf.output = swapExt(chunkDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
-          vcfWithVcf.fields ::= ("AF", "AF_exac", None)
-          add(vcfWithVcf)
-          outputFile = vcfWithVcf.output
-        case _ =>
-      }
-
-      outputFile
-    }
-
     val cv = new CatVariants(this)
     cv.inputFiles = outputVcfFiles.toList
     cv.outputFile = (gonlVcfFile, exacVcfFile) match {
       case (Some(_), Some(_)) => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.gonl.exac.vcf.gz")
-      case (Some(_), _) => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
-      case (_, Some(_)) => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
-      case _ => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.vcf.gz")
+      case (Some(_), _)       => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
+      case (_, Some(_))       => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
+      case _                  => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.vcf.gz")
     }
     add(cv)