Style changes

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala

@@ -7,8 +7,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
-  * Created by pjvanthof on 30/03/16.
-  */
+ * Created by pjvanthof on 30/03/16.
+ */
 class Grep(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input file", required = true)
   var input: File = _

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -274,7 +274,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
     (v1, v2) match {
       case (x1: Int, x2: Int) => x1 + x2
-      case _ => throw new IllegalStateException("Value are not Int's, unable to sum them up")
+      case _                  => throw new IllegalStateException("Value are not Int's, unable to sum them up")
     }
   }
 

toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.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.pipelines.toucan
 
 import java.io.File
@@ -31,10 +31,10 @@ import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
 import org.broadinstitute.gatk.queue.QScript
 
 /**
-  * Pipeline to annotate a vcf file with VEP
-  *
-  * Created by ahbbollen on 15-1-15.
-  */
+ * Pipeline to annotate a vcf file with VEP
+ *
+ * Created by ahbbollen on 15-1-15.
+ */
 class Toucan(val root: Configurable) extends QScript with BiopetQScript with SummaryQScript with Reference {
   def this() = this(null)
 
@@ -78,58 +78,58 @@ 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}-${region.end}"
-      val chunkDir = new File(outputDir, "chunk" + File.separator + chunkName)
-      val sv = new SelectVariants(this)
-      sv.inputFiles :+= useVcf
-      sv.outputFile = new File(chunkDir, chunkName + ".vcf.gz")
-      sv.isIntermediate = true
-      add(sv)
-
-      val vep = new VariantEffectPredictor(this)
-      vep.input = sv.outputFile
-      vep.output = new File(chunkDir, chunkName + ".vep.vcf")
-      vep.isIntermediate = true
-      add(vep)
-      addSummarizable(vep, "variant_effect_predictor")
-
-      val normalizer = new VepNormalizer(this)
-      normalizer.inputVCF = vep.output
-      normalizer.outputVcf = new File(chunkDir, chunkName + ".normalized.vcf.gz")
-      normalizer.isIntermediate = true
-      add(normalizer)
-
-      var outputFile = normalizer.outputVcf
-
-      gonlVcfFile match {
-        case Some(gonlFile) =>
-          val vcfWithVcf = new VcfWithVcf(this)
-          vcfWithVcf.input = outputFile
-          vcfWithVcf.secondaryVcf = gonlFile
-          vcfWithVcf.output = swapExt(chunkDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
-          vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
-          vcfWithVcf.isIntermediate = true
-          add(vcfWithVcf)
-          outputFile = vcfWithVcf.output
-        case _ =>
+        val chunkName = s"${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")
+        normalizer.isIntermediate = true
+        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)
+            vcfWithVcf.isIntermediate = true
+            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)
+            vcfWithVcf.isIntermediate = true
+            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)
-          vcfWithVcf.isIntermediate = true
-          add(vcfWithVcf)
-          outputFile = vcfWithVcf.output
-        case _ =>
-      }
-
-      outputFile
-    }
-
     val cv = new CatVariants(this)
     cv.inputFiles = outputVcfFiles.toList
     cv.outputFile = (gonlVcfFile, exacVcfFile) match {
@@ -144,14 +144,14 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
   }
 
   /**
-    * Performs the varda import and activate for one sample
-    *
-    * @param sampleID the sampleID to be used
-    * @param inputVcf the input VCF
-    * @param gVCF the gVCF for coverage
-    * @param annotation: ManweDownloadAnnotateVcf object of annotated vcf
-    * @return
-    */
+   * Performs the varda import and activate for one sample
+   *
+   * @param sampleID the sampleID to be used
+   * @param inputVcf the input VCF
+   * @param gVCF the gVCF for coverage
+   * @param annotation: ManweDownloadAnnotateVcf object of annotated vcf
+   * @return
+   */
   def importAndActivateSample(sampleID: String, sampleGroups: List[String], inputVcf: File,
                               gVCF: File, annotation: ManweAnnotateVcf): ManweActivateAfterAnnotImport = {
 
@@ -215,12 +215,12 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
   }
 
   /**
-    * Perform varda analysis
-    *
-    * @param vcf input vcf
-    * @param gVcf The gVCF to be used for coverage calculations
-    * @return return vcf
-    */
+   * Perform varda analysis
+   *
+   * @param vcf input vcf
+   * @param gVcf The gVCF to be used for coverage calculations
+   * @return return vcf
+   */
   def varda(vcf: File, gVcf: File): File = {
 
     val annotationQueries: List[String] = config("annotation_queries", default = List("GLOBAL *"), namespace = "manwe")