Style changes

public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala

@@ -66,25 +66,26 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
       val cvTotal = new CatVariants(this)
       cvTotal.assumeSorted = true
       cvTotal.outputFile = new File(outputDirGens, "merge.gens.vcf.gz")
-      val chrGens = inputGens.groupBy(_.contig).map { case (contig, gens) =>
-        val cvChr = new CatVariants(this)
-        cvChr.assumeSorted = true
-        //cvChr.isIntermediate = true
-        cvChr.outputFile = new File(outputDirGens, s"${contig}.merge.gens.vcf.gz")
-        gens.zipWithIndex.foreach { gen =>
-          val gensToVcf = new GensToVcf(this)
-          gensToVcf.inputGens = gen._1.genotypes
-          gensToVcf.inputInfo = gen._1.info
-          gensToVcf.contig = gen._1.contig
-          gensToVcf.samplesFile = phenotypeFile
-          gensToVcf.outputVcf = new File(outputDirGens, gen._1.genotypes.getName + s".${gen._2}.vcf.gz")
-          gensToVcf.isIntermediate = true
-          add(gensToVcf)
-          cvChr.inputFiles :+= gensToVcf.outputVcf
-        }
-        add(cvChr)
-        cvTotal.inputFiles :+= cvChr.outputFile
-        contig -> cvChr.outputFile
+      val chrGens = inputGens.groupBy(_.contig).map {
+        case (contig, gens) =>
+          val cvChr = new CatVariants(this)
+          cvChr.assumeSorted = true
+          //cvChr.isIntermediate = true
+          cvChr.outputFile = new File(outputDirGens, s"${contig}.merge.gens.vcf.gz")
+          gens.zipWithIndex.foreach { gen =>
+            val gensToVcf = new GensToVcf(this)
+            gensToVcf.inputGens = gen._1.genotypes
+            gensToVcf.inputInfo = gen._1.info
+            gensToVcf.contig = gen._1.contig
+            gensToVcf.samplesFile = phenotypeFile
+            gensToVcf.outputVcf = new File(outputDirGens, gen._1.genotypes.getName + s".${gen._2}.vcf.gz")
+            gensToVcf.isIntermediate = true
+            add(gensToVcf)
+            cvChr.inputFiles :+= gensToVcf.outputVcf
+          }
+          add(cvChr)
+          cvTotal.inputFiles :+= cvChr.outputFile
+          contig -> cvChr.outputFile
       }
       add(cvTotal)
       (cvTotal.outputFile, Map[String, File]())