diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala index 8774bdc985be4e03c6e09cec23d4070373c79866..ccd47d551363be2bf65d0fd0176f02f8092060a1 100644 --- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala +++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala @@ -35,7 +35,6 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum var inputVCF: File = _ def init(): Unit = { - } override def defaults = ConfigUtils.mergeMaps(Map( @@ -63,28 +62,26 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum var outputFile = normalizer.outputVcf gonlVcfFile match { - case Some(gonlVcfFile) => { + case Some(gonlFile) => val vcfWithVcf = new VcfWithVcf(this) vcfWithVcf.input = outputFile - vcfWithVcf.secondaryVcf = gonlVcfFile + vcfWithVcf.secondaryVcf = gonlFile vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz") vcfWithVcf.fields ::= ("AF", "AF_gonl", None) add(vcfWithVcf) outputFile = vcfWithVcf.output - } case _ => } exacVcfFile match { - case Some(exacVcfFile) => { + case Some(exacFile) => val vcfWithVcf = new VcfWithVcf(this) vcfWithVcf.input = outputFile - vcfWithVcf.secondaryVcf = exacVcfFile + vcfWithVcf.secondaryVcf = exacFile vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz") vcfWithVcf.fields ::= ("MAF", "MAF_exac", None) add(vcfWithVcf) outputFile = vcfWithVcf.output - } case _ => } }