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 6ee0776713a5391296719ac6edc83819777fcf31..423d51ee84495b645b9a9a30fe15f7e58407f4fe 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 @@ -48,6 +48,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum val vep = new VariantEffectPredictor(this) vep.input = inputVCF vep.output = new File(outputDir, inputVCF.getName.stripSuffix(".gz").stripSuffix(".vcf") + ".vep.vcf") + vep.failed = true vep.isIntermediate = true add(vep) @@ -80,7 +81,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum vcfWithVcf.input = outputFile vcfWithVcf.secondaryVcf = exacFile vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz") - vcfWithVcf.fields ::= ("MAF", "MAF_exac", None) + vcfWithVcf.fields ::= ("AF", "AF_exac", None) add(vcfWithVcf) outputFile = vcfWithVcf.output case _ =>