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..552eff8792021a662322c4c247d17d0dc7f7bfd2 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 @@ -39,7 +39,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum } override def defaults = Map( - "varianteffectpredictor" -> Map("everything" -> true) + "varianteffectpredictor" -> Map("everything" -> true, "failed" -> true) ) //defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true)) @@ -80,7 +80,7 @@ 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 _ =>