diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala index 5878d03f32d5b9943bfb4e734b2c5f7d0b806a41..8543b7706670ef40d9a877f27a0bf1b1ed3d77a9 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala @@ -45,7 +45,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion { var inputVCF: File = null @Output(doc = "Output VCF", shortName = "OutputFile", required = true) - var outputVCF: File = null + var outputVcf: File = null var mode: String = config("mode", default = "explode") var doNotRemove: Boolean = config("donotremove", default = false) @@ -54,7 +54,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion { override def commandLine = super.commandLine + required("-I", inputVCF) + - required("-O", outputVCF) + + required("-O", outputVcf) + required("-m", mode) + conditional(doNotRemove, "--do-not-remove") }