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biopet.biopet
Commit 369147f4 authored by Sander Bollen's avatar Sander Bollen
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parent c6a78d0d
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public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @ 369147f4
......@@ -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))
......@@ -48,7 +48,6 @@ 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)
......
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