From 369147f48877bb843461f299cb1a5db32456c67f Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 29 Oct 2015 17:56:13 +0100
Subject: [PATCH] blah
---
.../scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
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 423d51ee8..552eff879 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))
@@ -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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