From c6a78d0dfe6a97d7e6019fbe83b09d690079d7b8 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 29 Oct 2015 17:44:24 +0100
Subject: [PATCH] see #231
---
.../scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
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 6ee077671..423d51ee8 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 _ =>
--
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