Commit c6a78d0d authored by Sander Bollen's avatar Sander Bollen

see #231

parent 9c5c1703
......@@ -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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