Commit f32902a4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge remote-tracking branch 'remotes/origin/develop' into fix-shiva_fails

parents ef064a1b a53e20d9
......@@ -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))
......@@ -80,7 +80,7 @@ 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 _ =>
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment