Commit 556ca42a authored by Peter van 't Hof's avatar Peter van 't Hof

Fix compile errors

parent a09badf6
......@@ -85,14 +85,14 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
BedRecordList.fromList(List(region)).writeToFile(bedFile)
bedFile.deleteOnExit()
val sv = new SelectVariants(this)
sv.inputFiles :+= useVcf
sv.outputFile = new File(chunkDir, chunkName + ".vcf.gz")
sv.variant = useVcf
sv.out = new File(chunkDir, chunkName + ".vcf.gz")
sv.intervals :+= bedFile
sv.isIntermediate = true
add(sv)
val vep = new VariantEffectPredictor(this)
vep.input = sv.outputFile
vep.input = sv.out
vep.output = new File(chunkDir, chunkName + ".vep.vcf")
vep.isIntermediate = true
add(vep)
......@@ -136,7 +136,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
}
val cv = new CatVariants(this)
cv.inputFiles = outputVcfFiles.toList
cv.variant = outputVcfFiles.toList
cv.outputFile = (gonlVcfFile, exacVcfFile) match {
case (Some(_), Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.exac.vcf.gz")
case (Some(_), _) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
......
Markdown is supported
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