Commit fd872a57 authored by Peter van 't Hof's avatar Peter van 't Hof

Make chunk files intermediate

parent 7961846b
......@@ -94,6 +94,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val normalizer = new VepNormalizer(this)
normalizer.inputVCF = vep.output
normalizer.outputVcf = new File(chunkDir, chunkName + ".normalized.vcf.gz")
normalizer.isIntermediate = true
add(normalizer)
var outputFile = normalizer.outputVcf
......@@ -105,6 +106,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
vcfWithVcf.secondaryVcf = gonlFile
vcfWithVcf.output = swapExt(chunkDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
vcfWithVcf.isIntermediate = true
add(vcfWithVcf)
outputFile = vcfWithVcf.output
case _ =>
......@@ -117,6 +119,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
vcfWithVcf.secondaryVcf = exacFile
vcfWithVcf.output = swapExt(chunkDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_exac", None)
vcfWithVcf.isIntermediate = true
add(vcfWithVcf)
outputFile = vcfWithVcf.output
case _ =>
......
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