Commit a36ce065 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove Some()

parent 7439f3d4
......@@ -97,8 +97,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val cvRaw = CombineVariants(this, allRawVcfFiles.toList, outputDir + "variantcalling/multisample.raw.vcf.gz")
add(cvRaw)
multisampleVariantcalling.preProcesBams = Some(false)
multisampleVariantcalling.doublePreProces = Some(false)
multisampleVariantcalling.preProcesBams = false
multisampleVariantcalling.doublePreProces = false
multisampleVariantcalling.inputBams = allBamfiles.toList
multisampleVariantcalling.rawVcfInput = cvRaw.out
multisampleVariantcalling.outputDir = outputDir + "variantcalling"
......@@ -135,10 +135,10 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val gatkVariantcalling = new GatkVariantcalling(this)
gatkVariantcalling.inputBams = libraryBamfiles
gatkVariantcalling.outputDir = sampleDir + "/variantcalling/"
gatkVariantcalling.preProcesBams = Some(false)
gatkVariantcalling.preProcesBams = false
if (!singleSampleCalling) {
gatkVariantcalling.useHaplotypecaller = Some(false)
gatkVariantcalling.useUnifiedGenotyper = Some(false)
gatkVariantcalling.useHaplotypecaller = false
gatkVariantcalling.useUnifiedGenotyper = false
}
gatkVariantcalling.sampleID = sampleID
gatkVariantcalling.init
......
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