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