From a36ce0659489051184e4f6ce6a0f53c427399220 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Nov 2014 09:56:38 +0100
Subject: [PATCH] Remove Some()
---
.../lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index be951c2f1..aef4254d3 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -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
--
GitLab