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biopet.biopet
Commits
a36ce065
Commit
a36ce065
authored
Nov 17, 2014
by
Peter van 't Hof
Browse files
Remove Some()
parent
7439f3d4
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
a36ce065
...
...
@@ -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
...
...
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