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biopet.biopet
Commits
8fa9668a
Commit
8fa9668a
authored
Apr 14, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 14, 2017
Browse files
Merge pull request #69 from biopet/fix-BIOPET-654
Remove default arguments
parents
8c5573ad
310bcfe4
Changes
1
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @
8fa9668a
...
...
@@ -36,11 +36,6 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {
override
def
fixedValues
=
Map
(
"haplotypecaller"
->
Map
(
"emitRefConfidence"
->
"GVCF"
))
override
def
defaults
=
Map
(
"haplotypecaller"
->
Map
(
"variant_index_type"
->
"LINEAR"
,
"variant_index_parameter"
->
128000
)
)
def
biopetScript
()
{
gVcfFiles
=
for
((
sample
,
inputBam
)
<-
inputBams
)
yield
{
val
hc
=
gatk
.
HaplotypeCaller
(
this
,
List
(
inputBam
),
new
File
(
outputDir
,
sample
+
".gvcf.vcf.gz"
))
...
...
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