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biopet.biopet
Commits
369147f4
Commit
369147f4
authored
Oct 29, 2015
by
Sander Bollen
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parent
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public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+1
-2
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public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
369147f4
...
...
@@ -39,7 +39,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
}
override
def
defaults
=
Map
(
"varianteffectpredictor"
->
Map
(
"everything"
->
true
)
"varianteffectpredictor"
->
Map
(
"everything"
->
true
,
"failed"
->
true
)
)
//defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
...
...
@@ -48,7 +48,6 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val
vep
=
new
VariantEffectPredictor
(
this
)
vep
.
input
=
inputVCF
vep
.
output
=
new
File
(
outputDir
,
inputVCF
.
getName
.
stripSuffix
(
".gz"
).
stripSuffix
(
".vcf"
)
+
".vep.vcf"
)
vep
.
failed
=
true
vep
.
isIntermediate
=
true
add
(
vep
)
...
...
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