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biopet.biopet
Commits
f32902a4
Commit
f32902a4
authored
Nov 02, 2015
by
Peter van 't Hof
Browse files
Merge remote-tracking branch 'remotes/origin/develop' into fix-shiva_fails
parents
ef064a1b
a53e20d9
Changes
1
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public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
f32902a4
...
...
@@ -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))
...
...
@@ -80,7 +80,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
vcfWithVcf
.
input
=
outputFile
vcfWithVcf
.
secondaryVcf
=
exacFile
vcfWithVcf
.
output
=
swapExt
(
outputDir
,
outputFile
,
".vcf.gz"
,
".exac.vcf.gz"
)
vcfWithVcf
.
fields
::=
(
"
M
AF"
,
"
M
AF_exac"
,
None
)
vcfWithVcf
.
fields
::=
(
"AF"
,
"AF_exac"
,
None
)
add
(
vcfWithVcf
)
outputFile
=
vcfWithVcf
.
output
case
_
=>
...
...
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