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biopet.biopet
Commits
c6a78d0d
Commit
c6a78d0d
authored
Oct 29, 2015
by
Sander Bollen
Browse files
see #231
parent
9c5c1703
Changes
1
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Inline
Side-by-side
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
c6a78d0d
...
...
@@ -48,6 +48,7 @@ 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
)
...
...
@@ -80,7 +81,7 @@ 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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