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biopet.biopet
Commits
544eb3a0
Commit
544eb3a0
authored
Mar 09, 2015
by
bow
Browse files
Merge branch 'patch-toucan' into 'develop'
Patch toucan Fix output directory path in Toucan See merge request !123
parents
118f09fd
a9645551
Changes
1
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public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
544eb3a0
...
...
@@ -30,7 +30,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript {
def
biopetScript
()
:
Unit
=
{
val
vep
=
new
VariantEffectPredictor
(
this
)
vep
.
input
=
inputVCF
vep
.
output
=
outputDir
+
inputVCF
.
getName
.
stripSuffix
(
".gz"
).
stripSuffix
(
".vcf"
)
+
".vep.vcf"
vep
.
output
=
new
File
(
outputDir
,
inputVCF
.
getName
.
stripSuffix
(
".gz"
).
stripSuffix
(
".vcf"
)
+
".vep.vcf"
)
vep
.
isIntermediate
=
true
add
(
vep
)
...
...
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