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biopet.biopet
Commits
8fc17a50
Commit
8fc17a50
authored
May 11, 2016
by
Peter van 't Hof
Browse files
Fixed file names
parent
ab0764f7
Changes
1
Hide whitespace changes
Inline
Side-by-side
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
8fc17a50
...
...
@@ -45,11 +45,13 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
@Input
(
doc
=
"Input GVCF file"
,
shortName
=
"gvcf"
,
required
=
false
)
var
inputGvcf
:
Option
[
File
]
=
None
def
outputName
=
inputVcf
.
getName
.
stripSuffix
(
".vcf.gz"
)
def
outputVcf
:
File
=
(
gonlVcfFile
,
exacVcfFile
)
match
{
case
(
Some
(
_
),
Some
(
_
))
=>
swapExt
(
outputDir
,
inputVcf
,
".vcf.gz"
,
"
.vep.normalized.gonl.exac.vcf.gz"
)
case
(
Some
(
_
),
_
)
=>
swapExt
(
outputDir
,
inputVcf
,
".vcf.gz"
,
"
.vep.normalized.gonl.vcf.gz"
)
case
(
_
,
Some
(
_
))
=>
swapExt
(
outputDir
,
inputVcf
,
".vcf.gz"
,
"
.vep.normalized.exac.vcf.gz"
)
case
_
=>
swapExt
(
outputDir
,
inputVcf
,
".vcf.gz"
,
"
.vep.normalized.vcf.gz"
)
case
(
Some
(
_
),
Some
(
_
))
=>
new
File
(
outputDir
,
s
"$outputName
.vep.normalized.gonl.exac.vcf.gz"
)
case
(
Some
(
_
),
_
)
=>
new
File
(
outputDir
,
s
"$outputName
.vep.normalized.gonl.vcf.gz"
)
case
(
_
,
Some
(
_
))
=>
new
File
(
outputDir
,
s
"$outputName
.vep.normalized.exac.vcf.gz"
)
case
_
=>
new
File
(
outputDir
,
s
"$outputName
.vep.normalized.vcf.gz"
)
}
lazy
val
minScatterGenomeSize
:
Long
=
config
(
"min_scatter_genome_size"
,
default
=
75000000
)
...
...
@@ -114,7 +116,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
cv
.
variant
=
outputVcfFiles
.
toList
cv
.
outputFile
=
outputVcf
add
(
cv
)
}
else
runChunk
(
useVcf
,
outputDir
,
"toucan"
)
}
else
runChunk
(
useVcf
,
outputDir
,
outputName
)
addSummaryJobs
()
}
...
...
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