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biopet.biopet
Commits
946ea4c2
Commit
946ea4c2
authored
Nov 24, 2015
by
Peter van 't Hof
Browse files
Fixed outputDirs
parent
60fc26c3
Changes
2
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
946ea4c2
...
...
@@ -57,7 +57,10 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
require
(
inputBams
.
nonEmpty
,
"No input bams found"
)
require
(
callers
.
nonEmpty
,
"must select at least 1 SV caller, choices are: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
callers
.
foreach
(
add
)
callers
.
foreach
{
caller
=>
caller
.
outputDir
=
new
File
(
outputDir
,
caller
.
name
)
add
(
caller
)
}
addSummaryJobs
()
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
946ea4c2
...
...
@@ -87,6 +87,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript
for
(
caller
<-
callers
)
{
caller
.
inputBams
=
inputBams
caller
.
namePrefix
=
namePrefix
caller
.
outputDir
=
new
File
(
outputDir
,
caller
.
name
)
add
(
caller
)
addStats
(
caller
.
outputFile
,
caller
.
name
)
val
normalize
:
Boolean
=
config
(
"execute_vt_normalize"
,
default
=
false
,
submodule
=
caller
.
configName
)
...
...
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