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biopet.biopet
Commits
d2673ec5
Commit
d2673ec5
authored
May 11, 2016
by
Peter van 't Hof
Browse files
Fixed compile error
parent
e2b5ad1d
Changes
1
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Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
d2673ec5
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.extensions.gatk._
import
nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
...
...
@@ -164,7 +164,7 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
}
else
None
lazy
val
cnvCalling
=
if
(
config
(
"cnv_calling"
,
default
=
false
).
asBoolean
)
{
Some
(
new
Kopisu
(
)(
this
))
Some
(
new
Kopisu
(
this
))
}
else
None
lazy
val
annotation
=
if
(
multisampleVariantCalling
.
isDefined
&&
...
...
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