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biopet.biopet
Commits
6c15d952
Commit
6c15d952
authored
May 11, 2016
by
Peter van 't Hof
Browse files
Added cnv calling to shiva
parent
b500ee16
Changes
2
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shiva/pom.xml
View file @
6c15d952
...
...
@@ -40,6 +40,11 @@
<artifactId>
Mapping
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Kopisu
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Toucan
</artifactId>
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
6c15d952
...
...
@@ -15,10 +15,11 @@
*/
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
import
nl.lumc.sasc.biopet.pipelines.kopisu.Kopisu
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -162,6 +163,10 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
Some
(
new
ShivaSvCalling
(
this
))
}
else
None
lazy
val
cnvCalling
=
if
(
config
(
"cnv_calling"
,
default
=
false
).
asBoolean
)
{
Some
(
new
Kopisu
()(
this
))
}
else
None
lazy
val
annotation
=
if
(
multisampleVariantCalling
.
isDefined
&&
config
(
"annotation"
,
default
=
false
).
asBoolean
)
{
Some
(
new
Toucan
(
this
))
...
...
@@ -183,11 +188,17 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
}
})
svCalling
.
foreach
(
sv
=>
{
svCalling
.
foreach
{
sv
=>
sv
.
outputDir
=
new
File
(
outputDir
,
"sv_calling"
)
sv
.
inputBams
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
preProcessBam
.
map
(
sampleId
->
_
)
}
add
(
sv
)
})
}
cnvCalling
.
foreach
{
cnv
=>
cnv
.
outputDir
=
new
File
(
outputDir
,
"cnv_calling"
)
cnv
.
inputBams
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
preProcessBam
.
map
(
sampleId
->
_
)
}
add
(
cnv
)
}
}
/** Location of summary file */
...
...
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