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biopet.biopet
Commits
8e606123
Commit
8e606123
authored
Aug 01, 2015
by
Peter van 't Hof
Browse files
Adding toucan to shiva
parent
d7efc98b
Changes
2
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public/shiva/pom.xml
View file @
8e606123
...
...
@@ -40,6 +40,11 @@
<artifactId>
Mapping
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Toucan
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
org.testng
</groupId>
<artifactId>
testng
</artifactId>
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
8e606123
...
...
@@ -24,6 +24,7 @@ import nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
SamToFastq
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import
scala.collection.JavaConversions._
...
...
@@ -292,6 +293,16 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
vc
.
biopetScript
()
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
if
(
config
(
"annotation"
,
default
=
true
).
asBoolean
)
{
val
toucan
=
new
Toucan
(
this
)
toucan
.
outputDir
=
new
File
(
outputDir
,
"annotation"
)
toucan
.
inputVCF
=
vc
.
finalFile
toucan
.
init
()
toucan
.
biopetScript
()
addAll
(
toucan
.
functions
)
addSummaryQScript
(
toucan
)
}
})
svCalling
.
foreach
(
sv
=>
{
...
...
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