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biopet.biopet
Commits
0d7fce54
Commit
0d7fce54
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
Add ShiveGatk
parent
492b1223
Changes
3
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protected/biopet-gatk-pipelines/pom.xml
View file @
0d7fce54
...
...
@@ -39,5 +39,10 @@
<artifactId>
Mapping
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Shiva
</artifactId>
<version>
${project.version}
</version>
</dependency>
</dependencies>
</project>
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaGatk.scala
0 → 100644
View file @
0d7fce54
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
ShivaTrait
,
Shiva
}
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 2/26/15.
*/
class
ShivaGatk
(
val
root
:
Configurable
)
extends
QScript
with
ShivaTrait
{
def
this
()
=
this
(
null
)
override
def
makeSample
(
id
:
String
)
=
new
this
.
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
super
.
Sample
(
sampleId
)
{
override
def
makeLibrary
(
id
:
String
)
=
new
this
.
Library
(
id
)
class
Library
(
libId
:
String
)
extends
super
.
Library
(
libId
)
{
override
def
preProcess
(
input
:
File
)
:
Option
[
File
]
=
{
//TODO: add preproces
None
}
}
override
def
doublePreProcess
(
input
:
List
[
File
],
isIntermediate
:
Boolean
=
false
)
:
Option
[
File
]
=
{
if
(
input
.
size
<=
1
)
super
.
doublePreProcess
(
input
)
else
{
super
.
doublePreProcess
(
input
)
//TODO: Add indel realignment
}
}
}
}
object
ShivaGatk
extends
PipelineCommand
\ No newline at end of file
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
View file @
0d7fce54
...
...
@@ -12,6 +12,7 @@ object BiopetExecutableProtected extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVariantcalling
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkPipeline
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVariantRecalibration
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
ShivaGatk
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
)
def
tools
=
BiopetExecutablePublic
.
tools
...
...
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