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biopet.biopet
Commits
2fe05703
Commit
2fe05703
authored
Aug 01, 2015
by
Peter van 't Hof
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Add summary to toucan
parent
3584a778
Changes
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7 additions
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+7
-1
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+7
-1
No files found.
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
2fe05703
...
...
@@ -16,6 +16,7 @@
package
nl.lumc.sasc.biopet.pipelines.toucan
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
import
nl.lumc.sasc.biopet.tools.VepNormalizer
...
...
@@ -27,7 +28,7 @@ import org.broadinstitute.gatk.queue.QScript
*
* Created by ahbbollen on 15-1-15.
*/
class
Toucan
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
with
Reference
{
class
Toucan
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
with
SummaryQScript
with
Reference
{
def
this
()
=
this
(
null
)
@Input
(
doc
=
"Input VCF file"
,
shortName
=
"Input"
,
required
=
true
)
...
...
@@ -56,6 +57,11 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Ref
add
(
normalizer
)
}
def
summaryFile
=
new
File
(
outputDir
,
"Toucan.summary.json"
)
def
summaryFiles
=
Map
()
def
summarySettings
=
Map
()
}
object
Toucan
extends
PipelineCommand
\ No newline at end of file
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