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biopet.biopet
Commits
298ca175
Commit
298ca175
authored
Apr 26, 2016
by
Peter van 't Hof
Browse files
Switch to biopet scattering
parent
85bf7a10
Changes
14
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Inline
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
View file @
298ca175
...
...
@@ -26,7 +26,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
GATKScatterFunction
,
LocusScatterFunction
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
class
AnalyzeCovariates
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
View file @
298ca175
...
...
@@ -50,7 +50,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.Argument
import
org.broadinstitute.gatk.utils.commandline.Gather
import
org.broadinstitute.gatk.utils.commandline.Input
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @
298ca175
...
...
@@ -28,7 +28,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
GATKScatterFunction
,
ReadScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
//TODO: check gathering
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
View file @
298ca175
...
...
@@ -26,7 +26,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Input
,
Output
,
_
}
class
CombineGVCFs
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
View file @
298ca175
...
...
@@ -26,7 +26,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
class
CombineVariants
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
298ca175
...
...
@@ -49,7 +49,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
class
GenotypeGVCFs
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
298ca175
...
...
@@ -79,7 +79,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk._
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
_
}
class
HaplotypeCaller
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
View file @
298ca175
...
...
@@ -34,7 +34,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
BamGatherFunction
,
GATKScatterFunction
,
ReadScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
class
IndelRealigner
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
View file @
298ca175
...
...
@@ -26,7 +26,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
BamGatherFunction
,
GATKScatterFunction
,
ReadScatterFunction
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline._
class
PrintReads
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
View file @
298ca175
...
...
@@ -28,7 +28,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
_
}
class
RealignerTargetCreator
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
View file @
298ca175
...
...
@@ -26,7 +26,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
class
SelectVariants
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @
298ca175
...
...
@@ -60,7 +60,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather
.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.core
.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Input
,
Output
,
_
}
class
UnifiedGenotyper
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
View file @
298ca175
...
...
@@ -26,10 +26,10 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
class
VariantAnnotator
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
analysisName
=
"VariantAnnotator"
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala
0 → 100644
View file @
298ca175
package
nl.lumc.sasc.biopet.core
/**
* Created by pjvan_thof on 4/26/16.
*/
trait
ScatterGatherableFunction
extends
BiopetCommandLineFunction
with
org
.
broadinstitute
.
gatk
.
queue
.
function
.
scattergather
.
ScatterGatherableFunction
{
scatterCount
=
config
(
"scatter_count"
,
freeVar
=
true
)
}
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