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biopet.biopet
Commits
a81bce67
Commit
a81bce67
authored
Sep 10, 2015
by
Peter van 't Hof
Browse files
Moved config to utils
parent
10e09e28
Changes
189
Hide whitespace changes
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
AnalyzeCovariates
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
AnalyzeCovariates
with
GatkGeneral
{
}
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
ApplyRecalibration
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
ApplyRecalibration
with
GatkGeneral
{
scatterCount
=
config
(
"scattercount"
,
default
=
0
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
BaseRecalibrator
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
,
default
=
1
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
CombineGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineGVCFs
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
CombineVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineVariants
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
GenotypeGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
GenotypeGVCFs
with
GatkGeneral
{
annotation
++=
config
(
"annotation"
,
default
=
Seq
(
"FisherStrand"
,
"QualByDepth"
,
"ChromosomeCounts"
)).
asStringList
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
a81bce67
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class
HaplotypeCaller
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
HaplotypeCaller
with
GatkGeneral
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
IndelRealigner
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
IndelRealigner
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
PrintReads
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
PrintReads
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
RealignerTargetCreator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
RealignerTargetCreator
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
SelectVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
SelectVariants
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @
a81bce67
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
UnifiedGenotyper
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
UnifiedGenotyper
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
VariantAnnotator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantAnnotator
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
class
VariantEval
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantEval
with
GatkGeneral
{
override
def
beforeGraph
()
{
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
class
VariantRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantRecalibrator
with
GatkGeneral
{
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
View file @
a81bce67
...
...
@@ -6,7 +6,7 @@
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.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
View file @
a81bce67
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
View file @
a81bce67
...
...
@@ -5,7 +5,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
GenotypeGVCFs
,
SelectVariants
}
import
org.broadinstitute.gatk.queue.QScript
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
a81bce67
...
...
@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.
{
MultiSampleQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
CombineGVCFs
,
CombineVariants
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
SamToFastq
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
View file @
a81bce67
...
...
@@ -6,7 +6,7 @@
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.
core
.config.Configurable
import
nl.lumc.sasc.biopet.
utils
.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
ApplyRecalibration
,
VariantAnnotator
,
VariantRecalibrator
}
import
org.broadinstitute.gatk.queue.QScript
...
...
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