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biopet.biopet
Commits
72761225
Commit
72761225
authored
Oct 01, 2015
by
Peter van 't Hof
Browse files
Switch to CommandLineResources
parent
1199a39e
Changes
6
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
View file @
72761225
...
...
@@ -14,8 +14,8 @@ class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk
override
val
defaultThreads
=
3
override
def
beforeGraph
()
{
super
.
beforeGraph
()
override
def
freezeFieldValues
()
{
super
.
freezeFieldValues
()
nt
=
Option
(
getThreads
)
memoryLimit
=
Option
(
nt
.
getOrElse
(
1
)
*
2
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @
72761225
...
...
@@ -20,7 +20,6 @@ object BaseRecalibrator {
val
br
=
new
BaseRecalibrator
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
br
.
beforeGraph
()
br
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
View file @
72761225
...
...
@@ -5,17 +5,19 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetJavaCommandLineFunction
}
import
nl.lumc.sasc.biopet.core.
{
CommandLineResources
,
Reference
,
BiopetJavaCommandLineFunction
}
import
org.broadinstitute.gatk.engine.phonehome.GATKRunReport
import
org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait
GatkGeneral
extends
CommandLineGATK
with
BiopetJava
CommandLine
Function
with
Reference
{
trait
GatkGeneral
extends
CommandLineGATK
with
CommandLine
Resources
with
Reference
{
memoryLimit
=
Option
(
3
)
override
def
subPath
=
"gatk"
::
super
.
subPath
jarFile
=
config
(
"gatk_jar"
)
reference_sequence
=
referenceFasta
()
override
def
defaultCoreMemory
=
4.0
override
def
faiRequired
=
true
...
...
@@ -33,14 +35,9 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
if
(
config
.
contains
(
"gatk_key"
))
gatk_key
=
config
(
"gatk_key"
)
if
(
config
.
contains
(
"pedigree"
))
pedigree
=
config
(
"pedigree"
)
override
def
versionRegex
=
"""(.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
override
def
versionCommand
=
executable
+
" -jar "
+
jarFile
+
" -version"
override
def
getVersion
=
super
.
getVersion
.
collect
{
case
v
=>
"Gatk "
+
v
}
//override def versionRegex = """(.*)""".r
//override def versionExitcode = List(0, 1)
//override def versionCommand = executable + " -jar " + jarFile + " -version"
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
reference_sequence
==
null
)
reference_sequence
=
referenceFasta
()
}
//override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
72761225
...
...
@@ -38,8 +38,8 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
override
def
beforeGraph
()
{
super
.
beforeGraph
()
override
def
freezeFieldValues
()
{
super
.
freezeFieldValues
()
if
(
bamOutput
!=
null
&&
nct
.
getOrElse
(
1
)
>
1
)
{
logger
.
warn
(
"BamOutput is on, nct/threads is forced to set on 1, this option is only for debug"
)
}
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @
72761225
...
...
@@ -28,8 +28,8 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
override
val
defaultThreads
=
1
override
def
beforeGraph
()
{
super
.
beforeGraph
()
override
def
freezeFieldValues
()
{
super
.
freezeFieldValues
()
genotype_likelihoods_model
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
genotyper
.
GenotypeLikelihoodsCalculationModel
.
Model
.
BOTH
nct
=
Some
(
getThreads
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
View file @
72761225
...
...
@@ -10,9 +10,6 @@ import java.io.File
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
()
{
super
.
beforeGraph
()
}
}
object
VariantEval
{
...
...
@@ -22,7 +19,6 @@ object VariantEval {
vareval
.
eval
=
Seq
(
sample
)
vareval
.
comp
=
Seq
(
compareWith
)
vareval
.
out
=
output
vareval
.
beforeGraph
()
vareval
}
...
...
@@ -36,7 +32,6 @@ object VariantEval {
vareval
.
ST
=
ST
vareval
.
noEV
=
true
vareval
.
EV
=
EV
vareval
.
beforeGraph
()
vareval
}
...
...
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