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biopet.biopet
Commits
fbff5f3d
Commit
fbff5f3d
authored
Nov 10, 2014
by
Peter van 't Hof
Browse files
Change default threads to 1
parent
b457ed22
Changes
2
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
View file @
fbff5f3d
...
...
@@ -11,7 +11,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
this
.
sample_ploidy
=
config
(
"ploidy"
)
nct
=
config
(
"threads"
,
default
=
3
)
nct
=
config
(
"threads"
,
default
=
1
)
bamOutput
=
config
(
"bamOutput"
)
memoryLimit
=
Option
(
nct
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"allSitePLs"
))
this
.
allSitePLs
=
config
(
"allSitePLs"
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
View file @
fbff5f3d
...
...
@@ -10,7 +10,7 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
this
.
sample_ploidy
=
config
(
"ploidy"
)
nct
=
config
(
"threads"
,
default
=
3
)
nct
=
config
(
"threads"
,
default
=
1
)
memoryLimit
=
Option
(
nct
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"allSitePLs"
))
this
.
allSitePLs
=
config
(
"allSitePLs"
)
if
(
config
.
contains
(
"output_mode"
))
{
...
...
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