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biopet.biopet
Commits
09bf4a36
Commit
09bf4a36
authored
Dec 04, 2014
by
Peter van 't Hof
Browse files
No default limitation on variantcalling when target_bed is given
parent
ecff240c
Changes
2
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Inline
Side-by-side
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
09bf4a36
...
@@ -49,9 +49,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
...
@@ -49,9 +49,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
}
def
init
()
{
def
init
()
{
if
(
config
.
contains
(
"target_bed"
))
{
defaults
++=
Map
(
"gatk"
->
Map
((
"intervals"
->
config
(
"target_bed"
).
asStringList
)))
}
if
(
config
.
contains
(
"gvcfFiles"
))
if
(
config
.
contains
(
"gvcfFiles"
))
for
(
file
<-
config
(
"gvcfFiles"
).
asList
)
for
(
file
<-
config
(
"gvcfFiles"
).
asList
)
gvcfFiles
:+=
file
.
toString
gvcfFiles
:+=
file
.
toString
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
09bf4a36
...
@@ -35,8 +35,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
...
@@ -35,8 +35,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
override
val
defaultVmem
=
"6G"
override
val
defaultVmem
=
"6G"
memoryLimit
=
Option
(
2.0
)
memoryLimit
=
Option
(
2.0
)
if
(
config
.
contains
(
"target_bed"
))
defaults
++=
Map
(
"samtoolsmpileup"
->
Map
(
"interval_bed"
->
config
(
"target_bed"
).
asStringList
.
head
,
defaults
++=
Map
(
"samtoolsmpileup"
->
Map
(
"disable_baq"
->
true
,
"min_map_quality"
->
1
))
"disable_baq"
->
true
,
"min_map_quality"
->
1
))
override
def
afterGraph
{
override
def
afterGraph
{
super
.
afterGraph
super
.
afterGraph
...
...
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