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biopet.biopet
Commits
afa1608d
Commit
afa1608d
authored
Jul 24, 2017
by
Peter van 't Hof
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Make it possible to disable gubbins
parent
9c297111
Changes
1
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9 additions
and
5 deletions
+9
-5
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+9
-5
No files found.
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
afa1608d
...
...
@@ -45,6 +45,8 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
val
numBoot
:
Int
=
config
(
"boot_runs"
,
default
=
100
,
namespace
=
"raxml"
).
asInt
val
executeGubbins
:
Boolean
=
config
(
"execute_gubbins"
,
default
=
true
)
override
def
defaults
=
Map
(
"ploidy"
->
1
,
"variantcallers"
->
variantcallers
...
...
@@ -192,11 +194,13 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
raxmlBi
.
w
=
dirSufixRaxml
add
(
raxmlBi
)
val
gubbins
=
new
RunGubbins
(
this
)
gubbins
.
fastafile
=
concensusVariants
gubbins
.
startingTree
=
raxmlBi
.
getBipartitionsFile
gubbins
.
outputDirectory
=
dirSufixGubbins
add
(
gubbins
)
if
(
executeGubbins
)
{
val
gubbins
=
new
RunGubbins
(
this
)
gubbins
.
fastafile
=
concensusVariants
gubbins
.
startingTree
=
raxmlBi
.
getBipartitionsFile
gubbins
.
outputDirectory
=
dirSufixGubbins
add
(
gubbins
)
}
}
addTreeJobs
(
catVariantsSnps
.
output
,
...
...
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