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biopet.biopet
Commits
98db90f1
Commit
98db90f1
authored
Dec 02, 2014
by
Peter van 't Hof
Browse files
Added snp + indels tree
parent
1b9ceb90
Changes
1
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Inline
Side-by-side
protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
98db90f1
...
...
@@ -56,13 +56,16 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add
(
catConsensusVariantsSnps
)
val
seed
:
Int
=
config
(
"seed"
,
default
=
12345
)
def
addRaxml
(
input
:
File
,
outputDir
:
String
,
outputName
:
String
)
{
def
addTreeJobs
(
input
:
File
,
outputDir
:
String
,
outputName
:
String
)
{
val
dirSufixRaxml
=
if
(
outputDir
.
endsWith
(
File
.
separator
))
"raxml"
else
File
.
separator
+
"raxml"
val
dirSufixGubbins
=
if
(
outputDir
.
endsWith
(
File
.
separator
))
"gubbins"
else
File
.
separator
+
"gubbins"
val
raxmlMl
=
new
Raxml
(
this
)
raxmlMl
.
input
=
input
raxmlMl
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlMl
.
p
=
seed
raxmlMl
.
n
=
outputName
+
"_ml"
raxmlMl
.
w
=
outputDir
raxmlMl
.
w
=
outputDir
+
dirSufixRaxml
raxmlMl
.
N
=
config
(
"ml_runs"
,
default
=
20
,
submodule
=
"raxml"
)
add
(
raxmlMl
)
...
...
@@ -75,7 +78,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBoot
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlBoot
.
p
=
seed
raxmlBoot
.
b
=
math
.
abs
(
r
.
nextInt
)
raxmlBoot
.
w
=
outputDir
raxmlBoot
.
w
=
outputDir
+
dirSufixRaxml
raxmlBoot
.
N
=
1
raxmlBoot
.
n
=
outputName
+
"_boot_"
+
t
add
(
raxmlBoot
)
...
...
@@ -93,17 +96,18 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBi
.
p
=
seed
raxmlBi
.
f
=
"b"
raxmlBi
.
n
=
outputName
+
"_bi"
raxmlBi
.
w
=
outputDir
raxmlBi
.
w
=
outputDir
+
dirSufixRaxml
add
(
raxmlBi
)
val
gubbins
=
new
RunGubbins
(
this
)
gubbins
.
fastafile
=
input
gubbins
.
startingTree
=
raxmlBi
.
getBipartitionsFile
gubbins
.
outputDirectory
=
outputDir
+
"/g
ubbins
/"
gubbins
.
outputDirectory
=
outputDir
+
dirSufixG
ubbins
add
(
gubbins
)
}
addRaxml
(
catVariantsSnps
.
output
,
outputDir
+
"raxml"
,
"snps"
)
addTreeJobs
(
catVariantsSnps
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_only"
,
"snps_only"
)
addTreeJobs
(
catVariantsSnps
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_indels"
,
"snps_indels"
)
}
// Called for each sample
...
...
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