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biopet.biopet
Commits
fbdd632c
Commit
fbdd632c
authored
Dec 02, 2014
by
Peter van 't Hof
Browse files
Fix bug on gubbins
parent
deab689c
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 @
fbdd632c
...
...
@@ -56,12 +56,12 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add
(
catConsensusVariantsSnps
)
val
seed
:
Int
=
config
(
"seed"
,
default
=
12345
)
def
addTreeJobs
(
input
:
File
,
outputDir
:
String
,
outputName
:
String
)
{
def
addTreeJobs
(
variants
:
File
,
concensusVariants
:
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
.
input
=
variants
raxmlMl
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlMl
.
p
=
seed
raxmlMl
.
n
=
outputName
+
"_ml"
...
...
@@ -74,7 +74,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
val
bootList
=
for
(
t
<-
0
until
numBoot
)
yield
{
val
raxmlBoot
=
new
Raxml
(
this
)
raxmlBoot
.
threads
=
1
raxmlBoot
.
input
=
input
raxmlBoot
.
input
=
variants
raxmlBoot
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlBoot
.
p
=
seed
raxmlBoot
.
b
=
math
.
abs
(
r
.
nextInt
)
...
...
@@ -89,7 +89,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add
(
cat
)
val
raxmlBi
=
new
Raxml
(
this
)
raxmlBi
.
input
=
input
raxmlBi
.
input
=
concensusVariants
raxmlBi
.
t
=
raxmlMl
.
getBestTreeFile
raxmlBi
.
z
=
cat
.
output
raxmlBi
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
...
...
@@ -100,14 +100,14 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add
(
raxmlBi
)
val
gubbins
=
new
RunGubbins
(
this
)
gubbins
.
fastafile
=
input
gubbins
.
fastafile
=
concensusVariants
gubbins
.
startingTree
=
raxmlBi
.
getBipartitionsFile
gubbins
.
outputDirectory
=
outputDir
+
dirSufixGubbins
add
(
gubbins
)
}
addTreeJobs
(
catVariantsSnps
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_only"
,
"snps_only"
)
addTreeJobs
(
catVariants
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_indels"
,
"snps_indels"
)
addTreeJobs
(
catVariantsSnps
.
output
,
catConsensusVariants
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_only"
,
"snps_only"
)
addTreeJobs
(
catVariants
.
output
,
catConsensusVariantsSnps
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_indels"
,
"snps_indels"
)
}
// Called for each sample
...
...
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