Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
05a50457
Commit
05a50457
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
General update for clever
parent
5396b8df
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
View file @
05a50457
...
...
@@ -9,11 +9,12 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class
CleverCaller
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
{
executable
=
config
(
"exe"
,
default
=
"clever"
)
private
lazy
val
version
e
xecutable
:
File
=
config
(
"version_exe"
,
default
=
new
File
(
executable
).
getParent
+
"/ctk-version"
)
private
lazy
val
version
E
xecutable
:
File
=
config
(
"version_exe"
,
default
=
new
File
(
executable
).
getParent
+
"/ctk-version"
)
override
def
defaultThreads
=
8
override
def
defaultCoreMemory
=
3.0
override
def
versionCommand
=
version
e
xecutable
.
getAbsolutePath
override
def
versionCommand
=
version
E
xecutable
.
getAbsolutePath
override
def
versionRegex
=
"""(.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
...
...
@@ -23,17 +24,17 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
@Input
(
doc
=
"Reference"
)
var
reference
:
File
=
_
var
workDir
:
File
=
_
protected
def
workDir
:
File
=
new
File
(
cwd
,
"work"
)
var
cwd
:
File
=
_
@Output
(
doc
=
"Clever VCF output"
)
lazy
val
outputvcf
:
File
=
{
new
File
(
cwd
+
"predictions.vcf"
)
new
File
(
cwd
,
"predictions.vcf"
)
}
@Output
(
doc
=
"Clever raw output"
)
lazy
val
outputraw
:
File
=
{
new
File
(
workDir
+
"predictions.raw.txt"
)
new
File
(
workDir
,
"predictions.raw.txt"
)
}
// var T: Option[Int] = config("T", default = defaultThreads)
...
...
@@ -52,7 +53,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
def
cmdLine
=
required
(
executable
)
+
" --sorted "
+
" --use_xa "
+
optional
(
"-T"
,
nCoresRequest
)
+
optional
(
"-T"
,
threads
)
+
conditional
(
f
,
"-f"
)
+
conditional
(
a
,
"-a"
)
+
conditional
(
k
,
"-k"
)
+
...
...
@@ -63,11 +64,10 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
}
object
CleverCaller
{
def
apply
(
root
:
Configurable
,
input
:
File
,
svDir
:
File
,
runDir
:
File
)
:
CleverCaller
=
{
def
apply
(
root
:
Configurable
,
input
:
File
,
svDir
:
File
)
:
CleverCaller
=
{
val
clever
=
new
CleverCaller
(
root
)
clever
.
input
=
input
clever
.
cwd
=
svDir
clever
.
workDir
=
runDir
clever
}
}
\ No newline at end of file
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
05a50457
...
...
@@ -120,7 +120,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
//TODO: check double directories
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
cleverDir
=
new
File
(
outputDir
,
sample
)
val
clever
=
CleverCaller
(
qscript
,
bamFile
,
cleverDir
,
cleverDir
)
val
clever
=
CleverCaller
(
qscript
,
bamFile
,
cleverDir
)
add
(
clever
)
}
}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment