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biopet.biopet
Commits
1b56691e
Commit
1b56691e
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
Changed default options
parent
a91e1f83
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
View file @
1b56691e
...
...
@@ -2,31 +2,30 @@ package nl.lumc.sasc.biopet.extensions.delly
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.Ln
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.extensions.gatk.CatVariants
class
Delly
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
class
Delly
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
with
Reference
{
def
this
()
=
this
(
null
)
@Input
(
doc
=
"Input file (bam)"
)
var
input
:
File
=
_
@Argument
(
doc
=
"Work directory"
)
var
workdir
:
String
=
_
var
workdir
:
File
=
_
@Output
(
doc
=
"Delly result VCF"
)
var
outputvcf
:
File
=
_
var
outputBaseName
:
String
=
_
var
outputBaseName
:
File
=
_
// select the analysis types DEL,DUP,INV,TRA
var
del
:
Boolean
=
config
(
"DEL"
,
default
=
fals
e
)
var
dup
:
Boolean
=
config
(
"DUP"
,
default
=
fals
e
)
var
inv
:
Boolean
=
config
(
"INV"
,
default
=
fals
e
)
var
tra
:
Boolean
=
config
(
"TRA"
,
default
=
fals
e
)
var
del
:
Boolean
=
config
(
"DEL"
,
default
=
tru
e
)
var
dup
:
Boolean
=
config
(
"DUP"
,
default
=
tru
e
)
var
inv
:
Boolean
=
config
(
"INV"
,
default
=
tru
e
)
var
tra
:
Boolean
=
config
(
"TRA"
,
default
=
tru
e
)
override
def
init
()
{
}
...
...
@@ -77,13 +76,11 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript {
var
finalVCF
=
if
(
vcfFiles
.
size
>
1
)
{
// do merging
// CatVariants is a $org.broadinstitute.gatk.utils.commandline.CommandLineProgram$;
//TODO: convert to biopet extension
val
variants
=
new
CatVariants
()
variants
.
jobResourceRequests
:+=
"h_vmem=4G"
variants
.
nCoresRequest
=
1
variants
.
memoryLimit
=
Option
(
2.0
)
variants
.
variant
=
vcfFiles
.
values
.
toList
variants
.
reference
=
config
(
"reference"
)
variants
.
outputFile
=
this
.
outputvcf
variants
.
reference
=
referenceFasta
()
// add the job
add
(
variants
)
this
.
outputvcf
...
...
@@ -103,7 +100,7 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript {
object
Delly
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/extensions/svcallers/Delly/Delly.class"
def
apply
(
root
:
Configurable
,
input
:
File
,
runDir
:
String
)
:
Delly
=
{
def
apply
(
root
:
Configurable
,
input
:
File
,
runDir
:
File
)
:
Delly
=
{
val
dellypipeline
=
new
Delly
(
root
)
dellypipeline
.
input
=
input
dellypipeline
.
workdir
=
runDir
...
...
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