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biopet.biopet
Commits
3c2bd820
Commit
3c2bd820
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
Add gatk variantcalling with haplotypecaller
parent
05273365
Changes
4
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Inline
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaGatk.scala
View file @
3c2bd820
...
...
@@ -3,15 +3,27 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.pipelines.shiva.ShivaTrait
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
ShivaVariantcallingTrait
,
ShivaVariantcalling
,
ShivaTrait
}
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 2/26/15.
*/
class
ShivaGatk
(
val
root
:
Configurable
)
extends
QScript
with
ShivaTrait
{
qscript
=>
def
this
()
=
this
(
null
)
override
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
:
ShivaVariantcallingTrait
=
{
if
(
multisample
)
new
ShivaVariantcallingGatk
(
qscript
)
{
override
def
namePrefix
=
"multisample."
override
def
configName
=
"shivavariantcalling"
override
def
configPath
:
List
[
String
]
=
super
.
configPath
:::
"multisample"
::
Nil
}
else
new
ShivaVariantcallingGatk
(
qscript
)
{
override
def
configName
=
"shivavariantcalling"
}
}
override
def
makeSample
(
id
:
String
)
=
new
this
.
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
super
.
Sample
(
sampleId
)
{
override
def
makeLibrary
(
id
:
String
)
=
new
this
.
Library
(
id
)
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatk.scala
0 → 100644
View file @
3c2bd820
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller
import
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 2/26/15.
*/
class
ShivaVariantcallingGatk
(
val
root
:
Configurable
)
extends
QScript
with
ShivaVariantcallingTrait
{
qscript
=>
def
this
()
=
this
(
null
)
override
def
callers
=
new
Haplotypecaller
::
super
.
callers
class
Haplotypecaller
extends
Variantcaller
{
val
name
=
"haplotypecaller"
protected
val
defaultPrio
=
1
protected
val
defaultUse
=
true
def
outputFile
=
new
File
(
outputDir
,
namePrefix
+
"haplotypecaller.vcf.gz"
)
def
addJobs
()
{
val
hc
=
new
HaplotypeCaller
(
qscript
)
hc
.
input_file
=
inputBams
hc
.
out
=
outputFile
add
(
hc
)
}
}
}
object
ShivaVariantcallingGatk
extends
PipelineCommand
\ No newline at end of file
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
3c2bd820
...
...
@@ -26,7 +26,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
addSummaryJobs
}
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
=
{
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
:
ShivaVariantcallingTrait
=
{
if
(
multisample
)
new
ShivaVariantcalling
(
qscript
)
{
override
def
namePrefix
=
"multisample."
override
def
configName
=
"shivavariantcalling"
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
3c2bd820
...
...
@@ -29,13 +29,15 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
}
def
init
:
Unit
=
{
if
(!
namePrefix
.
isEmpty
&&
!
namePrefix
.
endsWith
(
"."
))
namePrefix
+=
"."
}
def
finalFile
=
new
File
(
outputDir
,
namePrefix
+
"final.vcf.gz"
)
def
biopetScript
:
Unit
=
{
val
cv
=
new
CombineVariants
(
qscript
)
cv
.
outputFile
=
new
File
(
outputDir
,
namePrefix
+
".final.vcf.gz"
)
for
(
caller
<-
callers
)
{
cv
.
outputFile
=
finalFile
cv
.
setKey
=
"VariantCaller"
for
(
caller
<-
usedCallers
)
{
caller
.
addJobs
()
cv
.
addInput
(
caller
.
outputFile
,
caller
.
name
)
}
...
...
@@ -44,7 +46,9 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
addSummaryJobs
}
def
callers
=
List
(
new
RawVcf
).
filter
(
_
.
use
)
def
callers
:
List
[
Variantcaller
]
=
List
(
new
RawVcf
)
def
usedCallers
:
List
[
Variantcaller
]
=
callers
.
filter
(
_
.
use
)
trait
Variantcaller
{
val
name
:
String
...
...
@@ -96,5 +100,5 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
def
summarySettings
=
Map
()
def
summaryFiles
=
Map
(
)
def
summaryFiles
:
Map
[
String
,
File
]
=
usedCallers
.
map
(
x
=>
(
x
.
name
->
x
.
outputFile
)).
toMap
+
(
"final"
->
finalFile
)
}
\ No newline at end of file
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