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biopet.biopet
Commits
99f18f74
Commit
99f18f74
authored
Mar 04, 2015
by
Peter van 't Hof
Browse files
Rename pipelines
parent
9c83fc47
Changes
4
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva
Gatk
.scala
→
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
99f18f74
...
...
@@ -9,17 +9,17 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 2/26/15.
*/
class
Shiva
Gatk
(
val
root
:
Configurable
)
extends
QScript
with
ShivaTrait
{
class
Shiva
(
val
root
:
Configurable
)
extends
QScript
with
ShivaTrait
{
qscript
=>
def
this
()
=
this
(
null
)
override
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
:
ShivaVariantcallingTrait
=
{
if
(
multisample
)
new
ShivaVariantcalling
Gatk
(
qscript
)
{
if
(
multisample
)
new
ShivaVariantcalling
(
qscript
)
{
override
def
namePrefix
=
"multisample"
override
def
configName
=
"shivavariantcalling"
override
def
configPath
:
List
[
String
]
=
super
.
configPath
:::
"multisample"
::
Nil
}
else
new
ShivaVariantcalling
Gatk
(
qscript
)
{
else
new
ShivaVariantcalling
(
qscript
)
{
override
def
configName
=
"shivavariantcalling"
}
}
...
...
@@ -47,9 +47,9 @@ class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
}
}
override
def
d
oublePreProcess
(
input
:
List
[
File
],
isIntermediate
:
Boolean
=
false
)
:
Option
[
File
]
=
{
if
(
input
.
size
<=
1
)
super
.
d
oublePreProcess
(
input
)
else
super
.
d
oublePreProcess
(
input
,
true
).
collect
{
override
protected
def
addD
oublePreProcess
(
input
:
List
[
File
],
isIntermediate
:
Boolean
=
false
)
:
Option
[
File
]
=
{
if
(
input
.
size
<=
1
)
super
.
addD
oublePreProcess
(
input
)
else
super
.
addD
oublePreProcess
(
input
,
true
).
collect
{
case
file
=>
{
config
(
"use_indel_realign"
,
default
=
true
).
asBoolean
match
{
case
true
=>
addIndelRealign
(
file
,
sampleDir
,
false
)
...
...
@@ -98,4 +98,4 @@ class ShivaGatk(val root: Configurable) extends QScript with ShivaTrait {
}
}
object
ShivaGatk
extends
PipelineCommand
\ No newline at end of file
object
Shiva
extends
PipelineCommand
\ No newline at end of file
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling
Gatk
.scala
→
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
View file @
99f18f74
...
...
@@ -9,7 +9,7 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 2/26/15.
*/
class
ShivaVariantcalling
Gatk
(
val
root
:
Configurable
)
extends
QScript
with
ShivaVariantcallingTrait
{
class
ShivaVariantcalling
(
val
root
:
Configurable
)
extends
QScript
with
ShivaVariantcallingTrait
{
qscript
=>
def
this
()
=
this
(
null
)
...
...
@@ -104,4 +104,4 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
}
}
object
ShivaVariantcallingGatk
extends
PipelineCommand
\ No newline at end of file
object
ShivaVariantcalling
extends
PipelineCommand
\ No newline at end of file
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva
Gatk
Test.scala
→
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
99f18f74
...
...
@@ -15,11 +15,11 @@ import org.testng.annotations.{ Test, DataProvider }
/**
* Created by pjvan_thof on 3/2/15.
*/
class
Shiva
Gatk
Test
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Shiva
Gatk
=
{
new
Shiva
Gatk
()
{
class
ShivaTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Shiva
=
{
new
Shiva
()
{
override
def
configName
=
"shiva"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
Shiva
Gatk
Test
.
config
))
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaTest
.
config
))
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
...
...
@@ -40,10 +40,10 @@ class ShivaGatkTest extends TestNGSuite with Matchers {
multi
:
Boolean
,
single
:
Boolean
,
library
:
Boolean
,
dbsnp
:
Boolean
,
covariates
:
Boolean
,
realign
:
Boolean
,
baseRecalibration
:
Boolean
)
:
Unit
=
{
val
map
=
{
var
m
:
Map
[
String
,
Any
]
=
Shiva
Gatk
Test
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
Shiva
Gatk
Test
.
sample1
,
m
.
toMap
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
Shiva
Gatk
Test
.
sample2
,
m
.
toMap
)
if
(
sample3
)
m
=
ConfigUtils
.
mergeMaps
(
Shiva
Gatk
Test
.
sample3
,
m
.
toMap
)
var
m
:
Map
[
String
,
Any
]
=
ShivaTest
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample1
,
m
.
toMap
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample2
,
m
.
toMap
)
if
(
sample3
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample3
,
m
.
toMap
)
if
(
dbsnp
)
m
=
ConfigUtils
.
mergeMaps
(
Map
(
"dbsnp"
->
"test"
),
m
.
toMap
)
ConfigUtils
.
mergeMaps
(
Map
(
"multisample_sample_variantcalling"
->
multi
,
"single_sample_variantcalling"
->
single
,
...
...
@@ -80,7 +80,7 @@ class ShivaGatkTest extends TestNGSuite with Matchers {
}
}
object
Shiva
Gatk
Test
{
object
ShivaTest
{
val
outputDir
=
Files
.
createTempDir
()
val
config
=
Map
(
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling
Gatk
Test.scala
→
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
99f18f74
...
...
@@ -19,11 +19,11 @@ import scala.collection.mutable.ListBuffer
/**
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaVariantcalling
Gatk
Test
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
ShivaVariantcalling
Gatk
=
{
new
ShivaVariantcalling
Gatk
()
{
class
ShivaVariantcallingTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
ShivaVariantcalling
=
{
new
ShivaVariantcalling
()
{
override
def
configName
=
"shivavariantcalling"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaVariantcalling
Gatk
Test
.
config
))
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
ShivaVariantcallingTest
.
config
))
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
...
...
@@ -94,11 +94,11 @@ class ShivaVariantcallingGatkTest extends TestNGSuite with Matchers {
}
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
ShivaVariantcalling
Gatk
Test
.
outputDir
)
FileUtils
.
deleteDirectory
(
ShivaVariantcallingTest
.
outputDir
)
}
}
object
ShivaVariantcalling
Gatk
Test
{
object
ShivaVariantcallingTest
{
val
outputDir
=
Files
.
createTempDir
()
val
config
=
Map
(
...
...
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