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biopet.biopet
Commits
4078fca2
Commit
4078fca2
authored
Dec 28, 2015
by
Peter van 't Hof
Browse files
Fix format
parent
f2c27a88
Changes
4
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
4078fca2
...
...
@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Output
}
class
GenotypeGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
GenotypeGVCFs
with
GatkGeneral
{
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
4078fca2
...
...
@@ -68,7 +68,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
val
file
=
addIndelRealign
(
bamFile
.
get
,
libDir
,
isIntermediate
=
true
)
addBaseRecalibrator
(
file
,
libDir
,
libraries
.
size
>
1
)
}
else
if
(
useIndelRealigner
)
{
addIndelRealign
(
bamFile
.
get
,
libDir
,
libraries
.
size
>
1
)
addIndelRealign
(
bamFile
.
get
,
libDir
,
libraries
.
size
>
1
)
}
else
if
(
useBaseRecalibration
)
{
addBaseRecalibrator
(
bamFile
.
get
,
libDir
,
libraries
.
size
>
1
)
}
...
...
@@ -87,7 +87,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
super
.
addJobs
()
if
(
useIndelRealigner
&&
libraries
.
values
.
flatMap
(
_
.
preProcessBam
).
size
>
1
)
{
addIndelRealign
(
bamFile
.
get
,
sampleDir
,
libraries
.
size
>
1
)
addIndelRealign
(
bamFile
.
get
,
sampleDir
,
libraries
.
size
>
1
)
}
}
}
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
View file @
4078fca2
...
...
@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.File
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
,
MultiSampleQScript
}
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
,
MultiSampleQScript
}
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
,
AddOrReplaceReadGroups
,
SamToFastq
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
,
AddOrReplaceReadGroups
,
SamToFastq
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -16,8 +16,8 @@ import MultisampleMapping.MergeStrategy
import
scala.collection.JavaConversions._
/**
* Created by pjvanthof on 18/12/15.
*/
* Created by pjvanthof on 18/12/15.
*/
trait
MultisampleMappingTrait
extends
MultiSampleQScript
with
Reference
{
qscript
:
QScript
=>
...
...
@@ -25,7 +25,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
val
value
:
String
=
config
(
"merge_strategy"
,
default
=
"preprocessmarkduplicates"
)
MergeStrategy
.
values
.
find
(
_
.
toString
.
toLowerCase
==
value
)
match
{
case
Some
(
v
)
=>
v
case
_
=>
throw
new
IllegalArgumentException
(
s
"merge_strategy '$value' does not exist"
)
case
_
=>
throw
new
IllegalArgumentException
(
s
"merge_strategy '$value' does not exist"
)
}
}
...
...
@@ -55,8 +55,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
def
summaryFiles
:
Map
[
String
,
File
]
=
(
inputR1
.
map
(
"input_R1"
->
_
)
::
inputR2
.
map
(
"input_R2"
->
_
)
::
inputBam
.
map
(
"input_bam"
->
_
)
::
bamFile
.
map
(
"output_bam"
->
_
)
::
preProcessBam
.
map
(
"output_preProcessBam"
->
_
)
::
Nil
).
flatten
.
toMap
inputBam
.
map
(
"input_bam"
->
_
)
::
bamFile
.
map
(
"output_bam"
->
_
)
::
preProcessBam
.
map
(
"output_preProcessBam"
->
_
)
::
Nil
).
flatten
.
toMap
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
...
...
@@ -75,9 +75,9 @@ trait MultisampleMappingTrait extends MultiSampleQScript
}
else
None
def
bamFile
=
mapping
match
{
case
Some
(
m
)
=>
Some
(
m
.
finalBamFile
)
case
Some
(
m
)
=>
Some
(
m
.
finalBamFile
)
case
_
if
inputBam
.
isDefined
=>
Some
(
new
File
(
libDir
,
s
"$sampleId-$libId.bam"
))
case
_
=>
None
case
_
=>
None
}
def
preProcessBam
=
bamFile
...
...
@@ -166,9 +166,9 @@ trait MultisampleMappingTrait extends MultiSampleQScript
mergeStrategy
match
{
case
MergeStrategy
.
None
=>
case
(
MergeStrategy
.
MergeSam
|
MergeStrategy
.
MarkDuplicates
)
if
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
size
==
1
=>
add
(
Ln
.
linkBamFile
(
qscript
,
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
head
,
bamFile
.
get
)
:_
*
)
add
(
Ln
.
linkBamFile
(
qscript
,
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
head
,
bamFile
.
get
)
:
_
*
)
case
(
MergeStrategy
.
PreProcessMergeSam
|
MergeStrategy
.
PreProcessMarkDuplicates
)
if
libraries
.
flatMap
(
_
.
_2
.
preProcessBam
).
size
==
1
=>
add
(
Ln
.
linkBamFile
(
qscript
,
libraries
.
flatMap
(
_
.
_2
.
preProcessBam
).
head
,
bamFile
.
get
)
:_
*
)
add
(
Ln
.
linkBamFile
(
qscript
,
libraries
.
flatMap
(
_
.
_2
.
preProcessBam
).
head
,
bamFile
.
get
)
:
_
*
)
case
MergeStrategy
.
MergeSam
=>
add
(
MergeSamFiles
(
qscript
,
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
toList
,
bamFile
.
get
))
case
MergeStrategy
.
PreProcessMergeSam
=>
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
4078fca2
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import
nl.lumc.sasc.biopet.pipelines.mapping.
{
MultisampleMappingTrait
}
import
nl.lumc.sasc.biopet.pipelines.mapping.
{
MultisampleMappingTrait
}
import
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -86,7 +86,6 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
}
lazy
val
variantcalling
=
if
(
config
(
"single_sample_variantcalling"
,
default
=
false
).
asBoolean
)
{
Some
(
makeVariantcalling
(
multisample
=
false
))
}
else
None
...
...
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