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biopet.biopet
Commits
98b792b5
Commit
98b792b5
authored
Jan 08, 2016
by
Wai Yi Leung
Browse files
Less errorprone approach of storing the path to outputfiles for the svcallers.
parent
3babdbc3
Changes
5
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
98b792b5
...
...
@@ -67,15 +67,20 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
for
((
sample
,
bamFile
)
<-
inputBams
)
{
var
sampleVcfs
:
List
[
File
]
=
List
()
callers
.
foreach
{
caller
=>
sampleVcfs
:+=
caller
.
output
Files
(
sample
)
sampleVcfs
:+=
caller
.
output
VCF
(
sample
)
.
get
}
val
mergeSVcalls
=
new
Pysvtools
(
this
)
mergeSVcalls
.
input
=
sampleVcfs
mergeSVcalls
.
output
=
new
File
(
outputDir
,
sample
+
".merged.vcf"
)
add
(
mergeSVcalls
)
outputFiles
+=
(
sample
->
mergeSVcalls
.
output
)
//
outputFiles += (sample -> mergeSVcalls.output)
}
// merging the VCF calls by project
// basicly this will do all samples from this pipeline run
// group by "tags"
// sample tagging is however not available within this pipeline
addSummaryJobs
()
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
View file @
98b792b5
...
...
@@ -19,7 +19,7 @@ class Breakdancer(val root: Configurable) extends SvCaller {
val
bdvcf
=
BreakdancerVCF
(
this
,
breakdancer
.
output
,
new
File
(
breakdancerSampleDir
,
sample
+
".breakdancer.vcf"
))
add
(
bdcfg
,
breakdancer
,
bdvcf
)
outputFiles
+=
(
sample
->
bdvcf
.
output
)
addVCF
(
sample
,
bdvcf
.
output
)
}
}
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
View file @
98b792b5
...
...
@@ -14,7 +14,7 @@ class Clever(val root: Configurable) extends SvCaller {
val
clever
=
CleverCaller
(
this
,
bamFile
,
cleverDir
)
add
(
clever
)
outputFiles
+=
(
sample
->
clever
.
outputvcf
)
addVCF
(
sample
,
clever
.
outputvcf
)
}
}
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
View file @
98b792b5
...
...
@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import
nl.lumc.sasc.biopet.extensions.gatk.CatVariants
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler delly */
/** Script for sv cal
l
er delly */
class
Delly
(
val
root
:
Configurable
)
extends
SvCaller
{
def
name
=
"delly"
...
...
@@ -54,8 +54,7 @@ class Delly(val root: Configurable) extends SvCaller {
}
add
(
catVariants
)
outputFiles
+=
(
sample
->
catVariants
.
outputFile
)
addVCF
(
sample
,
catVariants
.
outputFile
)
}
}
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
View file @
98b792b5
...
...
@@ -15,5 +15,15 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
var
inputBams
:
Map
[
String
,
File
]
=
_
def
outputVCF
(
sample
:
String
)
:
Option
[
File
]
=
{
outputVcfs
.
get
(
sample
)
}
protected
var
outputVcfs
:
Map
[
String
,
File
]
=
_
protected
def
addVCF
(
sampleId
:
String
,
outputVCF
:
File
)
=
{
outputVcfs
+=
(
sampleId
->
outputVCF
)
}
def
init
()
=
{}
}
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