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biopet.biopet
Commits
89b2c3cd
Commit
89b2c3cd
authored
Jan 27, 2015
by
Peter van 't Hof
Browse files
Mask yamsvp code
parent
4b16b7cd
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
View file @
89b2c3cd
...
...
@@ -20,8 +20,7 @@
package
nl.lumc.sasc.biopet.pipelines.yamsvp
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
MultiSampleQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.sambamba.
{
SambambaIndex
,
SambambaMerge
}
import
nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
...
...
@@ -33,12 +32,12 @@ import org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.function._
import
org.broadinstitute.gatk.queue.engine.JobRunInfo
class
Yamsvp
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
{
class
Yamsvp
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
//with
MultiSampleQScript {
def
this
()
=
this
(
null
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
finalBamFiles
:
List
[
File
]
=
Nil
/*
class LibraryOutput extends AbstractLibraryOutput {
var mappedBamFile: File = _
}
...
...
@@ -47,7 +46,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
var vcf: Map[String, List[File]] = Map()
var mappedBamFile: File = _
}
*/
override
def
init
()
{
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Output directory is not specified in the config / argument"
)
...
...
@@ -61,7 +60,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
// read config and set all parameters for the pipeline
logger
.
info
(
"Starting YAM SV Pipeline"
)
runSamplesJobs
//
runSamplesJobs
//
}
...
...
@@ -69,7 +68,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
override
def
onExecutionDone
(
jobs
:
Map
[
QFunction
,
JobRunInfo
],
success
:
Boolean
)
{
logger
.
info
(
"YAM SV Pipeline has run ......................."
)
}
/*
def runSingleSampleJobs(sampleID: String): SampleOutput = {
val sampleOutput = new SampleOutput
var libraryBamfiles: List[File] = List()
...
...
@@ -160,6 +159,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
// logger.debug(outputFiles)
// return outputFiles
}
*/
}
object
Yamsvp
extends
PipelineCommand
\ No newline at end of file
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