Commit 89b2c3cd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Mask yamsvp code

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