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 @@
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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