Commit a50fc782 authored by Peter van 't Hof's avatar Peter van 't Hof

Output centrifuge as gz files

parent a8a0e1b0
......@@ -2,7 +2,8 @@ package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.SampleLibraryTag
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
import nl.lumc.sasc.biopet.extensions.Gzip
import nl.lumc.sasc.biopet.extensions.centrifuge.{Centrifuge, CentrifugeKreport}
import nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......@@ -27,15 +28,17 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
}
def biopetScript(): Unit = {
val centrifugeOutput = new File(outputDir, s"$outputName.centrifuge.gz")
val centrifuge = new Centrifuge(this)
centrifuge.inputR1 = fastqR1
centrifuge.inputR2 = fastqR2
centrifuge.output = new File(outputDir, s"$outputName.centrifuge")
centrifuge.report = Some(new File(outputDir, s"$outputName.centrifuge.report"))
add(centrifuge)
val cmd = centrifuge | new Gzip(this) > centrifugeOutput
cmd.threadsCorrection = -1
add(cmd)
makeKreport(List(centrifuge.output), "centrifuge", unique = false)
makeKreport(List(centrifuge.output), "centrifuge_unique", unique = true)
makeKreport(List(centrifugeOutput), "centrifuge", unique = false)
makeKreport(List(centrifugeOutput), "centrifuge_unique", unique = true)
addSummaryJobs()
}
......
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