Commit ff5e56e1 authored by Peter van 't Hof's avatar Peter van 't Hof

Switch to fifo pipe

parent 785d5a26
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.SampleLibraryTag
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat }
import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
......@@ -46,10 +46,12 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
protected def makeKreport(name: String, unique: Boolean): Unit = {
val fifo = new File(outputDir, s"$outputName.$name.fifo")
val centrifugeKreport = new CentrifugeKreport(this)
centrifugeKreport.centrifugeOutputFiles :+= fifo
centrifugeKreport.output = new File(outputDir, s"$outputName.$name.kreport")
centrifugeKreport.onlyUnique = unique
add(centrifugeOutput :<: Zcat(this) | centrifugeKreport)
add(new BiopetFifoPipe(this, List(centrifugeKreport, Zcat(this, centrifugeOutput, fifo))))
val krakenReportJSON = new KrakenReportToJson(this)
krakenReportJSON.inputReport = centrifugeKreport.output
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