Commit 3b55324c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added count seqs

parent 03c15ef3
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.{BiopetQScript, SampleLibraryTag}
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.tools.SageCountFastq
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 12/29/15.
*/
class GearsSeqCount(val root: Configurable) extends QScript with BiopetQScript with SampleLibraryTag {
var fastqInput: File = _
def countFile = swapExt(outputDir, fastqInput, ".fastq.gz", ".counts.txt")
/** Init for pipeline */
def init(): Unit = {
}
/** Pipeline itself */
def biopetScript(): Unit = {
val seqCount = new SageCountFastq(this)
seqCount.input = fastqInput
seqCount.output = countFile
add(seqCount)
}
}
......@@ -44,6 +44,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
lazy val krakenScript = if (config("gears_use_kraken", default = true)) Some(new GearsKraken(this)) else None
lazy val qiimeRatx = if (config("gear_use_qiime_rtax", default = false)) Some(new GearsQiimeRtax(this)) else None
lazy val qiimeClosed = if (config("gear_use_qiime_closed", default = false)) Some(new GearsQiimeClosed(this)) else None
lazy val seqCount = if (config("gear_use_seq_count", default = false)) Some(new GearsSeqCount(this)) else None
/** Executed before running the script */
def init(): Unit = {
......@@ -137,6 +138,12 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
//TODO: Plots
}
seqCount.foreach { seqCount =>
seqCount.fastqInput = combinedFastq
seqCount.outputDir = new File(outputDir, "seq_count")
add(seqCount)
}
addSummaryJobs()
}
......
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