Commit c15b307b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

removed qscript key

parent 6598b281
......@@ -77,7 +77,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
new File(outputDir, s"$outputName.unmapped.R2.fq.gz")
)
samToFastq.isIntermediate = true
qscript.add(samToFastq)
add(samToFastq)
// sync the fastq records
val fastqSync = new FastqSync(qscript)
......@@ -87,7 +87,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
fastqSync.outputFastq1 = new File(outputDir, s"$outputName.unmapped.R1.sync.fq.gz")
fastqSync.outputFastq2 = new File(outputDir, s"$outputName.unmapped.R2.sync.fq.gz")
fastqSync.outputStats = new File(outputDir, s"$outputName.sync.stats.json")
qscript.add(fastqSync)
add(fastqSync)
List(fastqSync.outputFastq1, fastqSync.outputFastq2)
}.getOrElse(List(fastqFileR1, fastqFileR2).flatten)
......@@ -99,7 +99,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
krakenAnalysis.paired = true
krakenAnalysis.classified_out = Option(new File(outputDir, s"$outputName.krkn.classified.fastq"))
krakenAnalysis.unclassified_out = Option(new File(outputDir, s"$outputName.krkn.unclassified.fastq"))
qscript.add(krakenAnalysis)
add(krakenAnalysis)
// create kraken summary file
......@@ -107,7 +107,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
krakenReport.input = krakenAnalysis.output
krakenReport.show_zeros = true
krakenReport.output = new File(outputDir, s"$outputName.krkn.full")
qscript.add(krakenReport)
add(krakenReport)
addSummaryJobs()
}
......
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