Commit 72aa3362 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Add todo to GEARS pipeline.

parent f2a3ee03
......@@ -85,6 +85,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
fastqSync.inputFastq1 = samToFastq.fastqR1
fastqSync.inputFastq2 = samToFastq.fastqR2
fastqSync.outputFastq1 = new File(outputDir, s"$outputName.unmapped.R1.sync.fq.gz")
// TODO: need some sanity check on whether R2 is really containing reads (e.g. Single End libraries)
fastqSync.outputFastq2 = new File(outputDir, s"$outputName.unmapped.R2.sync.fq.gz")
fastqSync.outputStats = new File(outputDir, s"$outputName.sync.stats.json")
add(fastqSync)
......@@ -96,7 +98,9 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
val krakenAnalysis = new Kraken(qscript)
krakenAnalysis.input = fastqFiles
krakenAnalysis.output = new File(outputDir, s"$outputName.krkn.raw")
krakenAnalysis.paired = true
krakenAnalysis.paired = (fastqFiles.length == 2)
krakenAnalysis.classified_out = Option(new File(outputDir, s"$outputName.krkn.classified.fastq"))
krakenAnalysis.unclassified_out = Option(new File(outputDir, s"$outputName.krkn.unclassified.fastq"))
add(krakenAnalysis)
......
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