From 72aa33627f2ddf005c2832800f98f74b918a1e21 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Tue, 29 Sep 2015 15:56:02 +0200
Subject: [PATCH] Add todo to GEARS pipeline.
---
.../scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index ef0b2426a..cfddf6047 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -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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