Commit 481a7a96 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Skip extractIfNeeded on R2 when not paired

parent 2838b39a
......@@ -146,8 +146,10 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
chunks += (chunkDir -> (removeGz(chunkDir + input_R1.getName),
if (paired) removeGz(chunkDir + input_R2.get.getName) else ""))
}
else chunks += (outputDir -> (flexiprep.extractIfNeeded(input_R1, flexiprep.outputDir),
flexiprep.extractIfNeeded(input_R2.getOrElse(null), flexiprep.outputDir)))
else chunks += (outputDir -> (
flexiprep.extractIfNeeded(input_R1, flexiprep.outputDir),
if (paired) flexiprep.extractIfNeeded(input_R2.get, flexiprep.outputDir) else "")
)
if (chunking) {
val fastSplitter_R1 = new FastqSplitter(this)
......
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