Commit 699c7baf authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Removed zcat step

parent 2156f192
......@@ -184,12 +184,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
chunkDir -> (new File(chunkDir, input_R1.getName),
if (paired) Some(new File(chunkDir, input_R2.get.getName)) else None)
} else if (skipFlexiprep) {
Map(outputDir -> (
extractIfNeeded(input_R1, flexiprep.outputDir),
if (paired) Some(extractIfNeeded(input_R2.get, outputDir)) else None)
} else Map(outputDir -> (flexiprep.input_R1, flexiprep.input_R2))
} else if (skipFlexiprep) Map(outputDir -> (input_R1, (if (paired) input_R2 else None)))
else Map(outputDir -> (flexiprep.input_R1, flexiprep.input_R2))
if (chunking) {
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