Commit 2b989a5a authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'feature-fixMappingPipeline-zcat' into 'develop'

zcat fix for mapping pipeline

This fix makes sure that the pipeline first performs a zcat on gzipped fastq files.

See merge request !161
parents a4e47ce4 5c4cdff6
......@@ -176,7 +176,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
extractIfNeeded(input_R1, flexiprep.outputDir),
if (paired) Some(extractIfNeeded(input_R2.get, outputDir)) else None)
} else Map(outputDir -> (input_R1, input_R2))
} else Map(outputDir -> (flexiprep.outputFiles("fastq_input_R1"), flexiprep.outputFiles.get("fastq_input_R2")))
if (chunking) {
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