Commit 46f8b1b5 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change to compressed output

parent 43a4bc76
......@@ -144,8 +144,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
config("bam_to_fastq", default = false).asBoolean match {
case true =>
val samToFastq = SamToFastq(qscript, config("bam"),
new File(libDir, sampleId + "-" + libId + ".R1.fastq"),
new File(libDir, sampleId + "-" + libId + ".R2.fastq"))
new File(libDir, sampleId + "-" + libId + ".R1.fq.gz"),
new File(libDir, sampleId + "-" + libId + ".R2.fq.gz"))
samToFastq.isIntermediate = true
qscript.add(samToFastq)
mapping.foreach(mapping => {
......
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