Commit f24db978 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix intermediate

parent 38566ec8
......@@ -119,7 +119,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
val samToFastq = SamToFastq(qscript, inputBam.get,
new File(libDir, sampleId + "-" + libId + ".R1.fq.gz"),
new File(libDir, sampleId + "-" + libId + ".R2.fq.gz"))
samToFastq.isIntermediate = true
samToFastq.isIntermediate = libraries.size > 1
qscript.add(samToFastq)
mapping.foreach(m => {
m.input_R1 = samToFastq.fastqR1
......
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