Commit 337ef542 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed default aligner to bowtie

parent 34f65445
......@@ -96,6 +96,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
val mapping = new Mapping(this)
mapping.skipFlexiprep = true
mapping.skipMarkduplicates = true
mapping.defaultAligner = "bowtie"
mapping.input_R1 = prefixFastq.output
mapping.RGLB = runConfig("ID").toString
mapping.RGSM = sampleConfig("ID").toString
......
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