Commit cf99b25d authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Set default star to output unmapped reads also in the bamfile

parent a4c324e1
......@@ -98,7 +98,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** location of summary file */
def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".summary.json")
override def defaults = Map("gsnap" -> Map("batch" -> 4))
override def defaults = Map(
"gsnap" -> Map("batch" -> 4),
"star" -> Map("outSAMunmapped" -> "Within")
)
override def fixedValues = Map(
"gsnap" -> Map("format" -> "sam"),
......
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