Commit baa5ab44 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix-star-mapping-keep-unmapped' into 'develop'

Fix star mapping keep unmapped reads in bamfile

An addition of a config value to the `Mapping` pipeline. Let Star output unmapped reads.

See merge request !416
parents bfdad518 5665f7e9
......@@ -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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