Commit ae0a5dfd authored by rhpvorderman's avatar rhpvorderman

Fix outputname issue

parent 865f33cf
......@@ -56,12 +56,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
if (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on GearsSingle module")
if (outputName == null) {
if (fastqR1.nonEmpty) outputName = fastqR1.headOption.map(_.getName
.stripSuffix(".gz")
.stripSuffix(".fastq")
.stripSuffix(".fq"))
.getOrElse("noName")
else outputName = bamFile.map(_.getName.stripSuffix(".bam")).getOrElse("noName")
outputName = sampleId.getOrElse("noName") + libId.map("-" + _).getOrElse("")
}
if (fastqR1.nonEmpty) {
......
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