Commit ae0a5dfd authored by Ruben Vorderman's avatar Ruben Vorderman
Browse files

Fix outputname issue

parent 865f33cf
...@@ -56,12 +56,7 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript ...@@ -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 (sampleId == null || sampleId == None) Logging.addError("Missing sample ID on GearsSingle module")
if (outputName == null) { if (outputName == null) {
if (fastqR1.nonEmpty) outputName = fastqR1.headOption.map(_.getName outputName = sampleId.getOrElse("noName") + libId.map("-" + _).getOrElse("")
.stripSuffix(".gz")
.stripSuffix(".fastq")
.stripSuffix(".fq"))
.getOrElse("noName")
else outputName = bamFile.map(_.getName.stripSuffix(".bam")).getOrElse("noName")
} }
if (fastqR1.nonEmpty) { if (fastqR1.nonEmpty) {
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment