Commit b0ef88db authored by pjvan_thof's avatar pjvan_thof

Adding missing argument

parent 76e1a93b
......@@ -49,7 +49,7 @@ class RefflatStats(val parent: Configurable) extends ToolCommandFunction with Re
if (reference == null) reference = referenceFasta()
}
override def cmdLine =
override def cmdLine: String =
super.cmdLine +
required("-a", refflatFile) +
required("-R", reference) +
......
......@@ -237,6 +237,8 @@ class Gentrap(val parent: Configurable)
new File(outputDir, "expression_measures" + File.separator + "transcript.stats")
refflatStats.exonOutput =
new File(outputDir, "expression_measures" + File.separator + "exon.stats")
refflatStats.intronOutput =
new File(outputDir, "expression_measures" + File.separator + "intron.stats")
refflatStats.jobOutputFile = new File(outputDir, ".reflatstats.out")
add(refflatStats)
......
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