Commit 3fbbc7b9 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing output files of sambamba markdup

parent 8a0e0c8e
......@@ -40,6 +40,13 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
override def defaultThreads = 4
override def defaultCoreMemory = 4.0
@Output
private var indexOutput: File = _
override def beforeGraph(): Unit = {
indexOutput = new File(output + ".bai")
}
/** Returns command to execute */
def cmdLine: String = required(executable) +
required("markdup") +
......
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