Commit dbda4819 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix command

parent c0f8f2a3
......@@ -44,8 +44,8 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
*/
def cmdLine: String = executable +
//TODO: Options
optional("--threads", threads)
required("-x", index) +
optional("--threads", threads) +
required("-x", index) +
(inputR2 match {
case Some(r2) => required("-1", inputR1) + required("-2", r2)
case _ => required("-U", inputR1)
......
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