Commit e40baa30 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed output pipeline

parent 2ada4499
......@@ -33,7 +33,7 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
stdoutFile = stdoutFile.map(_.getAbsoluteFile)
stdinFile = stdinFile.map(_.getAbsoluteFile)
if (stdoutFile.isDefined) {
if (stdoutFile.isDefined || _outputAsStdout) {
commands.last.stdoutFile = None
commands.last._outputAsStdout = true
}
......
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