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Test-drive the GATK tools and Best Practices pipelines on Terra
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Queue deletes all files in working directory
I'm running Queue-3.3-0 on an Ubuntu server, and running it deletes every file in the working directory. I've only tried this on one machine so far, but I reproduced this behavior repeatedly in different situations and confirmed that the directory emptied is the precisely the current directory, at least in my setup.
This behavior seems dangerous to me. I can submit a detailed bug report.