Hi there @lmanchon!
QIIME 2 uses your system’s temp dir to handle automatic cleanup of temp files (at the interval defined by your operating system). Are you overriding the
TMPDIR env var? If so, then those files will most likely not be covered by your system’s machinery for temporary file cleanup.
At the end of the day, all temporary files generated by QIIME 2 should be deleted by your system’s temp file machinery — QIIME 2 behaves like any other unix tool in that respect.
In a way this flag exists — by leaving your
TMPDIR env var setting as your system default, this is saying “let my files be cleaned up at the system’s defined interval”. If I set the
TMPDIR var to a new value, this is saying “don’t delete my temporary files, let me do it on my own.”
Yep, we love that idea, and it is something that we have been stewing on for a while now. Maybe some time in 2019?