Running on SLURM does not delete all temp files

[cnluzon]

This may be a snakemake issue or related to it.

I have seen this a few times, but I was not sure that the problem was not something crashing during the pipeline. But at this point I have run minute-testdata-0.9.tar.gz test data in several ways and I always end up with tmp/4-mapped/*.bam files there, where everything seemed to have run smoothly.

This reproduces with minute-testdata-0.9.tar.gz running in cluster mode. I ran it with my attempt at cluster profiles, which can be found at /proj/<projcode>/minute-uppmax-conf/minute_rackham.sbatch, where <projcode> is the Uppmax computing project. That could also be the cause, but I think I recall running it in the old cluster mode with the same result.

It also happens if run on Snowy.

[cnluzon]

This has not happened in a very long time either, so it was probably fixed in our own code or upon Snakemake updates.