Peter Van Dyken

One clarification: sub-snakemake instances on the cluster actually do **not** automatically delete the temp files (they get called with `--notemp`). This behaviour is fine, it just means this PR more...

@DrYak Ah, no worries, I was clarifying myself because I made a mistake in the initial post. I wanted to correct it for the record.

See here #1488 for why this isn't super viable right now and for other workarounds.

Exactly the same way you call from the cli ``` snakemake.main(["--profile", "profile_name", "other_arg", "other_arg2", ...]) ```

If it's one specific tool that's causing trouble, you could probably work around it manually within the rule by using `shadow="shallow"` and adding something like this to your shell: ```py...

> Thanks for the post Johannes, this helps. One additional question: Say I modify a rule and want to cleanup the metadata for multiple files, either say the output file...

@jdblischak, did you specify the maximum number of threads using `--cores ` or `-c`?

> I tried out using `--cores` and `--resources mem_mb=x`. I have to admit that I find it difficult to reason about. When I use one or the other, both of...

@uweschmitt, just found this thread and realized it's related to a PR I just drafted involving group jobs and temp files #1765. I'm not sure what causes the bug here,...

Cool, I'm actually surprised, because my PR doesn't actually adjust the deleting of temp files, it just tells Snakemake to (sometimes) not worry about temp files already deleted. But if...