Entering edit mode
6 weeks ago
hamarillo
▴
80
Hi, does anyone know of the effects of using both temp() and directory() in snakemake's output?
e.g.
rule:
output: temp(directory("bowtie/{samp}/global_alignment"))
Yep, this behavior is easy to confirm with a couple of test rules and something like
shell: "sleep 60"
in the last one, so you can see the temp directory outputs get removed before the whole workflow is done running. That distinction (versus removal at the very end) can matter if you have big workflows with multiple batches of temporary files.I'm pretty sure that Snakemake implicitly sets rule priorities to try to get temp outputs cleared out sooner rather than later, too, but I can't find this in the docs. (Maybe implied by the help text for
--scheduler
where it "aims to reduce runtime and hdd usage by best possible use of resources"? I could have sworn I saw it described somewhere but can't find it now.)