feat: support --qos as a resource

[kdm9]

A cluster I am using requires setting --qos to enable jobs with longer runtimes. it would be convenient to be directly able to use slurm_qos as a resource, like one can do for partition & account, so I've implemented that. Also fixed some typos in the docs.

best
K

[fgvieira]

Can't you use slurm_extra to pass the qos?

[cmeesters]

Essentially, this is all covered by slurm_extra. However, the documentation needs an update in that regard (and I do not seem to get to it all too soon) and there has been a bug.

Please update to snakemake v8.4.3 or higher, that should fix working with slurm_extra. Yet, there is another bug, see PR #2627 and the discussion to #2555.

Note, that the idea behind this executor is to provide all relevant submission flags, but to catch cluster relevant flags, like qos (where some admins hide their accelerators, instead of gres) or flags introduced by spank plugins or all the nifty detail flags, sbatch provides with slurm_extra. If we were to include all flags explicetly, we would have to include a hundred ifs in the code.

[kdm9]

How about something like:

for resource, value in job.resources.items:
    if not resource.startswith("slurm_"):
        continue
    slurmarg = resource.replace("slurm_", "")
    args += f" --{slurmarg}={value}"

In other words, to submit with sbatch --arg=value, provide "slurm_arg=value" as a resource.

That should handle partition as it happens now (perhaps updating job.resources["slurm_partition"] using the existing logic), and would allow users direct control over the submission command.

[cmeesters]

I am closing this pull request: The current release is working with slurm_extra as intended, offering to set qos.