Using a cluster profile no longer works with snakemake >8.0.0

[sterrettJD]

Snakemake 8 overhauled cluster job submission such that it broke compatibility with the cookiecutter slurm/etc profiles. From the cookiecutter profile:

Snakemake version 8 currently unsupported
Snakemake version 8 introduces breaking changes with respect to the Snakemake cookiecutter profile. One new feature is that execution of jobs on a cluster or the cloud is handled by executor plugins. For instance, there is a dedicated executor plugin for SLURM that provides much of the functionality that was previously catered for by this snakemake profile. Profiles are still needed, but their role changes somewhat to that of fine-tuning executor plugins for particular sites, only requiring the yaml configuration file.

With this in mind, support for Snakemake version 8 has currently been put on hold and I recommend that users consult the executor plugin documentation for slurm.

It looks like snakemake, much like nextflow is trying to have built in support for clusters/cloud batch job systems, and HoMi should migrate toward using the built in support executors.