snakemake 8.16 incompatibility

Problem: On the cluster, snakemake was updated from Version 7.32.4 to 8.16. In the latest version, some of the flags provided in Profiles/Slurm/config.yaml are deprecated.

Bug: executing the commands as described in the git using snakemake 8.16 result in the following error:

snakemake: error: ambiguous option: --cluster=sbatch -t {resources.time_min} --mem {resources.mem_mb} -c {resources.cpus} -o Logs/{rule}_%j.log -e Logs/{rule}_%j.log --parsable --exclude smer16-4,smeb01-[1-4],smeb02-[1-4],smeb03-[1-4],smeb04-[1-4],smeb05-[1-4],smeb06-[1-4],smeb07-[1-4],smeb08-[1-4],smeb09-[1-4],smeb10-[1-4],smeb11-[1-4],smeb12-[1-4],smeb13-[1-4],smeb14-[1-4],smer01-[1-4],smer02-[1-4],smer03-[1-4],smer04-[1-4],smer05-[1-4],smer06-[1-4],smer07-[1-4],smer08-[1-4],smer09-[1-4],smer10-[1-4],smer11-[1-4],smer12-[1-4],smer13-[1-4],smer14-[1-4],smer15-[1-4],smer16-[1-3],smer17-[1-4],smer18-[1-4],smer19-[1-4],smer20-[1-4],smer21-4,smer24-4,smer26-1,smer27-[1,3],smer28-[1-2,4],smer29-[1-4],smer30-[2,4],smum[01-14] could match --cluster-generic-submit-cmd, --cluster-generic-status-cmd, --cluster-generic-cancel-cmd, --cluster-generic-cancel-nargs, --cluster-generic-sidecar-cmd, --cluster-sync-submit-cmd

Solution option 1: change cluster to cluster-generic-submit-cmd in the slurm/config.yaml file. When re-run with this adaptation, another error is called:

snakemake: error: unrecognized arguments: --cluster-status=Profiles/Slurm/status.py

I was not able to figure out how to resolve this error. My assumption is that, due to the modularization of snakemake 8 the cluster interactions are integrated in a different manner.

Solution option 2: run

module load snakemake/7.32.4-foss-2022b instead of module load snakemake

This reverts some other dependencies, but enables the usage of the snakemake pipeline as is