SLURM cluster_config not recognized

[meixilin]

Hi,

I am trying to run grenepipe with SLURM. When I use the v0.13.1 release with a new install of micromamba, I get this error:

No SLURM account given, trying to guess.
Guessed SLURM account: xxx
No wall time information given. This might or might not work on your cluster. If not, specify the resource runtime in your rule or as a reasonable default via --default-resources.
No job memory information ('mem_mb' or 'mem_mb_per_cpu') is given - submitting without. This might or might not work on your cluster.
....
WorkflowError:
SLURM job submission failed. The error message was sbatch: error: Batch job submission failed: Time limit specification required, but not provided

I think this issue can be fixed with updating the workflow/profiles/slurm/config.yaml file. When I add the following lines to the workflow/profiles/slurm/config.yaml file, my job can start.

default-resources:
    slurm_partition: "xxx"
    slurm_account:   "yyy"
    runtime: 60

However, when I add these lines to cluster_config.yaml, snakemake can't recognize it and have the same error. I think the cluster_config.yaml file might be discontinued?

By the way, other variables (e.g. time needs to become runtime, details here) might have to be updated as well.

Best, M