Slurm execution¶

The CLI is a submitter. A normal workflow command performs preflight validation, writes a resolved run configuration and controller script, and submits that controller with sbatch. The controller runs Snakemake and dispatches worker jobs through the packaged Slurm profile.

login shell
└── omnomnomics ...
    └── controller Slurm job
        └── Snakemake worker jobs

Do not wrap the CLI invocation in another sbatch command.

Site configuration defines controller resources, worker defaults, partition, maximum concurrent jobs, and scheduler pacing. Conservative defaults for max_jobs_per_second and max_status_checks_per_second reduce transient Slurm submission failures on busy clusters.

Inspect jobs¶

squeue -u "$USER"
scontrol show job JOB_ID

Cancel a workflow¶

Cancel the controller and its worker jobs before modifying or removing active outputs. Job names and IDs are visible in squeue; rule logs are preserved in slurm_logs/.

After an interrupted run, make sure no jobs remain before clearing a stale Snakemake lock. See Troubleshooting.