slurm.conf

# This is an example of how you can use Cromwell to interact with SLURM
# workload manager. *This is not a complete configuration file!* The
# content here should be copy pasted into the backend -> providers section
# of the cromwell.examples.conf in the root of the repository. You should
# uncomment lines that you want to define, and read carefully to customize
# the file. If you have any questions, please open an issue at
# https://www.github.com/broadinstitute/cromwell/issues

# Documentation
# https://cromwell.readthedocs.io/en/stable/backends/SLURM/

backend {
	default = slurm

	providers {
		slurm {
			actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
			config {
				runtime-attributes = """
					Int runtime_minutes = 600
					Int cpu = 1
					Int requested_memory_mb_per_core = 768
					String queue = "prod"
				"""

				# If an 'exit-code-timeout-seconds' value is specified:
				# - check-alive will be run at this interval for every job
				# - if a job is found to be not alive, and no RC file appears after this interval
				# - Then it will be marked as Failed.
				# Warning: If set, Cromwell will run 'check-alive' for every job at this interval

				# exit-code-timeout-seconds = 120

				submit = """
					sbatch -J ${job_name} -D ${cwd} -o ${out} -e ${err} \
						--time ${runtime_minutes} \
						--partition ${queue} \
						--ntasks ${cpu} \
						--mem-per-cpu ${requested_memory_mb_per_core} \
						--wrap "/usr/bin/env bash ${script}"
				"""
				kill = "scancel ${job_id}"
				check-alive = "squeue -j ${job_id}"
				job-id-regex = "Submitted batch job (\\d+).*"
			}
		}
	}
}