singularity.slurm.conf

# This is an example of how you can use Singularity containers with Cromwell
# *This is not a complete configuration file!* The
# content here should be copy pasted into the backend -> providers section
# of cromwell.example.backends/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/develop/tutorials/Containers/#job-schedulers

backend {
  default = slurm

  providers {
    slurm {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"                                                                                     
      config {
        runtime-attributes = """
        Int runtime_minutes = 600
        Int cpus = 2
        Int requested_memory_mb_per_core = 8000
        String? docker
        """

        submit = """
            sbatch \
              --wait \
              -J ${job_name} \
              -D ${cwd} \
              -o ${out} \
              -e ${err} \
              -t ${runtime_minutes} \
              ${"-c " + cpus} \
              --mem-per-cpu=${requested_memory_mb_per_core} \
              --wrap "/bin/bash ${script}"
        """

        submit-docker = """
            # Ensure singularity is loaded if it's installed as a module
            module load Singularity/3.0.1

            # Build the Docker image into a singularity image
            IMAGE=${cwd}/${docker}.sif
            singularity build $IMAGE docker://${docker}

            # Submit the script to SLURM
            sbatch \
              --wait \
              -J ${job_name} \
              -D ${cwd} \
              -o ${cwd}/execution/stdout \
              -e ${cwd}/execution/stderr \
              -t ${runtime_minutes} \
              ${"-c " + cpus} \
              --mem-per-cpu=${requested_memory_mb_per_core} \
              --wrap "singularity exec --bind ${cwd}:${docker_cwd} $IMAGE ${job_shell} ${script}"
        """

        kill = "scancel ${job_id}"
        check-alive = "squeue -j ${job_id}"
        job-id-regex = "Submitted batch job (\\d+).*"
      }
    }
  }
}