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Generate mafs pipeline

Prior to kicking off the command, make sure to create a logs directory in the same directory as the snakemake file in order for the logs to be saved. The logs directory can also be configured in the config.yaml file under log_dir: to any other location.

Run the following command:

CLUSTER_CMD=("bsub -n {threads} -R {cluster.resources} -M {cluster.memory} -o {cluster.output} -J {cluster.name} -W {cluster.time}")

snakemake --jobs 500 --skip-script-cleanup \
  --cluster-config cluster.yaml \
  --cluster "${CLUSTER_CMD}" \
  --use-singularity \
  --singularity-args "--bind /juno"