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Choosing an executor

The workflow ships with several profiles under workflow/profiles/. Each cluster profile names the executor plugin it needs and marks the site-specific values with CHANGE_ME; run any of them with snakemake --workflow-profile workflow/profiles/<name> -j <max_parallel_jobs>.

  • default/ — local execution, auto-loaded. Snakemake picks this up automatically, so snakemake -j <cores> just runs on the current machine with no extra flags and no scheduler.
  • slurm/ — generic SLURM (pip install snakemake-executor-plugin-slurm).
  • lsf/ — generic LSF (pip install snakemake-executor-plugin-lsf); uses the dedicated LSF plugin with native lsf_queue / lsf_project resources. These are untested profiles so they may require some tailoring.
  • bsc/ — the authors' Barcelona Supercomputing Center profile, kept for reference and reproducibility.

The heavy rules request up to 112 cores; on smaller nodes, lower the values in the profile's set-threads block (a commented example is included in each cluster profile).