Quick Start#

  • Configuration: Create a params.yaml file defining your input, output, and processing options (reference below sections).

  • Basic Execution: Once you’re in the relevant folder with the Snakefile present, run the workflow through the following command:

    cd finaletoolkit_workflow # Enter the folder with the workflow Snakefile

# --cores: Number of CPU cores to use.
# --jobs: Maximum number of concurrent jobs (limited by --cores).
snakemake --configfile params.yaml --cores <cores> --jobs <jobs>

  • SLURM Execution: Submit to SLURM to run the workflow through the command below (see slurm_profile/config.yaml for default settings).

    cd finaletoolkit_workflow # Enter the folder with the workflow Snakefile

# Runs the command through params specified in slurm_profile/config.yaml in the background (&),
# Redirects all command-related output to snakemake.log
snakemake  --profile slurm_profile > snakemake.log 2>&1 &

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