Batch Submission Using Snakemake

Batch Submission Using Snakemake#

This workflow demonstrates how to use fpocketR with Snakemake to efficiently run pocket-finding jobs in parallel.

See the README in the demo folder for full details.

Overview#

  • Configure batch runs in a YAML file

  • Run the Snakemake workflow to process jobs in parallel

  • Output and log files are organized by parameter set and sample

Example Snakemake Command#

snakemake --use-envmodules --use-conda --conda-frontend conda --cores all --rerun-incomplete --latency-wait 15 --keep-going &