snakemake-workflow-manager

# Snakemake Workflow Manager Skill ## Purpose Enable Snakemake workflow management for rule-based pipeline execution. ## Capabilities - DAG-based workflow execution - Cluster/cloud execution - Conda environment management - Checkpointing and resume - Benchmark collection - Report generation ## Usage Guidelines - Define rules with clear inputs/outputs - Use Conda for environment management - Configure for cluster execution - Enable checkpointing for large workflows - Collect benchmarks for optimization - Generate workflow reports ## Dependencies - Snakemake - Conda - Bioconda ## Process Integration - Reproducible Research Workflow (reproducible-research) - Analysis Pipeline Validation (pipeline-validation)