name: snakemake-workflow-manager description: Snakemake workflow management skill for rule-based pipeline execution allowed-tools:

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• Bash metadata: version: "1.0" category: bioinformatics tags:
  • infrastructure
  • workflow
  • snakemake
  • reproducibility

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)