Agent-Skills.md

Agent Skills: Snakemake Workflow Manager Skill

Snakemake workflow management skill for rule-based pipeline execution

bioinformaticsID: a5c-ai/babysitter/snakemake-workflow-manager

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

Install this agent skill to your local

pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/snakemake-workflow-manager

Skill Files

Browse the full folder contents for snakemake-workflow-manager.

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plugins/babysitter/skills/babysit/process/specializations/domains/science/bioinformatics/skills/snakemake-workflow-manager/SKILL.md

Skill Metadata

Name
snakemake-workflow-manager
Description
Snakemake workflow management skill for rule-based pipeline execution

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)