snakemake-workflow-manager
// Snakemake workflow management skill for rule-based pipeline execution
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stars:384
forks:73
updated:March 4, 2026
SKILL.mdreadonly
SKILL.md Frontmatter
namesnakemake-workflow-manager
descriptionSnakemake workflow management skill for rule-based pipeline execution
allowed-toolsRead,Write,Glob,Grep,Edit,WebFetch,WebSearch,Bash
metadata[object Object]
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)