ReddRadar
Agent skill
snakemake-workflow-manager
Snakemake workflow management skill for rule-based pipeline execution
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/bioinformatics/skills/snakemake-workflow-manager
Metadata
Additional technical details for this skill
- tags
-
infrastructure workflow snakemake reproducibility
- version
- 1.0
- category
- bioinformatics
SKILL.md
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)
Recommended Agent Skills
Expand your agent's capabilities with these related and highly-rated skills.
a5c-ai/babysitter
gsd-tools
Central utility skill for GSD operations. Provides config parsing, slug generation, timestamps, path operations, and orchestrates calls to other specialized skills. Acts as the unified entry point that the original gsd-tools.cjs provided via its lib/ modules (commands, config, core, init).
a5c-ai/babysitter
model-profile-resolution
Resolve model profile (quality/balanced/budget) at orchestration start and map agents to specific models. Enables cost/quality tradeoffs by selecting appropriate AI models for each agent role.
a5c-ai/babysitter
verification-suite
Plan structure validation, phase completeness checks, reference integrity verification, and artifact existence confirmation. Provides the structured verification layer ensuring GSD artifacts are well-formed and complete.
a5c-ai/babysitter
state-management
STATE.md reading, writing, and field-level updates. Provides cross-session state persistence via .planning/STATE.md with structured fields for current task, completed phases, blockers, decisions, and quick tasks.
a5c-ai/babysitter
git-integration
Git commit patterns, formats, and conventions for GSD methodology. Provides atomic commits per task, structured commit messages, planning file commits, branch management, and milestone tag operations.
a5c-ai/babysitter
frontmatter-parsing
YAML frontmatter parsing and manipulation for .planning/ documents. Provides read, write, update, query, and validation operations on frontmatter blocks in GSD markdown artifacts.
Didn't find tool you were looking for?