bio-workflow-management-snakemake-workflows - Author reproducible bioinformatics pipelines with Snakemake.
Authors Snakemake pipelines using output-pattern rules, wildcards, checkpoints, resource escalation, and conda or container deployment.
Tags
Updated: 2026-10-06Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Author Snakemake pipelines
- Wire rules by output patterns
- Fan out samples with wildcards
- Handle unknown outputs with checkpoints
- Diagnose rerun triggers
- Escalate resources on retry
- Deploy software with conda or containers
- Port Snakemake execution commands
Inputs
- Target files
- Sample metadata
- Configuration files
- Input datasets
- Resource and retry settings
- Software environment specifications
- Execution backend settings
Outputs
- Snakemake workflow files
- DAG and dry-run results
- Bioinformatics result files
- Execution logs and reports
- Job scheduling status
Requirements
- Snakemake 8.0 or later
- Python 3.11 or later
- Version-compatible CLI and APIs
- Conda or container runtime when used
- Executor or storage plugins when selected