Nextflow Pipeline Executor Skill
Purpose
Provide Nextflow workflow management for reproducible bioinformatics pipelines.
Capabilities
- DSL2 workflow execution
- Container integration (Docker/Singularity)
- Cloud execution (AWS, GCP, Azure)
- Pipeline parameterization
- Resume and caching
- Execution reports and timelines
Usage Guidelines
- Use DSL2 for modular pipelines
- Containerize processes for reproducibility
- Configure for target execution environment
- Enable resume for fault tolerance
- Generate execution reports
- Document pipeline versions
Dependencies
- Nextflow
- nf-core
- Snakemake
Process Integration
- Reproducible Research Workflow (reproducible-research)
- Analysis Pipeline Validation (pipeline-validation)
- All analysis pipelines