# Nextflow Pipeline Executor

> Nextflow workflow management skill for reproducible bioinformatics pipelines

- Skill: `a5c-ai/nextflow-pipeline-executor` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/nextflow-pipeline-executor`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/nextflow-pipeline-executor/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/nextflow-pipeline-executor

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# 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