# Nextflow Dsl2 Generator

> Generates production Nextflow DSL2 process modules, handles tuple channel mapping, pins Docker containers, and configures AWS Batch / SLURM profiles.

- Skill: `yulianuzhnenko/nextflow-dsl2-generator` (Agent Skill)
- Install (CLI): `npx skillmds@latest add yulianuzhnenko/nextflow-dsl2-generator`
- Raw SKILL.md: https://api.skillmd.com/api/skills/yulianuzhnenko/nextflow-dsl2-generator/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- Author: YuliaNuzhnenko (https://skillmd.com/u/yulianuzhnenko)
- Updated: 2026-09-22
- Page: https://skillmd.com/skills/yulianuzhnenko/nextflow-dsl2-generator

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# Agent Skill: Nextflow DSL2 Cloud Pipeline Generator Skill

[![Domain](https://img.shields.io/badge/Domain-Cloud%20HPC%20&%20Workflows-00f0ff?style=flat-square)](#)
[![Version](https://img.shields.io/badge/Version-1.0.0-green?style=flat-square)](#)

## 📌 Description
Generates production Nextflow DSL2 process modules, handles tuple channel mapping, pins Docker containers, and configures AWS Batch / SLURM profiles.

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## 🤖 Agent Execution Protocol

When an AI Agent is tasked with `nextflow-dsl2-generator`:
1. **Input Validation**: Verify that the required input files or coordinates are supplied.
2. **Environment Check**: Ensure dependencies (`Nextflow DSL2, Docker, AWS Batch, SLURM`) are installed.
3. **Execution**: Run the protocol pipeline snippet below.
4. **Output Generation**: Produce actionable Markdown/JSON summaries with publication figures.

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## 💻 Protocol Code Snippet

```python
// Nextflow DSL2 Agent Template
process FASTQC {
    container 'biocontainers/fastqc:v0.11.9_cv8'
    input: tuple val(id), path(reads)
    output: path "*.html", emit: html
    script: "fastqc ${reads}"
}

```

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## 📥 Input & Output Specifications

### Input Contract
* **Target Files**: Valid input data matching domain formats.
* **Parameters**: Quality thresholds and cutoffs.

### Output Contract
* **Results Table**: Structured summary dataframe or matrix.
* **Visualization**: Rendered SVG/PNG figures.

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## 📄 License
Distributed under the MIT License. See `LICENSE` for details.