Nextflow Dsl2 Generator

Agent Skill: Nextflow DSL2 Cloud Pipeline Generator Skill

📌 Description

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

🤖 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.

💻 Protocol Code Snippet

// 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}"
}

📥 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.

📄 License

Distributed under the MIT License. See LICENSE for details.