add-subworkflow

What problem does it solve?

Scaffold a reusable Bactopia subworkflow that orchestrates one or more existing modules. It creates a main.nf file wired with GroovyDoc comments and a standard test scaffold, reducing boilerplate and ensuring a consistent interface for workflows.

Core Features & Use Cases

• Scaffold a subworkflow that wires modules together and provides a GroovyDoc-enabled main.nf.
• Generate tests for the subworkflow, including nf-test specs, nextflow.config, and test configuration files.
• Operate in an interactive fashion to determine which modules are included and how test data should be discovery-driven.
• Ideal for adding new subworkflows to glue existing modules into a cohesive orchestration layer.

Quick Start

Ask the AI to scaffold a new Bactopia subworkflow; it will create main.nf and the accompanying tests and config files.