bacass

What problem does it solve?

This Skill helps you run the nf-core/bacass pipeline correctly without guessing release-specific flags, parameter names, or required inputs.

Core Features & Use Cases

• Runs bacterial assembly and annotation workflows for short-read, long-read, and hybrid sequencing data.
• Exposes the release-pinned input schema, parameter groups, defaults, and allowed values so agents can choose valid options.
• Produces standard pipeline outputs, MultiQC reports, and provenance for reproducible reruns.
• Use case: an analyst provides a samplesheet and desired profile, and the Skill guides a clean run for a bacterial isolate assembly project.

Quick Start

Use the bacass Skill to run the pipeline for your samplesheet and output directory, then add only the validated optional parameters needed for your sequencing data and environment.