mag

What problem does it solve?

This Skill removes the complexity of running nf-core/mag by turning a large metagenomics workflow into a guided, validated run with the right inputs, parameters, and provenance captured automatically.

Core Features & Use Cases

• End-to-End Metagenomics: Handles read preprocessing, assembly, binning, bin QC, taxonomic profiling, virus identification, and genome annotation in one workflow.
• Strict Input Validation: Uses a required CSV samplesheet and schema-backed parameters so runs fail fast on invalid paths, flags, or values.
• Reproducible Execution: Tracks the pinned pipeline release, commit, exact command, and run provenance for reliable reruns and auditing.
• Use Case: A researcher can submit short-read, long-read, or hybrid metagenomic data and obtain assembled contigs, bins, QC reports, and MultiQC summaries without manually wiring pipeline modules together.

Quick Start

Ask the assistant to run the mag metagenomics pipeline with my samplesheet, output directory, and preferred profile, then generate the command and validate the required parameters.