FAQ

Is MICOS-2024 a workflow engine?

No. It is better described as a metagenomics platform shell with:

• a stable Python CLI,
• workflow assets under steps/,
• environment assets under deploy/ and containers/.

Is every script in scripts/ part of the stable public interface?

No. Several scripts are specialist tools or expansion surfaces. The CLI reference documents the narrower stable command contract.

Should I use the shell wrappers or the Python CLI?

Prefer the Python CLI for new automation and documentation. Use the wrappers when maintaining compatibility with existing shell-first workflows.

Why are the configuration templates broader than the CLI surface?

Because the repository ambition is broader than the currently unified runtime surface. The templates capture that broader platform direction.

Does the Docker Compose file run the full analysis pipeline?

It provides a reproducible environment scaffold and service example. It should not be read as a guarantee that every pipeline concern is fully automated through Compose alone.

Where should a reviewer start?

Start with the homepage, then:

1. Academy / Pipeline Foundations
2. Architecture / System Overview
3. Reference / CLI Reference

That path gives the clearest signal about maturity and boundaries.