Introduction
============

RAFT provides a consistent, reproducible way to run bioinformatics analyses
across samples, environments, and workflow versions. Whether you are processing
a single patient or a large cohort, every RAFT project follows the same
structure — from setup through results.

What RAFT does
--------------

- **Manages projects** — initializes a standard layout and tracks what ran,
  when, and with what inputs
- **Runs versioned workflows** — pulls specific workflow versions from GitLab
  and executes them through Nextflow
- **Stages inputs** — helps you build sample manifests, download public
  datasets, and wire inputs together before execution
- **Surfaces results** — launches a browser-based viewer for QC metrics,
  reports, and workflow outputs
- **Works anywhere** — runs on a local cluster (SLURM and others) or your own
  GCP infrastructure

How a RAFT project works
------------------------

RAFT projects all follow the same basic flow:

1. **Set up your workspace**
2. **Choose a workflow** 
3. **Prepare inputs**
4. **Run the analysis**
5. **Review results**

Where to start
--------------

**New to RAFT?**
   Follow :doc:`quick-start` to install RAFT and run a demo in minutes.

**Ready to run your own data?**
   Use :doc:`choosing-your-environment` to decide between local and cloud,
   then follow the relevant setup guide.

**Looking for a specific command or option?**
   See :doc:`running-raft-locally`, :doc:`running-raft-on-the-cloud`, and
   :doc:`manifest` for execution guidance and manifest details.