Welcome to RAFT
===============

**RAFT** (Reproducible Analyses Framework and Tools) is a workflow manager
for multi-sample bioinformatics analyses that allows users to focus on the biology.

**New here?** Start with :doc:`quick-start` to be up and running in minutes.

.. toctree::
   :caption: Getting started
   :maxdepth: 1

   introduction
   quick-start

.. toctree::
   :caption: User guide
   :maxdepth: 1

   choosing-your-environment
   workflows
   datasets
   running-raft
   accessing-and-reviewing-outputs
   managing-raft-projects
   helpful-raft-options
   troubleshooting

.. toctree::
   :caption: Reference
   :maxdepth: 1
   :hidden:

   which-command
   inspecting-workflow-details
   manifest
   ui
   outputs
   modules
   manual-workflow-assembly
   ots-workflows
   workflow-ui-templates
   workflow-package-contract
   ui-specifications
   experimental-command-aliases
   rftpkg
   code-status
   changelog
   project-status
   feature-availability