Welcome to the RAFT documentation!

RAFT (Reproducible Analyses Framework and Tools) turns complex, multi-sample bioinformatics workflows into versioned, reproducible projects that can run locally, on clusters, or in user-owned cloud infrastructure.

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Getting started

• Introduction
• Quick start

User guide

• Installing RAFT
• Choosing your environment
• Choosing a workflow
• Preparing your samples
• Running RAFT
• Accessing and reviewing outputs
• Managing RAFT projects
• Reproducibility and archiving
• Helpful RAFT options

Help

• Frequently asked questions
  • What is RAFT?
  • What directory should I run RAFT from?
  • Do I need a manifest before I create a project?
  • Can I build a manifest without creating a project?
  • What does --setup-only do?
  • How do I rerun an existing project?
  • How do I see what happened in a project?
  • Where are my workflow outputs?
  • Can I run RAFT without a default Nextflow profile?
  • How do I update references for an off-the-shelf workflow?
  • How do I open the report viewer?
  • How much disk space do I need?
  • Can several people share one reference set?
  • How do I check that my dependencies actually work?
• Troubleshooting
  • pip says error: externally-managed-environment
  • Extracting a reference fails with lbzip2: Cannot exec
  • Nextflow fails with CAPSULE EXCEPTION: Error resolving dependencies
  • check-manifest reports multiple samples of the same type
  • RAFT refuses to run an existing project
  • Where should I run RAFT commands?
  • How do I check project status?
  • Why are there no reports after a setup-only run?
  • Why can’t RAFT find my manifest?
  • How do I create a manifest?
  • What does the missing Nextflow profile warning mean?
  • My workflow failed. What do I check first?
  • How do I list available workflow steps?
  • Why aren’t files preloading in the report viewer?
  • Can I skip downloads during setup?
  • Related pages