RAFT

Reproducible Analyses Framework and Tools

RAFT is a Python package and CLI for running and managing bioinformatics workflows built on Nextflow DSL2. The repository also includes browser-based tools for manifest/config generation, a report viewer, and a Bring Your Own Cloud (BYOC) launcher for running on GCP Batch.

What RAFT does

• Creates and manages reproducible workflow projects
• Runs off-the-shelf workflows from versioned definitions
• Validates manifests before execution
• Launches browser UIs for manifest editing, config generation, report viewing, and BYOC setup
• Supports local execution and BYOC submission to GCP Batch

Installation

RAFT installs a raft command-line entry point. Install it into an environment of its own — current Debian and Ubuntu releases enforce PEP 668 and refuse to let pip install into the system Python (error: externally-managed-environment), including with --user.

sudo apt install -y pipx
pipx ensurepath
pipx install reproducible-analyses-framework-and-tools

Or, without pipx:

python3 -m venv ~/raft-venv
~/raft-venv/bin/pip install reproducible-analyses-framework-and-tools
export PATH="$HOME/raft-venv/bin:$PATH"

On older distributions that predate PEP 668 enforcement, pip install --user reproducible-analyses-framework-and-tools still works.

Runtime prerequisites for most workflow execution paths:

• Python 3.9+
• Nextflow
• Java
• wget
• tar, gzip, and the bzip2 helper this system's tar calls (lbzip2 on Debian, bzip2 on Ubuntu) for reference archive extraction; raft install-dependencies installs whichever one applies
• Singularity/Apptainer

Quick Start

Initialize a RAFT workspace in the current directory:

raft setup --default

List available off-the-shelf workflows:

raft available-workflows
raft available-workflows --workflow lens

Create and run a new workflow project:

raft run \
  --project-id demo-lens \
  --workflow lens \
  --version 1.9.0

If --manifest is omitted for a new project, RAFT launches the manifest generator UI. If --workflow-profile is not provided, RAFT can also launch the config generator UI. Use --workflow-profile standard to apply the base workflow configuration non-interactively.

Launch the report viewer for an existing project:

raft generate-reports --project-id demo-lens

Main Commands

• raft setup: create .raft.cfg and standard workspace directories, including inputs/
• raft run: run an existing project, or create and run a new workflow project
• raft run-demo: create and run a demo workflow
• raft available-workflows: inspect workflow definitions
• raft check-manifest: validate a manifest
• raft generate-reports: open the workflow report viewer

Documentation In This Repo

• User docs: docs/source
• Runner container: containers/raft-runner

Cloud / BYOC

The repository includes:

• A browser-based BYOC launcher for GCP Batch
• A runner container image used by Batch jobs
• Local raft run --bucket ... support for advanced cases

Start with:

• docs/source/running-raft-on-the-cloud.rst
• containers/raft-runner/README.md