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:

Metadata

Release files for reproducible-analyses-framework-and-tools 1.5.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for reproducible-analyses-framework-and-tools 1.5.2
File	Size	Uploaded
reproducible_analyses_framework_and_tools-1.5.2.tar.gz	3.0 MB	Sep 17, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for reproducible-analyses-framework-and-tools 1.5.2
File	Interpreter	ABI	Platform	Reset
reproducible_analyses_framework_and_tools-1.5.2-py3-none-any.whl 2.9 MB Sep 17, 2026	Python 3	none	any	Details

Total release size: 5.9 MB

Release files / reproducible_analyses_framework_and_tools-1.5.2.tar.gz

Download URL	reproducible_analyses_framework_and_tools-1.5.2.tar.gz
Size	3.0 MB
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Uploaded via	`twine/7.0.0 CPython/3.14.3`

Release files / reproducible_analyses_framework_and_tools-1.5.2-py3-none-any.whl

Download URL	reproducible_analyses_framework_and_tools-1.5.2-py3-none-any.whl
Size	2.9 MB
Tags	Python 3
SHA-256 checksum How to use checksums	`fec6cca50093bf833445cd78531fa717eb570d63b7a62af5b5f28188c54e2b25`
BLAKE2b-256 checksum How to use checksums	`9aff9abdfe85aedacc5fb30dfb9bbd410f07a51a628182cb9cc192f706f4f6e9`
Upload date	Sep 17, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/7.0.0 CPython/3.14.3`