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.
pip install --user reproducible-analyses-framework-and-tools
Runtime prerequisites for most workflow execution paths:
- Python 3.9+
- Nextflow
- Java
wget- 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 v1.9-dev
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.cfgand standard workspace directories, includinginputs/raft run: run an existing project, or create and run a new workflow projectraft run-demo: create and run a demo workflowraft available-workflows: inspect workflow definitionsraft check-manifest: validate a manifestraft 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:
1 maintainer
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