NF-Core RNA-seq App

A proof-of-concept B-Fabric WebApp for invoking bulk transcriptomics processing with NF-Core pipelines, tightly integrated with B-Fabric.

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Note: This repository was forked from the bfabric-web-app-template, and was built using the bfabric-web-apps Python library.

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About

The NF-Core RNA-seq App demonstrates integration between B-Fabric, the Nextflow/NF-Core RNA-seq pipeline, and a Redis-based compute backend. Built using Dash and the bfabric-web-apps module, it enables a structured, interactive interface for RNA-seq data analysis.

• Retrieves and displays sample metadata from B-Fabric.
• Enqueues jobs for NF-Core RNA-seq execution using Redis.
• Links results back to B-Fabric automatically.

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Features

• Dash web UI with form-based job submission.
• Automated retrieval of metadata via B-Fabric API.
• Redis-powered job dispatch to remote compute server.
• Integrated output registration in B-Fabric.

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Built With

• Python
• Dash
• Plotly
• Flask
• bfabric-web-apps

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Quickstart

Follow these steps to install and run the app locally:

1. Clone the Repository

git clone https://github.com/GWCustom/rnaseq.git
cd rnaseq

2. Create and Activate a Virtual Environment

Using virtualenv (Linux/Mac):

python3 -m venv venv
source venv/bin/activate

Using virtualenv (Windows):

python -m venv venv
venv\Scripts\activate

Or use conda:

conda create -n rnaseq-app pip
conda activate rnaseq-app

3. Install Dependencies

pip install -r requirements.txt

4. Set Up .bfabricpy.yml

Create a file in your home directory at ~/.bfabricpy.yml with your credentials:

GENERAL:
  default_config: PRODUCTION

PRODUCTION:
  login: your_username
  password: your_password
  base_url: https://your-bfabric-api-endpoint

This file is required to authenticate with the B-Fabric API.

5. Run the Application

python3 index.py

Then open http://localhost:8050 in your browser.

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License

Distributed under the MIT License. See LICENSE for details.

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Contact

GWC GmbH - GitHub
Griffin White - LinkedIn
Marc Zuber - LinkedIn