quality-control_pipeline

Variant Calling Pipeline

A comprehensive bioinformatics pipeline for variant calling, featuring a Nextflow-based workflow, a FastAPI backend, and a modern React frontend.

Features

• Nextflow Pipeline: Automated workflow for Quality Control, Trimming, Alignment, and Variant Calling.
• Interactive Dashboard: React-based UI to upload files, monitor jobs, and view results.
• Real-time Monitoring: Track pipeline progress and view logs directly from the browser.
• QC Reports: Integrated MultiQC/FastQC-style reporting (Falco/Fastp).

Prerequisites

Ensure you have the following installed:

• Conda (or Mamba)
• Nextflow (Requires Java 11+)
• Node.js (v16+ recommended)

Installation

1. Clone the repository:

   git clone https://github.com/YOUR_USERNAME/bioinfo-pipeline.git
   cd bioinfo-pipeline
   

2. Set up the Conda Environment: This environment includes all necessary bioinformatics tools (bcftools, fastp, falco, etc.) and Python dependencies.

   conda env create -f environment.yml
   

3. Set up the FastApi backend Environment:

    python -m venv .venv
    source .venv/bin/activate
    pip install -r requirements.txt
    deactivate
   

4. Install Frontend Dependencies:

   cd frontend
   npm install
   cd ..
   

Running the Application

You need to run both the backend and frontend servers.

1. Start the Backend (API)

From the root directory of the project:

# Make sure your both environment is activated
conda activate variant-calling
source .venv/bin/activate

# Run the FastAPI server
uvicorn api:app --reload

The API will be available at http://localhost:8000.

2. Start the Frontend

Open a new terminal window, navigate to the frontend directory, and start the development server:

cd frontend
npm run dev

The application will be accessible at http://localhost:5173.

Usage

1. Open your browser and go to http://localhost:5173.
2. Upload Data: Upload your paired-end FASTQ files (_R1, _R2).
3. Select Reference: Upload a reference genome (.fna / .fasta) if running the full pipeline.
4. Configure: Choose the pipeline stage:
   • QC Only: Generates quality reports.
   • Trim & QC: Trims reads and generates reports.
   • Full Pipeline: Performs alignment and variant calling.
5. Run: Start the job and monitor the progress in the “Jobs” tab.

Project Structure

• api.py: FastAPI backend server.
• main.nf: Nextflow pipeline definition.
• frontend/: React frontend application.
• environment.yml: Conda environment specification.
• data_test/ & ref_test/: Directories for storing uploaded test data which are created on runtime.
• results_test/: Output directory for pipeline results.