Getting Started

CheckRef is a Nextflow pipeline designed for detecting and correcting allele switches between target VCF files and reference panel legend files. This guide will help you get up and running with the pipeline.

Prerequisites

Before you begin, ensure you have the following installed:

• Nextflow (version 21.04.0 or later)
• Container engine: Docker, Singularity, Podman, Shifter, Charliecloud, or Conda
• Java 11 or later (required for Nextflow)

Quick Installation

1. Install Nextflow

# Install Nextflow
curl -s https://get.nextflow.io | bash

# Make it executable and move to PATH
chmod +x nextflow
sudo mv nextflow /usr/local/bin/

# Verify installation
nextflow -version

2. Install Container Engine

Choose one of the following:

Docker (Recommended for local systems):

# Follow instructions at https://docs.docker.com/get-docker/

Singularity (Recommended for HPC):

# Follow instructions at https://sylabs.io/guides/latest/user-guide/

3. Test the Installation

Run the pipeline with test data to verify everything is working:

Option A: Quick Test (recommended)

# Clone repository with test data
git clone https://github.com/AfriGen-D/checkref.git
cd checkref

# Run with included test data
nextflow run main.nf \
    --targetVcfs "test_data/chr22/*.vcf.gz" \
    --referenceDir "test_data/reference/" \
    --legendPattern "*.legend.gz" \
    --outdir test_results \
    -profile docker

Option B: Pull from GitHub

nextflow run AfriGen-D/checkref -profile test,docker --outdir test_results

This will:

• Download the CheckRef pipeline from GitHub
• Pull the required Docker container
• Run on chr22 sample data (~1000 variants)
• Generate results in test_results/
• Complete in ~2-5 minutes

Verify Results:

ls test_results/
# Expected files:
# - chr22_allele_switch_results.tsv
# - chr22_allele_switch_summary.txt
# - chr22.noswitch.vcf.gz
# - all_chromosomes_summary.txt

What's Next?

• Installation - Detailed installation instructions
• Quick Start - Run your first analysis
• Configuration - Customize the pipeline for your needs
• Input Files - Understand input file requirements

Getting Help

If you encounter any issues:

1. Check the troubleshooting guide
2. Search existing GitHub issues
3. Create a new issue with details about your problem
4. Contact the AfriGen-D team at helpdesk.afrigen-d.org