Quickstart Guide

This guide will help you get the pipeline up and running as quickly as possible.

Step 1: Clone the Repository

git clone https://github.com/bibymaths/nf-illumina2lineage.git
cd nf-illumina2lineage

Step 2: Install Mamba (if not already installed)

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh"
bash Mambaforge-Linux-x86_64.sh

Step 3: Create and Activate the Environment

conda update -y conda
mamba env create -p --file environment.yaml
mamba activate sars_genome_assembly

Set up Java and Nexflow

curl -s https://get.sdkman.io | bash

In new terminal

sdk install java 17.0.10-tem  
java -version

curl -s https://get.nextflow.io | bash  
chmod +x nextflow 
mkdir -p $HOME/.local/bin/
mv nextflow $HOME/.local/bin/ 
nextflow info

Before you launch Nextflow, unset the Conda‐JDK variables and point to SDKMAN’s inside the conda environment. 

unset JAVA_CMD JAVA_HOME
export JAVA_HOME="$HOME/.sdkman/candidates/java/current"
export JAVA_CMD="$JAVA_HOME/bin/java"

Nextflow requires Bash 3.2 (or later) and Java 17 (or later, up to 24) to be installed. More information on Nextflow installation.

Step 4: Run the Pipeline with Nextflow

nextflow run main.nf

To use a Docker profile:

nextflow run main.nf -profile docker

Input Data Requirements

  • Illumina paired-end FASTQ files
  • SARS-CoV-2 reference genome (automatically downloaded by the pipeline)

Output Overview

  • Cleaned FASTQ files and QC reports
  • Sorted, indexed BAM files
  • VCF variant files
  • Consensus sequences (FASTA)
  • Pangolin lineage assignments
  • Phylogenetic tree (Newick format)

For advanced configuration, see the parameters section.

💡 Tip: Use multiqc to summarize all QC results in one place.

You're now ready to use the pipeline!