Quickstart Guide

This guide will help you get the pipeline up and running as quickly as possible. To use your own data, you must override the input parameters or modify the downloadData process, as the current script hardcodes a download from OSF.

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 nf-illumina2lineage

Set up Java and Nexflow if not already installed

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

In a 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

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!