Quickstart
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¶
Step 2: Install Pixi¶
Install Pixi using the official installer:
Restart your shell, or reload your shell configuration:
Verify the installation:
Step 3: Install and Use the Environment¶
From the root directory of this pipeline, install the Pixi environment:
Run commands inside the environment using:
For example:
To enter the environment shell:
If your environment is named illumina2lineage instead of default, use this version:
Step 3: Install and Use the Environment¶
From the root directory of this pipeline, install the Pixi environment:
Run commands inside the environment using:
For example:
To enter the environment shell:
Set up Java and Nexflow if not already installed¶
In a new terminal:
curl -s https://get.nextflow.io | bash
chmod +x nextflow
mkdir -p $HOME/.local/bin/
mv nextflow $HOME/.local/bin/
nextflow info
unset JAVA_CMD JAVA_HOME
export JAVA_HOME="$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¶
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
multiqcto summarize all QC results in one place.
You're now ready to use the pipeline!