Container Support¶

This pipeline supports containerized execution using Docker, which ensures reproducibility and simplifies environment setup.

Using Docker¶

To run the pipeline with Docker:

nextflow run main.nf -profile docker

Make sure Docker is installed and the current user has permission to run Docker commands (e.g., add user to docker group).

A Dockerfile is provided to build a custom container image:

docker build -t nf-illumina2lineage .

Use your image with:

nextflow run main.nf -with-docker nf-illumina2lineage

Customize container settings in nextflow.config:

process.container = 'nf-illumina2lineage'
docker.enabled = true

📦 Using containers is recommended for dependency consistency and reproducibility across systems.