Nextflow Pipeline

Run py-gbcms at scale on HPC clusters with automatic parallelization.

Overview

The Nextflow workflow provides:

• Automatic parallelization across samples

• SLURM/HPC integration with resource management

• Containerization with Docker/Singularity

• Resume capability for failed runs

Quick Start

nextflow run nextflow/main.nf \
    --input samplesheet.csv \
    --variants variants.vcf \
    --fasta reference.fa \
    -profile docker

Documentation

Page	Description
Samplesheet	Input CSV format
Parameters	All configuration options
Examples	Common usage patterns

Related

• CLI Reference — For processing few samples

• Troubleshooting — Common issues