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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