Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker and singularity containers making installation trivial and results highly reproducible.

Quick Start

i. Install nextflow

ii. Install one of docker, singularity or conda

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run https://forgemia.inra.fr/get-nextflow-ngl-bi/template-nf -profile test,<docker/singularity/conda>

singularity pull template.sif oras://registry.forgemia.inra.fr/get-nextflow-ngl-bi/template-nf/template-nf:latest

nextflow run main.nf -with-singularity template.sif