OmicsBox Engine Workflows

A collection of Nextflow and Snakemake pipelines that orchestrate the OmicsBox Engine CLI. Each workflow wires together a sequence of omicsbox commands into a reproducible pipeline; OmicsBox itself runs the heavy bioinformatics analyses in the cloud and handles parallelization, resource allocation and input validation, while these workflows take care of sequencing the steps, wiring inputs/outputs together and laying out the results. To ensure a seamless user experience, every pipeline is driven by a self-documenting configuration template. You can easily customize any underlying OmicsBox parameter or advanced option simply by filling in or uncommenting pre-defined flags directly in the config file, without needing to memorize complex CLI syntax.

Prerequisites

• Nextflow v25.04.0 or later — to run the pipelines under nextflow/
• Snakemake v9.23.0 or later — to run the pipelines under snakemake/
• OmicsBox Engine CLI (omicsbox) — installed, licensed, and available on PATH

Quick Start

There are two ways to run any of these pipelines: cloning the repository and running the workflow locally (the one shown below), or running it directly from GitHub without cloning. See the Wiki for the full breakdown of both options.

The commands below only fetch each workflow's configuration template and exit — no OmicsBox cloud job is launched, so no credentials or cost are involved. Replace <workflow> with the name of any pipeline from the list below.

Nextflow

git clone https://github.com/BioBam/omicsbox-engine-workflows.git
cd omicsbox-engine-workflows
nextflow run nextflow/workflows/<workflow>/<workflow>.nf --dump_config

Snakemake

git clone https://github.com/BioBam/omicsbox-engine-workflows.git
cd omicsbox-engine-workflows
snakemake -s snakemake/workflows/<workflow>/Snakefile dump_config --cores 1

---

For detailed execution guides, self-documenting configuration templates, OmicsBox integration details, and developer instructions on how to modify workflows, please see our Wiki.