Home

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.

About BioBam & OmicsBox

BioBam Bioinformatics is a bioinformatics solution provider whose stated mission is "to transform complex data analysis procedures into attractive and interactive tasks", closing the gap between experimental work, bioinformatics analysis, and applied research. Its flagship product, OmicsBox, is an all-in-one platform for end-to-end NGS data analysis of genomes, transcriptomes, and metagenomes, organised into five modules: Functional Analysis,Transcriptomics, Genetic Variation, Metagenomics, and Genome Analysis. It is widely used in the study of non-model organisms and in fields such as agricultural genomics, microbiology, and environmental NGS research. A distinctive feature of the platform is its integrated cloud computing: compute-intensive steps such as BLAST, InterProScan, and EggNOG searches are dispatched to OmicsBox's cloud infrastructure, so users do not need to provision local compute or maintain large reference databases themselves.

OmicsBox traces its origins to Blast2GO, published in 2005 (Conesa, Götz et al., Bioinformatics 21:3674–3676, doi:10.1093/bioinformatics/bti610) and since cited in more than 10,000 scientific papers. Blast2GO established the functional annotation methodology — high-throughput BLAST and InterProScan searches followed by Gene Ontology mapping, annotation, and enrichment analysis — that remains at the core of the platform today, and since the release of OmicsBox in early 2019 it lives on as its Functional Analysis module. The workflows in this repository build directly on that lineage: rather than reimplementing any of these analyses, they drive the OmicsBox Engine CLI from Nextflow and Snakemake, turning the same validated, citable methods into reproducible, scriptable pipelines that fit naturally into automated and high-throughput environments.

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

Authentication

Before you can run any workflow, the OmicsBox Engine CLI must be authenticated on the machine that will execute the pipeline steps. Authentication is a one-time setup per machine and involves two independent credentials: a subscription key (a 45-character key that unlocks the analysis modules) and a BioBam account sign-in (which grants access to the OmicsBox cloud, where the analyses actually run). A single command covers both: omicsbox activate <key> validates the key against BioBam's licence server, stores it, and then automatically opens a browser sign-in flow. Both credentials are persisted to ~/.omicsboxEngine/properties/, a location deliberately kept separate from the OmicsBox desktop application's own store, so signing in with the CLI never disturbs a desktop session.

From that point on the workflows themselves need no credentials of any kind — none of the pipelines in this repository accept a key, token, or login parameter. Each step simply invokes omicsbox <tool>, and the CLI resolves the stored credentials from the home directory of the process that runs it.

omicsbox activate <45-character-key>   # validates the key, stores it, then signs you in
omicsbox whoami                        # check activation and sign-in status

If a workflow is started without valid credentials, the very first step fails immediately with an explicit message. No cloud analysis is submitted in that case, so nothing is consumed or billed.

To sign out, use omicsbox logout (add --forget-key to remove the stored subscription key as well).

Where to Go Next

Page	Covers
Nextflow Available Workflows	The published Nextflow pipelines, each linking to its own reference page
Nextflow Architecture	How the module library, workflow entry points and configuration layers fit together
Nextflow Execution & Configuration	Running with or without a clone, the configuration template workflow, output layout
Nextflow Developer Guide	Adding a module or a new pipeline, and the conventions to follow
Snakemake Available Workflows	Which pipelines are ported to Snakemake and their current status
Snakemake Architecture	The rule library, the use rule … as … instantiation pattern and the shared defaults
Snakemake Execution & Configuration	Launch options, run_id semantics and deterministic output paths
Snakemake Developer Guide	Writing a .smk rule and porting a Nextflow pipeline

License & Contact

The workflows in this repository are released by BioBam Bioinformatics S.L. under the Apache License 2.0, which allows you to use, modify, and redistribute them freely — including in commercial and closed-source settings — provided you retain the licence and copyright notices and state any changes you have made. Please note that this licence covers only the pipeline definitions in this repository: the Nextflow and Snakemake code, its modules and its configuration files. It does not extend to the OmicsBox Engine CLI or to the OmicsBox cloud service, which are commercial products requiring a valid OmicsBox subscription and governed by BioBam's terms of service. In short, the pipelines themselves are free and open, but running them requires a licensed OmicsBox installation.

The full licence text is in the LICENSE file at the repository root.

For questions, bug reports, feature requests about these workflows or anything concerning OmicsBox itself please contact BioBam:

Enquiry	Channel
Technical support	support@biobam.com, or the Customer Support Centre at https://account.biobam.com
Subscriptions & sales	sales@biobam.com
Training	training@biobam.com
General enquiries	contact@biobam.com