EN:CloWM Joins the NFDI4Biodiversity Service Catalog for Biodiversity Data Analysis

With CloWM, NFDI4Biodiversity expands its portfolio with a cloud-based platform for reproducible bioinformatics analyses directly in the web browser. Researchers can use established workflows such as APSCALE without requiring their own computing infrastructure.

Following approval by the NFDI4Biodiversity steering committee on February 27, 2026, the Cloud-based Workflow Manager (CloWM) [1] is now an official service in the NFDI4Biodiversity service catalog.

Developed and operated by the Bielefeld Institute for Bioinformatics Infrastructure (BIBI) at Bielefeld University together with the German Network for Bioinformatics Infrastructure (de.NBI), CloWM enables biodiversity researchers to run curated best-practice bioinformatics workflows through a web browser without needing their own computing infrastructure or local software installations.

What CloWM offers

CloWM is a platform for scalable and reproducible workflow execution. Through a web interface, users can access curated and version-controlled analysis workflows that run on cloud-based computing infrastructure and use integrated S3-based data storage. The workflows are implemented in Nextflow, a workflow language commonly used in bioinformatics.

Users authenticate with their Life Science Login or NFDI Login credentials. The platform currently provides more than 50 production-ready workflows covering research areas such as metagenomics, metabarcoding, genome assembly, transcriptomics, and phylogenomics. To date, CloWM has more than 200 active users and has supported over 2,700 workflow executions.

A key strength of CloWM is that it makes complex command-line-based analysis workflows accessible through a web interface. Instead of installing and running software manually, researchers can configure workflow parameters, upload or link their data, and start analyses directly in the browser. The platform automatically manages workflow execution, compute scheduling, and result storage.

Connecting biodiversity workflows to the cloud

CloWM joins the NFDI4Biodiversity service catalog as part of the Processing & Visualizing category of the data lifecycle. This category includes services for analysing and processing biodiversity data.

One workflow that is particularly relevant for the biodiversity community is APSCALE [2], which was integrated into CloWM in collaboration with NFDI4Microbiota during the first funding phase of NFDI4Biodiversity. APSCALE is used for the analysis of DNA metabarcoding data derived from environmental samples. Instead of managing software installations and access to compute clusters themselves, researchers can now upload raw DNA sequencing data from environmental samples directly to CloWM and run the APSCALE workflow through the web interface.

The resulting metabarcoding data can then be used for downstream steps such as taxonomic assignment and submission to biodiversity repositories via the GFBIo Submission Service.

Getting started

CloWM is freely accessible at https://clowm.bi.denbi.de. Users can log in with their Life Science Login or NFDI credentials to browse and run the available workflows.

For questions and support, contact the CloWM team at support@clowm.bi.denbi.de or the NFDI4Biodiversity Helpdesk.

References

1] Göbel, D., Stoye, J., Sczyrba, A., & Beckstette, M. (2024). The Cloud-based Workflow Manager (CloWM) - An integrated platform for highly scalable workflow execution. German Conference on Bioinformatics 2024 (GCB), Bielefeld. Zenodo. https://doi.org/10.5281/zenodo.14039069

[2] Buchner, D., Macher, T.-H., & Leese, F. (2022). APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data. Bioinformatics, 38(20), 4817–4819. https://doi.org/10.1093/bioinformatics/btac588