Cloudgene is an open-source platform that turns Nextflow analysis pipelines into web services, helping researchers make computational workflows easier to deploy, run, and share. Created by Lukas Forer and Sebastian Schönherr and licensed under the MIT License, Cloudgene 3 connects pipeline development with an accessible web application through a simple configuration file.

Users can integrate individual Nextflow pipelines or combine multiple workflows into tailored services. The platform provides features such as user management, data transfer, error handling, job management, and results delivery. Applications can be shared through HTTP, GitHub, or S3, allowing others to install and run them on their own infrastructure. Cloudgene also supports deployment to in-house clusters and public cloud environments, including Amazon AWS, and can be used to offer services to other scientists.

Examples of applications using Cloudgene include the Michigan Imputation Server 2, which provides genotype imputation, and mtDNA-Server 2 and Haplocheck, which support mitochondrial variant detection and contamination analysis. Cloudgene offers documentation, installation guidance, command-line tools, and a REST API for managing jobs and applications.