Robrecht Cannoodt

Robrecht Cannoodt, Hendrik Cannoodt, Eric Van de Kerckhove et al.

Most bioinformatics pipelines consist of software components that are tightly coupled to the logic of the pipeline itself. This limits reusability of the individual components in the pipeline or introduces maintenance overhead when they need to be reimplemented in multiple pipelines. We introduce Viash, a tool for speeding up development of robust pipelines through "code-first" prototyping, separation of concerns and code generation of modular pipeline components. By decoupling the component functionality from the pipeline logic, component functionality becomes fully pipeline-agnostic, and conversely the resulting pipelines are agnostic towards specific component requirements. This separation of concerns improves reusability of components and facilitates multidisciplinar and pan-organisational collaborations. It has been applied in a variety of projects, from proof-of-concept pipelines to supporting an international data science competition. Viash is available as an open-source project at https://github.com/viash-io/viash and documentation is available at https://viash.io.

Daniel Nüst, Dirk Eddelbuettel, Dom Bennett et al.

The Rocker Project provides widely used Docker images for R across different application scenarios. This article surveys downstream projects that build upon the Rocker Project images and presents the current state of R packages for managing Docker images and controlling containers. These use cases cover diverse topics such as package development, reproducible research, collaborative work, cloud-based data processing, and production deployment of services. The variety of applications demonstrates the power of the Rocker Project specifically and containerisation in general. Across the diverse ways to use containers, we identified common themes: reproducible environments, scalability and efficiency, and portability across clouds. We conclude that the current growth and diversification of use cases is likely to continue its positive impact, but see the need for consolidating the Rockerverse ecosystem of packages, developing common practices for applications, and exploring alternative containerisation software.