Viash: from scripts to pipelines
This addresses the issue of inefficient pipeline development and collaboration in bioinformatics, though it is incremental as it builds on existing modularization concepts.
The paper tackles the problem of tightly coupled bioinformatics pipeline components limiting reusability and increasing maintenance overhead by introducing Viash, a tool that enables 'code-first' prototyping and modular component generation, which has been applied in projects ranging from proof-of-concept pipelines to international data science competitions.
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.