Software Engineering for Reproducible Pipeline Development in Bioinformatics

Abstract

Reproducibility in bioinformatics remains challenging despite the availability of workflow management systems and mature computational infrastructures. This work presents a software-engineering perspective for developing reproducible bioinformatics pipelines, with emphasis on pipeline-specific code. We reinterpret the SOLID principles in this context at two levels: workflow management systems (e.g., Nextflow, Snakemake, and Compi) and pipeline implementation. Our approach promotes pipeline designs based on well-defined task interfaces, explicit input/output specifications, and a clear separation between compute tasks and glue/adaptation tasks, in order to improve flexibility, reuse, and maintainability. The paper provides practical guidance for robust and reproducible pipeline development, including systematic validation checks (environment, inputs, and runtime), standardized project organization, and comprehensive testing strategies using both real and synthetic data within continuous integration workflows. It also discusses how modular ecosystems (such as nf-core modules and Snakemake wrappers) support these principles in community-driven environments. Finally, we relate these recommendations to FAIR-oriented research software guidelines (FAIR4RS and FAIRsoft), showing how core engineering practices strengthen robustness, portability, and long-term sustainability, thereby supporting reproducibility in bioinformatics pipelines.