From Abandoned Scripts to FAIR Community Pipelines: Rescuing Orphan Bioinformatics Workflows with nf-core - Lessons from Light-Sheet Fluorescence Microscopy

Authors

Schwitalla, C., Kuhn Cuellar, L., Hoertenhuber, M., Grote, N., Woller, T., Lamberti, I., Pavie, B., Kuestner, T., Kyere, F. A., Curtin, I., Stein, J. L., Nahnsen, S.

Abstract

Abstract Background Research software is essential for modern data analysis but is often developed and maintained by a small number of researchers. When developers leave, software may become orphaned, limiting reuse and risking the loss of valuable domain knowledge and computational methods. While the FAIR Principles for Research Software (FAIR4RS) provide an essential foundation for improving the reuse of research software, compliance with these principles alone does not guarantee practical reusability. Here, we investigate whether orphaned scientific software can be systematically rescued and transformed into sustainable, reusable workflows using established software engineering practices and community standards. Findings We re-engineered the abandoned MATLAB-based NuMorph toolkit for large-scale light-sheet microscopy image analysis into nf-core/lsmquant, a Nextflow-based workflow developed according to nf-core community guidelines. The re-engineered workflow preserved the original scientific methods at comparable computational cost while improving the software's FAIRness, portability, and reproducibility. Integration into the nf-core ecosystem provides a community-driven framework that supports software sustainability through distributed maintenance and shared development practices, while the modular workflow architecture simplified adaptation of nf-core/lsmquant to additional light-sheet microscopy datasets beyond the original application Conclusion Our work demonstrates that orphaned scientific software can be successfully rescued through systematic re-engineering guided by FAIR and software sustainability principles. By transforming a legacy codebase into a community-maintained workflow, we preserve valuable domain-specific methods while improving usability, maintainability, and reproducibility. This approach provides a practical strategy for recovering orphan research software and integrating it into modern, reusable research ecosystems. Keywords Light-sheet fluorescence microscopy, Nextflow, nf-core, re-engineering, sustainable software

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 04 Aug 2026.

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