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

作者：Carolin Schwitalla, Luis Kuhn Cuellar, Matthias Hörtenhuber, Niklas Grote, Tatiana Woller, Irene Lamberti, Benjamin Pavie, Thomas Küstner, Felix A. Kyere, Ian Curtin, Jason L. Stein, Sven Nahnsen · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2026 · DOI：10.64898/2026.07.29.741447 · 研究领域：Cell Image Analysis Techniques、Scientific Computing and Data Management、Research Data Management Practices

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 orp...