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bioRxiv · 10.1101/2025.09.15.672424

TAFFISH: A lightweight, modular, and containerized workflow framework for reproducible bioinformatics analyses

Han, K.·Wang, T.·Yuan, S.-S.·Ma, C.-Y.·Su, W.·Deng, K.·Lv, H.·Lin, H.
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Abstract

SummaryBioinformatics analyses often rely on shell commands and small shell scripts whose executable context is difficult to preserve, inspect and reuse. TAFFISH addresses this gap by packaging command-line tool calls and lightweight shell flows as installable, versioned and inspectable executable units. Through a curated public Hub, TAFFISH indexes command interfaces, execution backends, platform constraints, release metadata and smoke-test/validation records. Together, these components provide a command-level reproducibility layer that works directly in ordinary shells and can also be invoked from existing workflow systems. Availability and ImplementationTAFFISH is implemented in Common Lisp and released under Apache-2.0. TAFFISH version 0.10.1, together with the source code, documentation and public Hub resources, is available at https://github.com/taffish/taffish, https://taffish.com, https://taffish.github.io and https://github.com/taffish/. The submitted software release, frozen Hub snapshot, test data, command logs, checksums and reproducibility package are archived at https://doi.org/10.5281/zenodo.21054185. The authors will maintain the software and public resources for at least two years after publication. ContactHao Lyu: hao.lyu@uestc.edu.cn; Hao Lin: hlin@uestc.edu.cn; Kejun Deng: dengkj@uestc.edu.cn Supplementary informationSupplementary data are available online.

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Han, K., Wang, T., Yuan, S.-S., Ma, C.-Y., Su, W., Deng, K., Lv, H., Lin, H.. 2025-09-16. TAFFISH: A lightweight, modular, and containerized workflow framework for reproducible bioinformatics analyses. https://doi.org/10.1101/2025.09.15.672424

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