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通过nf-test提高生物信息管道的可靠性,质量和可维护性

Lukas Forer¹, Sebastian Schönherr¹

¹Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.

|October 22, 2025

概括

nf-test是一个新的模块化框架,用于生物信息学下一流管道的自动化单元测试. 它提高了软件质量,并通过实现孤立测试和优化资源使用,减少了开发时间.

科学领域:

生物信息学是一种生物信息学.
计算生物学计算生物学
软件工程软件工程软件工程

背景情况:

下一流和nf-core社区已经为生物信息学工作流创造了一个重要的生态系统.
确保复杂的Nextflow管道的正确性和可靠性是具有挑战性的,因为没有统一的,自动化的单元测试框架.

研究的目的:

引入nf-test,一个模块化测试框架,旨在解决Nextflow管道缺乏自动化单元测试的问题.
让用户能够测试单个组件和整个管道,有效验证他们的输出.

主要方法:

开发了nf-test,语法类似于Nextflow DSL2.
实现了诸如快照测试和智能测试等功能,通过仅测试修改模块来优化资源使用.
证明了该框架在多个生物信息学管道中的有效性.

主要成果:

nf-test可最大限度地缩短开发时间,并将测试执行时间缩短高达80%.
通过早期检测错误和问题来提高软件质量.
证明可以提高生物信息管道的稳定性,可维护性和可靠性.

结论:

nf-test为Nextflow管道提供了一个统一的,自动化的单元测试解决方案.
该框架显著改善了生物信息学软件的开发生命周期和质量.
已经被许多管道采用了,nf-test是生物信息学社区的宝贵工具.

关键词:

下一个流程下一个流程管道测试管道测试测试自动化测试自动化

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