Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
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DOI：
10.1038/s41592-021-01254-9
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发表时间：
2021-09-23
期刊：
影响因子：
48
通讯作者：
Goke, Jonathan
中科院分区：
文献类型：
--
作者：
Wratten, Laura;Wilm, Andreas;Goke, Jonathan
高通量技术的快速发展改变了生物医学研究。随着数据量和复杂性的增加，可扩展性和可重复性不仅对实验至关重要，而且对计算分析也至关重要。但是，将数据转换为信息涉及到运行大量工具、优化参数以及集成动态变化的参考数据。工作流管理器是为了应对这些挑战而开发的。它们简化了管道开发、优化资源使用、处理软件安装和版本，并在不同的计算平台上运行，从而实现工作流程的可移植性和共享。在这个角度来看，我们强调工作流管理器的主要功能，比较常用的方法，生物信息学工作流，并提供了一个指南，计算和非计算用户。我们概述了社区策划的管道计划，使新手和经验丰富的用户能够执行复杂的最佳实践分析，而无需手动组装工作流。总之，我们说明了工作流管理器如何有助于使生物医学研究中的计算分析可共享，可扩展和可复制。这个角度突出了工作流管理器，这是有用的开发和管理复杂的生物信息学管道。
The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not just for experiments, but also for computational analysis. However, transforming data into information involves running a large number of tools, optimizing parameters, and integrating dynamically changing reference data. Workflow managers were developed in response to such challenges. They simplify pipeline development, optimize resource usage, handle software installation and versions, and run on different compute platforms, enabling workflow portability and sharing. In this Perspective, we highlight key features of workflow managers, compare commonly used approaches for bioinformatics workflows, and provide a guide for computational and noncomputational users. We outline community-curated pipeline initiatives that enable novice and experienced users to perform complex, best-practice analyses without having to manually assemble workflows. In sum, we illustrate how workflow managers contribute to making computational analysis in biomedical research shareable, scalable, and reproducible.This Perspective highlights workflow managers, which are useful for developing and managing complex bioinformatics pipelines.