SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines. Issue 5 (26th April 2019)

• Record Type: Journal Article
• Authors: Lampa, Samuel; Dahlö, Martin; Alvarsson, Jonathan; Spjuth, Ola
• Is Part Of: GigaScience. Volume 8:Issue 5(2019)
• Publication Date: 2019-04-26
• Subjects: scientific workflow management systems -- pipelines -- reproducibility -- machine learning -- flow-based programming -- Go -- Golang; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giz044
• Languages: English
• ISSNs: 2047-217X

Abstract

Abstract: Background: The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines, assist with job automation, and aid reproducibility of analyses. Many contemporary workflow tools are specialized or not designed for highly complex workflows, such as with nested loops, dynamic scheduling, and parametrization, which is common in, e.g., machine learning. Findings: SciPipe is a workflow programming library implemented in the programming language Go, for managing complex and dynamic pipelines in bioinformatics, cheminformatics, and other fields. SciPipe helps in particular with workflow constructs common in machine learning, such as extensive branching, parameter sweeps, and dynamic scheduling and parametrization of downstream tasks. SciPipe builds on flow-based programming principles to support agile development of workflows based on a library of self-contained, reusable components. It supports running subsets of workflows for improved iterative development and provides a data-centric audit logging feature that saves a full audit trace for every output file of a workflow, which can be converted to other formats such as HTML, TeX, and PDF on demand. The utility of SciPipe is demonstrated with a machine learning pipeline, a genomics, and a transcriptomics pipeline. Conclusions: SciPipe provides a solution for agile development of complex and dynamic pipelines, especially in machine learning, through a flexible application programming interface suitable for scientists used to programming or scripting.