Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics [version 2; peer review: 1 approved, 2 approved with reservations]

• Published in: F1000Research
• Main Authors: Manabu Ishii, Bruno P. Kinoshita, Hirotaka Suetake, Tomoya Tanjo, Takatomo Fujisawa, Takeo Igarashi, Osamu Ogasawara, Tazro Ohta, Masanori Arita, Tsukasa Fukusato, Yuichi Kodama, Atsushi Shimizu, Takeshi Fujino, Tsuyoshi Hachiya
• Format: Article
• Language: English
• Published: F1000 Research Ltd 2024-06-01
• Subjects: workflow; workflow language; workflow execution service; open science; eng
• Online Access: https://f1000research.com/articles/11-889/v2

The increased demand for efficient computation in data analysis encourages researchers in biomedical science to use workflow systems. Workflow systems, or so-called workflow languages, are used for the description and execution of a set of data analysis steps. Workflow systems increase the productivity of researchers, specifically in fields that use high-throughput DNA sequencing applications, where scalable computation is required. As systems have improved the portability of data analysis workflows, research communities are able to share workflows to reduce the cost of building ordinary analysis procedures. However, having multiple workflow systems in a research field has resulted in the distribution of efforts across different workflow system communities. As each workflow system has its unique characteristics, it is not feasible to learn every single system in order to use publicly shared workflows. Thus, we developed Sapporo, an application to provide a unified layer of workflow execution upon the differences of various workflow systems. Sapporo has two components: an application programming interface (API) that receives the request of a workflow run and a browser-based client for the API. The API follows the Workflow Execution Service API standard proposed by the Global Alliance for Genomics and Health. The current implementation supports the execution of workflows in four languages: Common Workflow Language, Workflow Description Language, Snakemake, and Nextflow. With its extensible and scalable design, Sapporo can support the research community in utilizing valuable resources for data analysis.