Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud

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Published: 2018-12-07

Formatted citation

Moreno P, Pireddu L, Roger P, Goonasekera N, Afgan E, Beek Mvd, He S, Larsson A, Ruttkies C, Schober D, Johnson D, Rocca-Serra P, Weber RJM, Gruening B, Salek B, Kale N, Perez-Riverol Y, Papatheodorou I, Spjuth O, Neumann D. Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud.
bioRxiv. 488643 (2018). DOI: 10.1101/488643


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 and assist with job automation and aids reproducibility of analyses. Many contemporary workflow tools are specialized and 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, re-usable 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 leaning, through a flexible programming API suitable for scientists used to programming or scripting.