Approaches for containerized scientific workflows in cloud environments with applications in life science

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Published: 2018-08-25

Formatted citation

Spjuth O, Capuccini M, Carone M, Larsson A, Schaal W, Novella J, Di Tommaso P, Notredame C, Moreno P, Khoonsari PE, Herman S, Kultima K, Lampa S. Approaches for containerized scientific workflows in cloud environments with applications in life science.
PeerJ Preprints. 6, e27141v1 (2018). DOI: 10.7287/peerj.preprints.27141v1

Abstract

Containers are gaining popularity in life science research as they encompass all dependencies of provisioned tools and simplifies software installations for end users, as well as offering a form of isolation between processes. Scientific workflows are ideal to chain containers into data analysis pipelines to sustain reproducible science. In this manuscript we review the different approaches to use containers inside the workflow tools Nextflow, Galaxy, Pachyderm, Luigi, and SciPipe when deployed in cloud environments. A particular focus is placed on the workflow tool’s interaction with the Kubernetes container orchestration framework.