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

Ola Spjuth, Marco Capuccini, Matteo Carone, Anders Larsson, Wesley Schaal, Jon Ander Novella, Oliver Stein, Morgan Ekmefjord, Paolo Di Tommaso, Evan Floden, Cedric Notredame, Pablo Moreno (+5 others)
2021 F1000Research  
Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible analyses. In this article, we review a number of approaches to using containers as implemented in the workflow tools Nextflow, Galaxy, Pachyderm,
more » ... Kubeflow, 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.
doi:10.12688/f1000research.53698.1 fatcat:qy3gnqbsavcctctanch25ukgie