Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis


This paper is published in Data Science and Engineering, to appear in special issue “HPC-enabled Modelling for Big Data Problems in Life, Socio-Economical and Physical Sciences“. The Common Workflow Language is a core part of the Workflows component of BioExcel.

Abstract

Information integration and workflow technologies for data analysis have always been major fields of investigation in bioinformatics. A range of popular workflow suites are available to support analyses in computational biology. Commercial providers tend to offer prepared applications remote to their clients. However, for most academic environments with local expertise, novel data collection techniques or novel data analysis, it is essential to have all the flexibility of open source tools and open source workflow descriptions.

Workflows in data-driven science such as computational biology have considerably gained in complexity. New tools or new releases with additional features arrive at an enormous pace, new reference data or concepts for quality control are emerging. A well-abstracted workflow and the exchange of the same across work groups has an enormous impact on the efficiency of research and the further development of the field. High-throughput sequencing adds to the avalanche of data available in the field; efficient computation and, in particular, parallel execution motivate the transition from traditional scripts and Makefiles to workflows.

We here review the extant software development and distribution model with a focus on the role of integration testing and discuss the effect of Common Workflow Language (CWL) on distributions of open source scientific software to swiftly and reliably provide the tools demanded for the execution of such formally described workflows. It is contended that, alleviated from technical differences for the execution on local machines, clusters or the cloud, communities also gain the technical means to test workflow-driven interaction across several software packages.

Citation

Möller, Steffen; Prescott, Stuart W.; Wirzenius, Lars; Reinholdtsen, Petter; Chapman, Brad; Prins, Pjotr; Soiland-Reyes, Stian; Klötzl, Fabian; Bagnacani, Andrea; Kalaš, Matúš; Tille, Andreas; Crusoe, Michael R. (2017): Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis. Data Science and Engineering. https://doi.org/10.1007/s41019-017-0050-4

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