Wratten, L., Wilm, A., Göke, J. (2021). Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nature Methods, 18(10), 1161–1168. https://doi.org/10.1038/s41592-021-01254-9
Abstract:
The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not just for experiments, but also for computational analysis. However, transforming data into information involves running a large number of tools, optimizing parameters, and integrating dynamically changing reference data. Workflow managers were developed in response to such challenges. They simplify pipeline development, optimize resource usage, handle software installation and versions, and run on different compute platforms, enabling workflow portability and sharing. In this Perspective, we highlight key features of workflow managers, compare commonly used approaches for bioinformatics workflows, and provide a guide for computational and noncomputational users. We outline community-curated pipeline initiatives that enable novice and experienced users to perform complex, best-practice analyses without having to manually assemble workflows. In sum, we illustrate how workflow managers contribute to making computational analysis in biomedical research shareable, scalable, and reproducible.
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Funding Info:
This research is supported by core funding from: Agency for Science, Technology and Research
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This research / project is supported by the National Medical Research Council - Individual Research Grant funding scheme
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This research / project is supported by the Agency for Science, Technology and Research - Singapore International Pre-Graduate Award (SIPGA)
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This research / project is supported by the Australian Department of Foreign Affairs and Trade - New Colombo Plan Scholarship
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Description:
This version of the article has been accepted for publication, after peer review (when applicable) and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: https://doi.org/10.1038/s41592-021-01254-9