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Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
- Source :
- Nature Methods. 18:1161-1168
- Publication Year :
- 2021
- Publisher :
- Springer Science and Business Media LLC, 2021.
-
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.
- Subjects :
- Biomedical Research
business.industry
Computer science
Computational Biology
Reproducibility of Results
Cell Biology
Biochemistry
Pipeline (software)
Workflow
Pipeline transport
Software portability
Reference data
Resource (project management)
Installation
Scalability
Software engineering
business
Molecular Biology
Biotechnology
Subjects
Details
- ISSN :
- 15487105 and 15487091
- Volume :
- 18
- Database :
- OpenAIRE
- Journal :
- Nature Methods
- Accession number :
- edsair.doi.dedup.....c0c49545a71067e6d3a0697c0925bb63