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bioRxiv · 10.1101/2024.06.28.601236

Maloja: simple and scalable Snakemake workflow orchestration in the cloud

Giustizia, J.·Hodgson, W.·Andress, C.·Bilkhu, S.·Macklin, J.·Kess, T.
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Abstract

As sequencing technologies have matured, bioinformatics tasks have become more complex, computationally demanding, and data intensive. Workflow management software has been developed to aid in simplifying the replicable chaining of complex bioinformatics jobs, and cloud computing has emerged as a potential solution to the computational demands of this work. However, the capacity to effectively deploy these resources is limited by the expertise required to implement these solutions. Here, we develop Maloja, an easily deployed cloud workflow orchestrator. This tool interprets existing scientific workflows written in Snakemake and deploys them in appropriately scaled AWS cloud resources. We test the utility of this new toolset using previously published and custom built Snakemake workflows for ecological genomics tasks, revealing how this tool can facilitate the use of cloud resources without prior cloud architecture expertise.

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Giustizia, J., Hodgson, W., Andress, C., Bilkhu, S., Macklin, J., Kess, T.. 2024-07-02. Maloja: simple and scalable Snakemake workflow orchestration in the cloud. https://doi.org/10.1101/2024.06.28.601236

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