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SUMMARY: In the era of large data, the cloud is increasingly used as a computing environment, necessitating the development of cloud-compatible pipelines that can provide uniform analysis across disparate biological datasets. The Warp Analysis Research Pipelines (WARP) repository is a GitHub repository of open-source, cloud-optimized workflows for biological data processing that are semantically versioned, tested, and documented. A companion repository, WARP-Tools, hosts Docker containers and custom tools used in WARP workflows.AVAILABILITY AND IMPLEMENTATION: The WARP and WARP-Tools repositories and code are freely available at and , respectively. The pipelines are available for download from the WARP repository, can be exported from Dockstore, and can be imported to a bioinformatics platform such as Terra.