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All of Us Pipelines

All of Us Analysis Workflows
Reproducible pipelines for community review, reuse, and adaptation.

This section contains workflows used in support of genomic analyses for the All of Us Research Program. We release these pipelines to support reproducibility and to make methods easier for the community to review, reuse, and adapt.

Pipeline Overview​

The following All of Us analysis areas are currently available or in-progress in the WARP repository:

Versioning and Changelogs​

Version note: All of Us workflow versions (for example, aou_9.0.0) align to the release in which a pipeline was used.

Pipeline WDLs in this area include companion changelog files (for example, *.changelog.md). The All of Us versioning convention (for example, aou_9.0.0) reflects the release version in which the pipeline was used.

Docker Images​

Container note: Docker images for these workflows are maintained in the sister repository warp-tools.

Several Docker images used by these workflows are maintained in the sister repository warp-tools. These Dockers were created to ensure consistency across pipeline runs.

What to Expect​

Community expectations: Some analyses are still in progress, pipelines are provided as-is, and suggestions are welcome.
  • Some analyses in this folder are still in progress.
  • Pipelines are provided as-is. These pipelines are designed to run in a Cromwell environment such as Terra.
  • We welcome suggestions and improvement ideas from the community. Please post to warp-issues.