GoliathOmics documentation¶
This repository is the genomics product. It specializes GoliathApp and calls GoliathAlign and MethylExtractor as standalone utilities. GoliathApp does not reference this product. The two utilities do not reference GoliathApp or GoliathOmics. See Dependency direction.
GoliathWorkflow is not a run path.
Release 2026.10.27 follows the tag, assemble, and deploy process in operators/release.md.
Sections¶
| Section | What it covers |
|---|---|
| operators | Start a SamplePrep instance, release and enroll workers, process packs |
| usage | How to run studies, SamplePrep, and validation |
| theory | Statistical and biological background |
| architecture | Dependency direction and sample-prep tooling |
| regulatory | SaMD and operational controls |
| research | Notes and assessments. These are not the operator contract. |
| contracts | Features required from GoliathAlign and MethylExtractor |
| deploy-targets | Deploy profiles |
| rollouts | Deploy reporting |
The MkDocs Material site is published from main at https://goliath-research.github.io/GoliathOmics/. Pull request CI builds it and does not deploy. Local preview from the repository root: python -m pip install -r requirements-docs.txt && mkdocs serve.
Ownership¶
| Concern | Owner |
|---|---|
Gateway wheel, engine DDL, goliath-cfg, shared claim protocol |
GoliathApp. The installed console script is methyl-gateway. This repo does not contain workflow_engine/rest/. |
Science packages, DomainPrograms, profiles, analytes, methyl_worker handlers, science seeds |
GoliathOmics |
| Alignment image and binaries | GoliathAlign (GOLIATH_ALIGN_*; MOJO_ALIGN_* is a one-cycle alias) |
| Linear BAM to HDF5 | MethylExtractor |
Names¶
Older chapters say MethylPipeline. That name means this genomics product. methyl-* remains the CLI alias for one release cycle (methyl-workflow-run, methyl-cfg, methyl-study-start). Platform commands use the goliath prefix and are documented with GoliathApp.
Older chapters say mojo-align. That repository is GoliathAlign.
Chapters that link to docs/implementation/, docs/reference/, docs/deployment/, or docs/plans/ describe documents that are not in this tree. The operator guides and the code are the current contract. Theory and research notes stay as background.