Relationship to Theory and Implementation

This usage manual owns operator commands, stage handoffs, artifact gates, and deployment checklists. It does not derive statistical methods.

Need	Read
DMP detection math, assumptions, limitations	Theory book — start with ch.03
How this product sits on GoliathApp and the two utilities	Dependency direction
Start SamplePrep, release, enroll, process packs	Operators
Parameter keys used by SamplePrep QC	Sample prep and QC and Analyte profiles
Align path matrix	Alignment engines

docs/implementation/, docs/reference/, and docs/deployment/ are not in this tree. Where an older chapter links there, use the operator guides and the code paths they name.

SamplePrep instances are started with methyl-study-start sample-prep-start. That command calls finalize_instance_context and writes the instance to the workflow database.

Staged validation on a workstation uses methyl-workflow-run from the methyl-gateway wheel (GoliathApp), with a DomainProgram, a pipeline profile, and a /work study manifest. This repository does not declare that console script. See Orchestration.

Legacy orchestration: methyl-validation --stability/--freeze/--model and the file-queue subcommands (plan-runs, run-task) remain for transitional scripts and recovery.

Repo vs /work: profiles and programs live in the git repo. project_*.json and run artifacts live under /work. See Project config and layout.