Capstone Glossary

Use this page when the Snakemake capstone routes start sounding interchangeable. The goal is to keep workflow meaning, operating policy, publish trust, and stewardship review separate while you are inside the executable repository.

This glossary exists to keep capstone language from flattening into "run something bigger."

How to use this glossary

Open this page when two capstone terms sound close enough that your route choice is getting blurry.

It is most useful when:

• two proof routes sound similar but answer different questions
• policy language starts getting confused with workflow meaning
• publish review language starts drifting into general execution language
• you need to restate a capstone term in plainer words before continuing

Do not read it as a full capstone manual. Read it when vocabulary is blocking route choice.

Why this glossary exists

The capstone is larger than the module examples. That makes sloppy vocabulary more dangerous here.

This glossary keeps a few important distinctions stable:

• orientation route versus execution route
• workflow contract versus operating policy
• publish boundary versus internal run state
• saved evidence versus general repository output
• stewardship review versus ordinary walkthrough

Terms in this directory

Term	Meaning here	Use it when...
walkthrough	the bounded first pass through the workflow repository before stronger executed proof	you need orientation, not full execution
tour	one executed workflow story with saved evidence	you need the repository to become concrete without escalating to stewardship
rule contract	the explicit input, output, and log relationship a rule is allowed to promise	you are judging workflow meaning rather than helper detail
discovery evidence	the durable artifact that records what dynamic discovery found	you need discovery to stay reviewable after execution
operating policy	executor, resource, and environment settings that change how the workflow runs without redefining its meaning	you are comparing local, CI, and scheduler contexts
semantic drift	a change that alters workflow meaning rather than only execution policy	you suspect a context or profile change is too strong
publish boundary	the downstream-facing output surface another person is allowed to trust	you are reasoning from the consumer side
saved evidence bundle	an exported artifact set that lets a reviewer inspect the workflow later	you need proof that survives after the run is gone
stewardship review	the stronger route used when a maintainer must judge the whole repository, not only one run	the question is about migration, drift, or long-lived trust

Three distinctions that matter most

Walkthrough versus tour

• walkthrough is for bounded first understanding
• tour is for one executed workflow story

If you need the first story of the repository, start with walkthrough. If you need execution evidence, move to tour.

Operating policy versus semantic drift

• operating policy changes how work runs
• semantic drift changes what the workflow means

Confusing those two is one of the fastest ways to misread profiles.

Publish boundary versus internal run state

• the publish boundary is what downstream users may trust
• internal run state supports execution, debugging, or review but is not itself the public contract

This distinction matters every time a learner is tempted to treat results/ as public.

Good stopping point

Leave this page when:

• the route terms are distinct again
• you can explain the current capstone question in plainer words
• you know which page or command should come next