Reference Glossary¶
Use this glossary when the workflow idea is already recognizable but the support-page language still needs to be pinned down. This page keeps the course’s review and support vocabulary stable across modules, reference pages, and capstone routes.
This is not the place to memorize every Snakemake term. It is the place to stabilize the course’s support language so review decisions do not drift into vague administrative prose.
How to use this glossary¶
Open it when a term matters for a real decision, such as:
- where a change belongs
- which page owns the question
- which proof route should answer the claim
- what kind of judgment a page is asking you to make
Do not read it like a dictionary to finish. Read it when a term is blocking a judgment.
Why this glossary exists¶
This page is deliberately smaller than the course-wide technical vocabulary.
It exists to stabilize the support shelf itself:
- which review page to open
- what kind of judgment that page supports
- why one support route is better than another for the current question
- what "complete," "reviewable," or "boundary" means in this course
That keeps the support layer from becoming fuzzy even when the course gets large.
Terms in this directory¶
| Term | Meaning in Deep Dive Snakemake | Use it when... |
|---|---|---|
| Anti-Pattern Atlas | a symptom-led catalog of recurring workflow mistakes | you recognize the smell before you remember the lesson |
| Boundary Review Prompts | a page of sharper keep, change, or reject questions tied to boundaries | a review feels blurry and you need a clearer judgment |
| Completion Rubric | the page that separates recognition from real command | you think you are done and want an honest standard |
| Module Dependency Map | the reading-order map showing which modules support later ones | you need to know whether to go forward or backward |
| Practice Map | the crosswalk from modules to exercises, retained evidence, and proof loops | you know the concept and need the next practice move |
| Review Checklist | the page that turns a workflow concern into a bounded review | you want a trust judgment rather than a vibe |
| Self-Review Prompts | short prompts for recall, prediction, and plain-language explanation | you want to test whether the idea is actually yours yet |
| Topic Boundaries | the page that separates core course material from supportive or outer-boundary material | you are unsure whether the course should answer this question at all |
Two terms that learners often blur¶
Boundary¶
In this course, a boundary is a place where responsibility should stay explicit:
- workflow meaning versus policy
- internal run state versus published trust
- visible rule contract versus hidden helper behavior
If a boundary becomes blurry, the workflow may still run while becoming harder to review.
Proof route¶
A proof route is the smallest file, command, or saved bundle that can honestly answer the current claim.
It is not just "some command to run." It is the route whose size is proportionate to the question.
What this glossary is not¶
This page is not the place to define every technical Snakemake concept in the course.
Use the module glossaries for module-local terms and the capstone glossary for repository-specific support language.
Good stopping point¶
Leave this page when:
- the term is clear enough to support the decision in front of you
- you know which page should answer the next question
- the vocabulary is no longer the thing making the judgment fuzzy