Reference Glossary

Glossary Fit

flowchart TD
  directory["This directory"] --> glossary["Glossary"]
  glossary --> terms["Stable local terms"]
  terms --> reading["Reading and examples"]
  terms --> practice["Exercises and review"]
  terms --> proof["Capstone proof and discussion"]

flowchart TD
  pressure["Hit an unfamiliar term"] --> lookup["Open the glossary entry"]
  lookup --> confirm["Match the term to the local meaning"]
  confirm --> return["Return to the lesson or guide"]
  return --> reuse["Reuse the same wording in notes, code review, and proof"]

This glossary belongs to Reference in Deep Dive Snakemake. It keeps the language of this directory stable so the same ideas keep the same names across reading, practice, review, and capstone proof.

How to use this glossary

Read the directory index first, then return here whenever a page, command, or review discussion starts to feel more vague than the course intends. The goal is stable language, not extra theory.

Terms in this directory

Term	Meaning in this directory
Anti-Pattern Atlas	the recurring failure catalog for anti-pattern atlas, used to recognize defect shapes before they harden into local folklore.
Boundary Map	the routing surface for boundary map, used to find the right dependency, practice, or evidence path quickly.
Completion Rubric	the review surface for completion rubric, used to turn judgment into explicit keep, change, or reject calls.
Module Dependency Map	the routing surface for module dependency map, used to find the right dependency, practice, or evidence path quickly.
Practice Map	the routing surface for practice map, used to find the right dependency, practice, or evidence path quickly.
Repository Layer Guide	the durable vocabulary and review surface for repository layer guide, used to keep naming, scope, and proof expectations stable across the course.
Topic Boundaries	the durable rule surface for topic boundaries, used when a design or review decision needs stable language instead of intuition.