Module 00: Orientation and Study Practice

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Orientation"]
  page["Module 00: Orientation and Study Practice"]
  capstone["Capstone evidence"]

  family --> program --> section --> page
  page -.applies in.-> capstone

flowchart LR
  orient["Orient on the page map"] --> read["Read the main claim and examples"]
  read --> inspect["Inspect the related code, proof, or capstone surface"]
  inspect --> verify["Run or review the verification path"]
  verify --> apply["Apply the idea back to the module and capstone"]

This module exists to make the course legible before the first technical lesson starts. Deep Dive Snakemake is not a tour of commands. It is a course about truthful file contracts, explicit dynamic discovery, stable publish boundaries, operational policy that does not mutate workflow meaning, and the review habits that keep those claims honest.

Use this module when

• you want the course shape before committing to a reading path
• you need the shortest honest first session instead of browsing the whole shelf
• you want to know when the capstone helps and when it adds noise

Study rhythm

Keep the rhythm small and repeatable:

1. read until the current workflow question is clear
2. read a bounded cluster instead of the whole shelf
3. use the capstone only when it sharpens the current claim
4. stop once you can name one rule, one evidence surface, and one failure mode

Start here by question

If the question is...	Read this first
what journey does the whole course take	course-map.md
what should my first session look like	first-contact-map.md
how should I bridge from file contracts into scaling, publish trust, and operating contexts	mid-course-map.md
how should I re-enter the course for stewardship, migration, or trust review	mastery-map.md
which recurring terms matter before Module 01	Reference Glossary

What this course is trying to build

By the end of Deep Dive Snakemake, you should be able to:

• explain workflow behavior as a file-contract question rather than a CLI incantation
• keep checkpoints, profiles, and publish boundaries explicit and reviewable
• separate internal execution state from downstream trust surfaces
• judge when Snakemake still owns a concern and when another boundary should take over

First proof route

When you want one executable companion route without overcommitting to the capstone:

make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough

Use the walkthrough when the current module is clear enough that a repository specimen will help. Stay in the smaller lesson model when the capstone starts feeling larger than the concept you are studying.

Orientation files in this module

• course-map.md
• first-contact-map.md
• mid-course-map.md
• mastery-map.md

For stable vocabulary across the wider course, use Reference Glossary.