Deep Dive Snakemake Capstone Docs

Guide Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  guide["Capstone docs"]
  section["Docs"]
  page["Deep Dive Snakemake Capstone Docs"]
  proof["Proof route"]

  family --> program --> guide --> section --> page
  page -.checks against.-> proof

flowchart LR
  orient["Read the guide boundary"] --> inspect["Inspect the named files, targets, or artifacts"]
  inspect --> run["Run the confirm, demo, selftest, or proof command"]
  run --> compare["Compare output with the stated contract"]
  compare --> review["Return to the course claim with evidence"]

Use this shelf when the question is about the executable Snakemake capstone repository itself: public file contracts, review bundles, repository architecture, profile drift, or safe extension. These pages are not another first-contact route into the course. They are the stable public documentation set for the reference repository that the course points to.

Use this shelf when

• you are already inside the capstone repository or one of its saved review bundles
• a course page sends you to a repository-facing document rather than to a lesson
• you need the repository explanation of a file contract, bundle route, or profile surface

Do not use this shelf when

• you still need the concept introduced for the first time
• you need help choosing which course module or support page to read next
• you are browsing because the repository feels large instead of because the question is specific

Choose the document by question

If the question is...	Start here	Then use
what does this repository promise and how should I enter it	walkthrough-guide.md	proof-guide.md
which outputs are safe for downstream trust	file-api.md	publish-review-guide.md
what claim does a bundle or route actually prove	proof-guide.md	tour.md
which repository layer owns this change	architecture.md	extension-guide.md
how do local, CI, and scheduler policy differ	profile-audit-guide.md	proof-guide.md
what does this workflow produce and why does the domain matter	domain-guide.md	walkthrough-guide.md

Public project-doc set

• architecture.md for repository layers, ownership, and review boundaries
• domain-guide.md for the capstone’s domain story and output meaning
• extension-guide.md for safe repository evolution
• file-api.md for the downstream-facing file contract
• profile-audit-guide.md for execution-policy review
• proof-guide.md for claim-to-evidence routing
• publish-review-guide.md for downstream trust review
• tour.md for the executed repository proof bundle
• walkthrough-guide.md for the bounded first pass

Naming crosswalk

These exported pages use lowercase generated names. Inside the capstone repository, the source documents appear under docs/ with uppercase filenames such as docs/file-api.md.

Good stopping point

Stop when you can name the single project doc that owns the current repository question. If you are still opening several documents at once, the question is probably still too broad.