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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
do declared inputs trigger reruns and failed writers preserve trusted finals file-contract-audit-guide.md make file-contract-audit
how do local, CI, and scheduler policy differ profile-audit-guide.md proof-guide.md
does a module expose config, paths, and policy at its caller boundary module-interface-audit-guide.md make module-interface-audit
did a performance change remove work without removing guarantees performance-diagnostics-audit-guide.md make performance-diagnostics-audit
does a scheduler profile preserve declared resources and workflow meaning scheduler-policy-audit-guide.md make scheduler-policy-audit
do local, CI, and scheduler contexts preserve the same workflow meaning context-invariance-audit-guide.md make context-invariance-audit
does discovery expose the intended modules without hidden coupling discovery-integrity-audit-guide.md make discovery-integrity-audit
does a published bundle preserve its downstream compatibility promises publish-compatibility-audit-guide.md make publish-compatibility-audit
does software identity participate honestly in rebuild decisions software-boundary-audit-guide.md make software-boundary-audit
what does this workflow produce and why does the domain matter domain-guide.md walkthrough-guide.md

Public project-doc set

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.