Skip to content

Capstone Walkthrough

Guide Fit

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> pressure["A concrete learner or reviewer question"]
  pressure --> guide["Capstone Walkthrough"]
  guide --> next["Modules, capstone, and reference surfaces"]
flowchart TD
  question["Do you need a first pass or a deeper review?"] --> route["Choose one walkthrough depth"]
  route --> inspect["Read the matching guide and artifact"]
  inspect --> next_move["Stop when one honest workflow story is visible"]

Read the first diagram as a timing map: this page gives the capstone a teaching route, not just a repository map. Read the second diagram as the rule: choose one walkthrough depth, read the matching guide and artifact, then stop when one honest workflow story is visible.

First pass versus deeper pass

  • First pass: use the learner-first route when you need one bounded workflow story from file contract to executed proof.
  • Deeper pass: use the longer routes only when the question changes from entry to policy, publish, or stewardship review.

30-minute first pass

  1. Read Capstone Guide.
  2. Run make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough.
  3. Read the copied Snakefile, rule files, list-rules.txt, and dryrun.txt in that order.
  4. Read Capstone File Guide.
  5. Use Capstone Review Worksheet to record what is visible before execution.

Goal: leave with a clear picture of what the workflow claims to build, where dynamic discovery is declared, and which files are public contracts.

Executed workflow pass

Use this only after the first pass is clear.

  1. Run make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour.
  2. Read the executed proof bundle.
  3. Compare the bundle's publish artifacts against FILE_API.md.
  4. Follow one rule family back into workflow/rules/.

Goal: see how the planned workflow becomes executed evidence without losing contract clarity.

Good stopping point

Stop when you can explain one complete workflow story:

  • the public contract you started from
  • the rule or artifact that makes the contract visible
  • the next command that would strengthen the claim only if needed

If you cannot tell that story yet, do not widen the walkthrough. Repeat the smaller pass.