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Workflow Tour

Guide Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  guide["Capstone docs"]
  section["Docs"]
  page["Workflow Tour"]
  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"]

This tour is the executed proof route for the Snakemake capstone. It creates a bundle under artifacts/tour/reproducible-research/deep-dive-snakemake/ so you can inspect the workflow through declared rules, planned jobs, actual execution, published outputs, and the guides that explain what each surface should settle.

If the workflow has not been run yet, start with make walkthrough instead.

What the tour produces

  • list-rules.txt for the visible rule surface
  • dryrun.txt for the planned jobs before execution
  • run.txt for the real workflow execution log
  • summary.txt for Snakemake's post-run summary
  • verify.txt for publish verification output
  • discovered_samples.json for the durable checkpoint-resolved sample set
  • publish-manifest.json, summary.json, summary.tsv, provenance.json, and report/index.html for the published contract
  • copied guides for domain, walkthrough, publish trust, profile drift, proof routing, architecture, and extension ownership
  • bundle-manifest.json for the inventory of the tour bundle itself

Good first reading order

  1. README.md
  2. INDEX.md, DOMAIN_GUIDE.md, and WALKTHROUGH_GUIDE.md
  3. list-rules.txt and dryrun.txt
  4. discovered_samples.json, Snakefile, and dryrun.txt
  5. summary.txt, run.txt, and verify.txt
  6. publish-manifest.json, summary.json, summary.tsv, provenance.json, and report/index.html

That order keeps declared workflow meaning ahead of executed evidence, and executed evidence ahead of downstream trust.

When to step out of the tour

  • use PUBLISH_REVIEW_GUIDE.md when the question is specifically downstream trust
  • use PROFILE_AUDIT_GUIDE.md when the question is profile or executor drift
  • use PROOF_GUIDE.md when the question is determinism or route selection
  • use EXTENSION_GUIDE.md when you know the question but not the owning layer