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Proof Matrix

Guide Fit

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> pressure["A concrete learner or reviewer question"]
  pressure --> guide["Proof Matrix"]
  guide --> next["Modules, capstone, and reference surfaces"]
flowchart TD
  question["Name the exact question you need answered"] --> skim["Skim only the sections that match that pressure"]
  skim --> crosscheck["Open the linked module, proof surface, or capstone route"]
  crosscheck --> next_move["Leave with one next decision, page, or command"]

Read the first diagram as a timing map: this guide is for a named pressure, not for wandering the whole course-book. Read the second diagram as the guide loop: arrive with a concrete question, use only the matching sections, then leave with one smaller and more honest next move.

This page maps the course's main claims to the commands and files that prove them.

Use it when you care about a concept but want the fastest evidence route.

Core Workflow Claims

Claim Command File surfaces
the capstone has a bounded first-pass reading route make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough course-book/capstone/index.md, artifacts/make/workflow-walkthrough/
the workflow exposes its public rule surface clearly make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough capstone/Snakefile, artifacts/make/workflow-walkthrough/list-rules.txt
dynamic discovery becomes explicit evidence instead of a hidden side effect make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour capstone/results/discovered_samples.json, capstone/publish/v1/discovered_samples.json
profiles change execution policy without changing workflow meaning make PROGRAM=reproducible-research/deep-dive-snakemake capstone-profile-audit capstone/profiles/, capstone/Makefile
promoted outputs are smaller than the full internal repository state make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour publish-review-guide.md, capstone/publish/v1/, capstone/results/

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Operational Claims

Claim Command File surfaces
the workflow validates configuration before execution make PROGRAM=reproducible-research/deep-dive-snakemake capstone-validate-config capstone/config/config.yaml, capstone/config/schema.yaml
the workflow can explain its plan before a run make PROGRAM=reproducible-research/deep-dive-snakemake capstone-wf-dryrun artifacts/make/workflow-walkthrough/dryrun.txt, capstone/workflow/rules/
the publish bundle can defend itself after execution make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-artifacts capstone/publish/v1/manifest.json, capstone/publish/v1/provenance.json
the publish boundary is reviewable as a durable contract make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-report publish-review-guide.md, artifacts/proof/reproducible-research/deep-dive-snakemake/verify/
the repository can prove itself through one stronger end-to-end route make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm capstone/Makefile, capstone/tests/
workflow incidents can be reviewed with narrower evidence than a full rewrite make PROGRAM=reproducible-research/deep-dive-snakemake capstone-selftest or make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour capstone/tests/selftest.sh, capstone/logs/, artifacts/tour/reproducible-research/deep-dive-snakemake/
the executed workflow tour is reviewable as evidence make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour artifacts/make/workflow-tour/, capstone-walkthrough.md

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Review Questions

Question Best first command Best first file
where should a new learner start in the capstone make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough course-book/capstone/index.md
what does this workflow claim it will build make PROGRAM=reproducible-research/deep-dive-snakemake capstone-wf-dryrun capstone/Snakefile
what exactly is public for downstream trust make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-artifacts publish-review-guide.md
which surface explains dynamic discovery honestly make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour capstone/workflow/rules/preprocess.smk
what would I inspect before migration make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm course-book/capstone/index.md

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Companion Pages

The most useful companion pages for this matrix are:

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