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Command Guide

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Capstone"]
  page["Command Guide"]
  capstone["Capstone evidence"]

  family --> program --> section --> page
  page -.applies in.-> capstone
flowchart LR
  orient["Orient on the page map"] --> read["Read the main claim and examples"]
  read --> inspect["Inspect the related code, proof, or capstone surface"]
  inspect --> verify["Run or review the verification path"]
  verify --> apply["Apply the idea back to the module and capstone"]

Read the first diagram as a timing map: this page is for command choice, not for reading the whole capstone. Read the second diagram as the rule: choose the command layer that matches the current job, run the smallest honest command, then escalate only if the question changes.

Deep Dive Snakemake has three command layers: repository root, program directory, and capstone directory. The layers exist so you do not have to guess where a command belongs.

Choose the command layer

If you need... Use this layer Why
one stable entrypoint from the repository root repository root consistent commands across all programs
course-local commands while staying inside the program programs/reproducible-research/deep-dive-snakemake/ a smaller surface than the repo root
the raw executable workflow repository capstone/ direct access to the workflow itself

Start by job, not by directory

If the job is... Start here Do not start with
first-pass capstone reading make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm
executed workflow review make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour make PROGRAM=reproducible-research/deep-dive-snakemake proof
publish-boundary verification make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-report make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm
execution-policy comparison make PROGRAM=reproducible-research/deep-dive-snakemake capstone-profile-audit random make PROGRAM=reproducible-research/deep-dive-snakemake ... exploration
strongest final confirmation make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough

Repository root

Use root-level commands when you want one entrypoint that works across programs.

  • make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough
  • make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour
  • make PROGRAM=reproducible-research/deep-dive-snakemake proof
  • make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-report
  • make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm

Program directory

Use programs/reproducible-research/deep-dive-snakemake/ when you want the course-local surface.

  • make capstone-walkthrough
  • make capstone-tour
  • make proof
  • make capstone-profile-audit
  • make capstone-confirm

Capstone directory

Use capstone/ when you want the raw reference workflow.

  • make walkthrough
  • make verify
  • make tour
  • make verify-report
  • make profile-audit
  • make confirm

Good stopping point

Stop when you can explain why the chosen command layer is proportionate to the current question. If the layer still feels too large, step down one layer before opening more targets.