Proposed chapter order

[lachlandeer]

Preface

• [x] Whats there without install guide

Part 0

• [ ] Motivation
• [x] Project Structure

Part I - Workflow Basics with Snakemake

After this we can run everything

• [x] Initial Steps / First Rule + Execution
• [x] Mutliple Rules
• [x] Target Rules

Part II - Minimizing Repititon + Simplifying XX

Making workflow more "powerful"

• [x] Wildcards
• [x] Expand (incl. multiple wildcards)
• [x] Glob_wildcards

Part III - Bringing Outputs Together

Apply concepts from Part II to get an end product

• [x] From Regression Results to Tables
• [x] One rule to rule them all
• [x] From Tables and Figs to Papers + Slides

Part IV - Optional Extras, but Useful? (written soonish - but not now)

• [ ] Log Files
• [ ] Params (i.e. Solow's constant?!)
• [ ] Self Documenting Help
• [ ] Splitting Workflow into multiple Snakefiles

Part V - Getting Boxy (not written anytime soon)

• [ ] renv for package control
• [ ] docker containers

Appendix

• [x] Install Guide
• [ ] DAGs (if we want boring details)

[lachlandeer]

We also need a chapter on visualizing the workflow (DAGS, filesgraphs etc..)

proposed location: Part 4, before log files?

thoughts @bergmul ?

[bergmul]

Agreed, beginning of Part 4 looks good.

[bergmul]

Replaces #3

[bergmul]

We also shouldn't forget to put Parts 4 and 5 into TBA status. Should we save the current state in a different branch, in a version of the master branch or in a _backup folder on the master branch. Thoughts, @lachlandeer?