Week 5: Pipeline Building and Automation

Learning goals

• Learn how to organize your project with a coherent directory structure
• Conceive your project as a pipeline
• Separate your code into smaller chunks (each one with inputs, transformations and outputs)
• Automate workflows and make them reproducible using make

Lecture

Laptop required!

• Tutorial (view slides, view complete tutorial)
• Check out the make cheatsheet!

Coaching session

• Work on your team goals for this course week (see coaching #4 on your workplan).

After the lecture

• Complete all after-class exercises for this week’s tutorial ( View, Download; right click - download file as)
• Watch (in this order…)
  • This is why you should automate the pipeline of your empirical research project
  • Four steps to automate & make reproducible your empirical research project
  • The content of the slides shown in the videos is available here.
• Read the building block “What are makefiles”
• Optional readings
  • Notes on Automating Your Pipeline
  • Revisit the slidedeck