Automating data analyses with make: Writing rules in makefiles to improve reproducibility (CC019)
Channel: Riffomonas Project
Date: 23/07/2020

In this screencast tutorial, Pat Schloss shows how you can use GNU Make to keep track of dependencies and automate steps in a data analysis workflow. Today we'll write rules in a Makefile to automate our earlier steps of downloading files and aligning sequences. The improved automation and better tracking of dependencies will improve the reproducibility of our analysis. Being able to write these types of rules will be critical as we determine the degree to which inter- and intra-genomic variation limit the interpretation of amplicon sequence variants (ASVs; aka exact sequence variants or ESVs).

Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make. He then turns viewers loose to work through several activities to answer related questions and finishes by giving his solutions.

The accompanying blog post contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2020-07-23-automating-analysis.



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