Snakemake is a powerful tool for keeping track of data dependencies and to automate data analysis pipelines. In this episode of Code Club, Pat Shares how to install snakemake, convert a driver script to a simple Snakemake file, troubleshoot problems, create rules, use parameters, and test snakemake files. The overall goal of this project is to highlight reproducible research practices using a number of tools. The specific output from this project will be a map-based visual that shows the level of drought across the globe.
You can find my blog post for this episode at https://www.riffomonas.org/code_club/2022-09-15-snakemake.
#snakemake #conda #bash #R #Rstats
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0:00 Introduction
3:30 Our first Snakemake rule
6:41 Installing snakemake with conda/mamba
9:33 Testing snakefile with --dry-run or -np
18:43 Creating and using a targets rule
21:13 Running snakefile
25:08 Visualizing the DAG
27:49 Cleaning up