Intro to Snakemake

GitHub Classroom Assignment

We’ll be going through the Snakemake Basics: An example workflow tutorial

Installing the Data

curl -L https://api.github.com/repos/snakemake/snakemake-tutorial-data/tarball -o snakemake-tutorial-data.tar.gz
tar --wildcards -xf snakemake-tutorial-data.tar.gz --strip 1 "*/data"

Tip

There’s a rule commented out in the Snakefile that will do this automatically

Criteria

To complete the assignment the following will be worth 2 points each:

1. Generate A.bam - snakemake --cores 1 mapped_reads/A.bam
2. Dry run of A.bam - snakemake -np mapped_reads/A.bam
3. Using snakefmt to format the code - snakefmt --check
4. Dry run of the entire workflow - snakemake -n
5. Full workflow runs - snakemake --cores 2
6. Bonus: Tests pass - pytest