Getting started with Snakemake

About this course | Before the session | About Snakemake  | Course material | Exercises

Exercise 0 - run your first snakefile

objective > setup > o1 > o2 > o3

In this Exercise, we will be taking our first steps with Snakemake. We will:
  • learn how to fetch (setup) and run a small Snakemake pipeline (o1)
  • understand the basic architecture of Snakemake files (o2)
  • get familiar with the output log (o3)

The pipeline that we will be running will fetch protein sequences from the UniProt database and align them using mafft. Graphically, we’ll be doing this:

ex0_workflow_complete

wget: fetches files from the web directly; cat: fuses 2 or more files together; mafft: aligns all sequences in a file

Don’t worry if you don’t understand exactly what it does and how…

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