Snakemake Profiles

Last updated on 2023-08-02 | Edit this page

Estimated time: 12 minutes

Overview

Questions

  • How can we encapsulate our desired snakemake configuration?
  • How do we balance non-reptition and customizability?

Objectives

  • Write a Snakemake profile for the cluster
  • Run the amdahl code with varying degrees of parallelism with the cluster profile.

Snakemake Profiles

Snakemake has a provision for profiles, which allow users to collect various common settings together in a special file that snakemake examines when it runs. This lets users avoid repetition and possible errors of omission for common settings, and encapsulates some of the cluster complexity we encoutered in the previous module.

Not all settings should be in the profile. Users can choose which ones to make static and which ones to make adjustable. In our case, we will want to have the freedom to choose the degree of parallelism, but most of the cluster arguments will not change, and so can be static in the profile.

Write a Profile

Do the thing.

Run Snakemake

Throw the switch!

Challenge

Write a profile that allows you to choose a different partition, in addition to the level of parallelism.

The profile files can have variables taken from the rule file, and in particular can refer to resources from a rule.

Key Points

  • Snakemake profiles encapsulate cluster complexity.
  • Retaining operational flexibliity is also important.