Tag Archives: snakemake

Slurm and Snakemake: a match made in HPC heaven

Snakemake is an incredibly useful workflow management tool that allows you to run pipelines in an automated way. Simply put, it allows you to define inputs and outputs for different steps that depend on each other, Snakemake will then run jobs only when the required inputs have been generated by previous steps. A previous blog post by Tobias is a good introduction to it – https://www.blopig.com/blog/2021/12/snakemake-better-workflows-with-your-code/. 

However, often pipelines are computationally intense and we would like to run them on our HPC. Snakemake allows us to do this on slurm using an extension package called snakemake-executor-plugin-slurm.

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snakeMAKE better workflows with your code

When developing your pipeline for processing, annotating and/or analyzing data, you will probably find yourself needing to continuously re-run it, as you play around with your code. This can become a problem when working with long pipelines, large datasets and cpu’s begging you not to run some pieces of code again.

Luckily, you are not the first one to have been annoyed by this and other related struggles. Some people were actually so annoyed that they created Snakemake. Snakemake can be used to create workflows and help solve problems, such as the one mentioned above. This is done using a Snakefile, which helps you split your pipeline into “rules”. To illustrate how this helps you create a better workflow, we will be looking at the example below.

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