Webinar: Workflow Management Using Snakemake

March 27, 2020 | Virtual

10am Pacific | 11am Mountain | 12noon Central | 1pm Eastern (DST)

Webinar Materials:

Snakemake Tutorial

Webinar Recording

Webinar Recording of Snakemake for an RNA-seq workflow

About this Webinar:

From where and how to get data for your analysis, to where and how to treat the outputs, workflow managers can help you achieve better scientific reproducibility and scalability. In this webinar, University of Arizona graduate student Sateesh Peri demonstrates Snakemake, an open source workflow management tool. Sateesh first identifies use cases where workflow managers are helpful for automation so that you can understand Snakefile components, such as the rules, inputs, outputs and actions. Then he leads us through how to write and run a Snakefile in CyVerse VICE (Visual and Interactive Compute Environment). Once you learn to properly use Snakemake (or similar workflow management tools), keeping track of and sharing your work becomes second nature, not only saving you time whenever you need to re-run all or part of an analysis but helping you reduce errors that naturally get introduced whenever a non-automated activity is done (i.e., you're a human, not a bot!).

About the Presenter: 

Sateesh Peri, Snakecharmer
Sateesh Peri

Sateesh Peri is a PhD candidate in Eric Lyon’s lab at the University of Arizona and also works at CyVerse as a graduate intern. His primary research focus is on identification and characterization of long non-coding RNAs (lincRNAs); in his spare time, Sateesh likes learning and teaching computational skills to biologists (which is why we love working with him at CyVerse!). He is an open-science evangelist and an active instructor for Data Carpentry and for CyVerse's Foundational Open Source Skills (FOSS) and Container Camp.