Introduction to Workflows using Snakemake PART I

Date/Time

Date(s) - 05/12/2021
Time - 9:00 am PDT - 11:00 am PDT

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Description

Learn to create reproducible and scalable data analyses using the Snakemake workflow management system. Snakemake is a text-based workflow system in which workflows are defined in terms of rules that connect input and output files. Snakemake offers many desired features such as flexibility to scale without modification, integration with package manager Conda and container engine Singularity and compatibility with cloud computing.

This free two part workshop series will cover basics of Snakemake including setup, installation, building and running an example workflow along with discussion on advanced features such as customizing computational threads, use of config file and use of arbitrary parameters.

This workshop will be conducted remotely via Zoom. The workshop Zoom link will be emailed to participants after registration closes.

Participants should plan to fill out a brief survey before and after the workshop.

Instructors

Titus Brown (UC Davis/Common Fund Data Ecosystem)

Prerequisites

No prior experience is needed, although some familiarity with bash command-line computing is helpful.

Who is offering this?

This workshop is a pilot workshop offered by the Lab for Data Intensive Biology as part of the NIH Common Fund Data Ecosystem training and engagement program.

Contact

Please contact us at training@cfde.atlassian.net with any questions you have!

 

Bookings