Workflows with Snakemake workshop, Nov 8 - 10

Overview

Researchers needing to implement data analysis workflows face a number of common challenges, including the need to organise tasks, make effective use of compute resources, handle any errors in processing, and document and share their methods. The Snakemake workflow system provides effective solutions to these problems. By the end of the course, you will be confident in using Snakemake to run real workflows in your day-to-day research.

Snakemake workflows are described by special scripts that define steps in the workflow as rules, and these are then used by Snakemake to construct and execute a sequence of shell commands to yield the desired output. Re-calculation of existing results is avoided where possible, so you can add or update input data, then efficiently generate an updated result. Workflows can be seamlessly scaled to server, cluster, grid and cloud environments without the need to modify the workflow definition.

This course is primarily intended for researchers who need to automate data analysis tasks for biological research involving next-generation sequence data, for example RNA-seq analysis, variant calling, CHIP-Seq, bacterial genome assembly, etc. However, Snakemake has many uses beyond this and the course does not assume any specialist biological knowledge. The language used to write Snakemake workflows is Python-based, but no prior knowledge of Python is required or assumed either. We do require that attendees must have familiarity with using the Linux command line (pipes, redirects, variables, …).

General Information

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: 8 - 10 November. 

Instructor: Tim Booth

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed.

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Schedule

Day 1 : 8th November (09:00 - 17:00)
Lessons
Introduction to Snakemake Running commands with Snakemake
Placeholders and Wildcards
Chaining Rules
How Snakemake plans what jobs to run
Breaks
Morning 10:30 - 10:45
Lunch 12:30 - 13:30
Afternoon 15:00 - 15:15
Day 2 : 9th November (09:00 - 17:00)
Lessons
Introduction to Snakemake - Cont. Processing lists of inputs
Handling awkward programs
Configuration workflows
Optimising workflow performance
Breaks
Morning 10:30 - 10:45
Lunch 12:30 - 13:30
Afternoon 15:00 - 15:15
Day 3 : 10th November (09:00 - 17:00)
Lessons
Introduction to Snakemake Input functions
Conda integration
Constructing a whole new workflow
Cleaning up
Breaks
Morning 10:30 - 10:45
Lunch 12:30 - 13:30
Afternoon 15:00 - 15:15

More information

Ed-DaSH homepage

Ed-DaSH contact