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 Nov 08 2022 09.00 - Nov 10 2022 17.00 Workflows with Snakemake workshop, Nov 8 - 10 This course is intended for researchers who need to automate data analysis tasks for biological research using next-generation sequencing data, e.g., RNA-seq analysis, variant calling, bacterial genome assembly, and beyond. Register here
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 Nov 08 2022 09.00 - Nov 10 2022 17.00 Workflows with Snakemake workshop, Nov 8 - 10 This course is intended for researchers who need to automate data analysis tasks for biological research using next-generation sequencing data, e.g., RNA-seq analysis, variant calling, bacterial genome assembly, and beyond. Register here
Nov 08 2022 09.00 - Nov 10 2022 17.00 Workflows with Snakemake workshop, Nov 8 - 10 This course is intended for researchers who need to automate data analysis tasks for biological research using next-generation sequencing data, e.g., RNA-seq analysis, variant calling, bacterial genome assembly, and beyond.
