Workflows with Nextflow

University of Edinburgh

Online

31 May - 2 Jun 2022

9:30 - 16:30

Instructors: Graeme Grimes

Helpers: Murray Wham, Breeshey Roskams-Hieter, Jesko Wagner

Overview

Workflows with Nextflow

This lesson is a three day introduction to the workflow manager Nextflow, and nf-core, a community effort to collect a curated set of analysis pipelines built using Nextflow.

Nextflow enables scalable and reproducible scientific workflows using software enviroments like conda. It allows the adaptation of pipelines written in the most common scripting languages such as Bash, R and Python. Nextflow is a Domain Specific Language (DSL) that simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters.

This lesson also introduces nf-core: a framework that provides a community-driven, peer reviewed platform for the development of best practice analysis pipelines written in Nextflow.

This lesson motivates the use of Nextflow and nf-core as a development tool for building and sharing computational pipelines that facilitate reproducible (data) science workflows.

Ed-DaSH

Ed-DaSH is a Data Science training programme for Health and Biosciences. The team has developed workshops using The Carpentries platform on the following topics. See workshops for dates and registration details. All workshops will be delivered remotely.

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: 31 May - 2 Jun 2022. Add to your Google Calendar.

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 (listed below).

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.

Contact: Please email for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Surveys

Please be sure to complete the workshop survey (can be completed before you attend).

Ed-DaSH Survey

Schedule

The lesson taught in this workshop is being piloted and a precise schedule is yet to be established.

Day 1 : 31st May 2022 (9:30 - 16:30)

Lessons
Introduction to Nextflow	Getting Started with Nextflow
	Workflow parameterization
	Channels
	Processes 1/2
Breaks
Morning	10:30 - 10:45
Lunch	12:30 - 13:30
Afternoon	15:00 - 15:15

Day 2 : 1st June 2022 (9:30 - 16:30)

Lessons
Introduction to Nextflow	Operators
	Workflow
	Nextflow Configuration
	Reporting
Breaks
Morning	10:30 - 10:45
Lunch	12:00 - 13:00
Afternoon	15:00 - 15:15

Day 3 : 2nd June 2022 (9:30 - 16:30)

Lessons
Introduction to Nextflow	Checkpointing and Caching
	Simple RNA-Seq pipeline
	Deploying nf-core pipelines
Breaks
Morning	10:30 - 10:45
Lunch	12:00 - 13:00
Afternoon	15:00 - 15:15

Setup

To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have the tool you are learing up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

Please check the “Setup” page of the lesson site for instructions to follow to obtain the software and data you will need to follow the lesson.