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General Information

Nextflow is a programming language used to code computational pipelines for multi-step data analyses and is particularly popular in the bioinformatics field. With Nextflow, you can run scientific pipelines in multi-platform and multi-cloud environments without changing the underlying pipeline code and these pipelines can be easily shared with the scientific community. We will use the Nextflow DSL2 syntax, which makes it easier to write well-structured modular code.

In this course you will learn to:

• Write Nextflow DSL2 scripts
• Develop Nextflow DSL2 workflows
• Run Nextflow DSL2 pipelines
• Develop Nextflow DSL2 modules and subworkflows
• Pass command line arguments to Nextflow
• Work with Nextflow configurations

Who: The course is aimed at graduate students, undergraduate students, summer students, postdoctoral fellows and any other researcher and it is intended for those who want to learn how to develop Nextflow pipelines. Some reasons Nextflow is popular include its provision of good parallelization, scalability, structure/compartmentalization, ability to resume failed jobs, and portability across a range of run-time environments (e.g. localhost, SLURM, GCP, AWS, Kubernetes). You don't need to have any previous knowledge of Nextflow or the tools that will be presented at the workshop but you should have basic bash skills to succeed in this course. In this class, we will use the Nextflow programming language to develop a simple bioinformatics pipeline.

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

When: Dec 6, 2022. Add to your Google Calendar.

Requirements: We assume ability to login to the JAX Sumner cluster, familiarity with bash, and basic understanding of one scripting or programming language (e.g. Python, Java, R, PHP, JavaScripts, bash scripting etc.). 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 susan.mcclatchy@jax.org or olaitan.awe@jax.org for more information.

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

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Surveys

Please be sure to complete this survey after the workshop.

Post-workshop Survey

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Schedule

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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 learning 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.