Nextflow

The Jackson Laboratory

Online

Dec 6, 2022

9:00 am - 4:00 pm EST

Instructors: Olaitan Awe

Helpers: Michael Blanchard

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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:

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.


Surveys

Please be sure to complete this survey after the workshop.

Post-workshop Survey


Schedule

Tue Dec 6

9:00 Workshop overview and introductions
9:15 Getting Started with Nextflow
9:45 Nextflow scripting
10:45 Break
11:00 Nextflow DSL2 Example Pipeline
12:00 Lunch
1:00 Nextflow DSL2 Workflow Definition
1:45 Subworkflows
2:30 Break
2:45 Working with Nextflow Configurations
3:05 Nextflow Configuration Profiles
3:30 Running nf-core pipelines
4:00 Wrap-up
4:30 END

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:

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

Nextflow

You must use a JAX-owned computer. Please ask the IT help desk if you need help to download and install software. For Windows users, you need to have an ssh client on your laptop. Download and install MobaXterm (the free, home edition).