Training track for Nextflow Summit 2025
This training workshop is intended as a “getting started” course for students and early-career researchers who are completely new to Nextflow.
By the end of the course you will be able to:
Learn Core Nextflow Concepts
Understand the Nextflow language, essential commands, and structure, allowing users to build and run simple workflows locally.
Engage with nf-core Resources
Discover the benefits of nf-core, including how to access, customize, and utilize community-built pipelines for various bioinformatics tasks.
Hands-on Exercise
Create pipelines using the nf-core template, covering best practices for version control, collaboration, and troubleshooting common errors.
Overview
This training workshop is intended as a “getting started” course for students and early-career researchers who are completely new to Nextflow. It aims to equip participants with foundational knowledge and skills in three key areas: (1) understanding the logic of how data analysis workflows are constructed, (2) Nextflow language proficiency and (3) command-line interface (CLI) execution.
Additionally, participants will learn to leverage the resources and capabilities offered by the nf-core initiative and the Seqera platform.
- Audience: Beginners (no prior Nextflow experience)
- Required: basic experience with command line and scripting Some bioinformatics concepts will be introduced
By the end of the workshop, participants will be well-prepared for tackling the next steps in their journey to develop and apply reproducible workflows for their scientific computing needs. Additional study-at-home materials will be provided for them to continue learning and developing their skills further.
Getting Started with Nextflow
Based on Hello Nextflow, our popular intro-level tutorial for learning how to develop pipelines with Nextflow.
Participants will be guided through hands-on, goal-oriented exercises that will allow them to develop the following skills:
- Use core components of the Nextflow language to construct simple multi-step workflows effectively.
- Launch Nextflow workflows locally, navigate output directories to access results, interpret log outputs for insights into workflow execution, and troubleshoot basic issues that may arise during workflow execution.
This tutorial is entirely domain-agnostic and does not assume any prior scientific knowledge.
Nextflow for Science
Based on Nextflow for RNAseq, a step-by-step tutorial demonstrating how to develop a pipeline for processing bulk RNAseq data.
In this half-day session, participants will learn how to apply the concepts and mechanisms they learned on the first day to an actual scientific use case. This will enable them to make the connection between the introductory examples and how to solve real scientific analysis problems with Nextflow.
This tutorial assumes some basic knowledge of RNAseq data formats and tools. Pre-read materials will be provided ahead of the course, and critical information will be recapitulated at the start of the tutorial as necessary.
Collaborative pipeline development with nf-core and Seqera Platform
In this final half-day session, participants will learn to use open-source pipelines and tools from the nf-core project, as well as Seqera platform to take their pipeline development to the next level of collaboration and reproducibility within their team or organization.