Description
Instructors: Geraldine Van der Auwera
This hands-on workshop introduces researchers to using Nextflow pipelines from the nf-core project (https://nf-co.re/) for reproducible and scalable omics analyses. Through guided exercises and group activities, you will learn how to find, evaluate, and run community-curated nf-core workflows, interpret outputs and execution logs, and address common challenges encountered in real-world analyses. You will leave with the skills and confidence to apply nf-core pipelines effectively to your own scientific questions.
Competency requirements: Participants are expected to be familiar with basic command-line usage and general scripting concepts (as found in Python, R etc). Scripting proficiency is not required.
Note: This workshop covers different material from the Nextflow workshop held at ASHG in 2025.
Session Details:
- Part 1 will consist of instructor-led hands-on exercises in which participants will learn and practice basic usage of nf-core resources using a simple demonstration pipeline. [60 minutes]
- Part 2 will consist of a group activity in which participants will team up based on their domain interests (e.g. genomics, transcriptomics, proteomics etc) to find and apply a pipeline to a specific scientific question. This will provide them with the opportunity to practice applying the skills they learned in Phase 1 to a real-world example. [50 minutes, with 10-minute mid-point break]
- Part 3 will consist of a brief discussion followed by instructor-led hands-on exercises in which participants will learn to address key challenges related to real-world application of the domain-specific pipelines they evaluated. This will cover common challenges such as managing and formatting inputs, identifying and solving computational bottlenecks, and troubleshooting data quality issues. [60 minutes]
Learning Objectives:
- Summarize the general structure, input requirements and usage of nf-core pipelines
- Launch and manage pipeline execution
- Retrieve and parse outputs and execution logs
- Identify and test-run domain-specific pipelines
- Evaluate the appropriateness of a pipeline for addressing a specific scientific question
- Identify and address key challenges for real-world application of nf-core pipelines
Additional Information:
Intermediate level; Participants must have a Github account and verify they are able to access Github Codespaces OR have a local installation of the materials. The training materials will be open-source and freely available on the Nextflow training portal. These will become available in Fall 2026.
