Nextflow in Genomics 2025
Welcome to the 2nd Workshop & Hackathon of Nextflow In Genomics organized by the Institute of Genetic Epidemiology, Medical University of Innsbruck.
The aim of this workshop is to facilitate communication between researchers working on data analysis using Nextflow, especially in the area of Austria, Italy and Germany.
Topic: Nextflow and Michigan Imputation Server 2
Date: Thursday 30.01.2025 - Friday 31.01.2025
Location: Medical University of Innsbruck, Schöpfstrasse 3, UG
Registration: Want to participate? Please contact the workshop organizers.
Important Update
Note: The room for the workshop has changed. The new location is Medical University of Innsbruck, Schöpfstrasse 3, UG.
Prerequisites
- Setup Eduroam
- Install Nextflow locally installed on your computer *or** use a Gitpod Cloud Environment
- Familiarise yourself with the basics of Nextflow
- For Windows users: Install Nextflow on Windows
- Set-up a GitHub account
Projects
| Topic 1 | Getting Started with Nextflow |
| Topic 2 | Setting up a local server instance and enhance documentation. (Docs repo: https://github.com/genepi/michigan-imputationserver) |
| Topic 3 | Write documentation for setting up a local PGS server. (Docs repo: https://github.com/genepi/michigan-imputationserver) |
| Topic 4 | Integrating GLIMPSE2 as a new genotype imputation method |
| Topic 5 | Integrating SHAPEIT5 as a new genotype phasing method |
| Topic 6 | Detailed analysis and best practices for configuring SLURM |
| Topic 7 | Test and improve reference panel generation pipeline. (Repo: https://github.com/seppinho/nf-imputationserver-panels) |
| Topic 8 | Test and improve pre-imputation pipeline. (Repo: https://github.com/genepi/pre-imputation-qc) |
| Topic 9 | Test and improve chip simulation pipeline. (Repo: https://github.com/genepi/microarray-eval-nf) |
Program
Day 1 (Thu 30.01.2025)
| 09:30-10:00 | WELCOME |
| 10:00-12:00 | 1st session |
| 12:00-13:00 | Lunch |
| 13:00-15:00 | 2nd session |
| 15:00-15:30 | Coffee break |
| 15:30-17:00 | 3rd session |
| 17:00-17:30 | Wrap up |
| 17:30-21:00 | Social Event |
Day 2 (Fri 31.01.2025)
| 8:30-9:00 | Morning Coffee |
| 9:00-10:30 | 1st Session |
| 10:30-11:00 | Coffee Break |
| 11:00-12:30 | 2nd Session |
| 12:30-13:00 | Wrap up |
Organizers
Lukas Forer, PhD
Assistant Professor of Genome Informatics
+43 512 9003 70562
lukas.forer@i-med.ac.at
Assistant Professor of Genome Informatics
+43 512 9003 70562
lukas.forer@i-med.ac.at
Sebastian Schönherr, Dr.techn.
Professor of Computational Genomics
+43 512 9003 70579
sebastian.schoenherr@i-med.ac.at
Professor of Computational Genomics
+43 512 9003 70579
sebastian.schoenherr@i-med.ac.at
