Scientific Computing Facility

Introduction to Nextflow

by Andre Gohr (MPI-CBG, Scientific Computing Facility)

→ Europe/Berlin
Top-floor seminar room (CSBD)

Top-floor seminar room

CSBD
Description

Nextflow is workflow management software which allows users to create scalable and reproducible data-analysis pipelines in bioinformatics and any other area of data-analysis. It can integrate various software package and environment management systems such as Docker, Singularity, and Conda. It allows for existing analysis scripts written in common scripting languages, such as R and Python, to be seamlessly coupled together. It implements a Domain Specific Language (DSL) that simplifies the implementation and running of workflows on cloud or high-performance computing (HPC) infrastructures. 

Objectives: 

  1. The learner will understand the fundamental components of a Nextflow script, including channels, processes and operators.
  2. The learner will be able to write a Nextflow configuration file to alter the computational resources allocated to a process.

Level:         Intermediate

Format:      Instructor explains the material and does live-coding. Learners follow live-coding examples and solve exercises on their laptops.

Who can participate / Capacity: CBG members. 15 places.

Prerequisites:

  1. Be firm with the Unix shell ie. navigating through files/directories and calling software from within the shell.
  2. Have experience with connecting to remote computers via ssh.
  3. Have experience in Bash scripting; Ideally you have set up already a small workflow with Bash or other scripting languages.
  4. Be firm in the use of at least one terminal-based text editor like Nano, Vim, Gedit.
  5. Bring your own laptop
  6. Programming experience in a programming language will be helpful, but not essential.

Source: This workshop follows and uses the material of the Software Carpentries workshop Introduction to Bioinformatics workflows with Nextflow and nf-core

Resources:

  1. Nextflow
  2. Nextflow documentation
  3. Nextflow training
  4. Collection of more recommended training resources 2023

 

This workshop is part of the workshop series on reproducibility and good IT practices offered by the Scientific Computing Facility in September 2025.

Organised by

Andre Gohr (MPI-CBG, Scientific Computing Facility)