Pipiline implementation workshop

Trainer: Geraldine Van der Auwera

Nextflow is a powerful and flexible open-source workflow management system that simplifies the development, execution, and scalability of data-driven computational pipelines. It is widely used in bioinformatics and related scientific fields to automate complex analyses, making it easier to manage and reproduce large-scale data analysis workflows. Complementing this system is the nf-core project, a collaborative effort to develop and maintain high-quality open-source bioinformatics pipelines for a wide range of research applications.

This training section was designed as a “getting started” workshop for students and early-career researchers who are completely new to Nextflow and nf-core.

Learning outcomes

By the end of this session you should be able to:

• Identify how core components of the Nextflow language are used 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.
• Apply these learnings to a transcriptomics use case to read and execute a simplified RNA-seq pipeline.
• Take the next step in your journey to develop and apply reproducible workflows for your scientific computing needs.

Materials:

• https://training.nextflow.io/
• https://training.nextflow.io/latest/hello_nextflow/
• https://training.nextflow.io/latest/nf4_science/rnaseq/
• Forum: https://community.seqera.io/
• Training week: https://community.seqera.io/t/nextflow-training-week-instructions/1774