Empowering bioinformatics communities with Nextflow and nf-core.

Area of Science:

• Bioinformatics
• Computational Biology
• Data Science

Background:

• Standardized analysis pipelines are crucial for FAIR data principles (Findability, Accessibility, Interoperability, Reusability) in bioinformatics research.
• Command-line tools like Nextflow and Snakemake are gaining traction, complementing graphical platforms such as Galaxy.
• The nf-core framework aims to standardize bioinformatics workflows.

Purpose of the Study:

• To report recent developments in the nf-core framework, specifically the adoption of Nextflow DSL2.
• To highlight the utility of nf-core's extensive library of modules and subworkflows.
• To showcase the adoption and impact of nf-core within research communities, particularly in farmed animal research.

Main Methods:

• Development and implementation of Nextflow DSL2 within the nf-core framework.
• Creation of a comprehensive library of reusable modules and subworkflows.
• Case studies demonstrating nf-core adoption by research consortia.

Main Results:

• The nf-core framework now supports Nextflow DSL2, enhancing workflow development.
• An extensive library of modules and subworkflows facilitates progressive adoption of common standards.
• nf-core has been successfully adopted by six EuroFAANG farmed animal research consortia.

Conclusions:

• The nf-core framework, with Nextflow DSL2, effectively supports FAIR data principles and collaboration in bioinformatics.
• Its modular design and extensive library enable research communities to adopt standardized practices.
• nf-core adoption demonstrates its value in large-scale research initiatives like EuroFAANG.