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Empowering bioinformatics communities with Nextflow and nf-core.

Björn E Langer1, Andreia Amaral2,3, Marie-Odile Baudement4

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The nf-core framework, utilizing Nextflow DSL2, enhances bioinformatics research by promoting FAIR data principles and collaboration. It offers a modular library supporting community standards and adoption, as seen in farmed animal research consortia.

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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.