Cédric Notredame, Professor of Computational Biology at the Mohamed bin Zayed University of Artificial Intelligence (MBZUAI) will present our next virtual lunch on Nextflow

Title 

Nextflow and nf-core: A Virtual Infrastructure for the Next Generation of Bioinformatics Pipelines
 

Abstract

Biology generates data at a scale that outpaces existing computational capacity. Turning this raw material into knowledge requires workflows that are reproducible, portable and community-owned. Nextflow, together with nf-core, has become the de facto framework for this purpose: a virtual infrastructure on which thousands of groups build, share and run their analyses.

I will first retrace how Nextflow and nf-core evolved into a cooperation platform for bioinformatics. The strength of the framework lies less in its workflow engine than in the network it has brokered, with scientists across institutions coordinating through shared tooling, common standards and joint governance. A turning point was the move to DSL2 and the resulting library of modules and subworkflows. Contributors now exchange reusable building blocks rather than complete workflows, each independently tested, versioned and maintained. The result is a steady convergence toward FAIR workflows, adopted by consortia as diverse as EuroFAANG, Darwin Tree of Life and Genomics England.

This modular foundation called for a further step: the pipeline hub. Hubs turn workflows into versioned, peer-reviewed scientific objects, but their defining contribution is to let alternative methods for the same task be compared directly, side by side, on the same data and under the same conditions. I will illustrate this with nf-core/multiplesequencealign (Santus et al., 2025), which benchmarks alignment strategies against structural and evolutionary references. I will close with applications in comparative genomics, including multistrap, which combines sequence and structural information to improve bootstrap support in phylogenetic trees (Baltzis et al., 2025).

Lien de connexion : to come