Sharing Nextflow code across organizations using the nf-core infrastructure

Description

Abstract (English)

    nf-core (https://nf-co.re/) is a community of hundreds of bioinformaticians promoting and supporting the development of bioinformatics pipelines in the Nextflow language. They provide infrastructure and tooling for constructing, hosting, and using, the components of pipelines, which are called modules and sub-workflows, in an efficient and reliable manner. The nf-core organization on GitHub contains a central repository of ready-to-use modules and sub-workflows, which is open-source and co-developed by the wider community.

    The nf-core community maintains a software suite that enables the creation of data pipelines, leveraging on this infrastructure. In particular, a command-line tool facilitates the incorporation of pre-built code, modules and sub-workflows, into them. The command-line tool, however, restricts users from using components that are built across multiple modules / sub-workflows repositories. This limitation hinders the adoption of Nextflow and nf-core in organizations that cannot deposit all their modules and sub-workflows in the nf-core repository. In this work, we aim to facilitate the incorporation of sub-workflows built across repositories and organizations, further enabling collaborative efforts. By extending the YAML metadata already present in sub-workflows, we, in collaboration with the nf-core community, implemented a new feature for the tool that makes it possible for users to build these components. This new feature makes it possible for multiple institutions to reuse the same, well-tested Nextflow code, but still be able to build upon it and make their own modifications with ease.

Notes (English)