Utilising nf-core and associated tooling with in-house pipelines

At Genomics England we are migrating existing and developing new pipelines in Nextflow. We are largely aligning our code and work with the best practices of the community as defined by nf-core. The comprehensive tooling provided by nf-core allows us to streamline workflows and increase developer productivity. In parallel with public nf-core modules we maintain an internal remote for sharing modules with proprietary code across pipelines. Internal tools are containerised in both docker and singularity and CI/CD testing is performed using a minimal datasets held in S3 storage. Internally we have adopted much of the `nf-core` specification and standards so there is a pathway to open-sourcing work at a later stage if appropriate and collaboration with the community is easier, whilst allowing us flexibility to tailor aspects to the architecture and requirements of the business.