nf-core

nf-core is an open community project that provides a curated catalog of Nextflow-based bioinformatics pipelines, companion tooling, templates and best-practice modules. Launched in 2018 and published in peer-reviewed venues, nf-core enforces strict pipeline guidelines so that any compliant pipeline behaves consistently: pipelines are versioned via GitHub releases, run across laptops, HPC clusters and clouds, and ship with extensive documentation and reporting to support reproducible analyses. At its core nf-core leverages Nextflow as the workflow engine. All nf-core pipelines require Nextflow to run; installation is typically a simple single-user Nextflow install (recommended for reproducibility and easy upgrades). Pipelines manage their software stacks using container technologies (Docker or Singularity/Apptainer) and many also support Conda/Bioconda environments. Nextflow's native support for containers means nf-core pipelines can automatically fetch the correct runtime images or package environments, avoiding manual tool installation and improving reproducibility across different compute platforms. The project provides more than a hundred full pipelines and many hundreds of reusable modules and subworkflows covering a wide set of use cases: RNA‑seq (bulk and single‑cell), variant calling (WGS/WES), methylation and bisulfite sequencing, metagenomics and taxonomic profiling, genome assembly and annotation, proteomics workflows, ancient DNA, spatial transcriptomics, and specialised pipelines for HLA typing, epitope prediction, CRISPR analysis and more. Pipelines are designed to be production-ready: they include configurable reporting, QA/QC steps and are validated with continuous-integration tests (releases are tested on AWS after every release). This makes nf-core suitable for everything from exploratory work on a laptop to high-throughput analyses on institutional clusters or cloud batch services. For developers and power users, nf-core provides a structured development ecosystem: a canonical pipeline template, a library of reusable modules, and the nf-core companion (CLI) tool. The companion tool helps you list and download pipelines, generate commented config templates, create offline copies for air-gapped environments, and provides an interactive launch wizard. The project also publishes configuration profiles for many institutional clusters and cloud environments (an extensive nf-core/configs collection) so you can pick a ready-made profile for SLURM, LSF, AWS Batch, Google Cloud, Azure and many university HPC setups. Testing and reproducibility are further supported by nf-test utilities and nft-utils, plugins that help snapshot outputs, sort and cleanse version YAML files, create temporary module libraries for tests, and manage other pipeline testing tasks. Typical usage is straightforward: after installing Nextflow you can run a pipeline directly from GitHub (Nextflow will fetch the pipeline). For example, launching an RNA‑seq workflow or a metagenomics pipeline is as simple as running nextflow run nf-core/<pipeline-name> with appropriate inputs and a profile. If you need to modify pipeline logic you can fork the repository and run a local copy; for configuration-only changes nf-core encourages using custom config files or selecting from the many existing institutional profiles to avoid forking and remain upgradable. The community is active and welcoming: contributions range from documentation fixes and new modules to full pipeline additions, and collaboration is coordinated via GitHub and Slack, with periodic hackathons and talks. Integrations cover the entire Nextflow ecosystem: container registries, Conda/Bioconda, cloud batch systems, and GitHub Actions (there are actions to install Nextflow for CI). The project's licensing (MIT) and open development model make pipelines fully inspectable and modifiable. One practical caution: Nextflow is a required dependency, and if you rely on automatic pipeline downloads you need network access; nf-core provides utilities for offline downloads and explicit guidance (e.g., for Windows via WSL2). Overall, nf-core is a mature, well-documented solution for teams that want reproducible, portable, tested bioinformatics workflows with community support and a rich set of ready-to-run pipelines and components.