nf-core

nf-core [options] command [subcommand] [args]

nf-core is the command-line interface for the nf-core community, which curates a collection of high-quality bioinformatics pipelines built with Nextflow. The tool helps users find, download, launch, and develop pipelines following community best practices.
The download command fetches pipelines along with their Singularity or Docker container images for use in offline or air-gapped environments. The launch command provides an interactive interface for setting pipeline parameters, generating a params file, and starting a run.
For pipeline developers, create scaffolds a new pipeline from the nf-core template with CI, documentation, and testing built in. The lint command validates that a pipeline follows nf-core guidelines for code quality, documentation, and reproducibility.

--help

Display help information.

Show version.

Increase output verbosity.

Do not show progress bars.

Save log output to a file.

pipelines list

List available nf-core pipelines with stars, releases, and descriptions.

Download a pipeline and its container images for offline use.

Interactively configure and launch a pipeline run.

Create a new pipeline from the nf-core template.

Check pipeline code against nf-core best practices.

Show detailed information about a pipeline.

Manage pipeline parameter schema files.

Requires Python 3.8 or later. Nextflow must be installed separately to actually run pipelines. Pipeline downloads can be large when including container images. Internet access is required for listing and downloading pipelines.

nf-core was established in 2018 as a community effort to create a curated set of Nextflow pipelines following best practices for reproducibility and portability. The project was published in Nature Biotechnology in 2020. It has grown to include over 100 pipelines covering genomics, proteomics, imaging, and other bioinformatics domains.

nextflow(1), conda(1), docker(1)