nf-core

List existing pipelines on nf-core

$ nf-core list

$ nf-core create

$ nf-core lint [path/to/directory]

$ nf-core bump-version [path/to/directory] [new_version]

$ nf-core launch [pipeline_name]

$ nf-core download [pipeline_name]

nf-core [options] [arguments]

Common Usage Examples:
nf-core list
nf-core download [version]
nf-core create pipeline
nf-core launch --id

list
    Lists all available nf-core pipelines and modules, with optional filters for keywords or specific versions.

download
    Downloads a specified nf-core pipeline or module version to a local directory, preparing it for execution.

create
    Generates a new pipeline, module, or subworkflow project from the official nf-core template, facilitating rapid development.

launch
    Interactively guides the user through pipeline parameter input, then generates and optionally executes the Nextflow command.

lint
    Checks a local pipeline directory against the extensive nf-core best practice guidelines, identifying deviations and suggesting fixes.

modules
    Manages nf-core DSL2 modules, allowing users to pull, create, update, and lint individual modular components.

subworkflows
    Manages nf-core DSL2 subworkflows, providing similar functionality to modules for larger, reusable workflow blocks.

sync
    Synchronizes a local pipeline with the latest changes from the official nf-core template, applying updates while preserving local modifications.

update
    Updates a downloaded nf-core pipeline to its latest official release, ensuring users benefit from the most recent features and bug fixes.

--version
    Displays the installed version of the nf-core command-line tool.

nf-core is a community-driven initiative that provides a collection of standardized, high-quality, and reproducible Nextflow pipelines for bioinformatics. The nf-core command-line tool serves as the primary interface for interacting with this ecosystem. It significantly simplifies the process of finding, downloading, validating, and launching these complex pipelines.

Users leverage nf-core to ensure their bioinformatics analyses adhere to community best practices, fostering easier collaboration and consistent results. The tool also streamlines pipeline development, offering features for creating new pipelines, modules, and subworkflows from templates, alongside robust linting capabilities to enforce adherence to the nf-core guidelines. This standardization greatly enhances pipeline maintainability, scalability, and reusability across diverse computational environments.

Running nf-core pipelines requires a separate installation of Nextflow. While nf-core streamlines setup, actual pipeline execution can still be computationally intensive and may require careful configuration for specific high-performance computing (HPC) environments or cloud platforms. The full benefits of nf-core's linting and syncing features are primarily for pipelines developed adhering to the nf-core guidelines.

nf-core boasts an active Slack community and extensive, well-maintained documentation, offering comprehensive support for both users and developers alike.

All nf-core pipelines are rigorously tested and leverage containerization technologies (Docker/Singularity) to ensure consistent and reproducible results across diverse computational environments.

Leveraging Nextflow's DSL2, nf-core pipelines are built from highly modular components (modules and subworkflows), which simplifies pipeline construction, maintenance, and reuse.

The nf-core project was initiated in 2018 by Phil Ewels and others, born from a growing need for standardized, high-quality, and reproducible bioinformatics pipelines using Nextflow. It rapidly evolved into a thriving open-source community, providing not just pipelines but also the nf-core command-line interface tool to facilitate their management. The project's development has closely mirrored advancements in Nextflow, particularly the adoption of DSL2, which significantly enhanced pipeline modularity and maintainability.

nextflow(1), git(1), docker(1), singularity(1)