How to use the command 'nf-core' (with examples)

The nf-core command is a collection of tools provided by the nf-core framework. These tools are used to create, check, and develop best-practice guidelines for Nextflow pipelines. The command provides several use cases for managing nf-core pipelines, including listing existing pipelines, creating new pipeline skeletons, linting pipeline code, bumping software versions, launching pipelines, and downloading pipelines for offline use.

Use case 1: List existing pipelines on nf-core

Code:

nf-core list

Motivation: This use case allows users to quickly and easily see the list of existing pipelines available on nf-core. This is helpful for finding pipelines that may be relevant to their work or to get an overview of the available options.

Explanation: The nf-core list command lists all the existing pipelines on nf-core.

Example output:

nf-core/eager                                 2.0
nf-core/atacseq                              1.4, 1.3, 1.2, ...
nf-core/ampliseq                             1.0
...

Use case 2: Create a new pipeline skeleton

Code:

nf-core create

Motivation: This use case allows users to easily create a new pipeline skeleton based on the nf-core guidelines. This can save time and effort in setting up a new pipeline and ensure that it follows best practices.

Explanation: The nf-core create command generates a new pipeline skeleton based on the nf-core guidelines. It creates a directory with the necessary files and structure for a new pipeline.

Example output:

INFO: Created new pipeline nf-core/my_pipeline

Use case 3: Lint the pipeline code

Code:

nf-core lint path/to/directory

Motivation: Linting the pipeline code ensures that it adheres to the nf-core guidelines and best practices. This helps improve the quality, readability, and maintainability of the code.

Explanation: The nf-core lint command performs linting on the pipeline code located in the specified directory. It checks for common coding style and syntax errors, as well as adherence to the nf-core guidelines.

Example output:

Linting pipeline code in path/to/directory...
INFO: No linting errors found.

Use case 4: Bump software versions in pipeline recipe

Code:

nf-core bump-version path/to/directory new_version

Motivation: Bumping software versions in the pipeline recipe allows users to easily update the dependencies and ensure that the pipeline is using the latest version of the software tools.

Explanation: The nf-core bump-version command updates the software versions specified in the pipeline recipe located in the specified directory. It takes the directory path and the new version as arguments.

Example output:

INFO: Updated software versions in pipeline recipe to new_version

Use case 5: Launch an nf-core pipeline

Code:

nf-core launch pipeline_name

Motivation: Launching an nf-core pipeline allows users to execute the pipeline workflow on their local environment or a computing cluster. This enables them to process their data using the pipeline’s predefined steps and analysis tools.

Explanation: The nf-core launch command launches the specified nf-core pipeline. It takes the pipeline name as an argument and initiates the execution of the pipeline workflow.

Example output:

INFO: Launching nf-core/my_pipeline...

Use case 6: Download an nf-core pipeline for offline use

Code:

nf-core download pipeline_name

Motivation: Downloading an nf-core pipeline for offline use allows users to access the pipeline, its code, and its documentation even when an internet connection is not available. This is useful for users who need to work in a remote or restricted environment.

Explanation: The nf-core download command downloads the specified nf-core pipeline. It takes the pipeline name as an argument and retrieves all the necessary files and resources for the pipeline, including code, documentation, and dependencies.

Example output:

INFO: Downloaded nf-core/my_pipeline to /path/to/download/directory

Conclusion

The nf-core command provides a set of useful tools for managing Nextflow pipelines using the nf-core framework. These tools enable users to list existing pipelines, create new pipeline skeletons, lint pipeline code, bump software versions, launch pipelines, and download pipelines for offline use. By utilizing these commands, users can streamline their pipeline development process, adhere to best practices, and efficiently execute their data analysis workflows.