nf-modules

Prerequisites

• nf-core tools: module load cellgen/nf-core/3.2.0

Usage

List all modules

This will show all all the modules available in the repository.

nf-core modules -g https://github.com/cellgeni/nf-modules.git list remote

List all subworkflows

This will show all the subworkflows available in the repository.

nf-core subworkflows -g https://github.com/cellgeni/nf-modules.git list remote

Install a subworkflow

This will install a subworkflow, along with the used modules, from the repository. so, you shouldn't manually install modules from the repository unless is not used in a subworkflow.

nf-core subworkflows -g https://github.com/cellgeni/nf-modules.git install <subworkflow_name>

Install a module

If the module is not used in a subworkflow, you can install it directly from the repository.

nf-core modules -g https://github.com/cellgeni/nf-modules.git install <module_name>

List installed modules

This will show all the modules installed in your local repository.

nf-core modules -g https://github.com/cellgeni/nf-modules.git list local

Remove a module

If you want to remove a module, you can do it with the following command:

nf-core modules -g https://github.com/cellgeni/nf-modules.git remove <module_name>

List all installed subworkflows

This will show all the subworkflows installed in your local repository.

nf-core subworkflows -g https://github.com/cellgeni/nf-modules.git list local

Remove a subworkflow

If you want to remove a subworkflow, you can do it with the following command:

nf-core subworkflows -g https://github.com/cellgeni/nf-modules.git remove <subworkflow_name>