Remote component repositories

The modules and subworkflows command groups come with two flags for specifying a custom remote:

  • --git-remote <git remote url>: Specify the repository from which the modules / subworkflows should be fetched as a git URL. Defaults to the github repository of nf-core/modules.
  • --branch <branch name>: Specify the branch from which the modules / subworkflows should be fetched. Defaults to the default branch of your repository.

For example, if you want to install the fastqc module from the repository nf-core/modules-test hosted at gitlab.com, you can use the following command:

nf-core modules --git-remote git@gitlab.com:nf-core/modules-test.git install fastqc

Or if you want to install the bam_stats_samtools subworkflow, you can use the following command:

nf-core subworkflows --git-remote git@gitlab.com:nf-core/modules-test.git --branch subworkflows install bam_stats_samtools

Note that a custom remote must follow a similar directory structure to that of nf-core/moduleÅ› for the nf-core modules / nf-core subworkflows commands to work properly.

The directory where modules / subworkflows are installed will be prompted or obtained from org_path in the .nf-core.yml file if available. If your modules are located at modules/my-folder/TOOL/SUBTOOL your .nf-core.yml should have:

org_path: my-folder

Please avoid installing the same tools from two different remotes, as this can lead to further errors.

The modules commands will during initalisation try to pull changes from the remote repositories. If you want to disable this, for example due to performance reason or if you want to run the commands offline, you can use the flag --no-pull. Note however that the commands will still need to clone repositories that have previously not been used.

Private remote repositories

You can use the modules command with private remote repositories. Make sure that your local git is correctly configured with your private remote and then specify the remote the same way you would do with a public remote repository.