Pipeline sync

Over time, the main nf-core pipeline template is updated. To keep all nf-core pipelines up to date, we synchronise these updates automatically when new versions of nf-core/tools are released. This is done by maintaining a special TEMPLATE branch, containing a vanilla copy of the nf-core template with only the variables used when it first ran (name, description etc.). This branch is updated and a pull-request can be made with just the updates from the main template code.

Note that pipeline synchronisation happens automatically each time nf-core/tools is released, creating an automated pull-request on each pipeline. As such, you do not normally need to run this command yourself!

This command takes a pipeline directory and attempts to run this synchronisation. Usage is nf-core sync, eg:

The sync command tries to check out the TEMPLATE branch from the origin remote or an existing local branch called TEMPLATE. It will fail if it cannot do either of these things. The nf-core create command should make this template automatically when you first start your pipeline. Please see the nf-core website sync documentation if you have difficulties.

To specify a directory to sync other than the current working directory, use the --dir <pipline_dir>.

By default, the tool will collect workflow variables from the current branch in your pipeline directory. You can supply the --from-branch flag to specific a different branch.

Finally, if you give the --pull-request flag, the command will push any changes to the remote and attempt to create a pull request using the GitHub API. The GitHub username and repository name will be fetched from the remote url (see git remote -v | grep origin), or can be supplied with --username and --github-repository.

To create the pull request, a personal access token is required for API authentication. These can be created at https://github.com/settings/tokens. Supply this using the --auth-token flag.