Manually syncing your pipeline

In rare cases, you need to trigger synchronisation manually. This applies when automated sync did not run during an nf-core/tools release on GitHub, when you want to perform a targeted sync, or when you maintain a custom pipeline created with nf-core pipelines create.

Sync an official nf-core pipeline

Use this approach when working with an official nf-core pipeline that needs manual synchronisation:

1. Navigate to your pipeline directory and check out your development branch:

   cd <pipeline-name>
   git checkout dev

2. If you work on a fork, pull the TEMPLATE branch from the upstream nf-core repository:

   git remote add upstream https://github.com/nf-core/<pipeline-name>.git
   git checkout --track upstream/TEMPLATE
   git checkout dev

3. Run the sync command:

   nf-core pipelines sync

The sync command creates a merge that you can resolve locally, similar to automated sync pull requests.

Sync a custom pipeline with a pull request

Use this approach when you maintain a custom pipeline and want to create a pull request to your dev branch:

1. Navigate to your pipeline directory:

   cd <pipeline-name>

2. Run the sync command with pull request options:

   nf-core pipelines sync \
      --dir <pipeline-directory> \
      --from-branch dev \
      --pull-request \
      --username <github-username> \
      --github-repository <github-repository-url>

This creates a pull request in your repository that you can review and merge through the GitHub interface.