Adding your pipeline to the nf-core organisation

Ok, so you’re essentially finished. Your pipeline is written, the tests pass and you’re ready to add your workflow to nf-core.

First, go to the settings of your repository. Under the General page, in the ‘Danger Zone’ you should have an option to Transfer Ownership. Transfer this to the nf-core organisation.

Tip

You must make sure you are already a part of the nf-core organisation to allow transferring to nf-core. Alternatively you can add a core-team member to your repository, and ask them to do the transfer you.

Once transferred, go to the transferred repository on nf-core, and make a new fork back to your user name or organisation to continue development on a fork.

Info

Repositories should be transferred instead of forking to nf-core. If we fork the original repository to nf-core whenever anyone opens a pull-request, it defaults to going to the original user’s fork of the repository, not the nf-core repo. In this case the only way to fix to request manual detachment from GitHub support.

Branch setup

All nf-core pipelines use branches called dev and master. The master branch should contain the code from the latest stable release, dev should have the latest development code. We want people to run the latest development code by default up until the first release. To do this, we set dev as the default repository branch. After an initial release is created, we set the default branch back to master so that the default action is to run the latest stable release code.

Once you have forked the repository, create a new branch called dev for the active development. In the repository settings, set dev to be the default branch.

Repository setup

Remember to configure the repository on the GitHub website with the following:

  • A description, the https://nf-co.re URL and lots of keywords!
  • Issues enabled, disable Wiki and Projects
  • A protected master branch that requires review and passing tests
  • Write permissions for nf-core/all and admin permissions for nf-core/admin

You can check that all of these settings are done correctly by referring to your pipeline in the nf-core Repository health web page. This reports the status of various checks and also has the option of fixing errors for you via the GitHub API.

Differences to your own fork

The main difference when working with the main nf-core fork of your workflow is that tests for pull-requests against the master branch will fail. This is because the master branch should only ever contain code from the last release. Instead, use the dev branch for new work and always make pull-requests against that. Then the tests should pass.

Tutorial: Adding a pipeline

11 Overview 22 Creating a pipeline 33 Test data 44 Move to nf-core org 55 First release 66 Next steps
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