This is a step-by-step guide for running a Nextflow pipeline on One Codex workflows. By following this guide, you will be able to create a new Nextflow pipeline using nf-core-tools then run it on One Codex. If you already have an existing Nextflow pipeline created using nf-core-tools; skip to Step 3.

You will need the following tools in order to follow this tutorial:

The first step is to create a new Nextflow pipeline. To do so, run nf-core create and follow the instructions:

When prompted, you can skip any of the template areas.

Create the repository on GitHub and push your pipeline code. If you choose to make your repository private; you will need to follow the guide on GitHub Integration with One Codex.

Log in to One Codex, go to the "Run Workflows" page and click "Create a New Workflow"

Select "Nextflow Pipeline" under Workflow Type and enter the Github URL under "Git Repository"

You should now see the "Arguments" section populated by the input arguments defined by your pipeline's nextflow_schema.json . You can read more about how configuring your workflow and defining arguments here.

Click "Save Draft" to create your Workflow

Your new Nextflow Workflow will now be available on the "Run Workflows" page. Select a sample and click "Run" next to your Workflow. This will bring you to the confirmation where you can configure the run by specifying values for its arguments.

Click "Run". You can view the status of your Workflow(s) by clicking "View Workflow Runs":

Clicking "Details" will bring you to a page where you can view the logs of your Workflow in real-time:

That's it! Hopefully things went well and your workflow has completed. From here, you might want to read more about how update and manage versions of your workflow in Workflows States and Permissions.