Add pipelines

The Launchpad lists the preconfigured Nextflow pipelines that you can run on the compute environments in your workspace.

You can import pipelines to your workspace Launchpad in two ways: directly from Seqera Pipelines, or manually with Add pipeline in Seqera Platform.

Import from Seqera Pipelines

Seqera Pipelines is a curated collection of open-source pipelines that you can import directly to your workspace Launchpad. Each pipeline includes a dataset for a test run that confirms compute environment compatibility.

To import a pipeline:

1. Select Launch next to the pipeline name in the list. In the Add pipeline tab, select Cloud or Enterprise depending on your Platform account type, then provide the information needed for Seqera Pipelines to access your Platform instance:
   • Seqera Cloud: Paste your Platform Access token and select Next.
   • Seqera Enterprise: Specify the Seqera Platform URL (hostname) and Base API URL for your Enterprise instance, then paste your Platform Access token and select Next.
   note

   If you do not have a Platform access token, select Get your access token from Seqera Platform to open the Access tokens page in a new browser window.

2. Select the Platform Organization, Workspace, and Compute environment for the imported pipeline.
3. (Optional) Customize the Pipeline Name and Pipeline Description.
   note

   Pipeline names must be unique per workspace.

4. Select Add Pipeline.

Add from the Launchpad

From your workspace Launchpad, select Add Pipeline and specify the following pipeline details:

• (Optional) Image: Select the Edit icon on the pipeline image to open the Edit image window. From here, select Upload file to browse for an image file, or drag and drop the image file directly. Images must be in JPG or PNG format, with a maximum file size of 200 KB.
  note

  You can upload custom icons when adding or updating a pipeline. If no user-uploaded icon is defined, Platform retrieves and attaches a pipeline icon in the following order of precedence:

  1. A valid icon key:value pair defined in the manifest object of the nextflow.config file.
  2. The GitHub organization avatar (if the repository is hosted on GitHub).
  3. If none of the above are defined, Platform auto-generates and attaches a pipeline icon.
• Name: A custom name of your choice. Pipeline names must be unique per workspace.
• (Optional) Description: A summary of the pipeline, or any information useful to workspace participants when they select a pipeline to launch.
• (Optional) Labels: Categorize the pipeline by criteria such as research group or reference genome version to help workspace participants select the right pipeline for their analysis.
• Compute environment: Select an existing workspace compute environment.
• Pipeline to launch: The URL of any public or private Git repository that contains Nextflow source code.
• Revision: A valid repository commit ID, tag, or branch name. Determines the version of the pipeline to launch.
  tip

  Selecting a specific pipeline version is important for reproducibility. Each run with the same input data then generates the same results.

• Commit ID: Pin pipeline revision to the most recent HEAD commit ID. If no commit ID is pinned, the latest revision of the repository branch or tag is used.
• Pull latest: Fetch the most recent HEAD commit ID of the pipeline revision at launch time. Unpins the Commit ID, if set.
  info

  See Git revision management for more information on Commit ID, Pull latest, and Revision behavior.

• (Optional) Config profiles: Select a predefined profile for the Nextflow pipeline.
  info

  nf-core pipelines include a test profile that is associated with a minimal test dataset. This profile runs the pipeline with heavily sub-sampled input data for the purposes of CI/CD and to quickly confirm that the pipeline runs on your infrastructure.

• (Optional) Pipeline parameters: Set custom pipeline parameters that are prepopulated when users launch the pipeline from the Launchpad. For example, set the path to local reference genomes so users don't need to locate these files at launch.
• (Optional) Pre-run script: Define Bash code that executes before the pipeline launches in the same environment where Nextflow runs.
  info

  Pre-run scripts are useful for defining executor settings, troubleshooting, and defining a specific version of Nextflow with the NXF_VER environment variable.

note

Workspace participants with the necessary permissions can override pre-filled pipeline settings (such as compute environment, config profiles, and pipeline parameters) during pipeline launch.

After you fill in the fields, select Add. Your pipeline is now available for workspace participants to launch in the preconfigured compute environment.