Launch pipelines

View, configure, and launch pipelines from your workspace Launchpad.

Launchpad

The Launchpad enables workspace users to launch pre-configured pipelines, add new pipelines, or perform a quick launch of unsaved pipelines. Use the Sort by: dropdown to sort pipelines, either by name or most-recently updated.

A pipeline is a repository containing a Nextflow workflow, a compute environment, and pipeline parameters.

The list layout is the default Launchpad view. Use the toggle next to the Search field to switch between the list and tile views. Both views display the compute environment of each pipeline for easy reference.

Launch form

In Platform Enterprise version 24.2, the stepped launch form described below is enabled for all user and organization workspaces by default. You can disable the new launch form in some or all organization workspaces with the TOWER_STEPPED_LAUNCH_FORM_ALLOWED_WORKSPACES environment variable.

Platform Cloud accounts use the new launch form in all user and organization workspaces.

The launch form is used to launch pipelines and to add pipelines to the Launchpad. Select Launch next to a saved pipeline in the list, or select launch a run without configuration to perform a quick launch of an unsaved pipeline.

The launch form consists of General config, Run parameters, and Advanced options sections to specify your run parameters before execution, and an execution summary. Use section headings or select the Previous and Next buttons at the bottom of the page to navigate between sections.

For saved pipelines, General config and Run parameters fields are prefilled and can be edited before launch.

General config

• Pipeline to launch: A Git repository name or URL. For saved pipelines, this is prefilled and cannot be edited. Private repositories require access credentials.

  Nextflow pipelines are Git repositories that can reside on any public or private Git-hosting platform. See Git integration in the Seqera docs and Pipeline sharing in the Nextflow docs for more details.

• Revision number: A valid repository commit ID, tag, or branch name. For saved pipelines, this is prefilled and cannot be edited.
• Config profiles: One or more configuration profile names to use for the execution. Config profiles must be defined in the nextflow.config file in the pipeline repository.
• Workflow run name: A unique identifier for the run, pre-filled with a random name. This can be customized.
• Labels: Assign new or existing labels to the run.
• Compute environment: The compute environment where the run will be launched.
• Work directory: The cloud storage or file system path where pipeline scratch data is stored. Seqera will create a scratch sub-folder if only a cloud bucket location is specified. Use file system paths for local or HPC compute environments.

  The credentials associated with the compute environment must have access to the work directory.

Config profiles

The dropdown of available config profiles is populated by inspecting the Nextflow configuration in the pipeline repository. A limited form of static analysis is used to detect profiles in the main configuration and included configurations that match any of the following patterns:

• Includes with a static string:

  includeConfig 'conf/profiles.config'
  includeConfig 'http://...'

• Includes with dynamic string that depends on parameters defined in the config:

  includeConfig params.custom_config
  includeConfig "${params.custom_config_base}/nfcore_custom.config"

• Includes with a ternary expression:

  includeConfig params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

  Only the "true" branch is inspected.

• Includes within a try-catch statement:

  try {
      includeConfig "${params.custom_config_base}/nfcore_custom.config"
  } catch (Exception e) {
      // ...
  }

Run parameters

There are three ways to enter Run parameters prior to launch:

• The Input form view displays form fields to enter text, select attributes from dropdowns, and browse input and output locations with Data Explorer.
• The Config view displays a raw schema that you can edit directly. Select JSON or YAML format from the View as dropdown.
• Upload params file allows you to upload a JSON or YAML file with run parameters.

Seqera uses a nextflow_schema.json file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters. Most pipelines contain at least input and output parameters:

• input Specify compatible input datasets manually or from the dropdown menu. Select Browse to view the available datasets or browse for files in Data Explorer. The Data Explorer tab allows you to select input datasets that match your pipeline schema mimetype criteria (text/csv for CSV files, or text/tsv for TSV files).

• outdir Specify the output directory where run results will be saved manually, or select Browse to choose a cloud storage directory using Data Explorer.

The remaining fields will vary for each pipeline, dependent on the parameters specified in the pipeline schema.

Advanced settings

Enter resource labels, pipeline secrets, and advanced options before launch.

Resource labels

Use resource labels to tag the computing resources created during the workflow execution. While resource labels for the run are inherited from the compute environment and pipeline, admins can override them from the launch form. Applied resource label names must be unique.

Pipeline secrets

Secrets are used to store keys and tokens used by workflow tasks to interact with external systems. Enter the names of any stored user or workspace secrets required for the workflow execution.

In AWS Batch compute environments, Seqera passes stored secrets to jobs as part of the Seqera-created job definition. Seqera secrets cannot be used in Nextflow processes that use a custom job definition.

Advanced options

See Advanced options.

After you have filled the necessary launch details, select Launch. The Runs tab shows your new run in a submitted status at the top of the list. Select the run name to navigate to the View Workflow Run page and view the configuration, parameters, status of individual tasks, and run report.

For more information on relaunch and resume, see Nextflow cache and resume.

Add new pipeline

From the Launchpad, select Add pipeline to add a new pipeline with pre-saved parameters to your workspace. The fields on the new pipeline form are similar to the pipeline launch form.

See Add pipelines for instructions to add pipelines to your workspace via Seqera Pipelines or the Launchpad.

Pipeline names must be unique per workspace.

To create your own customized Nextflow schema for your pipeline, see Pipeline schema and the nf-core workflows that have adopted this. nf-core/eager and nf-core/rnaseq are good examples.

Email notifications

You can receive email notifications upon completion or failure of a workflow execution.

Select Your profile from the user menu, then toggle Send notification email on workflow completion at the bottom of the page.

Edit pipeline

Workspace maintainers can edit existing pipeline details. Select the options menu next to the pipeline in the Launchpad list, then select Edit to load the pipeline parameters form with pre-filled existing pipeline details to be edited.

Select Update when you are ready to save the updated pipeline.

Workspace maintainers can edit pipeline names from the Edit pipeline page. Pipeline names must be unique per workspace.