Launch pipelines

Use the Seqera Platform Launchpad to launch pre-configured pipelines, add new pipelines, or quick-launch unsaved pipelines.

Sort and filter pipelines

Select the Sort by: dropdown to sort pipelines by name or by most-recently updated. Select the filter icon to filter by workspace and labels.

The list layout is the default Launchpad view. Select the tiles icon to switch between the list and tile layout. Both views display the compute environment of each pipeline.

note

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

Launch pipelines

Use the launch form to launch pipelines and add pipelines to the Launchpad. Select Launch next to a saved pipeline in the list, or select Quick launch to quick-launch an unsaved pipeline.

The launch form consists of General config, Run parameters, Advanced settings, and Summary tabs to configure and view your run before execution. Use section headings or select Previous or Next 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.

info

The launch form accepts URL query parameters. See URL query parameters for more information.

General config

Configure the core settings for your run, including the pipeline source, compute environment, and work directory:

Run setup

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

  note

  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.

• Version name: The pipeline version name selected as the default for this run. See [Pipeline versioning][pipeline-version] for details.

• Version ID: The pipeline version ID selected as the default for this run. See Pipeline versioning for details.

• Revision: A valid repository commit ID, tag, or branch name. Determines the version of the pipeline to launch.

• Commit ID: The pipeline revision commit ID. If no commit ID is pinned, the latest revision of the repository branch or tag is used.

• Pull latest: Pull 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 Revision, Commit ID, and Pull latest, behavior.

• Main script: The script file to execute (default: main.nf). Config profile suggestions may update when this field changes. See Main script for custom script paths.

• 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.

  How config profiles are detected

  Seqera Platform populates the Config profiles dropdown by statically analyzing the pipeline's Nextflow configuration. The analysis detects profiles in the main configuration and in includeConfig statements that match any of these patterns:

  • A static string:

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

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

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

  • A ternary expression (only the true branch is inspected):

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

  • An include within a try-catch statement:

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

• Workflow run name: A unique identifier for the run, pre-filled with a random name that you can customize.

• Labels: Assign new or existing labels to the run.

• Compute environment: The compute environment where the run launches.

• Work directory: The cloud storage or file system path where pipeline scratch data is stored. Seqera Platform creates a scratch sub-folder if you specify only a cloud bucket location. Use file system paths for local or high-performance computing (HPC) compute environments.

  note

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

• Schema: The pipeline schema to validate pipeline parameters and prevent runtime failures. Options include Repository default, Repository path, and Seqera Platform schema.

Run parameters

Enter Run parameters in one of four ways before 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 Params file view displays a raw schema that you can edit directly. Select JSON or YAML format from the View as dropdown.
• Use Upload params file to upload a JSON or YAML file with run parameters.
• Specify run parameters with query parameters in the launch URL. See URL query parameters for more information.

If the pipeline includes a nextflow_schema.json file in its repository root, Seqera Platform uses it to dynamically generate a form with that pipeline's parameters. The fields shown vary by pipeline, depending on the parameters defined in the schema.

Common parameters include:

• Input data: If the pipeline defines an input parameter, specify compatible datasets manually or from the dropdown menu. Select Browse to view the available datasets or browse for files in Data Explorer. Use the Data Explorer tab to select input datasets that match your pipeline schema mimetype criteria (text/csv for CSV files, or text/tsv for TSV files).
• Output directory: If the pipeline defines an output directory parameter, specify it manually or select Browse to choose a cloud storage directory using Data Explorer.

Advanced settings

Configure platform resources, pipeline secrets, and advanced Nextflow options before launch.

Platform config

• Resource labels: Resource labels to tag the computing resources created during a run. The run inherits resource labels from the compute environment and pipeline, but admins can override them from the launch form. Applied resource label names must be unique.

Pipeline secrets

• Workspace's pipeline secrets: Secrets defined in the current workspace, available to all members.
• User's pipeline secrets: Secrets defined in your personal account.

note

In AWS Batch compute environments, Seqera Platform passes stored secrets to jobs as part of the job definition it creates. You cannot use Seqera secrets in Nextflow processes that use a custom job definition.

Advanced options

• Nextflow config file: Additional Nextflow configuration settings.
• Seqera Cloud config file: Additional Seqera Cloud configuration settings to override the tower.yml file.
• Pre-run scripts: Custom shell commands to run before the execution.
• Post-run scripts: Custom shell commands to run after the execution.
• Stub run: Replace process commands with stubs, where defined, before execution.
• Enable Nextflow syntax parser v2: Run the pipeline with the v2 Nextflow language parser.
• Workflow entry name: A named DSL2 workflow other than the default.
• Schema name: The name of a pipeline schema file in the workflow repository root folder to override the default nextflow_schema.json.
• Head job CPUs: The number of CPUs for the Nextflow head job. Fields are only displayed for runs executing on AWS Batch and Azure Batch compute environments.
• Head job memory: The memory for the Nextflow head job, in MiB. Fields are only displayed for runs executing on AWS Batch and Azure Batch compute environments.

See Advanced options for detailed guidance.

Summary

Review your General config and Run parameters settings, then select Launch.

The Runs tab shows your new run in a submitted status at the top of the list. Select the run name to open the View Workflow Run page and view the configuration, parameters, status of individual tasks, and run report.

tip

You can receive email notifications when a run completes or fails. Select Manage your account from the user menu, then toggle Send notification email on workflow completion at the bottom of the page.

Add new pipelines

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.

note

Pipeline names must be unique per workspace.

Edit pipelines

Workspace maintainers can edit existing pipeline details. Select the options menu next to the pipeline in the Launchpad list, then select Edit to open the pipeline parameters form, pre-filled with the pipeline's existing details. See Add from the Launchpad for more information on the pipeline parameters form fields.

Select Update to save the updated pipeline.

URL query parameters

The launch form can populate fields with values passed as URL query parameters. For example, append ?revision=master to your launch URL to prefill the Revision field with master. Platform administrators can use custom launch URLs to hard-code required run and pipeline parameters for every run.

Seqera Platform validates run parameters passed in the launch URL as follows:

• Parameter names are not validated. You must provide valid and supported parameters to populate launch form fields without error. See supported parameter names in the following section.
• Seqera Platform validates parameter values and shows warnings for any invalid values.
• Disabled launch form fields, such as the pipeline field when launching a pre-saved pipeline, cannot be populated by URL.

For parameters that accept arrays (multiple values), specify the parameter name for each value. For example:

?labelIds=<label_1_id>&labelIds=<label_2_id>

Pass pipeline-specific run parameters with the paramsText query parameter. Include the name and value for any parameter defined in your pipeline schema, in JSON format:

?paramsText={"key1": "value1", "key2": "value2"}

note

When you submit JSON-formatted paramsText input, Seqera Platform percent-encodes spaces, brackets, and other non-standard URL characters. For example:

?paramsText={"key1": "value1", "key2": "value2"}

is formatted and added to the relevant launch form fields with this syntax:

%7B"key1":%20"value1",%20"key2":%20"value2"%7D

Seqera Platform ignores the added percent-encoding characters in form fields. You do not need to remove them manually before submitting your pipeline launch.

The following table lists the supported URL query parameters and their corresponding launch form fields:

Launch form field	Query parameter name
Run setup
Pipeline to launch	pipeline
Revision number	revision
Config profiles	configProfiles
Workflow run name	runName
Labels	labelIds
Compute environment	computeEnvId
Work directory	workDir
Run parameters
Pipeline-specific run parameters	paramsText
Advanced settings
Resource labels	resourceLabelIds
Nextflow config file	configText
Seqera Cloud config file	towerConfig
Pull latest	pullLatest
Stub run	stubRun
Main script	mainScript
Workflow entry name	entryName
Schema name	schemaName
Head job CPUs	headJobCpus
Head job memory	headJobMemoryMb
Workspace's pipeline secrets	workspaceSecrets
User's pipeline secrets	userSecrets
Pre-run script	preRunScript
Post-run script	postRunScript