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Version: 23.4

Launch pipelines

Seqera Platform Launch makes it easy for users without Nextflow expertise to configure pipeline parameters and launch workflows. View, configure, and launch pipelines on the Launch Pipeline page, accessed 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: drop-down 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 to the right of 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​

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

Launch a saved pipeline

Select Launch next to the pipeline of your choice to open the pipeline launch form.

Seqera uses a nextflow_schema.json file in the root of the pipeline repository to dynamically create a form with the necessary pipeline parameters.

All pipelines contain at least these parameters:

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. Input/output options: Specify paths to pipeline input datasets, output directories, and other pipeline-specific I/O options. input and outdir are required fields common to most pipelines:

  • input Specify compatible input datasets manually or from the drop-down menu. Select Browse to view the available datasets or browse for Data Explorer files in a popup window. 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. Specify the directory path manually, or select Browse to specify a cloud storage directory using Data Explorer.

The remaining fields of the pipeline parameters form will vary for each pipeline, dependent on the parameters specified in the pipeline schema. When you have filled the necessary launch form 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 Cache and resume.

Quick launch an unconfigured pipeline

  1. Select launch a run without configuration below the Launchpad heading.

  2. On the Launch form, enter an optional Workflow run name (or keep the randomly assigned default) and assign optional labels to the run.

  3. Select a Compute environment from the available options. See Compute environments to learn how to create an environment for your preferred execution platform.

  4. Enter a repository URL for the Pipeline to launch (e.g., https://github.com/nf-core/rnaseq.git).

    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.

  5. Select a Revision number to use a specific version of the pipeline (optional). The Git default branch (e.g. main or master) or manifest.defaultBranch in the Nextflow configuration will be used by default.

  6. Enter the Work directory, which corresponds to the Nextflow work directory. You can also Browse for a cloud storage directory with Data Explorer. The default work directory of the compute environment will be used by default.

    The credentials associated with the compute environment must have access to the work directory (e.g., an S3 bucket).

  7. Select any Config profiles you wish to use. See Nextflow Config profiles for more details.

  8. Enter any Pipeline parameters in YAML or JSON format:

    reads: 's3://nf-bucket/exome-data/ERR013140_{1,2}.fastq.bz2'
    paired_end: true

    In YAML, quotes should be used for paths but not for numbers or Boolean values.

  9. Select or create resource labels to apply to the resources consumed by the run, if needed.

  10. Expand the Pipeline secrets dropdown to select user or workspace secrets to be used during the run, if needed.

    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.

  11. Apply any Advanced options, if needed.

  12. When you have filled the necessary launch form details, select Launch. The Runs tab shows your new run in a submitted status on the top of the list. Select the run name to navigate to the run detail page and view the configuration, parameters, status of individual tasks, and run report.

For more information on relaunch and resume, see 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.

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 excellent 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 mainainers can edit existing pipeline details. Select the options menu to the right of your 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.