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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

  1. Select Launch next to the pipeline of your choice.

  2. Launchpad detects the presence of a nextflow_schema.json file in the root of the pipeline repository and dynamically creates a form to enter 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 workflow run.
    • Input/output options: Specify paths to pipeline input datasets and output directories.

    The input field drop-down menu only displays datasets of the file type specified in the mimetype field of your pipeline schema (text/csv for CSV files, or text/tsv for TSV files).

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

  3. 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.

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.

    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:

    1
2
    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. Once 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.

Relaunch pipeline run#

An effective way to troubleshoot a workflow execution is to relaunch it with different parameters. Navigate to the Runs tab and select Relaunch from the options menu to the right of the run of your choice to launch a new run with edited parameters, such as Pipeline to launch and Revision number, before launch. The relaunch option executes the run from scratch.

The Relaunch option is only available for runs launched from the Seqera Platform interface.

Resume pipeline run#

Seqera Platform enables you to use Nextflow's resume functionality to resume a workflow run with the same parameters, using the cached results of previously completed tasks and only executing failed and pending tasks. Select Resume from the options menu to the right of the run of your choice to launch a resumed run of the same workflow, with the option to edit some parameters before launch. Unlike a relaunch, you cannot edit the pipeline to launch or the work directory during a run resume.

The Resume option is only available for runs launched from the Seqera Platform interface.

For a detailed explanation of the Nextflow resume feature, see Demystifying Nextflow resume (Part 1 and Part 2) in the Nextflow blog.

Change compute environment during run resume#

Available from Seqera Platform 22.4.0

Users with appropriate permissions can change the compute environment when resuming a run. The new compute environment must have access to the original run work directory. This means that the new compute environment must have a work directory that matches the root path of the original pipeline work directory. For example, if the original pipeline work directory is s3://foo/work/12345, the new compute environment must have access to s3://foo/work.

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.

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.

From version 23.2, workspace maintainers can edit pipeline names from the Edit pipeline page.

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