Skip to main content

Launch pipelines

Launch a pipeline from your workspace Launchpad and set its run parameters. The examples use nf-core/rnaseq.

Prerequisites

You need the following:

Open the launch form​

The launch form starts with the settings saved with the Launchpad pipeline. You can change them for this run.

To open the launch form:

  1. In your workspace, select Launchpad.
  2. Select Launch next to your pipeline.

The form has four steps. To move between them, select a step name, or select Previous and Next.

Check the general config​

General config sets what runs and where. Check these fields:

  • Revision: The Git tag, branch, or commit ID of the pipeline to run.
  • Config profiles: The Nextflow configuration profiles to use, such as test.
  • Workflow run name: A random name. Change it to a name you recognize.
  • Labels: Optional labels to filter runs by later.
  • Compute environment: The compute environment that runs the pipeline.
  • Work directory: The storage path for intermediate files. The compute environment credentials must be able to write to it.

General config step

See General config for every field.

Set the run parameters​

Run parameters shows the parameters defined in the pipeline's schema. Enter values in the form, or switch to Params file view to edit them as JSON or YAML. To load values from a file, select Upload params file.

Most pipelines need an input and an output location. For nf-core/rnaseq:

  1. In input, select Browse and choose your samplesheet:
    • On the Datasets tab, select a dataset.
    • On the Data Explorer tab, open a data repository, browse to the samplesheet, then select Select next to it.
  2. In outdir, enter the path where the pipeline writes its results, such as s3://my-bucket/rnaseq/results. Select Browse to choose a folder with Data Explorer. Use a different path for each run, so a run doesn't overwrite earlier results.

Change other parameters as needed. For example, to trim reads with fastp instead of Trim Galore, expand Read trimming options and set trimmer to fastp.

Read trimming options

Review advanced settings​

Advanced settings is optional. Use it to label the cloud resources the run creates with resource labels. You can also select pipeline secrets, add Nextflow configuration, and set pre-run and post-run scripts. See Advanced settings and Advanced options.

Launch the run​

Check your settings, then start the run:

  1. Select Summary to review the run settings.
  2. Select Launch.

Summary step

Platform opens the Runs page. Your run appears at the top of the list with a Submitted status. Select the run name to view its run details.

Next steps​

Your run is submitted. Next, monitor it:

On this Page