Advanced options

You can modify the configuration and execution of a pipeline with advanced launch options.

Nextflow config file

Add settings to the Nextflow configuration file. This must follow the same syntax as the Nextflow configuration file.

For example, modify the manifest section to give the pipeline a name and description that will show up in the Seqera monitoring section:

    manifest {
        name = 'My_RNASeq_Pipeline'
        description = 'Generates RNASeq results using a test profile'
        mainScript = 'main.nf'
        defaultBranch = 'master'
    }

Nextflow configuration order of priority

When launcing pipelines in Platform, Nextflow configuration values can be supplied from the nextflow.config file in the pipeline repository and the Nextflow config file field in the pipeline launch form. If different values of the same configuration parameter are defined, Nextflow parameters defined in the launch form Nextflow config file field override the same parameters in your nextflow.config file.

Configuration values set in the Global Nextflow config field during compute environment creation are pre-filled in the Nextflow config file field during pipeline launch. These pre-filled values from the compute environment can be overridden manually during launch.

Nextflow configuration order of priority (highest to lowest)
Pipeline launch form Nextflow config file field
Compute environment Global Nextflow config field
Pipeline repository nextflow.config file

For example, if:

1. The nextflow.config file in your pipeline repository contains this manifest:

   Pipeline repository config file

   manifest {
       name = 'A'
       description = 'Pipeline description A'
       mainScript = 'main.nf'
       defaultBranch = 'master'
   }

2. Your compute environment Global Nextflow config field contains this manifest:

   Compute environment Global Nextflow config field

   manifest {
       name = 'B'
       description = 'Pipeline description B'
       mainScript = 'main.nf'
       defaultBranch = 'master'
   }

3. You specify this manifest in the Nextflow config file field on the pipeline launch form:

   Pipeline launch form Nextflow config file field

   manifest {
       name = 'C'
       description = 'Pipeline description C'
       mainScript = 'main.nf'
       defaultBranch = 'master'
   }

The resolved configuration will contain the Nextflow config file field's manifest:

Pipeline launch form Nextflow config file field

manifest {
    name = 'C'
    description = 'Pipeline description C'
    mainScript = 'main.nf'
    defaultBranch = 'master'
}

Seqera Cloud config file

Configure per-pipeline Seqera reporting behavior. Settings specified here override the same settings in the tower.yml configuration file for this execution. Use the reports key to specify report paths, titles, and MIME types:

reports:
  reports/multiqc/index.html:
    display: "MultiQC Reports"
    mimeType: "text/html"

Pre and post-run scripts

Run custom code either before or after the execution of the Nextflow script. These fields allow you to enter shell commands.

Pre-run scripts are executed in the nf-launch script prior to invoking Nextflow processes. Pre-run scripts are useful for:

• Specifying an alternate Nextflow version to use for the run:

  nextflow self-update
  export NXF_VER=24.10.0

  nextflow self-update is required before updating a pre-24.10.0 version of Nextflow to version 24.10.0 or later.

• Executor setup, such as loading a private CA certificate.

• Troubleshooting. For example, add sleep 3600 to your pre-run script to instruct Nextflow to wait 3600 seconds (60 minutes) before process execution after the nf-launcher container is started, to create a window in which to test connectivity and other issues before your Nextflow processes execute.

Post-run scripts are executed after all Nextflow processes have completed. Post-run scripts are useful for triggering a third party service via API request.

Pull latest

Instruct Nextflow to pull the latest pipeline version from the Git repository. This is equivalent to using the -latest flag.

Stub run

Replace Nextflow process commands with command stubs, where defined, before execution.

Main script

Nextflow will attempt to run the script named main.nf in the project repository by default. You can configure a custom script filename in manifest.mainScript or you can provide the script filename in this field.

If you specify a custom script filename, the root of the default branch in your pipeline repository must still contain blank main.nf and nextflow.config files. See Nextflow configuration for more information on this known Nextflow behavior.

Workflow entry name

Nextflow DSL2 provides the ability to launch workflows with specific names. Enter the name of the workflow to be executed in this field.

Schema name

Specify the name of a pipeline schema file in the workflow repository root folder to override the default nextflow_schema.json.

Head job CPUs and memory

Specify the compute resources allocated to the Nextflow head job. These fields are only displayed for runs executing on AWS Batch and Azure Batch compute environments.