Advanced options

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

Nextflow config file

The Nextflow config file field allows you to add settings to the Nextflow configuration file.

Nextflow parameters defined in this field override the same parameters in your nextflow.config file.

This text should 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'
    }

Seqera Cloud config file

The Seqera Cloud config file field allows you to configure per-pipeline Seqera reporting behavior. Settings specified here override the same settings in the tower.yml 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

You can 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 executor setup (e.g., to load a private CA certificate) and 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

Enable this option to ensure that Nextflow pulls the latest version from the Git repository. This is equivalent to using the -latest flag.

Main script

Nextflow will attempt to run the script named main.nf in the project repository by default. You can change this with the manifest.mainScript option or by providing the script filename to run in this field.

If you specify a custom main script, the root of the default branch in your pipeline repository must still contain blank main.nf and nextflow.config files for Nextflow to interpret the pipeline correctly. 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.