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Advanced Options

Advanced launch options allow users to modify the configuration and execution of the pipeline.

Nextflow config file#

The Nextflow config field allows the addition of settings to the Nextflow configuration file.

This text should follow the same syntax as the Nextflow configuration file.

In the example below, we can modify the manifest section to give the pipeline a name and description which will show up in the Tower monitoring section.

After changing the name in the manifest, when monitoring the pipeline, the name has been overwritten.

Pre & post-run scripts#

It is possible to run custom code, either before and after the execution of the Nextflow script. These fields allow users to enter shell commands.

Pull latest#

Enabling this option ensures 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 project repository by default. This can be changed via either the manifest.mainScript option or by providing the script filename to run in this field.

Workflow entry name#

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