Configuration

Modules and subworkflows expose configuration endpoints that can be set at runtime. Look for the arguments section in the API documentation. Refer to the correct section below for information on the configuration procedure respective to each component.

Module Configuration

Modules are configured through the ext parameter mapping, exclusive to each of them. Configuration must be done inside nextflow.config files, it cannot be done in .nf files. The configuration endpoint is accessible in the process scope :

process {
    ext.parameter_one = "value"
}

To restrict the configuration to a specific module, say MODULE_1, use the withName process selector :

process {
    withName: "MODULE_1" {
        ext.parameter_one = "value"
    }
}

Refer to the arguments section of modules in the nf-neuro API documentation for available configuration endpoints and to the nextflow documentation for more information on configuration and process selectors.

Caution

By default, when configurations are provided by nf-neuro subworkflows, they use the lowest priority selector available. To ensure your selector targets the right module, in the right subworkflow, use its fully qualified name. For example, MODULE_1 inside of SUBWORKFLOW_2 has the fully qualified name : SUBWORKFLOW_2:MODULE_1.

Subworkflow configuration

Subworkflows expose params configuration endpoints directly. You can define them either in the nextflow.config or in the .nf file that includes it.

params {
    subworkflow_parameter = "value"
}