ext properties/keys

Ext properties or keys are special process directives (See: ext directive ) that insert strings into the module scripts. For example, an nf-core module uses the string assigned to ext.args ( or ext.args2, ext.args3, … ) to insert tool specific options in a module script:

Example:

The configuration

process {
  withName: 'TOOL_SUBTOOL' {
    ext.args = '-T -K'
  }
}

inserts the string -T -K as options to the module script:

process TOOL_SUBTOOL {
  input:
  tuple val(meta), path(bam)
 
  output:
  tuple val(meta), path("*.log"), emit: log
  path "versions.yml",            emit: versions
 
  script:
  def args   = task.ext.args ?: ''          // If ext.args is defined assign it to args
  def prefix = task.ext.prefix ?: meta.id   // If ext.prefix is defined assign it to prefix, otherwise assign meta.id value
  """
  tool subtool $args $bam > ${prefix}.log
  """
}

so the script becomes:

#! /usr/env/bin bash
tool subtool -T -K test.bam > test.log

Permitted ext keys

The following table lists the permitted keys used in nf-core modules. Other keys must be discussed with maintainers, and added here when permitted.

To see some more advanced examples of these keys in use see:

• Set ext.args based on parameter settings
• Set ext.prefix based on task inputs
• Set ext.args based on both parameters and task inputs

Rational

The ext keys are properties that are intended to allow a pipeline user to change via configuration file how a module behaves. They are not a means for a developer to bypass passing values via a module’s input:. The majority of optional command-line flags are passed through ext.args. If changing an ext key would lead to pipeline instability, it should be an input:. This allows module parameters to be fully described and documented.