Module parameters

The key words “MUST”, “MUST NOT”, “SHOULD”, etc. are to be interpreted as described in RFC 2119.

1 Module input and outputs

The module file SHOULD only define input and output files as command-line parameters to be executed within the process.

2 Use of parameters within modules

Initialise and use params only within the module in the local context of the module. Do not assume that named params defined in the parent workflow will be passed to the module to allow developers to call their parameters whatever they want. Use additional input value channels for such scenarios.

3 Specification of multiple-threads or cores

If the tool supports multi-threading, provide the appropriate parameter using the Nextflow task variable. For example, --threads $task.cpus.

4 Evaluation of parameter within a module

Define within the process any parameters that need to be evaluated in the context of a particular sample. For example, single-end/paired-end data.