Naming conventions

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

1 Name format of module files

Use all lowercase for the directory structure of the module name, without punctuation. For example, modules/nf-core/bwa/mem/.

Make the name of the software (i.e., bwa) and tool (i.e., mem) all one word.

The nf-core/tools command will validate the suggested name.

2 Name format of module processes

Make the process name in the module file all uppercase. For example, process BWA_MEM {. Make the name of the software (i.e., BWA) and tool (i.e., MEM) all one word separated by an underscore.

3 Name format of module parameters

Parameter names MUST follow the snake_case convention.

4 Name format of module functions

Function names MUST follow the camelCase convention.

5 Name format of module channels

Channel names MUST follow snake_case convention and be all lower case.

6 Command file output naming

Output file (and/or directory) names SHOULD consist of only ${prefix} and the file-format suffix (for example, ${prefix}.fq.gz or ${prefix}.bam).

• This provides re-usability, giving developers flexibility to name their output files when using the module.

• As a result of using this syntax, if the module could potentially have the same named inputs and outputs, add a line in the script section like below (another example here) which will raise an error asking the developer to change the ext.prefix variable to rename the output files so they don’t clash.

  script:
  if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"

• If the input and output files are likely to have the same name, set an appropriate default prefix, for example:

  def prefix = task.ext.prefix ?: "${meta.id}_sorted"