Create Minimap2 mapper index module

This module allow to create a Minimap2 mapper index with custom options. If this module is not declared in the workflow file, the default mapper index generator will be used if you want to use Minimap2 as mapper.

  • Internal name: minimap2indexgenerator
  • Available: Both local and distributed mode

  • Input ports:
    • genome: genome sequence file (format: genome_fasta)
    • genomedescription: genome description (automatically generated from genome sequence file)

  • Output port:
    • output: genome mapper index

  • Mandatory parameters: none

  • Optional parameters:
    • Parameter Type Description Default value
    indexer.arguments string Specifies the indexer arguments to use to build the index Not set
  • Configuration example:
    • <!-- Create Minimap2 index -->
<step skip="false">
	<module>minimap2indexgenerator</module>
	<parameters>
		<parameter>
			<name>indexer.arguments</name>
			<value>-x splice</value>
		</parameter>
	</parameters>
</step>