Add bwa-mem2-idx

[duartetorreserick]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

Often we use bwa in workflows for multiple samples, where the same index is created repeatedly—-hundreds or even thousands of times. This tool will allow the creation of an index before running bwa-mem2, so multiple bwa-mem2 instances can use the same index without creating it over and over again. This will require a modification to bwa-mem2 as well to be able to take advantage of the index.

[mvdbeek]

Can you create a subclass of the directory datatype for this in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/datatypes_conf.xml.sample?

Something like

<datatype extension="bwa_mem_2_index" type="galaxy.datatypes.data:Directory" display_in_upload="true" subclass="true"/>

Then you can move the index directory to $output.files_path, and in the same way the bwa_mem2 tool can consume the index directory from ``$output.extra_files_path`