Add ML warehouse JSON output capability to TreePublisher

[kjsanger]

The main Illumina pipeline iRODS publisher can produce a JSON dump containing metadata about the files it has deposited in iRODS.

Calback constructing the JSON here:

npg_irods/lib/WTSI/NPG/HTS/Illumina/RunPublisher.pm

Line 367 in 0b38502

my $mlwh_json_cb = sub {

We would like a similar capability for the the tree publisher https://github.com/wtsi-npg/npg_irods/blob/devel/lib/WTSI/NPG/HTS/TreePublisher.pm and to have that exposed through its CLI https://github.com/wtsi-npg/npg_irods/blob/devel/bin/npg_publish_tree.pl

• Propose a version of the JSON metadata generalised beyond the core Illumina pipeline

We will allow the metadata to describe just a collection path, being the root of the uploaded directory hierarchy,
without including paths of all the consitituent data objects.

• Propose a route for the metadata to reach the ML warehouse
• Add to the TreePublisher the option to create JSON file dump
• Expose the new option on the CLI