Add picrust2/pipeline module

[dialvarezs]

Adds https://github.com/picrust/picrust2 module

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[SPPearce]

Hmm, these are quite nested.
Is it sensible to copy these into the base directory with renaming them with ${prefix}?

[dialvarezs]

Hi @SPPearce! Sure, that makes sense to me.

[SPPearce]

How many files does this actually make? Do the downstream tools assume it'll need the subfolders?

[dialvarezs]

It depends on how many functions are enabled. EC and KO are enabled by default, and the full list includes: EC, KO, GO, PFAM, BIGG, CAZY, GENE_NAMES.

Each CSV file can be used independently, so it should be fine to move them out of the output directory (preferably as copies, in case the original directory structure needs to be preserved).

There are a few other files in the output directory (around 20, excluding intermediate files), but these are the main ones.