[Metagenomics Illumina] fix to single-end problem when running with new setup

[AstrobioMike]

Draft currently until i get confirmation this fixed it from the individual who hit the issue.

• fix to single-end humann3 run where the ref db for metaphlan needs to be explicitly specified
  • this wasn't always necessary, but it became so a little while back. A fix was already implemented for paired-end, but apparently i didn't catch it for single-end (and it wouldn't cause a problem unless it was the first time a workflow was run on a new system)
  • I have this marked as a draft to be left alone until i get confirmation from Ankur Naqib (works with Stefan Green at Rush) that this solved the issue for him
    • once that's confirmed, i'll update here