Custom PDB templates for AlphaFold Jobs

[maxbates]

Hi! I'd like to provide my own directory of PDB templates, on a per-job basis, for example to run AlphaFold with a single template and an empty MSA to validate a design.

I see that I can specify AlphaFold2Job.template_mmcif_dir to set the CIF files exposed to AlphaFold. However, this appears to only support paths on the instance, and there doesn't appear to be a way to stage additional paths as part of the job (beyond the fasta and MSAs).

Do you have any suggestions to support this, or is there a generic and not-too-hacky way to modify the command_list to include additional staged paths?