Add more gap filling options to HQTB cleanup

[cb-Hades]

Currently, only the GeneGapFIller and the COBRApy medium gap filling can be used inside the HQTB workflow during the cleanup step.

refineGEMs provides two more options, BioCycGapFiller and KEGGGapFIller. These might be a good addition for this workflows.

Issues

• if one where to add these two to the workflow, the amount of parameters becomes quite substatial. Therefore, it shozld be considered to add an extra configuration file or something similar for the gap filling only.
  • ❗ command access for model cleanup has already been disabled due to too many input params
• KEGGGapFiller requires a direct match to a KEGG organism ID -> wait for update in refineGEMs to let this be usedc with a similar strain as well, as this workflow has a strong focus on lab strain model generation, which are likely to not have a match in KEGG.