[Bug]: Panaroo gives error when trying to run mafft

[erinyoung]

What container were you trying to use, and how were you attempting to use it?

Someone messaged me this error on slack

panaroo --aligner mafft -i gff/*.gff -o core_aln4 --clean-mode strict -a pan
Erorr:
/opt/conda/lib/python3.9/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
  warnings.warn(
Need specified aligner to be installed 
Need specified aligner to be installed 

I need to look at the current file and add a test for using the mafft aligner in panaroo.

Relevant log output