Assuming that all your genomes end in .fna and that you use a bash shell:

for i in *.fna
do
prokka --kingdom Bacteria --outdir ${i%.fna} --force --prefix ${i%.fna} --locustag ${i%.fna} --addgenes --cpus # $i
done

For a (t)csh shell:

foreach i ( *.fna )
prokka --kingdom Bacteria --outdir $i:r --force --prefix $i:r --locustag $i:r --addgenes --cpus # $i
end

In both cases instead of # you should enter the actual number of CPUs allocated to this command, and prokka command may need to be customized a bit to match your needs.