Support compressed (e.g. gzipped) fasta files for cgMLST alleles

[samuell]

This is a suggestion to keep the allele files, which are currently uncompressed .fasta, as compressed e.g. with gzip, to lower the storage usage.

The background is that we are having a problem where we have trouble fitting our epidemological typing pipeline within the default limits for the CI images at GitHub actions. Turns out one of the parts taking the most space currently are the cgMLST allele files used by chewBBACA.

I'm happy to have a go at contributing with this, if this is something that you think sounds reasonable.

[ramirma]

Thanks for the suggestion @samuell . Something to think about.