[Feature Request] Enable compatibility for .gz, maybe .cr files

[Firedrops]

BWA can natively work with .fastq.gz files, but it appears the upstream pipeline does not directly pass the files to the aligner, but extracts information from it first. Hence .gz files do not appear to work currently.
The jobs stop at Parse FastQ data part, with no outputs.

It might also be a good idea to support cryfa encrypted files, which act as both compression and security in the future.