There is already a DECOMPRESS process which allows to decompress files:
https://github.com/bigbio/quantms/blob/4abe9d819a2bf9eb0030ac67603dc0fa7f3a9b3a/subworkflows/local/file_preparation.nf#L32-L35
One could investigate in nf-core modules or on Slack how to keep compress files in and out, but use uncompress in the actual process.