Replace local modules with nf-core modules

[CarsonJM]

Description of feature

Modules to be replaced (as of 2024/01/18)

• MERGE_FASTAS -> nf-core/modules CAT
• UNCOMPRESS_FASTA -> nf-core/modules GUNZIP
• WGSIM -> nf-core/modules WGSIM (should match in functionality: wgsim: add seed option, add stub, update test, match readsimulator pipeline modules#6544)