find

Loop over all files in all sub-directories

# show all .fasta files in all sub-directories of folder 'assembly'

find assembly/ -name "*.fasta"

assembly/projectA/run1.fasta

assembly/projectA/run2.fasta

assembly/projectB/run1.fasta

assembly/projectB/run2.fasta

assembly/final.fasta

# search for 'plasmid' in all fasta files (run command grep on all files) in folder 'assembly'

find assembly/ -name "*.fasta" -exec grep --with-filename plasmid {} \;

# compress all .fasta files using gzip, include all sub-directories of folder 'assembly'

find assembly/ -name "*.fasta" -exec gzip {} \;

General

find /path/ -name filter files -exec run command {} \;

-name # filter filenames

-exec # run command

{} # on each file

\; # pass files one by one to the command

https://help.ubuntu.com/community/find