I ran this annotation command: for k in *.fasta; do prokka $k --outdir "$k".prokka.output; echo $k; done
on hundreds of assembled sequences. Each sequence annotation output produced a folder named "sequence_name.prokka.output" but the actual files in the folders were named according to the date e.g. "PROKKA_03062020.gff" for all the folders.
Now I want the actual output be named with the actual FASTA file ID. Example: sequence ID of D02502 should be like this: "PROKKA_D02502.gff"
What do I add (or remove) from the code above?