FILENAMES=glob_wildcards('{g}_genomic.fna').g
print(FILENAMES)

rule all:
    input:
        expand("{g}_protein.faa", g=FILENAMES)

rule make_prots:
    input:
        "{filename}_genomic.fna"
    output:
        "{filename}_protein.faa"
    shell: """
        prodigal -i {input} -a {output}
    """