import glob, os.path

FILENAMES=glob.glob('podar-ref/*.fa')
FILENAMES = [ os.path.splitext(f)[0] for f in FILENAMES ]
FILENAMES = [ os.path.basename(f) for f in FILENAMES ]
print(FILENAMES)

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

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