configfile: "config/config.yaml" 

import os
import yaml
import logging
import glob
import gzip
from datetime import date

RESDIR = config["res_dir"]


def _all(wildcards):
    out = checkpoints.dm_download_checkpoint.get(**wildcards).output 
    assemblies = [] 
    genome_dir = os.path.join(RESDIR, "ncbi_dataset","data")
    for g in os.listdir(genome_dir):
        if g.startswith("GCA_") or g.startswith("GCF_"):
            assemblies.append(g)
    if assemblies : # There is no new assembly so we stop here.
        return os.path.join(RESDIR,"genomes.yaml"),
    else:
        return out
        
rule all:
    input:
        _all, 



        
include: "rules/translate.smk"
include: "rules/download.smk"
include: "rules/fetch.smk"