DownloadReference

import json
configfile: "config.yml"

shell.executable("/bin/bash")
shell.prefix("set -euo pipefail; ")

##########
# avoid recursion loop
wildcard_constraints:
    sample="[^/]+",
    
##########
# Download reference chloroplast genome
#  This genome is used to find chloroplast genomes within your read set
#  Need to install BioPython before this rule runs --> installed as part of Snakemake env.
#  If the computer or remote HPC you are working from has restricted access to external
#  data sources, you will need to comment out each line of this rule and manually download
#  each reference genome of interest and save it so it is identical to 'output' below

from snakemake.remote.NCBI import RemoteProvider as NCBIRemoteProvider
NCBI = NCBIRemoteProvider(email=config["my_Email"]) # email required by NCBI to prevent abuse
rule download_chloro_genome:
    input:
        NCBI.remote(config["NCBI_reference_accession"] +".fasta", db="nuccore")
    output:
        "chloro_assembly/reference/" + config["NCBI_reference_accession"] + "_single.fasta"
    benchmark:
        "chloro_assembly/benchmark/download_chloro_genome/" + config["NCBI_reference_accession"] + "_benchmark.txt"
    shell:
        """
        mv {input} {output}
        """