pipeline_variables.json

{


    "assembly_output" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/assembled",
    "prokka_output" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/prokka",
    "abricate_output" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/amr_genes",
    "busco_output" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/busco", 
    "path_to_referance_genome" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/referance/",
    "path_to_shuffled_reads" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/docker_output/shuffle_reads",
    "path_to_snp_output" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/docker_output/snp_output",
    "path_to_tree_output" :"/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/docker_output/snp_output",
    "path_to_pdf_output" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/result",
    "CDC_path_to_pdf_output" : "/home/ssh_user/WGS_Drive/Phoenix/Reports",
    "csv_path" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing",
    "CDC_csv_path" : "/home/ssh_user/WGS_Drive/Phoenix/sample_fastq",
    "StrainDB" : "/home/ssh_user/WGS_Drive/CRAB_WGS_Sequencing/strain_db/pan-genome-db.hdf5",
    "phoenix_p": "/home/ssh_user/Documents/GitHub/phoenix",
    "phoenix_output":"/home/ssh_user/WGS_Drive/Phoenix",
    "kraken_path":"/home/ssh_user/WGS_Drive/Minikraken2DB"


}