consensusGenome

var ConsensusGenomeCmd = &cobra.Command{
	Use:   "consensus-genome",
	Short: "Commands related to the consensus-genome pipeline",
	Long:  "Commands related to the consensus-genome pipeline",
	PersistentPreRun: func(cmd *cobra.Command, args []string) {
		if strings.ToLower(viper.GetString("accepted_user_agreement")) != "y" {
			fmt.Println("Cannot upload samples until the user agreement is accepted, run czid accept-user-agreement or set CZID_CLI_ACCEPTED_USER_AGREEMENT=Y")
			os.Exit(2)
		}
	},
}

var MedakaModels = map[string]string{
	"r941_min_fast_g303":     "r941_min_fast_g303",
	"r941_min_high_g303":     "r941_min_high_g303",
	"r941_min_high_g330":     "r941_min_high_g330",
	"r941_min_high_g340_rle": "r941_min_high_g340_rle",
	"r941_min_high_g344":     "r941_min_high_g344",
	"r941_min_high_g351":     "r941_min_high_g351",

	"r103_prom_high_g360":     "r103_prom_high_g360",
	"r103_prom_snp_g3210":     "r103_prom_snp_g3210",
	"r103_prom_variant_g3210": "r103_prom_variant_g3210",
	"r941_prom_fast_g303":     "r941_prom_fast_g303",
	"r941_prom_high_g303":     "r941_prom_high_g303",
	"r941_prom_high_g330":     "r941_prom_high_g330",
	"r941_prom_high_g344":     "r941_prom_high_g344",
	"r941_prom_high_g360":     "r941_prom_high_g360",
	"r941_prom_high_g4011":    "r941_prom_high_g4011",
	"r941_prom_snp_g303":      "r941_prom_snp_g303",
	"r941_prom_snp_g322":      "r941_prom_snp_g322",
	"r941_prom_snp_g360":      "r941_prom_snp_g360",
	"r941_prom_variant_g303":  "r941_prom_variant_g303",
	"r941_prom_variant_g322":  "r941_prom_variant_g322",
	"r941_prom_variant_g360":  "r941_prom_variant_g360",
	"":                        "",
}

var Technologies = map[string]string{
	"Illumina": "Illumina",
	"Nanopore": "ONT",
}

var WetlabProtocols = map[string]string{
	"ARTIC v4/ARTIC v4.1":                 "artic_v4",
	"ARTIC v3 - Short Amplicons (275 bp)": "artic_short_amplicons",
	"ARTIC v3":                            "artic",
	"AmpliSeq":                            "ampliseq",
	"Combined MSSPE & ARTIC v3":           "combined_msspe_artic",
	"MSSPE":                               "msspe",
	"SNAP":                                "snap",
	"COVIDseq":                            "covidseq",
	"Midnight":                            "midnight",
	"Varskip":                             "varskip",
}