metagenomics

var GuppyBasecallerSettings = map[string]string{
	"fast":  "fast",
	"hac":   "hac",
	"super": "super",
}

var MetagenomicsCmd = &cobra.Command{
	Use:   "metagenomics",
	Short: "Commands related to metagenomics pipelines",
	Long:  "Commands related to metagenomics pipelines",
	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 Technologies = map[string]string{
	"Illumina": "Illumina",
	"Nanopore": "ONT",
}