message: refactor: remove unused clade definitions from CLI interface
diff: @@ -4,7 +4,6 @@ import { AuspiceJsonV2 } from 'auspice'
  import { convertPcrPrimers } from 'src/algorithms/primers/convertPcrPrimers'
  import yargs from 'yargs'
  -import { validateClades } from 'src/algorithms/clades'
  import { AnalysisResult, Virus } from 'src/algorithms/types'
  import { getVirus } from 'src/algorithms/defaults/viruses'
  import { parseCsv } from 'src/io/parseCsv'
  @@ -51,19 +50,12 @@ export function parseCommandLine() {
  description:
  '(optional) Path to Auspice JSON v2 file containing custom reference tree. See https://nextstrain.org/docs/bioinformatics/data-formats',
  })
  - .option('input-clades', {
  - alias: 'l',
  - type: 'string',
  - description:
  - '(optional) Path to a JSON file containing custom clade definitions.\nFor an example see https://github.com/nextstrain/nextclade/blob/20a9fda5b8046ce26669de2023770790c650daae/packages/web/src/algorithms/defaults/sars-cov-2/clades.json',
  - })
  .option('input-qc-config', {
  alias: 'q',
  type: 'string',
  description:
  '(optional) Path to a JSON file containing custom configuration of Quality Control rules.\nFor an example format see: https://github.com/nextstrain/nextclade/blob/20a9fda5b8046ce26669de2023770790c650daae/packages/web/src/algorithms/defaults/sars-cov-2/qcRulesConfig.ts',
  })
  -
  .option('input-gene-map', {
  alias: 'g',
  type: 'string',
  @@ -132,7 +124,6 @@ export async function validateParams(params: CliParams) {
  const inputFasta = params['input-fasta']
  const inputRootSeq = params['input-root-seq']
  const inputTree = params['input-tree']
  - const inputClades = params['input-clades']
  const inputQcConfig = params['input-qc-config']
  const inputGeneMap = params['input-gene-map']
  const inputPcrPrimers = params['input-pcr-primers']
  @@ -150,7 +141,6 @@ export async function validateParams(params: CliParams) {
  inputFasta,
  inputRootSeq,
  inputTree,
  - inputClades,
  inputQcConfig,
  inputGeneMap,
  inputPcrPrimers,
  @@ -165,7 +155,6 @@ export interface ReadInputsParams {
  inputFasta: string
  inputRootSeq?: string
  inputTree?: string
  - inputClades?: string
  inputQcConfig?: string
  inputGeneMap?: string
  inputPcrPrimers?: string
  @@ -176,7 +165,6 @@ export async function readInputs({
  inputFasta,
  inputRootSeq,
  inputTree,
  - inputClades,
  inputQcConfig,
  inputGeneMap,
  inputPcrPrimers,
  @@ -200,13 +188,6 @@ export async function readInputs({
  }
  }
  - if (inputClades) {
  - const clades = validateClades(await fs.readJson(inputClades))
  - if (clades) {
  - virus = { ...virus, clades }
  - }
  - }
  -
  if (inputQcConfig) {
  const qcRulesConfig = qcRulesConfigValidate(await fs.readJson(inputQcConfig))
  virus = { ...virus, qcRulesConfig }
  @@ -273,7 +254,6 @@ export async function main() {
  inputFasta,
  inputRootSeq,
  inputTree,
  - inputClades,
  inputQcConfig,
  inputGeneMap,
  inputPcrPrimers,
  @@ -289,7 +269,6 @@ export async function main() {
  inputFasta,
  inputRootSeq,
  inputTree,
  - inputClades,
  inputQcConfig,
  inputGeneMap,
  inputPcrPrimers,
  