message: fix(cli): make sure the custom tree is used
diff: @@ -205,12 +205,14 @@ export async function main() {
  outputTree,
  inputQcConfig,
  inputRootSeq,
  + inputTree,
  } = await validateParams(params)
  const { input, rootSeq, qcRulesConfig, auspiceDataReference } = await readInputs({
  inputFasta,
  inputQcConfig,
  inputRootSeq,
  + inputTree,
  })
  const { results, auspiceData } = run(input, rootSeq, qcRulesConfig, auspiceDataReference)
  