We use drush cim partial command
drush cim --partial --source="directory path where the single yml is stored"
Drush always runs inside docroot, so if your single yml is stored in a directory outside docroot update the command accordingly. For example if you have a web folder structure like this ,

Here web is the docroot and we have partialconfig on the same level and drush runs from inside docroot, so in this case the command will be,
drush cim --partial --source="../partialconfig"
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