Sided with the Minutemen - check

Castle rebuilt - check

Drowned in Garvey's radiant quests - check

Institute infiltrated - check

On my first playthrough I sided with the Institute, now that I'm with the Minutemen I don't want to be involved with the Institute anymore, but what am I supposed to do next? I already met Shaun who assigned me the Synth Retention quest, can I just ignore it? If so, what are my options to deal with the Institute with the help of the Minutemen?