I thought that we were friends
Are both correct:
ich dachte, wir wären Freunde.
ich dachte, dass wir Freunde wären.
Thanks to EilliottofRivia, I now understand the importance of commas. See: https://www.duolingo.com/comment/26572354
commas in german language are quite complicated, even for native speakers. but it is importent since sometimes a wrong set or forgotten comma can change the hole meaning of the the sentence.
ex: wir essen jetzt, Opa : granpa, we are going to eat now.
wir essen jetzt Opa. : we are eating granpa now.