I'm sorry for your loss.
Yes, you'll need to indicate that they're deceased and enter their date of death.
You'll need to print and mail your spouse's tax return. The CRA excludes returns for people who passed away in 2016 or 2017 from using NETFILE.
http://www.cra-arc.gc.ca/esrvc-srvce/tx/ndvdls/netfile-impotnet/lgblty-eng.html#other
when I started to do 2016 I transferred over the info filled out both then wanted to put the date of death allowed me to do that, then the program but I have a problem I need to separate the two files but it will not allow me to remove the wife