The movie doesn't lift from any one Suicide Squad story
The movie makes plenty of changes to Squad lore: the sword-wielding heroine Katana has never been associated with the team. Neither has Batman's foe Killer Croc (with animalistic villains relegated to Wonder Woman's Cheetah and, more regularly, King Shark, a giant talking shark).
El Diablo and Slipknot are relatively minor villains appearing on the team. The pro: they're now played by men of color, adding a little diversity to the superhero genre. The con: they're insignificant. The most memorable thing Slipknot has done in the Suicide Squad comics is get his arm blown off during a mission. If anyone in the movie's going to die as an example of Waller's control over the group, I'd bet on Slipknot. Any takers?
The Suicide Squad issues you should read
The Suicide Squad can be found constantly wreaking havoc across DC titles like Superman, Booster Gold, Manhunter, and Green Lantern's Blackest Night. The original group makes an appearance in Darwyn Cooke's World War II-set miniseries, DC: The New Frontier, which presents an alternate take on all your favorite heroes. Suicide Squad Vol.1: Kicked in the Teeth, from DC's 2011 reboot, is actually the closest to the Suicide Squad movie: bonkers personality, lots of violence, and with Harley Quinn front and center.