Play anyway. Depending on how large your group is, you can probably do without a player or two. Go ahead without them. Their characters disappear for the events of that session, and don't earn karma for those plot points.
If you're equipped for it, you might allow up to one "teleplayer" per session. When someone can't show up in person but still wants to play, we'll set up a laptop in their place, point its webcam at the gaming table, and have them join virtually using Google Hangouts (or Skype or FaceTime). Works well enough, but only one person at a time and don't let them make a permanent thing out of it.
If you're missing too many players to go ahead with the campaign, then run a one-shot mini-mission for the ones who do show up. Just a simple courier job, surveillance, sabotage, bodyguarding, etc. Extra karma for those characters. Be sure to wrap it up in a single session, though, or you end up with multiple unfinished games in progress.
Or play Shadowrun: Crossfire or Shadowrun: Encounters instead.