I use this script for taking screenshots, bound to the Print Scrn key with i3wm. It dumps a screenshot into my 'Pictures' directory, and makes a beep. You can set it to make a notification if you want.
#!/bin/bash import -window root $HOME/Pictures/screenshot_`date +%y-%m-%d_%H-%M-%S`.png
Without beep:
#!/bin/bash import -silent -window root $HOME/Pictures/screenshot_`date +%y-%m-%d_%H-%M-%S`.png
Two main commands are convert and mogrify. The distinction is that the former makes new files, and the later can overwrite existing files.
This will convert all PNGs in the current directory to JPGs at quality 50 and scaled to 1200px width.
mogrify -format jpg -quality 50% -resize 1200x *.png
To create a PDF from a bunch of PNG files in a directory:
convert *.png [name].pdf