Question

If work done only has magnitude not direction then how can it be negative?

Answer 1

negative signature used for a physical quantity signifies the reaction of the body in opposite direction to that of favorable for instance lets take a case, A ball hit by a bat comes to rest after moving some distance on the ground. The frictional force acting opposite to the direction of motion of the ball works to stop the ball.

Similarly motion of the body results in the direction of force being applied and doesn't depend upon the work at all but work itself does depend on the force and its nature.It could be negative!