As mentioned in the existing answer, all junk can be deposited into your workshop store by approaching the store and pressing the Transfer button, then pressing the Transfer All Junk button.
However, there are a few things not mentioned in the existing answer that need clarification:
- All stores (workshop, weapons, armor, etc) share the same contents per settlement. This means if you have multiple settlements, contents in your store at one settlement will not be shared with another settlement
- You can set up a supply line using spare settlers to share store contents between multiple settlements, this essentially makes everything in a store at a linked settlement available as though it was in the local store
