height 100% in flex

You can overlap (nest) flex boxes :

html, body {
  margin: 0;
  padding: 0;
  height: 100%;
}

.wrapper {
  border: 1px solid red;
  padding: 20px;
  min-height: 100%;
  display: flex;
  /* change flex-direction from column to row will work */
  flex-direction: column;
  box-sizing:border-box;
}

.container {
  display:flex;
  flex-direction: column;/* up to your needs */
  border: 1px solid green;
  padding: 20px;
  flex: 1;
}

.content {
  border: 1px solid blue;
  flex:1;
}
<div class="wrapper">
  <div class="container">
    <div class="content">
      Hello there
    </div>
  </div>
</div>

You may also mind the box-sizing properties to include borders and padding in size calculation.