Creating embroidery designs (like the JEF for Janome machines) from PDF sources is perhaps somewhat odd choice, nonetheless should be possible. But only if the .pdf file in question some kind of graphics, preferably vector based image. This is typically the case for graphics exported from some vector graphics program, such as Adobe Illustrator.
If this is also your case, the best course of action would be to convert pdf to svg or back to AI (Illustrator graphics) and then convert that resulting file to JEF, or any related embroidery format which could then be converted to JEF. Should the .pdf document contain raster image, you can also achieve this, but the end result may be a little worse as it is generally harder to create embroidery design from raster graphics.Open PDF file Open JEF file