The order of processing affects the result.

When pre-processing videos for encoding, the order of the filters does have an effect on image quality and the processing time.
I always try to follow the order below for best results.

1) De-interlace if needed.
2) Frame rate conversion if smaller than original.
3) Cropping if needed.
4) Resize if reducing image size.
5) Color space conversion.
6) De-noise.
7) Resize if enlarging image.
8) Frame rate conversion if greater than original.
9) Sharpen or other enhancements as needed.

The idea is that first you start with a progressive image to then reduce the size and number of frames to work with smaller data sets. Perform color space conversions and apply any noise reduction if needed. If you are enlarging the image, do it after the color space conversion and noise reduction. Then apply frame rate conversions.
Finally perform any sharpening or other image enhancing filters to the final image.