To transcode every file in a directory to h265 (for example):

#!/bin/bash

find . -type f -name '*.mkv' -exec sh -c '
i="$0"
nice /opt/ffmpeg/bin/ffmpeg -i "$i" -map 0 -scodec copy -acodec copy -vf yadif -vcodec libx265 "$i.mkv"
mv "$i.mkv" "$i"
' {} ';'