Hi Nicola,
Naturally, this can be done with PixInsight. However, the command line is not the best option; you have to write either a script in the JavaScript language, or a module in C++. For relatively simple chained batch tasks like these, JavaScript is undoubtedly the best and fastest option. I know if you have no programming experience, this may sound quite daunting, but it is actually much easier than what may seem. You just have to put all of the data items in their correct places and call the correct tools to get the tasks done in sequence.