How to use analysis output in my pipeline

I am running an analysis and I want to edit the output that I received from that analysis. However I cannot define the output name in my pipeline, because after running the analysis it is asking me to name the output file. How can I include that output file in my pipeline ?

• Welcome to Bioinformatics.StackExchange! I would recommend reverting the edit you just made. The question is impossible to answer generically, since many tools have different ways to specify output filenames. My answer is only applicable to pepstats, like your original question asked. – Daniel Standage Mar 5 at 20:21

I assume you are referring to the pepstats program from EMBOSS. The program has a -outfile flag that allows you to specify your desired name for the output file when you're not running the program interactively.