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 ?
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.