text: user4216: 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 ?
  
  user96: 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.
  
original_text: 4216: <p>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 ?</p>
   96: <p>I assume you are referring to the <a href="http://emboss.sourceforge.net/apps/cvs/emboss/apps/pepstats.html" rel="nofollow noreferrer">pepstats program from EMBOSS</a>. The program has a <code>-outfile</code> flag that allows you to specify your desired name for the output file when you're not running the program interactively.</p>
  