I am new to this community and not sure how to best write a post. So please let me know if you need more information. I am trying to automate my workflow for differential expression. I would like to turn my lines of code into a script so I can make multiple scripts and eventually pipe them all together... make a pipeline from my workflow. This is my first time attempting to do this. I tried to add some comments in my bourne shell script. I am not sure why it is throwing an error. Please refer to the screenshot. Also, if you have any helpful tips for bash scripting and automating workflows through pipeline development then let me know!
Side note, I am PhD in Biology with Emphasis a Bioinformatics. I familiar with R and MATLAB scripting... not bash scripting. Trying to use the command line because most people in my lab are more familiar with tools on the command line.