What you're asking here is probably beyond the scope of a Q/A site. To properly review all of these steps and provide feedback and suggestions would take hours. If you really need that level of support, then you're going to want to pay someone a consulting fee to help you get your pipeline set up. If you have specific questions about individual steps or commands, then Biostar can be a great resource, and please do feel free to ask questions. I'd encourage you to look through old posts first, as many of these topics have been addressed individually in the past. - Chris Miller