Bioinformatics pipeline flow chart guidelines?
This sadly doesnt seem to be stated as a question proper for the site as noted in the comments. Perhaps you can rephrase it and add some examples.

From personal experience, UML is widely accepted for the symbols and flow of charts on various charts. There are software to so it easily like DIA (openware), flowchart (online) or Microsoft Visio. But there are plenty of sowftwares to do it. What you must abide to, however, is to be consistent.