if you export workflows it can happen that your *.ga file contains full-path informations to the chromosome len file. For example try to export the "mergeCols1" or the "trimmer" tool. The field chromInfo will have a full path attached. I don't think that will cause any harm, but it would be nice to omit this information.
Trello Card is here: https://trello.com/c/TNUvq8X3