The workflow looks connected correctly. I see one problem in the settings for BWA, that we have fixed but it is not yet published to usegalaxy.org yet (or anywhere else). However, that would result in a job failure at the BWA step (or possibly a warning). More is probably going on and we can help to find out what that is and get it fixed (server/tool side or the workflow itself).
@kriskris99 Would you please send in a link to a test history that contains all of the inputs and the results you get from executing the workflow. It would be best if this was isolated. So if you need to, copy the inputs into a new history, then execute the workflow, sending it back to the same history. Executing the workflow and sending it to a new history won’t include all of the inputs we’ll need to do troubleshooting tests.
Generate a history share link and put in a mail, along with the workflow share link again, and a link to this post (as reference) and send all to this mailing list: galaxy-bugs@lists.galaxyproject.org. This maintains your data privacy – only admins at usegalaxy.org will have access and only for troubleshooting purposes.
Note: Make sure all data is left undeleted. When you perform the share, click on the box to share “all objects” in the history before generating the link (unshare then re-share to double check this box is checked if you have already generated the link).
