Workflow doesn't execute all steps after successfully being invoked.



I’ve recently created a workflow for my ChIP-Seq analysis. I used the workflow to analyse new experiments and while there are 5 steps, only 3 steps are executed. I dont even see the other steps at all in the history.
Any suggestions on how to resolve this would be greatly appreciated.


Could you share the workflow with us? At least a screenshot.


Please see the workflow using the following link:

My history shows steps till bamCompare are executed while Compute Matrix and HeatMaps are not.


@jennaj could you please have a look, it seems valid to me at first glance


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 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: This maintains your data privacy – only admins at 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).