I am new to Galaxy. I recently created what i think is a simple workflow. (link below). When I go to execute my workflow, I get this confirmation message…
However, I look in my history, tried to refresh and everything, and nothing. It’s like the workflow hasn’t even started yet. I have been reading around and all i see is that this is a common issue, but no real solutions. Hoping if i asked here i would find one.
nb* I have ‘Send results to a new history = NO’, though I have tried with a ‘YES’ but this doesn’t seem to change anything.
Try adding an “input” to the workflow at the very start (under the tool menu section “Inputs”). This can be an individual dataset or a dataset collection of type “list” (based on your use case).
Then, disconnect all noodles between tools, and reconnect them starting from the chosen input through the remainder of downstream tools, in the order of data flow/execution.
Note: If you decide to change the input in the workflow editor in any way (individual dataset, collection, the collection “type”), or decide to modify options in tools that change an output datatype (intermediate tool or at the end, including post job actions), you’ll need to disconnect then reconnect all of the noodles again in the same way: start to finish (to reset metadata). We are going to make a change to have the workflow metadata reset real-time (during editing) but that is still a work-in-progress. If interested in full details, please see/follow the help here: https://github.com/galaxyproject/galaxy/issues/7431
Please give that a try and see if it resolves your execution problems. If not, please share the modified workflow and a history that contains a sample input dataset that runs through the tools correctly when executed directly within the history. We can troubleshoot further from there.
Hello,
I’ve also had this issue. It either invokes and does not show in history or invokes and won’t complete the workflow. Link to my workflow https://usegalaxy.org/u/genesandbones/w/ngs-pipeline. I have unattached and reattached all of the noodles as well.
@Dale_Calleja Very glad you have the workflow running now
@genesandbones, welcome to the forum! Sorry to hear you are having problems. I will review your workflow tomorrow morning (Monday) in more detail, but I can see that you are using a custom genome and indexing during execution (rather than creating the custom build first). Am wondering if that is problematic (fails for some reason – highly fragmented fasta datasets can be one reason). It would help if you shared a history link that contains the input datasets, to better allow a review/rerun to find where the issue is coming from. If you don’t want to publish the history link publically, you can send me a direct message here with the link, or email galaxy-bugs@lists.galaxyproject.org (our private support mailing list). If you decide to email, include a link to your post here with the workflow link, for context please, or include both the source history + workflow link in the email.
