I just ran (as in queued) FASTQC, Trimmomatic, HISAT2, StringTie, StringMerge, and DESeq2 on some RNA samples. My jobs currently display: “This job is waiting to run” or something similar. How long will it take for the entire job to complete (i.e., until I can download the tabular file with differential gene expression)?
Jobs queuing is normal. You are working a public server and the cluster resources are shared. Allow everything to queue then process. If you delete/rerun, the new jobs are added back to the end of the queue.
If any part of the workflow fails, try a rerun on the individual jobs first, then check the data for problems for any persistent failures. If you are using collections/workflow, you will be able to check an extra box on the tool form to “replace the original job” and any downstream tools that are paused will resume.
I added a tag to your post that links to prior questions about how the job queue works. Some have more details and links to FAQs.
Note: UseGalaxy.org server is very very busy right now, and jobs may queue for a bit longer than usual. But the same advice still applies: the fastest way to get work completed is to let jobs completely finish, undisturbed, and to use a workflow to “stream” the batch queuing and processing.
You can track the progress on the User → Workflow Invocations view.