Hi-I am trying to set up a workflow for RNAseq (FASTQC, TRIMMOMATIC,HISAT2, FEATURECOUNTS) but I cannot get the program to load new fastq files uploaded with NCBI. Is there anything going on with Galazy today>
The Galaxy Training Academy is indeed happening this week, which means there may be increased user activity on the platform. However, this higher traffic shouldn’t typically impact your ability to set up a workflow.
To help us troubleshoot the issue with your FASTQ files, could you provide more details about the error you’re encountering? Specifically:
- Are you seeing any error messages or status indicators (like red, yellow, or grey) next to the files in your history?
Any additional information you can provide will help us pinpoint the issue more effectively. Thank you!
Hi @pcarrico
I’ve got a test running here to see what happens.
This is what I did
- Imported your history
- Extracted a workflow from it
- Run the workflow, and sent the result to a new history
Maybe you can explain what you are doing differently?
So, the workflow seems like there is some loop where it keeps running trimmomatic on previously trimmed data?
Maybe this will help?
Hi @pcarrico
I see one of the Faster tools that extracts fastq reads has unconnected “noodles” in your workflow.
And, one of the Trimmomatic steps doesn’t have an input, so that will never run, and any downstream tool run dependent on it will never run.
Maybe you need to edit it to avoid doing that extraction step twice?
With the Extract Workflow function, you can choose what to extract, but sometimes it is easier to just get all it, then to edit the draft result after.
Screenshot
Thanks Jenna, I will give that a try!
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