Question: Sam-to-bam in workflow
gravatar for lucille.delisle
3.0 years ago by
lucille.delisle0 wrote:

I made a workflow in which I am using the tool SAM-to-BAM. I wanted to use a locally cached reference genome set at Runtime. My problem is that at Runtime there is no reference genome proposed. If I launch the workflow without specifying the the reference it does not work. How can I do?

Thank you,


galaxy samtools • 667 views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by lucille.delisle0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Thank you for reporting the behavior. This is how the tool currently functions, meaning that the genome must be set as a fixed choice within the workflow editor.

I did some other testing related to this and there are a few options for genome selection that could be tuned across tools. This issue tracks the current tool options and potential places for improvement:

Thanks again, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k
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