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Question: Sam-to-bam in workflow
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gravatar for lucille.delisle
3.0 years ago by
lucille.delisle • 0
Switzerland
lucille.delisle • 0 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,

Lucille
galaxy samtools • 667 views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by lucille.delisle • 0
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: https://github.com/galaxyproject/galaxy/issues/1132

Thanks again, Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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