After working on turning the workflow from Alevin into the new modular Alevin-fry workflow, I was getting failed runs for the later processes specific to the Alevin-fry steps. I was able to generate the RAD file using salmon alevin with the --justAlign option, but it fails after that. After looking into it more, I realized that the most recent Salmon container does not contain the functions needed for Alevin-fry. It looks like they don't have a public container for Alevin-fry so we need to build our own for use with this new workflow.
After working on turning the workflow from Alevin into the new modular Alevin-fry workflow, I was getting failed runs for the later processes specific to the Alevin-fry steps. I was able to generate the RAD file using
salmon alevinwith the--justAlignoption, but it fails after that. After looking into it more, I realized that the most recent Salmon container does not contain the functions needed for Alevin-fry. It looks like they don't have a public container for Alevin-fry so we need to build our own for use with this new workflow.