Hi @wormball – this tool has an option to accept a dataset in fasta format. This can be from an upstream tool or an input dataset.
You might need to disconnect all tools, then reconnect them starting from the input through the downstream tools, in the order of processing. I’m guessing that the tool had the setting originally to use a natively indexed genome, then it was changed to use a fasta from the history. Reconnecting the “noodles” resets the workflow’s metadata. If the genome is already an input dataset, you can also connect that input to multiple tools that need to incorporate it.