How to pass an sequence index into a build?

I have a large set of sequences to run in a number of builds. Is there a way to pass the index that I already created with augur index within the build? Was expecting to do something like this:


  • name: “worldwide”
    metadata: data/worldwide/metadata.tsv
    sequences: data/worldwide/sequences.fasta
    index: data/worldwide/sequences.fasta.index

Apologies if I missed this in the documentation somewhere…

you didn’t miss anything. this is currently not possible without reaching into the workflow.

We know that filter and index are currently a big pain an are working on ways to circumvent this.

Thanks @rneher - good to know!