Hi @gvestal, the current Nextstrain container doesn’t support conda, so I think this can be fixed by dropping the --use-conda argument (which is being passed to Snakemake running in the container).
nextstrain build --docker . --cores 4 --configfile ./my_profiles/fl_delta/builds.yaml
# P.S. the --docker argument isn't needed if docker is the default environment,
# run `nextstrain check-setup` to see the default
If you want to use conda to manage dependencies etc, then we can also run nextstrain “natively” (i.e. not within a container) via:
# ensure conda & snakemake are available in the current environment
nextstrain build --native . --cores 4 --use-conda –configfile ./my_profiles/fl_delta/builds.yaml