Hi @suskraem, when running the ncov workflow in a cluster environment, you can run Snakemake with --use-conda --conda-frontend mamba. This will tell Snakemake to create the proper Nextstrain conda environment and activate it before running each job. This approach works best on a cluster where you can install Conda yourself (e.g., in your home directory) and saves you the extra work of creating a custom Snakemake job script or asking the cluster IT staff to install and maintain Nextstrain software.
You can read more about this approach in this earlier post about reproducible workflows with conda environments.