Current Behavior

The Snakemake workflow now fails when not using the Docker runtime:

/bin/bash: line 1: nextalign2: command not found

and similar for nextclade2.

This is because the commands nextalign2/nextclade2 are only provided into the nextstrain/base Docker image after nextstrain/docker-base#54 and exclusively used by this workflow following merge of #963.

Expected behavior

Workflow should work for all runtimes.

How to reproduce

1. Set up a native environment following installation docs (simpler method proposed by docs: Remove note to install dependencies in Native runtime #967):

   mamba create -n nextstrain \
   -c conda-forge -c bioconda \
   nextstrain-cli augur auspice nextalign nextclade snakemake git epiweeks pangolin pangolearn \
   --yes

2. Run example data tutorial.

3. See error in logs/align_reference_data.txt

Possible solutions

• Alias nextclade2 -> nextclade / nextalign2 -> nextalign?
• Drop nextclade2 in the Docker image and make nextclade point to v2. If we want to allow users to still have access to v1, maybe have a nextclade1 command available similar to how nextclade2 is currently available.

cc @ivan-aksamentov