Updates in this release include:
- Outfile name now can be specified with an optional
--outfileargument - Bug fix Now won't max out bash args as instead of passing hashed taxon names through the cmd line, write to a temp config.yaml file with
query_sequencesspecified as a config key. The sub workflow accepts this with the--configfileargument. This then loads tax names into the new snakemake without having to be passed through the shell command or then parsed. Could in theory pass everything through this config file, but I think it's probably useful to have the other things printed as part of the snakemake command call. - Quite a lot of dev to the prep-pipeline in anticipation of the new data release tomorrow. Added in quite a lot of annotation and tomorrow will make it a flag in the pangolin command to prep your own pipeline, which will be fun.