Add INRB-specific build pipeline #287
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genehack
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This includes one modification to the shared snakemake rules - if a config defines both 'private_sequences' and 'private_metadata' then private data will be merged in. The script which merges them should be replaced by `augur merge` in the future.
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This branch represents (updated) code which has been in-use for a while now and generates the https://next.nextstrain.org/groups/inrb-mpox/clade-I build. The recent changes to ingested data (#283) has convinced me to merge this work into master in order to stay up-to-date and prevent the current situation where Eddy can't run the build until I update the branch he's using.
The changes in this PR are largely self-contained but do include one modification to the shared snakemake rules - if a config defines both 'private_sequences' and 'private_metadata' then private data will be merged in. The script which merges them should be replaced by
augur mergein the future.I'm awaiting confirmation from INRB that this is working well from them, and plan to merge once I know it's working so that they can then work from the master branch and as such stay up-to-date with the canonical pipeline.