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Update README
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Data source paths had changed via #22
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jameshadfield committed May 8, 2024
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Expand Up @@ -60,7 +60,7 @@ Note that you may need to remove any existing data in `results/` in order for sn

Run `snakemake` / `nextstrain build` with `--snakefile Snakefile.genome`

Currently this is only set up for the "h5n1-cattle-outbreak" build, and restricts the build to a set of strains where we think there's no reassortment (`config/include_strains_h5n1-cattle-outbreak.txt`). Output files will be placed in `results/h5n1-cattle-outbreak/genome`. Input files must be created by running (part of) the main workflow to produce `results/sequences_h5n1_{segment}.fasta` and `results/metadata_h5n1_{segment}.tsv` files. See `Snakefile.genome` for more details.
Currently this is only set up for the "h5n1-cattle-outbreak" build, and restricts the build to a set of strains where we think there's no reassortment (`config/include_strains_h5n1-cattle-outbreak.txt`). Output files will be placed in `results/h5n1-cattle-outbreak/genome`. Input files must be created by running (part of) the main workflow to produce `data/sequences_h5n1_{segment}.fasta` and `data/metadata_h5n1.tsv` files. See `Snakefile.genome` for more details.


### To modify this build to work with your own data
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