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jameshadfield added a commit to nextstrain/fauna that referenced this pull request Dec 2, 2024
Very ad-hoc / temporary approach I used to generate FASTA files which I could then use as inputs for avian-flu builds. Avoids any use of the rethink db. See <nextstrain/avian-flu#108> for the corresponding avian-flu work.
Requires custom data via fauna to be present in the `ingest/fauna/data` directory. Reference genomes are from H7N9 and should be improved. Ingest: ``` cd ingest snakemake --cores 1 -pf all ``` Phylo: ``` snakemake --cores 4 -pf -s gisaid/Snakefile --configfile config/h7n6.yaml ```
jameshadfield force-pushed the james/h7n6 branch from 04f527d to 12f45f0 Compare jameshadfield force-pushed the james/config-schema branch from 557bf38 to 9e71d58 Compare jameshadfield added a commit that referenced this pull request Mar 4, 2025
This reduces the conditional logic used to special-case the workflows which wanted to filter on GenoFLU by shifting the entire query arg into the config YAML. A (not unintentional) side effect is that future builds which want to analyse different subtypes such as H7N6 <#108> are possible to set-up using only a config overlay.
jameshadfield added a commit that referenced this pull request Mar 5, 2025
This reduces the conditional logic used to special-case the workflows which wanted to filter on GenoFLU by shifting the entire query arg into the config YAML. A (not unintentional) side effect is that future builds which want to analyse different subtypes such as H7N6 <#108> are possible to set-up using only a config overlay.
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Requires custom data via fauna to be present in the
ingest/fauna/datadirectory.Reference genomes are from H7N9 and should be improved.
Ingest:
Phylo: