Upload regional contexts to S3
Updates the existing global context input of the upload rule to include
all Nextstrain regional builds. As a result, all subsampled sequences
and metadata for each regional build should get uploaded to S3 during
each run of the ncov workflow.
@@ -211,8 +211,8 @@ rule upload:
expand("results/masked_{origin}.fasta", origin=config["S3_DST_ORIGINS"]), # from `rule mask`
expand("results/filtered_{origin}.fasta", origin=config["S3_DST_ORIGINS"]), # from `rule filter`
expand("results/mutation_summary_{origin}.tsv", origin=config["S3_DST_ORIGINS"]), # from `rule mutation_summary
- "results/global/global_subsampled_sequences.fasta",
- "results/global/global_subsampled_metadata.tsv"
+ expand("results/{build_name}/{build_name}_subsampled_sequences.fasta", build_name=config["builds"]),
+ expand("results/{build_name}/{build_name}_subsampled_metadata.tsv", build_name=config["builds"]),
params:
s3_bucket = config["S3_DST_BUCKET"],
compression = config["S3_DST_COMPRESSION"]
