Use compressed metadata and sequences files
Use the newly available, compressed, `metadata.tsv.gz` and
`sequences.fasta.gz` files to reduce network transfer time.
@@ -76,8 +76,8 @@ rule download:
metadata = config["metadata"]
shell:
"""
- aws s3 cp s3://nextstrain-ncov-private/metadata.tsv {output.metadata:q}
- aws s3 cp s3://nextstrain-ncov-private/sequences.fasta {output.sequences:q}
+ aws s3 cp s3://nextstrain-ncov-private/metadata.tsv.gz - | gunzip -cq > {output.metadata:q}
+ aws s3 cp s3://nextstrain-ncov-private/sequences.fasta.gz - | gunzip -cq > {output.sequences:q}
"""
rule filter:
