Snakefile: Conditionally include --no-sign-request option

Conditionally include `--no-sign-request` option for download rules
if the sequence/metadata S3 URLs point to the public Nextstrain S3
bucket (s3://nextstrain-data/).

This means AWS credentials are no longer necessary for the public
h5n1-cattle-outbreak genome builds.

README.md

@@ -46,7 +46,7 @@ These use NCBI data including consensus genomes and SRA data assembled via the A
 snakemake --cores 1 -pf --configfile config/h5n1-cattle-outbreak.yaml
 ```
 
-This pipeline starts by downloading data from a public S3 bucket, however credentials may still be required to interact with AWS S3 buckets.
+This pipeline starts by downloading data from a public S3 bucket.
 
 
 **Genome builds**

Snakefile

@@ -17,6 +17,7 @@ for rule_file in config.get('custom_rules', []):
 # (2) Filter the other segments by simply force-including the same strains as (1)
 SAME_STRAINS = bool(config.get('same_strains_per_segment', False))
 
+NEXTSTRAIN_PUBLIC_BUCKET = "s3://nextstrain-data/"
 S3_SRC = config.get('s3_src', {})
 LOCAL_INGEST = config.get('local_ingest', None)
 
@@ -90,20 +91,22 @@ rule download_sequences:
     output:
         sequences = f"data/{S3_SRC.get('name', None)}/sequences_{{segment}}.fasta",
     params:
-        address=lambda w: S3_SRC.get('sequences', None).format(segment=w.segment)
+        address=lambda w: S3_SRC.get('sequences', None).format(segment=w.segment),
+        no_sign_request=lambda w: "--no-sign-request" if S3_SRC.get('sequences', "").startswith(NEXTSTRAIN_PUBLIC_BUCKET) else ""
     shell:
         """
-        aws s3 cp {params.address:q} - | zstd -d > {output.sequences}
+        aws s3 cp {params.no_sign_request:q} {params.address:q} - | zstd -d > {output.sequences}
         """
 
 rule download_metadata:
     output:
         metadata = f"data/{S3_SRC.get('name', None)}/metadata.tsv",
     params:
         address=S3_SRC.get('metadata', None),
+        no_sign_request=lambda w: "--no-sign-request" if S3_SRC.get('metadata', "").startswith(NEXTSTRAIN_PUBLIC_BUCKET) else ""
     shell:
         """
-        aws s3 cp {params.address:q} - | zstd -d > {output.metadata}
+        aws s3 cp {params.no_sign_request:q} {params.address:q} - | zstd -d > {output.metadata}
         """