diff --git a/ingest/Snakefile b/ingest/Snakefile index 4e829ea4..168dd2a7 100644 --- a/ingest/Snakefile +++ b/ingest/Snakefile @@ -32,7 +32,7 @@ def _get_all_targets(wildcards): print( f"Skipping file upload for {target!r} because there are duplicate remote file names." ) - elif not params.get("dst"): + elif not params.get("s3_dst"): print( f"Skipping file upload for {target!r} because the destintion was not defined." ) diff --git a/ingest/config/optional.yaml b/ingest/config/optional.yaml index b361327a..5a3cb028 100644 --- a/ingest/config/optional.yaml +++ b/ingest/config/optional.yaml @@ -1,10 +1,10 @@ # Optional configs used by Nextstrain team # Params for uploads +# AWS S3 Bucket with prefix +s3_dst: 's3://nextstrain-data/files/workflows/monkeypox' upload: # Upload params for AWS S3 s3: - # AWS S3 Bucket with prefix - dst: 's3://nextstrain-data/files/workflows/monkeypox' # Files to upload to S3 that are in the `data` directory files_to_upload: [ 'genbank.ndjson', diff --git a/ingest/workflow/snakemake_rules/upload.smk b/ingest/workflow/snakemake_rules/upload.smk index fd4d3305..94afc3f3 100644 --- a/ingest/workflow/snakemake_rules/upload.smk +++ b/ingest/workflow/snakemake_rules/upload.smk @@ -52,7 +52,7 @@ rule upload_to_s3: "data/upload/s3/{file_to_upload}-to-{remote_file_name}.done", params: quiet="" if send_notifications else "--quiet", - s3_dst=config["upload"].get("s3", {}).get("dst", ""), + s3_dst=config.get("s3_dst", ""), cloudfront_domain=config["upload"].get("s3", {}).get("cloudfront_domain", ""), shell: """