ingest: Upload Nextclade TSV output

Keep a copy of the full Nextclade TSV output from ingest on S3
since we won't necessarily join all columns with the metadata output.

ingest/Snakefile

@@ -20,6 +20,7 @@ rule upload_all:
     input:
         sequences=expand("fauna/s3/sequences_{segment}.done", segment=config["segments"]),
         metadata="fauna/s3/metadata.done",
+        nextclade="fauna/s3/nextclade.done",
 
 include: "rules/ingest_fauna.smk"
 include: "rules/merge_segment_metadata.smk"

ingest/build-configs/ncbi/Snakefile

@@ -40,6 +40,7 @@ rule upload_all_ncbi:
         expand([
             "{data_source}/s3/sequences_{segment}.done",
             "{data_source}/s3/metadata.done",
+            "{data_source}/s3/nextclade.done",
         ], data_source=NCBI_DATA_SOURCES, segment=config["segments"]),
 
 

ingest/rules/upload_to_s3.smk

@@ -37,3 +37,21 @@ rule upload_metadata:
             {params.s3_dst:q}/metadata.tsv.zst \
             {params.cloudfront_domain} 2>&1 | tee {output.flag}
         """
+
+
+rule upload_nextclade_tsv:
+    input:
+        nextclade="{data_source}/results/nextclade.tsv",
+    output:
+        flag="{data_source}/s3/nextclade.done",
+    params:
+        s3_dst=lambda wildcards: config["s3_dst"][wildcards.data_source],
+        cloudfront_domain=config.get("cloudfront_domain", ""),
+    shell:
+        """
+        ./vendored/upload-to-s3 \
+            --quiet \
+            {input.nextclade:q} \
+            {params.s3_dst:q}/nextclade.tsv.zst \
+            {params.cloudfront_domain} 2>&1 | tee {output.flag}
+        """