fixup: conform to pathogen-repo-guide

Match the upload rules in nextstrain/pathogen-repo-guide#36

ingest/build-configs/nextstrain-automation/upload.smk

@@ -18,39 +18,11 @@ send_notifications = (
 )
 
 
-def _get_upload_inputs(wildcards):
-    """
-    If the file_to_upload has Slack notifications that depend on diffs with S3 files,
-    then we want the upload rule to run after the notification rule.
-
-    This function is mostly to keep track of which flag files to expect for
-    the rules in `slack_notifications.smk`, so it only includes flag files if
-    `send_notifications` is True.
-    """
-    inputs = {
-        "file_to_upload": config["files_to_upload"][
-            wildcards.remote_file_name
-        ],
-    }
-
-    if send_notifications:
-        flag_file = []
-
-        if file_to_upload == "data/genbank.ndjson":
-            flag_file = "data/notify/genbank-record-change.done"
-        elif file_to_upload == "results/metadata.tsv":
-            flag_file = "data/notify/metadata-diff.done"
-
-        inputs["notify_flag_file"] = flag_file
-
-    return inputs
-
-
 rule upload_to_s3:
     input:
-        unpack(_get_upload_inputs),
+        file_to_upload=lambda wildcards: config["files_to_upload"][wildcards.remote_file],
     output:
-        "data/upload/s3/{remote_file_name}.done",
+        "results/upload/{remote_file}.upload",
     params:
         quiet="" if send_notifications else "--quiet",
         s3_dst=config["s3_dst"],
@@ -60,6 +32,16 @@ rule upload_to_s3:
         ./vendored/upload-to-s3 \
             {params.quiet} \
             {input.file_to_upload:q} \
-            {params.s3_dst:q}/{wildcards.remote_file_name:q} \
+            {params.s3_dst:q}/{wildcards.remote_file:q} \
             {params.cloudfront_domain} 2>&1 | tee {output}
         """
+
+
+rule upload_all:
+    input:
+        uploads=[
+            f"results/upload/{remote_file}.upload"
+            for remote_file in config["files_to_upload"].keys()
+        ],
+    output:
+        touch("results/upload_all.done")