entrypoint-aws-batch: Upload .snakemake/metadata/ too

Snakemake stores state information per input/output here and uses it to
determine if it needs to re-run rules or not.  It seems akin to the file
mtimes which we already take care to preserve on upload/download.
Additionally, the metadata recorded is used in Snakemake's report
generation and is generally useful for looking at workflow statistics.

Continue to not upload all of .snakemake/ en masse because it can
potentially contain files that interfere with local usage and/or are
large and unnecessary.

Resolves: <nextstrain/cli#373>
Related-to: <nextstrain/cli#374>

Author: tsibley

entrypoint-aws-batch

@@ -40,8 +40,8 @@ case "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" in
                 return "$zipstatus"
             fi
         }
-        zip -u "$PWD.zip" -r . --exclude ".snakemake/*"     || succeed-when-nothing-to-update $?
-        zip -u "$PWD.zip" -r . --include ".snakemake/log/*" || succeed-when-nothing-to-update $?
+        zip -u "$PWD.zip" -r . --exclude ".snakemake/*"                             || succeed-when-nothing-to-update $?
+        zip -u "$PWD.zip" -r . --include ".snakemake/log/*" ".snakemake/metadata/*" || succeed-when-nothing-to-update $?
         aws s3 cp --no-progress "$PWD.zip" "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL"
         ;;
     s3://*)