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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>
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