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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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entrypoint-aws-batch

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

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