From 442a5b757735363be5f5c3c8b2cb6811618110dd Mon Sep 17 00:00:00 2001 From: Thomas Sibley Date: Mon, 17 Jun 2024 14:35:23 -0700 Subject: [PATCH] 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: Related-to: --- entrypoint-aws-batch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/entrypoint-aws-batch b/entrypoint-aws-batch index ae92419b..a56371cb 100755 --- a/entrypoint-aws-batch +++ b/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://*)