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nextstrain-public/all_deploy: remove log directive
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We were running into the Snakemake issue where the log directive in
the default rule causes it to skip tasks.¹ This issue has been fixed
since Snakemake 7.25.1, but we are still pinned to 7.24.1 in
nextstrain/docker-base.²

Just removing the log directive here is the simplest fix for this
particular issue. We'll still be able to see the upload logs in
the AWS Batch logs.

¹ snakemake/snakemake#2142
² https://github.com/nextstrain/docker-base/blob/95cea4f44a803ce27992706c87a7237492dbb083/Dockerfile#L277
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joverlee521 committed Aug 9, 2023
1 parent 04dd991 commit 087558c
Showing 1 changed file with 1 addition and 3 deletions.
4 changes: 1 addition & 3 deletions profiles/nextstrain-public/deploy.smk
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,9 @@ Depends on the `all_public` rule from rename.smk

rule all_deploy:
input: rules.all_public.input
log:
"logs/all_deploy.txt"
params:
s3_dst = config["deploy_url"]
shell:
"""
nextstrain remote upload {params.s3_dst} {input} 2>&1 | tee {log}
nextstrain remote upload {params.s3_dst} {input}
"""

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