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Merged
tsibley merged 1 commit into from
Jun 17, 2024
Merged

runner.aws_batch: Download .snakemake/metadata/ too #374

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15 changes: 15 additions & 0 deletions CHANGES.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,21 @@ development source code and as such may not be routinely kept up to date.

# __NEXT__

## Improvements

* Snakemake's per-input/output file metadata (stored in `.snakemake/metadata/`)
is now downloaded from AWS Batch builds by default. Like file modification
times (mtimes), which are already preserved from the remote build, this
additional metadata is used by Snakemake to track when inputs have changed
and when it should regenerate outputs. The metadata is also used in
[Snakemake report generation](https://snakemake.readthedocs.io/en/v8.14.0/snakefiles/reporting.html#rendering-reports)
and can be useful for gathering ad-hoc workflow statistics.

The runtime image used must be at least `nextstrain/base:build-20240617T235011Z`
for these Snakemake metadata files to be available for download from the AWS
Batch job.
([#374](https://github.com/nextstrain/cli/pull/374))


# 8.4.0 (29 May 2024)

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6 changes: 5 additions & 1 deletion nextstrain/cli/runner/aws_batch/s3.py
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Expand Up @@ -119,8 +119,12 @@ def download_workdir(remote_workdir: S3Object, workdir: Path, patterns: List[str
])

included = path_matcher([
# But we do want the Snakemake logs to come over.
# But we do want the Snakemake logs to come over…
".snakemake/log/",

# …and the input/output metadata Snakemake tracks (akin to mtimes,
# which we also preserve).
".snakemake/metadata/",
])

if patterns:
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