entrypoint-aws-batch: Upload .snakemake/storage/ too #259
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joverlee521 merged 2 commits intomasterfrom Jul 21, 2025
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entrypoint-aws-batch: Upload .snakemake/storage/ too #259joverlee521 merged 2 commits intomasterfrom
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When using Snakemakes storage support to download remote files, Snakemake stores the downloaded files in `.snakemake/storage` by default. This allows users to keep the remote files that were downloaded during the build on AWS Batch. Note that the storage path is configurable via Snakemake's `--local-storage-prefix`.¹ So if someone configures the storage path to a custom path within `.snakemake`, e.g. `.snakemake/foo`, then it would not be available in their downloaded workdir. I'm not even sure it's possible to configure the path in entrypoint-aws-batch for the docker-base image, so I've added a warning against using the Snakemake option if using the aws-batch runtime. Resolves #453 Related to nextstrain/docker-base#259 ¹ <https://github.com/snakemake/snakemake/blob/v9.6.3/src/snakemake/cli.py#L1463-L1469>
When using Snakemakes storage support to download remote files, Snakemake stores the downloaded files in `.snakemake/storage` by default. This allows users to keep the remote files that were downloaded during the build on AWS Batch. Note that the storage path is configurable via Snakemake's `--local-storage-prefix`.¹ So if someone configures the storage path to a custom path within `.snakemake`, e.g. `.snakemake/foo`, then it would not be available in their workdir. I'm not sure it's even possible to make this path configurable here, so I'm just going to warn against using it from the Nextstrain CLI. Related to nextstrain/cli#460 ¹ <https://github.com/snakemake/snakemake/blob/v9.6.3/src/snakemake/cli.py#L1456-L1462>
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victorlin
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Worked as expected in nextstrain/cli#460 (comment) |
joverlee521
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When using Snakemakes storage support to download remote files, Snakemake stores the downloaded files in `.snakemake/storage` by default. This allows users to keep the remote files that were downloaded during the build on AWS Batch. Note that the storage path is configurable via Snakemake's `--local-storage-prefix`.¹ So if someone configures the storage path to a custom path within `.snakemake`, e.g. `.snakemake/foo`, then it would not be available in their downloaded workdir. I'm not even sure it's possible to configure the path in entrypoint-aws-batch for the docker-base image, so I've added a warning against using the Snakemake option if using the aws-batch runtime. Resolves #453 Related to nextstrain/docker-base#259 ¹ <https://github.com/snakemake/snakemake/blob/v9.6.3/src/snakemake/cli.py#L1463-L1469>
joverlee521
added a commit
to nextstrain/cli
that referenced
this pull request
Jul 21, 2025
When using Snakemakes storage support to download remote files, Snakemake stores the downloaded files in `.snakemake/storage` by default. This allows users to keep the remote files that were downloaded during the build on AWS Batch. Note that the storage path is configurable via Snakemake's `--local-storage-prefix`.¹ So if someone configures the storage path to a custom path within `.snakemake`, e.g. `.snakemake/foo`, then it would not be available in their downloaded workdir. I'm not even sure it's possible to configure the path in entrypoint-aws-batch for the docker-base image, so I've added a warning against using the Snakemake option if using the aws-batch runtime. Resolves #453 Related to nextstrain/docker-base#259 ¹ <https://github.com/snakemake/snakemake/blob/v9.6.3/src/snakemake/cli.py#L1463-L1469>
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Description of proposed changes
When using Snakemakes storage support to download remote files, Snakemake stores
the downloaded files in
.snakemake/storageby default. This allows users tokeep the remote files that were downloaded during the build on AWS Batch.
Note that the storage path is configurable via Snakemake's
--local-storage-prefix.¹ So if someone configures the storage path to a custompath within
.snakemake, e.g..snakemake/foo, then it would not be availablein their workdir. I'm not sure it's even possible to make this path configurable
here, so I'm just going to warn against using it from the Nextstrain CLI.
Related to nextstrain/cli#460
¹ https://github.com/snakemake/snakemake/blob/v9.6.3/src/snakemake/cli.py#L1456-L1462
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