Inject mem_mb into existing resources#514
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Match Snakemake's own argument handling by treating -- as the end of option parsing.
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joverlee521
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Mar 24, 2026
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Nice to tackle this longstanding TODO! I'm not sure --resources concurrent_deploys=2 is the way we want work around setdefault described in nextstrain/public#37, but good to have it as a fallback option.
The trick with stack-walking --log-handler-script is a clever hack, but it relies on Snakemake's internal implementation. Instead, parse the arguments for resources and either (1) update them in-place or (2) append the option at the end as done previously.
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joverlee521
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Mar 25, 2026
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Description of proposed changes
The trick with stack-walking
--log-handler-scriptis a clever hack, but it relies on Snakemake's internal implementation.Instead, parse the arguments for resources and either (1) update them in-place or (2) append the option at the end as done previously.
Related issue(s)
Addresses the removed TODO:
cli/nextstrain/cli/command/build.py
Lines 284 to 307 in 1867fd6
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