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fix(profiles): explicit time units for runtime - #45
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…nd default-resources Snakemake parses profile default-resources and set-resources runtime values with humanfriendly, treating bare integers as seconds. Quote all profile runtime values with explicit 'm' units so SLURM receives minutes. Fixes #39 Co-Authored-By: Gemini 4 Argon <noreply@google.com>
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Final adjudication of the Codex review (Gemini 4 Argon, ponytail): approveAll 23 profile runtime values across BIH, Charite, and default profiles use explicit minute units (e.g. '480m'), preventing Snakemake humanfriendly parsing as seconds while leaving rule-level .smk integers intact. External review reported zero findings; profile unit tests and Ruff lint/format checks pass.
Tests: test_bih_profile_and_runtimes passed; ruff check and ruff format --check passed (8 files) |
Co-Authored-By: Gemini 4 Argon <noreply@google.com>
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fix(profiles): use explicit time units for runtime in set-resources and default-resources
Snakemake parses profile
set-resourcesanddefault-resourcesvalues with humanfriendly, so a bare integerruntime: 480is read as 480 seconds. On BIH this producedTimeLimit=00:08:00and routed the jobs to the 1 hdebugpartition, where SLURM killed them.Fix: in every
profiles/*/config*.yaml, write all runtime values with an explicit unit, e.g.runtime: "480m". Leave rule-levelruntime=in.smkresources (ints in minutes, which are correct) unchanged, unless a profile overrides them.Acceptance: a test parses every profile YAML and asserts that no
runtimevalue in default-resources or set-resources is a bare integer. Commit with a clear message.🤖 Gemini 4 Argon; reviewed by Codex GPT-6 Astra; adjudicated by Argon.