Document GPU configuration flow across pipelines, modules, and profiles - #4352
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mahesh-panchal wants to merge 7 commits into
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Document GPU configuration flow across pipelines, modules, and profiles#4352mahesh-panchal wants to merge 7 commits into
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Clarify that `accelerator` is a map (`request`/`type`), not a plain integer, and explain how a GPU request flows from module -> pipeline config -> institutional profile -> user override. Add a GPU resource requests section to the institutional profiles guide (with a `--gres` vs `--gpus` SLURM note), update the example gpu profile to read `task.accelerator` via a closure instead of hardcoding `--gres=gpu:1`, and add a new running/configuration guide for pipeline users. Remove the now-unused `ext.use_gpu` key from the ext-args reference. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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@nf-core-bot fix linting |
pontus
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Aug 14, 2026
mashehu
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just some nitpicks, can be ignored if you disagree
pontus
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pontus
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Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Pontus Freyhult <pontus_github@soua.net> Co-authored-by: Cormac Kinsella <27350062+CormacKinsella@users.noreply.github.com>
Reword the module-detection rationale to state the actual mechanical reason (task.accelerator is readable inside the process body, a label is not) and decouple it from the separate question of whether GPU use is opt-in by default. Simplify the institutional profile GPU example to a single process scope instead of a withLabel block, drop the profile-order note and duplicated accelerator-map explanation, and clean up stray blank lines. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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@nf-core-bot fix linting |
The distinction is already covered by the "SLURM: --gres vs --gpus" note earlier in the GPU resource requests section. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Co-authored-by: Cormac Kinsella <27350062+CormacKinsella@users.noreply.github.com>
This was referenced Aug 18, 2026
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Summary
acceleratoris a map (request/typekeys), not a plain integer, and document how a GPU request flows: module -> pipeline config -> institutional profile -> user override.--gresvs--gpuson SLURM, and update the examplegpuprofile to readtask.acceleratorvia a closure instead of hardcoding--gres=gpu:1.running/configuration/gpu-pipelines.mdguide aimed at pipeline users.ext.use_gpukey from theext-argsreference.@netlify /docs/running/configuration/gpu-pipelines