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Module-specific default profile not being used #24

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fwzhao opened this issue Sep 19, 2024 · 1 comment
Open

Module-specific default profile not being used #24

fwzhao opened this issue Sep 19, 2024 · 1 comment
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@fwzhao
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fwzhao commented Sep 19, 2024

Snakemake8 (v8.20.3)
atacseq_pipeline (v2.0.0) - global defaults: partition shortq
cemm.slurm.cm (v.3.0.0) - global defaults: partition tinyq

For project using multiple modules, module-specific default profile does not seem to be used.
Behavior:
When sbatch snakemake conductor.sh --> the global default are used (partition: tinyq) for job rather than the module specific defaults (partition: shortq)
When the respective lines for global defaults are commented out, no partition is assigned, leading to -

WorkflowError:
SLURM job submission failed. The error message was sbatch: error: Batch job submission failed: No partition specified or system default partition

@sreichl sreichl self-assigned this Sep 19, 2024
@sreichl
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sreichl commented Sep 19, 2024

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