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fix: Apply max_time_hr to sample_level_ibd rule (issue #334) #342

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merged 1 commit into from
Oct 3, 2024
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fix: Apply max_time_hr to sample_level_ibd rule (issue #334) #342

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2 changes: 1 addition & 1 deletion src/cgr_gwas_qc/models/config/workflow_params.py
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Expand Up @@ -92,7 +92,7 @@ class WorkflowParams(BaseModel):

max_time_hr: Optional[int] = Field(
None,
description="Allocates the specified number of hours for the execution of the ``sample_concordance_plink`` and ``population_level_ibd`` rules.",
description="Allocates the specified number of hours to the following rules: ``sample_concordance_plink``, ``sample_concordance_king``, ``sample_concordance_summary``, ``sample_level_ibd``, and ``population_level_ibd``.",
)

time_start: str = Field(
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3 changes: 3 additions & 0 deletions src/cgr_gwas_qc/workflow/sub_workflows/sample_qc.smk
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Expand Up @@ -335,6 +335,9 @@ use rule genome from plink as sample_level_ibd with:
out_prefix="sample_level/call_rate_2/samples_maf{maf}_ld{ld}",
output:
"sample_level/call_rate_2/samples_maf{maf}_ld{ld}.genome",
resources:
mem_mb=lambda wildcards, attempt, input: max((attempt + 1) * input.size_mb, 1024),
time_hr=lambda wildcards, attempt: BIG_TIME[attempt],


rule sample_concordance_plink:
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