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Update temporary directory size limit #156

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Dec 5, 2024
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2 changes: 1 addition & 1 deletion src/argowrapper/argo_workflows_templates/header.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,6 @@ spec:
volumes:
- name: workdir
emptyDir:
sizeLimit: "3Gi"
sizeLimit: "20Gi"
workflowTemplateRef:
name: gwas-template-integration-test
7 changes: 5 additions & 2 deletions src/argowrapper/workflows/argo_workflows/gwas.py
Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,7 @@ def _add_spec_volumes(self):
)
logger.info(f"pvc {pvc_name} is used as storage gateway pvc")
self.spec.add_persistent_volume_claim("gateway", pvc_name)
self.spec.add_empty_dir("workdir", "10Gi")
self.spec.add_empty_dir("workdir", "20Gi")

def _add_spec_podMetadata_annotations(self):
self.spec.add_pod_metadata_annotation("gen3username", self.username)
Expand All @@ -199,7 +199,10 @@ def interpret_gwas_workflow_error(step_name: str, step_log: str) -> str:
"""A static method to interpret the error message in the main-log file
of Failed Retry node
"""
if step_name in ["run-null-model", "run-single-assoc"] and "system is exactly singular" in step_log:
if (
step_name in ["run-null-model", "run-single-assoc"]
and "system is exactly singular" in step_log
):
show_error = "The error occurred due to small cohort size or unbalanced cohort sizes. Please ensure that the cohorts selected for your analysis are sufficiently large and balanced."
elif (
step_name in ["run-null-model", "run-single-assoc"]
Expand Down
2 changes: 1 addition & 1 deletion workflow_examples/gwas_header.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,6 @@ spec:
claimName: va-input-nfs-pvc
- name: workdir
emptyDir:
sizeLimit: "10Gi"
sizeLimit: "20Gi"
workflowTemplateRef:
name: gwas-template
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