diff --git a/src/argowrapper/argo_workflows_templates/header.yaml b/src/argowrapper/argo_workflows_templates/header.yaml index c7e7c8c..e1361c3 100644 --- a/src/argowrapper/argo_workflows_templates/header.yaml +++ b/src/argowrapper/argo_workflows_templates/header.yaml @@ -104,6 +104,6 @@ spec: volumes: - name: workdir emptyDir: - sizeLimit: "3Gi" + sizeLimit: "20Gi" workflowTemplateRef: name: gwas-template-integration-test diff --git a/src/argowrapper/workflows/argo_workflows/gwas.py b/src/argowrapper/workflows/argo_workflows/gwas.py index 62ad2d6..4d25fe9 100644 --- a/src/argowrapper/workflows/argo_workflows/gwas.py +++ b/src/argowrapper/workflows/argo_workflows/gwas.py @@ -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) @@ -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"] diff --git a/workflow_examples/gwas_header.yaml b/workflow_examples/gwas_header.yaml index 027bc50..4e137f9 100644 --- a/workflow_examples/gwas_header.yaml +++ b/workflow_examples/gwas_header.yaml @@ -101,6 +101,6 @@ spec: claimName: va-input-nfs-pvc - name: workdir emptyDir: - sizeLimit: "10Gi" + sizeLimit: "20Gi" workflowTemplateRef: name: gwas-template