kemal
5463f489a3
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End-to-end variant interpretation platform for rare genetic disease research: SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline, LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure. Public test data only; no clinical claims.
38 lines
1.3 KiB
YAML
38 lines
1.3 KiB
YAML
# Triggered by an Argo Events sensor listening on the Pub/Sub topic "vcf-uploaded".
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apiVersion: argoproj.io/v1alpha1
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kind: WorkflowTemplate
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metadata: { name: annotate-vcf, namespace: rarelens }
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spec:
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entrypoint: nextflow
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arguments:
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parameters:
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- { name: job_id }
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- { name: vcf_uri }
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templates:
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- name: nextflow
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inputs:
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parameters: [{ name: job_id }, { name: vcf_uri }]
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serviceAccountName: rarelens-pipeline
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container:
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image: europe-west2-docker.pkg.dev/PROJECT/rarelens/pipeline:latest
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command: [nextflow]
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args:
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- run
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- /pipeline/main.nf
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- -profile
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- gcp
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- --vcf
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- "{{inputs.parameters.vcf_uri}}"
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- --job_id
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- "{{inputs.parameters.job_id}}"
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- --db_url
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- "$(DATABASE_URL)"
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envFrom: [{ secretRef: { name: api-secrets } }]
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resources: { requests: { cpu: "2", memory: 4Gi } }
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- name: score
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# Optional GPU step for the deep-learning baseline; Autopilot schedules on an L4 node.
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nodeSelector: { cloud.google.com/gke-accelerator: nvidia-l4 }
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container:
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image: europe-west2-docker.pkg.dev/PROJECT/rarelens/ml:latest
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resources: { limits: { nvidia.com/gpu: 1 } }
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