# 02b-job-sra-download-extra.yaml
apiVersion: batch/v1
kind: Job
metadata:
  name: sra-download-extra
  namespace: rnaseq
spec:
  backoffLimit: 2
  template:
    spec:
      restartPolicy: Never
      initContainers:
        - name: download-sra
          image: ncbi/sra-tools:3.0.0
          command: ["/bin/sh", "-c"]
          args:
            - |
              set -e
              for acc in ERR458494 ERR458495 ERR458501 ERR458502; do
                echo "=== Downloading $acc ==="
                fasterq-dump $acc --outdir /data/raw --temp /tmp --threads 4
              done
              gzip /data/raw/*.fastq
              ls -lh /data/raw/
          resources:
            requests: { memory: "1Gi", cpu: "2" }
            limits: { memory: "2Gi", cpu: "4" }
          volumeMounts:
            - name: workspace
              mountPath: /data
      containers:
        - name: verify
          image: busybox:1.36
          command: ["/bin/sh", "-c"]
          args: ["ls -lh /data/raw/"]
          volumeMounts:
            - name: workspace
              mountPath: /data
      volumes:
        - name: workspace
          persistentVolumeClaim:
            claimName: rnaseq-workspace