# 02-job-sra-download.yaml
apiVersion: batch/v1
kind: Job
metadata:
  name: sra-download
  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
              mkdir -p /data/raw

              echo "=== Downloading ERR458493 (WT, single-end) ==="
              fasterq-dump ERR458493 --outdir /data/raw --temp /tmp --threads 4

              echo "=== Downloading ERR458500 (snf2 mutant, single-end) ==="
              fasterq-dump ERR458500 --outdir /data/raw --temp /tmp --threads 4

              echo "=== Compressing ==="
              gzip /data/raw/*.fastq

              echo "=== Done ==="
              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:
            - |
              echo "=== Raw files ==="
              ls -lh /data/raw/
          volumeMounts:
            - name: workspace
              mountPath: /data

      volumes:
        - name: workspace
          persistentVolumeClaim:
            claimName: rnaseq-workspace