# 04b-job-star-extra.yaml
apiVersion: batch/v1
kind: Job
metadata:
  name: star-align-extra
  namespace: rnaseq
spec:
  backoffLimit: 1
  template:
    spec:
      restartPolicy: Never

      containers:
        - name: star
          image: quay.io/biocontainers/star:2.7.10a--h9ee0642_0
          command: ["/bin/sh", "-c"]
          args:
            - |
              set -e
              for acc in ERR458494 ERR458495 ERR458501 ERR458502; do
                echo "=== Aligning $acc ==="
                mkdir -p /data/aligned/$acc
                STAR \
                  --runMode alignReads \
                  --genomeDir /data/reference/star_index \
                  --readFilesIn /data/raw/$acc.fastq.gz \
                  --readFilesCommand zcat \
                  --outSAMtype BAM SortedByCoordinate \
                  --outSAMattributes NH HI AS NM \
                  --outFileNamePrefix /data/aligned/$acc/ \
                  --runThreadN 4
              done

              echo "=== Done ==="
              for acc in ERR458494 ERR458495 ERR458501 ERR458502; do
                ls -lh /data/aligned/$acc/
              done
          resources:
            requests:
              memory: "6Gi"
              cpu: "4"
            limits:
              memory: "10Gi"
              cpu: "4"
          volumeMounts:
            - name: workspace
              mountPath: /data

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