# 04-job-star.yaml
apiVersion: batch/v1
kind: Job
metadata:
  name: star-align
  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

              echo "=== Aligning ERR458493 (WT) ==="
              mkdir -p /data/aligned/ERR458493
              STAR \
                --runMode alignReads \
                --genomeDir /data/reference/star_index \
                --readFilesIn /data/raw/ERR458493.fastq.gz \
                --readFilesCommand zcat \
                --outSAMtype BAM SortedByCoordinate \
                --outSAMattributes NH HI AS NM \
                --outFileNamePrefix /data/aligned/ERR458493/ \
                --runThreadN 4

              echo "=== Aligning ERR458500 (snf2 mutant) ==="
              mkdir -p /data/aligned/ERR458500
              STAR \
                --runMode alignReads \
                --genomeDir /data/reference/star_index \
                --readFilesIn /data/raw/ERR458500.fastq.gz \
                --readFilesCommand zcat \
                --outSAMtype BAM SortedByCoordinate \
                --outSAMattributes NH HI AS NM \
                --outFileNamePrefix /data/aligned/ERR458500/ \
                --runThreadN 4

              echo "=== Done ==="
              ls -lh /data/aligned/ERR458493/
              ls -lh /data/aligned/ERR458500/
          resources:
            requests:
              memory: "6Gi"
              cpu: "4"
            limits:
              memory: "10Gi"
              cpu: "4"
          volumeMounts:
            - name: workspace
              mountPath: /data

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