# 05-job-featurecounts.yaml
apiVersion: batch/v1
kind: Job
metadata:
  name: featurecounts-v2
  namespace: rnaseq
spec:
  backoffLimit: 2
  template:
    spec:
      restartPolicy: Never

      containers:
        - name: featurecounts
          image: quay.io/biocontainers/subread:2.0.6--he4a0461_0
          command: ["/bin/sh", "-c"]
          args:
            - |
              set -e
              echo "=== Running featureCounts on 6 samples ==="
              featureCounts \
                -a /data/reference/annotation.gtf \
                -o /data/counts/gene_counts.txt \
                -T 4 \
                /data/aligned/ERR458493/Aligned.sortedByCoord.out.bam \
                /data/aligned/ERR458494/Aligned.sortedByCoord.out.bam \
                /data/aligned/ERR458495/Aligned.sortedByCoord.out.bam \
                /data/aligned/ERR458500/Aligned.sortedByCoord.out.bam \
                /data/aligned/ERR458501/Aligned.sortedByCoord.out.bam \
                /data/aligned/ERR458502/Aligned.sortedByCoord.out.bam

              echo "=== Done ==="
              cat /data/counts/gene_counts.txt.summary
          resources:
            requests:
              memory: "1Gi"
              cpu: "2"
            limits:
              memory: "2Gi"
              cpu: "4"
          volumeMounts:
            - name: workspace
              mountPath: /data

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