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

      containers:
        - name: fastqc
          image: biocontainers/fastqc:v0.11.9_cv8
          command: ["/bin/sh", "-c"]
          args:
            - |
              set -e
              echo "=== Running FastQC on all samples ==="
              fastqc \
                /data/raw/ERR458493.fastq.gz \
                /data/raw/ERR458500.fastq.gz \
                --outdir /data/fastqc \
                --threads 4

              echo "=== Done ==="
              ls -lh /data/fastqc/
          resources:
            requests:
              memory: "1Gi"
              cpu: "2"
            limits:
              memory: "2Gi"
              cpu: "4"
          volumeMounts:
            - name: workspace
              mountPath: /data

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