Initial RNA-seq DESeq2 pipeline manifests

2026-06-21 06:39:53 -04:00
commit 395c18a9e6
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+# 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