Initial RNA-seq DESeq2 pipeline manifests

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