Initial RNA-seq DESeq2 pipeline manifests

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