# 06-job-deseq2.yaml
apiVersion: batch/v1
kind: Job
metadata:
  name: deseq2-v2
  namespace: rnaseq
spec:
  backoffLimit: 1
  template:
    spec:
      restartPolicy: Never

      containers:
        - name: deseq2
          image: quay.io/biocontainers/bioconductor-deseq2:1.46.0--r44he5774e6_1
          command: ["/bin/sh", "-c"]
          args:
            - |
              set -e
              cat <<'EOF' > /tmp/deseq2_analysis.R
              library(DESeq2)

              counts_raw <- read.table("/data/counts/gene_counts.txt",
                                        header = TRUE, skip = 1, row.names = 1)

              counts <- counts_raw[, 6:11]
              colnames(counts) <- c("WT_1", "WT_2", "WT_3",
                                     "SNF2_1", "SNF2_2", "SNF2_3")

              coldata <- data.frame(
                condition = factor(c("WT", "WT", "WT",
                                      "SNF2", "SNF2", "SNF2"),
                                    levels = c("WT", "SNF2"))
              )
              rownames(coldata) <- colnames(counts)

              dds <- DESeqDataSetFromMatrix(countData = counts,
                                             colData = coldata,
                                             design = ~ condition)

              dds <- DESeq(dds)
              res <- results(dds)
              res <- res[order(res$padj), ]

              write.csv(as.data.frame(res), "/data/results/deseq2_results.csv")

              cat("=== Summary ===\n")
              summary(res)

              cat("\n=== Top 10 genes by adjusted p-value ===\n")
              print(head(as.data.frame(res), 10))
              EOF

              Rscript /tmp/deseq2_analysis.R
          resources:
            requests:
              memory: "2Gi"
              cpu: "2"
            limits:
              memory: "4Gi"
              cpu: "4"
          volumeMounts:
            - name: workspace
              mountPath: /data

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