From 983a2c3246cae4e9509df1c1c7b5f400e549ba30 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Thu, 26 Mar 2026 19:27:11 +0100
Subject: [PATCH] Add debug_pvc.nf to inspect PVC contents

---
 debug_pvc.nf | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 debug_pvc.nf

diff --git a/debug_pvc.nf b/debug_pvc.nf
new file mode 100644
index 0000000..979a751
--- /dev/null
+++ b/debug_pvc.nf
@@ -0,0 +1,45 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl=2
+
+params.outdir = '/omic/eureka/digital-patients'
+
+process DEBUG_PVC {
+    container 'harbor.cluster.omic.ai/omic/digital-patients/corto:latest'
+
+    script:
+    """
+    echo "=== PVC mount check ==="
+    echo "Current dir: \$(pwd)"
+    echo ""
+    echo "=== /omic/eureka contents ==="
+    ls -la /omic/eureka/ 2>&1 | head -20
+    echo ""
+    echo "=== /omic/eureka/digital-patients/ ==="
+    ls -la /omic/eureka/digital-patients/ 2>&1 | head -30
+    echo ""
+    echo "=== /omic/eureka/digital-patients/imputed/ ==="
+    ls -la /omic/eureka/digital-patients/imputed/ 2>&1 | head -20
+    echo ""
+    echo "=== /omic/eureka/digital-patients/healthy/ ==="
+    ls -la /omic/eureka/digital-patients/healthy/ 2>&1 | head -20
+    echo ""
+    echo "=== /omic/eureka/digital-patients/supporting-data/ ==="
+    ls -laR /omic/eureka/digital-patients/supporting-data/ 2>&1 | head -30
+    echo ""
+    echo "=== Check for assembled files ==="
+    ls -lh /omic/eureka/digital-patients/imputed/F5_SCHIZO* 2>&1
+    ls -lh /omic/eureka/digital-patients/healthy/gnomad* 2>&1
+    ls -lh /omic/eureka/digital-patients/supporting-data/genome/hg38* 2>&1
+    echo ""
+    echo "=== Small files check ==="
+    ls -lh /omic/eureka/digital-patients/MANE* 2>&1
+    ls -lh /omic/eureka/digital-patients/regulon* 2>&1
+    ls -lh /omic/eureka/digital-patients/LM22* 2>&1
+    ls -lh /omic/eureka/digital-patients/ukbb* 2>&1
+    echo "=== DEBUG COMPLETE ==="
+    """
+}
+
+workflow {
+    DEBUG_PVC()
+}