Simplified PVC debug script

debug_pvc.nf

@@ -1,45 +1,22 @@
-#!/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'
-
+process DEBUG {
+    container 'harbor.cluster.omic.ai/omic/digital-patients/synthea:cudf'
     script:
     """
-    echo "=== PVC mount check ==="
-    echo "Current dir: \$(pwd)"
-    echo ""
-    echo "=== /omic/eureka contents ==="
-    ls -la /omic/eureka/ 2>&1 | head -20
-    echo ""
+    echo "PWD: \$(pwd)"
+    echo "=== /omic/eureka/ ==="
+    ls /omic/eureka/ 2>&1 | head -20
     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 ==="
+    echo "=== Test write ==="
+    echo "test" > /omic/eureka/digital-patients/write_test.txt && echo "WRITE OK" || echo "WRITE FAILED"
+    echo "DONE"
     """
 }
-
-workflow {
-    DEBUG_PVC()
-}
+workflow { DEBUG() }